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Sample records for single panmictic population

  1. Multi-Genetic Marker Approach and Spatio-Temporal Analysis Suggest There Is a Single Panmictic Population of Swordfish Xiphias gladius in the Indian Ocean

    Science.gov (United States)

    Muths, Delphine; Le Couls, Sarah; Evano, Hugues; Grewe, Peter; Bourjea, Jerome

    2013-01-01

    Genetic population structure of swordfish Xiphias gladius was examined based on 2231 individual samples, collected mainly between 2009 and 2010, among three major sampling areas within the Indian Ocean (IO; twelve distinct sites), Atlantic (two sites) and Pacific (one site) Oceans using analysis of nineteen microsatellite loci (n = 2146) and mitochondrial ND2 sequences (n = 2001) data. Sample collection was stratified in time and space in order to investigate the stability of the genetic structure observed with a special focus on the South West Indian Ocean. Significant AMOVA variance was observed for both markers indicating genetic population subdivision was present between oceans. Overall value of F-statistics for ND2 sequences confirmed that Atlantic and Indian Oceans swordfish represent two distinct genetic stocks. Indo-Pacific differentiation was also significant but lower than that observed between Atlantic and Indian Oceans. However, microsatellite F-statistics failed to reveal structure even at the inter-oceanic scale, indicating that resolving power of our microsatellite loci was insufficient for detecting population subdivision. At the scale of the Indian Ocean, results obtained from both markers are consistent with swordfish belonging to a single unique panmictic population. Analyses partitioned by sampling area, season, or sex also failed to identify any clear structure within this ocean. Such large spatial and temporal homogeneity of genetic structure, observed for such a large highly mobile pelagic species, suggests as satisfactory to consider swordfish as a single panmictic population in the Indian Ocean. PMID:23717447

  2. Panmictic and Clonal Evolution on a Single Patchy Resource Produces Polymorphic Foraging Guilds.

    Science.gov (United States)

    Getz, Wayne M; Salter, Richard; Lyons, Andrew J; Sippl-Swezey, Nicolas

    2015-01-01

    We develop a stochastic, agent-based model to study how genetic traits and experiential changes in the state of agents and available resources influence individuals' foraging and movement behaviors. These behaviors are manifest as decisions on when to stay and exploit a current resource patch or move to a particular neighboring patch, based on information of the resource qualities of the patches and the anticipated level of intraspecific competition within patches. We use a genetic algorithm approach and an individual's biomass as a fitness surrogate to explore the foraging strategy diversity of evolving guilds under clonal versus hermaphroditic sexual reproduction. We first present the resource exploitation processes, movement on cellular arrays, and genetic algorithm components of the model. We then discuss their implementation on the Nova software platform. This platform seamlessly combines the dynamical systems modeling of consumer-resource interactions with agent-based modeling of individuals moving over a landscapes, using an architecture that lays transparent the following four hierarchical simulation levels: 1.) within-patch consumer-resource dynamics, 2.) within-generation movement and competition mitigation processes, 3.) across-generation evolutionary processes, and 4.) multiple runs to generate the statistics needed for comparative analyses. The focus of our analysis is on the question of how the biomass production efficiency and the diversity of guilds of foraging strategy types, exploiting resources over a patchy landscape, evolve under clonal versus random hermaphroditic sexual reproduction. Our results indicate greater biomass production efficiency under clonal reproduction only at higher population densities, and demonstrate that polymorphisms evolve and are maintained under random mating systems. The latter result questions the notion that some type of associative mating structure is needed to maintain genetic polymorphisms among individuals

  3. Panmictic and Clonal Evolution on a Single Patchy Resource Produces Polymorphic Foraging Guilds.

    Directory of Open Access Journals (Sweden)

    Wayne M Getz

    Full Text Available We develop a stochastic, agent-based model to study how genetic traits and experiential changes in the state of agents and available resources influence individuals' foraging and movement behaviors. These behaviors are manifest as decisions on when to stay and exploit a current resource patch or move to a particular neighboring patch, based on information of the resource qualities of the patches and the anticipated level of intraspecific competition within patches. We use a genetic algorithm approach and an individual's biomass as a fitness surrogate to explore the foraging strategy diversity of evolving guilds under clonal versus hermaphroditic sexual reproduction. We first present the resource exploitation processes, movement on cellular arrays, and genetic algorithm components of the model. We then discuss their implementation on the Nova software platform. This platform seamlessly combines the dynamical systems modeling of consumer-resource interactions with agent-based modeling of individuals moving over a landscapes, using an architecture that lays transparent the following four hierarchical simulation levels: 1. within-patch consumer-resource dynamics, 2. within-generation movement and competition mitigation processes, 3. across-generation evolutionary processes, and 4. multiple runs to generate the statistics needed for comparative analyses. The focus of our analysis is on the question of how the biomass production efficiency and the diversity of guilds of foraging strategy types, exploiting resources over a patchy landscape, evolve under clonal versus random hermaphroditic sexual reproduction. Our results indicate greater biomass production efficiency under clonal reproduction only at higher population densities, and demonstrate that polymorphisms evolve and are maintained under random mating systems. The latter result questions the notion that some type of associative mating structure is needed to maintain genetic polymorphisms among

  4. Unravelling population genetic structure with mitochondrial DNA in a notional panmictic coastal crab species: sample size makes the difference.

    Science.gov (United States)

    Fratini, Sara; Ragionieri, Lapo; Deli, Temim; Harrer, Alexandra; Marino, Ilaria A M; Cannicci, Stefano; Zane, Lorenzo; Schubart, Christoph D

    2016-07-26

    The extent of genetic structure of a species is determined by the amount of current gene flow and the impact of historical and demographic factors. Most marine invertebrates have planktonic larvae and consequently wide potential dispersal, so that genetic uniformity should be common. However, phylogeographic investigations reveal that panmixia is rare in the marine realm. Phylogeographic patterns commonly coincide with geographic transitions acting as barriers to gene flow. In the Mediterranean Sea and adjoining areas, the best known barriers are the Atlantic-Mediterranean transition, the Siculo-Tunisian Strait and the boundary between Aegean and Black seas. Here, we perform the so far broadest phylogeographic analysis of the crab Pachygrapsus marmoratus, common across the north-eastern Atlantic Ocean, Mediterranean and Black seas. Previous studies revealed no or weak genetic structuring at meso-geographic scale based on mtDNA, while genetic heterogeneity at local scale was recorded with microsatellites, even if without clear geographic patterns. Continuing the search for phylogeographic signal, we here enlarge the mtDNA dataset including 51 populations and covering most of the species' distribution range. This enlarged dataset provides new evidence of three genetically separable groups, corresponding to the Portuguese Atlantic Ocean, Mediterranean Sea plus Canary Islands, and Black Sea. Surprisingly, hierarchical AMOVA and Principal Coordinates Analysis agree that our Canary Islands population is closer to western Mediterranean populations than to mainland Portugal and Azores populations. Within the Mediterranean Sea, we record genetic homogeneity, suggesting that population connectivity is unaffected by the transition between the western and eastern Mediterranean. The Mediterranean metapopulation seems to have experienced a relatively recent expansion around 100,000 years ago. Our results suggest that the phylogeographic pattern of P. marmoratus is shaped by the

  5. Genome-wide single-generation signatures of local selection in the panmictic European eel

    DEFF Research Database (Denmark)

    Pujolar, J. M.; Jacobsen, M. W.; Als, Thomas Damm

    2014-01-01

    –receptor interaction and circadian rhythm. Remarkably, one of the candidate genes identified is PERIOD, possibly related to differences in local photoperiod associated with the >30° difference in latitude between locations. Genes under selection were spread across the genome, and there were no large regions...

  6. Global Asymptotic Stability for Discrete Single Species Population Models

    Directory of Open Access Journals (Sweden)

    A. Bilgin

    2017-01-01

    Full Text Available We present some basic discrete models in populations dynamics of single species with several age classes. Starting with the basic Beverton-Holt model that describes the change of single species we discuss its basic properties such as a convergence of all solutions to the equilibrium, oscillation of solutions about the equilibrium solutions, Allee’s effect, and Jillson’s effect. We consider the effect of the constant and periodic immigration and emigration on the global properties of Beverton-Holt model. We also consider the effect of the periodic environment on the global properties of Beverton-Holt model.

  7. Modeling bacterial population growth from stochastic single-cell dynamics.

    Science.gov (United States)

    Alonso, Antonio A; Molina, Ignacio; Theodoropoulos, Constantinos

    2014-09-01

    A few bacterial cells may be sufficient to produce a food-borne illness outbreak, provided that they are capable of adapting and proliferating on a food matrix. This is why any quantitative health risk assessment policy must incorporate methods to accurately predict the growth of bacterial populations from a small number of pathogens. In this aim, mathematical models have become a powerful tool. Unfortunately, at low cell concentrations, standard deterministic models fail to predict the fate of the population, essentially because the heterogeneity between individuals becomes relevant. In this work, a stochastic differential equation (SDE) model is proposed to describe variability within single-cell growth and division and to simulate population growth from a given initial number of individuals. We provide evidence of the model ability to explain the observed distributions of times to division, including the lag time produced by the adaptation to the environment, by comparing model predictions with experiments from the literature for Escherichia coli, Listeria innocua, and Salmonella enterica. The model is shown to accurately predict experimental growth population dynamics for both small and large microbial populations. The use of stochastic models for the estimation of parameters to successfully fit experimental data is a particularly challenging problem. For instance, if Monte Carlo methods are employed to model the required distributions of times to division, the parameter estimation problem can become numerically intractable. We overcame this limitation by converting the stochastic description to a partial differential equation (backward Kolmogorov) instead, which relates to the distribution of division times. Contrary to previous stochastic formulations based on random parameters, the present model is capable of explaining the variability observed in populations that result from the growth of a small number of initial cells as well as the lack of it compared to

  8. The confounding effect of population structure on bayesian skyline plot inferences of demographic history

    DEFF Research Database (Denmark)

    Heller, Rasmus; Chikhi, Lounes; Siegismund, Hans

    2013-01-01

    Many coalescent-based methods aiming to infer the demographic history of populations assume a single, isolated and panmictic population (i.e. a Wright-Fisher model). While this assumption may be reasonable under many conditions, several recent studies have shown that the results can be misleading...... when it is violated. Among the most widely applied demographic inference methods are Bayesian skyline plots (BSPs), which are used across a range of biological fields. Violations of the panmixia assumption are to be expected in many biological systems, but the consequences for skyline plot inferences...... the best scheme for inferring demographic change over a typical time scale. Analyses of data from a structured African buffalo population demonstrate how BSP results can be strengthened by simulations. We recommend that sample selection should be carefully considered in relation to population structure...

  9. Population genetic structure of Meccus longipennis (Hemiptera, Reduviidae, Triatominae), vector of Chagas disease in West Mexico.

    Science.gov (United States)

    Brenière, Simone Frédérique; Waleckx, Etienne; Magallón-Gastélum, Ezequiel; Bosseno, Marie-France; Hardy, Xavier; Ndo, Cyrille; Lozano-Kasten, Felipe; Barnabé, Christian; Kengne, Pierre

    2012-03-01

    The originally wild species of the Meccus complex are important vectors of Chagas disease in Mexico. In West Mexico, Meccus longipennis plays an important epidemiological role. To understand the genetic structure of the domestic and wild populations of this species, a preliminary study with five polymorphic microsatellite loci was conducted. The population genetics analysis showed high structuring between peridomestic biotopes, with breeding subunits detected in a single peridomestic structure. In the wild environment, two genetic patterns were observed according to the biotope, possible breeding subunits in large rocky formations and a larger panmictic unit in agropastoral areas, suggesting considerable dispersal of bugs in this biotope. Moreover, the discovery of two foci of wild populations at the edge of Guadalajara city raises the question of new urban areas where the phenomenon of bug incursions into households could constitute a risk of transmission of Chagas disease. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Novel RAD sequence data reveal a lack of genomic divergence between dietary ecotypes in a landlocked salmonid population

    Science.gov (United States)

    Limborg, Morten T.; Larson, Wesley; Shedd, Kyle; Seeb, Lisa W.; Seeb, James E.

    2017-01-01

    Preservation of heritable ecological diversity within species and populations is a key challenge for managing natural resources and wild populations. Salmonid fish are iconic and socio-economically important species for commercial, aquaculture, and recreational fisheries across the globe. Many salmonids are known to exhibit ecological divergence within species, including distinct feeding ecotypes within the same lakes. Here we used 5559 SNPs, derived from RAD sequencing, to perform population genetic comparisons between two dietary ecotypes of sockeye salmon (Oncorhynchus nerka) in Jo-Jo Lake, Alaska (USA). We tested the standing hypothesis that these two ecotypes are currently diverging as a result of adaptation to distinct dietary niches; results support earlier conclusions of a single panmictic population. The RAD sequence data revealed 40 new SNPs not previously detected in the species, and our sequence data can be used in future studies of ecotypic diversity in salmonid species.

  11. Single bumps in a 2-population homogenized neuronal network model

    Science.gov (United States)

    Kolodina, Karina; Oleynik, Anna; Wyller, John

    2018-05-01

    We investigate existence and stability of single bumps in a homogenized 2-population neural field model, when the firing rate functions are given by the Heaviside function. The model is derived by means of the two-scale convergence technique of Nguetseng in the case of periodic microvariation in the connectivity functions. The connectivity functions are periodically modulated in both the synaptic footprint and in the spatial scale. The bump solutions are constructed by using a pinning function technique for the case where the solutions are independent of the local variable. In the weakly modulated case the generic picture consists of two bumps (one narrow and one broad bump) for each admissible set of threshold values for firing. In addition, a new threshold value regime for existence of bumps is detected. Beyond the weakly modulated regime the number of bumps depends sensitively on the degree of heterogeneity. For the latter case we present a configuration consisting of three coexisting bumps. The linear stability of the bumps is studied by means of the spectral properties of a Fredholm integral operator, block diagonalization of this operator and the Fourier decomposition method. In the weakly modulated regime, one of the bumps is unstable for all relative inhibition times, while the other one is stable for small and moderate values of this parameter. The latter bump becomes unstable as the relative inhibition time exceeds a certain threshold. In the case of the three coexisting bumps detected in the regime of finite degree of heterogeneity, we have at least one stable bump (and maximum two stable bumps) for small and moderate values of the relative inhibition time.

  12. On the apllication of single specie dynamic population model | Iguda ...

    African Journals Online (AJOL)

    The Method of mathematical models of Malthus and Verhults were applied on ten years data collected from Magaram Poultry Farm to determine the nature of population growth, population decay or constant ... Keywords: Birth rate, sustainable population, overcrowding, harvesting, independent t-test and one way Anova.

  13. A single nucleotide polymorphism (SNP) assay for population ...

    African Journals Online (AJOL)

    Therefore, we developed the first SNP assay to test stratification between Chinese and Japanese populations living in East Asia. The ancestry ... The SNP assay showed excellent promise as a highly potential application to test population stratification in case-control studies of association in Eastern Asians. Key words: ...

  14. Spatially-explicit estimation of Wright's neighborhood size in continuous populations

    Science.gov (United States)

    Andrew J. Shirk; Samuel A. Cushman

    2014-01-01

    Effective population size (Ne) is an important parameter in conservation genetics because it quantifies a population's capacity to resist loss of genetic diversity due to inbreeding and drift. The classical approach to estimate Ne from genetic data involves grouping sampled individuals into discretely defined subpopulations assumed to be panmictic. Importantly,...

  15. Single-Phase Mail Survey Design for Rare Population Subgroups

    Science.gov (United States)

    Brick, J. Michael; Andrews, William R.; Mathiowetz, Nancy A.

    2016-01-01

    Although using random digit dialing (RDD) telephone samples was the preferred method for conducting surveys of households for many years, declining response and coverage rates have led researchers to explore alternative approaches. The use of address-based sampling (ABS) has been examined for sampling the general population and subgroups, most…

  16. Mathematical Modeling in Population Dynamics: The Case of Single ...

    African Journals Online (AJOL)

    kofimereku

    formulated by the logistic growth function, where ε is the intrinsic rate of increase and )0(. ≥. µ represents the effect of intraspecific competition on the reproduction rate. Fisher (1937) first proposed this equation as a model in population genetics to describe the process of spatial spread when mutant individuals with higher ...

  17. on the apllication of single specie dynamic population model 306

    African Journals Online (AJOL)

    pc

    used to compare the predicted values and observed values in order to find out whether there is significant difference between the observed and predicted values using these two models. Keywords: Birth rate, sustainable population, overcrowding, harvesting, independent t-test and ..... 95% confidence interval of the.

  18. Defense of single-factor models of population regulation

    International Nuclear Information System (INIS)

    Tamarin, R.H.

    1978-01-01

    I reject a multifactorial approach to the study of the regulation of animal populations for two reasons. First, a mechanism suggested by Chitty, that has natural selection at its base, has not been adequately tested. Second, the multifactorial model suggested by Lidicker is untestable because of its vagueness. As a middle ground, I suggest a model that has natural selection as its mechanism, but is multifacturial because it allows many parameters to be the selective agents. I particularly emphasize prediction and selective dispersal. Methods to test this model are suggested

  19. Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history.

    Science.gov (United States)

    Zhu, Yuan O; Aw, Pauline P K; de Sessions, Paola Florez; Hong, Shuzhen; See, Lee Xian; Hong, Lewis Z; Wilm, Andreas; Li, Chen Hao; Hue, Stephane; Lim, Seng Gee; Nagarajan, Niranjan; Burkholder, William F; Hibberd, Martin

    2017-10-27

    Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge. Here we applied BAsE-Seq, an Illumina-based single-virion sequencing technology, to eight samples from four chronic hepatitis B (CHB) patients - once before antiviral treatment and once after viral rebound due to resistance. With single-virion sequencing, we obtained 248-8796 single-virion sequences per sample, which allowed us to find evidence for both hard and soft selective sweeps. We were able to reconstruct population demographic history that was independently verified by clinically collected data. We further verified four of the samples independently through PacBio SMRT and Illumina Pooled deep sequencing. Overall, we showed that single-virion sequencing yields insight into viral evolution and population dynamics in an efficient and high throughput manner. We believe that single-virion sequencing is widely applicable to the study of viral evolution in the context of drug resistance and host adaptation, allows differentiation between soft or hard selective sweeps, and may be useful in the reconstruction of intra-host viral population demographic history.

  20. Genetic approaches to understanding the population-level impact of wind energy development on migratory bats

    Energy Technology Data Exchange (ETDEWEB)

    Vonhof, Maarten J. [Western Michigan Univ., Kalamazoo MI (United States); Russell, Amy L. [Grand Valley State Univ. Allendale, MI (United States)

    2013-09-30

    Documented fatalities of bats at wind turbines have raised serious concerns about the future impacts of increased wind power development on populations of migratory bat species. Yet there is little data on bat population sizes and trends to provide context for understanding the consequences of mortality due to wind power development. Using a large dataset of both nuclear and mitochondrial DNA variation for eastern red bats, we demonstrated that: 1) this species forms a single, panmictic population across their range with no evidence for the historical use of divergent migratory pathways by any portion of the population; 2) the effective size of this population is in the hundreds of thousands to millions; and 3) for large populations, genetic diversity measures and at least one coalescent method are insensitive to even very high rates of population decline over long time scales and until population size has become very small. Our data provide important context for understanding the population-level impacts of wind power development on affected bat species.

  1. Concurrent Isolation of 3 Distinct Cardiac Stem Cell Populations From a Single Human Heart Biopsy.

    Science.gov (United States)

    Monsanto, Megan M; White, Kevin S; Kim, Taeyong; Wang, Bingyan J; Fisher, Kristina; Ilves, Kelli; Khalafalla, Farid G; Casillas, Alexandria; Broughton, Kathleen; Mohsin, Sadia; Dembitsky, Walter P; Sussman, Mark A

    2017-07-07

    The relative actions and synergism between distinct myocardial-derived stem cell populations remain obscure. Ongoing debates on optimal cell population(s) for treatment of heart failure prompted implementation of a protocol for isolation of multiple stem cell populations from a single myocardial tissue sample to develop new insights for achieving myocardial regeneration. Establish a robust cardiac stem cell isolation and culture protocol to consistently generate 3 distinct stem cell populations from a single human heart biopsy. Isolation of 3 endogenous cardiac stem cell populations was performed from human heart samples routinely discarded during implantation of a left ventricular assist device. Tissue explants were mechanically minced into 1 mm 3 pieces to minimize time exposure to collagenase digestion and preserve cell viability. Centrifugation removes large cardiomyocytes and tissue debris producing a single cell suspension that is sorted using magnetic-activated cell sorting technology. Initial sorting is based on tyrosine-protein kinase Kit (c-Kit) expression that enriches for 2 c-Kit + cell populations yielding a mixture of cardiac progenitor cells and endothelial progenitor cells. Flowthrough c-Kit - mesenchymal stem cells are positively selected by surface expression of markers CD90 and CD105. After 1 week of culture, the c-Kit + population is further enriched by selection for a CD133 + endothelial progenitor cell population. Persistence of respective cell surface markers in vitro is confirmed both by flow cytometry and immunocytochemistry. Three distinct cardiac cell populations with individualized phenotypic properties consistent with cardiac progenitor cells, endothelial progenitor cells, and mesenchymal stem cells can be successfully concurrently isolated and expanded from a single tissue sample derived from human heart failure patients. © 2017 American Heart Association, Inc.

  2. Integrated Spectral Energy Distributions and Absorption Feature Indices of Single Stellar Populations

    OpenAIRE

    Zhang, Fenghui; Han, Zhanwen; Li, Lifang; Hurley, Jarrod R.

    2004-01-01

    Using evolutionary population synthesis, we present integrated spectral energy distributions and absorption-line indices defined by the Lick Observatory image dissector scanner (referred to as Lick/IDS) system, for an extensive set of instantaneous burst single stellar populations (SSPs). The ages of the SSPs are in the range 1-19 Gyr and the metallicities [Fe/H] are in the range -2.3 - 0.2. Our models use the rapid single stellar evolution algorithm of Hurley, Pols and Tout for the stellar e...

  3. Spatio-temporal population structuring and genetic diversity retention in depleted Atlantic Bluefin tuna of the Mediterranean Sea

    Science.gov (United States)

    Riccioni, Giulia; Landi, Monica; Ferrara, Giorgia; Milano, Ilaria; Cariani, Alessia; Zane, Lorenzo; Sella, Massimo; Barbujani, Guido; Tinti, Fausto

    2010-01-01

    Fishery genetics have greatly changed our understanding of population dynamics and structuring in marine fish. In this study, we show that the Atlantic Bluefin tuna (ABFT, Thunnus thynnus), an oceanic predatory species exhibiting highly migratory behavior, large population size, and high potential for dispersal during early life stages, displays significant genetic differences over space and time, both at the fine and large scales of variation. We compared microsatellite variation of contemporary (n = 256) and historical (n = 99) biological samples of ABFTs of the central-western Mediterranean Sea, the latter dating back to the early 20th century. Measures of genetic differentiation and a general heterozygote deficit suggest that differences exist among population samples, both now and 96–80 years ago. Thus, ABFTs do not represent a single panmictic population in the Mediterranean Sea. Statistics designed to infer changes in population size, both from current and past genetic variation, suggest that some Mediterranean ABFT populations, although still not severely reduced in their genetic potential, might have suffered from demographic declines. The short-term estimates of effective population size are straddled on the minimum threshold (effective population size = 500) indicated to maintain genetic diversity and evolutionary potential across several generations in natural populations. PMID:20080643

  4. Paternity in the Addo elephant population, South Africa. Is a single ...

    African Journals Online (AJOL)

    The hypothesis that a single dominant male (GAA) monopolized all matings within the elephant population of South Africa's Addo Elephant National Park between 1982 and 1996 was tested using microsatellite analysis. In addition, behavioural data on male musth periods, female oestrous periods, and observations of ...

  5. Neglect of bandwidth of Odontocetes echo location clicks biases propagation loss and single hydrophone population estimates

    NARCIS (Netherlands)

    Ainslie, M.A.

    2013-01-01

    Passive acoustic monitoring with a single hydrophone has been suggested as a cost-effective method to monitor population density of echolocating marine mammals, by estimating the distance at which the hydrophone is able to intercept the echolocation clicks and distinguish these from the background.

  6. Deconstructing stem cell population heterogeneity: Single-cell analysis and modeling approaches

    Science.gov (United States)

    Wu, Jincheng; Tzanakakis, Emmanuel S.

    2014-01-01

    Isogenic stem cell populations display cell-to-cell variations in a multitude of attributes including gene or protein expression, epigenetic state, morphology, proliferation and proclivity for differentiation. The origins of the observed heterogeneity and its roles in the maintenance of pluripotency and the lineage specification of stem cells remain unclear. Addressing pertinent questions will require the employment of single-cell analysis methods as traditional cell biochemical and biomolecular assays yield mostly population-average data. In addition to time-lapse microscopy and flow cytometry, recent advances in single-cell genomic, transcriptomic and proteomic profiling are reviewed. The application of multiple displacement amplification, next generation sequencing, mass cytometry and spectrometry to stem cell systems is expected to provide a wealth of information affording unprecedented levels of multiparametric characterization of cell ensembles under defined conditions promoting pluripotency or commitment. Establishing connections between single-cell analysis information and the observed phenotypes will also require suitable mathematical models. Stem cell self-renewal and differentiation are orchestrated by the coordinated regulation of subcellular, intercellular and niche-wide processes spanning multiple time scales. Here, we discuss different modeling approaches and challenges arising from their application to stem cell populations. Integrating single-cell analysis with computational methods will fill gaps in our knowledge about the functions of heterogeneity in stem cell physiology. This combination will also aid the rational design of efficient differentiation and reprogramming strategies as well as bioprocesses for the production of clinically valuable stem cell derivatives. PMID:24035899

  7. Microselection - Affinity Selecting Antibodies against a Single Rare Cell in a Heterogeneous Population

    DEFF Research Database (Denmark)

    Sørensen, Morten Dræby; Agerholm, Inge Errebo; Christensen, Britta

    2009-01-01

    antibodies. Here we have generated a microselection method allowing antibody selection, by phage display, targeting a single cell in a heterogeneous population. One K562 cell (female origin) was positioned on glass-slide among millions of lymphocytes from male donor, identifying the K562 cell by FISH (XX......). Several single cell selections were performed on such individual slides. The phage particles bound to the target cell is protected by a minute disc, while inactivating all remaining phage by UV-irradiation; leaving only the phage bound to the target cell viable. We hereby retrieved up to eight antibodies...

  8. Identification of Diagnostic Mitochondrial DNA Single Nucleotide Polymorphisms Specific to Sumatran Orangutan (Pongo abelii Populations

    Directory of Open Access Journals (Sweden)

    Puji Rianti

    2015-10-01

    Full Text Available The hypervariable region I of mitochondrial DNA has frequently been used to distinguish among populations, in particular in species with strong female philopatry. In such cases, populations are expected to diverge rapidly for hypervariable region I markers because of the smaller effective population size and thus increased genetic drift. This rapid divergence leads to the accumulation of mutations exclusively found in one population, which may serve as diagnostic single nucleotide polymorphisms (SNPs. To date, diagnostic SNPs distinctive to Sumatran orangutan populations have not yet been described. However, given the continuously declining numbers of Sumatran orangutans, this information can be vital for effective conservation measures, especially regarding reintroductions of orangutans in rehabilitation centers. Phylogenetic analyses of 54 samples of Sumatran orangutans from nine sampling sites with good provenance, we found five major clades and a total of 20 haplotypes. We propose a total of 52 diagnostic SNPs that are specific to Sumatran orangutan populations. Data can be used to develop restriction fragment length polymorphism assays to carry out genetic assignments using basic laboratory equipment to assign Sumatran orangutan to their population of origin.

  9. Inequivalence of single-particle and population lifetimes in a cuprate superconductor

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Shuolong [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); Sobota, J. A. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Leuenberger, D. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); He, Y. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); Hashimoto, M. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Lu, D. H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Eisaki, H. [National Institute of Advanced Industrial Science and Technology, Ibaraki (Japan); Kirchmann, P. S. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Shen, Z. -X. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States)

    2015-06-15

    We study optimally doped Bi-2212 (Tc=96 K) using femtosecond time- and angle-resolved photoelectron spectroscopy. Energy-resolved population lifetimes are extracted and compared with single-particle lifetimes measured by equilibrium photoemission. The population lifetimes deviate from the single-particle lifetimes in the low excitation limit by 1–2 orders of magnitude. Fundamental considerations of electron scattering unveil that these two lifetimes are in general distinct, yet for systems with only electron-phonon scattering they should converge in the low-temperature, low-fluence limit. As a result, the qualitative disparity in our data, even in this limit, suggests that scattering channels beyond electron-phonon interactions play a significant role in the electron dynamics of cuprate superconductors.

  10. Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains

    Science.gov (United States)

    Onken, Arno; Liu, Jian K.; Karunasekara, P. P. Chamanthi R.; Delis, Ioannis; Gollisch, Tim; Panzeri, Stefano

    2016-01-01

    Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons. This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension (differences in stimulus tuning across neurons at different locations), in their temporal dimension (temporal neural response variations), or in their combination (temporally coordinated neural population firing). Here we investigate the utility of tensor factorizations of population spike trains along space and time. These factorizations decompose a dataset of single-trial population spike trains into spatial firing patterns (combinations of neurons firing together), temporal firing patterns (temporal activation of these groups of neurons) and trial-dependent activation coefficients (strength of recruitment of such neural patterns on each trial). We validated various factorization methods on simulated data and on populations of ganglion cells simultaneously recorded in the salamander retina. We found that single-trial tensor space-by-time decompositions provided low-dimensional data-robust representations of spike trains that capture efficiently both their spatial and temporal information about sensory stimuli. Tensor decompositions with orthogonality constraints were the most efficient in extracting sensory information, whereas non-negative tensor decompositions worked well even on non-independent and overlapping spike patterns, and retrieved informative firing patterns expressed by the same population in response to novel stimuli. Our method showed that populations of retinal ganglion cells carried information in their spike timing on the ten-milliseconds-scale about spatial details of natural images. This information could not be recovered from the spike counts of these cells. First-spike latencies carried the majority of information provided by the whole spike train about fine-scale image

  11. Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains.

    Directory of Open Access Journals (Sweden)

    Arno Onken

    2016-11-01

    Full Text Available Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons. This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension (differences in stimulus tuning across neurons at different locations, in their temporal dimension (temporal neural response variations, or in their combination (temporally coordinated neural population firing. Here we investigate the utility of tensor factorizations of population spike trains along space and time. These factorizations decompose a dataset of single-trial population spike trains into spatial firing patterns (combinations of neurons firing together, temporal firing patterns (temporal activation of these groups of neurons and trial-dependent activation coefficients (strength of recruitment of such neural patterns on each trial. We validated various factorization methods on simulated data and on populations of ganglion cells simultaneously recorded in the salamander retina. We found that single-trial tensor space-by-time decompositions provided low-dimensional data-robust representations of spike trains that capture efficiently both their spatial and temporal information about sensory stimuli. Tensor decompositions with orthogonality constraints were the most efficient in extracting sensory information, whereas non-negative tensor decompositions worked well even on non-independent and overlapping spike patterns, and retrieved informative firing patterns expressed by the same population in response to novel stimuli. Our method showed that populations of retinal ganglion cells carried information in their spike timing on the ten-milliseconds-scale about spatial details of natural images. This information could not be recovered from the spike counts of these cells. First-spike latencies carried the majority of information provided by the whole spike train about fine

  12. The reverse effects of random perturbation on discrete systems for single and multiple population models

    International Nuclear Information System (INIS)

    Kang, Li; Tang, Sanyi

    2016-01-01

    Highlights: • The discrete single species and multiple species models with random perturbation are proposed. • The complex dynamics and interesting bifurcation behavior have been investigated. • The reverse effects of random perturbation on discrete systems have been discussed and revealed. • The main results can be applied for pest control and resources management. - Abstract: The natural species are likely to present several interesting and complex phenomena under random perturbations, which have been confirmed by simple mathematical models. The important questions are: how the random perturbations influence the dynamics of the discrete population models with multiple steady states or multiple species interactions? and is there any different effects for single species and multiple species models with random perturbation? To address those interesting questions, we have proposed the discrete single species model with two stable equilibria and the host-parasitoid model with Holling type functional response functions to address how the random perturbation affects the dynamics. The main results indicate that the random perturbation does not change the number of blurred orbits of the single species model with two stable steady states compared with results for the classical Ricker model with same random perturbation, but it can strength the stability. However, extensive numerical investigations depict that the random perturbation does not influence the complexities of the host-parasitoid models compared with the results for the models without perturbation, while it does increase the period of periodic orbits doubly. All those confirm that the random perturbation has a reverse effect on the dynamics of the discrete single and multiple population models, which could be applied in reality including pest control and resources management.

  13. Bet-hedging in bacteriocin producing Escherichia coli populations: the single cell perspective

    Science.gov (United States)

    Bayramoglu, Bihter; Toubiana, David; van Vliet, Simon; Inglis, R. Fredrik; Shnerb, Nadav; Gillor, Osnat

    2017-02-01

    Production of public goods in biological systems is often a collaborative effort that may be detrimental to the producers. It is therefore sustainable only if a small fraction of the population shoulders the cost while the majority reap the benefits. We modelled this scenario using Escherichia coli populations producing colicins, an antibiotic that kills producer cells’ close relatives. Colicin expression is a costly trait, and it has been proposed that only a small fraction of the population actively expresses the antibiotic. Colicinogenic populations were followed at the single-cell level using time-lapse microscopy, and showed two distinct, albeit dynamic, subpopulations: the majority silenced colicin expression, while a small fraction of elongated, slow-growing cells formed colicin-expressing hotspots, placing a significant burden on expressers. Moreover, monitoring lineages of individual colicinogenic cells showed stochastic switching between expressers and non-expressers. Hence, colicin expressers may be engaged in risk-reducing strategies—or bet-hedging—as they balance the cost of colicin production with the need to repel competitors. To test the bet-hedging strategy in colicin-mediated interactions, competitions between colicin-sensitive and producer cells were simulated using a numerical model, demonstrating a finely balanced expression range that is essential to sustaining the colicinogenic population.

  14. The population of single and binary white dwarfs of the Galactic bulge

    Science.gov (United States)

    Torres, S.; García-Berro, E.; Cojocaru, R.; Calamida, A.

    2018-02-01

    Recent Hubble Space Telescope observations have unveiled the white dwarf cooling sequence of the Galactic bulge. Although the degenerate sequence can be well fitted employing the most up-to-date theoretical cooling sequences, observations show a systematic excess of red objects that cannot be explained by the theoretical models of single carbon-oxygen white dwarfs of the appropriate masses. Here we present a population synthesis study of the white dwarf cooling sequence of the Galactic bulge that takes into account the populations of both single white dwarfs and binary systems containing at least one white dwarf. These calculations incorporate state-of-the-art cooling sequences for white dwarfs with hydrogen-rich and hydrogen-deficient atmospheres, for both white dwarfs with carbon-oxygen and helium cores, and also take into account detailed prescriptions of the evolutionary history of binary systems. Our Monte Carlo simulator also incorporates all the known observational biases. This allows us to model with a high degree of realism the white dwarf population of the Galactic bulge. We find that the observed excess of red stars can be partially attributed to white dwarf plus main sequence binaries, and to cataclysmic variables or dwarf novae. Our best fit is obtained with a higher binary fraction and an initial mass function slope steeper than standard values, as well as with the inclusion of differential reddening and blending. Our results also show that the possible contribution of double degenerate systems or young and thick-disk bulge stars is negligible.

  15. The population of single and binary white dwarfs of the Galactic bulge

    Science.gov (United States)

    Torres, S.; García-Berro, E.; Cojocaru, R.; Calamida, A.

    2018-05-01

    Recent Hubble Space Telescope observations have unveiled the white dwarf cooling sequence of the Galactic bulge. Although the degenerate sequence can be well fitted employing the most up-to-date theoretical cooling sequences, observations show a systematic excess of red objects that cannot be explained by the theoretical models of single carbon-oxygen white dwarfs of the appropriate masses. Here, we present a population synthesis study of the white dwarf cooling sequence of the Galactic bulge that takes into account the populations of both single white dwarfs and binary systems containing at least one white dwarf. These calculations incorporate state-of-the-art cooling sequences for white dwarfs with hydrogen-rich and hydrogen-deficient atmospheres, for both white dwarfs with carbon-oxygen and helium cores, and also take into account detailed prescriptions of the evolutionary history of binary systems. Our Monte Carlo simulator also incorporates all the known observational biases. This allows us to model with a high degree of realism the white dwarf population of the Galactic bulge. We find that the observed excess of red stars can be partially attributed to white dwarf plus main sequence binaries, and to cataclysmic variables or dwarf novae. Our best fit is obtained with a higher binary fraction and an initial mass function slope steeper than standard values, as well as with the inclusion of differential reddening and blending. Our results also show that the possible contribution of double degenerate systems or young and thick-discbulge stars is negligible.

  16. Establishing the evolutionary compatibility of potential sources of colonizers for overfished stocks: a population genomics approach.

    Science.gov (United States)

    Gonçalves da Silva, Anders; Appleyard, Sharon A; Upston, Judy

    2015-02-01

    Identifying fish stock structure is fundamental to pinpoint stocks that might contribute colonizers to overfished stocks. However, a stock's potential to contribute to rebuilding hinges on demographic connectivity, a challenging parameter to measure. With genomics as a new tool, fisheries managers can detect signatures of natural selection and thus identify fishing areas likely to contribute evolutionarily compatible colonizers to an overfished area (i.e. colonizers that are not at a fitness disadvantage in the overfished area and able to reproduce at optimal rates). Identifying evolutionarily compatible stocks would help narrow the focus on establishing demographic connectivity where it matters. Here, we genotype 4723 SNPs in 616 orange roughy (Hoplostethus atlanticus) across five fishing areas off the Tasmanian coast in Australia. We ask whether these areas form a single genetic unit, and test for signatures of local adaptation. Results from amova, structure, discriminant analysis of principal components, BAYESASS and isolation by distance suggest that sampled locations are subjected to geneflow amounts that are above what is needed to establish 'drift connectivity'. However, it remains unclear whether there is a single panmictic population or several highly connected populations. Most importantly, we did not find any evidence of local adaptation, suggesting that the examined orange roughy stocks are evolutionarily compatible. The data have helped test an assumption of the orange roughy management programme and to formulate hypotheses regarding stock demographic connectivity. Overall, our results demonstrate the potential of genomics to inform fisheries management, even when evidence for stock structure is sparse. © 2014 John Wiley & Sons Ltd.

  17. Performance of autofocusing schemes for single target and populated scenes behind unknown walls

    Science.gov (United States)

    Ahmad, Fauzia; Amin, Moeness G.

    2007-04-01

    The quality and reliability of through-the-wall radar imagery is governed, among other things, by the knowledge of the wall characteristics. Ambiguity in wall characteristics has a two-fold effect. It smears and blurs the image, and also shifts the imaged target positions. Higher order standardized moments have been shown to be suitable measures of the degree of smearing and blurriness of through-the-wall images. These moments can be used to tune the wall variables to achieve autofocusing. It is noted that the solution to the autofocusing problem is not unique, and there exist several assumed wall characteristics, in addition to the exact, that lead to similar focused images. In this paper, we analyze the dependency of the estimated autofocusing wall parameters on the imaged scene, specifically target density and location, in the presence of single uniform wall. We consider single and multiple target cases with different scene complexity and population. Supporting simulation results are also provided.

  18. In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians.

    Science.gov (United States)

    Molinaro, Alyssa M; Pearson, Bret J

    2016-04-27

    The planarian Schmidtea mediterranea is a master regenerator with a large adult stem cell compartment. The lack of transgenic labeling techniques in this animal has hindered the study of lineage progression and has made understanding the mechanisms of tissue regeneration a challenge. However, recent advances in single-cell transcriptomics and analysis methods allow for the discovery of novel cell lineages as differentiation progresses from stem cell to terminally differentiated cell. Here we apply pseudotime analysis and single-cell transcriptomics to identify adult stem cells belonging to specific cellular lineages and identify novel candidate genes for future in vivo lineage studies. We purify 168 single stem and progeny cells from the planarian head, which were subjected to single-cell RNA sequencing (scRNAseq). Pseudotime analysis with Waterfall and gene set enrichment analysis predicts a molecularly distinct neoblast sub-population with neural character (νNeoblasts) as well as a novel alternative lineage. Using the predicted νNeoblast markers, we demonstrate that a novel proliferative stem cell population exists adjacent to the brain. scRNAseq coupled with in silico lineage analysis offers a new approach for studying lineage progression in planarians. The lineages identified here are extracted from a highly heterogeneous dataset with minimal prior knowledge of planarian lineages, demonstrating that lineage purification by transgenic labeling is not a prerequisite for this approach. The identification of the νNeoblast lineage demonstrates the usefulness of the planarian system for computationally predicting cellular lineages in an adult context coupled with in vivo verification.

  19. Single species victory in a two-site, two-species model of population dispersion

    Science.gov (United States)

    Waddell, Jack; Sander, Len; Kessler, David

    2008-03-01

    We study the behavior of two species, differentiated only by their dispersal rates in an environment providing heterogeneous growth rates. Previous deterministic studies have shown that the slower-dispersal species always drives the faster species to extinction, while stochastic studies show that the opposite case can occur given small enough population and spatial heterogeneity. Other models of similar systems demonstrate the existence of an optimum dispersal rate, suggesting that distinguishing the species as faster or slower is insufficient. We here study the interface of these models for a small spatial system and determine the conditions of stability for a single species outcome.

  20. Quantitative single cell analysis of cell population dynamics during submandibular salivary gland development and differentiation

    Science.gov (United States)

    Nelson, Deirdre A.; Manhardt, Charles; Kamath, Vidya; Sui, Yunxia; Santamaria-Pang, Alberto; Can, Ali; Bello, Musodiq; Corwin, Alex; Dinn, Sean R.; Lazare, Michael; Gervais, Elise M.; Sequeira, Sharon J.; Peters, Sarah B.; Ginty, Fiona; Gerdes, Michael J.; Larsen, Melinda

    2013-01-01

    Summary Epithelial organ morphogenesis involves reciprocal interactions between epithelial and mesenchymal cell types to balance progenitor cell retention and expansion with cell differentiation for evolution of tissue architecture. Underlying submandibular salivary gland branching morphogenesis is the regulated proliferation and differentiation of perhaps several progenitor cell populations, which have not been characterized throughout development, and yet are critical for understanding organ development, regeneration, and disease. Here we applied a serial multiplexed fluorescent immunohistochemistry technology to map the progressive refinement of the epithelial and mesenchymal cell populations throughout development from embryonic day 14 through postnatal day 20. Using computational single cell analysis methods, we simultaneously mapped the evolving temporal and spatial location of epithelial cells expressing subsets of differentiation and progenitor markers throughout salivary gland development. We mapped epithelial cell differentiation markers, including aquaporin 5, PSP, SABPA, and mucin 10 (acinar cells); cytokeratin 7 (ductal cells); and smooth muscle α-actin (myoepithelial cells) and epithelial progenitor cell markers, cytokeratin 5 and c-kit. We used pairwise correlation and visual mapping of the cells in multiplexed images to quantify the number of single- and double-positive cells expressing these differentiation and progenitor markers at each developmental stage. We identified smooth muscle α-actin as a putative early myoepithelial progenitor marker that is expressed in cytokeratin 5-negative cells. Additionally, our results reveal dynamic expansion and redistributions of c-kit- and K5-positive progenitor cell populations throughout development and in postnatal glands. The data suggest that there are temporally and spatially discreet progenitor populations that contribute to salivary gland development and homeostasis. PMID:23789091

  1. Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations.

    Science.gov (United States)

    Jordan, Michael R; Kearney, Mary; Palmer, Sarah; Shao, Wei; Maldarelli, Frank; Coakley, Eoin P; Chappey, Colombe; Wanke, Christine; Coffin, John M

    2010-09-01

    To compare standard PCR/cloning and single genome sequencing (SGS) in their ability to reflect actual intra-patient polymorphism of HIV-1 populations, a total of 530 HIV-1 pro-pol sequences obtained by both sequencing techniques from a set of 17 ART naïve patient specimens was analyzed. For each specimen, 12 and 15 sequences, on average, were characterized by the two techniques. Using phylogenetic analysis, tests for panmixia and entropy, and Bland-Altman plots, no difference in population structure or genetic diversity was shown in 14 of the 17 subjects. Evidence of sampling bias by the presence of subsets of identical sequences was found by either method. Overall, the study shows that neither method was more biased than the other, and providing that an adequate number of PCR templates is analyzed, and that the bulk sequencing captures the diversity of the viral population, either method is likely to provide a similar measure of population diversity. Copyright 2010 Elsevier B.V. All rights reserved.

  2. CYP3A5*3 and *6 single nucleotide polymorphisms in three distinct Asian populations.

    Science.gov (United States)

    Balram, C; Zhou, Qingyu; Cheung, Yin Bun; Lee, Edmund J D

    2003-06-01

    To determine the frequencies of two functional single nucleotide polymorphisms, CYP3A5*3 and CYP3A5*6, in the CYP3A5 gene in three distinct Asian ethnic groups, namely, the Chinese, Malays and Indians. Single nucleotide polymorphism analyses of CYP3A5*1, *3 and *6 were performed in 296 healthy subjects (108 Chinese, 98 Malays and 90 Indians) using the polymerase chain reaction-restriction fragment length polymorphism method. The *1 allele frequency was 25% in Chinese compared with 40% in Malays and Indians ( P=0.001). The *3 allele frequency was also higher in the Chinese population, being 76% versus 60% in the Malays and Indians ( P=0.001). The Malays and Indians also had allele frequencies significantly different from Caucasian, Japanese and African-American populations (each Pliterature. The *6 allele was not detected in any the three Asian ethnic groups analysed. These results seem to suggest that genetic polymorphisms in CYP3A5 in Asians, in particular Malays and Indians but also Chinese although to a lesser extent, may be an important genetic contributor to interindividual as well as interethnic differences in clearance of CYP3A substrates.

  3. Pharmacokinetic study of single- and multiple-dosing with metolazone tablets in healthy Chinese population.

    Science.gov (United States)

    Li, Xueqing; Wang, Rutao; Liu, Yang; Liu, Yun; Zheng, Heng; Feng, Yabo; Zhao, Na; Geng, Hongbin; Zhang, Wanzhi; Wen, Aidong

    2017-11-16

    Metolazone is a diuretic, saluretic and antihypertensive chemical compound from the quinazoline category that possesses medicinal features similar to those of other thiazide diuretic drugs. However, the pharmacokinetics of metolazone in the Chinese population has rarely been studied. This study aimed to examine the pharmacokinetic characteristics, safety characteristic, and tolerability of metolazone in healthy Chinese subjects after single and multiple doses taken orally as well as the effects that food and gender have on oral metolazone pharmacokinetic parameters. An open-label, randomized, and single- and multiple-dosing investigation was performed in healthy Chinese subjects. The investigation included 3 study groups: the 0.5 mg, 1 mg and 2 mg dose groups were the single-dose study groups in the first stage. Eligible volunteers were randomly and orally administered a single 0.5 mg, 1 mg, or 2 mg metolazone tablet. The 0.5 mg dose group was also part of the multiple-dose study group, and the 1 mg dose group was the food-effect study group in the second stage. Human plasma samples were gathered pre-dosing and up to 48 h after dosing. The human plasma sample concentration of metolazone was quantified using a validated liquid chromatography tandem mass spectrometry method. Pharmacokinetic data were calculated by a noncompartmental analysis method using WinNonlin version 6.4. Tolerability was evaluated based on adverse events, medical examination, 12-lead ECG, and other clinical laboratory exams. Thirty eligible subjects (15 men and 15 women) were registered in our investigation and completed all of the study stages. The AUC and C max showed dose proportionality after a single dose based on the linear-regression analysis. A comparison of the pharmacokinetic data revealed that the differences between the male and female groups were not statistically significant. The t max of metolazone was increased by approximately 100% in the fed condition. Metolazone was

  4. Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population

    Directory of Open Access Journals (Sweden)

    Jessica eLabonté

    2015-04-01

    Full Text Available A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a three km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32 % of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment.

  5. Mitochondrial Genome Diversity of Native Americans Supports a Single Early Entry of Founder Populations into America

    Science.gov (United States)

    Silva Jr., Wilson A.; Bonatto, Sandro L.; Holanda, Adriano J.; Ribeiro-dos-Santos, Andrea K.; Paixão, Beatriz M.; Goldman, Gustavo H.; Abe-Sandes, Kiyoko; Rodriguez-Delfin, Luis; Barbosa, Marcela; Paçó-Larson, Maria Luiza; Petzl-Erler, Maria Luiza; Valente, Valeria; Santos, Sidney E. B.; Zago, Marco A.

    2002-01-01

    There is general agreement that the Native American founder populations migrated from Asia into America through Beringia sometime during the Pleistocene, but the hypotheses concerning the ages and the number of these migrations and the size of the ancestral populations are surrounded by controversy. DNA sequence variations of several regions of the genome of Native Americans, especially in the mitochondrial DNA (mtDNA) control region, have been studied as a tool to help answer these questions. However, the small number of nucleotides studied and the nonclocklike rate of mtDNA control-region evolution impose several limitations to these results. Here we provide the sequence analysis of a continuous region of 8.8 kb of the mtDNA outside the D-loop for 40 individuals, 30 of whom are Native Americans whose mtDNA belongs to the four founder haplogroups. Haplogroups A, B, and C form monophyletic clades, but the five haplogroup D sequences have unstable positions and usually do not group together. The high degree of similarity in the nucleotide diversity and time of differentiation (i.e., ∼21,000 years before present) of these four haplogroups support a common origin for these sequences and suggest that the populations who harbor them may also have a common history. Additional evidence supports the idea that this age of differentiation coincides with the process of colonization of the New World and supports the hypothesis of a single and early entry of the ancestral Asian population into the Americas. PMID:12022039

  6. Elective single-embryo transfer: persuasive communication strategies can affect choice in a young British population.

    Science.gov (United States)

    van den Akker, O B A; Purewal, S

    2011-12-01

    This study tested the effectiveness of the framing effect and fear appeals to inform young people about the risks of multiple births and the option of selecting elective single-embryo transfer (eSET). A non-patient student sample (age (mean±SD) 23±5.5 years; n=321) were randomly allocated to one of seven groups: (1) framing effect: (1a) gain and (1b) loss frame; (2) fear appeal: (2a) high, (2b) medium and (2c) low fear; or (3) a control group: (3a) education and (3b) non-education. The primary outcome measure was the Attitudes towards Single Embryo Transfer questionnaire, before exposure to the messages (time 1) and immediately afterwards (time 2). Results revealed participants in the high fear, medium fear and gain condition demonstrated the most positive and significant differences (Ppersuasive communication techniques on a student population to promote immediate and hypothetical eSET preferences is more successful at promoting eSET than merely reporting educational content. Future research should investigate its application in a clinical population. A multiple pregnancy is a health risk to both infant and mother following IVF treatment. The aims of this study were to test the effectiveness of two persuasive communication techniques (the framing effect and fear appeals) to inform young people about the risks of multiple births and the hypothetical option of selecting elective single-embryo transfer (eSET) (i.e., only one embryo is transferred to the uterus using IVF treatment). A total of 321 non-patient student sample (mean age 23) were randomly allocated to read a message from one of seven groups: (1) framing effect: (1a) gain and (1b) loss frame; (2) fear appeal: (2a) high, (2b) medium and (2c) low fear; or (3) a control group: education (3a) and (3b) non-education. Participants completed the Attitudes towards Single Embryo Transfer questionnaire, before exposure to the messages (time 1) and immediately afterwards (time 2). Results revealed that participants

  7. HLA antigen distribution in Jain population from Mumbai, Maharashtra, India.

    Science.gov (United States)

    Chhaya, S U; Shankarkumar, U

    2001-07-01

    The Indian population is well known for its genetic diversity. Among the numerous endogamous communities, the Jain community from Mumbai is very restricted by custom, marriage and occupation. We present here the HLA antigen distribution of individuals belonging to this endogamous community. A total of 161 healthy individuals of the Jain community working or studying in a hospital at Mumbai were selected randomly during 1985-1988. HLA class I and class II antigens were identified by using the standard National Institutes of Health (NIH) microlymphocytotoxicity assay. The phenotypic frequencies of HLA A1, A2, A9, A11, A24, B5, B35, B40, Cw4, DR2, DR3, DR4, DR5 and DR7 were increased while frequencies of HLA A10, A19, A26, A32, B7, B14, B16, B21, B22, B27, B37, Cw2, DR1 and DR9 were decreased when compared with other populations from, Maharashtra. The phenotype frequencies of HLA A26, A28, A30, B18, B40, B56, Cw3, Cw4, DR3, DR4 and DR5 were increased while the frequencies of HLA B7, B15, B16, B22, B37, Cw2, Cw6, DR1 and DR9 were decreased when compared with frequencies in other Indian populations. Two locus haplotype analyses revealed that A9-B5, B35-Cw4, DR2-DQ1 and DR7-DQ2 were significant haplotypes among the positive linkage disequilibrium haplotypes. Whereas A9-B35, B35-Cw1 and DR1-DQ2 were significant haplotypes among the negative linkage disequilibrium haplotypes. The study revealed that the Jain population of Mumbai cannot be considered as a single panmictic population with reference to genetic characteristics, this may have a clinical relevance in unrelated donor selection for allogenic bone marrow transplantation in India.

  8. Series solution for continuous population models for single and interacting species by the homotopy analysis method

    Directory of Open Access Journals (Sweden)

    Magdy A. El-Tawil

    2012-07-01

    Full Text Available The homotopy analysis method (HAM is used to find approximate analytical solutions of continuous population models for single and interacting species. The homotopy analysis method contains the auxiliary parameter $hbar,$ which provides us with a simple way to adjust and control the convergence region of series solution. the solutions are compared with the numerical results obtained using NDSolve, an ordinary differential equation solver found in the Mathematica package and a good agreement is found. Also the solutions are compared with the available analytic results obtained by other methods and more accurate and convergent series solution found. The convergence region is also computed which shows the validity of the HAM solution. This method is reliable and manageable.

  9. Lyman alpha evolution at high resolution: evidence for a single population?

    International Nuclear Information System (INIS)

    Giallongo, E.

    1991-01-01

    Recent high-resolution spectroscopic data on the Lyman alpha absorption lines allow a statistical investigation of the cosmological evolution of Ly α clouds from z = 1.8 to 3.8. The maximum likelihood analysis shows that the number density evolution is differential, being progressively slower for stronger lines. There are discrepancies in the derived evolution for lines with equivalent widths W>0.3 A from line samples obtained at high and intermediate resolutions. A possible explanation is given in terms of line blending. A differential evolution of this type seems to imply a unified evolutionary scheme which incorporates Ly α and metal-line systems in a single population. (author)

  10. Stochastic adaptation and fold-change detection: from single-cell to population behavior

    Directory of Open Access Journals (Sweden)

    Leier André

    2011-02-01

    Full Text Available Abstract Background In cell signaling terminology, adaptation refers to a system's capability of returning to its equilibrium upon a transient response. To achieve this, a network has to be both sensitive and precise. Namely, the system must display a significant output response upon stimulation, and later on return to pre-stimulation levels. If the system settles at the exact same equilibrium, adaptation is said to be 'perfect'. Examples of adaptation mechanisms include temperature regulation, calcium regulation and bacterial chemotaxis. Results We present models of the simplest adaptation architecture, a two-state protein system, in a stochastic setting. Furthermore, we consider differences between individual and collective adaptive behavior, and show how our system displays fold-change detection properties. Our analysis and simulations highlight why adaptation needs to be understood in terms of probability, and not in strict numbers of molecules. Most importantly, selection of appropriate parameters in this simple linear setting may yield populations of cells displaying adaptation, while single cells do not. Conclusions Single cell behavior cannot be inferred from population measurements and, sometimes, collective behavior cannot be determined from the individuals. By consequence, adaptation can many times be considered a purely emergent property of the collective system. This is a clear example where biological ergodicity cannot be assumed, just as is also the case when cell replication rates are not homogeneous, or depend on the cell state. Our analysis shows, for the first time, how ergodicity cannot be taken for granted in simple linear examples either. The latter holds even when cells are considered isolated and devoid of replication capabilities (cell-cycle arrested. We also show how a simple linear adaptation scheme displays fold-change detection properties, and how rupture of ergodicity prevails in scenarios where transitions between

  11. Tourette's syndrome in a special education population: a pilot study involving a single school district.

    Science.gov (United States)

    Kurlan, R; Whitmore, D; Irvine, C; McDermott, M P; Como, P G

    1994-04-01

    To determine whether children requiring special education represent a high-risk group for identifying Tourette's syndrome (TS), we performed direct examinations for the presence of tics in 35 special education and 35 regular classroom students from a single school district. Of the special education students, nine (26%) had definite or probable tics as compared with only two (6%) of the regular classroom students. About one-third of the students with tics currently meet diagnostic criteria for TS and probably more will do so in the future. About one-half of the subjects with tics have evidence of obsessive-compulsive behavior (OCB) or an attention-deficit hyperactivity disorder (ADHD). For three randomly selected students with definite tics, direct examinations of first-degree relatives revealed the presence of tics in all families. Subjects to the limitations of this pilot study, we conclude that TS and related tic disorders are commonly associated with the need for special education in this single school district. TS might also be an important contributor to school problems in the childhood population at large and may be a highly prevalent condition. In addition, we conclude that childhood tics are associated with OCB and ADHD, are genetically determined, and are part of the TS clinical spectrum.

  12. Genetic homogeneity of the invasive lionfish across the Northwestern Atlantic and the Gulf of Mexico based on Single Nucleotide Polymorphisms.

    Science.gov (United States)

    Pérez-Portela, R; Bumford, A; Coffman, B; Wedelich, S; Davenport, M; Fogg, A; Swenarton, M K; Coleman, F; Johnston, M A; Crawford, D L; Oleksiak, M F

    2018-03-22

    Despite the devastating impact of the lionfish (Pterois volitans) invasion on NW Atlantic ecosystems, little genetic information about the invasion process is available. We applied Genotyping by Sequencing techniques to identify 1,220 single nucleotide polymorphic sites (SNPs) from 162 lionfish samples collected between 2013 and 2015 from two areas chronologically identified as the first and last invaded areas in US waters: the east coast of Florida and the Gulf of Mexico. We used population genomic analyses, including phylogenetic reconstruction, Bayesian clustering, genetic distances, Discriminant Analyses of Principal Components, and coalescence simulations for detection of outlier SNPs, to understand genetic trends relevant to the lionfish's long-term persistence. We found no significant differences in genetic structure or diversity between the two areas (F ST p-values > 0.01, and t-test p-values > 0.05). In fact, our genomic analyses showed genetic homogeneity, with enough gene flow between the east coast of Florida and Gulf of Mexico to erase previous signals of genetic divergence detected between these areas, secondary spreading, and bottlenecks in the Gulf of Mexico. These findings suggest rapid genetic changes over space and time during the invasion, resulting in one panmictic population with no signs of divergence between areas due to local adaptation.

  13. Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

    Science.gov (United States)

    Chiu, Isaac M; Barrett, Lee B; Williams, Erika K; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D; Lou, Shan; Bryman, Gregory S; Roberson, David P; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos, Enrique J; Stucky, Cheryl L; Ma, Qiufu; Liberles, Stephen D; Woolf, Clifford J

    2014-01-01

    The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4+SNS-Cre/TdTomato+, 2) IB4−SNS-Cre/TdTomato+, and 3) Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation. DOI: http://dx.doi.org/10.7554/eLife.04660.001 PMID:25525749

  14. Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure.

    Science.gov (United States)

    Albaina, A; Iriondo, M; Velado, I; Laconcha, U; Zarraonaindia, I; Arrizabalaga, H; Pardo, M A; Lutcavage, M; Grant, W S; Estonba, A

    2013-12-01

    The optimal management of the commercially important, but mostly over-exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded FST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between-ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17-SNP panel was developed in Atlantic BFT by cross-species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (FST  = 0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories. © 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics.

  15. The challenges of detecting subtle population structure and its importance for the conservation of emperor penguins.

    Science.gov (United States)

    Younger, Jane L; Clucas, Gemma V; Kao, Damian; Rogers, Alex D; Gharbi, Karim; Hart, Tom; Miller, Karen J

    2017-08-01

    Understanding the boundaries of breeding populations is of great importance for conservation efforts and estimates of extinction risk for threatened species. However, determining these boundaries can be difficult when population structure is subtle. Emperor penguins are highly reliant on sea ice, and some populations may be in jeopardy as climate change alters sea-ice extent and quality. An understanding of emperor penguin population structure is therefore urgently needed. Two previous studies have differed in their conclusions, particularly whether the Ross Sea, a major stronghold for the species, is isolated or not. We assessed emperor penguin population structure using 4,596 genome-wide single nucleotide polymorphisms (SNPs), characterized in 110 individuals (10-16 per colony) from eight colonies around Antarctica. In contrast to a previous conclusion that emperor penguins are panmictic around the entire continent, we find that emperor penguins comprise at least four metapopulations, and that the Ross Sea is clearly a distinct metapopulation. Using larger sample sizes and a thorough assessment of the limitations of different analytical methods, we have shown that population structure within emperor penguins does exist and argue that its recognition is vital for the effective conservation of the species. We discuss the many difficulties that molecular ecologists and managers face in the detection and interpretation of subtle population structure using large SNP data sets, and argue that subtle structure should be taken into account when determining management strategies for threatened species, until accurate estimates of demographic connectivity among populations can be made. © 2017 John Wiley & Sons Ltd.

  16. Association ofinterleukin-10gene single nucleotide polymorphisms with rheumatoid arthritis in a Chinese population.

    Science.gov (United States)

    Zhang, Tian-Ping; Lv, Tian-Tian; Xu, Shu-Zhen; Pan, Hai-Feng; Ye, Dong-Qing

    2018-02-27

    Increasing numbers of studies show that interleukin (IL)-10 plays a key role in the pathogenesis of autoimmune diseases including rheumatoid arthritis (RA) and acts as an immunomodulatory cytokine. The purpose of the present study was to analyse the relationship between gene single nucleotide polymorphisms (SNPs) in the IL-10 gene and RA susceptibility. We genotyped three SNPs (rs1800890, rs3024495, rs3024505) of the IL-10 gene in a Chinese population of 354 RA patients and 367 controls. Genotyping was conducted using TaqMan SNP genotyping assays. Plasma IL-10 levels were measured by ELISA. The A allele of the rs1800890 variant was significantly related to decreased risk for RA compared with the T allele (A vs T: OR 0.580, 95% CI 0.345 to 0.975, P=0.038). No significant association between the genotype distribution of these SNPs and RA susceptibility was detected. The genotype effect of the dominant model was also evaluated, but no statistical difference was found. Further analysis in RA patients demonstrated that none of these SNPs were associated with rheumatoid factor (RF) or anti-citrullinated protein antibody (anti-CCP). In addition, no significant differences in plasma IL-10 levels were observed among RA patients with different genotypes. The IL-10 rs1800890 variant might contribute to RA susceptibility in the Chinese population. Replication studies in different ethnic groups are required to further examine the critical role of IL-10 gene variation in the pathogenesis of RA. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  17. Common single nucleotide polymorphisms and keratoconus in the Han Chinese population.

    Science.gov (United States)

    Wang, Yani; Jin, Tianbo; Zhang, Xuehui; Wei, Wei; Cui, Yan; Geng, Tingting; Liu, Qianping; Gao, Jing; Liu, Ming; Chen, Chao; Zhang, Changning; Zhu, Xiuping

    2013-09-01

    To investigate whether the tag single nucleotide polymorphisms (tSNPs) in VSX1, COL4A3, COL4A4, IL1A and IL1B genes were associated with keratoconus (KTCN) in the Han Chinese population. Ninety-seven KTCN patients and 101 healthy controls were enrolled in this study. All cases were diagnosed on the basis of clinical examination. Twenty-one tSNPs were selected for association study in five genes. SNP genotyping was performed by Sequenom MassARRAY RS1000. Sequenom Typer 4.0 Software, PLINK, Haploview and SHEsis software platform were used to perform data management and analyses. Three tSNPs in the VSX1 gene were observed to be associated with KTCN risk at a 5% level by χ(2) test (rs56157240 and rs12480307, p = 0.0499, OR: 6.42, 95% CI: 0.77-53.78; rs6050307, p = 1.22 × 10(-7), OR: 0.05, 95% CI: 0.01-0.23). Rs2071376 in the IL1A gene was also associated with KTCN (p = 0.0487, OR: 1.51, 95% CI: 1.00-2.26). Three haplotypes in the VSX1 gene were found to be associated with risk of KTCN (p < 0.05). Our findings confirmed previous reports that polymorphisms of VSX1 and IL1A genes were associated with risk of KTCN in the Chinese population, suggesting an important determinant of KTCN development by VSX1 and IL1A genes.

  18. Emergence of cytotoxic resistance in cancer cell populations: Single-cell mechanisms and population-level consequences

    International Nuclear Information System (INIS)

    Lorenzi, Tommaso; Chisholm, Rebecca H.; Lorz, Alexander; Neves de Almeida, Luís; Clairambault, Jean; Larsen, Annette K.; Escargueil, Alexandre

    2016-01-01

    We formulate an individual-based model and a population model of phenotypic evolution, under cytotoxic drugs, in a cancer cell population structured by the expression levels of survival-potential and proliferation-potential. We apply these models to a recently studied experimental system. Our results suggest that mechanisms based on fundamental laws of biology can reversibly push an actively-proliferating, and drug-sensitive, cell population to transition into a weakly-proliferative and drug-tolerant state, which will eventually facilitate the emergence of more potent, proliferating and drug-tolerant cells.

  19. Emergence of cytotoxic resistance in cancer cell populations: Single-cell mechanisms and population-level consequences

    Energy Technology Data Exchange (ETDEWEB)

    Lorenzi, Tommaso [Centre de Mathématiques et de Leurs Applications, ENS Cachan, CNRS, Cachan 94230 Cedex, France & INRIA-Paris-Rocquencourt, MAMBA Team, Domaine de Voluceau, BP105, 78153 Le Chesnay Cedex (France); Chisholm, Rebecca H. [School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052 (Australia); Lorz, Alexander; Neves de Almeida, Luís; Clairambault, Jean [Sorbonne Universités, UPMC Univ Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris (France); CNRS, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris (France); INRIA-Paris-Rocquencourt, MAMBA Team, Domaine de Voluceau, BP105, 78153 Le Chesnay Cedex (France); Larsen, Annette K.; Escargueil, Alexandre [Sorbonne Universités, UPMC Univ Paris 06, F-75005, Paris (France); INSERM, UMR-S 938, Laboratory of “Cancer Biology and Therapeutics”, F-75012, Paris (France)

    2016-06-08

    We formulate an individual-based model and a population model of phenotypic evolution, under cytotoxic drugs, in a cancer cell population structured by the expression levels of survival-potential and proliferation-potential. We apply these models to a recently studied experimental system. Our results suggest that mechanisms based on fundamental laws of biology can reversibly push an actively-proliferating, and drug-sensitive, cell population to transition into a weakly-proliferative and drug-tolerant state, which will eventually facilitate the emergence of more potent, proliferating and drug-tolerant cells.

  20. Metabolic diversity and ecological niches of Achromatium populations revealed with single-cell genomic sequencing

    Directory of Open Access Journals (Sweden)

    Muammar eMansor

    2015-08-01

    Full Text Available Large, sulfur-cycling, calcite-precipitating bacteria in the genus Achromatium represent a significant proportion of bacterial communities near sediment-water interfaces throughout the world. Our understanding of their potentially crucial roles in calcium, carbon, sulfur, nitrogen, and iron cycling is limited because they have not been cultured or sequenced using environmental genomics approaches to date. We utilized single-cell genomic sequencing to obtain one incomplete and two nearly complete draft genomes for Achromatium collected at Warm Mineral Springs, FL. Based on 16S rRNA gene sequences, the three cells represent distinct and relatively distant Achromatium populations (91-92% identity. The draft genomes encode key genes involved in sulfur and hydrogen oxidation; oxygen, nitrogen and polysulfide respiration; carbon and nitrogen fixation; organic carbon assimilation and storage; chemotaxis; twitching motility; antibiotic resistance; and membrane transport. Known genes for iron and manganese energy metabolism were not detected. The presence of pyrophosphatase and vacuolar (V-type ATPases, which are generally rare in bacterial genomes, suggests a role for these enzymes in calcium transport, proton pumping, and/or energy generation in the membranes of calcite-containing inclusions.

  1. Associations between single nucleotide polymorphisms in iron-related genes and iron status in multiethnic populations.

    Directory of Open Access Journals (Sweden)

    Christine E McLaren

    Full Text Available The existence of multiple inherited disorders of iron metabolism suggests genetic contributions to iron deficiency. We previously performed a genome-wide association study of iron-related single nucleotide polymorphisms (SNPs using DNA from white men aged ≥ 25 y and women ≥ 50 y in the Hemochromatosis and Iron Overload Screening (HEIRS Study with serum ferritin (SF ≤ 12 µg/L (cases and controls (SF >100 µg/L in men, SF >50 µg/L in women. We report a follow-up study of white, African-American, Hispanic, and Asian HEIRS participants, analyzed for association between SNPs and eight iron-related outcomes. Three chromosomal regions showed association across multiple populations, including SNPs in the TF and TMPRSS6 genes, and on chromosome 18q21. A novel SNP rs1421312 in TMPRSS6 was associated with serum iron in whites (p = 3.7 × 10(-6 and replicated in African Americans (p = 0.0012.Twenty SNPs in the TF gene region were associated with total iron-binding capacity in whites (p<4.4 × 10(-5; six SNPs replicated in other ethnicities (p<0.01. SNP rs10904850 in the CUBN gene on 10p13 was associated with serum iron in African Americans (P = 1.0 × 10(-5. These results confirm known associations with iron measures and give unique evidence of their role in different ethnicities, suggesting origins in a common founder.

  2. Clonal diversity and population genetic structure of arbuscular mycorrhizal fungi (Glomus spp.) studied by multilocus genotyping of single spores

    DEFF Research Database (Denmark)

    Holtgrewe-Stukenbrock, Eva; Rosendahl, Søren

    2005-01-01

    A nested multiplex PCR (polymerase chain reaction) approach was used for multilocus genotyping of arbuscular mycorrhizal fungal populations. This method allowed us to amplify multiple loci from Glomus single spores in a single PCR amplification. Variable introns in the two protein coding genes Gm......FOX2 and GmTOR2 were applied as codominant genetic markers together with the LSU rDNA.   Genetic structure of Glomus spp. populations from an organically and a conventionally cultured field were compared by hierarchical sampling of spores from four plots in each field. Multilocus genotypes were...

  3. The evolutionary dynamics of the lion Panthera leo revealed by host and viral population genomics.

    Science.gov (United States)

    Antunes, Agostinho; Troyer, Jennifer L; Roelke, Melody E; Pecon-Slattery, Jill; Packer, Craig; Winterbach, Christiaan; Winterbach, Hanlie; Hemson, Graham; Frank, Laurence; Stander, Philip; Siefert, Ludwig; Driciru, Margaret; Funston, Paul J; Alexander, Kathy A; Prager, Katherine C; Mills, Gus; Wildt, David; Bush, Mitch; O'Brien, Stephen J; Johnson, Warren E

    2008-11-01

    The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA), paternal (Y-chromosome), and biparental nuclear (nDNA) genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIV(Ple)), a lentivirus analogous to human immunodeficiency virus (HIV). In spite of the ability of lions to disperse long distances, patterns of lion genetic diversity suggest substantial population subdivision (mtDNA Phi(ST) = 0.92; nDNA F(ST) = 0.18), and reduced gene flow, which, along with large differences in sero-prevalence of six distinct FIV(Ple) subtypes among lion populations, refute the hypothesis that African lions consist of a single panmictic population. Our results suggest that extant lion populations derive from several Pleistocene refugia in East and Southern Africa ( approximately 324,000-169,000 years ago), which expanded during the Late Pleistocene ( approximately 100,000 years ago) into Central and North Africa and into Asia. During the Pleistocene/Holocene transition ( approximately 14,000-7,000 years), another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIV(Ple) variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently.

  4. The evolutionary dynamics of the lion Panthera leo revealed by host and viral population genomics.

    Directory of Open Access Journals (Sweden)

    Agostinho Antunes

    2008-11-01

    Full Text Available The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA, paternal (Y-chromosome, and biparental nuclear (nDNA genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIV(Ple, a lentivirus analogous to human immunodeficiency virus (HIV. In spite of the ability of lions to disperse long distances, patterns of lion genetic diversity suggest substantial population subdivision (mtDNA Phi(ST = 0.92; nDNA F(ST = 0.18, and reduced gene flow, which, along with large differences in sero-prevalence of six distinct FIV(Ple subtypes among lion populations, refute the hypothesis that African lions consist of a single panmictic population. Our results suggest that extant lion populations derive from several Pleistocene refugia in East and Southern Africa ( approximately 324,000-169,000 years ago, which expanded during the Late Pleistocene ( approximately 100,000 years ago into Central and North Africa and into Asia. During the Pleistocene/Holocene transition ( approximately 14,000-7,000 years, another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIV(Ple variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently.

  5. Single-Cell Behavior and Population Heterogeneity: Solving an Inverse Problem to Compute the Intrinsic Physiological State Functions

    OpenAIRE

    Spetsieris, Konstantinos; Zygourakis, Kyriacos

    2011-01-01

    The dynamics of isogenic cell populations can be described by cell population balance models that account for phenotypic heterogeneity. To utilize the predictive power of these models, however, we must know the rates of single-cell reaction and division and the bivariate partition probability density function. These three intrinsic physiological state (IPS) functions can be obtained by solving an inverse problem that requires knowledge of the phenotypic distributions for the overall cell popu...

  6. Brief communication genotyping of Burkholderia pseudomallei revealed high genetic variability among isolates from a single population group

    OpenAIRE

    Zueter, Abdelrahman Mohammad; Rahman, Zaidah Abdul; Yean, Chan Yean; Harun, Azian

    2015-01-01

    Burkholderia pseudomallei is a soil dwelling Gram-negative bacteria predominates in Southeast Asia zone and the tropical part of Australia. Genetic diversity has been explored among various populations and environments worldwide. To date, little data is available on MLST profiling of clinical B. pseudomallei isolates in peninsular Malaysia. In this brief report, thirteen culture positive B. pseudomallei cases collected from a single population of Terengganu state in the Western Peninsular Mal...

  7. Models of synchronized hippocampal bursts in the presence of inhibition. I. Single population events.

    Science.gov (United States)

    Traub, R D; Miles, R; Wong, R K

    1987-10-01

    1. We constructed model networks with 520 or 1,020 cells intended to represent the CA3 region of the hippocampus. Model neurons were simulated in enough detail to reproduce intrinsic bursting and the electrotonic flow of currents along dendritic cables. Neurons exerted either excitatory or inhibitory postsynaptic actions on other cells. The network models were simulated with different levels of excitatory and inhibitory synaptic strengths in order to study epileptic and other interesting collective behaviors in the system. 2. Excitatory synapses between neurons in the network were powerful enough so that burst firing in a presynaptic neuron would evoke bursting in its connected cells. Since orthodromic or antidromic stimulation evokes both a fast and a slow phase of inhibition, two types of inhibitory cells were simulated. The properties of these inhibitory cells were modeled to resemble those of two types of inhibitory cells characterized by dual intracellular recordings in the slice preparation. 3. With fast inhibition totally blocked, a stimulus to a single cell lead to a synchronized population burst. Thus the principles of our epileptic synchronization model, developed earlier, apply even when slow inhibitory postsynaptic potentials (IPSPs) are present, as apparently occurs in the epileptic hippocampal slice. The model performs in this way because bursting can propagate through several generations in the network before slow inhibition builds up enough to block burst propagation. This can occur, however, only if connectivity is sufficiently large. With very low connection densities, slow IPSPs will prevent the development of full synchronization. 4. We performed multiple simulations in which the fast inhibitory conductance strength was kept fixed at various levels while the strength of the excitatory synapses was varied. In each simulation, we stimulated either one or four cells. For each level of inhibition, the peak number of cells bursting depended

  8. Genetics of single-cell protein abundance variation in large yeast populations

    Science.gov (United States)

    Albert, Frank W.; Treusch, Sebastian; Shockley, Arthur H.; Bloom, Joshua S.; Kruglyak, Leonid

    2014-02-01

    Variation among individuals arises in part from differences in DNA sequences, but the genetic basis for variation in most traits, including common diseases, remains only partly understood. Many DNA variants influence phenotypes by altering the expression level of one or several genes. The effects of such variants can be detected as expression quantitative trait loci (eQTL). Traditional eQTL mapping requires large-scale genotype and gene expression data for each individual in the study sample, which limits sample sizes to hundreds of individuals in both humans and model organisms and reduces statistical power. Consequently, many eQTL are probably missed, especially those with smaller effects. Furthermore, most studies use messenger RNA rather than protein abundance as the measure of gene expression. Studies that have used mass-spectrometry proteomics reported unexpected differences between eQTL and protein QTL (pQTL) for the same genes, but these studies have been even more limited in scope. Here we introduce a powerful method for identifying genetic loci that influence protein expression in the yeast Saccharomyces cerevisiae. We measure single-cell protein abundance through the use of green fluorescent protein tags in very large populations of genetically variable cells, and use pooled sequencing to compare allele frequencies across the genome in thousands of individuals with high versus low protein abundance. We applied this method to 160 genes and detected many more loci per gene than previous studies. We also observed closer correspondence between loci that influence protein abundance and loci that influence mRNA abundance of a given gene. Most loci that we detected were clustered in `hotspots' that influence multiple proteins, and some hotspots were found to influence more than half of the proteins that we examined. The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell

  9. Two Positive Periodic Solutions for a Neutral Delay Model of Single-Species Population Growth with Harvesting

    OpenAIRE

    Fang, Hui

    2012-01-01

    By coincidence degree theory for k-set-contractive mapping, this paper establishes a new criterion for the existence of at least two positive periodic solutions for a neutral delay model of single-species population growth with harvesting. An example is given to illustrate the effectiveness of the result.

  10. Two Positive Periodic Solutions for a Neutral Delay Model of Single-Species Population Growth with Harvesting

    Directory of Open Access Journals (Sweden)

    Hui Fang

    2012-01-01

    Full Text Available By coincidence degree theory for k-set-contractive mapping, this paper establishes a new criterion for the existence of at least two positive periodic solutions for a neutral delay model of single-species population growth with harvesting. An example is given to illustrate the effectiveness of the result.

  11. Early and late preterm delivery rates - a comparison of differing tocolytic policies in a single urban population.

    LENUS (Irish Health Repository)

    Hehir, Mark P

    2012-11-01

    Preterm delivery results in neonatal morbidity and mortality. We set out to estimate the difference in rates of preterm delivery in two institutions, serving a single population, with differing policies regarding use of tocolytic drugs for the prevention of preterm delivery.

  12. A panel of 130 autosomal single-nucleotide polymorphisms for ancestry assignment in five Asian populations and in Caucasians.

    Science.gov (United States)

    Hwa, Hsiao-Lin; Lin, Chih-Peng; Huang, Tsun-Ying; Kuo, Po-Hsiu; Hsieh, Wei-Hsin; Lin, Chun-Yen; Yin, Hsiang-I; Tseng, Li-Hui; Lee, James Chun-I

    2017-06-01

    Ancestry informative single-nucleotide polymorphism (AISNP) panels for differentiating between East and Southeast Asian populations are scarce. This study aimed to identify AISNPs for ancestry assignment of five East and Southeast Asian populations, and Caucasians. We analyzed 145 autosomal SNPs of the 627 DNA samples from individuals of six populations (234 Taiwanese Han, 91 Filipinos, 79 Indonesians, 60 Thais, 71 Vietnamese, and 92 Caucasians) using arrays. The multiple logistic regression model and a multi-tier approach were used for ancestry classification. We observed that 130 AISNPs were effective for classifying the ethnic origins with fair accuracy. Among the 130 AISNPs, 122 were useful for stratification between these five Asian populations and 64 were effective for differentiating between Caucasians and these Asian populations. For differentiation between Caucasians and Asians, an accuracy rate of 100% was achieved in these 627 subjects with 50 optimal AISNPs among the 64 effective SNPs. For classification of the five Asian populations, the accuracy rates of ancestry inference using 20 to 57 SNPs for each of the two Asian populations ranged from 74.1% to 100%. Another 14 degraded DNA samples with incomplete profiling were analyzed, and the ancestry of 12 (85.7%) of those subjects was accurately assigned. We developed a 130-AISNP panel for ethnic origin differentiation between the five East and Southeast Asian populations and Caucasians. This AISNP set may be helpful for individual ancestral assignment of these populations in forensic casework.

  13. Single-cell behavior and population heterogeneity: solving an inverse problem to compute the intrinsic physiological state functions.

    Science.gov (United States)

    Spetsieris, Konstantinos; Zygourakis, Kyriacos

    2012-04-15

    The dynamics of isogenic cell populations can be described by cell population balance models that account for phenotypic heterogeneity. To utilize the predictive power of these models, however, we must know the rates of single-cell reaction and division and the bivariate partition probability density function. These three intrinsic physiological state (IPS) functions can be obtained by solving an inverse problem that requires knowledge of the phenotypic distributions for the overall cell population, the dividing cell subpopulation and the newborn cell subpopulation. We present here a robust computational procedure that can accurately estimate the IPS functions for heterogeneous cell populations. A detailed parametric analysis shows how the accuracy of the inverse solution is affected by discretization parameters, the type of non-parametric estimators used, the qualitative characteristics of phenotypic distributions and the unknown partitioning probability density function. The effect of finite sampling and measurement errors on the accuracy of the recovered IPS functions is also assessed. Finally, we apply the procedure to estimate the IPS functions of an E. coli population carrying an IPTG-inducible genetic toggle network. This study completes the development of an integrated experimental and computational framework that can become a powerful tool for quantifying single-cell behavior using measurements from heterogeneous cell populations. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. Predicting the effects of climate change on population connectivity and genetic diversity of an imperiled freshwater mussel, Cumberlandia monodonta (Bivalvia: Margaritiferidae), in riverine systems.

    Science.gov (United States)

    Inoue, Kentaro; Berg, David J

    2017-01-01

    In the face of global climate change, organisms may respond to temperature increases by shifting their ranges poleward or to higher altitudes. However, the direction of range shifts in riverine systems is less clear. Because rivers are dendritic networks, there is only one dispersal route from any given location to another. Thus, range shifts are only possible if branches are connected by suitable habitat, and stream-dwelling organisms can disperse through these branches. We used Cumberlandia monodonta (Bivalvia: Unionoida: Margaritiferidae) as a model species to investigate the effects of climate change on population connectivity because a majority of contemporary populations are panmictic. We combined ecological niche models (ENMs) with population genetic simulations to investigate the effects of climate change on population connectivity and genetic diversity of C. monodonta. The ENMs were constructed using bioclimatic and landscape data to project shifts in suitable habitat under future climate scenarios. We then used forward-time simulations to project potential changes in genetic diversity and population connectivity based on these range shifts. ENM results under current conditions indicated long stretches of highly suitable habitat in rivers where C. monodonta persists; populations in the upper Mississippi River remain connected by suitable habitat that does not impede gene flow. Future climate scenarios projected northward and headwater-ward range contraction and drastic declines in habitat suitability for most extant populations throughout the Mississippi River Basin. Simulations indicated that climate change would greatly reduce genetic diversity and connectivity across populations. Results suggest that a single, large population of C. monodonta will become further fragmented into smaller populations, each of which will be isolated and begin to differentiate genetically. Because C. monodonta is a widely distributed species and purely aquatic, our

  15. Population pharmacokinetics of recombinant coagulation factor VIII-SingleChain in patients with severe hemophilia A.

    Science.gov (United States)

    Zhang, Y; Roberts, J; Tortorici, M; Veldman, A; St Ledger, K; Feussner, A; Sidhu, J

    2017-06-01

    Essentials rVIII-SingleChain is a unique recombinant factor VIII (FVIII) molecule. A population pharmacokinetic model was based on FVIII activity of severe hemophilia A patients. The model was used to simulate factor VIII activity-time profiles for various dosing scenarios. The model supports prolonged dosing of rVIII-SingleChain with intervals of up to twice per week. Background Single-chain recombinant coagulation factor VIII (rVIII-SingleChain) is a unique recombinant coagulation factor VIII molecule. Objectives To: (i) characterize the population pharmacokinetics (PK) of rVIII-SingleChain in patients with severe hemophilia A; (ii) identify correlates of variability in rVIII-SingleChain PK; and (iii) simulate various dosing scenarios of rVIII-SingleChain. Patients/Methods A population PK model was developed, based on FVIII activity levels of 130 patients with severe hemophilia A (n = 91 for ≥ 12-65 years; n = 39 for  85% and > 93% of patients were predicted to maintain FVIII activity level above 1 IU dL -1 , at all times with three-times-weekly dosing (given on days 0, 2, and 4.5) at the lowest (20 IU kg -1 ) and highest (50 IU kg -1 ) doses, respectively. For twice weekly dosing (days 0 and 3.5) of 50 IU kg -1 rVIII-SingleChain, 62-80% of patients across all ages were predicted to maintain a FVIII activity level above 1 IU dL -1 at day 7. Conclusions The population PK model adequately characterized rVIII-SingleChain PK, and the model can be utilized to simulate FVIII activity-time profiles for various dosing scenarios. © 2017 The Authors. Journal of Thrombosis and Haemostasis published by Wiley Periodicals, Inc. on behalf of International Society on Thrombosis and Haemostasis.

  16. Analysis of single hyphal growth and fragmentation in submerged cultures using a population model

    DEFF Research Database (Denmark)

    Krabben, Preben; Nielsen, Søren; Michelsen, Michael Locht

    1997-01-01

    Descriptions of population dynamics in submerged cultures are important when studying the mechanisms of growth and fragmentation of filamentous microorganisms. Population models are traditionally formulated as population balance equations. Population models of filamentous morphology are difficult...... to solve because of random fragmentation, which introduces an integral term into the population balance equations. Balances for the systemic properties, e.g. concentration of hyphal elements, substrate concentration, average total hyphal length, and average number of growing tips, are set up. Based...... on these balances one can solve the inverse problem, i.e. determination of kinetic parameters directly from measurements of the hyphal morphology. Both a Monte Carlo method and a discretization method have been used to calculate the steady-state population distribution. The two methods are compared and the Monte...

  17. Comparison on genomic predictions using three GBLUP methods and two single-step blending methods in the Nordic Holstein population

    Directory of Open Access Journals (Sweden)

    Gao Hongding

    2012-07-01

    Full Text Available Abstract Background A single-step blending approach allows genomic prediction using information of genotyped and non-genotyped animals simultaneously. However, the combined relationship matrix in a single-step method may need to be adjusted because marker-based and pedigree-based relationship matrices may not be on the same scale. The same may apply when a GBLUP model includes both genomic breeding values and residual polygenic effects. The objective of this study was to compare single-step blending methods and GBLUP methods with and without adjustment of the genomic relationship matrix for genomic prediction of 16 traits in the Nordic Holstein population. Methods The data consisted of de-regressed proofs (DRP for 5 214 genotyped and 9 374 non-genotyped bulls. The bulls were divided into a training and a validation population by birth date, October 1, 2001. Five approaches for genomic prediction were used: 1 a simple GBLUP method, 2 a GBLUP method with a polygenic effect, 3 an adjusted GBLUP method with a polygenic effect, 4 a single-step blending method, and 5 an adjusted single-step blending method. In the adjusted GBLUP and single-step methods, the genomic relationship matrix was adjusted for the difference of scale between the genomic and the pedigree relationship matrices. A set of weights on the pedigree relationship matrix (ranging from 0.05 to 0.40 was used to build the combined relationship matrix in the single-step blending method and the GBLUP method with a polygenetic effect. Results Averaged over the 16 traits, reliabilities of genomic breeding values predicted using the GBLUP method with a polygenic effect (relative weight of 0.20 were 0.3% higher than reliabilities from the simple GBLUP method (without a polygenic effect. The adjusted single-step blending and original single-step blending methods (relative weight of 0.20 had average reliabilities that were 2.1% and 1.8% higher than the simple GBLUP method, respectively. In

  18. Putative panmixia in restricted populations of Trypanosoma cruzi isolated from wild Triatoma infestans in Bolivia.

    Directory of Open Access Journals (Sweden)

    Christian Barnabe

    Full Text Available Trypanosoma cruzi, the causative agent of Chagas disease, is subdivided into six discrete typing units (DTUs; TcI-TcVI of which TcI is ubiquitous and genetically highly variable. While clonality is the dominant mode of propagation, recombinant events play a significant evolutive role. Recently, foci of wild Triatoma infestans have been described in Bolivia, mainly infected by TcI. Hence, for the first time, we evaluated the level of genetic exchange within TcI natural potentially panmictic populations (single DTU, host, area and sampling time. Seventy-nine TcI stocks from wild T. infestans, belonging to six populations were characterized at eight microsatellite loci. For each population, Hardy-Weinberg equilibrium (HWE, linkage disequilibrium (LD, and presence of repeated multilocus genotypes (MLG were analyzed by using a total of seven statistics, to test the null hypothesis of panmixia (H0. For three populations, none of the seven statistics allowed to rejecting H0; for another one the low size did not allow us to conclude, and for the two others the tests have given contradictory results. Interestingly, apparent panmixia was only observed in very restricted areas, and was not observed when grouping populations distant of only two kilometers or more. Nevertheless it is worth stressing that for the statistic tests of "HWE", in order to minimize the type I error (i. e. incorrect rejection of a true H0, we used the Bonferroni correction (BC known to considerably increase the type II error ( i. e. failure to reject a false H0. For the other tests (LD and MLG, we did not use BC and the risk of type II error in these cases was acceptable. Thus, these results should be considered as a good indicator of the existence of panmixia in wild environment but this must be confirmed on larger samples to reduce the risk of type II error.

  19. Harlequin Duck recovery from the Exxon Valdez oil spill: A population genetics perspective

    Science.gov (United States)

    Lanctot, R.; Goatcher, B.; Scribner, K.; Talbot, S.; Pierson, B.; Esler, Daniel; Zwiefelhofer, D.

    1999-01-01

    Concerns about Harlequin Duck (Histrionicus histrionicus) population recovery following the Exxon Valdez oil spill led biologists to ask whether birds located in different molting and wintering areas belong to genetically distinct and, thus, demographically independent populations. Owing to the lack of direct observations of movements among marine areas, three classes of genetic markers that differed in mode of inheritance were used to evaluate the degree of genetic differentiation among wintering areas within Prince William Sound (PWS) and the Alaska Peninsula and Kodiak Archipelago (APKA). We could not reject the null hypothesis that the wintering aggregations within each region are composed of a single genetically panmictic population. Differences in genotype frequencies among wintering locations within PWS and APKA were low and nonsignificant for all three classes of markers. Furthermore, we saw no evidence for deviations in Hardy-Weinberg equilibrium or gametic disequilibrium between loci within a winter collection site as would be expected if these locales were composed of individuals from reproductively isolated (and genetically distinct) breeding locales. Finally, no evidence for significant structuring was noted between PWS and APKA. Lack of spatial genetic structuring could be due to the cumulative effects of low levels of gene flow over long time periods, low levels of gene flow by immature birds moving between marine habitats, or to episodic dispersal caused by habitat alteration (e.g. volcanic eruptions). Harlequin Ducks are likely to recolonize or enhance populations in areas recovering from environmental damage via emigration of birds from non-affected areas. Demographic studies suggest, however, that levels of movements are low, and that population recovery by emigration is a long-term process.

  20. Putative Panmixia in Restricted Populations of Trypanosoma cruzi Isolated from Wild Triatoma infestans in Bolivia

    Science.gov (United States)

    Barnabe, Christian; Buitrago, Rosio; Bremond, Philippe; Aliaga, Claudia; Salas, Renata; Vidaurre, Pablo; Herrera, Claudia; Cerqueira, Frédérique; Bosseno, Marie-France; Waleckx, Etienne; Breniere, Simone Frédérique

    2013-01-01

    Trypanosoma cruzi, the causative agent of Chagas disease, is subdivided into six discrete typing units (DTUs; TcI–TcVI) of which TcI is ubiquitous and genetically highly variable. While clonality is the dominant mode of propagation, recombinant events play a significant evolutive role. Recently, foci of wild Triatoma infestans have been described in Bolivia, mainly infected by TcI. Hence, for the first time, we evaluated the level of genetic exchange within TcI natural potentially panmictic populations (single DTU, host, area and sampling time). Seventy-nine TcI stocks from wild T. infestans, belonging to six populations were characterized at eight microsatellite loci. For each population, Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), and presence of repeated multilocus genotypes (MLG) were analyzed by using a total of seven statistics, to test the null hypothesis of panmixia (H0). For three populations, none of the seven statistics allowed to rejecting H0; for another one the low size did not allow us to conclude, and for the two others the tests have given contradictory results. Interestingly, apparent panmixia was only observed in very restricted areas, and was not observed when grouping populations distant of only two kilometers or more. Nevertheless it is worth stressing that for the statistic tests of "HWE", in order to minimize the type I error (i. e. incorrect rejection of a true H0), we used the Bonferroni correction (BC) known to considerably increase the type II error ( i. e. failure to reject a false H0). For the other tests (LD and MLG), we did not use BC and the risk of type II error in these cases was acceptable. Thus, these results should be considered as a good indicator of the existence of panmixia in wild environment but this must be confirmed on larger samples to reduce the risk of type II error. PMID:24312410

  1. Assessment of host-associated genetic differentiation among phenotypically divergent populations of a coral-eating gastropod across the Caribbean.

    Directory of Open Access Journals (Sweden)

    Lyza Johnston

    Full Text Available Host-associated adaptation is emerging as a potential driver of population differentiation and speciation for marine organisms with major implications for ecosystem structure and function. Coralliophila abbreviata are corallivorous gastropods that live and feed on most of the reef-building corals in the tropical western Atlantic and Caribbean. Populations of C. abbreviata associated with the threatened acroporid corals, Acropora palmata and A. cervicornis, display different behavioral, morphological, demographic, and life-history characteristics than those that inhabit other coral host taxa, indicating that host-specific selective forces may be acting on C. abbreviata. Here, we used newly developed polymorphic microsatellite loci and mitochondrial cytochrome b sequence data to assess the population genetic structure, connectivity, and demographic history of C. abbreviata populations from three coral host taxa (A. palmata, Montastraea spp., Mycetophyllia spp. and six geographic locations across the Caribbean. Analysis of molecular variance provided some evidence of weak and possibly geographically variable host-associated differentiation but no evidence of differentiation among sampling locations or major oceanographic regions, suggesting high gene flow across the Caribbean. Phylogenetic network and bayesian clustering analyses supported a hypothesis of a single panmictic population as individuals failed to cluster by host or sampling location. Demographic analyses consistently supported a scenario of population expansion during the Pleistocene, a time of major carbonate reef development in the region. Although further study is needed to fully elucidate the interactive effects of host-associated selection and high gene flow in this system, our results have implications for local and regional community interactions and impact of predation on declining coral populations.

  2. Assessment of host-associated genetic differentiation among phenotypically divergent populations of a coral-eating gastropod across the Caribbean.

    Science.gov (United States)

    Johnston, Lyza; Miller, Margaret W; Baums, Iliana B

    2012-01-01

    Host-associated adaptation is emerging as a potential driver of population differentiation and speciation for marine organisms with major implications for ecosystem structure and function. Coralliophila abbreviata are corallivorous gastropods that live and feed on most of the reef-building corals in the tropical western Atlantic and Caribbean. Populations of C. abbreviata associated with the threatened acroporid corals, Acropora palmata and A. cervicornis, display different behavioral, morphological, demographic, and life-history characteristics than those that inhabit other coral host taxa, indicating that host-specific selective forces may be acting on C. abbreviata. Here, we used newly developed polymorphic microsatellite loci and mitochondrial cytochrome b sequence data to assess the population genetic structure, connectivity, and demographic history of C. abbreviata populations from three coral host taxa (A. palmata, Montastraea spp., Mycetophyllia spp.) and six geographic locations across the Caribbean. Analysis of molecular variance provided some evidence of weak and possibly geographically variable host-associated differentiation but no evidence of differentiation among sampling locations or major oceanographic regions, suggesting high gene flow across the Caribbean. Phylogenetic network and bayesian clustering analyses supported a hypothesis of a single panmictic population as individuals failed to cluster by host or sampling location. Demographic analyses consistently supported a scenario of population expansion during the Pleistocene, a time of major carbonate reef development in the region. Although further study is needed to fully elucidate the interactive effects of host-associated selection and high gene flow in this system, our results have implications for local and regional community interactions and impact of predation on declining coral populations.

  3. Non-invasive single-trial detection of variable population spike responses in human somatosensory evoked potentials.

    Science.gov (United States)

    Waterstraat, Gunnar; Scheuermann, Manuel; Curio, Gabriel

    2016-03-01

    Somatosensory evoked potentials (SEPs) around 600 Hz ('σ-bursts') are correlates of cortical population spikes. Recently, single-trial σ-bursts were detected in human scalp EEG using 29-channel low-noise recordings in an electromagnetically shielded room. To achieve clinical applicability, this study aimed to establish a protocol using only 8 EEG channels in an unshielded environment and to quantify the variability of σ-bursts. Median nerve SEPs were recorded in 10 healthy subjects using a custom-built low-noise EEG amplifier. A detection algorithm for single-trial σ-bursts was trained as combination of spatio-temporal filters and a non-linear classifier. The single-trial responses were probed for the presence of significant increases of amplitude and variability. Single-trial σ-burst detection succeeded with Detection Rates and Positive Predictive Values above 80% in subjects with high SNR. A significant inter-trial variability in the amplitudes of early low-frequency SEPs and σ-bursts could be demonstrated. Single-trial σ-bursts can be detected on scalp-EEG using only 8 EEG channels in an electromagnetically disturbed environment. The combination of dedicated hardware and detection algorithms allows quantifying and describing their variability. The variability of population spikes in the human somatosensory cortex can be traced non-invasively in a clinical setting. Copyright © 2015 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

  4. Complete transfer of populations from a single state to a preselected superposition of states using piecewise adiabatic passage: Experiment

    International Nuclear Information System (INIS)

    Zhdanovich, S.; Shapiro, E. A.; Hepburn, J. W.; Shapiro, M.; Milner, V.

    2009-01-01

    We demonstrate a method of adiabatic population transfer from a single quantum state into a coherent superposition of states. The transfer is executed with femtosecond pulses, spectrally shaped in a simple and intuitive manner, which does not require iterative feedback-controlled loops. In contrast to nonadiabatic methods of excitation, our approach is not sensitive to the exact value of laser intensity. We show that the population transfer is complete, and analyze the possibility of controlling the relative phases and amplitudes of the excited eigenstates. We discuss the limitations of the proposed control methods due to the dynamic level shifts and suggest ways of reducing their influence.

  5. Population Pharmacokinetic Modelling of FE 999049, a Recombinant Human Follicle-Stimulating Hormone, in Healthy Women After Single Ascending Doses

    OpenAIRE

    Rose, Trine H?yer; R?shammar, Daniel; Erichsen, Lars; Grundemar, Lars; Ottesen, Johnny T.

    2016-01-01

    Objective The purpose of this analysis was to develop a population pharmacokinetic model for a novel recombinant human follicle-stimulating hormone (FSH) (FE 999049) expressed from a human cell line of foetal retinal origin (PER.C6?) developed for controlled ovarian stimulation prior to assisted reproductive technologies. Methods Serum FSH levels were measured following a single subcutaneous FE 999049 injection of 37.5, 75, 150, 225 or 450?IU in 27 pituitary-suppressed healthy female subjects...

  6. Mitochondrial Genome Diversity of Native Americans Supports a Single Early Entry of Founder Populations into America

    OpenAIRE

    Silva Jr., Wilson A.; Bonatto, Sandro L.; Holanda, Adriano J.; Ribeiro-dos-Santos, Andrea K.; Paixão, Beatriz M.; Goldman, Gustavo H.; Abe-Sandes, Kiyoko; Rodriguez-Delfin, Luis; Barbosa, Marcela; Paçó-Larson, Maria Luiza; Petzl-Erler, Maria Luiza; Valente, Valeria; Santos, Sidney E. B.; Zago, Marco A.

    2002-01-01

    There is general agreement that the Native American founder populations migrated from Asia into America through Beringia sometime during the Pleistocene, but the hypotheses concerning the ages and the number of these migrations and the size of the ancestral populations are surrounded by controversy. DNA sequence variations of several regions of the genome of Native Americans, especially in the mitochondrial DNA (mtDNA) control region, have been studied as a tool to help answer these questions...

  7. Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range.

    Science.gov (United States)

    Clucas, Gemma V; Younger, Jane L; Kao, Damian; Rogers, Alex D; Handley, Jonathan; Miller, Gary D; Jouventin, Pierre; Nolan, Paul; Gharbi, Karim; Miller, Karen J; Hart, Tom

    2016-10-13

    Seabirds are important components of marine ecosystems, both as predators and as indicators of ecological change, being conspicuous and sensitive to changes in prey abundance. To determine whether fluctuations in population sizes are localised or indicative of large-scale ecosystem change, we must first understand population structure and dispersal. King penguins are long-lived seabirds that occupy a niche across the sub-Antarctic zone close to the Polar Front. Colonies have very different histories of exploitation, population recovery, and expansion. We investigated the genetic population structure and patterns of colonisation of king penguins across their current range using a dataset of 5154 unlinked, high-coverage single nucleotide polymorphisms generated via restriction site associated DNA sequencing (RADSeq). Despite breeding at a small number of discrete, geographically separate sites, we find only very slight genetic differentiation among colonies separated by thousands of kilometers of open-ocean, suggesting migration among islands and archipelagos may be common. Our results show that the South Georgia population is slightly differentiated from all other colonies and suggest that the recently founded Falkland Island colony is likely to have been established by migrants from the distant Crozet Islands rather than nearby colonies on South Georgia, possibly as a result of density-dependent processes. The observed subtle differentiation among king penguin colonies must be considered in future conservation planning and monitoring of the species, and demographic models that attempt to forecast extinction risk in response to large-scale climate change must take into account migration. It is possible that migration could buffer king penguins against some of the impacts of climate change where colonies appear panmictic, although it is unlikely to protect them completely given the widespread physical changes projected for their Southern Ocean foraging grounds

  8. New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)

    Science.gov (United States)

    Doyle, Jacqueline M.; Bell, Douglas A.; Bloom, Peter H.; Emmons, Gavin; Fesnock, Amy; Katzner, Todd; LePre, Larry; Leonard, Kolbe; SanMiguel, Phillip; Westerman, Rick; DeWoody, J. Andrew

    2018-01-01

    BackgroundManagement requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species’ range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge.ResultsWe sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated > 16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring > 140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~ 100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population.ConclusionsOur study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating

  9. A Chrysodeixis chalcites single-nucleocapsid nucleopolyhedrovirus population from the Canary Islands is genotypically structured to maximize survival.

    Science.gov (United States)

    Bernal, Alexandra; Simón, Oihane; Williams, Trevor; Muñoz, Delia; Caballero, Primitivo

    2013-12-01

    A Chrysodeixis chalcites single-nucleocapsid nucleopolyhedrovirus wild-type isolate from the Canary Islands, Spain, named ChchSNPV-TF1 (ChchTF1-wt), appears to have great potential as the basis for a biological insecticide for control of the pest. An improved understanding of the genotypic structure of this wild-type strain population should facilitate the selection of genotypes for inclusion in a bioinsecticidal product. Eight genetically distinct genotypes were cloned in vitro: ChchTF1-A to ChchTF1-H. Quantitative real-time PCR (qPCR) analysis confirmed that ChchTF1-A accounted for 36% of the genotypes in the wild-type population. In bioassays, ChchTF1-wt occlusion bodies (OBs) were significantly more pathogenic than any of the component single-genotype OBs, indicating that genotype interactions were likely responsible for the pathogenicity phenotype of wild-type OBs. However, the wild-type population was slower killing and produced higher OB yields than any of the single genotypes alone. These results strongly suggested that the ChchTF1-wt population is structured to maximize its transmission efficiency. Experimental OB mixtures and cooccluded genotype mixtures containing the most abundant and the rarest genotypes, at frequencies similar to those at which they were isolated, revealed a mutualistic interaction that restored the pathogenicity of OBs. In OB and cooccluded mixtures containing only the most abundant genotypes, ChchTF1-ABC, OB pathogenicity was even greater than that of wild-type OBs. The ChchTF1-ABC cooccluded mixture killed larvae 33 h faster than the wild-type population and remained genotypically and biologically stable throughout five successive passages in vivo. In conclusion, the ChchTF1-ABC mixture shows great potential as the active ingredient of a bioinsecticide to control C. chalcites in the Canary Islands.

  10. Small Scale Genetic Population Structure of Coral Reef Organisms in Spermonde Archipelago, Indonesia

    Directory of Open Access Journals (Sweden)

    Janne Timm

    2017-09-01

    Full Text Available Small island archipelagos with fringing and dispersed reef systems represent special marine ecosystems, providing a patchy habitat for many coral reef organisms. Although geographic distances may be short, it is still unclear if such environments are inhabited evenly with panmictic conditions or if limited connectivity between marine populations, even on small geographic scales, leads to genetic differentiation between areas within the archipelago or even single reef structures. To study diversity patterns and connectivity between reefs of the Spermonde Archipelago, Indonesia, population genetic analyses of two reef organisms were performed by using the mitochondrial control region and microsatellite markers. A vertebrate (clown anemonefish and an invertebrate species (sea squirt were studied in parallel to investigate if there are general patterns of connectivity in Spermonde for sessile or site attached marine species, which can be extrapolated to a larger group. The genetic population structures revealed restrictions in gene flow in the clown anemone fish (Amphiprion ocellaris, especially between near-shore reefs in the South of the archipelago. This indicates very localized genetic exchange and may also reflect the high self-recruitment typical for these fish. The northern reefs show higher connectivity despite geographic distances being larger. The filter-feeding sessile sea squirt, Polycarpa aurata, features similar population patterns, especially in the southern area. However, connectivity is generally higher in the middle and shelf edge areas of Spermonde for this species. The results underline that there are restrictions to gene flow even on very small geographic scales in the studied organisms, with many barriers to gene flow in the southern shallower shelf area. Weaker currents in this area may lead to more influence of biological factors for dispersal, such as larval behavior, motility and competition for suitable habitat. The

  11. Population Pharmacokinetic Modelling of FE 999049, a Recombinant Human Follicle-Stimulating Hormone, in Healthy Women After Single Ascending Doses

    DEFF Research Database (Denmark)

    Rose, Trine Høyer; Röshammar, Daniel; Erichsen, Lars

    2016-01-01

    Objective: The purpose of this analysis was to develop a population pharmacokinetic model for a novel recombinant human follicle-stimulating hormone (FSH) (FE 999049) expressed from a human cell line of foetal retinal origin (PER.C6) developed for controlled ovarian stimulation prior to assisted...... effects population pharmacokinetic modelling in NONMEM 7.2.0. Results: A one-compartment model with first-order absorption and elimination rates was found to best describe the data. A transit model was introduced to describe a delay in the absorption process. The apparent clearance (CL/F) and apparent...... volume of distribution (V/F) estimates were found to increase with body weight. Body weight was included as an allometrically scaled covariate with a power exponent of 0.75 for CL/F and 1 for V/F. Conclusions: The single-dose pharmacokinetics of FE 999049 were adequately described by a population...

  12. Single cell cytometry of protein function in RNAi treated cells and in native populations

    Directory of Open Access Journals (Sweden)

    Hill Andrew

    2008-08-01

    Full Text Available Abstract Background High Content Screening has been shown to improve results of RNAi and other perturbations, however significant intra-sample heterogeneity is common and can complicate some analyses. Single cell cytometry can extract important information from subpopulations within these samples. Such approaches are important for immune cells analyzed by flow cytometry, but have not been broadly available for adherent cells that are critical to the study of solid-tumor cancers and other disease models. Results We have directly quantitated the effect of resolving RNAi treatments at the single cell level in experimental systems for both exogenous and endogenous targets. Analyzing the effect of an siRNA that targets GFP at the single cell level permits a stronger measure of the absolute function of the siRNA by gating to eliminate background levels of GFP intensities. Extending these methods to endogenous proteins, we have shown that well-level results of the knockdown of PTEN results in an increase in phospho-S6 levels, but at the single cell level, the correlation reveals the role of other inputs into the pathway. In a third example, reduction of STAT3 levels by siRNA causes an accumulation of cells in the G1 phase of the cell cycle, but does not induce apoptosis or necrosis when compared to control cells that express the same levels of STAT3. In a final example, the effect of reduced p53 levels on increased adriamycin sensitivity for colon carcinoma cells was demonstrated at the whole-well level using siRNA knockdown and in control and untreated cells at the single cell level. Conclusion We find that single cell analysis methods are generally applicable to a wide range of experiments in adherent cells using technology that is becoming increasingly available to most laboratories. It is well-suited to emerging models of signaling dysfunction, such as oncogene addition and oncogenic shock. Single cell cytometry can demonstrate effects on cell

  13. Not a single but multiple populations of GABAergic neurons control sleep.

    Science.gov (United States)

    Luppi, Pierre-Hervé; Peyron, Christelle; Fort, Patrice

    2017-04-01

    The role of gamma-amino butyric acid (GABA) in sleep induction and maintenance is well accepted since most insomnia treatments target GABAa receptors. However, the population(s) of GABAergic neurons involved in the beneficial effect of GABA on sleep remains to be identified. This is not an easy task since GABAergic neurons are widely distributed in all brain structures. A recently growing number of populations of GABAergic neurons have been involved in sleep control. We first review here possible candidates for inducing non-rapid eye movement (NREM) sleep including the GABAergic neurons of the ventrolateral preoptic area, the parafacial zone in the brainstem, the nucleus accumbens and the cortex. We also discuss the role of several populations of GABAergic neurons in rapid eye movement (REM) sleep control. Indeed, it is well accepted that muscle atonia occurring during REM sleep is due to a GABA/glycinergic hyperpolarization of motoneurons. Recent evidence strongly suggests that these neurons are located in the ventral medullary reticular formation. It has also recently been shown that neurons containing the neuropeptide melanin concentrating hormone and GABA located in the lateral hypothalamic area control REM sleep expression. Finally, a population of REM-off GABAergic neurons located in the ventrolateral periaqueductal gray has been shown to gate REM sleep by inhibiting glutamatergic neurons located in the sublaterodorsal tegmental nucleus. In summary, recent data clearly indicate that multiple populations of GABAergic neurons located throughout the brain from the cortex to the medulla oblongata control NREM and REM sleep. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Heterogeneity of Metazoan Cells and Beyond: To Integrative Analysis of Cellular Populations at Single-Cell Level.

    Science.gov (United States)

    Barteneva, Natasha S; Vorobjev, Ivan A

    2018-01-01

    In this paper, we review some of the recent advances in cellular heterogeneity and single-cell analysis methods. In modern research of cellular heterogeneity, there are four major approaches: analysis of pooled samples, single-cell analysis, high-throughput single-cell analysis, and lately integrated analysis of cellular population at a single-cell level. Recently developed high-throughput single-cell genetic analysis methods such as RNA-Seq require purification step and destruction of an analyzed cell often are providing a snapshot of the investigated cell without spatiotemporal context. Correlative analysis of multiparameter morphological, functional, and molecular information is important for differentiation of more uniform groups in the spectrum of different cell types. Simplified distributions (histograms and 2D plots) can underrepresent biologically significant subpopulations. Future directions may include the development of nondestructive methods for dissecting molecular events in intact cells, simultaneous correlative cellular analysis of phenotypic and molecular features by hybrid technologies such as imaging flow cytometry, and further progress in supervised and non-supervised statistical analysis algorithms.

  15. Laser capture microdissection of enriched populations of neurons or single neurons for gene expression analysis after traumatic brain injury.

    Science.gov (United States)

    Boone, Deborah R; Sell, Stacy L; Hellmich, Helen Lee

    2013-04-10

    Long-term cognitive disability after TBI is associated with injury-induced neurodegeneration in the hippocampus-a region in the medial temporal lobe that is critical for learning, memory and executive function. Hence our studies focus on gene expression analysis of specific neuronal populations in distinct subregions of the hippocampus. The technique of laser capture microdissection (LCM), introduced in 1996 by Emmert-Buck, et al., has allowed for significant advances in gene expression analysis of single cells and enriched populations of cells from heterogeneous tissues such as the mammalian brain that contains thousands of functional cell types. We use LCM and a well established rat model of traumatic brain injury (TBI) to investigate the molecular mechanisms that underlie the pathogenesis of TBI. Following fluid-percussion TBI, brains are removed at pre-determined times post-injury, immediately frozen on dry ice, and prepared for sectioning in a cryostat. The rat brains can be embedded in OCT and sectioned immediately, or stored several months at -80 °C before sectioning for laser capture microdissection. Additionally, we use LCM to study the effects of TBI on circadian rhythms. For this, we capture neurons from the suprachiasmatic nuclei that contain the master clock of the mammalian brain. Here, we demonstrate the use of LCM to obtain single identified neurons (injured and degenerating, Fluoro-Jade-positive, or uninjured, Fluoro-Jade-negative) and enriched populations of hippocampal neurons for subsequent gene expression analysis by real time PCR and/or whole-genome microarrays. These LCM-enabled studies have revealed that the selective vulnerability of anatomically distinct regions of the rat hippocampus are reflected in the different gene expression profiles of different populations of neurons obtained by LCM from these distinct regions. The results from our single-cell studies, where we compare the transcriptional profiles of dying and adjacent surviving

  16. Single stellar populations in the near-infrared. I. Preparation of the IRTF spectral stellar library

    NARCIS (Netherlands)

    Meneses-Goytia, S.; Peletier, R. F.; Trager, S. C.; Falcón-Barroso, J.; Koleva, M.; Vazdekis, A.

    2015-01-01

    We present a detailed study of the stars of the NASA InfraRed Telescope Facility (IRTF) spectral library to understand its full extent and reliability for use with stellar population (SP) modeling. The library consist of 210 stars, with a total of 292 spectra, covering the wavelength range of 0.94

  17. Impact of environmental colored noise in single-species population dynamics

    Science.gov (United States)

    Spanio, Tommaso; Hidalgo, Jorge; Muñoz, Miguel A.

    2017-10-01

    Variability on external conditions has important consequences for the dynamics and the organization of biological systems. In many cases, the characteristic timescale of environmental changes as well as their correlations play a fundamental role in the way living systems adapt and respond to it. A proper mathematical approach to understand population dynamics, thus, requires approaches more refined than, e.g., simple white-noise approximations. To shed further light onto this problem, in this paper we propose a unifying framework based on different analytical and numerical tools available to deal with "colored" environmental noise. In particular, we employ a "unified colored noise approximation" to map the original problem into an effective one with white noise, and then we apply a standard path integral approach to gain analytical understanding. For the sake of specificity, we present our approach using as a guideline a variation of the contact process—which can also be seen as a birth-death process of the Malthus-Verhulst class—where the propagation or birth rate varies stochastically in time. Our approach allows us to tackle in a systematic manner some of the relevant questions concerning population dynamics under environmental variability, such as determining the stationary population density, establishing the conditions under which a population may become extinct, and estimating extinction times. We focus on the emerging phase diagram and its possible phase transitions, underlying how these are affected by the presence of environmental noise time-correlations.

  18. Social perceptions of single-use plastic consumption of the Balinese population

    OpenAIRE

    Lopez Murcia Martin, Javier

    2015-01-01

    The island of Bali has suffered from an increasing amount of single-use plastics being littered into the environment during the past few years. This research aims to determine the social perceptions of plastic bags and bottles in particular, through consumption habits, the degree of awareness of environmental impacts and the willingness to reduce their consumption. The methodology is based on a survey approach and literature review contrasting the characteristics of plastic bottles and bags, ...

  19. Increased frequency of single base substitutions in a population of transcripts expressed in cancer cells

    Directory of Open Access Journals (Sweden)

    Bianchetti Laurent

    2012-11-01

    Full Text Available Abstract Background Single Base Substitutions (SBS that alter transcripts expressed in cancer originate from somatic mutations. However, recent studies report SBS in transcripts that are not supported by the genomic DNA of tumor cells. Methods We used sequence based whole genome expression profiling, namely Long-SAGE (L-SAGE and Tag-seq (a combination of L-SAGE and deep sequencing, and computational methods to identify transcripts with greater SBS frequencies in cancer. Millions of tags produced by 40 healthy and 47 cancer L-SAGE experiments were compared to 1,959 Reference Tags (RT, i.e. tags matching the human genome exactly once. Similarly, tens of millions of tags produced by 7 healthy and 8 cancer Tag-seq experiments were compared to 8,572 RT. For each transcript, SBS frequencies in healthy and cancer cells were statistically tested for equality. Results In the L-SAGE and Tag-seq experiments, 372 and 4,289 transcripts respectively, showed greater SBS frequencies in cancer. Increased SBS frequencies could not be attributed to known Single Nucleotide Polymorphisms (SNP, catalogued somatic mutations or RNA-editing enzymes. Hypothesizing that Single Tags (ST, i.e. tags sequenced only once, were indicators of SBS, we observed that ST proportions were heterogeneously distributed across Embryonic Stem Cells (ESC, healthy differentiated and cancer cells. ESC had the lowest ST proportions, whereas cancer cells had the greatest. Finally, in a series of experiments carried out on a single patient at 1 healthy and 3 consecutive tumor stages, we could show that SBS frequencies increased during cancer progression. Conclusion If the mechanisms generating the base substitutions could be known, increased SBS frequency in transcripts would be a new useful biomarker of cancer. With the reduction of sequencing cost, sequence based whole genome expression profiling could be used to characterize increased SBS frequency in patient’s tumor and aid diagnostic.

  20. Increased frequency of single base substitutions in a population of transcripts expressed in cancer cells

    International Nuclear Information System (INIS)

    Bianchetti, Laurent; Kieffer, David; Féderkeil, Rémi; Poch, Olivier

    2012-01-01

    Single Base Substitutions (SBS) that alter transcripts expressed in cancer originate from somatic mutations. However, recent studies report SBS in transcripts that are not supported by the genomic DNA of tumor cells. We used sequence based whole genome expression profiling, namely Long-SAGE (L-SAGE) and Tag-seq (a combination of L-SAGE and deep sequencing), and computational methods to identify transcripts with greater SBS frequencies in cancer. Millions of tags produced by 40 healthy and 47 cancer L-SAGE experiments were compared to 1,959 Reference Tags (RT), i.e. tags matching the human genome exactly once. Similarly, tens of millions of tags produced by 7 healthy and 8 cancer Tag-seq experiments were compared to 8,572 RT. For each transcript, SBS frequencies in healthy and cancer cells were statistically tested for equality. In the L-SAGE and Tag-seq experiments, 372 and 4,289 transcripts respectively, showed greater SBS frequencies in cancer. Increased SBS frequencies could not be attributed to known Single Nucleotide Polymorphisms (SNP), catalogued somatic mutations or RNA-editing enzymes. Hypothesizing that Single Tags (ST), i.e. tags sequenced only once, were indicators of SBS, we observed that ST proportions were heterogeneously distributed across Embryonic Stem Cells (ESC), healthy differentiated and cancer cells. ESC had the lowest ST proportions, whereas cancer cells had the greatest. Finally, in a series of experiments carried out on a single patient at 1 healthy and 3 consecutive tumor stages, we could show that SBS frequencies increased during cancer progression. If the mechanisms generating the base substitutions could be known, increased SBS frequency in transcripts would be a new useful biomarker of cancer. With the reduction of sequencing cost, sequence based whole genome expression profiling could be used to characterize increased SBS frequency in patient’s tumor and aid diagnostic

  1. Association analysis of two single-nucleotide polymorphisms of the RELN gene with autism in the South African population

    KAUST Repository

    Sharma, Jyoti Rajan

    2013-02-01

    Background: Autism (MIM209850) is a neurodevelopmental disorder characterized by a triad of impairments, namely impairment in social interaction, impaired communication skills, and restrictive and repetitive behavior. A number of family and twin studies have demonstrated that genetic factors play a pivotal role in the etiology of autistic disorder. Various reports of reduced levels of reelin protein in the brain and plasma in autistic patients highlighted the role of the reelin gene (RELN) in autism. There is no such published study on the South African (SA) population. Aims: The aim of the present study was to find the genetic association of intronic rs736707 and exonic rs362691 (single-nucleotide polymorphisms [SNPs] of the RELN gene) with autism in a SA population. Methods: Genomic DNA was isolated from cheek cell swabs from autistic (136) as well as control (208) subjects. The TaqMan ® Real-Time polymerase chain reaction and genotyping assay was utilized to determine the genotypes. Results: A significant association of SNP rs736707, but not for SNP rs362691, with autism in the SA population is observed. Conclusion: There might be a possible role of RELN in autism, especially for SA populations. The present study represents the first report on genetic association studies on the RELN gene in the SA population. © 2013, Mary Ann Liebert, Inc.

  2. Using enhanced green fluorescent protein (EGFP) promoter fusions to study gene regulation at single cell and population levels.

    Science.gov (United States)

    Utratna, Marta; O'Byrne, Conor P

    2014-01-01

    Reporter gene fusions based on the enhanced green fluorescent protein (EGFP) are powerful experimental tools that allow real-time changes in gene expression to be monitored both in single cells and in populations. Here we describe the development of a chromosomally integrated transcriptional reporter fusion in Listeria monocytogenes that allows real-time measurements of gene expression. To construct a single copy of an EGFP-based fluorescent reporter fused to a promoter of interest (Px) in L. monocytogenes, a suicide shuttle vector carrying the Px::egfp gene fusion is first constructed in Escherichia coli (as an intermediate host). Then, the vector is transformed into L. monocytogenes and integrated into its chromosome by homologous recombination within the selected promoter region. Subsequently, analysis of fluorescence exhibited by cells carrying a single copy reporter can be performed under selected experimental conditions by stringent sample preparation, optimized image acquisition, and processing of the digital data with the image analysis freeware ImageJ. Thus, the methodology described here can be adapted to investigate the activity and regulation of any promoter in L. monocytogenes both at the cell and population levels.

  3. Single locus typing of MHC class I and class II B loci in a population of red jungle fowl.

    Science.gov (United States)

    Worley, K; Gillingham, M; Jensen, P; Kennedy, L J; Pizzari, T; Kaufman, J; Richardson, D S

    2008-05-01

    In species with duplicated major histocompatibility complex (MHC) genes, estimates of genetic variation often rely on multilocus measures of diversity. It is possible that such measures might not always detect more detailed patterns of selection at individual loci. Here, we describe a method that allows us to investigate classical MHC diversity in red jungle fowl (Gallus gallus), the wild ancestor of the domestic chicken, using a single locus approach. This is possible due to the well-characterised gene organisation of the 'minimal essential' MHC (BF/BL region) of the domestic chicken, which comprises two differentially expressed duplicated class I (BF) and two class II B (BLB) genes. Using a combination of reference strand-mediated conformation analysis, cloning and sequencing, we identify nine BF and ten BLB alleles in a captive population of jungle fowl. We show that six BF and five BLB alleles are from the more highly expressed locus of each gene, BF2 and BLB2, respectively. An excess of non-synonymous substitutions across the jungle fowl BF/BL region suggests that diversifying selection has acted on this population. Importantly, single locus screening reveals that the strength of selection is greatest on the highly expressed BF2 locus. This is the first time that a population of red jungle fowl has been typed at the MHC region, laying the basis for further research into the underlying processes acting to maintain MHC diversity in this and other species.

  4. Estimates for Genetic Variance Components in Reciprocal Recurrent Selection in Populations Derived from Maize Single-Cross Hybrids

    Directory of Open Access Journals (Sweden)

    Matheus Costa dos Reis

    2014-01-01

    Full Text Available This study was carried out to obtain the estimates of genetic variance and covariance components related to intra- and interpopulation in the original populations (C0 and in the third cycle (C3 of reciprocal recurrent selection (RRS which allows breeders to define the best breeding strategy. For that purpose, the half-sib progenies of intrapopulation (P11 and P22 and interpopulation (P12 and P21 from populations 1 and 2 derived from single-cross hybrids in the 0 and 3 cycles of the reciprocal recurrent selection program were used. The intra- and interpopulation progenies were evaluated in a 10×10 triple lattice design in two separate locations. The data for unhusked ear weight (ear weight without husk and plant height were collected. All genetic variance and covariance components were estimated from the expected mean squares. The breakdown of additive variance into intrapopulation and interpopulation additive deviations (στ2 and the covariance between these and their intrapopulation additive effects (CovAτ found predominance of the dominance effect for unhusked ear weight. Plant height for these components shows that the intrapopulation additive effect explains most of the variation. Estimates for intrapopulation and interpopulation additive genetic variances confirm that populations derived from single-cross hybrids have potential for recurrent selection programs.

  5. Brief communication genotyping of Burkholderia pseudomallei revealed high genetic variability among isolates from a single population group.

    Science.gov (United States)

    Zueter, Abdelrahman Mohammad; Rahman, Zaidah Abdul; Yean, Chan Yean; Harun, Azian

    2015-01-01

    Burkholderia pseudomallei is a soil dwelling Gram-negative bacteria predominates in Southeast Asia zone and the tropical part of Australia. Genetic diversity has been explored among various populations and environments worldwide. To date, little data is available on MLST profiling of clinical B. pseudomallei isolates in peninsular Malaysia. In this brief report, thirteen culture positive B. pseudomallei cases collected from a single population of Terengganu state in the Western Peninsular Malaysia and were confirmed by In-house TTS1-PCR. Isolates were subjected for multi-locus sequence typing (MLST) to explore their genotypic diversity and to investigate for possible clonal clustering of a certain sequence type. Patient's clinical information was examined to investigate for clinical correlation among the different genotypes. In spite of small sample set, MLST results indicated predictive results; considerable genotypic diversity, predominance and novelty among B. pseudomallei collected over a single geographically-located population in Malaysia. Massive genotypic heterogeneity was observed; 8 different sequence types with predominance of sequence type 54 and discovery of two novel sequence types. However, no clear pathogenomic or organ tropism clonal relationships were predicted.

  6. Diversity of knockdown resistance alleles in a single house fly population facilitates adaptation to pyrethroid insecticides.

    Science.gov (United States)

    Kasai, S; Sun, H; Scott, J G

    2017-02-01

    Insecticide use exerts a tremendous selection force on house fly populations, but the frequencies of the initial resistance mutations may not reach high levels if they have a significant fitness cost in the absence of insecticides. However, with the continued use of the same (or similar) insecticides, it is expected that new mutations (conferring equal or greater resistance, but less of a fitness cost) will evolve. Pyrethroid insecticides target the insect voltage sensitive sodium channel (VSSC) and have been widely used for control of house flies at animal production facilities for more than three decades. There are three Vssc mutations known that cause resistance to pyrethroids in house flies: knockdown resistance (kdr, L1014F), kdr-his (L1014H) and super-kdr (M918T + L1014F). Whether or not there are any new mutations in house fly populations has not been examined for decades. We collected house flies from a dairy in Kansas (USA) and selected this population for three generations. We discovered multiple new Vssc alleles, including two that give very high levels of resistance to most pyrethroids. The importance of these findings to understanding the evolution of insecticide resistance, designing appropriate resistance monitoring and management schemes, and the future of pyrethroids for house fly control are discussed. © 2016 The Royal Entomological Society.

  7. Population pharmacokinetics of artesunate and dihydroartemisinin following single- and multiple-dosing of oral artesunate in healthy subjects

    Directory of Open Access Journals (Sweden)

    Kirsch Lee E

    2009-12-01

    Full Text Available Abstract Background The population pharmacokinetics of artesunate (AS and its active metabolite dihydroartemisinin (DHA were studied in healthy subjects receiving single- or multiple-dosing of AS orally either in combination with pyronaridine (PYR or as a monotherapy with or without food. Methods Data from 118 concentration-time profiles arising from 91 healthy Korean subjects were pooled from four Phase I clinical studies. Subjects received 2-5 mg/kg of single- and multiple-dosing of oral AS either in combination with PYR or as a monotherapy with or without food. Plasma AS and DHA were measured simultaneously using a validated liquid chromatography- mass spectrometric method with a lower limit of quantification of 1 ng/mL for both AS and DHA. Nonlinear mixed-effect modelling was used to obtain the pharmacokinetic and variability (inter-individual and residual variability parameter estimates. Results A novel parent-metabolite pharmacokinetic model consisting of a dosing compartment, a central compartment for AS, a central compartment and a peripheral compartment for DHA was developed. AS and DHA data were modelled simultaneously assuming stoichiometric conversion to DHA. AS was rapidly absorbed with a population estimate of absorption rate constant (Ka of 3.85 h-1. The population estimates of apparent clearance (CL/F and volume of distribution (V2/F for AS were 1190 L/h with 36.2% inter-individual variability (IIV and 1210 L with 57.4% IIV, respectively. For DHA, the population estimates of apparent clearance (CLM/F and central volume of distribution (V3/F were 93.7 L/h with 28% IIV and 97.1 L with 30% IIV, respectively. The population estimates of apparent inter-compartmental clearance (Q/F and peripheral volume of distribution (V4/F for DHA were 5.74 L/h and 18.5 L, respectively. Intake of high-fat and high-caloric meal prior to the drug administration resulted in 84% reduction in Ka. Body weight impacted CLM/F, such that a unit change in

  8. In-vitro activity of taurolidine on single species and a multispecies population associated with periodontitis.

    Science.gov (United States)

    Zollinger, Lilly; Schnyder, Simone; Nietzsche, Sandor; Sculean, Anton; Eick, Sigrun

    2015-04-01

    The antimicrobial activity of taurolidine was compared with minocycline against microbial species associated with periodontitis (four single strains and a 12-species mixture). Minimal inhibitory concentrations (MICs) and minimal bactericidal concentrations (MBCs), killing as well as activities on established and forming single-species biofilms and a 12-species biofilm were determined. The MICs of taurolidine against single species were always 0.31 mg/ml, the MBCs were 0.64 mg/ml. The used mixed microbiota was less sensitive to taurolidine, MIC and the MBC was 2.5 mg/ml. The strains and the mixture were completely killed by 2.5 mg/ml taurolidine, whereas 256 μg/ml minocycline reduced the bacterial counts of the mixture by 5 log10 colony forming units (cfu). Coating the surface with 10 mg/ml taurolidine or 256 μg/ml minocycline prevented completely biofilm formation of Porphyromonas gingivalis ATCC 33277 but not of Aggregatibacter actinomycetemcomitans Y4 and the mixture. On 4.5 d old biofilms, taurolidine acted concentration dependent with a reduction by 5 log10 cfu (P. gingivalis ATCC 33277) and 7 log10 cfu (A. actinomycetemcomitans Y4) when applying 10 mg/ml. Minocycline decreased the cfu counts by 1-2 log10 cfu independent of the used concentration. The reduction of the cfu counts in the 4.5 d old multi-species biofilms was about 3 log10 cfu after application of any minocycline concentration and after using 10 mg/ml taurolidine. Taurolidine is active against species associated with periodontitis, even within biofilms. Nevertheless a complete elimination of complex biofilms by taurolidine seems to be impossible and underlines the importance of a mechanical removal of biofilms prior to application of taurolidine. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka populations

    Directory of Open Access Journals (Sweden)

    Habicht Christopher

    2011-02-01

    Full Text Available Abstract Background Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP multilocus genotypes for 31 sockeye salmon (Oncorhynchus nerka populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance and ecology (spawning habitat and timing driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s may maintain the genetic variation of outlier loci. Results For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection. Conclusions First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second

  10. Elucidating distinct ion channel populations on the surface of hippocampal neurons via single-particle tracking recurrence analysis

    Science.gov (United States)

    Sikora, Grzegorz; Wyłomańska, Agnieszka; Gajda, Janusz; Solé, Laura; Akin, Elizabeth J.; Tamkun, Michael M.; Krapf, Diego

    2017-12-01

    Protein and lipid nanodomains are prevalent on the surface of mammalian cells. In particular, it has been recently recognized that ion channels assemble into surface nanoclusters in the soma of cultured neurons. However, the interactions of these molecules with surface nanodomains display a considerable degree of heterogeneity. Here, we investigate this heterogeneity and develop statistical tools based on the recurrence of individual trajectories to identify subpopulations within ion channels in the neuronal surface. We specifically study the dynamics of the K+ channel Kv1.4 and the Na+ channel Nav1.6 on the surface of cultured hippocampal neurons at the single-molecule level. We find that both these molecules are expressed in two different forms with distinct kinetics with regards to surface interactions, emphasizing the complex proteomic landscape of the neuronal surface. Further, the tools presented in this work provide new methods for the analysis of membrane nanodomains, transient confinement, and identification of populations within single-particle trajectories.

  11. Syncope unit in the paediatric population: A single-centre experience.

    Science.gov (United States)

    Courtheix, Mathieu; Jalal, Zakaria; Bordachar, Pierre; Iriart, Xavier; Pillois, Xavier; Escobedo, Cécile; Rabot, Catherine; Tribout, Laetitia; Thambo, Jean-Benoit

    2016-03-01

    Syncopes are frequent in the paediatric population. Most are benign, but rare cases are caused by cardiac life-threatening diseases. Syncope units developed in the adult population have demonstrated improvement in evaluation and treatment, with a reduction in hospitalization. We report our experience of paediatric syncope management in a dedicated unit, and analyse the value of different elements in the identification of cardiac causes. This prospective study included 97 consecutive patients (mean age: 12.1±3.3 years) referred between January 2011 and June 2013 to a syncope unit with a paediatric cardiologist, a nurse, a physiotherapist and a psychologist. Patients were classified into diagnostic categories after an initial evaluation that included history, physical examination, electrocardiography, echocardiography and Holter monitoring. The most common diagnosis was neurocardiogenic syncope (n=69, 70.4%). Fifty-two cases (81.3%) had no or less recurrence after specific management that included physiotherapy and psychological support (follow-up: 11.5±5.4 months). Psychogenic pseudosyncopes affected 20 children (20.6%). Two patients had epileptic seizures. There were five cases of cardiac syncope (5.1%): two long QT syndromes and a catecholaminergic polymorphic ventricular tachycardia received beta-blockers; two atrioventricular complete blocks required pacemakers. One case was of indeterminate cause and received an insertable loop recorder after exhaustive investigations. Exercise-induced syncopes were significantly associated with cardiac origins (P=0.003), such as electrocardiographic abnormalities (PSyncope units in the paediatric population may be useful in the diagnostic process, to help identify rare cardiac aetiologies, and could decrease recurrence through specific management. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  12. Strategies for imputation to whole genome sequence using a single or multi-breed reference population in cattle

    DEFF Research Database (Denmark)

    Brøndum, Rasmus Froberg; Guldbrandtsen, Bernt; Sahana, Goutam

    2014-01-01

    autosome 29 using 387,436 bi-allelic variants and 13,612 SNP markers from the bovine HD panel. Results A combined breed reference population led to higher imputation accuracies than did a single breed reference. The highest accuracy of imputation for all three test breeds was achieved when using BEAGLE...... with un-phased reference data (mean genotype correlations of 0.90, 0.89 and 0.87 for Holstein, Jersey and Nordic Red respectively) but IMPUTE2 with un-phased reference data gave similar accuracies for Holsteins and Nordic Red. Pre-phasing the reference data only lead to a minor decrease in the imputation...

  13. Effects of extracellular nucleotides on single cells and populations of human osteoblasts: contribution of cell heterogeneity to relative potencies

    OpenAIRE

    Jane Dixon, C; Bowler, Wayne B; Walsh, Catherine A; Gallagher, James A

    1997-01-01

    Human osteoblasts responded to the application of extracellular nucleotides, acting at P2-receptors, with increases in cytosolic free calcium concentration ([Ca2+]i).In populations of human osteoblasts, adenosine 5′-diphosphate (ADP) evoked a rise in [Ca2+]i with less than 40% of the amplitude of that induced by adenosine 5′-triphosphate (ATP).ATP and uridine 5′-triphosphate (UTP) were applied to single human osteoblasts and induced [Ca2+]i rises of comparable amplitude in every cell tested.H...

  14. The Bifurcation and Control of a Single-Species Fish Population Logistic Model with the Invasion of Alien Species

    Directory of Open Access Journals (Sweden)

    Yi Zhang

    2014-01-01

    Full Text Available The objective of this paper is to study systematically the bifurcation and control of a single-species fish population logistic model with the invasion of alien species based on the theory of singular system and bifurcation. It regards Spartina anglica as an invasive species, which invades the fisheries and aquaculture. Firstly, the stabilities of equilibria in this model are discussed. Moreover, the sufficient conditions for existence of the trans-critical bifurcation and the singularity induced bifurcation are obtained. Secondly, the state feedback controller is designed to eliminate the unexpected singularity induced bifurcation by combining harvested effort with the purification capacity. It obviously inhibits the switch of population and makes the system stable. Finally, the numerical simulation is proposed to show the practical significance of the bifurcation and control from the biological point of view.

  15. Single-nucleotide polymorphism-based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographic sites.

    Science.gov (United States)

    Gutacker, Michaela M; Mathema, Barun; Soini, Hanna; Shashkina, Elena; Kreiswirth, Barry N; Graviss, Edward A; Musser, James M

    2006-01-01

    We studied genetic relationships among 5069 Mycobacterium tuberculosis strains recovered from patients enrolled in 4 population-based studies in the United States and Europe, by analysis of 36 synonymous single-nucleotide polymorphisms (SNPs). All strains were assigned to 1 of 9 major genetic clusters based on sSNP profile. The same 9 genetic clusters were revealed by analysis of 227 nonsynonymous SNPs, 121 intergenic SNPs, and concatenated profiles of 578 SNPs available for a subset of 48 representative strains. IS6110 profiles, spoligotypes, and mycobacterial interspersed repetitive unit patterns were nonrandomly associated with SNP-based phylogenetic lineages, together indicating a strongly clonal population structure. Isolates of the 9 genetic clusters were not distributed with equal frequency in all localities, reflecting geographic subdivision. The SNP-based phylogenetic framework provides new insight into the worldwide evolution of M. tuberculosis and a gateway for investigating genotype-disease phenotype relationships in large samples of strains.

  16. Single Cell Dynamics Causes Pareto-Like Effect in Stimulated T Cell Populations.

    Science.gov (United States)

    Cosette, Jérémie; Moussy, Alice; Onodi, Fanny; Auffret-Cariou, Adrien; Neildez-Nguyen, Thi My Anh; Paldi, Andras; Stockholm, Daniel

    2015-12-09

    Cell fate choice during the process of differentiation may obey to deterministic or stochastic rules. In order to discriminate between these two strategies we used time-lapse microscopy of individual murine CD4 + T cells that allows investigating the dynamics of proliferation and fate commitment. We observed highly heterogeneous division and death rates between individual clones resulting in a Pareto-like dominance of a few clones at the end of the experiment. Commitment to the Treg fate was monitored using the expression of a GFP reporter gene under the control of the endogenous Foxp3 promoter. All possible combinations of proliferation and differentiation were observed and resulted in exclusively GFP-, GFP+ or mixed phenotype clones of very different population sizes. We simulated the process of proliferation and differentiation using a simple mathematical model of stochastic decision-making based on the experimentally observed parameters. The simulations show that a stochastic scenario is fully compatible with the observed Pareto-like imbalance in the final population.

  17. Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay.

    Directory of Open Access Journals (Sweden)

    Adam F Prasanphanich

    2016-11-01

    Full Text Available The side population (SP assay, a technique used in cancer and stem cell research, assesses the activity of ABC transporters on Hoechst staining in the presence and absence of transporter inhibition, identifying SP and non-SP cell (NSP subpopulations by differential staining intensity. The interpretation of the assay is complicated because the transporter-mediated mechanisms fail to account for cell-to-cell variability within a population or adequately control the direct role of transporter activity on staining intensity. We hypothesized that differences in dye kinetics at the single-cell level, such as ABCG2 transporter-mediated efflux and DNA binding, are responsible for the differential cell staining that demarcates SP/NSP identity. We report changes in A549 phenotype during time in culture and with TGFβ treatment that correlate with SP size. Clonal expansion of individually sorted cells re-established both SP and NSPs, indicating that SP membership is dynamic. To assess the validity of a purely kinetics-based interpretation of SP/NSP identity, we developed a computational approach that simulated cell staining within a heterogeneous cell population; this exercise allowed for the direct inference of the role of transporter activity and inhibition on cell staining. Our simulated SP assay yielded appropriate SP responses for kinetic scenarios in which high transporter activity existed in a portion of the cells and little differential staining occurred in the majority of the population. With our approach for single-cell analysis, we observed SP and NSP cells at both ends of a transporter activity continuum, demonstrating that features of transporter activity as well as DNA content are determinants of SP/NSP identity.

  18. Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay

    Science.gov (United States)

    Prasanphanich, Adam F.; White, Douglas E.; Gran, Margaret A.

    2016-01-01

    The side population (SP) assay, a technique used in cancer and stem cell research, assesses the activity of ABC transporters on Hoechst staining in the presence and absence of transporter inhibition, identifying SP and non-SP cell (NSP) subpopulations by differential staining intensity. The interpretation of the assay is complicated because the transporter-mediated mechanisms fail to account for cell-to-cell variability within a population or adequately control the direct role of transporter activity on staining intensity. We hypothesized that differences in dye kinetics at the single-cell level, such as ABCG2 transporter-mediated efflux and DNA binding, are responsible for the differential cell staining that demarcates SP/NSP identity. We report changes in A549 phenotype during time in culture and with TGFβ treatment that correlate with SP size. Clonal expansion of individually sorted cells re-established both SP and NSPs, indicating that SP membership is dynamic. To assess the validity of a purely kinetics-based interpretation of SP/NSP identity, we developed a computational approach that simulated cell staining within a heterogeneous cell population; this exercise allowed for the direct inference of the role of transporter activity and inhibition on cell staining. Our simulated SP assay yielded appropriate SP responses for kinetic scenarios in which high transporter activity existed in a portion of the cells and little differential staining occurred in the majority of the population. With our approach for single-cell analysis, we observed SP and NSP cells at both ends of a transporter activity continuum, demonstrating that features of transporter activity as well as DNA content are determinants of SP/NSP identity. PMID:27851764

  19. Spontaneous Coronary Artery Dissection as a Cause of Acute Myocardial Infarction in Young Female Population: A Single-center Study.

    Science.gov (United States)

    Meng, Pei-Na; Xu, Chen; You, Wei; Wu, Zhi-Ming; Xie, Du-Jiang; Zhang, Hang; Pan, Chang; Ye, Fei

    2017-07-05

    Spontaneous coronary artery dissection (SCAD) is a nonatherosclerotic but a rare and extremely dangerous clinical entity, it has a high prevalence in young female population with acute myocardial infarction (AMI). The previous reports were restricted to other countries' population, but rare in China. Hence, this study aimed to focus on the characteristics of SCAD as a cause of young female AMI population in Jiangsu, China. This study enrolled young female AMI patients aged ≤50 years who underwent coronary angiography (CAG) and intracoronary imaging in our center between January 2013 and December 2016. Their clinical presentations, risk factors, and CAG characteristics were analyzed. A total of 60 young female AMI (SCAD in young female AMI population was 35% (21/60), the prevalence of coronary atherosclerostic heart disease was 65% (39/60). In the SCAD group, 43% (9/21) presented with non-ST-elevation myocardial infarction (NSTEMI) and the remainder presenting as STEMI. SCAD usually occurred in a single vessel (20/21, 95%), especially in left anterior descending artery (14/21, 67%). Eighteen patients (18/21, 86%) underwent conservative treatment, whereas the remaining three patients (3/21, 14%) underwent percutaneous coronary intervention. Regarding the angiographic results of SCAD lesions, intramural hematoma was discriminated in 95% (20/21), and Type I imaging was observed in 5% (1/21), Type II was observed in 67% (14/21), and Type III was 29% (6/21). The average stenosis in the group was 76.9% ± 20.6%, and the mean lesion length was 36.6 ± 8.6 mm. SCAD has a high prevalence in young female AMI population in Jiangsu, China. Discriminating the cause of AMI in young female population is very important.

  20. Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas.

    Science.gov (United States)

    Fagundes, Nelson J R; Kanitz, Ricardo; Eckert, Roberta; Valls, Ana C S; Bogo, Mauricio R; Salzano, Francisco M; Smith, David Glenn; Silva, Wilson A; Zago, Marco A; Ribeiro-dos-Santos, Andrea K; Santos, Sidney E B; Petzl-Erler, Maria Luiza; Bonatto, Sandro L

    2008-03-01

    It is well accepted that the Americas were the last continents reached by modern humans, most likely through Beringia. However, the precise time and mode of the colonization of the New World remain hotly disputed issues. Native American populations exhibit almost exclusively five mitochondrial DNA (mtDNA) haplogroups (A-D and X). Haplogroups A-D are also frequent in Asia, suggesting a northeastern Asian origin of these lineages. However, the differential pattern of distribution and frequency of haplogroup X led some to suggest that it may represent an independent migration to the Americas. Here we show, by using 86 complete mitochondrial genomes, that all Native American haplogroups, including haplogroup X, were part of a single founding population, thereby refuting multiple-migration models. A detailed demographic history of the mtDNA sequences estimated with a Bayesian coalescent method indicates a complex model for the peopling of the Americas, in which the initial differentiation from Asian populations ended with a moderate bottleneck in Beringia during the last glacial maximum (LGM), around approximately 23,000 to approximately 19,000 years ago. Toward the end of the LGM, a strong population expansion started approximately 18,000 and finished approximately 15,000 years ago. These results support a pre-Clovis occupation of the New World, suggesting a rapid settlement of the continent along a Pacific coastal route.

  1. Response of single bacterial cells to stress gives rise to complex history dependence at the population level

    Science.gov (United States)

    Mathis, Roland; Ackermann, Martin

    2016-01-01

    Most bacteria live in ever-changing environments where periods of stress are common. One fundamental question is whether individual bacterial cells have an increased tolerance to stress if they recently have been exposed to lower levels of the same stressor. To address this question, we worked with the bacterium Caulobacter crescentus and asked whether exposure to a moderate concentration of sodium chloride would affect survival during later exposure to a higher concentration. We found that the effects measured at the population level depended in a surprising and complex way on the time interval between the two exposure events: The effect of the first exposure on survival of the second exposure was positive for some time intervals but negative for others. We hypothesized that the complex pattern of history dependence at the population level was a consequence of the responses of individual cells to sodium chloride that we observed: (i) exposure to moderate concentrations of sodium chloride caused delays in cell division and led to cell-cycle synchronization, and (ii) whether a bacterium would survive subsequent exposure to higher concentrations was dependent on the cell-cycle state. Using computational modeling, we demonstrated that indeed the combination of these two effects could explain the complex patterns of history dependence observed at the population level. Our insight into how the behavior of single cells scales up to processes at the population level provides a perspective on how organisms operate in dynamic environments with fluctuating stress exposure. PMID:26960998

  2. Fasciola hepatica demonstrates high levels of genetic diversity, a lack of population structure and high gene flow: possible implications for drug resistance.

    Science.gov (United States)

    Beesley, Nicola J; Williams, Diana J L; Paterson, Steve; Hodgkinson, Jane

    2017-01-01

    Fasciola hepatica, the liver fluke, is a trematode parasite of considerable economic importance to the livestock industry and is a re-emerging zoonosis that poses a risk to human health in F. hepatica-endemic areas worldwide. Drug resistance is a substantial threat to the current and future control of F. hepatica, yet little is known about how the biology of the parasite influences the development and spread of resistance. Given that F. hepatica can self-fertilise and therefore inbreed, there is the potential for greater population differentiation and an increased likelihood of recessive alleles, such as drug resistance genes, coming together. This could be compounded by clonal expansion within the snail intermediate host and aggregation of parasites of the same genotype on pasture. Alternatively, widespread movement of animals that typically occurs in the UK could promote high levels of gene flow and prevent population differentiation. We identified clonal parasites with identical multilocus genotypes in 61% of hosts. Despite this, 84% of 1579 adult parasites had unique multilocus genotypes, which supports high levels of genotypic diversity within F. hepatica populations. Our analyses indicate a selfing rate no greater than 2%, suggesting that this diversity is in part due to the propensity for F. hepatica to cross-fertilise. Finally, although we identified high genetic diversity within a given host, there was little evidence for differentiation between populations from different hosts, indicating a single panmictic population. This implies that, once those emerge, anthelmintic resistance genes have the potential to spread rapidly through liver fluke populations. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  3. Properties of the single Jovian planet population and the pursuit of Solar system analogues

    Science.gov (United States)

    Agnew, Matthew T.; Maddison, Sarah T.; Horner, Jonathan

    2018-04-01

    While the number of exoplanets discovered continues to increase at a rapid rate, we are still to discover any system that truly resembles the Solar system. Existing and near future surveys will likely continue this trend of rapid discovery. To see if these systems are Solar system analogues, we will need to efficiently allocate resources to carry out intensive follow-up observations. We seek to uncover the properties and trends across systems that indicate how much of the habitable zone is stable in each system to provide focus for planet hunters. We study the dynamics of all known single Jovian planetary systems, to assess the dynamical stability of the habitable zone around their host stars. We perform a suite of simulations of all systems where the Jovian planet will interact gravitationally with the habitable zone, and broadly classify these systems. Besides the system's mass ratio (Mpl/Mstar), and the Jovian planet's semi-major axis (apl) and eccentricity (epl), we find that there are no underlying system properties which are observable that indicate the potential for planets to survive within the system's habitable zone. We use Mpl/Mstar, apl and epl to generate a parameter space over which the unstable systems cluster, thus allowing us to predict which systems to exclude from future observational or numerical searches for habitable exoplanets. We also provide a candidate list of 20 systems that have completely stable habitable zones and Jovian planets orbiting beyond the habitable zone as potential first order Solar system analogues.

  4. SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations.

    Directory of Open Access Journals (Sweden)

    Unitsa Sangket

    Full Text Available Influenza virus (IFV can evolve rapidly leading to genetic drifts and shifts resulting in human and animal influenza epidemics and pandemics. The genetic shift that gave rise to the 2009 influenza A/H1N1 pandemic originated from a triple gene reassortment of avian, swine and human IFVs. More minor genetic alterations in genetic drift can lead to influenza drug resistance such as the H274Y mutation associated with oseltamivir resistance. Hence, a rapid tool to detect IFV mutations and the potential emergence of new virulent strains can better prepare us for seasonal influenza outbreaks as well as potential pandemics. Furthermore, identification of specific mutations by closely examining single nucleotide polymorphisms (SNPs in IFV sequences is essential to classify potential genetic markers associated with potentially dangerous IFV phenotypes. In this study, we developed a novel R library called "SNPer" to analyze quantitative variants in SNPs among IFV subpopulations. The computational SNPer program was applied to three different subpopulations of published IFV genomic information. SNPer queried SNPs data and grouped the SNPs into (1 universal SNPs, (2 likely common SNPs, and (3 unique SNPs. SNPer outperformed manual visualization in terms of time and labor. SNPer took only three seconds with no errors in SNP comparison events compared with 40 hours with errors using manual visualization. The SNPer tool can accelerate the capacity to capture new and potentially dangerous IFV strains to mitigate future influenza outbreaks.

  5. Psidium guajava: A Single Plant for Multiple Health Problems of Rural Indian Population.

    Science.gov (United States)

    Daswani, Poonam G; Gholkar, Manasi S; Birdi, Tannaz J

    2017-01-01

    The rural population in India faces a number of health problems and often has to rely on local remedies. Psidium guajava Linn. (guava), a tropical plant which is used as food and medicine can be used by rural communities due to its several medicinal properties. A literature search was undertaken to gauge the rural health scenario in India and compile the available literature on guava so as to reflect its usage in the treatment of multiple health conditions prevalent in rural communities. Towards this, electronic databases such as Pubmed, Science Direct, google scholar were scanned. Information on clinical trials on guava was obtained from Cochrane Central Register of Controlled Trials and Clinicaltrial.gov. The literature survey revealed that guava possesses various medicinal properties which have been reported from across the globe in the form of ethnobotanical/ethnopharmacological surveys, laboratory investigations and clinical trials. Besides documenting the safety of guava, the available literature shows that guava is efficacious against the following conditions which rural communities would encounter. (a) Gastrointestinal infections; (b) Malaria; (c)Respiratory infections; (d) Oral/dental infections; (e) Skin infections; (f) Diabetes; (g) Cardiovascular/hypertension; (h) Cancer; (i) Malnutrition; (j) Women problems; (k) Pain; (l) Fever; (m) Liver problems; (n) Kidney problems. In addition, guava can also be useful for treatment of animals and explored for its commercial applications. In conclusion, popularization of guava, can have multiple applications for rural communities.

  6. The Fitness Effects of Men's Family Investments : A Test of Three Pathways in a Single Population.

    Science.gov (United States)

    Winking, Jeffrey; Koster, Jeremy

    2015-09-01

    Men's investments in parenting and long-term reproductive relationships are a hallmark feature of human reproduction and life history. The uniqueness of such male involvement among catarrhines has driven an extensive debate surrounding the selective pressures that led to and maintain such capacities in men. Three major pathways have been proposed through which men's involvement might confer fitness benefits: enhancing child well-being, increasing couple fertility, and decreasing likelihood of partner desertion. Previous research has explored the impact of father involvement on these factors individually, but here we present novel research that explores all three pathways within the same population, the Mayangna/Miskito horticulturalists of Nicaragua. Furthermore, we expand the traditional dichotomous measure of father presence/absence by using a continuous measure of overall male investment, as well as two continuous measures of its subcomponents: direct care and wealth. We find that men's investments are associated with children's growth and possibly with wife's marital satisfaction; however, they are not associated with couple fertility.

  7. Unrelated hematopoietic stem cell transplantation in the pediatric population: single institution experience

    Directory of Open Access Journals (Sweden)

    Daniela Hespanha Marinho

    2015-08-01

    Full Text Available OBJECTIVE: Hematopoietic stem cell transplantation has been successfully used to treat the pediatric population with malignant and non-malignant hematological diseases. This paper reports the results up to 180 days after the procedure of all unrelated hematopoietic stem cell transplantations in pediatric patients that were performed in one institution.METHODS: A retrospective review was performed of all under 18-year-old patients who received unrelated transplantations between 1995 and 2009. Data were analyzed using the log-rank test, Cox stepwise model, Kaplan-Meier method, Fine and Gray model and Fisher's exact test.RESULTS: This study included 118 patients (46.8% who received bone marrow and 134 (53.2% who received umbilical cord blood transplants. Engraftment occurred in 89.47% of the patients that received bone marrow and 65.83% of those that received umbilical cord blood (p-value < 0.001. Both neutrophil and platelet engraftments were faster in the bone marrow group. Acute graft-versus-host disease occurred in 48.6% of the patients without statistically significant differences between the two groups (p-value = 0.653. Chronic graft-versus-host disease occurred in 9.2% of the patients with a higher incidence in the bone marrow group (p-value = 0.007. Relapse occurred in 24% of the 96 patients with malignant disease with 2-year cumulative incidences of 45% in the bone marrow group and 25% in the umbilical cord blood group (p-value = 0.117. Five-year overall survival was 47%, with an average survival time of 1207 days, and no significant differences between the groups (p-value = 0.4666.CONCLUSION: Despite delayed engraftment in the umbilical cord blood group, graft-versus-host disease, relapse and survival were similar in both groups.

  8. Management, treatment and outcomes of acute appendicitis in an elderly population: a single-center experience.

    Science.gov (United States)

    Cohen-Arazi, O; Dabour, K; Bala, M; Haran, A; Almogy, G

    2017-10-01

    Only 5-10% of cases of acute appendicitis (AA) are diagnosed above the age of 60 years. Complicated AA is more common in the elderly, who also have more comorbidities. The goals of this study were to describe our experience with elderly patients and identify predictors of increased morbidity. Patients ≥65 years who were treated for AA between 2006 and 2013 were selected. The control consisted of patients aged 20-45 years, who were randomly selected from a pool of 900 patients. Seventy-four patients ≥65 years, mean age of 74.6 ± 7.4, were included. Time from onset of symptoms to surgery was similar between the groups. CT scan was performed for all patients in the elderly group compared to 55.6% in the younger group (p < 0.001). 77% of the younger patients underwent laparoscopic appendectomy compared to 43.2% of the elderly patients (p < 0.001). Pathological findings of severe appendicitis were significantly more common in the elderly group (39.2 vs. 10.5%, p < 0.001). Sixteen elderly patients (21.6%) developed complications, compared with 4 patients (3.2%) in the younger group (p < 0.001). The length of stay was longer in the elderly group and even longer for patients with complications (p < 0.001). There was no mortality. Cardiac disease was the only independent predictor of peri-operative complications (OR = 4.2). Severe forms of acute appendicitis and post-operative morbidity are higher in the elderly population. Cardiac disease is the only predictor for increased morbidity. Although CT scan was performed universally in the elderly group, it did not appear to increase time from presentation to surgery.

  9. A single population of red globular clusters around the massive compact galaxy NGC 1277

    Science.gov (United States)

    Beasley, Michael A.; Trujillo, Ignacio; Leaman, Ryan; Montes, Mireia

    2018-03-01

    Massive galaxies are thought to form in two phases: an initial collapse of gas and giant burst of central star formation, followed by the later accretion of material that builds up their stellar and dark-matter haloes. The systems of globular clusters within such galaxies are believed to form in a similar manner. The initial central burst forms metal-rich (spectrally red) clusters, whereas more metal-poor (spectrally blue) clusters are brought in by the later accretion of less-massive satellites. This formation process is thought to result in the multimodal optical colour distributions that are seen in the globular cluster systems of massive galaxies. Here we report optical observations of the massive relic-galaxy candidate NGC 1277—a nearby, un-evolved example of a high-redshift ‘red nugget’ galaxy. We find that the optical colour distribution of the cluster system of NGC 1277 is unimodal and entirely red. This finding is in strong contrast to other galaxies of similar and larger stellar mass, the cluster systems of which always exhibit (and are generally dominated by) blue clusters. We argue that the colour distribution of the cluster system of NGC 1277 indicates that the galaxy has undergone little (if any) mass accretion after its initial collapse, and use simulations of possible merger histories to show that the stellar mass due to accretion is probably at most ten per cent of the total stellar mass of the galaxy. These results confirm that NGC 1277 is a genuine relic galaxy and demonstrate that blue clusters constitute an accreted population in present-day massive galaxies.

  10. A single, plastic population of Mycosphaerella pinodes causes ascochyta blight on winter and spring peas (Pisum sativum) in France.

    Science.gov (United States)

    Le May, Christophe; Guibert, Michèle; Leclerc, Aurélie; Andrivon, Didier; Tivoli, Bernard

    2012-12-01

    Plant diseases are caused by pathogen populations continuously subjected to evolutionary forces (genetic flow, selection, and recombination). Ascochyta blight, caused by Mycosphaerella pinodes, is one of the most damaging necrotrophic pathogens of field peas worldwide. In France, both winter and spring peas are cultivated. Although these crops overlap by about 4 months (March to June), primary Ascochyta blight infections are not synchronous on the two crops. This suggests that the disease could be due to two different M. pinodes populations, specialized on either winter or spring pea. To test this hypothesis, 144 pathogen isolates were collected in the field during the winter and spring growing seasons in Rennes (western France), and all the isolates were genotyped using amplified fragment length polymorphism (AFLP) markers. Furthermore, the pathogenicities of 33 isolates randomly chosen within the collection were tested on four pea genotypes (2 winter and 2 spring types) grown under three climatic regimes, simulating winter, late winter, and spring conditions. M. pinodes isolates from winter and spring peas were genetically polymorphic but not differentiated according to the type of cultivars. Isolates from winter pea were more pathogenic than isolates from spring pea on hosts raised under winter conditions, while isolates from spring pea were more pathogenic than those from winter pea on plants raised under spring conditions. These results show that disease developed on winter and spring peas was initiated by a single population of M. pinodes whose pathogenicity is a plastic trait modulated by the physiological status of the host plant.

  11. Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep

    Directory of Open Access Journals (Sweden)

    Andrés N Grasso

    2014-06-01

    Full Text Available The aim of this study was to investigate the genetic diversity within and among three breeds of sheep: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10 were genotyped using the Illumina Ovine SNP50 beadchip®. Genetic diversity was evaluated by comparing the minor allele frequency (MAF among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA and fixation index (F ST. Fixed markers (MAF = 0 that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs, PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively and moderate genetic differentiation (F ST = 0.08 between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (F ST = 0.17 for both breeds. Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds.

  12. Different risk-increasing drugs in recurrent versus single fallers: are recurrent fallers a distinct population?

    Science.gov (United States)

    Askari, Marjan; Eslami, Saied; Scheffer, Alice C; Medlock, Stephanie; de Rooij, Sophia E; van der Velde, Nathalie; Abu-Hanna, Ameen

    2013-10-01

    classes that showed significant association with recurrent falls. In part, these classes may act as markers of frailty and comorbidity, or they may reflect differences in the risk factors affecting the older, frailer population that tends to sustain recurrent falls. Further investigation is needed to elucidate causes and ways to prevent recurrent falls.

  13. Population.

    Science.gov (United States)

    International Planned Parenthood Federation, London (England).

    In an effort to help meet the growing interest and concern about the problems created by the rapid growth of population, The International Planned Parenthood Federation has prepared this booklet with the aim of assisting the study of the history and future trends of population growth and its impact on individual and family welfare, national,…

  14. Patients come from populations and populations contain patients. A two-stage scientific and ethics review: The next adaptation for single institutional review boards.

    Science.gov (United States)

    Knopman, David; Alford, Eli; Tate, Kaitlin; Long, Mark; Khachaturian, Ara S

    2017-08-01

    For nearly 50 years, institutional review boards (IRB) and independent ethics committees have featured local oversight as a core function of research ethics reviews. However growing complexity in Alzheimer's clinical research suggests current approaches to research volunteer safety is hampering development of new therapeutics. As a partial response to this challenge, the NIH has mandated that all NIH-funded multi-site studies will use a single Institutional Review Board. The perspective describes a joint program to provide a single IRB of record (sIRB) for phases of multi-site studies. The approach follows two steps. One, an expert Scientific Review Committee (SRC) of senior researchers in the field will conduct the review principally of scientific merit, significance, feasibility, and the likelihood of meaningful results. The second step will be the IRB's regulatory and ethics review. The IRB will apply appropriate regulatory criteria for approval including minimization of risks to subjects and risks reasonable in relation to anticipated benefits, equitable subject selection, informed consent, protections for vulnerable populations, and application of local context considerations, among others. There is a steady demand for scientific, ethical and regulatory review of planned Alzheimer's studies. As of January 15, 2017, there are nearly 400 open studies, Phase II and III, industry and NIH sponsored trials on disease indications affecting memory, movement and mood in the US. The effort will initially accept protocols for studies of Alzheimer's disease, dementia, and related disorders effecting memory, movement and mood. Future aims will be to provide scientific review and, where applicable, regulatory and ethical review in an international context outside North America with sites possibly in Asia, Europe and Australia. Copyright © 2017 the Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

  15. COMPARISON OF SINGLE NUCLEOTIDE POLYMORPHISMS AND MICROSATELLITES IN NON-INVASIVE GENETIC MONITORING OF A WOLF POPULATION

    DEFF Research Database (Denmark)

    Fabbri, Elena; Caniglia, R.; Mucci, Nadia

    2012-01-01

    Single nucleotide polymorphisms (SNPs) which represent the most widespread source of sequence variation in genomes, are becoming a routine application in several fields such as forensics, ecology and conservation genetics. Their use, requiring short amplifications, may allow a more efficient...... genotyping of degraded DNA. We provide the first application of SNP genotyping in an Italian non-invasive genetic monitoring project of the wolf. We compared three different techniques for genotyping SNPs: pyrosequencing, SNaPshot* and TaqMan* Probe Assay in Real-Time PCR. We successively genotyped nine SNPs....... We evaluated the cost, laboratory effort and reliability of these different markers and discuss the possible future use of VeraCode, SNPlex and Fluidigm EP1 system in wild population monitoring....

  16. Frequency of single nucleotide polymorphisms of some immune response genes in a population sample from São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    Léa Campos de Oliveira

    2011-09-01

    Full Text Available Objective: To present the frequency of single nucleotide polymorphismsof a few immune response genes in a population sample from SãoPaulo City (SP, Brazil. Methods: Data on allele frequencies ofknown polymorphisms of innate and acquired immunity genes werepresented, the majority with proven impact on gene function. Datawere gathered from a sample of healthy individuals, non-HLA identicalsiblings of bone marrow transplant recipients from the Hospital dasClínicas da Faculdade de Medicina da Universidade de São Paulo,obtained between 1998 and 2005. The number of samples variedfor each single nucleotide polymorphism analyzed by polymerasechain reaction followed by restriction enzyme cleavage. Results:Allele and genotype distribution of 41 different gene polymorphisms,mostly cytokines, but also including other immune response genes,were presented. Conclusion: We believe that the data presentedhere can be of great value for case-control studies, to define whichpolymorphisms are present in biologically relevant frequencies and toassess targets for therapeutic intervention in polygenic diseases witha component of immune and inflammatory responses.

  17. Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations.

    Science.gov (United States)

    Yáñez, J M; Naswa, S; López, M E; Bassini, L; Correa, K; Gilbey, J; Bernatchez, L; Norris, A; Neira, R; Lhorente, J P; Schnable, P S; Newman, S; Mileham, A; Deeb, N; Di Genova, A; Maass, A

    2016-07-01

    A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype-phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from American and European salmon populations. A total of 9 736 473 nonredundant SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs were selected to develop an Affymetrix Axiom(®) myDesign Custom Array. This array was used to genotype 480 fish representing wild and farmed salmon from Europe, North America and Chile. A total of 159 099 (79.6%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs against 238 572 markers currently available in two other Atlantic salmon arrays, only 4.6% of the SNP overlapped with the panel developed in this study. This novel high-density SNP panel will be very useful for the dissection of economically and ecologically relevant traits, enhancing breeding programmes through genomic selection as well as supporting genetic studies in both wild and farmed populations of Atlantic salmon using high-resolution genomewide information. © 2016 John Wiley & Sons Ltd.

  18. Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias

    Science.gov (United States)

    2013-01-01

    Background Deep sequencing is a powerful tool for assessing viral genetic diversity. Such experiments harness the high coverage afforded by next generation sequencing protocols by treating sequencing reads as a population sample. Distinguishing true single nucleotide variants (SNVs) from sequencing errors remains challenging, however. Current protocols are characterised by high false positive rates, with results requiring time consuming manual checking. Results By statistical modelling, we show that if multiple variant sites are considered at once, SNVs can be called reliably from high coverage viral deep sequencing data at frequencies lower than the error rate of the sequencing technology, and that SNV calling accuracy increases as true sequence diversity within a read length increases. We demonstrate these findings on two control data sets, showing that SNV detection is more reliable on a high diversity human immunodeficiency virus sample as compared to a moderate diversity sample of hepatitis C virus. Finally, we show that in situations where probabilistic clustering retains false positive SNVs (for instance due to insufficient sample diversity or systematic errors), applying a strand bias test based on a beta-binomial model of forward read distribution can improve precision, with negligible cost to true positive recall. Conclusions By combining probabilistic clustering (implemented in the program ShoRAH) with a statistical test of strand bias, SNVs may be called from deeply sequenced viral populations with high accuracy. PMID:23879730

  19. Single nucleotide polymorphisms of ABCB1 (MDR1) gene and distinct haplotype profile in a West Black African population.

    Science.gov (United States)

    Allabi, Aurel C; Horsmans, Yves; Issaoui, Bouchra; Gala, Jean-Luc

    2005-04-01

    The ABCB1 (MDR1) multidrug transporter plays a key role in determining drug bioavailability. Differences in drug response exist among different ethnic groups. However, until now, no haplotype data are available in a Black African population. Exons 2, 7, 10, 11, 12, 14, 17, 21, 26, and the surrounding intronic regions were sequenced using genomic DNA from 111 Beninese subjects to examine 19 intragenic single nucleotide polymorphisms (SNPs). Linkage disequilibrium analysis and haplotypes were generated using the expectation-maximization algorithm. We identified 12 SNPs, 3 of which were novel: IVS9-57delA, IVS9-8T>A, 1662G>C (exon 14). The most common SNP was IVS14+38A>G. At the MRD1 locus, 53 haplotypes were inferred from the SNP data sets. The 4 SNPs, IVS6+139C>T, IVS9-44A>G, 1236C>T, and 3435C>T, showed strong linkage disequilibrium with each other, confirming the block concept. Moreover, our findings suggest that ABCB1 exonic SNPs are less frequently observed in our population than in African-Americans. Our data are compatible with a close evolutionary relationship in Black Africans from Benin.

  20. Integrative analysis of single nucleotide polymorphisms and gene expression efficiently distinguishes samples from closely related ethnic populations

    Directory of Open Access Journals (Sweden)

    Yang Hsin-Chou

    2012-07-01

    Full Text Available Abstract Background Ancestry informative markers (AIMs are a type of genetic marker that is informative for tracing the ancestral ethnicity of individuals. Application of AIMs has gained substantial attention in population genetics, forensic sciences, and medical genetics. Single nucleotide polymorphisms (SNPs, the materials of AIMs, are useful for classifying individuals from distinct continental origins but cannot discriminate individuals with subtle genetic differences from closely related ancestral lineages. Proof-of-principle studies have shown that gene expression (GE also is a heritable human variation that exhibits differential intensity distributions among ethnic groups. GE supplies ethnic information supplemental to SNPs; this motivated us to integrate SNP and GE markers to construct AIM panels with a reduced number of required markers and provide high accuracy in ancestry inference. Few studies in the literature have considered GE in this aspect, and none have integrated SNP and GE markers to aid classification of samples from closely related ethnic populations. Results We integrated a forward variable selection procedure into flexible discriminant analysis to identify key SNP and/or GE markers with the highest cross-validation prediction accuracy. By analyzing genome-wide SNP and/or GE markers in 210 independent samples from four ethnic groups in the HapMap II Project, we found that average testing accuracies for a majority of classification analyses were quite high, except for SNP-only analyses that were performed to discern study samples containing individuals from two close Asian populations. The average testing accuracies ranged from 0.53 to 0.79 for SNP-only analyses and increased to around 0.90 when GE markers were integrated together with SNP markers for the classification of samples from closely related Asian populations. Compared to GE-only analyses, integrative analyses of SNP and GE markers showed comparable testing

  1. Imputation Accuracy from Low to Moderate Density Single Nucleotide Polymorphism Chips in a Thai Multibreed Dairy Cattle Population

    Directory of Open Access Journals (Sweden)

    Danai Jattawa

    2016-04-01

    Full Text Available The objective of this study was to investigate the accuracy of imputation from low density (LDC to moderate density SNP chips (MDC in a Thai Holstein-Other multibreed dairy cattle population. Dairy cattle with complete pedigree information (n = 1,244 from 145 dairy farms were genotyped with GeneSeek GGP20K (n = 570, GGP26K (n = 540 and GGP80K (n = 134 chips. After checking for single nucleotide polymorphism (SNP quality, 17,779 SNP markers in common between the GGP20K, GGP26K, and GGP80K were used to represent MDC. Animals were divided into two groups, a reference group (n = 912 and a test group (n = 332. The SNP markers chosen for the test group were those located in positions corresponding to GeneSeek GGP9K (n = 7,652. The LDC to MDC genotype imputation was carried out using three different software packages, namely Beagle 3.3 (population-based algorithm, FImpute 2.2 (combined family- and population-based algorithms and Findhap 4 (combined family- and population-based algorithms. Imputation accuracies within and across chromosomes were calculated as ratios of correctly imputed SNP markers to overall imputed SNP markers. Imputation accuracy for the three software packages ranged from 76.79% to 93.94%. FImpute had higher imputation accuracy (93.94% than Findhap (84.64% and Beagle (76.79%. Imputation accuracies were similar and consistent across chromosomes for FImpute, but not for Findhap and Beagle. Most chromosomes that showed either high (73% or low (80% imputation accuracies were the same chromosomes that had above and below average linkage disequilibrium (LD; defined here as the correlation between pairs of adjacent SNP within chromosomes less than or equal to 1 Mb apart. Results indicated that FImpute was more suitable than Findhap and Beagle for genotype imputation in this Thai multibreed population. Perhaps additional increments in imputation accuracy could be achieved by increasing the completeness of pedigree information.

  2. Association of single nucleotide polymorphisms in TCF2 with type 2 diabetes susceptibility in a Han Chinese population.

    Directory of Open Access Journals (Sweden)

    Xuelong Zhang

    Full Text Available Hepatocyte nuclear factor 1β (HNF1β, a transcription factor encoded by the transcription factor 2 gene (TCF2, plays a critical role in pancreatic cell formation and glucose homeostasis. It has been suggested that single nucleotide polymorphisms (SNPs of TCF2 are associated with susceptibility to type 2 diabetes (T2D. However, published results are inconsistent and inclusive. To further investigate the role of these common variants, we examined the association of TCF2 polymorphisms with the risk of T2D in a Han population in northeastern China. We genotyped five SNPs in 624 T2D patients and 630 healthy controls by using a SNaPshot method, and evaluated the T2D risk conferred by individual SNPs and haplotypes. In the single-locus analysis, we found that rs752010, rs4430796 and rs7501939 showed allelic differences between T2D patients and healthy controls, with an OR of 1.26 (95% CI 1.08-1.51, P = 0.003, an OR of 1.23 (95% CI 1.06-1.55, P = 0.001 and an OR of 1.28 (95% CI 1.10-1.61, P = 0.001, respectively. Genotype association analysis of each locus also revealed that the homozygous carriers of the at-risk allele had a significant increased T2D risk compared to homozygous carriers of the other allele (OR 1.78, 95% CI 1.20-2.64 for rs752010; OR 1.82, 95% CI 1.24-2.67 for rs4430796; OR 1.95, 95% CI 1.31-2.90 for rs7501939, even after Bonferroni correction for multiple comparisons. Besides, the haplotype-based analysis demonstrated that AGT in block rs752010-rs4430796-rs7501939 was associated with about 30% increase in T2D risk (OR 1.31, 95% CI 1.09-1.57, P = 0.01. Our findings suggested that TCF2 variants may be involved in T2D risk in a Han population of northeastern China. Larger studies with ethnically diverse populations are warranted to confirm the results reported in this investigation.

  3. Differing effects of attention in single-units and populations are well predicted by heterogeneous tuning and the normalization model of attention.

    Science.gov (United States)

    Hara, Yuko; Pestilli, Franco; Gardner, Justin L

    2014-01-01

    Single-unit measurements have reported many different effects of attention on contrast-response (e.g., contrast-gain, response-gain, additive-offset dependent on visibility), while functional imaging measurements have more uniformly reported increases in response across all contrasts (additive-offset). The normalization model of attention elegantly predicts the diversity of effects of attention reported in single-units well-tuned to the stimulus, but what predictions does it make for more realistic populations of neurons with heterogeneous tuning? Are predictions in accordance with population-scale measurements? We used functional imaging data from humans to determine a realistic ratio of attention-field to stimulus-drive size (a key parameter for the model) and predicted effects of attention in a population of model neurons with heterogeneous tuning. We found that within the population, neurons well-tuned to the stimulus showed a response-gain effect, while less-well-tuned neurons showed a contrast-gain effect. Averaged across the population, these disparate effects of attention gave rise to additive-offsets in contrast-response, similar to reports in human functional imaging as well as population averages of single-units. Differences in predictions for single-units and populations were observed across a wide range of model parameters (ratios of attention-field to stimulus-drive size and the amount of baseline response modifiable by attention), offering an explanation for disparity in physiological reports. Thus, by accounting for heterogeneity in tuning of realistic neuronal populations, the normalization model of attention can not only predict responses of well-tuned neurons, but also the activity of large populations of neurons. More generally, computational models can unify physiological findings across different scales of measurement, and make links to behavior, but only if factors such as heterogeneous tuning within a population are properly accounted for.

  4. Population pharmacokinetics of a single dose of meloxicam after oral and intramuscular administration to captive lesser flamingos (Phoeniconaias minor).

    Science.gov (United States)

    Zordan, Martín A; Papich, Mark G; Pich, Ashley A; Unger, Katy M; Sánchez, Carlos R

    2016-12-01

    OBJECTIVE To determine the pharmacokinetics of a single dose of meloxicam after IM and oral administration to healthy lesser flamingos (Phoeniconaias minor) by use of a population approach. ANIMALS 16 healthy captive lesser flamingos between 1 and 4 years of age. PROCEDURES A single dose of meloxicam (0.5 mg/kg) was administered IM to each bird, and blood samples were collected from birds at 3 (n = 13 birds), 2 (2), or 1 (1) selected point between 0 and 13 hours after administration, with samples collected from birds at each point. After a 15-day washout period, the same dose of meloxicam was administered PO via a red rubber tube and blood samples were collected as described for IM administration. Pharmacokinetic values were determined from plasma concentrations measured by high-performance liquid chromatography. RESULTS Plasma drug concentrations after IM administration of meloxicam reached a mean ± SD maximum value of 6.01 ± 3.38 μg/mL. Mean area under the concentration-versus-time curve was 17.78 ± 2.79 μg•h/mL, and mean elimination half-life was 1.93 ± 0.32 hours. Plasma concentrations after oral administration reached a mean maximum value of 1.79 ± 0.33 μg/mL. Mean area under the curve was 22.16 ± 7.17 μg•h/mL, and mean elimination half-life was 6.05 ± 3.53 hours. CONCLUSIONS AND CLINICAL RELEVANCE In lesser flamingos, oral administration of meloxicam resulted in higher bioavailability and a longer elimination half-life than did IM administration, but the maximum plasma concentration was low and may be insufficient to provide analgesia in flamingos. Conversely, IM administration achieved the desired plasma concentration but would require more frequent administration.

  5. Effects of Single and Fractionated Irradiation on Natural Killer Cell Populations: Radiobiological Characteristics of Viability and Cytotoxicity In Vitro.

    Science.gov (United States)

    Hietanen, Tenho; Pitkänen, Maunu; Kapanen, Mika; Kellokumpu-Lehtinen, Pirkko-Liisa

    2015-10-01

    Natural killer (NK) cells are important in destroying tumor cells. However, they are damaged by radiation therapy. We studied the effects of single and fractionated irradiation on the viability and cytotoxicity of human non-selected NK cells and sub-groups with cluster of differentiation (CD) CD16(+) and CD56(+) in vitro. Only very few studies dealing with the standard radiobiological parameters for characterizing NK cells exist in the literature. NK cell populations were isolated from buffy coats using different methods and irradiated with single doses up to 80 Gy and fractionated doses of 10 or 30 Gy with different numbers of applications and at different intervals. The study end-points were viability using propidium iodide (PI), trypan blue and intracellular adenosine triphosphate (ATP) assays, and cytotoxicity using the (51)Cr-release assay. The standard radiobiological parameters α and β of the linear-quadratic (L-Q) model and the mean inactivation dose D̅ taken as the area under the curve (AUC) were calculated to characterize the radiosensitivity of different NK cell populations. The AUC values of the 51Cr release data in the dose range of 0-40 Gy were as follows: for non-selected NK cells, 23.6-20.9 Gy; for CD16(+) and CD56(+) cells, 14.5-13.2 Gy. The AUC values of ATP, trypan blue and propidium iodide methods equally well described the viability of irradiated NK cells. The α/β ratio for cytotoxicity and viability data in the L-Q model corresponded to the acutely responding tissues. Splitting a 30-Gy dose into two fractions applied at different intervals caused a significant rise in ATP levels and cytotoxicity. Dividing the total dose into four doses applied at fixed intervals also resulted in significant elevations of ATP content and cytotoxicity of NK cells at 10 Gy. According to the L-Q method, irradiated NK cells behaved similarly to acutely responding human tissues with respect to cytotoxicity and viability. The AUC proved very useful for comparing

  6. A Putative Association of a Single Nucleotide Polymorphism in GPR126 with Aggressive Periodontitis in a Japanese Population.

    Science.gov (United States)

    Kitagaki, Jirouta; Miyauchi, Shizuka; Asano, Yoshihiro; Imai, Atsuko; Kawai, Shinji; Michikami, Ikumi; Yamashita, Motozo; Yamada, Satoru; Kitamura, Masahiro; Murakami, Shinya

    2016-01-01

    Periodontitis is an inflammatory disease causing loss of tooth-supporting periodontal tissue. Disease susceptibility to the rapidly progressive form of periodontitis, aggressive periodontitis (AgP), appears to be influenced by genetic risk factors. To identify these in a Japanese population, we performed whole exome sequencing of 41 unrelated generalized or localized AgP patients. We found that AgP is putatively associated with single nucleotide polymorphism (SNP) rs536714306 in the G-protein coupled receptor 126 gene, GPR126 [c.3086 G>A (p.Arg1029Gln)]. Since GPR126 activates the cAMP/PKA signaling pathway, we performed cAMP ELISA analysis of cAMP concentrations, and found that rs536714306 impaired the signal transactivation of GPR126. Moreover, transfection of human periodontal ligament (HPDL) cells with wild-type or mutant GPR126 containing rs536714306 showed that wild-type GPR126 significantly increased the mRNA expression of bone sialoprotein, osteopontin, and Runx2 genes, while mutant GPR126 had no effect on the expression of these calcification-related genes. The increase in expression of these genes was through the GPR126-induced increase of bone morphogenic protein-2, inhibitor of DNA binding (ID) 2, and ID4 expression. These data indicate that GPR126 might be important in maintaining the homeostasis of periodontal ligament tissues through regulating the cytodifferentiation of HPDL cells. The GPR126 SNP rs536714306 negatively influences this homeostasis, leading to the development of AgP, suggesting that it is a candidate genetic risk factor for AgP in the Japanese population.

  7. Therapeutic dosage assessment based on population pharmacokinetics of a novel single-dose transdermal donepezil patch in healthy volunteers.

    Science.gov (United States)

    Choi, Hee Youn; Kim, Yo Han; Hong, Donghyun; Kim, Seong Su; Bae, Kyun-Seop; Lim, Hyeong-Seok

    2015-08-01

    We performed population pharmacokinetic (PK) analysis of a novel transdermal donepezil patch in healthy subjects who participated in a phase I trial. We also studied the optimal dosage regimen with repeated patch application for achieving a therapeutic range using a PK simulation model. This study used data from a randomized, single-dose escalation phase I clinical trial conducted in Korea. The population PK analysis was performed using NONMEM software, version 7.3. From the final PK model, we simulated repeat patch application results assuming various transdermal absorption rates. Based on the clinical trial data, novel donepezil patches with doses of 43.75 mg/12.5 cm(2), 87.5 mg/25 cm(2), and 175 mg/50 cm(2) were placed on each subject. A linear one-compartment, first-order elimination with sequential zero- and first-order absorption model best described the donepezil plasma concentrations after patch application. Simulated results on the basis of the PK model showed that repeat application of the patches of 87.5 mg/25 cm(2) and 175 mg/50 cm(2) every 72 h would cover the therapeutic range of donepezil and reach steady-state faster with fewer fluctuations in concentration compared to typical oral administrations. A linear one-compartment with sequential zero- and first-order absorption model was effective for describing the PKs of donepezil after application of patch. Based on this analysis, 87.5 mg/25 cm(2) or 175 mg/50 cm(2) patch application every 72 h is expected to achieve the desired plasma concentration of donepezil.

  8. A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina.

    Science.gov (United States)

    Kasulin, Luciana; Rowan, Beth A; León, Rolando J C; Schuenemann, Verena J; Weigel, Detlef; Botto, Javier F

    2017-07-01

    The growing collection of sequenced or genotyped Arabidopsis thaliana accessions includes mostly individuals from the native Eurasian and N. African range and introduced North American populations. Here, we describe the genetic and phenotypic diversity, along with habitats and life history, of A. thaliana plants collected at the southernmost end of its worldwide distribution. Seed samples were harvested from plants growing in four sites within a ~3500-km 2 -area in Patagonia, Argentina, and represent the first germplasm to be collected in South America for this species. Whole-genome resequencing revealed that plants from the four sites and a Patagonia herbarium specimen collected in 1967 formed a single haplogroup (Pat), indicating that the phenotypic variation observed in the field reflected plastic responses to the environment. admixture and principal components analyses suggest that the ancestor of the Pat haplogroup either came from Italy or the Balkan/Caucasus regions of Eurasia. In the laboratory, plants from the Pat haplogroup were hyposensitive to continuous red (Rc) and shade light, with corresponding changes in the expression of phytochrome signalling genes. Pat had higher PIF3 and PIF5 and lower HY5 expression under Rc light; and lower expression of PIL1, ATHB2 and HFR1 under shade compared to Col-0. In addition, Pat plants had a strong vernalization requirement associated with high levels of FLC expression. We conclude that including Pat in studies of natural variation and in comparison with other introduced populations will provide additional information for association studies and allow for a more detailed assessment of the demographic events following colonization. © 2017 John Wiley & Sons Ltd.

  9. Response of Listeria monocytogenes to disinfection stress at the single-cell and population levels as monitored by intracellular pH measurements and viable-cell counts

    DEFF Research Database (Denmark)

    Kastbjerg, Vicky Gaedt; Nielsen, Dennis S.; Arneborg, Nils

    2009-01-01

    of the bacterium. In situ analyses of Listeria monocytogenes single cells were performed during exposure to different concentrations of the disinfectant Incimaxx DES to study a possible population subdivision. Bacterial survival was quantified with plate counting and disinfection stress at the single-cell level...... by measuring intracellular pH (pHi) over time by fluorescence ratio imaging microscopy. pHi values were initially 7 to 7.5 and decreased in both attached and planktonic L. monocytogenes cells during exposure to sublethal and lethal concentrations of Incimaxx DES. The response of the bacterial population...... that a population of L. monocytogenes cells, whether planktonic or attached, is homogenous with respect to sensitivity to an acidic disinfectant studied on the single-cell level. Hence a major subpopulation more tolerant to disinfectants, and hence more persistent, does not appear to be present....

  10. QTLs Associated with Agronomic Traits in the Cutler × AC Barrie Spring Wheat Mapping Population Using Single Nucleotide Polymorphic Markers

    Science.gov (United States)

    Perez-Lara, Enid; Semagn, Kassa; Chen, Hua; Iqbal, Muhammad; N’Diaye, Amidou; Kamran, Atif; Navabi, Alireza; Pozniak, Curtis; Spaner, Dean

    2016-01-01

    We recently reported three earliness per se quantitative trait loci (QTL) associated with flowering and maturity in a recombinant inbred lines (RILs) population derived from a cross between the spring wheat (Triticum aestivum L.) cultivars ‘Cutler’ and ‘AC Barrie’ using 488 microsatellite and diversity arrays technology (DArT) markers. Here, we present QTLs associated with flowering time, maturity, plant height, and grain yield using high density single nucleotide polymorphic (SNP) markers in the same population. A mapping population of 158 RILs and the two parents were evaluated at five environments for flowering, maturity, plant height and grain yield under field conditions, at two greenhouse environments for flowering, and genotyped with a subset of 1809 SNPs out of the 90K SNP array and 2 functional markers (Ppd-D1 and Rht-D1). Using composite interval mapping on the combined phenotype data across all environments, we identified a total of 19 QTLs associated with flowering time in greenhouse (5), and field (6) conditions, maturity (5), grain yield (2) and plant height (1). We mapped these QTLs on 8 chromosomes and they individually explained between 6.3 and 37.8% of the phenotypic variation. Four of the 19 QTLs were associated with multiple traits, including a QTL on 2D associated with flowering, maturity and grain yield; two QTLs on 4A and 7A associated with flowering and maturity, and another QTL on 4D associated with maturity and plant height. However, only the QTLs on both 2D and 4D had major effects, and they mapped adjacent to well-known photoperiod response Ppd-D1 and height reducing Rht-D1 genes, respectively. The QTL on 2D reduced flowering and maturity time up to 5 days with a yield penalty of 436 kg ha-1, while the QTL on 4D reduced plant height by 13 cm, but increased maturity by 2 days. The high density SNPs allowed us to map eight moderate effect, two major effect, and nine minor effect QTLs that were not identified in our previous study

  11. Safety of and tolerance to adenosine infusion for myocardial perfusion single-photon emission computed tomography in a Japanese population.

    Science.gov (United States)

    Hatanaka, Kunihiko; Doi, Masayuki; Hirohata, Satoshi; Kamikawa, Shigeshi; Kaji, Yoko; Katoh, Tsutomu; Kusachi, Shozo; Ninomiya, Yoshifumi; Ohe, Tohru

    2007-06-01

    Adenosine has been available for use in myocardial perfusion single-photon emission computed tomography (SPECT) in Japan since 2005. The purpose of this study was to evaluate the safety of and tolerance to thallium-201 myocardial perfusion SPECT with intravenous adenosine infusion in Japanese patients with suspected coronary artery disease. Two hundred and six consecutive patients who underwent an adenosine infusion (120 mug . kg(-1) . min(-1)) SPECT at Sumitomo Besshi Hospital (Niihama, Japan) were investigated. The effects of adenosine infusion were monitored for each patient. A coronary angiography was performed in 81 patients. Adenosine infusion significantly decreased blood pressure and increased heart rate. Adverse reactions were observed in 161 patients (78.2%). Most reactions were transient, disappearing soon after the termination of adenosine infusion. No serious adverse reactions, such as acute myocardial infarction or death, occurred. Adenosine infusion was terminated in 3 patients (1.5%) because of near syncope or sustained 2:1 atrioventricular block. Electrocardiographic changes occurred in 15 patients (7.3%). Self-assessed scoring after SPECT showed that the patients were very tolerant (74.6% of 177 patients) of adenosine infusion myocardial SPECT. The sensitivity and specificity were 75.0% and 69.7%, respectively. Adenosine infusion myocardial SPECT is safe and well tolerated in the Japanese population, despite the frequent occurrence of minor adverse reactions.

  12. Comparison of single nucleotide polymorphisms and microsatellites in non-invasive genetic monitoring of a wolf population

    Directory of Open Access Journals (Sweden)

    Fabbri Elena

    2012-01-01

    Full Text Available Single nucleotide polymorphisms (SNPs which represent the most widespread source of sequence variation in genomes, are becoming a routine application in several fields such as forensics, ecology and conservation genetics. Their use, requiring short amplifications, may allow a more efficient genotyping of degraded DNA. We provide the first application of SNP genotyping in an Italian non-invasive genetic monitoring project of the wolf. We compared three different techniques for genotyping SNPs: pyrosequencing, SNaPshot® and TaqMan® Probe Assay in Real-Time PCR. We successively genotyped nine SNPs using the TaqMan Probe Assay in 51 Italian wolves, 57 domestic dogs, 15 wolf x dog hybrids and 313 wolf scats collected in the northern Apennines. The obtained results were used to estimate genetic variability and PCR error rates in SNP genotyping protocols compared to standard microsatellite analysis. We evaluated the cost, laboratory effort and reliability of these different markers and discuss the possible future use of VeraCode, SNPlex and Fluidigm EP1 system in wild population monitoring.

  13. A novel high-resolution single locus sequence typing scheme for mixed populations of Propionibacterium acnes in vivo.

    Directory of Open Access Journals (Sweden)

    Christian F P Scholz

    Full Text Available The Gram-positive anaerobic bacterium Propionibacterium acnes is a prevalent member of the normal skin microbiota of human adults. In addition to its suspected role in acne vulgaris it is involved in a variety of opportunistic infections. Multi-locus sequence-typing (MLST schemes identified distinct phylotypes associated with health and disease. Being based on 8 to 9 house-keeping genes these MLST schemes have a high discriminatory power, but their application is time- and cost-intensive. Here we describe a single-locus sequence typing (SLST scheme for P. acnes. The target locus was identified with a genome mining approach that took advantage of the availability of representative genome sequences of all known phylotypes of P. acnes. We applied this SLST on a collection of 188 P. acnes strains and demonstrated a resolution comparable to that of existing MLST schemes. Phylogenetic analysis applied to the SLST locus resulted in clustering patterns identical to a reference tree based on core genome sequences. We further demonstrate that SLST can be applied to detect multiple phylotypes in complex microbial communities by a metagenomic pyrosequencing approach. The described SLST strategy may be applied to any bacterial species with a basically clonal population structure to achieve easy typing and mapping of multiple phylotypes in complex microbiotas. The P. acnes SLST database can be found at http://medbac.dk/slst/pacnes.

  14. Chosen single nucleotide polymorphisms (SNPs) of enamel formation genes and dental caries in a population of Polish children.

    Science.gov (United States)

    Gerreth, Karolina; Zaorska, Katarzyna; Zabel, Maciej; Borysewicz-Lewicka, Maria; Nowicki, Michał

    2017-09-01

    It is increasingly emphasized that the influence of a host's factors in the etiology of dental caries are of most interest, particularly those concerned with genetic aspect. The aim of the study was to analyze the genotype and allele frequencies of single nucleotide polymorphisms (SNPs) in AMELX, AMBN, TUFT1, TFIP11, MMP20 and KLK4 genes and to prove their association with dental caries occurrence in a population of Polish children. The study was performed in 96 children (48 individuals with caries - "cases" and 48 free of this disease - "controls"), aged 20-42 months, chosen out of 262 individuals who had dental examination performed and attended 4 day nurseries located in Poznań (Poland). From both groups oral swab was collected for molecular evaluation. Eleven selected SNPs markers were genotyped by Sanger sequencing. Genotype and allele frequencies were calculated and a standard χ2 analysis was used to test for deviation from Hardy-Weinberg equilibrium. The association of genetic variations with caries susceptibility or resistance was assessed by the Fisher's exact test and p ≤ 0.05 was considered statistically significant. Five markers were significantly associated with caries incidence in children in the study: rs17878486 in AMELX (p caries occurrence in Polish children.

  15. Microelectromechanical System-Based Sensing Arrays for Comparative in Vitro Nanotoxicity Assessment at Single Cell and Small Cell-Population Using Electrochemical Impedance Spectroscopy.

    Science.gov (United States)

    Shah, Pratikkumar; Zhu, Xuena; Zhang, Xueji; He, Jin; Li, Chen-zhong

    2016-03-09

    The traditional in vitro nanotoxicity assessment approaches are conducted on a monolayer of cell culture. However, to study a cell response without interference from the neighbor cells, a single cell study is necessary; especially in cases of neuronal, cancerous, and stem cells, wherein an individual cell's fate is often not explained by the whole cell population. Nonetheless, a single cell does not mimic the actual in vivo environment and lacks important information regarding cell communication with its microenvironment. Both a single cell and a cell population provide important and complementary information about cells' behaviors. In this research, we explored nanotoxicity assessment on a single cell and a small cell population using electrochemical impedance spectroscopy and a microelectromechanical system (MEMS) device. We demonstrated a controlled capture of PC12 cells in different-sized microwells (to capture a different number of cells) using a combined method of surface functionalization and dielectrophoresis. The present approach provides a rapid nanotoxicity response as compared to other conventional approaches. This is the first study, to our knowledge, which demonstrates a comparative response of a single cell and small cell colonies on the same MEMS platform, when exposed to metaloxide nanoparticles. We demonstrated that the microenvironment of a cell is also accountable for cells' behaviors and their responses to nanomaterials. The results of this experimental study open up a new hypothesis to be tested for identifying the role of cell communication in spreading toxicity in a cell population.

  16. Association analysis of single nucleotide polymorphisms at five loci: comparison between atopic dermatitis and asthma in the Chinese Han population.

    Directory of Open Access Journals (Sweden)

    Hua-Yang Tang

    Full Text Available Atopic diseases, such as atopic dermatitis (AD and asthma, are closely related to clinical phenotypes with hypersensitivity, and often share some similar genetic and pathogenic bases. Our recent GWAS identified three susceptibility gene/loci FLG (rs11204971 and rs3126085, 5q22.1 (rs10067777, rs7701890, rs13360927 and rs13361382 and 20q13.33 (rs6010620 to AD. The effect of these AD associated polymorphisms in asthma is so far unknown. To investigate whether AD relevant genetic variants is identical to asthma and reveal the differences in genetic factors between AD and asthma in Chinese Han population, seven AD associated single nucleotide polymorphisms (SNPs as well as 3 other SNPs (rs7936562 and rs7124842 at 11q13.5 and rs4982958 at 14q11.2 from our previous AD GWAS were genotyped in 463 asthma patients and 985 controls using Sequenom MassArray system. We found rs4982958 at 14q11.2 was significantly associated with asthma (P = 3.04×10(-4, OR = 0.73. We also detected one significant risk haplotype GGGA from the 4 SNPs (rs10067777, rs7701890, rs13360927 and rs13361382 at 5q22.1 in AD cases (P(correction = 3.60×10(-10, OR = 1.26, and the haplotype was suggestive of risk in asthma cases in this study (P = 0.014, P(correction = 0.084, OR = 1.38. These SNPs (rs11204971, rs3126085, rs7936562, rs712484 and rs6010620 at AD susceptibility genes/loci FLG, 11q13.5 and 20q13.33 were not associated with asthma in this study. Our results further comfirmed that 14q11.2 was an important candidate locus for asthma and demonstrated that 5q22.1 might be shared by AD and asthma in Chinese Han population.

  17. Insertion sequence element single nucleotide polymorphism typing provides insights into the population structure and evolution of Mycobacterium ulcerans across Africa.

    Science.gov (United States)

    Vandelannoote, Koen; Jordaens, Kurt; Bomans, Pieter; Leirs, Herwig; Durnez, Lies; Affolabi, Dissou; Sopoh, Ghislain; Aguiar, Julia; Phanzu, Delphin Mavinga; Kibadi, Kapay; Eyangoh, Sara; Manou, Louis Bayonne; Phillips, Richard Odame; Adjei, Ohene; Ablordey, Anthony; Rigouts, Leen; Portaels, Françoise; Eddyani, Miriam; de Jong, Bouke C

    2014-02-01

    Buruli ulcer is an indolent, slowly progressing necrotizing disease of the skin caused by infection with Mycobacterium ulcerans. In the present study, we applied a redesigned technique to a vast panel of M. ulcerans disease isolates and clinical samples originating from multiple African disease foci in order to (i) gain fundamental insights into the population structure and evolutionary history of the pathogen and (ii) disentangle the phylogeographic relationships within the genetically conserved cluster of African M. ulcerans. Our analyses identified 23 different African insertion sequence element single nucleotide polymorphism (ISE-SNP) types that dominate in different areas where Buruli ulcer is endemic. These ISE-SNP types appear to be the initial stages of clonal diversification from a common, possibly ancestral ISE-SNP type. ISE-SNP types were found unevenly distributed over the greater West African hydrological drainage basins. Our findings suggest that geographical barriers bordering the basins to some extent prevented bacterial gene flow between basins and that this resulted in independent focal transmission clusters associated with the hydrological drainage areas. Different phylogenetic methods yielded two well-supported sister clades within the African ISE-SNP types. The ISE-SNP types from the "pan-African clade" were found to be widespread throughout Africa, while the ISE-SNP types of the "Gabonese/Cameroonian clade" were much rarer and found in a more restricted area, which suggested that the latter clade evolved more recently. Additionally, the Gabonese/Cameroonian clade was found to form a strongly supported monophyletic group with Papua New Guinean ISE-SNP type 8, which is unrelated to other Southeast Asian ISE-SNP types.

  18. Incidence and characteristics of acute referred orofacial pain caused by a posterior single tooth pulpitis in an Iranian population.

    Science.gov (United States)

    Hashemipour, Maryam Alsadat; Borna, Roya

    2014-02-01

    This study was designed to evaluate incidence and characteristics of acute referred orofacial pain caused by a posterior single tooth pulpitis in an Iranian population. In this cross-sectional study, 3,150 patients (1,400 males and 1,750 females) with pain in the orofacial region were evaluated via clinical and radiographic examination to determine their pain source. Patients completed a standardized clinical questionnaire consisting of a numerical rating scale for pain intensity and chose verbal descriptors from short form McGill questionnaire to describe the quality of their pain. Visual analog scale (VAS) was used to score pain intensity. In addition, patients indicated sites to which pain referred by drawing on an illustration of the head and neck. Data were analyzed using chi-square, fisher exact, and Mann-Whitney tests. Two thousand and hundred twenty patients (67/3%) reported pain in sites that diagnostically differed from the pain source. According to statistical analysis, sex (P = 0.02), intensity of pain (0.04), and quality (P = 0.001) of pain influenced its referral nature, while age of patients and kind of stimulus had no considerable effect on pain referral (P > 0.05). The results of the present study show the prevalence of referred pain in the head, face, and neck region is moderately high. Therefore, in patients with orofacial pain, it is essential to carefully examination before carrying out treatment that could be inappropriate. © 2013 The Authors Pain Practice © 2013 World Institute of Pain.

  19. Association of body mass index-related single nucleotide polymorphisms with psychiatric disease and memory performance in a Japanese population.

    Science.gov (United States)

    Ninomiya-Baba, Midori; Matsuo, Junko; Sasayama, Daimei; Hori, Hiroaki; Teraishi, Toshiya; Ota, Miho; Hattori, Kotaro; Noda, Takamasa; Ishida, Ikki; Shibata, Shigenobu; Kunugi, Hiroshi

    2017-10-01

    Obesity is a risk factor for psychiatric diseases. Recently, a number of single nucleotide polymorphisms (SNPs) have been shown to be related to body mass index (BMI). In this study, we investigated the association of BMI-related SNPs with psychiatric diseases and one of their endophenotypes, memory performance, in a Japanese population. The subjects were 1624 patients with one of three psychiatric diseases (799 patients with major depressive disorder, 594 with schizophrenia, and 231 with bipolar disorder) and 1189 healthy controls. Memory performance was assessed using the Wechsler Memory Scale - Revised (WMS-R). Genomic DNA was prepared from venous blood and used to genotype 23 BMI-related SNPs using the TaqMan 5'-exonuclease allelic discrimination assay. We then analysed the relationships between the SNPs and psychiatric disease and various subscales of the WMS-R. Three SNPs (rs11142387, rs12597579, and rs6548238) showed significant differences in the genotype or allele frequency between patients with any psychiatric diseases and controls. Furthermore, six SNPs (rs11142387, rs12597579, rs2815752, rs2074356, rs4776970, and rs2287019) showed significant differences in at least one subscale of the WMS-R depending on the genotypes of the healthy controls. Interestingly, rs11142387 near the Kruppel-like factor 9 (KLF9) was significantly associated with psychiatric disease and poor memory function. We identified three and six BMI-related SNPs associated with psychiatric disease and memory performance, respectively. In particular, carrying the A allele of rs11142387 near KLF9 was found to be associated with psychiatric disease and poor memory performance, which warrants further investigations.

  20. Correlation between single nucleotide polymorphisms of NADPH oxidase p22phox gene and ischemic stroke in Shanghai Han population

    Directory of Open Access Journals (Sweden)

    Wei XU

    2015-09-01

    Full Text Available Objective This paper aims to investigate the distribution of genotypes and alleles of nicotinamide adenine dinucleotide phosphate (NADPH oxidase p22phox -930A/G, 242C/T and -675A/T, so as to evaluate the association between three single-nucleotide polymorphisms (SNPs and risk of atherosclerotic ischemic stroke in permanent resident population of Han nationality living in Shanghai area. Methods The genotypes and allele frequencies of NADPH oxidase p22phox subunit -930A/G, 242C/T and -675A/T were detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP analysis in 205 patients with ischemic stroke and 136 healthy controls. Results In patients with ischemic stroke, the results of PCR-RFLP in variant genetic loci were different. For -930A/G, one band appeared at 268 bp of genotype AA; 2 bands appeared at 197 and 71 bp of genotype GG; 3 bands appeared at 268, 197 and 71 bp of genotype AG. For 242C/T, one band appeared at 348 bp of genotype CC; 2 bands appeared at 188 and 160 bp of genotype TT; 3 bands appeared at 348, 188 and 160 bp of genotype CT. For -675A/T, 2 bands appeared at 158 and 54 bp of genotype TT; 3 bands appeared at 212, 158 and 54 bp of genotype AT. The genotypes and allele frequency of all three SNPs of NADPH oxidase p22phox gene had no significant difference between ischemic stroke patients and healthy controls (P > 0.05. Conclusions The genetic polymorphism of NADPH oxidase p22phox gene -930A/G, 242C/T and -675A/T might have no association with ischemic stroke. DOI: 10.3969/j.issn.1672-6731.2015.09.011

  1. Haplotypes of nine single nucleotide polymorphisms on chromosome 19q13.2-3 associated with susceptibility of lung cancer in a Chinese population

    DEFF Research Database (Denmark)

    Yin, Jiaoyang; Vogel, Ulla Birgitte; Ma, Yegang

    2008-01-01

    To evaluate the joint effect of nine single nucleotide polymorphisms for three DNA repair genes in the region of chromosome 19q13.2-3 on susceptibility of lung cancer in a Chinese population, we conducted a hospital-based case-control study consisting of 247 lung cancer cases and 253 cancer...

  2. Dynamic single-cell analysis of Saccharomyces cerevisiae under process perturbation: Comparison of different methods for monitoring the intensity of population heterogeneity

    DEFF Research Database (Denmark)

    Delvigne, Frank; Baert, Jonathan; Gofflot, Sébastien

    2015-01-01

    BACKGROUND: Single cell biology has attracted a lot of attention in recent years and has led to numerous fundamental results pointing out the heterogeneity of clonal cell populations. In this context, microbial phenotypic heterogeneity under bioprocessing conditions needs to be further investigat...

  3. Genetic effects and reparation of single-stranded DNA breaks in Arabidopsis thaliana populations growing in the vicinity of the Chernobyl Nuclear Power Station

    International Nuclear Information System (INIS)

    Abramov, V.I.; Sergeeva, S.A.; Ptitsyna, S.N.; Semov, A.B.; Shevchenko, V.A.

    1992-01-01

    The genetic effects and efficiency of repair of single-stranded DNA breaks in natural populations of Arabidopsis growing within a thirty-kilometer zone of the Chernobyl Nuclear Power Station were studied. A direct relationship was found between the level of radioactive contamination and the frequency of embryonal lethal mutations in the Arabidopsis populations studied. A decrease in the efficiency of reparation of single-stranded DNA breaks was found in Arabidopsis plants growing in the contaminated sites. The level of efficiency of DNA reparation was dependent on the duration for which the Arabidopsis population had been growing in the contaminated sites and on the degree of radioactive contamination of the sites. 9 refs., 4 tabs

  4. Compilation of a panel of informative single nucleotide polymorphisms for bovine identification in the Northern Irish cattle population

    Directory of Open Access Journals (Sweden)

    Hartshorne David

    2010-01-01

    Full Text Available Abstract Background Animal identification is pivotal in governmental agricultural policy, enabling the management of subsidy payments, movement of livestock, test scheduling and control of disease. Advances in bovine genomics have made it possible to utilise inherent genetic variability to uniquely identify individual animals by DNA profiling, much as has been achieved with humans over the past 20 years. A DNA profiling test based on bi-allelic single nucleotide polymorphism (SNP markers would offer considerable advantages over current short tandem repeat (STR based industry standard tests, in that it would be easier to analyse and interpret. In this study, a panel of 51 genome-wide SNPs were genotyped across panels of semen DNA from 6 common breeds for the purposes of ascertaining allelic frequency. For SNPs on the same chromosome, the extent of linkage disequilbrium was determined from genotype data by Expectation Maximization (EM algorithm. Minimum probabilities of unique identification were determined for each breed panel. The usefulness of this SNP panel was ascertained by comparison to the current bovine STR Stockmarks II assay. A statistically representative random sampling of bovine animals from across Northern Ireland was assembled for the purposes of determining the population allele frequency for these STR loci and subsequently, the minimal probability of unique identification they conferred in sampled bovine animals from Northern Ireland. Results 6 SNPs exhibiting a minor allele frequency of less than 0.2 in more than 3 of the breed panels were excluded. 2 Further SNPs were found to reside in coding areas of the cattle genome and were excluded from the final panel. The remaining 43 SNPs exhibited genotype frequencies which were in Hardy Weinberg Equilibrium. SNPs on the same chromosome were observed to have no significant linkage disequilibrium/allelic association. Minimal probabilities of uniquely identifying individual animals from

  5. Study of GABAergic extra-synaptic tonic inhibition in single neurons and neural populations by traversing neural scales: application to propofol-induced anaesthesia.

    Science.gov (United States)

    Hutt, Axel; Buhry, Laure

    2014-12-01

    Anaesthetic agents are known to affect extra-synaptic GABAergic receptors, which induce tonic inhibitory currents. Since these receptors are very sensitive to small concentrations of agents, they are supposed to play an important role in the underlying neural mechanism of general anaesthesia. Moreover anaesthetic agents modulate the encephalographic activity (EEG) of subjects and hence show an effect on neural populations. To understand better the tonic inhibition effect in single neurons on neural populations and hence how it affects the EEG, the work considers single neurons and neural populations in a steady-state and studies numerically and analytically the modulation of their firing rate and nonlinear gain with respect to different levels of tonic inhibition. We consider populations of both type-I (Leaky Integrate-and-Fire model) and type-II (Morris-Lecar model) neurons. To bridge the single neuron description to the population description analytically, a recently proposed statistical approach is employed which allows to derive new analytical expressions for the population firing rate for type-I neurons. In addition, the work shows the derivation of a novel transfer function for type-I neurons as considered in neural mass models and studies briefly the interaction of synaptic and extra-synaptic inhibition. We reveal a strong subtractive and divisive effect of tonic inhibition in type-I neurons, i.e. a shift of the firing rate to higher excitation levels accompanied by a change of the nonlinear gain. Tonic inhibition shortens the excitation window of type-II neurons and their populations while maintaining the nonlinear gain. The gained results are interpreted in the context of recent experimental findings under propofol-induced anaesthesia.

  6. [Association between single nucleotide polymorphism in Wnt3 and nonsyndromic cleft lip with or without cleft palate in Hui and Han population of Ningxia Autonomous Region].

    Science.gov (United States)

    Xin, Yanhua; Ma, Lijuan; Zhai, Kun; Zhou, Zhongwei; Yang, Xiong; Ma, Jian; Wang, Yirui; Zhu, Jinfang; Jiang, Min; Huang, Yongqing

    2013-08-01

    To investigate the association between rs142167, rs7216231 single nucleotide polymorphism (SNP) in Wnt3 and nonsyndromic cleft lip and palate (NSCL/P) in Hui and Han population of Ningxia Autonomous Region. The study consisted of 371 NSCL/P patients from Ningxia Hui and Han population (Han population 166, Hui population 205), their parents (196 fathers, 224 mothers, 150 trios) and 258 normal controls (Han population 190, Hui population 68). Polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) was used to identify rs142167, rs7216231 genotypes of the samples. The data was analyzed by case-control analysis, transmission disequilibrium test (TDT) and family based associated test (FBAT). Case-control study showed that no differences in cleft lip, cleft palate, cleft lip and palate, and the total case group compared with the control group at rs142167 and rs7216231 (P > 0.05) in Hui and Han population and in stratified comparison. TDT test showed that rs142167 and rs7216231's allele had not over-transmitted (P > 0.05) in NSCL/P. FBAT test showed that G-G specific haplotypes showed statistically significant (P Hui and Han population.

  7. A single-longitudinal-mode Brillouin fiber laser passively stabilized at the pump resonance frequency with a dynamic population inversion grating

    International Nuclear Information System (INIS)

    Spirin, V V; López-Mercado, C A; Kinet, D; Mégret, P; Fotiadi, A A; Zolotovskiy, I O

    2013-01-01

    We demonstrate a single-longitudinal-mode Brillouin ring fiber laser passively stabilized at the resonance frequency with a 1.7 m section that is an unpumped polarization-maintaining erbium-doped fiber. The two coupled all-fiber Fabry–Perot interferometers that comprise the cavity, in combination with the dynamical population inversion gratings self-induced in the active fiber, provide adaptive pump-mode selection and Stokes wave generation at the same time. The laser is shown to emit a single-frequency Stokes wave with a linewidth narrower than 100 Hz. (letter)

  8. Random population model to explain the recombination dynamics in single InAs/GaAs quantum dots under selective optical pumping

    Energy Technology Data Exchange (ETDEWEB)

    Gomis-Bresco, Jordi; Munoz-Matutano, Guillermo; Martinez-Pastor, Juan [Institut de Ciencies dels Materials de la Universitat de Valencia, Universitat de Valencia, Valencia (Spain); Alen, Benito [IMM, Instituto de Microelectronica de Madrid (CNM, CSIC), Isaac Newton 8, 28760 Tres Cantos, Madrid (Spain); Seravalli, Luca; Frigeri, Paola; Trevisi, Giovanna; Franchi, Secondo, E-mail: jrdi.gomis@icn.cat [CNR-IMEM Institute, Parco delle Scienze 37a, I-43100 Parma (Italy)

    2011-02-15

    We model the time-resolved and time-integrated photoluminescence of a single InAs/GaAs quantum dot (QD) using a random population description. We reproduce the joint power dependence of the single QD exciton complexes (neutral exciton, neutral biexciton and charged trions). We use the model to investigate the selective optical pumping phenomenon, a predominance of the negative trion observed when the optical excitation is resonant to a non-intentional impurity level. Our experiments and simulations determine that the negative charge confined in the QD after exciting resonance to the impurity level escapes in 10 ns.

  9. Extinction risk of Zamia inermis (Zamiaceae): a genetic approach for the conservation of its single natural population.

    Science.gov (United States)

    Zamia inermis, a narrowly endemic cycad has been classified under the IUCN Red List as Critically Endangered based on a 75% population decline over last 50 years. There is only one known population occupying an area of less than 10 km2 with 654 individuals with extremely low seed production and recr...

  10. Secreted protein gene derived-single nucleotide polymorphisms (SP-SNPs) reveal population diversity and differentiation of Puccinia striiformis f. sp. tritici in the United States.

    Science.gov (United States)

    Xia, Chongjing; Wan, Anmin; Wang, Meinan; Jiwan, Derick A; See, Deven R; Chen, Xianming

    2016-05-01

    Single nucleotide polymorphism (SNP) is a powerful molecular marker technique that has been widely used in population genetics and molecular mapping studies for various organisms. However, the technique has not been used for studying Puccinia striiformis f. sp. tritici (Pst), the wheat stripe rust pathogen. In this study, we developed over a hundred secreted protein gene-derived SNP (SP-SNP) markers and used 92 markers to study the population structure of Pst. From 352 isolates collected in the United States, we identified 242 multi-locus genotypes. The SP-SNP genotypes had a moderate, but significant correlation with the virulence phenotype data. Clustering of the multi-locus genotypes was consistent by various analyses, revealing distinct genetic groups. Analysis of molecular variance detected significant differences between the eastern and western US Pst populations. High heterozygosity was found in the US population with significant differences identified among epidemiological regions. Analysis of population differentiation revealed that populations between the eastern and western US were highly differentiated while moderate differentiation was found in populations within the western or eastern US. Isolates from the western US were more diverse than isolates from the eastern US. The information is useful for guiding the disease management in different epidemiological regions. Published by Elsevier Ltd.

  11. Reduction of a single granule drying model: An essential step in preparation of a population balance model with a continuous growth term

    DEFF Research Database (Denmark)

    Mortier, Séverine Thérèse F.C.; Daele, Timothy, Van; Gernaey, Krist V.

    2013-01-01

    for a single granule needs reduction in complexity. The starting point is a detailed model that describes the drying behavior of single pharmaceutical granules. A Global Sensitivity Analysis (GSA) was performed to detect the most sensitive degrees of freedom in the model as these need to be retained...... in the reduced model. Simulations of the complex drying model were, in a next phase, used to develop the reduced model, which describes the decrease of the moisture content in function of the gas temperature. The developed reduced model was then included in a Population Balance Equation (PBE) to describe......The development of a Population Balance Model (PBM) for a pharmaceutical granule drying process requires a continuous growth term; the latter actually represents the drying process as the moisture content is the internal coordinate of the PBM. To establish such a PBM, a complex drying model...

  12. Mitochondrial DNA evidences reflect an incipient population structure in Atlantic goliath grouper (Epinephelus itajara, Epinephelidae in Brazil

    Directory of Open Access Journals (Sweden)

    Júnio S. Damasceno

    2015-12-01

    Full Text Available The Atlantic goliath grouper is a critically endangered species that inhabits estuarine and reef environments and is threatened primarily by fishing activities and habitat destruction. Despite the urgent need for protection, its genetic conservation status remains unknown. The aim of the present study was to evaluate the gene flow among the populations of the species along the coast of Brazil based on the control region of the mitochondrial DNA. The results indicate low haplotype diversity (0.40-0.86 and very low nucleotide diversity (0.1-0.5%. They also show that the genetic diversity of the species varies considerably along the coast and that this finding may be especially important for the identification of priority areas for its conservation. The population analyses indicate a low but significant degree of genetic structuring (ΦST =0.111, probably due to the occurrence of rare haplotypes at some locations, although the genetic differentiation between sites was not correlated with geographic distance (r=0.0501; p=0.7719, and the shared haplotypes indicate that gene flow occurs among all locations along the Brazilian coast. The results of the pairwise FST indicate a high degree of genetic differentiation between locations. The incipient population structuring detected in the present study is not related systematically to the geological or physical features of the Brazilian coast. The complex interaction of fluctuations in sea level, marine currents, and the reproductive characteristics of the species hampers the identification of the specific role of each of these processes in the gene flow dynamics of the population units of the Atlantic goliath grouper. The low overall levels of genetic diversity, the pairwise FST values and the significant population structuring among groups (ΦCT identified in the present study all reinforce the critically endangered status of the species and are inconsistent with the presence of a single, panmictic

  13. Invasive cyprinid fish in Europe originate from the single introduction of an admixed source population followed by a complex pattern of spread.

    Directory of Open Access Journals (Sweden)

    Andrea Simon

    Full Text Available The Asian cyprinid fish, the topmouth gudgeon (Pseudorasbora parva, was introduced into Europe in the 1960s. A highly invasive freshwater fish, it is currently found in at least 32 countries outside its native range. Here we analyse a 700 base pair fragment of the mitochondrial cytochrome b gene to examine different models of colonisation and spread within the invasive range, and to investigate the factors that may have contributed to their invasion success. Haplotype and nucleotide diversity of the introduced populations from continental Europe was higher than that of the native populations, although two recently introduced populations from the British Isles showed low levels of variability. Based on coalescent theory, all introduced and some native populations showed a relative excess of nucleotide diversity compared to haplotype diversity. This suggests that these populations are not in mutation-drift equilibrium, but rather that the relative inflated level of nucleotide diversity is consistent with recent admixture. This study elucidates the colonisation patterns of P. parva in Europe and provides an evolutionary framework of their invasion. It supports the hypothesis that their European colonisation was initiated by their introduction to a single location or small geographic area with subsequent complex pattern of spread including both long distance and stepping-stone dispersal. Furthermore, it was preceded by, or associated with, the admixture of genetically diverse source populations that may have augmented its invasive-potential.

  14. Single nucleotide polymorphism rs1800872 in the promoter region of the IL10 gene is associated with predisposition to chronic hepatitis C in Russian population.

    Science.gov (United States)

    Barkhash, Andrey V; Kochneva, Galina V; Chub, Elena V; Romaschenko, Aida G

    2018-03-01

    Previously, we studied an association of two IL28B gene single nucleotide polymorphisms (SNPs) and three IL10 gene SNPs with predisposition to tick-borne encephalitis in a Russian population. In this study, a possible involvement of these SNPs in the development of predisposition to chronic hepatitis C (caused by structurally similar, related virus from the Flaviviridae family) was investigated in the same population. Only the IL10 promoter rs1800872 SNP was associated with predisposition to chronic hepatitis C. This SNP seems to be a common genetic marker of predisposition to two diseases caused by hepatitis C and tick-borne encephalitis viruses in Russian population. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  15. Single nucleotide polymorphisms of the SLC22A2 gene within the Xhosa population of South Africa.

    Science.gov (United States)

    Jacobs, Clifford; Pearce, Brendon; Du Plessis, Mornè; Hoosain, Nisreen; Benjeddou, Mongi

    2015-12-01

    Human organic cation transporter 2 (hOCT2) is thought to play a critical role in the uptake, pharmacological effects and/or adverse effects of many cationic clinical therapeutics and xenobiotics. Moreover, genetic variations in hOCT2 gene, SLC22A2, are increasingly being recognized as a possible mechanism that can explain individual variation in drug response. To screen for variations in this gene, SLC22A2 was directly sequenced in 96 healthy Xhosa individuals. A total of 27 variations, including three novel ones, were identified in SLC22A2: eight in exons, 15 in introns, and four in the 5'-untranslated region. The minor allele frequencies (MAF) of genetic variants observed in the Xhosa population were compared both to other African and other world populations. Seventeen of the variants observed in the SLC22A2 gene of the Xhosa population were specific to/or occurred at a higher frequency in African populations or populations with a recent connection to the African continent. Copyright © 2015 The Japanese Society for the Study of Xenobiotics. Published by Elsevier Ltd. All rights reserved.

  16. Population genetic structure in farm and feral American mink (Neovison vison) inferred from RAD sequencing-generated single nucleotide polymorphisms.

    Science.gov (United States)

    Thirstrup, J P; Ruiz-Gonzalez, A; Pujolar, J M; Larsen, P F; Jensen, J; Randi, E; Zalewski, A; Pertoldi, C

    2015-08-01

    Feral American mink populations (), derived from mink farms, are widespread in Europe. In this study we investigated genetic diversity and genetic differentiation between feral and farm mink using a panel of genetic markers (194 SNP) generated from RAD sequencing data. Sampling included a total of 211 individuals from 14 populations, 4 feral and 10 from farms, the latter including a total of 7 color types (Brown, Black, Mahogany, Sapphire, White, Pearl, and Silver). Our study revealed similar low levels of genetic diversity in both farm and feral mink. Results are consistent with small effective population size as a consequence of line selection in the farms and founder effects of a few escapees from the farms in feral populations. Moderately high genetic differentiation was found between farm and feral animals, suggesting a scenario in which wild populations were founded from farm escapes a few decades ago. Currently, escapes and gene flow are probably limited. Genetic differentiation was higher among farm color types than among farms, consistent with line selection using few individuals to create the lines. Finally, no indications of inbreeding were found in either farm or feral samples, with significant negative values found in most farm samples, showing farms are successful in avoiding inbreeding.

  17. The prospective association between obesity and major depression in the general population : does single or recurrent episode matter?

    NARCIS (Netherlands)

    Nigatu, Yeshambel T.; Bultmann, Ute; Reijneveld, Sijmen A.

    2015-01-01

    Background: Obesity and major depressive disorder (MDD) are important public health problems. MDD is a heterogeneous disorder and the direction of its association with obesity remains unclear. Evidence grows that recurrent MDD (MDD-R) differs in etiology and prognosis from single episode MDD

  18. Very high MHC Class IIB diversity without spatial differentiation in the mediterranean population of greater Flamingos.

    Science.gov (United States)

    Gillingham, Mark A F; Béchet, Arnaud; Courtiol, Alexandre; Rendón-Martos, Manuel; Amat, Juan A; Samraoui, Boudjéma; Onmuş, Ortaç; Sommer, Simone; Cézilly, Frank

    2017-02-20

    Selective pressure from pathogens is thought to shape the allelic diversity of major histocompatibility complex (MHC) genes in vertebrates. In particular, both local adaptation to pathogens and gene flow are thought to explain a large part of the intraspecific variation observed in MHC allelic diversity. To date, however, evidence that adaptation to locally prevalent pathogens maintains MHC variation is limited to species with limited dispersal and, hence, reduced gene flow. On the one hand high gene flow can disrupt local adaptation in species with high dispersal rates, on the other hand such species are much more likely to experience spatial variation in pathogen pressure, suggesting that there may be intense pathogen mediated selection pressure operating across breeding sites in panmictic species. Such pathogen mediated selection pressure operating across breeding sites should therefore be sufficient to maintain high MHC diversity in high dispersing species in the absence of local adaptation mechanisms. We used the Greater Flamingo, Phoenicopterus roseus, a long-lived colonial bird showing a homogeneous genetic structure of neutral markers at the scale of the Mediterranean region, to test the prediction that higher MHC allelic diversity with no population structure should occur in large panmictic populations of long-distance dispersing birds than in other resident species. We assessed the level of allelic diversity at the MHC Class IIB exon 2 from 116 individuals born in four different breeding colonies of Greater Flamingo in the Mediterranean region. We found one of the highest allelic diversity (109 alleles, 2 loci) of any non-passerine avian species investigated so far relative to the number of individuals and loci genotyped. There was no evidence of population structure between the four major Mediterranean breeding colonies. Our results suggest that local adaptation at MHC Class IIB in Greater Flamingos is constrained by high gene flow and high MHC diversity

  19. Characteristics and Outcomes of Open Globe Trauma in the Urban versus Rural Population: A Single Center Retrospective Review.

    Science.gov (United States)

    Fu, Roxana; Kancherla, Swarupa; Eller, Andrew W; Yu, Jenny Y

    2017-07-05

    To examine the characteristics and outcomes of open globe injuries sustained by the urban population compared to the rural population. This is a retrospective chart review of 429 patients presenting to University of Pittsburgh Medical Center (UPMC) Presbyterian Hospital with traumatic open globes from July 2005 to July 2013. Rural patients had a longer time which elapsed from injury to presentation (P = 0.023, average 12.04 hours vs 7.53 hours). There was a higher incidence of patient transfer prior to arrival to UPMC Presbyterian Hospital (P = 0.018), patient follow-up elsewhere (P = 0.049), and patients sustaining intraocular foreign bodies (IOFBs) (P = 0.009). Health care access is a well-known problem in rural areas and using rural-urban commuting area (RUCA) codes can help identify a population for risk factors or potential disparities in care. Rural patients sustained a higher rate of IOFBs; this should heighten the clinicians' suspicion during the evaluation of an open globe in other rural populations.

  20. Analysis of genetic diversity in Brown Swiss, Jersey and Holstein populations using genome-wide single nucleotide polymorphism markers

    Directory of Open Access Journals (Sweden)

    Melka Melkaye G

    2012-03-01

    Full Text Available Abstract Background Studies of genetic diversity are essential in understanding the extent of differentiation between breeds, and in designing successful diversity conservation strategies. The objective of this study was to evaluate the level of genetic diversity within and between North American Brown Swiss (BS, n = 900, Jersey (JE, n = 2,922 and Holstein (HO, n = 3,535 cattle, using genotyped bulls. GENEPOP and FSTAT software were used to evaluate the level of genetic diversity within each breed and between each pair of the three breeds based on genome-wide SNP markers (n = 50,972. Results Hardy-Weinberg equilibrium (HWE exact test within breeds showed a significant deviation from equilibrium within each population (P st indicated that the combination of BS and HO in an ideally amalgamated population had higher genetic diversity than the other pairs of breeds. Conclusion Results suggest that the three bull populations have substantially different gene pools. BS and HO show the largest gene differentiation and jointly the highest total expected gene diversity compared to when JE is considered. If the loss of genetic diversity within breeds worsens in the future, the use of crossbreeding might be an option to recover genetic diversity, especially for the breeds with small population size.

  1. Need for a nomogram of renal sizes in the Indian population- findings from a single centre sonographic study

    Directory of Open Access Journals (Sweden)

    Prakash Muthusami

    2014-01-01

    Full Text Available Background & objectives: Renal size is an important parameter used in the diagnosis and follow up of renal diseases. However, while making decisions, clinicians must be aware of the dependence of these dimensions on the ethnicity of the individual, independent of anthropometric indices. There is no established nomogram for renal sizes in the Indian population. The aim of this study was to assess the applicability of oft-quoted ranges of normal renal sizes in our population. Methods: Renal dimensions including length, width and parenchymal thickness were sonographically measured in 140 individuals with no renal disease. Analysis was done for differences due to age, gender and laterality. The correlation of renal dimensions with anthropometric parameters like weight, height, body mass index (BMI and body surface area (BSA was analyzed. Results: The means of length, width and parenchymal thickness of all 280 kidneys of 140 patients were 9.65 ± 0.63, 4.5 ± 0.42 and 2.04 ± 0.2 cm, respectively. There was a significant difference in parenchymal thickness between the right and left kidneys, while there was no significant right-left difference in length or width. Gender-wise analysis showed significant differences between male and female renal breadths but not length and parenchymal thickness. Age group-wise analysis showed significant decrease in renal length and parenchymal thickness beyond the seventh decade. There was a moderate positive correlation of bilateral renal length with body weight and BSA, and a weak positive correlation with body height and BMI. Interpretation & conclusions: Renal sizes in our population are in contrast to commonly quoted normal values in literature. Conclusions about renal sizes need to be made with reference to nomograms and should not be based upon data from other populations. We also present formulae whereby to derive renal sizes from anthropometric indices in our population.

  2. Population pharmacokinetics of methadone hydrochloride after a single intramuscular administration in adult Japanese sika deer (Cervus nippon nippon).

    Science.gov (United States)

    Scala, Christopher; Marsot, Amélie; Limoges, Marie-Josée; Locatelli, Yann; Simon, Nicolas; Alvarez, Jean-Claude

    2015-03-01

    To assess the population pharmacokinetics of methadone in deer. Prospective non-randomized experimental trial. Twelve healthy adult sika deer (nine males and three females). Deer received intramuscular administration of racemic methadone hydrochloride at 0.5 mg kg(-1) or 1 mg kg(-1) . Plasma methadone and its metabolite 2-Ethylidene-1,5-Dimethyl-3,3-Diphenyl-Pyrolidine (EDDP) concentrations were determined by validated liquid chromatography coupled to tandem mass spectrometry methods, at times 0, 30 minutes, 1, 2, 3, 4, 5, 6, 8, 12 and 24 hours. Population pharmacokinetics analysis was undertaken using a non-linear mixed effects modelling (NONMEM). A two-compartment linear disposition model best described observed time-concentration profiles of methadone and EDDP. Population parameter estimates of methadone were elimination clearance (17.3 L hour(-1) ), metabolic clearance (34.6 L hour(-1) ), volume of distribution of compartment 1 (216.0 L) and volume of distribution of compartment 2 (384.0 L). Population parameter estimates of EDDP were elimination clearance (121.0 L hour(-1) ), volume of distribution of compartment 3 (1.08 L) and volume of distribution of compartment 4 (499.5 L). The total clearance and total volume of distribution of methadone and EDDP were 51.9 L hour(-1) , 121.0 L hour (-1) , 600.0 L and 500.6 L, respectively. The methadone terminal elimination half-life was 8.19 hours. No adverse effects were observed after methadone administration. Following intramuscular injection, methadone was characterized by a large total volume of distribution, high systemic clearance and intermediate terminal half-life in sika deer. © 2014 Association of Veterinary Anaesthetists and the American College of Veterinary Anesthesia and Analgesia.

  3. You Can't Unscramble an Egg: Population Genetic Structure of Oncorhynchus mykiss in the California Central Valley Inferred from Combined Microsatellite and Single Nucleotide Polymorphism Data

    Directory of Open Access Journals (Sweden)

    Devon E. Pearse

    2015-12-01

    Full Text Available doi: http://dx.doi.org/10.15447/sfews.2015v13iss4art3Steelhead/rainbow trout (Oncorhynchus mykiss are found in all of the major tributaries of the Sacramento and San Joaquin rivers, which flow through California’s Central Valley and enter the ocean through San Francisco Bay and the Golden Gate. This river system is heavily affected by water development, agriculture, and invasive species, and salmon and trout hatchery propagation has been occurring for over 100 years. We collected genotype data for 18 highly variable microsatellite loci and 95 single nucleotide polymorphisms (SNPs from more than 1,900 fish from Central Valley drainages to analyze genetic diversity, population structure, differentiation between populations above and below dams, and the relationship of Central Valley O. mykiss populations to coastal California steelhead. In addition, we evaluate introgression by both hatchery rainbow trout strains, which have primarily native Central Valley ancestry, and imported coastal steelhead stocks. In contrast to patterns typical of coastal steelhead, Central Valley O. mykiss above and below dams within the same tributary were not found to be each others’ closest relatives, and we found no relationship between genetic and geographic distance among below-barrier populations. While introgression by hatchery rainbow trout strains does not appear to be widespread among above-barrier populations, steelhead in the American River and some neighboring tributaries have been introgressed by coastal steelhead. Together, these results demonstrate that the ancestral population genetic structure that existed among Central Valley tributaries has been significantly altered in contemporary populations. Future conservation, restoration, and mitigation efforts should take this into account when working to meet recovery planning goals.

  4. Genomic diversity and affinities in population groups of North West India: an analysis of Alu insertion and a single nucleotide polymorphism.

    Science.gov (United States)

    Saini, J S; Kumar, A; Matharoo, K; Sokhi, J; Badaruddoza; Bhanwer, A J S

    2012-12-15

    The North West region of India is extremely important to understand the peopling of India, as it acted as a corridor to the foreign invaders from Eurasia and Central Asia. A series of these invasions along with multiple migrations led to intermixture of variable populations, strongly contributing to genetic variations. The present investigation was designed to explore the genetic diversities and affinities among the five major ethnic groups from North West India; Brahmin, Jat Sikh, Bania, Rajput and Gujjar. A total of 327 individuals of the abovementioned ethnic groups were analyzed for 4 Alu insertion marker loci (ACE, PV92, APO and D1) and a Single Nucleotide Polymorphism (SNP) rs2234693 in the intronic region of the ESR1 gene. Statistical analysis was performed to interpret the genetic structure and diversity of the population groups. Genotypes for ACE, APO, ESR1 and PV92 loci were found to be in Hardy-Weinberg equilibrium in all the ethnic groups, while significant departures were observed at the D1 locus in every investigated population after Bonferroni's correction. The average heterozygosity for all the loci in these ethnic groups was fairly substantial ranging from 0.3927 ± 0.1877 to 0.4333 ± 0.1416. Inbreeding coefficient indicated an overall 10% decrease in heterozygosity in these North West Indian populations. The gene differentiation among the populations was observed to be of the order of 0.013. Genetic distance estimates revealed that Gujjars were close to Banias and Jat Sikhs were close to Rajputs. Overall the study favored the recent division of the populations of North West India into largely endogamous groups. It was observed that the populations of North West India represent a more or less homogenous genetic entity, owing to their common ancestral history as well as geographical proximity. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Positive Association of Metabolic Syndrome with a Single Nucleotide Polymorphism of Syndecan-3 (rs2282440 in the Taiwanese Population

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    Betty Chia-Chen Chang

    2018-01-01

    Full Text Available Background/Purpose. Metabolic syndrome (MetS poses a major public health burden on the general population worldwide. Syndecan-3 (SDC3, a heparin sulfate proteoglycan, had been found by previous studies to be linked with energy balance and obesity, but its association with MetS is not known. The objective of this study is to investigate whether SDC3 polymorphism (rs2282440 is associated with MetS in the Taiwanese population. Methods. Genotypes of SDC3 polymorphism (rs2282440 were analyzed in 545 Taiwanese adult subjects, of which 154 subjects had MetS. Results. Subjects with SDC3 rs2282440 TT homozygote had higher frequency of MetS than those with CC or CT genotype (p=0.0217. SDC3 rs2282440 TT homozygote had a 1.96-fold risk of being obese and 1.8-fold risk of having MetS (with CC genotype as reference. As for the individual components of MetS, subjects with SDC3 rs2282440 TT homozygote were more likely to have large waist circumference and low high-density lipoprotein cholesterol (OR = 1.75 and OR = 1.84, resp.. Conclusion. SDC3 rs2282440 polymorphism is positively associated with MetS in the Taiwanese population. Further investigation is needed to see if this association is mediated by mere adiposity or SDC3 polymorphism is also linked with other components of MetS such as lipid metabolism.

  6. Quantifying kinematic differences between land and water during squats, split squats, and single-leg squats in a healthy population.

    Directory of Open Access Journals (Sweden)

    Anna C Severin

    Full Text Available Aquatic exercises can be used in clinical and sporting disciplines for both rehabilitation and sports training. However, there is limited knowledge on the influence of water immersion on the kinematics of exercises commonly used in rehabilitation and fitness programs. The aim of this study was to use inertial sensors to quantify differences in kinematics and movement variability of bodyweight squats, split squats, and single-leg squats performed on dry land and whilst immersed to the level of the greater trochanter. During two separate testing sessions, 25 active healthy university students (22.3±2.9 yr. performed ten repetitions of each exercise, whilst tri-axial inertial sensors (100 Hz recorded their trunk and lower body kinematics. Repeated-measures statistics tested for differences in segment orientation and speed, movement variability, and waveform patterns between environments, while coefficient of variance was used to assess differences in movement variability. Between-environment differences in segment orientation and speed were portrayed by plotting the mean difference ±95% confidence intervals (CI throughout the tasks. The results showed that the depth of the squat and split squat were unaffected by the changed environment while water immersion allowed for a deeper single leg squat. The different environments had significant effects on the sagittal plane orientations and speeds for all segments. Water immersion increased the degree of movement variability of the segments in all exercises, except for the shank in the frontal plane, which showed more variability on land. Without compromising movement depth, the aquatic environment induces more upright trunk and shank postures during squats and split squats. The aquatic environment allows for increased squat depth during the single-leg squat, and increased shank motions in the frontal plane. Our observations therefore support the use of water-based squat tasks for rehabilitation as

  7. Quantifying kinematic differences between land and water during squats, split squats, and single-leg squats in a healthy population.

    Science.gov (United States)

    Severin, Anna C; Burkett, Brendan J; McKean, Mark R; Wiegand, Aaron N; Sayers, Mark G L

    2017-01-01

    Aquatic exercises can be used in clinical and sporting disciplines for both rehabilitation and sports training. However, there is limited knowledge on the influence of water immersion on the kinematics of exercises commonly used in rehabilitation and fitness programs. The aim of this study was to use inertial sensors to quantify differences in kinematics and movement variability of bodyweight squats, split squats, and single-leg squats performed on dry land and whilst immersed to the level of the greater trochanter. During two separate testing sessions, 25 active healthy university students (22.3±2.9 yr.) performed ten repetitions of each exercise, whilst tri-axial inertial sensors (100 Hz) recorded their trunk and lower body kinematics. Repeated-measures statistics tested for differences in segment orientation and speed, movement variability, and waveform patterns between environments, while coefficient of variance was used to assess differences in movement variability. Between-environment differences in segment orientation and speed were portrayed by plotting the mean difference ±95% confidence intervals (CI) throughout the tasks. The results showed that the depth of the squat and split squat were unaffected by the changed environment while water immersion allowed for a deeper single leg squat. The different environments had significant effects on the sagittal plane orientations and speeds for all segments. Water immersion increased the degree of movement variability of the segments in all exercises, except for the shank in the frontal plane, which showed more variability on land. Without compromising movement depth, the aquatic environment induces more upright trunk and shank postures during squats and split squats. The aquatic environment allows for increased squat depth during the single-leg squat, and increased shank motions in the frontal plane. Our observations therefore support the use of water-based squat tasks for rehabilitation as they appear to

  8. Temporal Variation in Single-Cell Power-Law Rheology Spans the Ensemble Variation of Cell Population.

    Science.gov (United States)

    Cai, PingGen; Takahashi, Ryosuke; Kuribayashi-Shigetomi, Kaori; Subagyo, Agus; Sueoka, Kazuhisa; Maloney, John M; Van Vliet, Krystyn J; Okajima, Takaharu

    2017-08-08

    Changes in the cytoskeletal organization within cells can be characterized by large spatial and temporal variations in rheological properties of the cell (e.g., the complex shear modulus G ∗ ). Although the ensemble variation in G ∗ of single cells has been elucidated, the detailed temporal variation of G ∗ remains unknown. In this study, we investigated how the rheological properties of individual fibroblast cells change under a spatially confined environment in which the cell translational motion is highly restricted and the whole cell shape remains unchanged. The temporal evolution of single-cell rheology was probed at the same measurement location within the cell, using atomic force microscopy-based oscillatory deformation. The measurements reveal that the temporal variation in the power-law rheology of cells is quantitatively consistent with the ensemble variation, indicating that the cell system satisfies an ergodic hypothesis in which the temporal statistics are identical to the ensemble statistics. The autocorrelation of G ∗ implies that the cell mechanical state evolves in the ensemble of possible states with a characteristic timescale. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  9. Intracellular Drug Uptake-A Comparison of Single Cell Measurements Using ToF-SIMS Imaging and Quantification from Cell Populations with LC/MS/MS.

    Science.gov (United States)

    Newman, Carla F; Havelund, Rasmus; Passarelli, Melissa K; Marshall, Peter S; Francis, Ian; West, Andy; Alexander, Morgan R; Gilmore, Ian S; Dollery, Colin T

    2017-11-21

    ToF-SIMS is a label-free imaging method that has been shown to enable imaging of amiodarone in single rat macrophage (NR8383) cells. In this study, we show that the method extends to three other cell lines relevant to drug discovery: human embryonic kidney (HEK293), cervical cancer (HeLa), and liver cancer (HepG2). There is significant interest in the variation of drug uptake at the single cell level, and we use ToF-SIMS to show that there is great diversity between individual cells and when comparing each of the cell types. These single cell measurements are compared to quantitative measurements of cell-associated amiodarone for the population using LC/MS/MS and cell counting with flow cytometry. NR8383 and HepG2 cells uptake the greatest amount of amiodarone with an average of 2.38 and 2.60 pg per cell, respectively, and HeLa and Hek 293 have a significantly lower amount of amiodarone at 0.43 and 0.36 pg per cell, respectively. The amount of cell-associated drug for the ensemble population measurement (LC/MS/MS) is compared with the ToF-SIMS single cell data: a similar amount of drug was detected per cell for the NR8383, and HepG2 cells at a greater level than that for the HEK293 cells. However, the two techniques did not agree for the HeLa cells, and we postulate potential reasons for this.

  10. The European and Japanese outbreaks of H5N8 derive from a single source population providing evidence for the dispersal along the long distance bird migratory flyways

    OpenAIRE

    Andrew R. Dalby; Munir Iqbal

    2015-01-01

    The origin of recent parallel outbreaks of the high pathogenicity H5N8 avian flu virus in Europe and in Japan can be traced to a single source population, which has most likely been spread by migratory birds. By using Bayesian coalescent methods to analyze the DNA sequences of the virus to find the times for divergence and combining this sequence data with bird migration data we can show the most likely locations and migratory pathways involved in the origin of the current outbreak. This popu...

  11. Population structure of Lactobacillus helveticus isolates from naturally fermented dairy products based on multilocus sequence typing.

    Science.gov (United States)

    Sun, Zhihong; Liu, Wenjun; Song, Yuqin; Xu, Haiyan; Yu, Jie; Bilige, Menghe; Zhang, Heping; Chen, Yongfu

    2015-05-01

    Lactobacillus helveticus is an economically important lactic acid bacterium used in industrial dairy fermentation. In the present study, the population structure of 245 isolates of L. helveticus from different naturally fermented dairy products in China and Mongolia were investigated using an multilocus sequence typing scheme with 11 housekeeping genes. A total of 108 sequence types were detected, which formed 8 clonal complexes and 27 singletons. Results from Structure, SplitsTree, and ClonalFrame software analyses demonstrated the presence of 3 subpopulations in the L. helveticus isolates used in our study, namely koumiss, kurut-tarag, and panmictic lineages. Most L. helveticus isolates from particular ecological origins had specific population structures. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  12. The European and Japanese outbreaks of H5N8 derive from a single source population providing evidence for the dispersal along the long distance bird migratory flyways.

    Science.gov (United States)

    Dalby, Andrew R; Iqbal, Munir

    2015-01-01

    The origin of recent parallel outbreaks of the high pathogenicity H5N8 avian flu virus in Europe and in Japan can be traced to a single source population, which has most likely been spread by migratory birds. By using Bayesian coalescent methods to analyze the DNA sequences of the virus to find the times for divergence and combining this sequence data with bird migration data we can show the most likely locations and migratory pathways involved in the origin of the current outbreak. This population was most likely located in the Siberian summer breeding grounds of long-range migratory birds. These breeding grounds provide a connection between different migratory flyways and explain the current outbreaks in remote locations. By combining genetic methods and epidemiological data we can rapidly identify the sources and the dispersion pathways for novel avian influenza outbreaks.

  13. The European and Japanese outbreaks of H5N8 derive from a single source population providing evidence for the dispersal along the long distance bird migratory flyways

    Directory of Open Access Journals (Sweden)

    Andrew R. Dalby

    2015-04-01

    Full Text Available The origin of recent parallel outbreaks of the high pathogenicity H5N8 avian flu virus in Europe and in Japan can be traced to a single source population, which has most likely been spread by migratory birds. By using Bayesian coalescent methods to analyze the DNA sequences of the virus to find the times for divergence and combining this sequence data with bird migration data we can show the most likely locations and migratory pathways involved in the origin of the current outbreak. This population was most likely located in the Siberian summer breeding grounds of long-range migratory birds. These breeding grounds provide a connection between different migratory flyways and explain the current outbreaks in remote locations. By combining genetic methods and epidemiological data we can rapidly identify the sources and the dispersion pathways for novel avian influenza outbreaks.

  14. Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale

    DEFF Research Database (Denmark)

    Liu, Siyang; Huang, Shujia; Rao, Junhua

    2015-01-01

    present a novel approach implemented in a single software package, AsmVar, to discover, genotype and characterize different forms of structural variation and novel sequence from population-scale de novo genome assemblies up to nucleotide resolution. Application of AsmVar to several human de novo genome......) as well as large deletions. However, these approaches consistently display a substantial bias against the recovery of complex structural variants and novel sequence in individual genomes and do not provide interpretation information such as the annotation of ancestral state and formation mechanism. We...... assemblies captures a wide spectrum of structural variants and novel sequences present in the human population in high sensitivity and specificity. Our method provides a direct solution for investigating structural variants and novel sequences from de novo genome assemblies, facilitating the construction...

  15. A replication study for association of 53 single nucleotide polymorphisms in ScoliScore test with adolescent idiopathic scoliosis in French-Canadian population.

    Science.gov (United States)

    Tang, Qi Lin; Julien, Cedric; Eveleigh, Robert; Bourque, Guillaume; Franco, Anita; Labelle, Hubert; Grimard, Guy; Parent, Stefan; Ouellet, Jean; Mac-Thiong, Jean-Marc; Gorman, Kristen F; Moreau, Alain

    2015-04-15

    A replication association study that used genomic data generated from French-Canadian case and control cohorts. To determine whether the 53 single nucleotide polymorphisms (SNPs) that were previously associated with spinal deformity progression in an American Caucasian cohort are similarly associated in French-Canadian population. It is widely accepted that genetic factors contribute to adolescent idiopathic scoliosis. The identification of genetic variants associated with the predisposition or progression of curvature could facilitate diagnostic/prognostic tool development. Although 53 SNPs have been associated with spinal curve progression in Caucasian cohorts in the United States, these associations were not replicated in a large Japanese population study, arguing that such a discrepancy could be explained by ethnicity, thus raising the importance of a replication study in an independent Caucasian population of European descent. Genomic data were collected from the French-Canadian population, using the Illumina HumanOmni 2.5M BeadChip. Fifty-two SNPs, tested in ScoliScore or in high linkage disequilibrium with SNPs in the test, were selected to assess their association with scoliosis generally, and with spinal curve progression. One SNP in ScoliScore, rs16909285, could not be evaluated in our Genome-Wide association study. None of the SNPs used in ScoliScore were associated with adolescent idiopathic scoliosis curve progression or curve occurrence in French-Canadian population. We evaluated 52 SNPs in severe patients by comparing risk allele frequencies with those in nonsevere patients and with those in control individuals. There was no significant difference between the severe group and the nonsevere group or between the severe group and the control group. Although the 52 SNPs studied here were previously associated with curve progression in an American population of European descent, we found no association in French-Canadian patients with adolescent

  16. Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

    Directory of Open Access Journals (Sweden)

    Meghann K. Devlin-Durante

    2017-11-01

    Full Text Available The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

  17. Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata.

    Science.gov (United States)

    Devlin-Durante, Meghann K; Baums, Iliana B

    2017-01-01

    The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata , to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

  18. Longitudinal transport coefficients of a magnetized plasma consisting of hydrogen and a single impurity element in arbitrarily populated charge states

    International Nuclear Information System (INIS)

    Claassen, H.A.; Gerhauser, H.; El-Sharif, R.N.

    1991-01-01

    The coefficients determining the transport processes along the magnetic field in a magnetized plasma consisting of electrons, protons/deuterons and impurity ions in various charge states have been calculated on the basis of Grad's 21 moment approximation. Assuming a single impurity element, the determinants appearing in the transport coefficients are evaluated analytically for arbitrary ratios m z /m + between the impurity and hydrogen masses. The general formulae are then simplified for the important case m z /m + ≥ 1 and compared with existing data given by V.M. Zhdanov et al. and Yu.L. Igitkhanov et al. Whereas with minor modifications the proton/deuteron and electron coefficients agree well, there are remarkable differences in the impurity ion transport coefficients, which are discussed. (orig.)

  19. Single and combined effects of microplastics and copper on the population growth of the marine microalgae Tetraselmis chuii

    Science.gov (United States)

    Davarpanah, Elham; Guilhermino, Lúcia

    2015-12-01

    As the accumulation of microplastics continues to rise in the marine environment, more knowledge on their potential toxic effects on marine organisms is needed to assess their risks to environmental and human health. Thus, the goal of the present study was to investigate the effects of fluorescent red polyethylene plastic micro-spheres 1-5 μm diameter (used as microplastic model and hereafter indicated as MP), alone and in mixture with copper, on the population growth of the marine microalgae Tetraselmis chuii. Two null hypotheses were tested: (H01) Exposure to MP concentrations in ppb range does not affect the average specific growth rate of T. chuii; (H02) MP do not interact with the toxicity of copper to T. chuii. In laboratory bioassays, T. chuii cultures were exposed for 96 h to MP concentrations ranging from 0.046 to 1.472 mg/l), concentrations of copper alone ranging from 0.02 to 0.64 mg/l, and the same concentrations of copper in the presence of 0.184 mg/l of MP in test media. No significant effects of MP on T. chuii population growth were found (p > 0.05), leading to the acceptance of H01. Copper alone significantly decreased the population growth of T. chuii with EC10, EC20 and EC50 of 0.009, 0.023 and 0.139 mg/l, respectively. The corresponding values in the presence of MP were 0.012, 0.029 and 0.145 mg/l, respectively. Moreover, the study found no significant differences between the toxicity curves of copper in the presence and absence of MP (p > 0.05), leading to the acceptance of H02. Despite these findings, because microplastics are known to adsorb and accumulate copper, aged pellets more than virgin ones, and the toxicity of smaller particles may be higher, further studies on the combined effects of copper and microplastics on microalgae should be performed, especially under long-term exposures to nano-sized aged microplastics.

  20. Safety and efficacy assessment of carotid artery stenting in a high-risk population in a single-centre registry.

    Science.gov (United States)

    Kosowski, Michał; Zimoch, Wojciech; Gwizdek, Tomasz; Konieczny, Radosław; Kübler, Piotr; Telichowski, Artur; Jankowska, Ewa A; Reczuch, Krzysztof

    2014-01-01

    Ischaemic stroke is the primary cause of long-term disability and the third most common cause of death. Internal carotid artery stenosis is an important risk factor for stroke and transient ischaemic attack (TIA). European Society of Cardiology (ESC) and American Heart Association (AHA) guidelines allow carotid artery stenting (CAS) as an alternative to endarterectomy in centres with low rates of death or stroke. To assess the safety and efficacy of CAS in a single-centre observation. We performed a retrospective analysis of all patients treated with CAS between March 2008 and July 2012. Clinical data and outcomes in both asymptomatic and symptomatic patients were analysed. A total of 214 consecutive patients were included in the registry. Symptomatic patients accounted for 57% of the study group and were more likely to have a history of stroke and/or TIA that occurred more than 6 months before the procedure (50% vs. 8%, p likely to have a history of coronary artery disease (88% vs. 61%, p < 0.001), and the rates of previous acute coronary syndrome and revascularisation were also higher in this group (58% vs. 41% and 71% vs. 52%, respectively, both p < 0.05). The symptomatic group had higher incidence of stroke in periprocedural and 30-day observation (4% vs. 0%, p < 0.05). There was no difference in incidence of adverse events in long-term observation. Carotid artery stenting is a safe and efficacious procedure. Every centre performing CAS should monitor the rate of periprocedural complications.

  1. The Association between Single-Nucleotide Polymorphisms of ORAI1 Gene and Breast Cancer in a Taiwanese Population

    Directory of Open Access Journals (Sweden)

    Wei-Chiao Chang

    2012-01-01

    Full Text Available Background. Breast cancer is the most common malignancy in women. There is increasing evidence suggesting that ORAI1, components of store-operated calcium channel, play a pivotal role in breast cancer progression and metastasis. Methods. A total of 384 female patients with breast cancer were included in this study. We selected five representative tagging ORAI1 SNPs from HapMap database with minimum allele frequency (MAF >10%. Genotyping was performed using TaqMan allelic discrimination assay. Chi-square (χ2 test was used to analyze statistical differences among control and patient groups in genotype and allelic frequencies. Results. Two of the ORAI1 SNPs (rs12320939 and rs12313273 were associated with estrogen receptors positive in breast cancer patients under the recessive model. When the Bonferroni correction was performed, the significance still existed. In addition, rs12320939 also associated with the lymph nodal involvement. Conclusion. We showed that genetic polymorphisms of ORAI1 associated strongly with lymph nodal involvement and estrogen receptors (ERs positive breast cancer patients in a Taiwanese population.

  2. Association between single-nucleotide polymorphism in CISH gene and susceptibility to tuberculosis in Chinese Han population.

    Science.gov (United States)

    Zhao, Lan; Chu, Haiqing; Xu, Xiaogang; Yue, Jun; Li, Huiping; Wang, Minggui

    2014-04-01

    The cytokine-inducible SRC homology 2 domain (CISH) gene is up-regulated by IL-2 in response to infection, and inhibits microbial infection. The objective of the present study was to examine whether genetic variants of CISH (SNPs) are associated with increased susceptibility to tuberculosis (TB) in individuals of Chinese Han ethnicity. We sequenced five previously identified SNPs of CISH in patients with TB or healthy controls. Three of the SNPs, rs148685070 [position -639; C/C], rs414171 [position -292; A/T], and rs6768300 [position -163; C/G]) are located in the promoter region, while the fourth (rs2239751 [position +1320; A/C]) near the translation start site, and the fifth (rs622502 [position +3415; C/G]) in the third intron. The AA genotypes of the SNPs rs2239751 and rs414171 were significantly associated with TB. Multivariate logistic regression analysis demonstrated that subjects with the rs414171 AA genotype were more likely to have TB than those with the AT genotype. By contrast, we did not observe genetic variants of the rs148685070 SNP. In conclusion, two genetic variants in CISH gene appear to increase susceptibility to TB in Chinese Han population.

  3. Etiology of Hypopituitarism in Adult Patients: The Experience of a Single Center Database in the Serbian Population

    Directory of Open Access Journals (Sweden)

    M. Doknić

    2017-01-01

    Full Text Available There are only a few published studies related to the population-based etiology of hypopituitarism. New risks for developing hypopituitarism have been recognized in the last 10 years. Aim. To present data regarding the etiology of hypopituitarism collected in a tertiary center over the last decade. This is a cross-sectional database study. Patients and Methods. We included 512 patients (pts with hypopituitarism, with a mean age of 45.9 ± 1.7 yrs (range: 18–82; male: 57.9%. Results. Nonfunctional pituitary adenomas were presented in 205 pts (40.5%, congenital causes in 74 pts (14.6%, while acromegaly and prolactinomas were presented in 37 (7.2% and 36 (7.0% patients, respectively. Craniopharyngiomas were detected in 30 pts (5.9%, and head trauma due to trauma brain injury-TBI and subarachnoid hemorrhage-SAH in 27 pts (5.4%. Survivors of hemorrhagic fever with renal syndrome (HFRS and those with previous cranial irradiation were presented in the same frequency (18 pts, 3.5% each. Conclusion. The most common causes of hypopituitarism in our database are pituitary adenomas. Increased awareness of the other causes of pituitary dysfunction, such as congenital, head trauma, extrapituitary cranial irradiation, and infections, is the reason for a higher frequency of these etiologies of hypopituitarism in the presented database.

  4. Single nucleotide polymorphisms of NR3C1 gene and recurrent depressive disorder in population of Poland.

    Science.gov (United States)

    Gałecka, Elżbieta; Szemraj, Janusz; Bieńkiewicz, Małgorzata; Majsterek, Ireneusz; Przybyłowska-Sygut, Karolina; Gałecki, Piotr; Lewiński, Andrzej

    2013-02-01

    Depressive disorder is a disease characterized by disturbances in the hypothalamo-pituitary-adrenal axis. Abnormalities include the increased level of glucocorticoids (GC) and changes in sensitivity to these hormones. The changes are related to glucocorticoid receptors gene (NR3C1) variants. The NR3C1 gene is suggested to be a candidate gene affecting depressive disorder risk and management. The aim of this study was to investigate polymorphisms within the NR3C1 gene and their role in the susceptibility to recurrent depressive disorder (rDD). 181 depressive patients and 149 healthy ethnically matched controls were included in the study. Single nucleotide polymorphisms were assessed using polymerase chain reaction/restriction fragment length polymorphism method. Statistical significance between rDD patients and controls was observed for the allele and genotype frequencies at three loci: BclI, N363S, and ER22/23EK. The presence of C allele, CC, and GC genotype of BclI polymorphism, G allele and GA genotype for N363S and ER22/23EK variants respectively were associated with increased rDD risk. Two haplotypes indicated higher susceptibility for rDD, while haplotype GAG played a protective role with OR(dis) 0.29 [95 % confidence interval (CI) = 0.13-0.64]. Data generated from this study support the earlier results that genetic variants of the NR3C1 gene are associated with rDD and suggest further consideration on the possible involvement of these variants in etiology of the disease.

  5. Pattern of glomerular disease in the Saudi population: A single-center, five-year retrospective study

    Directory of Open Access Journals (Sweden)

    Z Nawaz

    2013-01-01

    Full Text Available Glomerular diseases continue to be the leading cause of end-stage renal disease (ESRD globally. Hence, it is important to recognize the pattern of glomerular diseases in different geographical areas in order to understand the patho-biology, incidence and progression of the disorder. Published studies from different centers in Saudi Arabia have reported contradicting results. In this retrospective study, we report our experience at the Armed Forces Hospital, Riyadh, Saudi Arabia. A total of 348 native renal biopsies performed at our center on patients with proteinuria >1 g, hematuria and/or renal impairment during a period of 5 years (between January 2005 and December 2009 were studied by a histopathologist using light microscopy, immunofluorescence and electron microscopy, and were categorized. Results showed that primary glomerular disease accounted for 55.1% of all renal biopsies. The most common histological lesion was focal and segmental glomerulosclerosis (FSGS (27.6%, followed by minimal change disease (MCD (17.7% and membrano-proliferative glomerulonephritis (MPGN (13.0%. Secondary glomerular disease accounted for 37.9% of the glomerular diseases, with lupus nephritis (LN being the most common lesion (54.5%, followed by hypertensive nephrosclerosis (22%, post-infectious glomerulonephritis (7.5%, diabetic nephropathy (DN (6.8% and vasculitides (4.5%. Four percent of all biopsies turned out to be ESRD while biopsy was inadequate in 2.8% of the cases. In conclusion, our study showed that FSGS was the most common primary GN encountered, while LN was the most common secondary GN. We encountered 14 cases of crescentic glomerulonephritis. Also, the prevalence of MPGN, MCD, IgA nephropathy and membranous GN was many folds higher in males when compared with the Western data. We believe that it is mandatory to maintain a Saudi Arabian Renal Biopsy Registry to understand better the pattern of glomerular disease in the Saudi population and to follow

  6. Association between single nucleotide polymorphisms of sterol regulatory element binding protein-2 gene and risk of knee osteoarthritis in a Chinese Han population.

    Science.gov (United States)

    Qiu, Xiao-Ming; Jin, Cheng-Tao; Wang, Wei

    2014-04-01

    To investigate associations between single nucleotide polymorphisms (SNPs) rs2228314 and rs2267443 in the sterol regulatory element binding protein-2 gene (SREBP-2) and knee osteoarthritis (OA) susceptibility in a Chinese Han population. SREBP-2 rs2228314 and rs2267443 polymorphisms were genotyped in patients with knee OA and age- and sex-matched OA-free controls from a Chinese Han population. A total of 402 patients with knee OA and 410 controls were enrolled in the study. GC and CC genotypes of rs2228314, and variant C, were associated with a significantly increased risk of knee OA. On stratification analysis, the association between the risk of OA and rs2228314 GC heterozygotes compared with GG homozygotes was stronger in females and those aged >65 years. In contrast, the GA and AA genotypes of rs2267443 were not significantly associated with the risk of knee OA, even after further stratification analysis according to age or sex. SREBP-2 rs2228314 G to C change and variant C genotype may contribute to knee OA risk in a Chinese Han population.

  7. The optimal anatomic site for a single slice to estimate the total volume of visceral adipose tissue by using the quantitative computed tomography (QCT) in Chinese population.

    Science.gov (United States)

    Cheng, X; Zhang, Y; Wang, C; Deng, W; Wang, L; Duanmu, Y; Li, K; Yan, D; Xu, L; Wu, C; Shen, W; Tian, W

    2018-03-20

    To investigate the relationship between the cross-sectional visceral adipose tissue (VAT) areas at different anatomic sites and the total VAT volume in a healthy Chinese population using quantitative computed tomography (QCT), and to identify the optimal anatomic site for a single slice to estimate the total VAT volume. A total of 389 healthy Chinese subjects aged 19-63 years underwent lumbar spine QCT scans. The cross-sectional area of total adipose tissue and VAT were measured using the tissue composition module of the software (QCT Pro, Mindways) at each intervertebral disc level from T 12 /L 1 to L 5 /S 1 , as well as at the umbilical level. The total VAT volume was defined as the fat areas multiplied by the height of vertebral body for all six slices. Statistical analysis was performed to determine the correlation between single-slice VAT areas and the total VAT volume. Moreover, the optimal anatomic site for a single slice to estimate the total VAT volume was identified by multiple regression analysis. The cross-sectional area of VAT and subcutaneous adipose tissue (SAT) measured at each anatomic site was all highly correlated with the total VAT volume and the total SAT volume (r = 0.89-0.98). Additionally, the VAT area measured at the L 2 /L 3 level showed the strongest correlation with the total VAT volume (r = 0.98, P VAT volume. It is feasible to perform measurements of VAT area on a single slice at L 2 /L 3 level for estimating the total VAT volume.

  8. Understanding the formation and evolution of early-type galaxies based on newly developed single-burst stellar population synthesis models in the infrared

    Science.gov (United States)

    Roeck, Benjamin

    2015-12-01

    The detailed study of the different stellar populations which can be observed in galaxies is one of the most promising methods to shed light on the evolutionary histories of galaxies. So far, stellar population analysis has been carried out mainly in the optical wavelength range. The infrared spectral range, on the other hand, has been poorly studied so far, although it provides very important insights, particularly into the cooler stellar populations which are present in galaxies. However, in the last years, space telescopes like the Spitzer Space Telescope or the Wide-field Infrared Survey Explorer and instruments like the spectrograph X-Shooter on the Very Large Telescope have collected more and more photometric and spectroscopic data in this wavelength range. In order to analyze these observations, it is necessary to dispose of reliable and accurate stellar population models in the infrared. Only a small number of stellar population models in the infrared exist in the literature. They are mostly based on theoretical stellar libraries and very often cover only the near-infrared wavelength range at a rather low resolution. Hence, we developed new single-burst stellar population models between 8150 and 50000Å which are exclusively based on 180 spectra from the empirical Infrared Telescope Facility stellar library. We computed our single stellar population models for two different sets of isochrones and various types of initial mass functions of different slopes. Since the stars of the Infrared Telescope Facility library present only a limited coverage of the stellar atmospheric parameter space, our models are of sufficient quality only for ages larger than 1 Gyr and metallicities between [Fe/H] = 0.40 and 0.26. By combining our single stellar population models in the infrared with the extended medium-resolution Isaac Newton Telescope library of empirical spectra in the optical spectral range, we created the first single stellar population models covering the

  9. Estimating the effective number of breeders from single parr samples for conservation monitoring of wild populations of Atlantic salmon Salmo salar.

    Science.gov (United States)

    Bacles, C F E; Bouchard, C; Lange, F; Manicki, A; Tentelier, C; Lepais, O

    2018-03-01

    This study assesses whether the effective number of breeders (N b ) can be estimated using a time and cost-effective protocol using genetic sibship reconstruction from a single sample of young-of-the-year (YOY) for the purposes of Atlantic salmon Salmo salar population monitoring. N b was estimated for 10 consecutive reproductive seasons for S. salar in the River Nivelle, a small population located at the rear-edge of the species distribution area in France, chronically under its conservation limit and subjected to anthropogenic and environmental changes. Subsampling of real and simulated data showed that accurate estimates of N b can be obtained from YOY genotypes, collected at moderate random sampling intensity, achievable using routine juvenile electrofishing protocols. Spatial bias and time elapsed since spawning were found to affect estimates, which must be accounted for in sampling designs. N b estimated in autumn for S. salar in the River Nivelle was low and variable across years from 23 (95% C.I. 14-41) to 75 (53-101) and was not statistically correlated with the estimated number of returning adults, but it was positively correlated with the estimated number of YOY at age 9 months. N b was found to be lower for intermediate levels of redd aggregation, suggesting that the strength of the competition between males to access females affects reproductive success variance depending on redd spatial configuration. Thus, environmental factors such as habitat availability and quality for spawning and YOY development predominate over demographic ones (number of returning adults) in driving long-term population viability for S. salar in the River Nivelle. This study showcases N b as an integrated parameter, encompassing demographic and ecological information about a reproductive event, relevant to the assessment of both short-term effects of management practices and long-term population conservation status. © 2018 The Fisheries Society of the British Isles.

  10. Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations.

    Directory of Open Access Journals (Sweden)

    Jingjing Liang

    2017-05-01

    Full Text Available Hypertension is a leading cause of global disease, mortality, and disability. While individuals of African descent suffer a disproportionate burden of hypertension and its complications, they have been underrepresented in genetic studies. To identify novel susceptibility loci for blood pressure and hypertension in people of African ancestry, we performed both single and multiple-trait genome-wide association analyses. We analyzed 21 genome-wide association studies comprised of 31,968 individuals of African ancestry, and validated our results with additional 54,395 individuals from multi-ethnic studies. These analyses identified nine loci with eleven independent variants which reached genome-wide significance (P < 1.25×10-8 for either systolic and diastolic blood pressure, hypertension, or for combined traits. Single-trait analyses identified two loci (TARID/TCF21 and LLPH/TMBIM4 and multiple-trait analyses identified one novel locus (FRMD3 for blood pressure. At these three loci, as well as at GRP20/CDH17, associated variants had alleles common only in African-ancestry populations. Functional annotation showed enrichment for genes expressed in immune and kidney cells, as well as in heart and vascular cells/tissues. Experiments driven by these findings and using angiotensin-II induced hypertension in mice showed altered kidney mRNA expression of six genes, suggesting their potential role in hypertension. Our study provides new evidence for genes related to hypertension susceptibility, and the need to study African-ancestry populations in order to identify biologic factors contributing to hypertension.

  11. Vicariance and dispersal across Baja California in disjunct marine fish populations.

    Science.gov (United States)

    Bernardi, Giacomo; Findley, Lloyd; Rocha-Olivares, Axayacatl

    2003-07-01

    Population disjunctions, as a first step toward complete allopatry, present an interesting situation to study incipient speciation. The geological formation of the Baja California Peninsula currently divides 19 species of fish into disjunct populations that are found on its Pacific Coast and in the northern part of the Gulf of California (also called the Sea of Cortez), but are absent from the Cape (Cabo San Lucas) region. We studied the genetic makeup of disjunct populations for 12 of these 19 fish species. Phylogeographic patterns for the 12 species can be separated into two major classes: a first group (eight species) showed reciprocal monophyly and high genetic divergence between disjunct populations. A second group (four species) displayed what appeared to be panmictic populations. Population structure between Pacific Coast populations, across the Punta Eugenia biogeographic boundary, was also evaluated. While dispersal potential (inferred by pelagic larval duration) was a poor predictor of population structure between Gulf of California and Pacific populations, we found that population genetic subdivision along the Pacific Coast at Punta Eugenia was always positively correlated with differentiation between Pacific and Gulf of California populations. Vicariant events, ongoing gene flow, and ecological characteristics played essential roles in shaping the population structures observed in this study.

  12. A Single Transcriptome of a Green Toad (Bufo viridis Yields Candidate Genes for Sex Determination and -Differentiation and Non-Anonymous Population Genetic Markers.

    Directory of Open Access Journals (Sweden)

    Jörn F Gerchen

    Full Text Available Large genome size, including immense repetitive and non-coding fractions, still present challenges for capacity, bioinformatics and thus affordability of whole genome sequencing in most amphibians. Here, we test the performance of a single transcriptome to understand whether it can provide a cost-efficient resource for species with large unknown genomes. Using RNA from six different tissues from a single Palearctic green toad (Bufo viridis specimen and Hiseq2000, we obtained 22,5 Mio reads and publish >100,000 unigene sequences. To evaluate efficacy and quality, we first use this data to identify green toad specific candidate genes, known from other vertebrates for their role in sex determination and differentiation. Of a list of 37 genes, the transcriptome yielded 32 (87%, many of which providing the first such data for this non-model anuran species. However, for many of these genes, only fragments could be retrieved. In order to allow also applications to population genetics, we further used the transcriptome for the targeted development of 21 non-anonymous microsatellites and tested them in genetic families and backcrosses. Eleven markers were specifically developed to be located on the B. viridis sex chromosomes; for eight markers we can indeed demonstrate sex-specific transmission in genetic families. Depending on phylogenetic distance, several markers, which are sex-linked in green toads, show high cross-amplification success across the anuran phylogeny, involving nine systematic anuran families. Our data support the view that single transcriptome sequencing (based on multiple tissues provides a reliable genomic resource and cost-efficient method for non-model amphibian species with large genome size and, despite limitations, should be considered as long as genome sequencing remains unaffordable for most species.

  13. The Display of Single-Domain Antibodies on the Surfaces of Connectosomes Enables Gap Junction-Mediated Drug Delivery to Specific Cell Populations.

    Science.gov (United States)

    Gadok, Avinash K; Zhao, Chi; Meriwether, Amanda I; Ferrati, Silvia; Rowley, Tanner G; Zoldan, Janet; Smyth, Hugh D C; Stachowiak, Jeanne C

    2018-01-09

    Gap junctions, transmembrane protein channels that directly connect the cytoplasm of neighboring cells and enable the exchange of molecules between cells, are a promising new frontier for therapeutic delivery. Specifically, cell-derived lipid vesicles that contain functional gap junction channels, termed Connectosomes, have recently been demonstrated to substantially increase the effectiveness of small molecule chemotherapeutics. However, because gap junctions are present in nearly all tissues, Connectosomes have no intrinsic ability to target specific cell types, which potentially limits their therapeutic effectiveness. To address this challenge, here we display targeting ligands consisting of single-domain antibodies on the surfaces of Connectosomes. We demonstrate that these targeted Connectosomes selectively interact with cells that express a model receptor, promoting the selective delivery of the chemotherapeutic doxorubicin to this target cell population. More generally, our approach has the potential to boost cytoplasmic delivery of diverse therapeutic molecules to specific cell populations while protecting off-target cells, a critical step toward realizing the therapeutic potential of gap junctions.

  14. Comparison of the clinical effectiveness of a single and a triple-headed toothbrushes in a population of mentally retarded patients.

    Science.gov (United States)

    Sauvetre, E; Rozow, A; de Meel, H; Richebe, A; Abi-Khalil, M; Demeure, F

    1995-01-01

    Tooth brushing is a very simple and effective method for removing daily dental deposits and for preventing dental and periodontal diseases. However, it can cause considerable manipulative difficulties among some populations, e.g., young children, physically handicapped and mentally retarded patients. In order to test and compare the efficiency of a newly designed toothbrush (Superbrush), we have performed a pilot study on patients staying at the "Reine Fabiola Village No. 1", an institution for patients who are followed for mental retardation at different levels. 30 patients were included in the study, aged between 18 to 40 years. Among these 30, five had to be eliminated for their incapacity to follow the initial training in how to brush their teeth. The comparison was made with a normal single headed tooth brush, in a double blind trial, based on bleeding and plaque indexes, performed on 6 different teeth on day 0, 7 and 21. The results of this study indicate that there is no significant difference between the two types of toothbrushes with respect to the ability of plaque removing and gingivitis prevention, during the period of time of this study. However, the easiness of manipulating this newly designed toothbrush renders it a useful tool for the dental hygiene for this special part of the dental compromised population.

  15. Combination Testing Using a Single MSH5 Variant alongside HLA Haplotypes Improves the Sensitivity of Predicting Coeliac Disease Risk in the Polish Population.

    Directory of Open Access Journals (Sweden)

    Agnieszka Paziewska

    Full Text Available Assessment of non-HLA variants alongside standard HLA testing was previously shown to improve the identification of potential coeliac disease (CD patients. We intended to identify new genetic variants associated with CD in the Polish population that would improve CD risk prediction when used alongside HLA haplotype analysis. DNA samples of 336 CD and 264 unrelated healthy controls were used to create DNA pools for a genome wide association study (GWAS. GWAS findings were validated with individual HLA tag single nucleotide polymorphism (SNP typing of 473 patients and 714 healthy controls. Association analysis using four HLA-tagging SNPs showed that, as was found in other populations, positive predicting genotypes (HLA-DQ2.5/DQ2.5, HLA-DQ2.5/DQ2.2, and HLA-DQ2.5/DQ8 were found at higher frequencies in CD patients than in healthy control individuals in the Polish population. Both CD-associated SNPs discovered by GWAS were found in the CD susceptibility region, confirming the previously-determined association of the major histocompatibility (MHC region with CD pathogenesis. The two most significant SNPs from the GWAS were rs9272346 (HLA-dependent; localized within 1 Kb of DQA1 and rs3130484 (HLA-independent; mapped to MSH5. Specificity of CD prediction using the four HLA-tagging SNPs achieved 92.9%, but sensitivity was only 45.5%. However, when a testing combination of the HLA-tagging SNPs and the MSH5 SNP was used, specificity decreased to 80%, and sensitivity increased to 74%. This study confirmed that improvement of CD risk prediction sensitivity could be achieved by including non-HLA SNPs alongside HLA SNPs in genetic testing.

  16. Population transcriptomics with single-cell resolution: a new field made possible by microfluidics: a technology for high throughput transcript counting and data-driven definition of cell types.

    Science.gov (United States)

    Plessy, Charles; Desbois, Linda; Fujii, Teruo; Carninci, Piero

    2013-02-01

    Tissues contain complex populations of cells. Like countries, which are comprised of mixed populations of people, tissues are not homogeneous. Gene expression studies that analyze entire populations of cells from tissues as a mixture are blind to this diversity. Thus, critical information is lost when studying samples rich in specialized but diverse cells such as tumors, iPS colonies, or brain tissue. High throughput methods are needed to address, model and understand the constitutive and stochastic differences between individual cells. Here, we describe microfluidics technologies that utilize a combination of molecular biology and miniaturized labs on chips to study gene expression at the single cell level. We discuss how the characterization of the transcriptome of each cell in a sample will open a new field in gene expression analysis, population transcriptomics, that will change the academic and biomedical analysis of complex samples by defining them as quantified populations of single cells. Copyright © 2013 WILEY Periodicals, Inc.

  17. Genetic study of two single nucleotide polymorphisms within corresponding microRNAs and susceptibility to tuberculosis in a Chinese Tibetan and Han population.

    Science.gov (United States)

    Li, Dongdong; Li, Dingdong; Wang, Tingting; Song, Xingbo; Qucuo, MeiLang; Yang, Bin; Zhang, Junlong; Wang, Jun; Ying, Binwu; Tao, Chuanmin; Wang, Lanlan

    2011-07-01

    MicroRNAs (miRNA) are thought to play important roles in the pathogenesis of diseases. Single nucleotide polymorphisms (SNPs) within miRNAs can change their characteristics via altering their target selection and/or expression, resulting in functional and/or phenotypic changes. We decided to investigate the genetic association with pulmonary tuberculosis with 2 nucleotide variations within corresponding microRNAs regulating the Toll-like receptor (TLR)-mediating signal pathway. MiRNAs potentially regulating the TLR-mediating signal pathway were predicted via bioinformatics. Finally, 2 SNPs, rs2910164 G>C and rs3746444 T>C within miR-146a and miR-499, were selected as candidates in accordance with some criteria. SNPs were genotyped by polymerase chain reaction-restriction fragment length polymorphism and validated by sequencing to demonstrate their association with susceptibility to pulmonary tuberculosis (PTB) in 337 PTB cases and 738 healthy controls, including 318 Tibetan and 757 Han individuals. Bioinformatics databases were searched to support the association between miRNAs and PTB. There was no association between rs3746444 and PTB risk (p = 0.118) in the Han population, but subjects carrying the C allele exhibited decreased PTB risk (odds ratio [OR] = 0.403 [95% confidence interval (95% CI) 0.278-0.583]). However, there was an association between rs3746444 and PTB in the Tibetan population, and individuals carrying the C allele exhibited increased PTB risk (OR = 1.870 [95% CI 1.218-2.871]). A polymorphism (rs2910164 G>C) indicated an association with PTB risk in both Tibetan (p = 0.031) and Han (p = 0.000) populations. However, the role of the G allele of rs2910164, like the C allele in rs3746444, differed in the Tibetan (OR = 1.509, p tuberculosis with SNPs within the corresponding miRNAs potentially regulates the TLR signal pathway. It is interesting that both the G allele (rs2910164) and the C allele (rs3746444) play different roles in 2 populations

  18. All Wales Injury Surveillance System revised: development of a population-based system to evaluate single-level and multilevel interventions.

    Science.gov (United States)

    Lyons, Ronan A; Turner, Samantha; Lyons, Jane; Walters, Angharad; Snooks, Helen A; Greenacre, Judith; Humphreys, Ciaran; Jones, Sarah J

    2016-04-01

    Injury surveillance has been established since the 1990s, but is still largely based upon single-source data from sentinel sites. The growth of electronic health records and developments in privacy protecting linkage technologies provide an opportunity for more sophisticated surveillance systems. To describe the evolution of an injury surveillance system to support the evaluation of interventions, both simple and complex in terms of organisation. The paper describes the evolution of the system from one that relied upon data only from emergency departments to one that include multisource data and are now embedded in a total population privacy protecting data linkage system. Injury incidence estimates are compared by source and data linkage used to aid understanding of data quality issues. Examples of applications, challenges and solutions are described. The age profile and estimated incidence of injuries recorded in general practice, emergency departments and hospital admissions differ considerably. Data linkage has enabled the evaluation of complex interventions and measurement of longer-term impact of a wide range of exposures. Embedding injury surveillance within privacy protecting data linkage environment can transform the utility of a traditional single-source surveillance system to a multisource system. It also facilitates greater involvement in the evaluation of simple and complex healthcare and non-healthcare interventions and contributes to the growing evidence basis underlying the science of injury prevention and control. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  19. Evaluation of the Microbiological Efficacy of a Single 2-Gram Dose of Extended-Release Azithromycin by Population Pharmacokinetics and Simulation in Japanese Patients with Gonococcal Urethritis.

    Science.gov (United States)

    Soda, Midori; Ito, Shin; Matsumaru, Naoki; Nakamura, Sakiko; Nagase, Izumi; Takahashi, Hikari; Ohno, Yuta; Yasuda, Mitsuru; Yamamoto, Miho; Tsukamoto, Katsura; Itoh, Yoshinori; Deguchi, Takashi; Kitaichi, Kiyoyuki

    2018-01-01

    The objective of this study was to analyze the relationship between the pharmacokinetic (PK)/pharmacodynamic (PD) parameters of a single 2-g dose of extended-release formulation of azithromycin (AZM-SR) and its microbiological efficacy against gonococcal urethritis. Fifty male patients with gonococcal urethritis were enrolled in this study. In 36 patients, the plasma AZM concentrations were measured using liquid chromatography-tandem mass spectrometry, the AZM MIC values for the Neisseria gonorrhoeae isolates were determined, and the microbiological outcomes were assessed. AZM-SR monotherapy eradicated N. gonorrhoeae in 30 (83%) of the 36 patients. AZM MICs ranged from 0.03 to 2 mg/liter. The mean value of the area under the concentration-time curve (AUC), estimated by population PK analysis using a two-compartment model, was 20.8 mg · h/liter. Logistic regression analysis showed that the PK/PD target value required to predict an N. gonorrhoeae eradication rate of ≥95% was a calculated AUC/MIC of ≥59.5. The AUC/MIC value was significantly higher in patients who achieved microbiological cure than in patients who achieved microbiological failure. Monte Carlo simulation using this MIC distribution revealed that the probability that AZM-SR monotherapy would produce an AUC/MIC exceeding the AUC/MIC target of 59.5 was 47%. Furthermore, the MIC distribution for strains isolated in this study was mostly consistent with that for strains currently circulating in Japan. In conclusion, in Japan, AZM-SR monotherapy may not be effective against gonococcal urethritis. Therefore, use of a single 2-g dose of AZM-SR either with or without other antibiotics could be an option to treat gonococcal urethritis if patients are allergic to ceftriaxone and spectinomycin or are diagnosed to be infected with an AZM-sensitive strain. Copyright © 2017 American Society for Microbiology.

  20. Quantitative Review Finds No Evidence of Cognitive Effects in Healthy Populations From Single-session Transcranial Direct Current Stimulation (tDCS).

    Science.gov (United States)

    Horvath, Jared Cooney; Forte, Jason D; Carter, Olivia

    2015-01-01

    Over the last 15-years, transcranial direct current stimulation (tDCS), a relatively novel form of neuromodulation, has seen a surge of popularity in both clinical and academic settings. Despite numerous claims suggesting that a single session of tDCS can modulate cognition in healthy adult populations (especially working memory and language production), the paradigms utilized and results reported in the literature are extremely variable. To address this, we conduct the largest quantitative review of the cognitive data to date. Single-session tDCS data in healthy adults (18-50) from every cognitive outcome measure reported by at least two different research groups in the literature was collected. Outcome measures were divided into 4 broad categories: executive function, language, memory, and miscellaneous. To account for the paradigmatic variability in the literature, we undertook a three-tier analysis system; each with less-stringent inclusion criteria than the prior. Standard mean difference values with 95% CIs were generated for included studies and pooled for each analysis. Of the 59 analyses conducted, tDCS was found to not have a significant effect on any - regardless of inclusion laxity. This includes no effect on any working memory outcome or language production task. Our quantitative review does not support the idea that tDCS generates a reliable effect on cognition in healthy adults. Reasons for and limitations of this finding are discussed. This work raises important questions regarding the efficacy of tDCS, state-dependency effects, and future directions for this tool in cognitive research. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. [Association of the tagging single nucleotide polymorphisms in transforming growth factor beta-1 gene with hypertension in the Han nationality population in Xinjiang].

    Science.gov (United States)

    Yang, Jian-feng; Shi, Xiao-peng; Zhao, Dan; Deng, Feng-mei; Zhong, Hua; Wang, Gang; Wang, Zhen-huan; Chen, Xiong-ying; He, Fang

    2010-06-01

    Essential hypertension (EH) was a complex disease resulted from the interaction of cumulative effect of multiple genetic and environment factors. The relationship between the genetic polymorphisms in the transforming growth factor-beta1 (TGF-beta1), the blood levels and EH have been investigated, but the conclusions were different. Therefore, we investigate the relationship between the tagging single nucleotide polymorphisms (tSNPs) (rs1800469, rs2241716, rs11466345, rs2241715, rs4803455) in TGF-beta1 gene, blood levels and EH in the Han nationality population in Xinjiang, to clarity the pattern of linkage disequilibrium (LD) and the feature of the structure of haplotype. Based on the case-control study,we selected 732 (365 EH patients,367 controls) Han Chinese population from the Boertonggu countryside of Shawan region in the Xinjiang Uygur Autonomous Region of China by random cluster sampling. After questionnaire and physical examination, we collected blood samples, and the blood levels of TGF-beta1 were quantified using sandwich ELISA. The polymorphisms of TGF-beta1 gene in the study groups were detected with SNaPshot system. The case-control study in a large group was carried out separately for each of the tSNP and followed up by haplotypes analyses to determine the relation between tSNPs of TGF-beta1 gene and EH in the Han population. (1) The frequencies of alleles A, G of rs11466345 of TGF-beta1 gene in EH group and control group were as follows: 69.7%, 30.3%, 74.4%, 25.6%, respectively. It was demonstrated that the G allele of the rs11466345 polymorphism occurred at a significantly higher frequency in EH patients than in healthy controls (30.3% vs. 25.6%, P 0.05). (2)Except the site of rs11466345, the other tSNPs were in strong LD, and no statistical differences were observed in haplotypes distribution in the followup study between case-control groups (P > 0.05). (3) There were no difference of TGF-beta1 levels between the different genotypes and alleles in

  2. [A study on relationship between single nucleotide polymorphisms of vascular endothelial growth factor gene and susceptibility to systemic lupus erythematosus in China north Han population].

    Science.gov (United States)

    Lv, Hao-Zhe; Lin, Tao; Zhu, Xiang-Yang; Zhang, Jin-Tao; Lu, Jing

    2010-12-01

    To investigate relationship between single nucleotide polymorphism(SNP) of VEGF gene and susceptibility to systemic lupus erythematosus(SLE) in China north population. Six VEGF SNPs (rs2010963, rs3024994, rs3025000, rs3025010, rs3025035 and rs833070) of forty-four patients with SLE and one hundred healthy controls were examined by Sequenom chip-based MALDI-TOF mass spectomery platform. Different genotypes were analyzed statistically by SPSS 11.5. There was no significant difference between SLE patients and controls in frequency of rs2010963, rs3024994, rs3025000, rs3025010, rs3025035 genotype and allele (P>0.05). The frequency of rs833070 A allele was significantly higher in SLE than that in controls. (31.2% vs 20%, x(2);=4.547, P=0.033, OR=1.818 , 95% CI 1.045-3.162). In the patient with SLE, rs833070 G decreased the susceptibility of arthritis(56% vs 80.4%, x(2);=5.613, P=0.018, OR=0.336, 95% CI 0.134-0.843), while the genotype of rs833070 GG significantly decreased the susceptibility to arthritis(GGvsAG+AA: 28% vs 65.2%, x(2);=6.684, P=0.010, OR=0.207, 95% CI 0.061-0.705). VEGF rs833070 A may represent an inreased susceptibility to SLE in China north Han population. VEGF rs833070 G and rs833070 GG may play protective roles in the case of lupus arthritis.

  3. Optimisation of single-phase dry-thermophilic anaerobic digestion under high organic loading rates of industrial municipal solid waste: population dynamics.

    Science.gov (United States)

    Zahedi, S; Sales, D; Romero, L I; Solera, R

    2013-10-01

    Different high feed organic loading rates (OLRs) (from 5.7 g to 46.0 g TVS/l/d) or hydraulic retention times (HRTs) (from 15 d to 2 d) in single-phase dry-thermophilic anaerobic digestion (AD) of organic fraction municipal solid waste (OFMSW) were investigated. The specific gas production (SGP) values (0.25-0.53 m(3)/kg TVS) and the percentages of Eubacteria, Archaea, H2-utilising methanogens (HUMs) and acetate-utilising methanogens (AUMs) were stable within the ranges 80.2-91.1%, 12.4-18.5%, 4.4-9.8% and 5.5-10.9%, respectively. A HUM/AUM ratio greater than 0.7 seems to be necessary to maintain very low partial pressures of H2 required for dry AD process. Increasing OLR resulted in an increase in all the populations, except for propionate-utilising acetogens (PUAs). Optimal conditions were obtained at 3d HRT (OLR=30.7 g TVS/l/d), which is lower than the doubling time of acetogens and methanogens. The methane production (MP) was clearly higher than those reported in AD of OFMSW. Copyright © 2013 Elsevier Ltd. All rights reserved.

  4. Association of Single-Nucleotide Polymorphisms in Immune-Related Genes with Development of Dengue Hemorrhagic Fever in a Mexican Population.

    Science.gov (United States)

    Vargas-Castillo, Angélica Berenice; Ruiz-Tovar, Karina; Vivanco-Cid, Héctor; Quiroz-Cruz, Sarai; Escobar-Gutiérrez, Alejandro; Cerna-Cortes, Jorge Francisco; Vaughan, Gilberto; Fonseca-Coronado, Salvador

    2017-11-13

    Single-nucleotide polymorphisms (SNPs) occurring in immune-related genes have been associated with risk or protection for development of dengue, depending on ethnicity. Here, we genotyped seven SNPs located in immune response-related genes to identify their association with severe forms of dengue in patients from an endemic region in Mexico. One hundred and thirty-eight patients with dengue fever (DF), thirty-one dengue hemorrhagic fever (DHF) patients, as well as 304 healthy donors were genotyped by using a TaqMan-based approach. SNP analysis, including rs1800629 (TNF), rs4804803 (CD209), rs2780831 (JAK1), rs1801274 (FCGR2A), rs231775 (CTLA4), rs12979860, and rs8099917 (IFNL3), was performed. The rs1800629 A-allele in the TNF gene was associated with an increased risk of DHF (OR = 3.4, CI = 1.235-9.284 p = 0.0212) whereas SNPs rs4804803, rs2780831, rs1801274, rs231775, rs12979860, and rs8099917 showed no association in this cohort. These results show that allelic variations in TNF can play an important role in the development of DHF. However, the lack of association between all remaining SNPs and DHF suggests that the genetic background might directly modify the role of these immune-related molecules, leading to the milder illness often observed in a Mexican population.

  5. Obligatory versus elective single embryo transfer in in vitro fertilization. A population-based analysis of data from the U.K. Human Fertilisation and Embryology Authority.

    Science.gov (United States)

    Straughen, Jennifer K; Salihu, Hamisu M; Keith, Louis; Petrozzino, Jeffrey; Jones, Christopher

    2013-01-01

    To determine how obligatory single embryo transfer (SET) and elective SET influence pregnancy outcome. We compared women who underwent obligatory and elective SET using data from a comprehensive, population-based register from the United Kingdom Human Fertilisation and Embryology Authority, which contained all in vitro fertilization (IVF) treatments administered between 1991 and 1998. Generalized estimating equations were used to generate adjusted odds ratios (ORs) and 95% confidence intervals (CIs) to compare clinical pregnancy, live birth, and multiple birth rates. Obligatory and elective SET had similar clinical pregnancy and live birth rates and comparable multiple birth rates. Obligatory and elective SET were equally likely to end in a live birth (OR = 1.08; 95% CI = 0.90, 1.30). Similar results were found after restricting the data to women without previous IVF births (OR = 1.18; 95% CI = 0.98, 1.42) and without previous naturally conceived live births (OR = 1.16; 95% CI = 0.95, 1.43). This study suggests that obligatory SET can achieve pregnancy and live birth rates that are at least as good as elective SET. Equally important is the low multiple birth rate which was maintained in both forms of SET. More studies comparing elective versus obligatory SET can assist with achieving optimal pregnancy rates while preventing multiple births.

  6. Genetic analysis of allelic variants, single-step mutations, three allelic variants of the 15 STR loci in the population of Northeast Bosnia

    Directory of Open Access Journals (Sweden)

    Hadžiavdić Vesna

    2013-01-01

    Full Text Available Diversity of nuclear DNA microsatellite markers were analyzed in a reference sample of the population of northeast Bosnia. 437 samples taken from unrelated individuals were processed and three samples of paternity proof were shown. Detection effectiveness profile of the research, points to a valid choice of method of extraction, amplification and genotyping STR loci with PowerPlextm16. Genetic analysis of allelic variants of the 15 STR loci detected 17 samples determined as microvariants. Samples were divided into 15 different allelic variants at 7 different loci, and are: in locus D7S820, D16S539, D3S1358, D18S51, PENTA D, PENTA E and in locus vWA. Genetic analysis of mutations in cases of paternity determined three examples of single-step mutations in the loci FGA, Penta D and D3S1358. Genetic analysis of observed STR loci detected three allelic variant of genotype combination 7/10/11.3 in locus D7S820 Type II.

  7. Pharmacokinetic/pharmacodynamic evaluation of marbofloxacin as a single injection for Pasteurellaceae respiratory infections in cattle using population pharmacokinetics and Monte Carlo simulations.

    Science.gov (United States)

    Paulin, A; Schneider, M; Dron, F; Woehrle, F

    2018-02-01

    Population pharmacokinetic of marbofloxacin was investigated with 52 plasma concentration-time profiles obtained after intramuscular administration of Forcyl® in cattle. Animal's status, pre-ruminant, ruminant, or dairy cow, was retained as a relevant covariate for clearance. Monte Carlo simulations were performed using a stratification by status, and 1000 virtual disposition curves were generated in each bovine subpopulation for the recommended dosage regimen of 10 mg/kg as a single injection. The probability of target attainment (PTA) of pharmacokinetic/pharmacodynamic (PK/PD) ratios associated with clinical efficacy and prevention of resistance was determined in each simulated subpopulation. The cumulative fraction of response (CFR) of animals achieving a PK/PD ratio predictive of positive clinical outcome was then calculated for the simulated dosage regimen, taking into account the minimum inhibitory concentration (MIC) distribution of Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni. When considering a ratio of AUC 0-24 hr /MIC (area under the curve/minimum inhibitory concentration) greater than 125 hr, CFRs ranging from 85% to 100% against the three Pasteurellaceae in each bovine subpopulation were achieved. The PTA of the PK/PD threshold reflecting the prevention of resistances was greater than 90% up to MPC (mutant prevention concentration) values of 1 μg/ml in pre-ruminants and ruminants and 0.5 μg/ml in dairy cows. © 2017 The Authors. Journal of Veterinary Pharmacology and Therapeutics Published by John Wiley & Sons Ltd.

  8. ESR1 single nucleotide polymorphism rs1062577 (c.*3804T>A) alters the susceptibility of breast cancer risk in Iranian population.

    Science.gov (United States)

    Dehghan, Zahra; Sadeghi, Samira; Tabatabaeian, Hossein; Ghaedi, Kamran; Azadeh, Mansoureh; Fazilati, Mohammad; Bagheri, Fatemeh

    2017-05-05

    Albeit single nucleotide polymorphisms related to ESR1 gene have been studied, only a number of them have been reported to be associated with breast cancer risk. rs1062577 is one of the most recent microRNA-related ESR1 SNPs; however, no study has been conducted to investigate the significance this polymorphism in Iranian population. In this study, we aimed to investigate the frequency and also the association between rs1062577 and breast cancer. rs1062577 position was genotyped by Tetra-primer ARMS-PCR in totally 182 blood specimens obtained from breast cancer patients (n=86), and healthy blood donors (n=96). The distribution of different genotypes was statistically analyzed in terms of the potential association between rs1062577 different alleles, breast cancer risk and clinicopathological criteria of breast cancer patients. The statistical analyses confidently indicated that rs1062577 A allele is associated with the increased breast cancer risk in both univariate and multivariate regression models (Odds Ratio=8.403 and 32.602 respectively). rs1062577 T allele was statistically associated with stage I of breast cancer patients (p-value=0.025). In silico studies implied that rs1062577 A allele can alter the binding capacity of ESR1 mRNA and miRNAs via either breakage or formation of hydrogen bonds. rs1062577 A allele is significantly and dramatically associated with the elevated risk and greater stages of breast cancer. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data.

    Science.gov (United States)

    Cornuet, Jean-Marie; Pudlo, Pierre; Veyssier, Julien; Dehne-Garcia, Alexandre; Gautier, Mathieu; Leblois, Raphaël; Marin, Jean-Michel; Estoup, Arnaud

    2014-04-15

    DIYABC is a software package for a comprehensive analysis of population history using approximate Bayesian computation on DNA polymorphism data. Version 2.0 implements a number of new features and analytical methods. It allows (i) the analysis of single nucleotide polymorphism data at large number of loci, apart from microsatellite and DNA sequence data, (ii) efficient Bayesian model choice using linear discriminant analysis on summary statistics and (iii) the serial launching of multiple post-processing analyses. DIYABC v2.0 also includes a user-friendly graphical interface with various new options. It can be run on three operating systems: GNU/Linux, Microsoft Windows and Apple Os X. Freely available with a detailed notice document and example projects to academic users at http://www1.montpellier.inra.fr/CBGP/diyabc CONTACT: estoup@supagro.inra.fr Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. Cytogenetics of the Anopheles gambiae complex in Sudan, with special reference to An. arabiensis: relationships with East and West African populations.

    Science.gov (United States)

    Petrarca, V; Nugud, A D; Ahmed, M A; Haridi, A M; Di Deco, M A; Coluzzi, M

    2000-06-01

    The species composition of malaria vector mosquitoes belonging to the Anopheles gambiae complex (Diptera: Culicidae) from >40 localities in Sudan, representing most ecological situations, was determined by analysis of ovarian polytene chromosomes. Of 2162 females, 93% were identified as An. arabiensis Patton and 7% were An. gambiae Giles sensu stricto. No hybrids were found between the two species. Anopheles arabiensis occurred in all but two sites, whereas An. gambiae s.s. was effectively limited to the southernmost, more humid localities. For chromosomal paracentric inversions, the degree of polymorphism was low in An. gambiae s.s. (inversions 2La, 2Rb and 2Rd), higher in An. arabiensis (inversions Xe, 2Ra, b, bc, d1, s; 3Ra, d). Anopheles gambiae samples from Sudan were all apparently panmictic, i.e. they did not show restricted gene flow such as observed among West African populations (interpreted as incipient speciation). Chromosomal inversion patterns of An. gambiae in southern Sudan showed characteristics of intergrading Savanna/Forest populations similar to those observed in comparable eco-climatic situations of West Africa. Anopheles arabiensis was polymorphic for inversion systems recorded in West Africa (2Ra, 2Rb, 2Rdl, 3Ra) and for a novel 2Rs polymorphism, overlapping with inversion systems 2Rb and 2Rd1. Samples carrying the 2Rs inversion were mostly from Khashm-el-Girba area in central-eastern Sudan. In the great majority of the samples all polymorphic inversions were found to be in Hardy-Weinberg equilibrium. Sudan populations of An. arabiensis should therefore be considered as generally panmictic. Anopheles arabiensis shows more inversion polymorphism in west than in east African populations. Sudan populations have more evident similarities with those from westwards than those from eastwards of the Great Rift Valley. The possible influence of the Rift on evolution of An. arabiensis is discussed.

  11. Investigating population continuity with ancient DNA under a spatially explicit simulation framework.

    Science.gov (United States)

    Silva, Nuno Miguel; Rio, Jeremy; Currat, Mathias

    2017-12-15

    Recent advances in sequencing technologies have allowed for the retrieval of ancient DNA data (aDNA) from skeletal remains, providing direct genetic snapshots from diverse periods of human prehistory. Comparing samples taken in the same region but at different times, hereafter called "serial samples", may indicate whether there is continuity in the peopling history of that area or whether an immigration of a genetically different population has occurred between the two sampling times. However, the exploration of genetic relationships between serial samples generally ignores their geographical locations and the spatiotemporal dynamics of populations. Here, we present a new coalescent-based, spatially explicit modelling approach to investigate population continuity using aDNA, which includes two fundamental elements neglected in previous methods: population structure and migration. The approach also considers the extensive temporal and geographical variance that is commonly found in aDNA population samples. We first showed that our spatially explicit approach is more conservative than the previous (panmictic) approach and should be preferred to test for population continuity, especially when small and isolated populations are considered. We then applied our method to two mitochondrial datasets from Germany and France, both including modern and ancient lineages dating from the early Neolithic. The results clearly reject population continuity for the maternal line over the last 7500 years for the German dataset but not for the French dataset, suggesting regional heterogeneity in post-Neolithic migratory processes. Here, we demonstrate the benefits of using a spatially explicit method when investigating population continuity with aDNA. It constitutes an improvement over panmictic methods by considering the spatiotemporal dynamics of genetic lineages and the precise location of ancient samples. The method can be used to investigate population continuity between any pair

  12. Conservation genetics of American crocodile, Crocodylus acutus, populations in Pacific Costa Rica

    Science.gov (United States)

    Mauger, Laurie A.; Velez, Elizabeth; Cherkiss, Michael S.; Brien, Matthew L.; Mazzotti, Frank J.; Spotila, James R.

    2017-01-01

    Maintaining genetic diversity is crucial for the survival and management of threatened and endangered species. In this study, we analyzed genetic diversity and population genetic structure at neutral loci in American crocodiles, Crocodylus acutus, from several areas (Parque Nacional Marino Las Baulas, Parque Nacional Santa Rosa, Parque Nacional Palo Verde, Rio Tarcoles, and Osa Conservation Area) in Pacific Costa Rica. We genotyped 184 individuals at nine microsatellite loci to describe the genetic diversity and conservation genetics between and among populations. No population was at Hardy-Weinberg Equilibrium (HWE) over all loci tested and a small to moderate amount of inbreeding was present. Populations along the Pacific coast had an average heterozygosity of 0.572 across all loci. All populations were significantly differentiated from each other with both FST and RST measures of population differentiation with a greater degree of molecular variance (81%) found within populations. Our results suggest C. acutus populations in Pacific Costa Rica were not panmictic with moderate levels of genetic diversity. An effective management plan that maintains the connectivity between clusters is critical to the success of C. acutus in Pacific Costa Rica.

  13. Association of single nucleotide polymorphisms of IL23R and IL17 with ulcerative colitis risk in a Chinese Han population.

    Directory of Open Access Journals (Sweden)

    Pengli Yu

    Full Text Available BACKGROUND: Previous studies implicated that IL23R and IL17 genes play an important role in autoimmune inflammation. Genome-wide association studies have also identified multiple single nucleotide polymorphisms (SNPs in the IL23R gene region associated with inflammatory bowel diseases. This study examined the association of IL23R and IL17A gene SNPs with ulcerative colitis susceptibility in a population in China. METHODOLOGY: A total of 270 ulcerative colitis and 268 healthy controls were recruited for the analyses of 23 SNPs in the IL23R and IL17A regions. Genomic DNA was extracted and analysis of these 23 SNPs using ligase detection reaction allelic (LDR technology. Genotype and allele associations were calculated using SPSS 13.0 software package. PRINCIPAL FINDINGS: Compared to the healthy controls, the variant alleles IL23R rs7530511, and rs11805303 showed a statistically significant difference for ulcerative colitis susceptibility (0.7% vs 3.3%, P = 0.002; 60.4% vs 53.2%, P = 0.0017, respectively. The linkage disequilibrium (LD patterns of these SNPs were measured and three LD blocks from the SNPs of IL23R and one block from those of IL17A were identified. A novel association with ulcerative colitis susceptibility occurred in haplotypes of IL23R (Block1 H3 P = 0.02; Block2 H2 P = 0.019; Block3 H4 P = 0.029 and IL17A (H4 P = 0.034. Pair-wise analyses showed an interaction between the risk haplotypes in IL23R and IL17A (P = 0.014. CONCLUSIONS: Our study demonstrated that rs7530511, and rs11805303 of IL23R were significantly associated with ulcerative colitis susceptibility in the Chinese population. The most noticeable finding was the linkage of IL23R and IL17A gene region to ulcerative colitis risk due to the gene-gene interaction.

  14. Single Nucleotide Polymorphisms in Key One-Carbon Metabolism Genes and Their Association with Blood Folate and Homocysteine Levels in a Chinese Population in Yunnan.

    Science.gov (United States)

    Ni, Juan; Liu, Yaoxian; Zhou, Tao; Wu, Xiayu; Wang, Xu

    2018-02-16

    One-carbon metabolism (OCM) is essential for DNA synthesis and methylation. Single nucleotide polymorphisms (SNPs) within OCM genes may affect folic acid (FA) metabolism, disrupt homocysteine (Hcy) homeostasis, and increase the risk of disease. This study investigated the relationship between SNPs in key OCM genes and their association with blood FA and Hcy levels in a healthy population in Yunnan, China. Six SNPs within five key OCM genes (MTHFR C677T, MTHFR A1298C, MS A2756G, MTRR A66G, CBS T833C, and SHMT C1420T) were genotyped in 300 healthy volunteers (148 males and 152 females) using polymerase chain reaction/restriction fragment length polymorphism. Blood folate [serum FA (SFA) and red blood cell folate (RBC FA)] and Hcy levels were determined by chemiluminescence immunoassays and enzymatic assays. Subjects with the MTHFR 677TT genotype had significantly higher Hcy levels and RBC FA concentrations compared with those harboring the MTHFR 677CC/CT genotypes (p < 0.01). Both Hcy and blood FA concentrations were also increased in subjects with MS 2756AA, as well as those within CBS 833TT, when compared with those with MS 2756AG/GG (p < 0.05) and CBS 833TC/CC (p < 0.05) genotypes, respectively. Subjects harboring the combined genotype of MTHFR 677TT and MS 2756AA had a higher Hcy concentration than those carrying other MTHFR and MS combinations (p = 0.002). Similarly, subjects harboring the combination of CBS 833TT with MTHFR 677TT had higher Hcy concentrations than those harboring other CBS and MTHFR combinations (p = 0.011). The genotypes involving the MTHFR C677T, MS A2756G, and CBS T833C polymorphisms, including combinations of these genotypes, were the most important factors associated with blood FA and Hcy levels of the investigated SNPs in the OCM genes.

  15. Correlation between single nucleotide polymorphism of rs3811047 in IL-1 F7 gene and rheumatoid arthritis susceptibility among Han population in central plains of China.

    Science.gov (United States)

    Shi, Li-Pu; He, Ya; Liu, Zhi-Dui

    2013-01-01

    To discuss the association between single nucleotide polymorphism (SNP) of rs3811047 in IL-1 F7 gene and rheumatoid arthritis (RA) susceptibility among the Han population in central plains of China. A total of 276 RA patients admitted to our hospital from December 2009 to December 2011 together with 276 healthy physical examinees in the same period were chosen as the subjects. The typing for rs3811047 SNP in IL-1 F7 gene was carried out by using ligase detection reaction and polymerase chain reaction technique. And the frequency of each allele and genotypes distribution was calculated so as to evaluate the association between genotype distribution and RA susceptibility. The frequency of A allele of rs3811047 in IL-1 F7 gene in RA group and control group was 16.27% and 17.68%, respectively, and that of G allele in two groups was 83.73% and 82.32%, respectively. The difference between two groups wasn't statistical significant (P >0.05). The frequency of genotype AA, AG and GG in RA group was 2.19%, 27.84% and 69.97%, respectively, while that in control group was 2.94%, 29.78% and 67.28%, respectively. The difference of distribution of three genotypes was not statistically significant (P >0.05). RA patients with A allele were better than those without A allele in joint swelling index, rest pain, HAQ scoring and blood sedimentation. There was significant difference between two groups in above indexes (PF7 gene is observed. However, A allele of rs3811047 has certain influence on the condition of RA patients. Copyright © 2013 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

  16. SLC2A3 single-nucleotide polymorphism and duplication influence cognitive processing and population-specific risk for attention-deficit/hyperactivity disorder.

    Science.gov (United States)

    Merker, Sören; Reif, Andreas; Ziegler, Georg C; Weber, Heike; Mayer, Ute; Ehlis, Ann-Christine; Conzelmann, Annette; Johansson, Stefan; Müller-Reible, Clemens; Nanda, Indrajit; Haaf, Thomas; Ullmann, Reinhard; Romanos, Marcel; Fallgatter, Andreas J; Pauli, Paul; Strekalova, Tatyana; Jansch, Charline; Vasquez, Alejandro Arias; Haavik, Jan; Ribasés, Marta; Ramos-Quiroga, Josep Antoni; Buitelaar, Jan K; Franke, Barbara; Lesch, Klaus-Peter

    2017-07-01

    Attention-deficit/hyperactivity disorder (ADHD) is a common, highly heritable neurodevelopmental disorder with profound cognitive, behavioral, and psychosocial impairments with persistence across the life cycle. Our initial genome-wide screening approach for copy number variants (CNVs) in ADHD implicated a duplication of SLC2A3, encoding glucose transporter-3 (GLUT3). GLUT3 plays a critical role in cerebral glucose metabolism, providing energy for the activity of neurons, which, in turn, moderates the excitatory-inhibitory balance impacting both brain development and activity-dependent neural plasticity. We therefore aimed to provide additional genetic and functional evidence for GLUT3 dysfunction in ADHD. Case-control association analyses of SLC2A3 single-nucleotide polymorphisms (SNPs) and CNVs were conducted in several European cohorts of patients with childhood and adult ADHD (SNP, n = 1,886 vs. 1,988; CNV, n = 1,692 vs. 1,721). These studies were complemented by SLC2A3 expression analyses in peripheral cells, functional EEG recordings during neurocognitive tasks, and ratings of food energy content. Meta-analysis of all cohorts detected an association of SNP rs12842 with ADHD. While CNV analysis detected a population-specific enrichment of SLC2A3 duplications only in German ADHD patients, the CNV + rs12842 haplotype influenced ADHD risk in both the German and Spanish cohorts. Duplication carriers displayed elevated SLC2A3 mRNA expression in peripheral blood cells and altered event-related potentials reflecting deficits in working memory and cognitive response control, both endophenotypic traits of ADHD, and an underestimation of energy units of high-caloric food. Taken together, our results indicate that both common and rare SLC2A3 variation impacting regulation of neuronal glucose utilization and energy homeostasis may result in neurocognitive deficits known to contribute to ADHD risk. © 2017 Association for Child and Adolescent Mental Health.

  17. Use of Single- versus Multiple-Fraction Palliative Radiation Therapy for Bone Metastases: Population-Based Analysis of 16,898 Courses in a Canadian Province

    International Nuclear Information System (INIS)

    Olson, Robert A.; Tiwana, Manpreet S.; Barnes, Mark; Kiraly, Andrew; Beecham, Kwamena; Miller, Stacy; Hoegler, David; Olivotto, Ivo

    2014-01-01

    Purpose: There is abundant evidence that a single fraction (SF) of palliative radiation therapy (RT) for bone metastases is equivalent to more protracted and costly multiple fraction courses. Despite this, there is low utilization of SFRT internationally. We sought to determine the utilization of SFRT in a population-based, publicly funded health care system. Methods and Materials: All consecutive patients with bone metastases treated with RT during 2007 to 2011 in British Columbia (BC) were identified. Associations between utilization of SFRT and patient and provider characteristics were investigated. Results: A total of 16,898 courses of RT were delivered to 8601 patients. SFRT was prescribed 49% of the time. There were positive relationships among SFRT utilization and primary tumor group (P<.001; most commonly in prostate cancer), worse prognosis (P<.001), increasing physician experience (P<.001), site of metastases (P<.001; least for spine metastases), and area of training (P<.001; most commonly for oncologists trained in the United Kingdom). There was wide variation in the prescription of SFRT across 5 regional cancer centers, ranging from 25.5% to 73.4%, which persisted after controlling for other, potentially confounding factors (P<.001). Conclusions: The large variability in SFRT utilization across BC Cancer Agency (BCCA) cancer centers suggests there is a strong cultural effect, where physicians' use of SFRT is influenced by their colleagues' practice. SFRT use in BC was similar to that in other Canadian and western European reports but strikingly higher than in the United States. Further work is needed to standardize SFRT prescribing practices internationally for this common indication for RT, with the potential for huge health system cost savings and substantial improvements in patients' quality of life

  18. Single Nucleotide Polymorphisms in IL17A and IL6 Are Associated with Decreased Risk for Pulmonary Tuberculosis in Southern Brazilian Population.

    Directory of Open Access Journals (Sweden)

    Mariana Milano

    Full Text Available In Mycobacterium tuberculosis (MTB infection, the complex interaction of host immune system and the mycobacteria is associated with levels of cytokines production that play a major role in determining the outcome of the disease. Several single-nucleotide polymorphisms (SNPs in cytokine genes have been associated with tuberculosis (TB outcome. The aim of this study was to evaluate the association between previously reported SNPs IL2-330 T>G (rs2069762; IL4-590 C>T (rs2243250; IL6-174 G>C (rs1800795; IL10-592 A>C (rs1800872; IL10-1082 G>A (rs1800896; IL17A -692 C>T (rs8193036; IL17A -197 G>A (rs2275913; TNF -238 G>A (rs361525; TNF -308 G>A (rs1800629 and IFNG +874 T>A (rs2430561 and pulmonary TB (PTB susceptibility. We conducted a case-control study in individuals from Southern Brazil who were recruited between February 2012 and October 2013 in a high incidence TB city. We performed a multiplex genotyping assay in 191 patients with PTB and 175 healthy subjects. Our results suggest a decreased risk for PTB development associated with the IL17A -197A allele (OR = 0.29; p = 0.04, AA genotype (OR = 0.12; p = 0.04 and A carrier (AG/AA (OR = 0.29; p = 0.004 and IL6 -174C carrier (CC/CG (OR = 0.46; p = 0.04. We could not properly analyze IL17A -692 C>T (rs8193036 and IFNG +874T>A due to genotypic inconsistencies and found no evidence of association for the IL2, IL4, IL10 and TNF polymorphisms and PTB. In conclusion, our results show a protective effect of IL17 and IL6 polymorphisms on PTB outcome in Southern Brazilian population.

  19. Population genetics of Glossina palpalis palpalis from central African sleeping sickness foci

    Directory of Open Access Journals (Sweden)

    Solano Philippe

    2011-07-01

    Full Text Available Abstract Background Glossina palpalis palpalis (Diptera: Glossinidae is widespread in west Africa, and is the main vector of sleeping sickness in Cameroon as well as in the Bas Congo Province of the Democratic Republic of Congo. However, little is known on the structure of its populations. We investigated G. p. palpalis population genetic structure in five sleeping sickness foci (four in Cameroon, one in Democratic Republic of Congo using eight microsatellite DNA markers. Results A strong isolation by distance explains most of the population structure observed in our sampling sites of Cameroon and DRC. The populations here are composed of panmictic subpopulations occupying fairly wide zones with a very strong isolation by distance. Effective population sizes are probably between 20 and 300 individuals and if we assume densities between 120 and 2000 individuals per km2, dispersal distance between reproducing adults and their parents extends between 60 and 300 meters. Conclusions This first investigation of population genetic structure of G. p. palpalis in Central Africa has evidenced random mating subpopulations over fairly large areas and is thus at variance with that found in West African populations of G. p. palpalis. This study brings new information on the isolation by distance at a macrogeographic scale which in turn brings useful information on how to organise regional tsetse control. Future investigations should be directed at temporal sampling to have more accurate measures of demographic parameters in order to help vector control decision.

  20. Genetic structure within and among regional populations of the Eurasian badger (Meles meles) from Denmark and the Netherlands

    DEFF Research Database (Denmark)

    Zande, L. van de; Vliet, M. van de; Pertoldi, C.

    2007-01-01

    The Eurasian badger Meles meles has a wide distribution area ranging from Japan to Ireland. In western Europe badger habitats are severely disturbed by anthropogenic factors, leading to fragmentation into subpopulations and formation of a metapopulation substructuring of once continuous panmictic...... to this structuring of badger populations. In contrast, measures that improve migration and connection to other populations from neighboring countries may have prevented substructuring of the Dutch badger population....... populations. We have examined the genetic structure of Dutch and Danish badger populations on a relatively small scale (within countries) and a larger scale (between countries). The levels of genetic variation of populations were moderate and did not differ significantly among populations (overall HO=0.......30, overall HE=0.34). Considerable genetic differentiation between the Dutch and Danish populations was found (overall FST=0.32, mean pairwise Dutch-Danish FST=0.42), indicating a large-scale substructuring of these western European badger populations. Further analysis showed that the Danish badger population...

  1. Dynamic heterogeneity of DNA methylation and hydroxymethylation in embryonic stem cell populations captured by single-cell 3D high-content analysis

    Energy Technology Data Exchange (ETDEWEB)

    Tajbakhsh, Jian, E-mail: tajbakhshj@cshs.org [Chromatin Biology Laboratory, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Stefanovski, Darko [Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19348 (United States); Tang, George [Chromatin Biology Laboratory, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Wawrowsky, Kolja [Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Liu, Naiyou; Fair, Jeffrey H. [Department of Surgery and UF Health Comprehensive Transplant Center, University of Florida College of Medicine, Gainesville, FL 32608 (United States)

    2015-03-15

    Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a 10-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 3D high-content analysis, an essential tool in single-cell screening. In summary: 1) We did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU/day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17: 0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, global DNA methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC{sup +}/5mC{sup −}, 5hmC{sup +}/5mC{sup +}, and 5hmC{sup −}/5mC{sup +} cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC{sup +}/5mC{sup +} cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably

  2. Dynamic heterogeneity of DNA methylation and hydroxymethylation in embryonic stem cell populations captured by single-cell 3D high-content analysis

    International Nuclear Information System (INIS)

    Tajbakhsh, Jian; Stefanovski, Darko; Tang, George; Wawrowsky, Kolja; Liu, Naiyou; Fair, Jeffrey H.

    2015-01-01

    Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a 10-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 3D high-content analysis, an essential tool in single-cell screening. In summary: 1) We did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU/day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17: 0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, global DNA methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC + /5mC − , 5hmC + /5mC + , and 5hmC − /5mC + cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC + /5mC + cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably delineating chromatin domains in

  3. Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish.

    Science.gov (United States)

    Coleman, R A; Gauffre, B; Pavlova, A; Beheregaray, L B; Kearns, J; Lyon, J; Sasaki, M; Leblois, R; Sgro, C; Sunnucks, P

    2018-01-12

    Habitat loss and fragmentation often result in small, isolated populations vulnerable to environmental disturbance and loss of genetic diversity. Low genetic diversity can increase extinction risk of small populations by elevating inbreeding and inbreeding depression, and reducing adaptive potential. Due to their linear nature and extensive use by humans, freshwater ecosystems are especially vulnerable to habitat loss and fragmentation. Although the effects of fragmentation on genetic structure have been extensively studied in migratory fishes, they are less understood in low-mobility species. We estimated impacts of instream barriers on genetic structure and diversity of the low-mobility river blackfish (Gadopsis marmoratus) within five streams separated by weirs or dams constructed 45-120 years ago. We found evidence of small-scale (barriers, as expected for a fish with low mobility. Genetic diversity was lower above barriers in small streams only, regardless of barrier age. In particular, one isolated population showed evidence of a recent bottleneck and inbreeding. Differentiation above and below the barrier (F ST  = 0.13) was greatest in this stream, but in other streams did not differ from background levels. Spatially explicit simulations suggest that short-term barrier effects would not be detected with our data set unless effective population sizes were very small (barriers is reduced and requires more genetic markers compared to panmictic populations. We also demonstrate the importance of accounting for natural population genetic structure in fragmentation studies.

  4. Cytochrome b gene reveals panmixia among Japanese Threadfin Bream, Nemipterus japonicus (Bloch, 1791) populations along the coasts of Peninsular Malaysia and provides evidence of a cryptic species.

    Science.gov (United States)

    Lim, Hong-Chiun; Ahmad, Abu Talib; Nuruddin, Ahmad Adnan; Mohd Nor, Siti Azizah

    2016-01-01

    We evaluated genetic differentiation among ten presumed Japanese threadfin bream, Nemipterus japonicus populations along the coast of Peninsular Malaysia based on the partial sequence of the mitochondrial cytochrome b gene (982 bp). Genetic divergences (Kimura-2 parameter) ranged from 0.5% to 0.8% among nine of the ten populations while these nine populations were 4.4% to 4.6% diverged from the Kuala Besar population located at the Northeast coast. The constructed Neighbour Joining (NJ) phylogenetic trees based on haplotypes showed the Kuala Besar population forming an isolated cluster. The Analysis of Molecular Variance (AMOVA) of the ten populations a priori assigned into four regions, revealed that most of the variation occurred within population with a fairly low but significant level of regional differentiation (FST = 0.07, p 0.05 and FCT = 0.07, p population. p Value after Bonferroni correction revealed that only pairwise FST values involving the Kuala Besar population with the other nine populations were significant. Thus, this study revealed that the N. japonicus populations off Peninsular Malaysia were panmictic. However, the Kuala Besar population, although morphologically identical was composed of a genetically discrete taxon from the rest. These findings are important contributions in formulating sustainable fishery management policies for this important fishery in Peninsular Malaysia.

  5. Comparison on genomic predictions using GBLUP models and two single-step blending methods with different relationship matrices in the Nordic Holstein population

    DEFF Research Database (Denmark)

    Gao, Hongding; Christensen, Ole Fredslund; Madsen, Per

    2012-01-01

    traits in the Nordic Holstein population. Methods The data consisted of de-regressed proofs (DRP) for 5 214 genotyped and 9 374 non-genotyped bulls. The bulls were divided into a training and a validation population by birth date, October 1, 2001. Five approaches for genomic prediction were used: 1...

  6. Population Pharmacokinetic Characteristics of Amikacin in Suspected Cases of Neonatal Sepsis in a Low-Resource African Setting: A Prospective Nonrandomized Single-Site Study

    Directory of Open Access Journals (Sweden)

    Seth K. Amponsah, PhD

    2017-01-01

    Conclusions: The V and half-life of amikacin in this cohort varied from that reported in non-African populations, and the high trough and low peak amikacin concentrations in both term and preterm neonates suggest strategies to optimize amikacin dosing are required in this population.

  7. Single nucleotide polymorphisms of ADH1B, ADH1C and ALDH2 genes and esophageal cancer: A population-based case-control study in China

    NARCIS (Netherlands)

    Wu, M.; Chang, S.C.; Kampman, E.; Yang, J.; Wang, X.S.; Gu, X.P.; Han, R.Q.; Liu, A.M.; Wallar, G.; Zhou, J.Y.; Kok, F.J.; Zhao, J.K.; Zhang, Z.F.

    2013-01-01

    Alcohol drinking is a major risk factor for esophageal cancer (EC) and the metabolism of ethanol has been suggested to play an important role in esophageal carcinogenesis. Epidemiologic studies, including genomewide association studies (GWAS), have identified single nucleotide polymorphisms (SNPs)

  8. The population structure of Glossina palpalis gambiensis from island and continental locations in Coastal Guinea.

    Directory of Open Access Journals (Sweden)

    Philippe Solano

    Full Text Available We undertook a population genetics analysis of the tsetse fly Glossina palpalis gambiensis, a major vector of sleeping sickness in West Africa, using microsatellite and mitochondrial DNA markers. Our aims were to estimate effective population size and the degree of isolation between coastal sites on the mainland of Guinea and Loos Islands. The sampling locations encompassed Dubréka, the area with the highest Human African Trypanosomosis (HAT prevalence in West Africa, mangrove and savannah sites on the mainland, and two islands, Fotoba and Kassa, within the Loos archipelago. These data are discussed with respect to the feasibility and sustainability of control strategies in those sites currently experiencing, or at risk of, sleeping sickness.We found very low migration rates between sites except between those sampled around the Dubréka area that seems to contain a widely dispersed and panmictic population. In the Kassa island samples, various effective population size estimates all converged on surprisingly small values (10population sizes suggest high levels of inbreeding in tsetse flies within the island samples in marked contrast to the large diffuse deme in Dubréka zones. We discuss how these genetic results suggest that different tsetse control strategies should be applied on the mainland and islands.

  9. Population genetic analysis and trichothecene profiling of Fusarium graminearum from wheat in Uruguay.

    Science.gov (United States)

    Pan, D; Mionetto, A; Calero, N; Reynoso, M M; Torres, A; Bettucci, L

    2016-03-11

    Fusarium graminearum sensu stricto (F. graminearum s.s.) is the major causal agent of Fusarium head blight of wheat worldwide, and contaminates grains with trichothecene mycotoxins that cause serious threats to food safety and animal health. An important aspect of managing this pathogen and reducing mycotoxin contamination of wheat is knowledge regarding its population genetics. Therefore, isolates of F. graminearum s.s. from the major wheat-growing region of Uruguay were analyzed by amplified fragment length polymorphism assays, PCR genotyping, and chemical analysis of trichothecene production. Of the 102 isolates identified as having the 15-ADON genotype via PCR genotyping, all were DON producers, but only 41 strains were also 15-ADON producers, as determined by chemical analysis. The populations were genotypically diverse but genetically similar, with significant genetic exchange occurring between them. Analysis of molecular variance indicated that most of the genetic variability resulted from differences between isolates within populations. Multilocus linkage disequilibrium analysis suggested that the isolates had a panmictic population genetic structure and that there is significant recombination occurs in F. graminearum s.s. In conclusion, tour findings provide the first detailed description of the genetic structure and trichothecene production of populations of F. graminearum s.s. from Uruguay, and expands our understanding of the agroecology of F. graminearum and of the correlation between genotypes and trichothecene chemotypes.

  10. WNT3A gene polymorphisms are associated with bone mineral density variation in postmenopausal mestizo women of an urban Mexican population: findings of a pathway-based high-density single nucleotide screening

    OpenAIRE

    Velázquez-Cruz, Rafael; García-Ortiz, Humberto; Castillejos-López, Manuel; Quiterio, Manuel; Valdés-Flores, Margarita; Orozco, Lorena; Villarreal-Molina, Teresa; Salmerón, Jorge

    2014-01-01

    Osteoporosis (OP) is a common skeletal disorder characterized by low bone mineral density (BMD) and is a common health problem in Mexico. To date, few genes affecting BMD variation in the Mexican population have been identified. The aim of this study was to investigate the association of single nucleotide polymorphisms (SNPs) located in genes of the Wnt pathway with BMD variation at various skeletal sites in a cohort of postmenopausal Mexican women. A total of 121 SNPs in or near 15 Wnt signa...

  11. The allele frequency of two single nucleotide polymorphisms in the von Hippel-Lindau (VHL tumor suppressor gene in the Taiwanese population

    Directory of Open Access Journals (Sweden)

    Wen-Chung Wang

    2011-10-01

    Conclusion: We found that the G allele frequency at these two loci in the Taiwanese population is much lower than that in people from Western countries. This phenomenon may be attributed to ethnic effects.

  12. Combination of Single Nucleotide Polymorphism and Variable-Number Tandem Repeats for Genotyping a Homogenous Population of Mycobacterium tuberculosis Beijing Strains in China

    OpenAIRE

    Luo, Tao; Yang, Chongguang; Gagneux, Sebastien; Gicquel, Brigitte; Mei, Jian; Gao, Qian

    2012-01-01

    The standard 15- and 24-locus variable-number tandem repeat (VNTR) genotyping methods have demonstrated adequate discriminatory power and a small homoplasy effect for tracing tuberculosis (TB) transmission and predicting Mycobacterium tuberculosis lineages in European and North American countries. However, its validity for the definition of transmission in homogenous M. tuberculosis populations in settings with high TB burdens has been questioned. Here, we genotyped a population-based collect...

  13. Genetic Distance and Genetic Identity between Hindu and Muslim populations of Barak Valley for ABO and Rh genes

    Directory of Open Access Journals (Sweden)

    Supriyo CHAKRABORTY

    2010-09-01

    Full Text Available A genetic study was carried out in two endogamous populations namely Hindus and Muslims in the Barak Valley Zone of Assam in India. Nei�s genetic distance and genetic identity between two populations were calculated on the basis of estimated allele frequencies of ABO and Rh blood group genes. The genetic distance between Hindus and Muslims was 0.12% for ABO gene and 0.10% for Rh gene. The genetic identity between two populations was estimated as 99.88% for ABO gene and 99.90% for Rh gene suggesting very high genetic similarity between these two populations. Observed heterozygosity estimate was higher in Hindus (0.5598 for ABO gene and 0.2822 for Rh gene than Muslims (0.5346 for ABO gene and 0.2408 for Rh gene indicating lesser inbreeding in Hindus than Muslims. Fixation index was lower in Hindus (16.02% for ABO gene and 43.56% for Rh gene than Muslims (19.80% for ABO gene and 51.84% for Rh gene. Panmictic index was higher in Hindus than Muslims for both the genes. Fixation and panmictic indices revealed that during evolutionary process the Hindus maintained more outbreeding feature than the Muslims in the valley. In this study, the concepts of genetic load of a population and genotype fitness were extended to alleles to estimate the magnitude of allele genetic load (GL and allele fitness for 3 alleles in ABO gene and for 2 alleles in Rh gene in two populations. The genetic load for O, A and B alleles were lower in Hindus than Muslims. Similar results for genetic load were found for the alleles of Rh gene in the comparison of two populations. The fitness estimates of O, A and B alleles for ABO gene and D and d alleles for Rh gene were higher in Hindus than Muslims. A population with low allele genetic load (GL and high allele fitness (AF might have greater survival advantage in nature in the absence of heterozygote advantage and higher adaptive value of the allele with increased frequency.

  14. Investigation of population structure in Gulf of Mexico Seepiophila jonesi (Polychaeta, Siboglinidae using cross-amplified microsatellite loci

    Directory of Open Access Journals (Sweden)

    Chunya Huang

    2016-08-01

    presence of significant gene flow via larval dispersal in mixed oceanic currents. Discussion The ability to develop “universal” microsatellites reduces the costs associated with these analyses and allows researchers to track and investigate a wider array of taxa, which is particularly useful for organisms living at inaccessible locations such as the deep sea. Our study highlights that non-species specific microsatellites can be amplified across large evolutionary distances and still yield similar findings as species-specific loci. Further, these results show that S. jonesi collected from various localities in the GoM represents a single panmictic population, suggesting that dispersal of lecithotrophic larvae by deep sea currents is sufficient to homogenize populations. These data are consistent with the high levels of gene flow seen in Escarpia spp., which advocates that differences in microhabitats of seep localities lead to variation in biogeography of separate species.

  15. Characterization of Distinct Astrocytic Populations Responding with Different Volume Changes to Oxygen-Glucose Deprivation: 3d Confocal Morphometry And Single-Cell Gene Expression Profilig

    Czech Academy of Sciences Publication Activity Database

    Benešová, Jana; Rusňáková, Vendula; Honsa, Pavel; Pivoňková, Helena; Kubista, Mikael; Anděrová, Miroslava

    2011-01-01

    Roč. 59, Supplement 1 (2011), S126-S126 ISSN 0894-1491. [European meeting on Glial Cells in Health and Disease /10./. 13.09.2011-13.09.2011, Prague] Institutional research plan: CEZ:AV0Z50390703; CEZ:AV0Z50520701 Keywords : cell volume regulation * single-cell PCR profiling * ischemia Subject RIV: FH - Neurology

  16. Single Nucleotide Polymorphism rs10919543 in FCGR2A/FCGR3A Region Confers Susceptibility to Takayasu Arteritis in Chinese Population

    Directory of Open Access Journals (Sweden)

    Fang Qin

    2016-01-01

    Conclusions: Our findings revealed unique genetic pattern in Chinese TA patients that may be partly responsible for the higher risk of TA in this population. FCGR2A/FCGR3A-related immune disorder might contribute to the etiology of TA.

  17. Correlation analysis between single nucleotide polymorphisms of pulmonary surfactant protein A gene and pulmonary tuberculosis in the Han population in China

    Directory of Open Access Journals (Sweden)

    Hong-yi Yang

    2014-09-01

    Conclusions: SNP in SP-A is associated with PTB in the Han population in China. The G allele at aa91, T allele at aa140, and haplotype 6A11–1A8 are risk factors for PTB, but haplotype CGAAC–1A0 and 6A4–1A12 are protective factors for PTB.

  18. Population genetic structure in farm and feral American mink (Neovison vison) inferred from RAD sequencing-generated single nucleotide polymorphisms

    DEFF Research Database (Denmark)

    Thirstrup, Janne Pia; Ruiz-Gonzalez, Aritz; Pujolar, José Martin

    2015-01-01

    Feral American mink populations (Neovison vison), derived from mink farms, are widespread in Europe. In this study we investigated genetic diversity and genetic differentiation between feral and farm mink using a panel of genetic markers (194 SNP) generated from RAD sequencing data. Sampling incl...

  19. Eligibility of sacubitril-valsartan in a real-world heart failure population: a community-based single-centre study.

    Science.gov (United States)

    Norberg, Helena; Bergdahl, Ellinor; Lindmark, Krister

    2018-04-01

    This study aims to investigate the eligibility of the Prospective Comparison of Angiotensin Receptor-Neprilysin Inhibitor (ARNI) with ACE inhibitor to Determine Impact on Global Mortality and Morbidity in Heart Failure (PARADIGM-HF) study to a real-world heart failure population. Medical records of all heart failure patients living within the catchment area of Umeå University Hospital were reviewed. This district consists of around 150 000 people. Out of 2029 patients with a diagnosis of heart failure, 1924 (95%) had at least one echocardiography performed, and 401 patients had an ejection fraction of ≤35% at their latest examination. The major PARADIGM-HF criteria were applied, and 95 patients fulfilled all enrolment criteria and thus were eligible for sacubitril-valsartan. This corresponds to 5% of the overall heart failure population and 24% of the population with ejection fraction ≤ 35%. The eligible patients were significantly older (73.2 ± 10.3 vs. 63.8 ± 11.5 years), had higher blood pressure (128 ± 17 vs. 122 ± 15 mmHg), had higher heart rate (77 ± 17 vs. 72 ± 12 b.p.m.), and had more atrial fibrillation (51.6% vs. 36.2%) than did the PARADIGM-HF population. Only 24% of our real-world heart failure and reduced ejection fraction population was eligible for sacubitril-valsartan, and the real-world heart failure and reduced ejection fraction patients were significantly older than the PARADIGM-HF population. The lack of data on a majority of the patients that we see in clinical practice is a real problem, and we are limited to extrapolation of results on a slightly different population. This is difficult to address, but perhaps registry-based randomized clinical trials will help to solve this issue. © 2018 The Authors. ESC Heart Failure published by John Wiley & Sons Ltd on behalf of the European Society of Cardiology.

  20. Spectroscopy of low-lying single-particle states in $^{81}$Zn populated in the $^{80}$Zn(d,p) reaction

    CERN Multimedia

    The aim of this proposal is the study of single-particle states of $^{81}$Zn via the $^{80}$Zn(d,p) reaction in inverse kinematics. $^{81}$Zn will be produced by means of a laser-ionized, 5.5 MeV/u HIE-Isolde $^{80}$Zn beam impinging on a deuterated-polyethylene target. The protons and $\\gamma$-rays emitted in the reaction will be studied using the Miniball + T-REX setup. This experiment will constitute the first spectroscopic study of $^{81}$Zn, which is critically important to determine the energy and ordering of neutron single-particle orbits above the N=50 gap and the properties of $^{78}$Ni.

  1. Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations

    OpenAIRE

    Liang, Jingjing; Le, Thu H.; Edwards, Digna R. Velez; Tayo, Bamidele O.; Gaulton, Kyle J.; Smith, Jennifer A.; Lu, Yingchang; Jensen, Richard A.; Chen, Guanjie; Yanek, Lisa R.; Schwander, Karen; Tajuddin, Salman M.; Sofer, Tamar; Kim, Wonji; Kayima, James

    2017-01-01

    © 2017 Public Library of Science. All Rights Reserved. Hypertension is a leading cause of global disease, mortality, and disability. While individuals of African descent suffer a disproportionate burden of hypertension and its complications, they have been underrepresented in genetic studies. To identify novel susceptibility loci for blood pressure and hypertension in people of African ancestry, we performed both single and multiple-trait genome-wide association analyses. We analyzed 21 genom...

  2. Relationship between single and multiple perpetrator rape perpetration in South Africa: A comparison of risk factors in a population-based sample.

    Science.gov (United States)

    R, Jewkes; Y, Sikweyiya; K, Dunkle; R, Morrell

    2015-07-07

    Studies of rape of women seldom distinguish between men's participation in acts of single and multiple perpetrator rape. Multiple perpetrator rape (MPR) occurs globally with serious consequences for women. In South Africa it is a cultural practice with defined circumstances in which it commonly occurs. Prevention requires an understanding of whether it is a context specific intensification of single perpetrator rape, or a distinctly different practice of different men. This paper aims to address this question. We conducted a cross-sectional household study with a multi-stage, randomly selected sample of 1686 men aged 18-49 who completed a questionnaire administered using an Audio-enhanced Personal Digital Assistant. We attempted to fit an ordered logistic regression model for factors associated with rape perpetration. 27.6 % of men had raped and 8.8 % had perpetrated multiple perpetrator rape (MPR). Thus 31.9 % of men who had ever raped had done so with other perpetrators. An ordered regression model was fitted, showing that the same associated factors, albeit at higher prevalence, are associated with SPR and MPR. Multiple perpetrator rape appears as an intensified form of single perpetrator rape, rather than a different form of rape. Prevention approaches need to be mainstreamed among young men.

  3. Identification of Distinct Breast Cancer Stem Cell Populations Based on Single-Cell Analyses of Functionally Enriched Stem and Progenitor Pools

    Directory of Open Access Journals (Sweden)

    Nina Akrap

    2016-01-01

    Full Text Available The identification of breast cancer cell subpopulations featuring truly malignant stem cell qualities is a challenge due to the complexity of the disease and lack of general markers. By combining extensive single-cell gene expression profiling with three functional strategies for cancer stem cell enrichment including anchorage-independent culture, hypoxia, and analyses of low-proliferative, label-retaining cells derived from mammospheres, we identified distinct stem cell clusters in breast cancer. Estrogen receptor (ERα+ tumors featured a clear hierarchical organization with switch-like and gradual transitions between different clusters, illustrating how breast cancer cells transfer between discrete differentiation states in a sequential manner. ERα− breast cancer showed less prominent clustering but shared a quiescent cancer stem cell pool with ERα+ cancer. The cellular organization model was supported by single-cell data from primary tumors. The findings allow us to understand the organization of breast cancers at the single-cell level, thereby permitting better identification and targeting of cancer stem cells.

  4. Introgression of lineage c honey bees into black honey bee populations: a genome-wide estimation using single nucleotide polymorphisms (SNPS)

    OpenAIRE

    Henriques, Dora; Chavez-Galarza, Julio; Kryger, Per; Johnston, J. Spencer; De la Rúa, Pilar; Rufino, José; Dall'Olio, Raffaele; Garnery, Lionel; Pinto, M. Alice

    2012-01-01

    The black honey bee, Apis mellifera mellifera L., is probably the honey bee subspecies more threatened by introgression from foreign subspecies, specially lineage C A. m. carnica and A. m. ligustica. In fact, in some areas of its distributional range, intensive beekeeping with foreign subspecies has driven A. m. mellifera populations to nearly replacement. While massive and repeated introductions may lead to loss of native genetic patrimony, a low level of gene flow can also be detrimental be...

  5. The effect of the dispersal kernel on isolation-by-distance in a continuous population

    Directory of Open Access Journals (Sweden)

    Tara N. Furstenau

    2016-03-01

    Full Text Available Under models of isolation-by-distance, population structure is determined by the probability of identity-by-descent between pairs of genes according to the geographic distance between them. Well established analytical results indicate that the relationship between geographical and genetic distance depends mostly on the neighborhood size of the population which represents a standardized measure of gene flow. To test this prediction, we model local dispersal of haploid individuals on a two-dimensional landscape using seven dispersal kernels: Rayleigh, exponential, half-normal, triangular, gamma, Lomax and Pareto. When neighborhood size is held constant, the distributions produce similar patterns of isolation-by-distance, confirming predictions. Considering this, we propose that the triangular distribution is the appropriate null distribution for isolation-by-distance studies. Under the triangular distribution, dispersal is uniform over the neighborhood area which suggests that the common description of neighborhood size as a measure of an effective, local panmictic population is valid for popular families of dispersal distributions. We further show how to draw random variables from the triangular distribution efficiently and argue that it should be utilized in other studies in which computational efficiency is important.

  6. Inferences about the Global Population Structures of Cryptosporidium parvum and Cryptosporidium hominis▿ †

    Science.gov (United States)

    Tanrıverdi, Sultan; Grinberg, Alex; Chalmers, Rachel M.; Hunter, Paul R.; Petrovic, Zorana; Akiyoshi, Donna E.; London, Eric; Zhang, Linghui; Tzipori, Saul; Tumwine, James K.; Widmer, Giovanni

    2008-01-01

    Cryptosporidium parvum and Cryptosporidium hominis are two related species of apicomplexan protozoa responsible for the majority of human cases of cryptosporidiosis. In spite of their considerable public health impact, little is known about the population structures of these species. In this study, a battery of C. parvum and C. hominis isolates from seven countries was genotyped using a nine-locus DNA subtyping scheme. To assess the existence of geographical partitions, the multilocus genotype data were mined using a cluster analysis based on the nearest-neighbor principle. Within each country, the population genetic structures were explored by combining diversity statistical tests, linkage disequilibrium, and eBURST analysis. For both parasite species, a quasi-complete phylogenetic segregation was observed among the countries. Cluster analysis accurately identified recently introduced isolates. Rather than conforming to a strict paradigm of either a clonal or a panmictic population structure, data are consistent with a flexible reproductive strategy characterized by the cooccurrence of both propagation patterns. The relative contribution of each pattern appears to vary between the regions, perhaps dependent on the prevailing ecological determinants of transmission. PMID:18836013

  7. Immediate Implant Placement and Loading of Single Implants in the Esthetic Zone: Clinical Outcome and Esthetic Evaluation in a Japanese Population.

    Science.gov (United States)

    Takeshita, Kenji; Vandeweghe, Stefan; Vervack, Valentin; Sumi, Takashi; De Bruyn, Hugo; Jimbo, Ryo

    2015-01-01

    This study evaluated the clinical outcomes of immediately loaded maxillary anterior single implants placed in fresh extraction sockets. A patient cohort that was treated 1.5 years earlier was recalled, and 18 patients (6 men, 12 women) with 21 implants were included. Clinical photographs and periapical radiographs were taken at follow-up and baseline to determine the bone loss and change in esthetics. No marginal bone loss was detected at follow-up (mean bone level ± standard deviation = 0.32 ± 0.82 mm). Immediate implant placement and loading resulted in predictable clinical and esthetic outcomes, with soft and hard tissue levels remaining stable over time.

  8. Mitochondrial DNA variation in the East China Sea and Yellow Sea populations of swimming crab Ovalipes punctatus.

    Science.gov (United States)

    Zheng, Wei; Han, Zhiqiang; Chen, Guobao; Yu, Cungen; Gao, Tianxiang

    2015-08-01

    Swimming crab Ovalipes punctatus is a commercially important species in the East China Sea and Yellow Sea, but there is limited knowledge of its genetic population structure. The population genetic structure of O. punctatus in East China Sea and Yellow Sea was examined with a 658-bp segment of the mtDNA COI gene. A total of 60 individuals were collected from five locations and 48 haplotypes were obtained. Mean haplotype diversity and nucleotide diversity for the five populations were 0.9876 ± 0.0068 and 0.0074 ± 0.0041, respectively. Analysis of molecular variance (AMOVA) detected no significant differences at all hierarchical levels, and all FST values were non-significant, indicating that no significant population genetic structure exists in the East China Sea and Yellow Sea. These results supported the null hypothesis that O. punctatus within the East China Sea and Yellow Sea constitutes a panmictic mtDNA gene pool. Neutrality tests and mismatch distribution supported population expansion in this species, indicating that climate change could play an important role in affecting the demographic history of marine species. Strong dispersal capacity of larvae and adults, and ocean currents in the studied area could be the reasons for genetic homogeneity in this species in the East China Sea and Yellow Sea. Another explanation for the lack of phylogeographic structure in O. punctatus might reflect a recent range expansion after the last glacial maximum and insufficient time to attain migration-drift equilibrium.

  9. Comparison between Single-Dose Esomeprazole- and Pantoprazole-Based Triple Therapy on the Effectiveness for Helicobacter pylori Eradication in Taiwanese Population

    Directory of Open Access Journals (Sweden)

    Hsiang-Yao Shih

    2012-01-01

    Full Text Available Background and Study Aims. To compare the effectiveness of two regimens, single-dose esomeprazole- and pantoprazole-based triple therapy, for Helicobacter pylori (H. pylori eradication. Patients and Methods. A total of 453 patients were enrolled for H. pylori eradication. They were randomly assigned to either EAC group (Esomeprazole 40 mg once daily, Amoxicillin 1 g twice daily, Clarithromycin 500 mg twice daily for 7 days or PAC group (Pantoprazole 40 mg twice daily, Amoxicillin 1 g twice daily, Clarithromycin 500 mg twice daily for 7 days. Follow-up endoscopy or urea breath test was scheduled 12–16 weeks after the eradication to evaluate the therapeutic response. Results. Higher eradication rate in EAC group than PAC group was shown by intention-to-treat analysis (EAC 72% versus PAC 55%, P<0.05 and per-protocol analysis (EAC 91% versus PAC 72%, P<0.05. The incidence of adverse effects (EAC 19% versus PAC 17%, P=0.712 and the compliance (EAC 87% versus PAC 91%, P=0.083 were comparable between these 2 groups. Conclusions. Single-dose esomeprazole-based triple therapy is effective for H. pylori eradication.

  10. Association between Interleukin-1 Gene Single Nucleotide Polymorphisms and Ischemic Stroke Classified by TOAST Criteria in the Han Population of Northern China

    Directory of Open Access Journals (Sweden)

    Zheng Zhang

    2013-01-01

    Full Text Available Increasing evidence suggests that IL-1β (C-511T and IL-1α (C-889T genes polymorphisms are associated with the susceptibility to cardiocerebral vascular disease. In this paper, we investigated the relationships between these polymorphisms and the risk of ischemic stroke (IS classified by TOAST criteria in the north Chinese Han population. 440 cases of IS and 486 age- and gender-matched controls of Chinese Han population were enrolled. Association study showed that the TT genotype and T allele of IL-1α-889 C/T were significantly associated with IS of a large artery atherosclerosis (LAA (TT: OR = 2.01, 95% CI = 1.34–3.0, and P<0.001; T: OR = 1.44, 95% CI = 1.18–1.78, and P=0.001. However, there was no significant difference in the distribution of IL-1α-889 C/T genotypes and allele frequencies between the two subgroups (small-artery occlusion (SVD and cardioembolism (CE of IS and control groups. No significant association was also found between the IL-1β-511 TT genotype and T allele (TT: OR = 0.79, 95% CI = 0.56–1.11, and P=0.175; T: OR = 0.83, 95% CI = 0.68–1.01, and P=0.066 and IS as well as subgroups of CE and SVD. Our results implicated that IL-1α-889 C/T gene polymorphism might be associated with the susceptibility to IS, especially to IS with LAA, in a north Chinese Han population.

  11. Population fragmentation leads to spatial and temporal genetic structure in the endangered Spanish imperial eagle.

    Science.gov (United States)

    Martínez-Cruz, B; Godoy, J A; Negro, J J

    2007-02-01

    The fragmentation of a population may have important consequences for population genetic diversity and structure due to the effects of genetic drift and reduced gene flow. We studied the genetic consequences of the fragmentation of the Spanish imperial eagle (Aquila adalberti) population into small patches through a temporal analysis. Thirty-four museum individuals representing the population predating the fragmentation were analysed for a 345-bp segment of the mitochondrial control region and a set of 10 nuclear microsatellite loci. Data from a previous study on the current population (N = 79) were re-analysed for this subset of 10 microsatellite markers and results compared to those obtained from the historical sample. Three shared mitochondrial haplotypes were found in both populations, although fluctuations in haplotype frequencies and the occurrence of a fourth haplotype in the historical population resulted in lower current levels of haplotype and nucleotide diversity. However, microsatellite markers revealed undiminished levels of nuclear diversity. No evidence for genetic structure was observed for the historical Spanish imperial eagle population, suggesting that the current pattern of structure is the direct consequence of population fragmentation. Temporal fluctuations in mitochondrial and microsatellite allelic frequencies were found between the historical and the current population as well as for each pairwise comparison between historical and current Centro and historical and current Parque Nacional de Doñana nuclei. Our results indicate an ancestral panmictic situation for the species that management policies should aim to restore. A historical analysis like the one taken here provides the baseline upon which the relative role of recent drift in shaping current genetic patterns in endangered species can be evaluated and this knowledge is used to guide conservation actions.

  12. A non-synonymous single-nucleotide polymorphism in the gene encoding Toll-like Receptor 3 (TLR3) is associated with sero-negative Rheumatoid Arthritis (RA) in a Danish population

    DEFF Research Database (Denmark)

    Laska, Magdalena Janina; Hansen, Bettina; Troldborg, Anne

    2014-01-01

    in a predominantly Caucasian population from Denmark using a case-control approach. FINDINGS: DNA samples (3 university hospital outpatient clinics) were obtained from patients with RA (n = 704) and healthy controls (n = 639) in a Danish population. TLR single nucleotide polymorphisms (SNPs) were selected based...... in the TLR3 locus may be implicated in the pathogenesis of sero-negative RA. Since this TLR3 SNP has previously been associated with systemic lupus erythematous (SLE), the present findings support the notion that TLR3 genetic variants may represent a common risk factor in different chronic inflammatory......BACKGROUND: It has been suggested that polymorphisms in Toll-like Receptors (TLRs) are associated with Rheumatoid Arthritis (RA), but the implicated alleles have differed between studies. The aim of this investigation was to explore whether polymorphisms of TLR genes are associated with RA...

  13. Single live cell TGF-β signalling imaging: breast cancer cell motility and migration is driven by sub-populations of cells with dynamic TGF-β-Smad3 activity.

    Science.gov (United States)

    Luwor, Rodney B; Hakmana, Dulani; Iaria, Josephine; Nheu, Thao V; Simpson, Richard J; Zhu, Hong-Jian

    2015-02-22

    Metastasis is a process where only a small subset of cells is capable of successfully migrating to and propagating at secondary sites. TGF-β signalling is widely known for its role in cancer metastasis and is associated with cell migration in whole cell populations. We extend these findings by investigating the role of TGF-β signalling in promoting migration and motility by imaging the signalling activity in live, individual MDA-MB-231 cancer cells utilizing a novel Smad3 Td-Tomato reporter adenovirus. Here we find that not all MDA-MB-231 cancer cells have similar TGF-β mediated Smad3 transcription activity and display at least two distinct migratory populations. Importantly, Smad3 activity was significantly higher within migratory cells compared to non-migrated cells in wound healing and transwell assays. Furthermore, time-lapse experiments showed that MDA-MB-231 cells displaying Smad3 activity moved faster and a greater distance compared to cells not displaying Smad3 reporter activity. Interestingly, despite being more motile than cells with undetectable levels of Smad3 activity, high Smad3 activity was detrimental to cell motility compared to low and medium level of Smad3 activity. We have developed a method enabling real-time visualization of TGF-β signalling in single live cells. Breast cancer cell motility and migration is driven by sub-populations of cells with dynamic TGF-β-Smad3 activity. Those sub-populations may be responsible for tumor invasion and metastasis.

  14. Clozapine usage increases the incidence of pneumonia compared with risperidone and the general population: a retrospective comparison of clozapine, risperidone, and the general population in a single hospital over 25 months.

    Science.gov (United States)

    Stoecker, Zachary R; George, Wales T; O'Brien, Jeffrey B; Jancik, Jon; Colon, Eduardo; Rasimas, Joseph J

    2017-05-01

    The aim of this study was to determine whether the incidence of pneumonia in patients taking clozapine was more frequent compared with those taking risperidone or no atypical antipsychotics at all before admission to a tertiary care medical center. This was a retrospective, case-matched study of 465 general medicine patients over a 25 month period from 1 July 2010 to 31 July 2012. Detailed electronic medical records were analyzed to explore the association between the use of two atypical antipsychotics and incidence of pneumonia. Of the 155 patients in the clozapine group, 54 (34.8%) had documented pneumonia compared with 22 (14.2%) in the risperidone group and 18 (11.6%) in the general population group. Clozapine, when compared with the untreated general population, was associated with an increased risk of pneumonia (odds ratio=4.07; 95% confidence interval=2.25-7.36). There was, however, no significant increase in the risk of pneumonia associated with the use of risperidone (odds ratio=1.26; 95% confidence interval=0.65-2.45). Clozapine use is associated with increased risk of pneumonia that may be related to immunologic factors or side effects of sedation and drooling that make aspiration more likely, although causative mechanisms require further investigation. These findings suggest that providers should use added caution in choosing candidates for clozapine therapy.

  15. The influence of habitat structure on genetic differentiation in red fox populations in north-eastern Poland.

    Science.gov (United States)

    Mullins, Jacinta; McDevitt, Allan D; Kowalczyk, Rafał; Ruczyńska, Iwona; Górny, Marcin; Wójcik, Jan M

    2014-01-01

    The red fox ( Vulpes vulpes ) has the widest global distribution among terrestrial carnivore species, occupying most of the Northern Hemisphere in its native range. Because it carries diseases that can be transmitted to humans and domestic animals, it is important to gather information about their movements and dispersal in their natural habitat but it is difficult to do so at a broad scale with trapping and telemetry. In this study, we have described the genetic diversity and structure of red fox populations in six areas of north-eastern Poland, based on samples collected from 2002-2003. We tested 22 microsatellite loci isolated from the dog and the red fox genome to select a panel of nine polymorphic loci suitable for this study. Genetic differentiation between the six studied populations was low to moderate and analysis in Structure revealed a panmictic population in the region. Spatial autocorrelation among all individuals showed a pattern of decreasing relatedness with increasing distance and this was not significantly negative until 93 km, indicating a pattern of isolation-by-distance over a large area. However, there was no correlation between genetic distance and either Euclidean distance or least-cost path distance at the population level. There was a significant relationship between genetic distance and the proportion of large forests and water along the Euclidean distances. These types of habitats may influence dispersal paths taken by red foxes, which is useful information in terms of wildlife disease management.

  16. Breast cancer detection using single-reading of breast tomosynthesis (3D-mammography) compared to double-reading of 2D-mammography: Evidence from a population-based trial.

    Science.gov (United States)

    Houssami, Nehmat; Bernardi, Daniela; Pellegrini, Marco; Valentini, Marvi; Fantò, Carmine; Ostillio, Livio; Tuttobene, Paolina; Luparia, Andrea; Macaskill, Petra

    2017-04-01

    Most population breast cancer (BC) screening programs use double-reading of 2D-mammography. We recently reported the screening with tomosynthesis or standard mammography-2 (STORM-2) trial, showing that double-read tomosynthesis (pseudo-3D-mammography) detected more BC than double-read 2D-mammography. In this study, we compare screen-detection measures for single-reading of 3D-mammography with those for double-reading of 2D-mammography, to inform screening practice. This is a secondary analysis based on STORM-2 which prospectively compared 3D-mammography and 2D-mammography in sequential screen-readings. Asymptomatic women ≥49 years who attended population-based screening (Trento, 2013-2015) were recruited. Participants recalled at any screen-read from parallel double-reading arms underwent further testing and/or biopsy. Single-reading of 3D-mammography, integrated with acquired or synthetized 2D-mammograms, was compared to double-reading of 2D-mammograhy alone for screen-detection measures: number of detected BCs, cancer detection rate (CDR), number and percentage of false-positive recall (FPR). Paired binary data were compared using McNemar's test. Screening detected 90, including 74 invasive, BCs in 85 of 9672 participants. CDRs for single-reading using integrated 2D/3D-mammography (8.2 per 1000 screens; 95% CI 6.5-10.2) or 2D synthetic/3D-mammography (8.4 per 1000 screens; 95% CI: 6.7-10.4) were significantly higher than CDR for double-reading of 2D-mammography (6.3 per 1000 screens; 95% CI: 4.8-8.1), Pmammography (2.60%; 95% CI: 2.29-2.94), or single-read 2D synthetic/3D-mammography (2.76%; 95% CI: 2.45-3.11), were significantly lower than FPR% for double-read 2D-mammography (3.42%; 95% CI: 3.07-3.80), Pmammography (integrated 2D/3D or 2Dsynthetic/3D) detected more BC, and had lower FPR, compared to current practice of double-reading 2D-mammography alone - these findings have implications for population BC screening programs. Copyright © 2017 Elsevier Ltd

  17. A study on single nucleotide polymorphism of exon 7 T/C (locus 593 of platelet-activating factor acetylhydrolase gene in healthy Han population in the Shanghai region

    Directory of Open Access Journals (Sweden)

    Tian-bao XIA

    2012-08-01

    Full Text Available Objective To investigate the distribution of single nucleotide polymorphism (SNP in platelet-activating factor acetylhydrolase (PAF-AH gene exon 7 T/C (locus 593 in healthy Han population in Shanghai region and the features different from other races. Methods The SNP in PAF-AH gene exon 7 T/C (locus 593 was detected and analyzed by PCR and sequencing in 110 healthy Han people from Shanghai areas. The genotype and allele frequency were then calculated and compared with that in other races in combination with review of relevant literature. Results The amplified product of the SNP in PAF-AH gene exon 7 T/C (locus 593 was 240 bp in 110 healthy Han people, of whom 97 were with TT genotype and 13 with TC genotype, but no CC genotype was found. As to the allele frequency distribution, T type allele took the highest position, and C type followed. The genotype frequency of TT and TC was 88.2% and 11.8%, respectively, and they were markedly different from that in German population (0.95%, while not statistically significant different from that in British population (7.67%. Conclusions There exists SNP in PAF-AH gene exon 7 T/C (position 593 in healthy Han people in Shanghai region, with a higher frequency of T→C mutation. The mutational genotype frequency is found to be located at the locus 593 is 11.81%, and it is markedly different from that in German population, but not significantly different from that in British population.

  18. A risk prediction score model for predicting occurrence of post-PCI vasovagal reflex syndrome: a single center study in Chinese population.

    Science.gov (United States)

    Li, Hai-Yan; Guo, Yu-Tao; Tian, Cui; Song, Chao-Qun; Mu, Yang; Li, Yang; Chen, Yun-Dai

    2017-08-01

    The vasovagal reflex syndrome (VVRS) is common in the patients undergoing percutaneous coronary intervention (PCI). However, prediction and prevention of the risk for the VVRS have not been completely fulfilled. This study was conducted to develop a Risk Prediction Score Model to identify the determinants of VVRS in a large Chinese population cohort receiving PCI. From the hospital electronic medical database, we identified 3550 patients who received PCI (78.0% males, mean age 60 years) in Chinese PLA General Hospital from January 1, 2000 to August 30, 2016. The multivariate analysis and receiver operating characteristic (ROC) analysis were performed. The adverse events of VVRS in the patients were significantly increased after PCI procedure than before the operation (all P predicting the incidence of VVRS (all P prediction score model for VVRS. ROC analysis showed that the risk prediction score model was effectively predictive of the incidence of VVRS in patients receiving PCI (c-statistic 0.76, 95% CI: 0.72-0.79, P prediction score is quite efficient in predicting the incidence of VVRS in patients receiving PCI. In which, the following factors may be involved, the femoral puncture site, female gender, hypertension, primary PCI, and over 2 stents implanted in LAD.

  19. Single-photon emission computed tomography myocardial perfusion imaging-assessed stress perfusion defect severity is associated with mortality independent of ethnicity in an Asian population.

    Science.gov (United States)

    Chin, Chee Tang; Gao, Fei; Keng, Felix Y J; Shah, Bimal R; Koh, Angela S; Tan, Ru San; Chua, Terrance S J

    2014-12-01

    Ischemic heart disease is growing by epidemic proportions in Asia. Among patients in Western populations with similar myocardial perfusion imaging (MPI) ischemia severity, ethnicity is independently associated with mortality. We aimed to determine the differential prognostic value of MPI abnormality severity among three major Asian ethnic groups. From 16,921 consecutive patients, we used summed stress score to define increasing abnormal scan severity groups (minimal, mild, moderate, and severe) among Chinese, Indian, and Malay patients. We determined mortality from the national death registry. Using multivariable Cox regression models, we examined the association between ethnicity and mortality. Chinese patients were older than Indians or Malays. Annual all-cause death rates increased with increasing abnormal scan severity in all three ethnicities. After adjustment, ethnicity was not associated with mortality. With Chinese as the reference group, adjusted hazard ratio and 95% CI for Malays and Indians were 1.29 (0.95-1.77) and 1.06 (0.74-1.50) in the minimally abnormal scan group, and 1.20 (0.75-1.91) and 0.82 (0.47-1.45) in the severely abnormal scan group, respectively. Mortality risk is related to the severity of scan abnormality and is independent of ethnicity in Asians. Our findings emphasize the continued utility of MPI in guiding risk stratification in Asia.

  20. A single FTO gene variant rs9939609 is associated with body weight evolution in a multiethnic extremely obese population that underwent bariatric surgery.

    Science.gov (United States)

    Rodrigues, Gisele K; Resende, Cristina M M; Durso, Danielle F; Rodrigues, Lorena A A; Silva, José Luiz P; Reis, Rodrigo C; Pereira, Solange S; Ferreira, Daniela C; Franco, Gloria R; Alvarez-Leite, Jacqueline

    2015-01-01

    The rs9939609 single nucleotide polymorphism (SNP) in the fat mass and obesity-associated (FTO) gene is involved in obesity. Few studies have been conducted on patients who underwent bariatric surgery. The aim of this study was to evaluate the influence of FTO SNPs on body weight, body composition, and weight regain during a 60-mo follow-up period after bariatric surgery. The rs9939609 was genotyped in 146 individuals using a real-time polymerase chain reaction TaqMan assay. Data for lifestyle, comorbidities, body weight, body mass index (BMI), excess weight loss (EWL), and body composition were obtained before and 6, 12, 18, 24, 36, 48, and 60 mo after surgery. Data were analyzed by comparing two groups of patients according to rs9939609 FTO gene polymorphism. Mixed-regression models were constructed to evaluate the dynamics of body weight, BMI, and EWL over time in female patients. No differences were observed between the groups during the first 24 mo after surgery. After 36, 48, and 60 mo, body weight, fat mass, and BMI were higher, whereas fat-free mass and EWL were lower in the FTO-SNP patient group. Weight regain was more frequent and occurred sooner in the FTO-SNP group. There is a different evolution of weight loss in obese carriers of the FTO gene variant rs9939609 after bariatric surgery. However, this pattern was evident at only 2 y postbariatric surgery, inducing a lower proportion of surgery success and a greater and earlier weight regain. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Psychosocial and cessation-related differences between tobacco-marijuana co-users and single product users in a college student population.

    Science.gov (United States)

    Masters, Matthew N; Haardörfer, Regine; Windle, Michael; Berg, Carla

    2018-02-01

    Limited research has examined psychosocial factors that differ among cigarette users, marijuana users, and co-users and influence their cessation efforts. We examined: 1) sociodemographic, mental health, and other substance use in relation to user category; and 2) associations among these factors in relation to recent quit attempts and readiness to quit among single product versus co-users. We used a cross-sectional design to study college students aged 18-25 from seven Georgia campuses, focusing on the 721 reporting cigarette and/or marijuana use in the past 4months (238 cigarette-only; 331 marijuana-only; 152 co-users). Multinomial logistic regression showed that correlates (p'scolleges (vs. private) and not using little cigars/cigarillos (LCCs), e-cigarettes, and alcohol. Correlates of marijuana-only versus co-use included being Black or Hispanic (vs. White), not attending technical school, and not using LCCs and e-cigarettes. Importance was rated higher for quitting cigarettes versus marijuana, but confidence was rated lower for quitting cigarettes versus marijuana (p'smarijuana (p'smarijuana-only and 15.13% of cigarette-only users reported readiness to quit, 41.18% of cigarette-only and 21.75% of marijuana-only users reported recent quit attempts (p'smarijuana. Cessation efforts of the respective products must attend to co-use with the other product to better understand relative perceptions of importance and confidence in quitting and actual cessation efforts. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Diagnosis of adult-type hypolactasia/lactase persistence: genotyping of single nucleotide polymorphism (SNP C/T-13910 is not consistent with breath test in Colombian Caribbean population

    Directory of Open Access Journals (Sweden)

    Evelyn Mendoza Torres

    2012-03-01

    Full Text Available CONTEXT: Genotyping of single nucleotide polymorphism (SNP C/T-13910 located upstream of the lactase gene is used to determine adult-type hypolactasia/lactase persistence in North-European Caucasian subjects. The applicability of this polymorphism has been studied by comparing it with the standard diagnostic methods in different populations. OBJECTIVE: To compare the lactose hydrogen breath test with the genetic test in a sample of the Colombian Caribbean population. METHODS: Lactose hydrogen breath test and genotyping of SNP C/T-13910 were applied to 128 healthy individuals (mean age 35 ± 1. A positive lactose hydrogen breath test was indicative of hypolactasia. Genotyping was done using polymerase chain reaction/restriction fragment length polymorphism. The kappa index was used to establish agreement between the two methods. RESULTS: Seventy-six subjects (59% were lactose-maldigesters (hypolactasia and 52 subjects (41% were lactose-digesters (lactase persistence. The frequencies of the CC, CT and TT genotypes were 80%, 20% and 0%, respectively. Genotyping had 97% sensitivity and 46% specificity. The kappa index = 0.473 indicates moderate agreement between the genotyping of SNP C/T-13910 and the lactose hydrogen breath test. CONCLUSION: The moderate agreement indicates that the genotyping of the SNP C/T-13910 is not applicable to determine adult-type hypolactasia/lactase persistence in the population participating in this study.

  3. Single-nucleotide polymorphisms (SNPs) of the IRF6 and TFAP2A in non-syndromic cleft lip with or without cleft palate (NSCLP) in a northern Chinese population

    International Nuclear Information System (INIS)

    Shi, Jinna; Song, Tao; Jiao, Xiaohui; Qin, Chunlin; Zhou, Jin

    2011-01-01

    Highlights: → IRF6 rs642961 polymorphism is intensively associated with NSCLP. → IRF6 rs2235371 polymorphism is not associated with NSCLP in the northern Chinese population. → This investigation failed to yield any evidence for the involvement of TFAP2A polymorphisms in NSCLP in the northern Chinese population. -- Abstract: Non-syndromic cleft lip with or without cleft palate (NSCLP) is a common birth defect that is presumably caused by genetic factors alone or gene alterations in combination with environmental changes. A number of studies have shown an association between NSCLP and single-nucleotide polymorphisms (SNPs) in the interferon regulatory factor 6 (IRF6) gene in several populations. The transcription factor AP-2a (TFAP2A), which is involved in regulating mid-face development and upper lip fusion, has also be considered a candidate gene contributing to the etiology of NSCLP. The potential importance of IRF6 and TFAP2A in the NSCLP is further highlighted by a study showing that the two molecules are in the same developmental pathway. To further assess the roles of the IRF6 and TFAP2A in NSCLP, we investigated two identified IRF6 SNPs (rs2235371, rs642961) and three TFAP2A tag SNPs (rs3798691, rs1675414, rs303050) selected from HapMap data in a northern Chinese population, a group with a high prevalence of NSCLP. These SNPs were examined for association with NSCLP in 175 patients and 160 healthy controls. We observed a significant correlation between IRF6 rs642961 and NSCLP, and a lack of association between IRF6 rs2235371 polymorphisms and NSCLP in this population. This investigation indicated that there is no association between the three SNPs in the TFAP2A and NSCLP, suggesting that TFAP2A may not be involved in the development of NSCLP in the northern Chinese population. Our study provides further evidence regarding the role of IRF6 variations in NSCLP development and finds no significant association between TFAP2A and NSCLP in this northern

  4. Single-nucleotide polymorphisms (SNPs) of the IRF6 and TFAP2A in non-syndromic cleft lip with or without cleft palate (NSCLP) in a northern Chinese population

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Jinna, E-mail: kqkjk@yahoo.com.cn [Department of Periodontology, The First Affiliated Hospital, Harbin Medical University, Harbin (China); Song, Tao; Jiao, Xiaohui [Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin (China); Qin, Chunlin [Department of Biomedical Sciences, Texas A and M Health Science Center, Baylor College of Dentistry, Dallas, TX (United States); Zhou, Jin [Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin (China)

    2011-07-15

    Highlights: {yields} IRF6 rs642961 polymorphism is intensively associated with NSCLP. {yields} IRF6 rs2235371 polymorphism is not associated with NSCLP in the northern Chinese population. {yields} This investigation failed to yield any evidence for the involvement of TFAP2A polymorphisms in NSCLP in the northern Chinese population. -- Abstract: Non-syndromic cleft lip with or without cleft palate (NSCLP) is a common birth defect that is presumably caused by genetic factors alone or gene alterations in combination with environmental changes. A number of studies have shown an association between NSCLP and single-nucleotide polymorphisms (SNPs) in the interferon regulatory factor 6 (IRF6) gene in several populations. The transcription factor AP-2a (TFAP2A), which is involved in regulating mid-face development and upper lip fusion, has also be considered a candidate gene contributing to the etiology of NSCLP. The potential importance of IRF6 and TFAP2A in the NSCLP is further highlighted by a study showing that the two molecules are in the same developmental pathway. To further assess the roles of the IRF6 and TFAP2A in NSCLP, we investigated two identified IRF6 SNPs (rs2235371, rs642961) and three TFAP2A tag SNPs (rs3798691, rs1675414, rs303050) selected from HapMap data in a northern Chinese population, a group with a high prevalence of NSCLP. These SNPs were examined for association with NSCLP in 175 patients and 160 healthy controls. We observed a significant correlation between IRF6 rs642961 and NSCLP, and a lack of association between IRF6 rs2235371 polymorphisms and NSCLP in this population. This investigation indicated that there is no association between the three SNPs in the TFAP2A and NSCLP, suggesting that TFAP2A may not be involved in the development of NSCLP in the northern Chinese population. Our study provides further evidence regarding the role of IRF6 variations in NSCLP development and finds no significant association between TFAP2A and NSCLP in this

  5. Regularity of beating of small clusters of embryonic chick ventricular heart-cells: experiment vs. stochastic single-channel population model.

    Science.gov (United States)

    Krogh-Madsen, Trine; Kold Taylor, Louise; Skriver, Anne D; Schaffer, Peter; Guevara, Michael R

    2017-09-01

    The transmembrane potential is recorded from small isopotential clusters of 2-4 embryonic chick ventricular cells spontaneously generating action potentials. We analyze the cycle-to-cycle fluctuations in the time between successive action potentials (the interbeat interval or IBI). We also convert an existing model of electrical activity in the cluster, which is formulated as a Hodgkin-Huxley-like deterministic system of nonlinear ordinary differential equations describing five individual ionic currents, into a stochastic model consisting of a population of ∼20 000 independently and randomly gating ionic channels, with the randomness being set by a real physical stochastic process (radio static). This stochastic model, implemented using the Clay-DeFelice algorithm, reproduces the fluctuations seen experimentally: e.g., the coefficient of variation (standard deviation/mean) of IBI is 4.3% in the model vs. the 3.9% average value of the 17 clusters studied. The model also replicates all but one of several other quantitative measures of the experimental results, including the power spectrum and correlation integral of the voltage, as well as the histogram, Poincaré plot, serial correlation coefficients, power spectrum, detrended fluctuation analysis, approximate entropy, and sample entropy of IBI. The channel noise from one particular ionic current (I Ks ), which has channel kinetics that are relatively slow compared to that of the other currents, makes the major contribution to the fluctuations in IBI. Reproduction of the experimental coefficient of variation of IBI by adding a Gaussian white noise-current into the deterministic model necessitates using an unrealistically high noise-current amplitude. Indeed, a major implication of the modelling results is that, given the wide range of time-scales over which the various species of channels open and close, only a cell-specific stochastic model that is formulated taking into consideration the widely different

  6. The rs5934505 single nucleotide polymorphism (SNP) is associated with low testosterone and late-onset hypogonadism, but the rs10822184 SNP is associated with overweight and obesity in a Chinese Han population: a case-control study.

    Science.gov (United States)

    Chen, Y-P; Nie, L-L; Li, H-G; Liu, T-H; Fang, F; Zhao, K; Yang, R-F; Ma, X-L; Kong, X-B; Zhang, H-P; Guan, H-T; Xia, W; Hong, W-X; Duan, S; Zeng, X-C; Shang, X-J; Zhou, Y-Z; Gu, Y-Q; Wu, W-X; Xiong, C-L

    2016-01-01

    Low testosterone is associated with late-onset hypogonadism (LOH) and obesity. Recently, studies have shown that four single nucleotide polymorphisms (SNPs), rs12150660, rs727428, rs5934505, and rs10822184, are associated with testosterone levels in populations of European descent. Therefore, we investigated whether the SNP loci are related to low testosterone, LOH, or obesity in a Chinese Han population. Ruling out co-morbidities, DNA was prepared from 409 men (aged 40-65 years) with low serum testosterone (defined as total testosterone testosterone and calculated free testosterone (CFT) levels (p = 0.045 and p = 0.021). rs5934505 (C>T) was associated with an increased risk of low total testosterone, low CFT, and LOH and adjusted for other factors, with an odds ratio (OR) of 2.01 (1.34-3.01), 2.14 (1.42-3.20), and 1.64 (1.04-2.58). rs10822184 was significantly correlated with weight and BMI (p = 0.035 and p = 0.027). rs10822184 (T>C) was associated with an increased risk of overweight and obesity. We adjusted for other factors, with odds ratios (ORs) of 1.94 (1.36-2.78) and 1.56 (1.00-2.43). In summary, our study provided convincing evidence that rs5934505 (C>T) was associated with the risk of low testosterone and LOH in Chinese populations. We were the first to find that rs10822184 (T>C) was significantly correlated with the risk of overweight and obesity in Chinese populations. However, further large and functional studies are warranted to confirm our findings. © 2015 American Society of Andrology and European Academy of Andrology.

  7. IRF6 rs2235375 single nucleotide polymorphism is associated with isolated non-syndromic cleft palate but not with cleft lip with or without palate in south Indian population.

    Science.gov (United States)

    Gurramkonda, Venkatesh Babu; Syed, Altaf Hussain; Murthy, Jyotsna; Lakkakula, Bhaskar V K S

    2017-06-26

    Transcription factors are very diverse family of proteins involved in activating or repressing the transcription of a gene at a given time. Several studies using animal models demonstrated the role of transcription factor genes in craniofacial development. We aimed to investigate the association of IRF6 intron-6 polymorphism in the non-syndromic cleft lip with or without Palate in a south Indian population. 173 unrelated nonsyndromic cleft lip with or without Palate patients and 176 controls without clefts patients were genotyped for IRF6 rs2235375 variant by allele-specific amplification using the KASPar single nucleotide polymorphism genotyping system. The association between interferon regulatory factor-6 gene intron-6 dbSNP208032210:g.G>C (rs2235375) single nucleotide polymorphism and non-syndromic cleft lip with or without palate risk was investigated by chi-square test. There were significant differences in genotype or allele frequencies of rs2235375 single nucleotide polymorphism between controls and cases with non-syndromic cleft lip with or without palate. IRF6 rs2235375 variant was significantly associated with increased risk of non-syndromic cleft lip with or without palate in co-dominant, dominant (OR: 1.19; 95% CI 1.03-2.51; p=0.034) and allelic models (OR: 1.40; 95% CI 1.04-1.90; p=0.028). When subset analysis was applied significantly increased risk was observed in cleft palate only group (OR dominant: 4.33; 95% CI 1.44-12.97; p=0.005). These results suggest that IRF6 rs2235375 SNP play a major role in the pathogenesis and risk of developing non-syndromic cleft lip with or without palate. Copyright © 2017 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

  8. WNT3A gene polymorphisms are associated with bone mineral density variation in postmenopausal mestizo women of an urban Mexican population: findings of a pathway-based high-density single nucleotide screening.

    Science.gov (United States)

    Velázquez-Cruz, Rafael; García-Ortiz, Humberto; Castillejos-López, Manuel; Quiterio, Manuel; Valdés-Flores, Margarita; Orozco, Lorena; Villarreal-Molina, Teresa; Salmerón, Jorge

    2014-06-01

    Osteoporosis (OP) is a common skeletal disorder characterized by low bone mineral density (BMD) and is a common health problem in Mexico. To date, few genes affecting BMD variation in the Mexican population have been identified. The aim of this study was to investigate the association of single nucleotide polymorphisms (SNPs) located in genes of the Wnt pathway with BMD variation at various skeletal sites in a cohort of postmenopausal Mexican women. A total of 121 SNPs in or near 15 Wnt signaling pathway genes and 96 ancestry informative markers were genotyped in 425 postmenopausal women using the Illumina GoldenGate microarray SNP genotyping method. BMD was measured by dual-energy X-ray absorptiometry in total hip, femoral neck, Ward's triangle, and lumbar spine. Associations were tested by linear regression for quantitative traits adjusting for possible confounding factors. SNP rs752107 in WNT3A was strongly associated with decreased total hip BMD showing the highest significance under the recessive model (P = 0.00012). This SNP is predicted to disrupt a binding site for microRNA-149. In addition, a polymorphism of the Wnt antagonist DKK2 was associated with BMD in femoral neck under a recessive model (P = 0.009). Several LRP4, LRP5, and LRP6 gene variants showed site-specific associations with BMD. In conclusion, this is the first report associating Wnt pathway gene variants with BMD in the Mexican population.

  9. Nucleotide-binding oligomerization domain containing 1 (NOD1 haplotypes and single nucleotide polymorphisms modify susceptibility to inflammatory bowel diseases in a New Zealand caucasian population: a case-control study

    Directory of Open Access Journals (Sweden)

    Barclay Murray L

    2009-03-01

    Full Text Available Abstract Background The nucleotide-binding oligomerization domain containing 1 (NOD1 gene encodes a pattern recognition receptor that senses pathogens, leading to downstream responses characteristic of innate immunity. We investigated the role of NOD1 single nucleotide polymorphisms (SNPs on IBD risk in a New Zealand Caucasian population, and studied Nod1 expression in response to bacterial invasion in the Caco2 cell line. Findings DNA samples from 388 Crohn's disease (CD, 405 ulcerative colitis (UC, 27 indeterminate colitis patients and 201 randomly selected controls, from Canterbury, New Zealand were screened for 3 common SNPs in NOD1, using the MassARRAY® iPLEX Gold assay. Transcriptional activation of the protein produced by NOD1 (Nod1 was studied after infection of Caco2 cells with Escherichia coli LF82. Carrying the rs2075818 G allele decreased the risk of CD (OR = 0.66, 95% CI = 0.50–0.88, p Conclusion The NOD1 gene is important in signalling invasion of colonic cells by pathogenic bacteria, indicative of its' key role in innate immunity. Carrying specific SNPs in this gene significantly modifies the risk of CD and/or UC in a New Zealand Caucasian population.

  10. Standard Populations (Millions) for Age-Adjustment - SEER Population Datasets

    Science.gov (United States)

    Download files containing standard population data for use in statististical software. The files contain the same data distributed with SEER*Stat software. You can also view the standard populations, either 19 age groups or single ages.

  11. Genetic Population Structure and Demographic History of the Widespread Common Shipworm Teredo navalis Linnaeus 1758 (Mollusca: Bivalvia: Teredinidae in European Waters Inferred from Mitochondrial COI Sequence Data

    Directory of Open Access Journals (Sweden)

    Ronny Weigelt

    2017-06-01

    Full Text Available The first documented scientific reports of the common marine shipworm Teredo navalis (Bivalvia for Central European waters date back to the time between 1700 and 1730 in the Netherlands. During the following centuries there were several irregular mass occurrences reported for both the North Sea and the Baltic Sea. These events were accompanied by massive destruction of wooden ships and coastal protection structures. In this study, the first population analysis of T. navalis is presented with the aim to detect the genetic population structure in the waters of Central Europe. The mtDNA COI (cytochrome c oxidase subunit I locus was found as suitable molecular marker and hence a 675 bp gene fragment was studied. A total of 352 T. navalis specimens from 13 different sampling sites distributed across Central Europe were examined. Subsequently, various population genetic indices including FST values and an AMOVA analysis were applied for the description of the population structure. To visualize the distribution of haplotypes at the different sampling sites two median-joining networks were calculated. In addition, the past demographic structure of the T. navalis population was analyzed, among others by calculating Tajima's D, Fu's F and the mismatch distribution. Finally, all computations of the population genetic indices could not reveal differentiated populations or any kind of distinct population structure in T. navalis. The network analyses revealed “star-like” patterns without differentiated substructures or demes. Therefore, it can be assumed that a sudden expansion of this species took place without any indications of neither a bottleneck nor a founder effect for the study area. The results of this study support the concept of a regional panmictic population in the waters of Central Europe with unhindered migration of individuals (e.g., via pelagic larvae between the various sampling sites as reflected by a high gene flow.

  12. Prognostic value of myocardial perfusion single-photon emission computed tomography for the prediction of future cardiac events in a Japanese population. A middle-term follow-up study

    International Nuclear Information System (INIS)

    Matsumoto, Naoya; Sato, Yuichi; Suzuki, Yasuyuki

    2007-01-01

    The prognostic value of rest 201 Tl/stress 99m Tc-tetrofosmin myocardial perfusion single-photon emission computed tomography (SPECT) for the prediction of future hard cardiac events, including acute myocardial infarction (AMI), unstable angina (UAP) and cardiac death, and the implications for risk stratification has not yet been defined in a Japanese population. The 1,988 patients who underwent rest 201 Tl/stress 99m Tc-tetrofosmin SPECT were identified and followed up for the occurrence of AMI, UAP and cardiac death. The mean follow-up interval was 26.9±15.8 months. The 142 patients were revascularized within 60 days after SPECT and they were censored from the prognostic analysis. Summed stress score (SSS), summed rest score and summed difference score (SDS) were calculated using a 5-point scoring (Normal: 0, No uptake: 4) and a 20-segment model; 22 cases of myocardial infarction, 31 of UAP and 22 cardiac deaths occurred (1.2%, 1.7% and 1.2%, respectively). Multivariate Cox regression analysis showed that hypertension (Wald 6.37, p<0.05) and SDS (Wald 8.77, p<0.01) were independent predictors of AMI and UAP. Advanced age (Wald 16.0, p<0.001), SSS (Wald 10.9, p<0.01) and SDS (Wald 4.58, p<0.05) were independent predictors of cardiac death. Myocardial perfusion SPECT yields prognostic information toward the identification of acute coronary syndrome and cardiac death. (author)

  13. Bacteriophage populations

    International Nuclear Information System (INIS)

    Klieve, A.V.; Gilbert, R.A.

    2005-01-01

    Bacteriophages are ubiquitous to the rumen ecosystem; they have a role in nitrogen metabolism through bacterial lysis in the rumen, they may help to regulate bacterial population densities, be an agent for genetic exchange and be of use in biocontrol of bacterial populations through phage therapy. In Chapter 2.1, classical methodologies to enable the isolation, enumeration, storage and morphological characterization of phages were presented. In addition to these classic procedures, molecular biological techniques have resulted in a range of methodologies to investigate the type, topology and size of phage nucleic acids, to fingerprint individual phage strains and to create a profile of ruminal phage populations. Different phage families possess all the currently identified combinations of double-stranded or single-stranded RNA or DNA and may also possess unusual bases such as 5-hydroxymethylcytosine (found in T-even phage) or 5- hydroxymethyluracil and uracil in place of thymidine. In all morphological groups of phage except the filamentous phages, the nucleic acid is contained within a head or polyhedral structure, predominantly composed of protein. Filamentous phages have their nucleic acid contained inside the helical filament, occupying much of its length. Many of the procedures used with phage nucleic acids and double-stranded (ds) DNA, in particular, are not specific to ruminal phages but are the same as in other areas where nucleic acids are investigated and are covered elsewhere in the literature and this chapter. Most applications with rumen phages are similar to those reported for phages of non-ruminal bacteria and are covered in general texts such as Maniatis et al. In this chapter, we will concentrate on aspects of methodology as they relate to ruminal phages

  14. Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species.

    Science.gov (United States)

    Oono, Ryoko; Lutzoni, François; Arnold, A Elizabeth; Kaye, Laurel; U'Ren, Jana M; May, Georgiana; Carbone, Ignazio

    2014-08-01

    • Fungal endophytes comprise one of the most ubiquitous groups of plant symbionts, inhabiting healthy leaves and stems of all major lineages of plants. Together, they comprise immense species richness, but little is known about the fundamental processes that generate their diversity. Exploration of their population structure is needed, especially with regard to geographic distributions and host affiliations.• We take a multilocus approach to examine genetic variation within and among populations of Lophodermium australe, an endophytic fungus commonly associated with healthy foliage of pines in the southeastern United States. Sampling focused on two pine species ranging from montane to coastal regions of North Carolina and Virginia.• Our sampling revealed two genetically distinct groups within Lophodermium australe. Our analysis detected less than one migrant per generation between them, indicating that they are distinct species. The species comprising the majority of isolates (major species) demonstrated a panmictic structure, whereas the species comprising the minority of isolates (cryptic species) demonstrated isolation by distance. Distantly related pine species hosted the same Lophodermium species, and host species did not influence genetic structure.• We present the first evidence for isolation by distance in a foliar fungal endophyte that is horizontally transmitted. Cryptic species may be common among microbial symbionts and are important to delimit when exploring their genetic structure and microevolutionary processes. The hyperdiversity of endophytic fungi may be explained in part by cryptic species without apparent ecological and morphological differences as well as genetic diversification within rare fungal species across large spatial scales. © 2014 Botanical Society of America, Inc.

  15. Population genetic structure of Aedes polynesiensis in the Society Islands of French Polynesia: implications for control using a Wolbachia-based autocidal strategy

    Directory of Open Access Journals (Sweden)

    Brelsfoard Corey L

    2012-04-01

    Full Text Available Abstract Background Aedes polynesiensis is the primary vector of Wuchereria bancrofti in the South Pacific and an important vector of dengue virus. An improved understanding of the mosquito population genetics is needed for insight into the population dynamics and dispersal, which can aid in understanding the epidemiology of disease transmission and control of the vector. In light of the potential release of a Wolbachia infected strain for vector control, our objectives were to investigate the microgeographical and temporal population genetic structure of A. polynesiensis within the Society Islands of French Polynesia, and to compare the genetic background of a laboratory strain intended for release into its population of origin. Methods A panel of eight microsatellite loci were used to genotype A. polynesiensis samples collected in French Polynesia from 2005-2008 and introgressed A. polynesiensis and Aedes riversi laboratory strains. Examination of genetic differentiation was performed using F-statistics, STRUCTURE, and an AMOVA. BAYESASS was used to estimate direction and rates of mosquito movement. Results FST values, AMOVA, and STRUCTURE analyses suggest low levels of intra-island differentiation from multiple collection sites on Tahiti, Raiatea, and Maupiti. Significant pair-wise FST values translate to relatively minor levels of inter-island genetic differentiation between more isolated islands and little differentiation between islands with greater commercial traffic (i.e., Tahiti, Raiatea, and Moorea. STRUCTURE analyses also indicate two population groups across the Society Islands, and the genetic makeup of Wolbachia infected strains intended for release is similar to that of wild-type populations from its island of origin, and unlike that of A. riversi. Conclusions The observed panmictic population on Tahiti, Raiatea, and Moorea is consistent with hypothesized gene flow occurring between islands that have relatively high levels of air

  16. Population genetic structure of Aedes polynesiensis in the Society Islands of French Polynesia: implications for control using a Wolbachia-based autocidal strategy.

    Science.gov (United States)

    Brelsfoard, Corey L; Dobson, Stephen L

    2012-04-24

    Aedes polynesiensis is the primary vector of Wuchereria bancrofti in the South Pacific and an important vector of dengue virus. An improved understanding of the mosquito population genetics is needed for insight into the population dynamics and dispersal, which can aid in understanding the epidemiology of disease transmission and control of the vector. In light of the potential release of a Wolbachia infected strain for vector control, our objectives were to investigate the microgeographical and temporal population genetic structure of A. polynesiensis within the Society Islands of French Polynesia, and to compare the genetic background of a laboratory strain intended for release into its population of origin. A panel of eight microsatellite loci were used to genotype A. polynesiensis samples collected in French Polynesia from 2005-2008 and introgressed A. polynesiensis and Aedes riversi laboratory strains. Examination of genetic differentiation was performed using F-statistics, STRUCTURE, and an AMOVA. BAYESASS was used to estimate direction and rates of mosquito movement. FST values, AMOVA, and STRUCTURE analyses suggest low levels of intra-island differentiation from multiple collection sites on Tahiti, Raiatea, and Maupiti. Significant pair-wise FST values translate to relatively minor levels of inter-island genetic differentiation between more isolated islands and little differentiation between islands with greater commercial traffic (i.e., Tahiti, Raiatea, and Moorea). STRUCTURE analyses also indicate two population groups across the Society Islands, and the genetic makeup of Wolbachia infected strains intended for release is similar to that of wild-type populations from its island of origin, and unlike that of A. riversi. The observed panmictic population on Tahiti, Raiatea, and Moorea is consistent with hypothesized gene flow occurring between islands that have relatively high levels of air and maritime traffic, compared to that of the more isolated Maupiti

  17. A single blind randomized controlled trial of cognitive behavioural therapy in a help-seeking population with an At Risk Mental State for psychosis: the Dutch Early Detection and Intervention Evaluation (EDIE-NL trial

    Directory of Open Access Journals (Sweden)

    Delespaul Philippe

    2010-03-01

    Full Text Available Abstract Background Psychotic disorders are a serious mental health problem. Intervention before the onset of psychosis might result in delaying the onset, reducing the impact or even preventing the first episode of psychosis. This study explores the effectiveness of cognitive behavioural therapy (CBT in targeting cognitive biases that are involved in the formation of delusions in persons with an ultra-high risk for developing psychosis. A single blind randomised controlled trial compares CBT with treatment as usual in preventing or delaying the onset of psychosis. Method/design All help seeking patients aged 14 to 35 years referred to the mental health services in three regions in the Netherlands are pre-screened with the Prodromal Questionnaire during a period of two years. Patients with a score of 18 or more on the sub-clinical positive symptoms items (45 items in total will be assessed with the Comprehensive Assessment of At Risk Mental State (CAARMS. In a different pathway to care model all referrals from the mental health services in Amsterdam to the specialized psychosis clinic of the Academic Medical Centre in Amsterdam are also assessed with the CAARMS. The primary outcome is the transition rate to psychosis according to the CAARMS-criteria. Group differences will be analysed with chi-square tests and survival analyses. Discussion CBT is a highly tolerated treatment. The psycho-educational CBT approach may prove to be a successful strategy since most people with an At Risk Mental State (ARMS are distressed by odd disturbing experiences. Giving explanations for and normalising these experiences may reduce the arousal (distress and therefore may prevent people from developing a catastrophic delusional explanation for their odd experiences and thus prevent them from developing psychosis. Screening the entire help-seeking population referred to community mental health services with a two-stage strategy, as compared with traditional referral

  18. MT1A (A>G, MT1A (C>G, MT1M (A>C and MT4 (G>A single nucleotide polymorphism allele frequencies in Iranian populations

    Directory of Open Access Journals (Sweden)

    Javad Babaei

    2016-09-01

    Full Text Available It has been widely reported that metallothioneins (MTs play pivotal roles in the metabolism of the relatively nontoxic essential metals, as well as of toxic heavy metals. MT gene polymorphisms in an individual may increase or decrease the expression efficiency of the gene. The present study was aimed to investigate the frequency of genetic variation of four MTs in the Iranian population. Whole blood samples were collected from 300 Iranian healthy individuals. Polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP and automated Sanger sequencing were used for DNA genotype determination. The frequencies of major homozygous, heterozygous and minor homozygous genotypes in MT1 (A>G were, respectively, 76.0%, 24.0% and 0.0%; in MT1A (C>G, 88.0%, 12.0% and 0.0%; in MT1M (A>C, 86.0%, 14.0% and 0.0%; in MT4 (G>A, 80.0%, 18.7% and 1.3%. The present study showed for the first time that the polymorphism frequency distribution of these four MTs significantly differed between the studied Iranian population and other populations around the world, except for the MT4 polymorphism in the Iranian population and populations from the USA and New Zealand, which were similar. In conclusion, it could be suggested that regional and ethnic differences are the main reasons for this varied prevalence.

  19. Population Ethics

    OpenAIRE

    BLACKORBY, Charles; BOSSERT, Walter; DONALDSON, David

    2006-01-01

    This paper reviews the welfarist approach to population ethics. We provide an overview of the critical-level utilitarian population principles and their generalized counterparts, examine important properties of these principles and discuss their relationships to other variable-population social-evaluation rules. We illustrate the difficulties arising in population ethics by means of an impossibility result and present characterizations of the critical-level generalized-utilitarian principles ...

  20. Population Research.

    Science.gov (United States)

    National Inst. of Child Health and Human Development (NIH), Bethesda, MD.

    The scope of population research as carried on by the National Institute of Child Health and Human Development (NICHD) is set forth in this booklet. Population problems of the world, United States, and the individual are considered along with international population policies based on voluntary family planning programs. NICHD goals for biological…

  1. Population Education.

    Science.gov (United States)

    Shashidhar, B.; And Others

    Population education has assumed enormous importance in the national and international arena, since population changes influence the quality of life of individuals, families, the nation and the world as a whole. Population education has, however, special significance to India since young persons below the age of 15 are reported to form about 42%…

  2. Susceptibility of field populations of the fall armyworm (Lepidoptera: Noctuidae) from Florida and Puerto Rico to purified Cry1F protein and corn leaf tissue containing single and pyramided Bt genes

    Science.gov (United States)

    Larval survival of Cry1F-susceptible (FL), -resistant (PR and Cry1F-RR), and -heterozygous (FL x PR and Cry1F-RS) populations of the fall armyworm, Spodoptera frugiperda (J.E. Smith) to purified Cry1F protein and corn leaf tissue of seven Bacillus thuringiensis (Bt) corn hybrids and five non-Bt corn...

  3. Performance of maize single-crosses developed from populations improved by a modified reciprocal recurrent selection Performance de híbridos simples de milho desenvolvidos de populações melhoradas por seleção recorrente recíproca modificada

    Directory of Open Access Journals (Sweden)

    Cláudio Lopes de Souza Jr.

    2010-04-01

    Full Text Available Maize (Zea mays L. elite inbred lines developed from pedigree programs tend to be genetically related. Therefore, it is necessary to incorporate unrelated inbreds to those programs to allow the continued release of outstanding single-crosses. The objectives of this research were to compare the usefulness of a modified reciprocal recurrent selection procedure (MRRS to improve populations to be used as sources of elite inbreds and outstanding single-crosses to integrate pedigree programs, and to investigate the effects of selection on the relative contribution of general (GCA and specific combining (SCA abilities to the single-crosses variation. Eight and six S3 lines from populations IG-3-C1 and IG-4-C1, respectively, selected from the first cycle of the MRRS program were crossed in a partial-diallel mating design, and the 48 experimental and five commercial single-crosses were evaluated in six environments. Grain yield mean of the experimental single-crosses (9.57 t ha¹ did not differ from the commercial single-crosses (9.86 t ha¹, and ten of the 48 experimental single-crosses could be released as cultivars because they compared favorably to the currently used single-crosses. Thus, one cycle of the MRRS procedure improved efficiently the populations allowing the development of outstanding single-cross, but additional cycles of selection should be carried out since none of the experimental single-crosses outperformed the highest yielding commercial single-cross. The relative contribution of the GCA over SCA may have been affected by the MRRS, since the SCA was more important than GCA for some of the traits assessed.Linhagens elites de milho (Zea mays L. desenvolvidas em programas genealógicos tendem a ser geneticamente relacionadas. Portanto, é necessário incorporar linhagens não relacionadas a estes programas para permitir a liberação contínua de híbridos simples superiores. Comparou-se a utilidade de um procedimento modificado de sele

  4. [Population education].

    Science.gov (United States)

    1977-01-01

    Goal of population education is to raise knowledge and comprehension of causes and consequences, either personal or social, of excessive population growth. These days it is possible to plan the growth and evolution of the population to reach a level of balance and harmony between number of inhabitants of a country, and the country's natural resoruces. general objectives of population education are: 1) knowledge of basic demographic processes; 2) knowledge of effects of evolution and growth of population on social and economic life inside the family and inside society; 3) family size as related to nutrition, health, education, and job; and, 4) knowledge of population dynamics which the individual can influence through personal behavior, i.e. age at marriage, and spacing and number of children.

  5. Imaginary populations

    OpenAIRE

    Martínez-Abraín, Alejandro

    2010-01-01

    A few years ago, Camus & Lima (2002) wrote an essay to stimulate ecologists to think about how we define and use a fundamental concept in ecology: the population. They concluded, concurring with Berryman (2002), that a population is "a group of individuals of the same species that live together in an area of sufficient size to permit normal dispersal and/or migration behaviour and in which population changes are largely the results of birth and death processes". They pointed out that ecologis...

  6. Cancer predispostition, radiosensitivity and the risk of radiation-induced cancers. II. A mendelian single-locus model of cancer predisposition and radiosensitivity for predicting cancer risks in populations

    International Nuclear Information System (INIS)

    Chakraborty, R.; Sankaranarayanan, K.

    1995-01-01

    Individuals genetically predisposed to cancer may be more sensitive to cancers induced by ionizing radiation than those who are not so predisposed. Should this be true, under conditions of radiation exposure, a population consisting of cancer-predisposed and non-predisposed individuals will be expected to respond with a higher total frequency of induced cancers than one in which all the individuals are assumed to have the same sensitivity to radiation-induced cancers. To study this problem quantitatively, we have developed a Mendelian autosomal one-locus, two-allele model; this model assumes that one of the alleles is mutant and the genotypes carrying the mutant allele(s) are cancer-predisposed and are also more sensitive to radiation-induced cancer. Formal analytical predictions as well as numerical illustrations of this model show that: (1) when such heterogeneity with respect to cancer predisposition and radiosensitivity is present in the population, irradiation results in a greater increase in the frequency of induced cancers than when it is absent; (2) this increase is detectable only when the proportion of cancers due to genetic predisposition is large and when the degree of predisposition is considerable; and (3) even when the effect is small, most of the radiation-induced cancers will occur in predisposed individuals. These conclusions are valid for models of cancer when predisposition and radiosensitivity may be either dominant or recessive. The published data on breast cancers in Japanese A-bomb survivors show that at 1 Sv, the radiation-related excess relative risk in women irradiated before age 20 is 13 compared to about 2 for those irradiated at later ages. We examined the application of our model to the above data using two assumptions, namely, that the proportion of cancers due to genetic susceptibility at the BRCA1 locus and the frequency of the mutant allele estimated for Western populations are valid for Japanese women. 14 refs., 3 figs., 5 tabs

  7. Single-Gender Education: Educators' Perspective

    Science.gov (United States)

    Fry, John P.

    2009-01-01

    The examination of educator's views regarding single-gender education was the basis of this study. The significance of the intended study is to show the educator's view of single-gender education as it relates to student academic achievement and behavioral incidents. A quantitative study was conducted utilizing a sample population of regular and…

  8. 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.

  9. Inferred vs Realized Patterns of Gene Flow: An Analysis of Population Structure in the Andros Island Rock Iguana

    Science.gov (United States)

    Colosimo, Giuliano; Knapp, Charles R.; Wallace, Lisa E.; Welch, Mark E.

    2014-01-01

    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, p0.01). 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. PMID:25229344

  10. Inferred vs realized patterns of gene flow: an analysis of population structure in the Andros Island Rock Iguana.

    Science.gov (United States)

    Colosimo, Giuliano; Knapp, Charles R; Wallace, Lisa E; Welch, Mark E

    2014-01-01

    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.

  11. Population Blocks.

    Science.gov (United States)

    Smith, Martin H.

    1992-01-01

    Describes an educational game called "Population Blocks" that is designed to illustrate the concept of exponential growth of the human population and some potential effects of overpopulation. The game material consists of wooden blocks; 18 blocks are painted green (representing land), 7 are painted blue (representing water); and the remaining…

  12. Population crises and population cycles.

    Science.gov (United States)

    Russell, C; Russell, W M

    2000-01-01

    To prevent a population irretrievably depleting its resources, mammals have evolved a behavioural and physiological response to population crisis. When a mammalian population becomes dangerously dense, there is a reversal of behaviour. Co-operation and parental behaviour are replaced by competition, dominance and aggressive violence, leading to high mortality, especially of females and young, and a reduced population. The stress of overpopulation and the resulting violence impairs both the immune and the reproductive systems. Hence epidemics complete the crash of the population, and reproduction is slowed for three or four generations, giving the resources ample time to recover. In some mammal species, crisis and crisis response recur regularly, leading to cycles of population growth and relapse, oscillating about a fixed mean. Population crisis response and population cycles have been equally prominent in the history of human societies. But in man successive advances in food production have made possible growing populations, though with every such advance population soon outgrew resources again. Hence human cycles have been superimposed on a rising curve, producing a saw-tooth graph. Because advances in food production amounted to sudden disturbances in the relations between human populations and their environments, the crisis response in man has failed to avert famine and resource damage. In the large human societies evolved since the coming of settled agriculture and cities, the basic effects of violence, epidemics, famine and resource damage have been mediated by such specifically human disasters as inflation, unemployment, and political tyranny. An account of past crises, periods of relative relief from population pressure, and resulting cycles, is given for a number of regions: China, North Africa and Western Asia, the northern Mediterranean, and north-western Europe. The paper ends with an account of the present world-wide population crisis, and the solution

  13. Imaginary populations

    Directory of Open Access Journals (Sweden)

    A. Martínez–Abraín

    2010-01-01

    Full Text Available A few years ago, Camus & Lima (2002 wrote an essay to stimulate ecologists to think about how we define and use a fundamental concept in ecology: the population. They concluded, concurring with Berryman (2002, that a population is "a group of individuals of the same species that live together in an area of sufficient size to permit normal dispersal and/or migration behaviour and in which population changes are largely the results of birth and death processes". They pointed out that ecologists often forget "to acknowledge that many study units are neither natural nor even units in terms of constituting a population system", and hence claimed that we "require much more accuracy than in past decades in order to be more effective to characterize populations and predict their behaviour". They stated that this is especially necessary "in disciplines such as conservation biology or resource pest management, to avoid reaching wrong conclusions or making inappropriate decisions". As a population ecologist and conservation biologist I totally agree with these authors and, like them, I be¬lieve that greater precision and care is needed in the use and definition of ecological terms. The point I wish to stress here is that we ecologists tend to forget that when we use statistical tools to infer results from our sample to a population we work with what statisticians term "imaginary", "hypothetical" or "potential" popula¬tions. As Zar (1999 states, if our sample data consist of 40 measurements of growth rate in guinea pigs "the population about which conclusions might be drawn is the growth rates of all the guinea pigs that conceivably might have been administered the same food supplement under identical conditions". Such a population does not really exist, and hence it is considered a hypothetical or imaginary population. Compare that definition with the population concept that would be in our minds when performing such measurements. We would probably

  14. Population policy.

    Science.gov (United States)

    1987-03-01

    Participants in the Seminar on Population Policies for Top-level Policy Makers and Program Managers, meeting in Thailand during January 1987, examined the challenges now facing them regarding the implementation of fertility regulation programs in their respective countries -- Bangladesh, China, India, Indonesia, Malaysia, Nepal, Pakistan, the Philippines, the Republic of Korea, and Thailand. This Seminar was organized to coincide with the completion of an Economic and Social Commission for Asia and the Pacific (ESCAP) study investigating the impact and efficiency of family planning programs in the region. Country studies were reviewed at the Seminar along with policy issues about the status of women, incentive and disincentive programs, and socioeconomic factors affecting fertility. In Bangladesh the government recognizes population growth as its top priority problem related to the socioeconomic development of the country and is working to promote a reorientation strategy from the previous clinic-oriented to a multidimensional family welfare program. China's family planning program seeks to postpone marraige, space the births of children between 3-5 years, and promote the 1-child family. Its goal is to reduce the rate of natural increase from 12/1000 in 1978 to 5/1000 by 1985 and 0 by 2000. India's 7th Five-Year-Plan (1986-90) calls for establishing a 2-child family norm by 2000. In Indonesia the government's population policy includes reducing the rate of population growth, achieving a redistribution of the population, adjusting economic factors, and creating prosperous families. The government of Indonesia reversed its policy to reduce the population growth rate in 1984 and announced its goal of achieving a population of 70 million by 2100 in order to support mass consumption industries. It has created an income tax deduction system favoring large families and maternity benefits for women who have up to 5 children as incentives. Nepal's official policy is to

  15. Estimation of effective population size in continuously distributed populations: There goes the neighborhood

    Science.gov (United States)

    M. C. Neel; K. McKelvey; N. Ryman; M. W. Lloyd; R. Short Bull; F. W. Allendorf; M. K. Schwartz; R. S. Waples

    2013-01-01

    Use of genetic methods to estimate effective population size (Ne) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations with local mating...

  16. Population structure of Bactrocera dorsalis s.s., B. papayae and B. philippinensis (Diptera: Tephritidae) in southeast Asia: evidence for a single species hypothesis using mitochondrial DNA and wing-shape data.

    Science.gov (United States)

    Schutze, Mark K; Krosch, Matthew N; Armstrong, Karen F; Chapman, Toni A; Englezou, Anna; Chomič, Anastasija; Cameron, Stephen L; Hailstones, Deborah; Clarke, Anthony R

    2012-07-30

    Bactrocera dorsalis s.s. is a pestiferous tephritid fruit fly distributed from Pakistan to the Pacific, with the Thai/Malay peninsula its southern limit. Sister pest taxa, B. papayae and B. philippinensis, occur in the southeast Asian archipelago and the Philippines, respectively. The relationship among these species is unclear due to their high molecular and morphological similarity. This study analysed population structure of these three species within a southeast Asian biogeographical context to assess potential dispersal patterns and the validity of their current taxonomic status. Geometric morphometric results generated from 15 landmarks for wings of 169 flies revealed significant differences in wing shape between almost all sites following canonical variate analysis. For the combined data set there was a greater isolation-by-distance (IBD) effect under a 'non-Euclidean' scenario which used geographical distances within a biogeographical 'Sundaland context' (r(2) = 0.772, P Bactrocera dorsalis s.s., B. papayae and B. philippinensis likely represent one species structured around the South China Sea, having migrated from northern Thailand into the southeast Asian archipelago and across into the Philippines. No migration is apparent between the Philippines and Taiwan. This information has implications for quarantine, trade and pest management.

  17. Single Cell Isolation and Analysis

    Directory of Open Access Journals (Sweden)

    Ping Hu

    2016-10-01

    Full Text Available Increasing evidence shows that the heterogeneity of individual cells within a genetically identical population can be critical to their peculiar function and fate. Conventional cell based assays mainly analysis the average responses from a population cells, while the difference within individual cells may often be masked. The cell size, RNA transcripts and protein expression level are quite different within individual cells and these variations are key point to answer the problems in cancer, neurobiology, stem cell biology, immunology and developmental biology. To better understand the cell-to-cell variations, the single cell analysis can provide much more detailed information which may be helpful for therapeutic decisions in an increasingly personalized medicine. In this review, we will focus on the recent development in single cell analysis, including methods used in single cell isolation, analysis and some application examples. The review provides the historical background to single cell analysis, discusses limitations, and current and future possibilities in this exciting field of research.

  18. Single-Cell Genomic Analysis in Plants

    Directory of Open Access Journals (Sweden)

    Yuxuan Yuan

    2018-01-01

    Full Text Available Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis.

  19. Detecting deletions, insertions, and single nucleotide substitutions in cloned β-globin genes and new polymorphic nucleotide substitutions in β-globin genes in a Japanese population using ribonuclease cleavage at mismatches in RNA: DNA duplexes

    International Nuclear Information System (INIS)

    Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko.

    1990-08-01

    The applicability of ribonuclease (RNase) cleavage at mismatches in RNA:DNA duplexes (the RNase cleavage method) for determining nucleotide variant rates was examined in a Japanese population. DNA segments of various lengths obtained from four different regions of one normal and three thalassemic cloned human β-globin genes were inserted into transcription vectors. Sense and antisense RNA probes uniformly labeled with 32 P were prepared. When RNA probes of 771 nucleotides (nt) or less were hybridized with cloned DNAs and the resulting duplexes were treated with a mixture of RNases A and T1, the length of products agreed with theoretical values. Twelve possible mismatches were examined. Since both sense and antisense probes were used, uncleavable mismatches such as G:T and G:G which were made from one combination of RNA and DNA strands could be converted to the cleavable C:A and C:C mismatches, respectively, by using the opposite combination. Deletions and insertions of one (G), four(TTCT), five (ATTTT), and 10 (ATTTTATTTT) nt were easily detected. A polymorphic substitution of T to C at position 666 of the second intervening sequence (IVS2-666) of the β-globin gene was detected using genomic DNAs from cell lines established from the peripheral B lymphocytes of 59 unrelated Japanese from Hiroshima or those amplified by polymerase chain reaction (PCR). The frequency of the gene with C at the IVS2-666 (allele C) was 0.48 and that of the gene with T (allene T) was 0.52. Two new polymorphic substitutions of C to A and A to T were detected at nucleotide positions 1789 and 1945 from the capping site, respectively, using genomic DNAs amplified by PCR. We conclude that it would be feasible to use the RNase cleavage method combined with PCR for large-scale screening of variation in chromosomal DNA. (J.P.N.)

  20. Population structure of Bactrocera dorsalis s.s., B. papayae and B. philippinensis (Diptera: Tephritidae in southeast Asia: evidence for a single species hypothesis using mitochondrial DNA and wing-shape data

    Directory of Open Access Journals (Sweden)

    Schutze Mark K

    2012-07-01

    Full Text Available Abstract Background Bactrocera dorsalis s.s. is a pestiferous tephritid fruit fly distributed from Pakistan to the Pacific, with the Thai/Malay peninsula its southern limit. Sister pest taxa, B. papayae and B. philippinensis, occur in the southeast Asian archipelago and the Philippines, respectively. The relationship among these species is unclear due to their high molecular and morphological similarity. This study analysed population structure of these three species within a southeast Asian biogeographical context to assess potential dispersal patterns and the validity of their current taxonomic status. Results Geometric morphometric results generated from 15 landmarks for wings of 169 flies revealed significant differences in wing shape between almost all sites following canonical variate analysis. For the combined data set there was a greater isolation-by-distance (IBD effect under a ‘non-Euclidean’ scenario which used geographical distances within a biogeographical ‘Sundaland context’ (r2 = 0.772, P r2 = 0.217, P beast analysis provided a root age and location of 540kya in northern Thailand, with migration of B. dorsalis s.l. into Malaysia 470kya and Sumatra 270kya. Two migration events into the Philippines are inferred. Sequence data revealed a weak but significant IBD effect under the ‘non-Euclidean’ scenario (r2 = 0.110, P  Conclusions Bactrocera dorsalis s.s., B. papayae and B. philippinensis likely represent one species structured around the South China Sea, having migrated from northern Thailand into the southeast Asian archipelago and across into the Philippines. No migration is apparent between the Philippines and Taiwan. This information has implications for quarantine, trade and pest management.

  1. A pancreaticoduodenectomy risk model derived from 8575 cases from a national single-race population (Japanese) using a web-based data entry system: the 30-day and in-hospital mortality rates for pancreaticoduodenectomy.

    Science.gov (United States)

    Kimura, Wataru; Miyata, Hiroaki; Gotoh, Mitsukazu; Hirai, Ichiro; Kenjo, Akira; Kitagawa, Yuko; Shimada, Mitsuo; Baba, Hideo; Tomita, Naohiro; Nakagoe, Tohru; Sugihara, Kenichi; Mori, Masaki

    2014-04-01

    using a nationwide surgical database. PD outcomes in the national population were satisfactory, and the risk model could help improve surgical practice quality.

  2. Population dynamics

    Directory of Open Access Journals (Sweden)

    Cooch, E. G.

    2004-06-01

    Full Text Available Increases or decreases in the size of populations over space and time are, arguably, the motivation for much of pure and applied ecological research. The fundamental model for the dynamics of any population is straightforward: the net change over time in the abundance of some population is the simple difference between the number of additions (individuals entering the population minus the number of subtractions (individuals leaving the population. Of course, the precise nature of the pattern and process of these additions and subtractions is often complex, and population biology is often replete with fairly dense mathematical representations of both processes. While there is no doubt that analysis of such abstract descriptions of populations has been of considerable value in advancing our, there has often existed a palpable discomfort when the ‘beautiful math’ is faced with the often ‘ugly realities’ of empirical data. In some cases, this attempted merger is abandoned altogether, because of the paucity of ‘good empirical data’ with which the theoretician can modify and evaluate more conceptually–based models. In some cases, the lack of ‘data’ is more accurately represented as a lack of robust estimates of one or more parameters. It is in this arena that methods developed to analyze multiple encounter data from individually marked organisms has seen perhaps the greatest advances. These methods have rapidly evolved to facilitate not only estimation of one or more vital rates, critical to population modeling and analysis, but also to allow for direct estimation of both the dynamics of populations (e.g., Pradel, 1996, and factors influencing those dynamics (e.g., Nichols et al., 2000. The interconnections between the various vital rates, their estimation, and incorporation into models, was the general subject of our plenary presentation by Hal Caswell (Caswell & Fujiwara, 2004. Caswell notes that although interest has traditionally

  3. Populations games

    Czech Academy of Sciences Publication Activity Database

    Křivan, Vlastimil

    2015-01-01

    Roč. 2, č. 1 (2015), s. 14-19 ISSN 2367-5233. [Featuring International Conferences Biomath 2015. Blagoevgrad, 14.06.2015-19.06.2015] R&D Projects: GA MŠk(CZ) EE2.3.30.0032 Institutional support: RVO:60077344 Keywords : populations dynamics

  4. Stellar Populations

    NARCIS (Netherlands)

    Peletier, Reynier F.

    2013-01-01

    This is a summary of my lectures during the 2011 Canary Islands Winter School in Puerto de la Cruz. I give an introduction to the field of stellar populations in galaxies, and highlight some new results. Since the title of the Winter School is Secular Evolution in Galaxies I mostly concentrate on

  5. MAIZE POPULATIONS

    African Journals Online (AJOL)

    2003-06-17

    Jun 17, 2003 ... This study compared two maize populations, ZM601 and. ZM607 for drought tolerance during flowering, the most drought-vulnerable period for the maize plant. Cultivar. ZM601 had been improved through ...... Banziger, M., Pixley, K.V. and Zambezi, B.T.. 1999. Drought andNstress tolerance of maize.

  6. Spatial and temporal genetic homogeneity of the Monterey Spanish mackerel,Scomberomorus concolor, in the Gulf of California.

    Science.gov (United States)

    Magallón-Gayón, Erika; Diaz-Jaimes, Pindaro; Uribe-Alcocer, Manuel

    2016-01-01

    The genetic homogeneity of the Monterey Spanish mackerel Scomberomorus concolor population in the Gulf of California was confirmed using nine nuclear microsatellite loci in combination with mitochondrial cytochrome b gene sequences. Samples were collected from the upper and central Gulf areas, representing the two main biogeographical regions of the Gulf. The analyses support the existence of a single panmictic population of S. concolor inhabiting the Gulf of California which in terms of fishery management represents a single genetic stock. Additionally, the contemporary effective population size estimated for the S. concolor population (Ne = 3056.9) was high and similar to another pelagic species. The gene flow seems to be bidirectional between the upper and central Gulf, which coincides with the seasonal movements between both regions related to spawning and feeding activities. A population expansion event was detected, which agrees with a colonization-expansion hypothesis of the S. concolor population in the Gulf.

  7. Spatial and temporal genetic homogeneity of the Monterey Spanish mackerel, Scomberomorus concolor, in the Gulf of California

    Directory of Open Access Journals (Sweden)

    Erika Magallón-Gayón

    2016-10-01

    Full Text Available The genetic homogeneity of the Monterey Spanish mackerel Scomberomorus concolor population in the Gulf of California was confirmed using nine nuclear microsatellite loci in combination with mitochondrial cytochrome b gene sequences. Samples were collected from the upper and central Gulf areas, representing the two main biogeographical regions of the Gulf. The analyses support the existence of a single panmictic population of S. concolor inhabiting the Gulf of California which in terms of fishery management represents a single genetic stock. Additionally, the contemporary effective population size estimated for the S. concolor population (Ne = 3056.9 was high and similar to another pelagic species. The gene flow seems to be bidirectional between the upper and central Gulf, which coincides with the seasonal movements between both regions related to spawning and feeding activities. A population expansion event was detected, which agrees with a colonization-expansion hypothesis of the S. concolor population in the Gulf.

  8. Population Aging

    OpenAIRE

    David Weil

    2006-01-01

    Population aging is primarily the result of past declines in fertility, which produced a decades long period in which the ratio of dependents to working age adults was reduced. Rising old-age dependency in many countries represents the inevitable passing of this %u201Cdemographic dividend.%u201D Societies use three methods to transfer resources to people in dependent age groups: government, family, and personal saving. In developed countries, families are predominant in supporting children, w...

  9. Single Audit: Single Audit Act Effectiveness Issues

    National Research Council Canada - National Science Library

    Thompson, Sally

    2002-01-01

    As discussed in the report we are releasing today, our work to review agency actions to ensure that recipients take timely and appropriate corrective actions to fix audit findings contained in single...

  10. Single photon from a single trapped atom

    International Nuclear Information System (INIS)

    Dingjan, J.; Jones, M.P.A.; Beugnon, J.; Darquiee, B.; Bergamini, S.; Browaeys, A.; Messin, G.; Grangier, P.

    2005-01-01

    Full text: A quantum treatment of the interaction between atoms and light usually begins with the simplest model system: a two-level atom interacting with a monochromatic light wave. Here we demonstrate an elegant experimental realization of this system using an optically trapped single rubidium atom illuminated by resonant light pulses. We observe Rabi oscillations, and show that this system can be used as a highly efficient triggered source of single photons with a well-defined polarisation. In contrast to other sources based on neutral atoms and trapped ions, no optical cavity is required. We achieved a flux of single photons of about 10 4 s -1 at the detector, and observe complete antibunching. This source has potential applications for distributed atom-atom entanglement using single photons. (author)

  11. Stickleback Population

    Directory of Open Access Journals (Sweden)

    Ulrika Candolin

    2012-01-01

    Full Text Available Human-induced eutrophication has increased offspring production in a population of threespine stickleback Gasterosteus aculeatus in the Baltic Sea. Here, we experimentally investigated the effects of an increased density of juveniles on behaviours that influence survival and dispersal, and, hence, population growth—habitat choice, risk taking, and foraging rate. Juveniles were allowed to choose between two habitats that differed in structural complexity, in the absence and presence of predators and conspecific juveniles. In the absence of predators or conspecifics, juveniles preferred the more complex habitat. The preference was further enhanced in the presence of a natural predator, a perch Perca fluviatilis (behind a transparent Plexiglas wall. However, an increased density of conspecifics relaxed the predator-enhanced preference for the complex habitat and increased the use of the open, more predator-exposed habitat. Foraging rate was reduced under increased perceived predation risk. These results suggest that density-dependent behaviours can cause individuals to choose suboptimal habitats where predation risk is high and foraging rate low. This could contribute to the regulation of population growth in eutrophicated areas where offspring production is high.

  12. The population of Brazil

    Directory of Open Access Journals (Sweden)

    João Yunes

    1972-12-01

    Full Text Available In 1970 the population of Brazil with 94,508,554 inhabitants was extreme youth, since 42.67% was composed of children under 14 years old. In that year the proportion of female was 50.2%. The population density increased from 1.17 inhabitants /km² in 1872 to 11.18 in 1970, and in this last year the range was 1.03 in the North region and 43.90 in the South-East region. The urban population increased from 31.24% in 1940 to 55.98% in 1970 and for the first time the rural population was smaller than the urban population. In 1950 concerning with marital status 39% of the population 15 years old and over was single and 54% married. In 1970 this rate was respectively 35.4% and 56.6%. The population economically inactive increased from 49.17% in 1940 to 52.24% in 1970. The literacy ratio increased from 43% in 1940, to 48% in 1950 and 68.04% in 1970. The crude birth rate was 43/1000 live births in 1950 and fell to 37.7/1000 in 1970. The fertility rate decreased from 179.3/1000 women (15-49 years old} to 156.7/1000 in 1960/70. The crude death rate decreased from 20.60/1000 inhabitants in 1940/50 to 9.4/1000 in 1960/70. The infant mortality rate still remains high: 171/1000 live births in 1940/50 and 170/1000 in 1971. Concerning with the size of the cities, 8 in 1940 had 100,000 or more inhabitants and in 1970 this number increased to 94 cities. The population growth increased from 2.38% in 1940/50, to 2.99% in 1950/60 and 2.83% in 1960./70. Brazil is the first country in population size in Latin America and the eighth in the world. Concerning his area, Brazil is the fifth country in size.

  13. Single frequency intracavity SRO

    DEFF Research Database (Denmark)

    Abitan, Haim; Buchhave, Preben

    2000-01-01

    Summary form only given. A single resonance optical parametric oscillator (SRO) is inserted intracavity to a CW high power, single frequency, and ring Nd:YVO4 laser. We obtain a stable single frequency CW SRO with output at 1.7-1.9 μm (idler) and a resonating signal at 2.3-2.6 μm. The behavior...

  14. Indian populations

    CERN Document Server

    Spahni,J

    1974-01-01

    Le Prof. J.C. Spahni qui a parcouru les Andes, Vénezuela etc. parle de ses expériences et connaissances qu'il a vécu au cours des 14 ans parmi les populations indiennes de la Cordillière des Andes. Il a ramené des objets artisanals indiens lesquels l'auditoire peut acquérir. L'introduction-conférence est suivi d'un film, commenté par lui-même; après l'entracte il y un débat-dialogue avec le public.

  15. Single fatherhood due to cancer.

    Science.gov (United States)

    Yopp, Justin M; Rosenstein, Donald L

    2012-12-01

    Cancer is a leading cause of widowed fatherhood in the USA. Fathers whose spouses have died from cancer constitute a potentially vulnerable population as they adjust to their role as sole or primary caregiver while managing their own grief and that of their children. The importance of addressing the psychological needs of widowed fathers is underscored by data showing that father's coping and emotional availability are closely tied to their bereaved children's mental health. Surprisingly, scant attention has been given to the phenomenon of widowed fatherhood with virtually no clinical resources or research studies devoted to fathers who have lost their wives to cancer. This commentary highlights key challenges facing this underserved population of widowers and calls for development of research agendas and clinical interventions for single fathers due to cancer. Copyright © 2011 John Wiley & Sons, Ltd.

  16. Mathematical Modeling in Population Dynamics: The Case of Single ...

    African Journals Online (AJOL)

    kofimereku

    That is the solutions obtained should be consistent with physical intuition and evidence. The Biological Problem. Human activities have brought about drastic changes in the global environment. One grave consequence of this is the increased incidences of biological invasions and growth. In nature, all organisms reproduce,.

  17. Mathematical modeling in population dynamics: the case of single ...

    African Journals Online (AJOL)

    ... equations are tailored to describing the essential features of a continuous process. The trust of this paper is the application of mathematical models in helping to unravel the underlying mechanisms involved in biological and ecological processes. African Journal of Educational Studies in Mathematics and Sciences Vol.

  18. Single ventricle cardiac defect

    International Nuclear Information System (INIS)

    Eren, B.; Turkmen, N.; Fedakar, R.; Cetin, V.

    2010-01-01

    Single ventricle heart is defined as a rare cardiac abnormality with a single ventricle chamber involving diverse functional and physiological defects. Our case is of a ten month-old baby boy who died shortly after admission to the hospital due to vomiting and diarrhoea. Autopsy findings revealed cyanosis of finger nails and ears. Internal examination revealed; large heart, weighing 60 grams, single ventricle, without a septum and upper membranous part. Single ventricle is a rare pathology, hence, this paper aims to discuss this case from a medico-legal point of view. (author)

  19. Parallel single-cell analysis microfluidic platform

    NARCIS (Netherlands)

    van den Brink, Floris Teunis Gerardus; Gool, Elmar; Frimat, Jean-Philippe; Bomer, Johan G.; van den Berg, Albert; le Gac, Severine

    2011-01-01

    We report a PDMS microfluidic platform for parallel single-cell analysis (PaSCAl) as a powerful tool to decipher the heterogeneity found in cell populations. Cells are trapped individually in dedicated pockets, and thereafter, a number of invasive or non-invasive analysis schemes are performed.

  20. Sampling Lesbian, Gay, and Bisexual Populations

    Science.gov (United States)

    Meyer, Ilan H.; Wilson, Patrick A.

    2009-01-01

    Sampling has been the single most influential component of conducting research with lesbian, gay, and bisexual (LGB) populations. Poor sampling designs can result in biased results that will mislead other researchers, policymakers, and practitioners. Investigators wishing to study LGB populations must therefore devote significant energy and…

  1. Wolf population genetics in Europe

    DEFF Research Database (Denmark)

    Hindrikson, Maris; Remm, Jaanus; Pilot, Malgorzata

    2017-01-01

    , resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population...... genetic studies in Europe, covering major studies from the ‘pre-genomic era’ and the first insights of the ‘genomics era’. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal...... (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large-scale trends and patterns of genetic variation in European wolf populations, we conducted a meta-analysis based on the results of previous microsatellite studies and also included...

  2. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    IAS Admin

    GENERAL ARTICLE. Single-Molecule Spectroscopy. Every Molecule is Different! Kankan Bhattacharyya. Keywords. Single-molecule spectroscopy. (SMS), confocal microscopy,. FCS, sm-FRET, FLIM. 1 High-resolution spectrum re- fers to a spectrum consisting of very sharp lines. The sharp lines clearly display transitions to ...

  3. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    IAS Admin

    RESONANCE. February 2015. GENERAL ARTICLE. Single-Molecule Spectroscopy. Every Molecule is Different! Kankan Bhattacharyya. Keywords. Single-molecule ..... Resonance Energy. Transfer (FRET) is an elegant technique to measure the distance between a donor and an acceptor molecule. FRET refers to the.

  4. Single photon and nonlocality

    Indian Academy of Sciences (India)

    critical analysis of the concept of hidden variable used by the authors of [1] shows that the reasoning is not correct. Keywords. Nonlocality; single particle; hidden variables. PACS Nos 03.67.Ba; 03.65.Ta; 32.80.Lg; 07.79.Fc. 1. Introduction. Quantum nonlocality [2] for single particle is a subject of debate since the origin.

  5. Single gaze gestures

    DEFF Research Database (Denmark)

    Møllenbach, Emilie; Lilholm, Martin; Gail, Alastair

    2010-01-01

    This paper examines gaze gestures and their applicability as a generic selection method for gaze-only controlled interfaces. The method explored here is the Single Gaze Gesture (SGG), i.e. gestures consisting of a single point-to-point eye movement. Horizontal and vertical, long and short SGGs were...

  6. Understanding Single Adulthood.

    Science.gov (United States)

    Stein, Peter J.

    The life styles and life chances of the unmarried include elements of choices. Singles may be grouped and characterized according to whether their status may be considered stable or temporary. A life cycle, or continuum model of singlehood is reviewed, including its different factors, or phases. A new model for singles is proposed--a life spiral…

  7. Single-sided NMR

    CERN Document Server

    Casanova, Federico; Blümich, Bernhard

    2011-01-01

    Single-Sided NMR describes the design of the first functioning single-sided tomograph, the related measurement methods, and a number of applications. One of the key advantages to this method is the speed at which the images are obtained.

  8. Single molecules and nanotechnology

    CERN Document Server

    Vogel, Horst

    2007-01-01

    This book focuses on recent advances in the rapidly evolving field of single molecule research. These advances are of importance for the investigation of biopolymers and cellular biochemical reactions, and are essential to the development of quantitative biology. Written by leading experts in the field, the articles cover a broad range of topics, including: quantum photonics of organic dyes and inorganic nanoparticles their use in detecting properties of single molecules the monitoring of single molecule (enzymatic) reactions single protein (un)folding in nanometer-sized confined volumes the dynamics of molecular interactions in biological cells The book is written for advanced students and scientists who wish to survey the concepts, techniques and results of single molecule research and assess them for their own scientific activities.

  9. Single Nanoparticle Plasmonic Sensors

    Directory of Open Access Journals (Sweden)

    Manish Sriram

    2015-10-01

    Full Text Available The adoption of plasmonic nanomaterials in optical sensors, coupled with the advances in detection techniques, has opened the way for biosensing with single plasmonic particles. Single nanoparticle sensors offer the potential to analyse biochemical interactions at a single-molecule level, thereby allowing us to capture even more information than ensemble measurements. We introduce the concepts behind single nanoparticle sensing and how the localised surface plasmon resonances of these nanoparticles are dependent upon their materials, shape and size. Then we outline the different synthetic approaches, like citrate reduction, seed-mediated and seedless growth, that enable the synthesis of gold and silver nanospheres, nanorods, nanostars, nanoprisms and other nanostructures with tunable sizes. Further, we go into the aspects related to purification and functionalisation of nanoparticles, prior to the fabrication of sensing surfaces. Finally, the recent developments in single nanoparticle detection, spectroscopy and sensing applications are discussed.

  10. Single-photon imaging

    CERN Document Server

    Seitz, Peter

    2011-01-01

    The acquisition and interpretation of images is a central capability in almost all scientific and technological domains. In particular, the acquisition of electromagnetic radiation, in the form of visible light, UV, infrared, X-ray, etc. is of enormous practical importance. The ultimate sensitivity in electronic imaging is the detection of individual photons. With this book, the first comprehensive review of all aspects of single-photon electronic imaging has been created. Topics include theoretical basics, semiconductor fabrication, single-photon detection principles, imager design and applications of different spectral domains. Today, the solid-state fabrication capabilities for several types of image sensors has advanced to a point, where uncoooled single-photon electronic imaging will soon become a consumer product. This book is giving a specialist´s view from different domains to the forthcoming “single-photon imaging” revolution. The various aspects of single-photon imaging are treated by internati...

  11. Single-Phase PLLs

    DEFF Research Database (Denmark)

    Golestan, Saeed; Guerrero, Josep M.; Quintero, Juan Carlos Vasquez

    2017-01-01

    Single-phase phase-locked loops (PLLs) are popular for the synchronization and control of single-phase gridconnected converters. They are also widely used for monitoring and diagnostic purposes in the power and energy areas. In recent years, a large number of single-phase PLLs with different...... structures and properties have been proposed in the literature. The main aim of this paper is to provide a review of these PLLs. To this end, the single-phase PLLs are first classified into two major categories: 1) power-based PLLs (pPLLs), and 2) quadrature signal generation-based PLLs (QSG......-PLLs). The members of each category are then described and their pros and cons are discussed. This work provides a deep insight into characteristics of different single-phase PLLs and, therefore, can be considered as a reference for researchers and engineers....

  12. Refining population health comparisons

    DEFF Research Database (Denmark)

    Hussain, M. Azhar; Jørgensen, Mette Møller; Østerdal, Lars Peter Raahave

    2016-01-01

    How to determine if a population group has better overall (multidimensional) health status than another is a central question in the health and social sciences. We apply a multidimensional first order dominance concept that does not rely on assumptions about the relative importance of each...... dimension. In particular, we show how one can explore the “depth” of dominance relations by gradually refining the health dimensions to see which dominance relations persist. We analyze a Danish health survey with many health indicators. These are initially collapsed into a single composite health dimension...... and then refined to four, seven, and ten health dimensions, each representing an (increasingly refined) area of health. Overall we find that younger age groups dominate older age groups in up to four dimensions, but no dominance relations are present with a more refined view of health. Comparing education groups...

  13. Single Policy Study

    DEFF Research Database (Denmark)

    Kronsell, Annica; Manners, Ian James

    2015-01-01

    Single policy studies are the most common form of European Union (EU) research. Single policy studies are widely used to understand the role of the EU in a wide variety of sectors, together with their development over time, and often offer public policy prescriptions. This chapter discusses the r...... Policy (CSDP). The examples are illustrative of how single policy studies can be designed to use different approaches in the analysis: multiple streams approach to policy-making; a comparative hypothesis testing; and feminist institutional theory.......Single policy studies are the most common form of European Union (EU) research. Single policy studies are widely used to understand the role of the EU in a wide variety of sectors, together with their development over time, and often offer public policy prescriptions. This chapter discusses...... the relevance of single policy studies in EU research and give examples of how such research can be designed and carried out. The chapter reviews three examples of single policy studies using different methods based on EU environmental policy, the EU biofuels directive, and the EU Common Security and Defence...

  14. Epigenetics reloaded: the single-cell revolution.

    Science.gov (United States)

    Bheda, Poonam; Schneider, Robert

    2014-11-01

    Mechanistically, how epigenetic states are inherited through cellular divisions remains an important open question in the chromatin field and beyond. Defining the heritability of epigenetic states and the underlying chromatin-based mechanisms within a population of cells is complicated due to cell heterogeneity combined with varying levels of stability of these states; thus, efforts must be focused toward single-cell analyses. The approaches presented here constitute the forefront of epigenetics research at the single-cell level using classic and innovative methods to dissect epigenetics mechanisms from the limited material available in a single cell. This review further outlines exciting future avenues of research to address the significance of epigenetic heterogeneity and the contributions of microfluidics technologies to single-cell isolation and analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Single neuron computation

    CERN Document Server

    McKenna, Thomas M; Zornetzer, Steven F

    1992-01-01

    This book contains twenty-two original contributions that provide a comprehensive overview of computational approaches to understanding a single neuron structure. The focus on cellular-level processes is twofold. From a computational neuroscience perspective, a thorough understanding of the information processing performed by single neurons leads to an understanding of circuit- and systems-level activity. From the standpoint of artificial neural networks (ANNs), a single real neuron is as complex an operational unit as an entire ANN, and formalizing the complex computations performed by real n

  16. Single photon ECT

    International Nuclear Information System (INIS)

    Maeda, Toshio; Matsuda, Hiroshi; Tada, Akira; Bunko, Hisashi; Koizumi, Kiyoshi

    1982-01-01

    The detectability of lesions located deep in a body or overlapped with a physiologically increased activity improve with the help of single photon ECT. In some cases, the ECT is superior to the conventional gamma camera images and X-ray CT scans in the evaluation of the location and size of lesion. The single photon ECT of the brain compares favorably with the contrast enhansed X-ray CT scans. The most important adaptation of the single photon ECT are the detection of recurrent brain tumors after craniotomy and the evaluation of ischemic heart diseases. (author)

  17. Single Electron Tunneling

    International Nuclear Information System (INIS)

    Ruggiero, Steven T.

    2005-01-01

    Financial support for this project has led to advances in the science of single-electron phenomena. Our group reported the first observation of the so-called ''Coulomb Staircase'', which was produced by tunneling into ultra-small metal particles. This work showed well-defined tunneling voltage steps of width e/C and height e/RC, demonstrating tunneling quantized on the single-electron level. This work was published in a now well-cited Physical Review Letter. Single-electron physics is now a major sub-field of condensed-matter physics, and fundamental work in the area continues to be conducted by tunneling in ultra-small metal particles. In addition, there are now single-electron transistors that add a controlling gate to modulate the charge on ultra-small photolithographically defined capacitive elements. Single-electron transistors are now at the heart of at least one experimental quantum-computer element, and single-electron transistor pumps may soon be used to define fundamental quantities such as the farad (capacitance) and the ampere (current). Novel computer technology based on single-electron quantum dots is also being developed. In related work, our group played the leading role in the explanation of experimental results observed during the initial phases of tunneling experiments with the high-temperature superconductors. When so-called ''multiple-gap'' tunneling was reported, the phenomenon was correctly identified by our group as single-electron tunneling in small grains in the material. The main focus throughout this project has been to explore single electron phenomena both in traditional tunneling formats of the type metal/insulator/particles/insulator/metal and using scanning tunneling microscopy to probe few-particle systems. This has been done under varying conditions of temperature, applied magnetic field, and with different materials systems. These have included metals, semi-metals, and superconductors. Amongst a number of results, we have

  18. Stresses of Single Parenting

    Science.gov (United States)

    ... Text Size Email Print Share Stresses of Single Parenting Page Content Article Body What are some ways ... way. Check your local library for books on parenting. Local hospitals, the YMCA, and church groups often ...

  19. A Single Atom Antenna

    International Nuclear Information System (INIS)

    Trinter, Florian; Williams, Joshua B; Weller, Miriam; Waitz, Markus; Pitzer, Martin; Voigtsberger, Jörg; Schober, Carl; Kastirke, Gregor; Müller, Christian; Goihl, Christoph; Burzynski, Phillip; Wiegandt, Florian; Wallauer, Robert; Kalinin, Anton; Schmidt, Lothar Ph H; Schöffler, Markus S; Jahnke, Till; Dörner, Reinhard; Chiang, Ying-Chih; Gokhberg, Kirill

    2015-01-01

    Here we demonstrate the smallest possible implementation of an antenna-receiver complex which consists of a single (helium) atom acting as the antenna and a second (neon) atom acting as a receiver. (paper)

  20. Single Beam Holography.

    Science.gov (United States)

    Chen, Hsuan; Ruterbusch, Paul H.

    1979-01-01

    Discusses how holography can be used as part of undergraduate physics laboratories. The authors propose a single beam technique of holography, which will reduce the recording scheme as well as relax the isolation requirements. (HM)

  1. Population growth rates in perfect contraceptive populations.

    Science.gov (United States)

    Udry, J R; Bauman, K E; Chase, C L

    1973-07-01

    Abstract Eventually, world population must cease to grow. In many countries attempts are made to decrease population growth by providing family planning services to all who want to prevent pregnancies. In this paper we use the concept 'perfect contraceptive population',(1) - a population in which no unwanted births occur - to derive estimates of the maximum contribution that prevention of unwanted births might make toward attaining a zero rate of natural increase in population.

  2. Population Genetics with Fluctuating Population Sizes

    OpenAIRE

    Chotibut, Thiparat; Nelson, David R.

    2016-01-01

    Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is reviewed. We then study a situation such that the competing species are neutral at the equilibrium population size but population size fluctuations nevertheless favor fixation of one species over the other. In this case, a separation of timescales emerges natural...

  3. The population factor.

    Science.gov (United States)

    Kats, G

    1983-01-01

    that their children will survie; 3) the trend away from pills should ease the workload of clinics; 4) the government program to re-involve the dayas, traditional health workers whose primary function is that of midwife, in the government health care system, thus extending and enhancing its outreach and effectiveness; and 5) the government and the majority of Egyptians believe that population control is a pressing need. Increases in individual opportunities and income combined with a growing desire for material amentities will provide an economic incentive to keep families small. The single biggest challenge will be to reach the rural areas, especially in Upper Egypt, where illiteracy rates are high and access to radio and television is limited.

  4. Insecticidal Efficacy of Azadirachta indica, Nucleopolyhedrovirus and Chlorantraniliprole Singly or Combined against Field Populations fo Helicoverpa armigera Hübner (Lepidoptera: Noctuidae Eficacia Insecticida de Azadirachta indica, Nucleopolihedrovirus y Clorantraniliprol solo y sus Aplicaciones Integradas contra Poblaciones de Campo de Helicoverpa armigera Hübner (Lepidoptera: Noctuidae

    Directory of Open Access Journals (Sweden)

    Waqas Wakil

    2012-03-01

    Full Text Available The development of resistance in cosmopolitan insect Helicoverpa armigera Hubner (Lepidoptera: Noctuidae forced the researchers for alternative control measures. In the present study, insecticidal efficacy of formulations of Azadirachta indica, a Nucleopolyhedrovirus (NPV, and new anthranilic diamide insecticide (chlorantraniliprole formulations was determined against 2nd, through 5th larval instars of H. armigera collected from diverse geographical locations in the Punjab province, Pakistan. Azadirachta indica was applied at 5 μL L-1; NPV at 2.1 x 10(5 polyhedral occlusion bodies (POB mL4 and chlorantraniliprole at 0.01 μL L-1, either alone or in combinations with each other. The bioassays were conducted at 27 ± 1 °C and 65 ± 5% relative humidity. The mortality varied greatly among treatments, larval instars, and locations. The combinations of NPV with A. indica and chlorantraniliprole caused higher mortality, pupation and produced an additive effect compared to their application singly in all the tested populations. The population from Rawalpindi was always susceptible while the Gujranwala was the resistant. The results herein suggest that the effectiveness of NPV and A. indica can be improved by the presence of chlorantraniliprole against the larvae of H. armigera.Se determinó la eficacia insecticida de formulaciones de Azadirachta indica, Nucleopolihedrovirus (VPN y el nuevo insecticida diamida antranílico (clorantraniliprol en contra de segundo, tercero, cuarto y quinto estadios larvales de Helicoverpa armigera Hubner (Lepidoptera: Noctuidae recogidos de diversas ubicaciones geográficas de la provincia de Punjab, Pakistán. Azadirachta indica se aplicó en dosis de 5 μL L-1; VPN en dosis 2.1 x 10(5 POB mL-1 y clorantraniliprol fue 0,01 μL L-1 ya sea solos o en combinaciones. Los bioensayos se realizaron a 27 ± 1 °C y 65 ± 5% de humedad relativa. La mortalidad fue notablemente variada entre los tratamientos, estadios larvales y

  5. Review Single nucleotide polymorphism in genome-wide ...

    African Journals Online (AJOL)

    Genome-wide patterns of variation across individuals provide most powerful source of data for uncovering the history of migration, expansion, and adaptation of the human population. The arrival of new technologies that type more than millions of the single nucleotide polymorphisms (SNPs) in a single experiment has ...

  6. In-silico single nucleotide polymorphisms (SNP) mining of Sorghum ...

    African Journals Online (AJOL)

    Single nucleotide polymorphisms (SNPs) may be considered the ultimate genetic markers as they represent the finest resolution of a DNA sequence (a single nucleotide), and are generally abundant in populations with a low mutation rate. SNPs are important tools in studying complex genetic traits and genome evolution.

  7. Program computes single-point failures in critical system designs

    Science.gov (United States)

    Brown, W. R.

    1967-01-01

    Computer program analyzes the designs of critical systems that will either prove the design is free of single-point failures or detect each member of the population of single-point failures inherent in a system design. This program should find application in the checkout of redundant circuits and digital systems.

  8. Single-Mode VCSELs

    Science.gov (United States)

    Larsson, Anders; Gustavsson, Johan S.

    The only active transverse mode in a truly single-mode VCSEL is the fundamental mode with a near Gaussian field distribution. A single-mode VCSEL produces a light beam of higher spectral purity, higher degree of coherence and lower divergence than a multimode VCSEL and the beam can be more precisely shaped and focused to a smaller spot. Such beam properties are required in many applications. In this chapter, after discussing applications of single-mode VCSELs, we introduce the basics of fields and modes in VCSELs and review designs implemented for single-mode emission from VCSELs in different materials and at different wavelengths. This includes VCSELs that are inherently single-mode as well as inherently multimode VCSELs where higher-order modes are suppressed by mode selective gain or loss. In each case we present the current state-of-the-art and discuss pros and cons. At the end, a specific example with experimental results is provided and, as a summary, the most promising designs based on current technologies are identified.

  9. Single-Photon Optomechanics

    Science.gov (United States)

    Nunnenkamp, A.; Børkje, K.; Girvin, S. M.

    2011-08-01

    Optomechanics experiments are rapidly approaching the regime where the radiation pressure of a single photon displaces the mechanical oscillator by more than its zero-point uncertainty. We show that in this limit the power spectrum has multiple sidebands and that the cavity response has several resonances in the resolved-sideband limit. Using master-equation simulations, we also study the crossover from the weak-coupling many-photon to the single-photon strong-coupling regime. Finally, we find non-Gaussian steady states of the mechanical oscillator when multiphoton transitions are resonant. Our study provides the tools to detect and take advantage of this novel regime of optomechanics.

  10. Single well techniques

    International Nuclear Information System (INIS)

    Drost, W.

    1983-01-01

    The single well technique method includes measurement of parameters of groundwater flow in saturated rock. For determination of filtration velocity the dilution of radioactive tracer is measured, for direction logging the collimeter is rotated in the probe linked with the compass. The limiting factor for measurement of high filtration velocities is the occurrence of turbulent flow. The single well technique is used in civil engineering projects, water works and subsurface drainage of liquid waste from disposal sites. The radioactive tracer method for logging the vertical fluid movement in bore-holes is broadly used in groundwater survey and exploitation. (author)

  11. Biocatalytic Single Enzyme Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Grate, Jay W.; Kim, Jungbae

    2004-03-31

    As an innovative way of enzyme stabilization, we recently developed a new enzyme composite of nano-meter scale that we call "single-enzyme nanoparticles (SENs)" (9). Each enzyme molecule is surrounded with a porous composite organic/inorganic network of less than a few nanometers think. This approach represents a new type of enzyme-containing nanostructure. In experiments with perotease (chymotrypsin, CT), the activity of single enzyme nanoparticle form of the enzyme was greatly stabilized compared to the free form, without imposing a serious mass transfer limitation of substrates. In this chapter we will describe the synthesis, characterization and catalytic activity of the new SENs.

  12. Single port laparoscopic surgery

    DEFF Research Database (Denmark)

    Springborg, Henrik; Istre, Olav

    2012-01-01

    potential benefits. Theoretically, cosmetic outcomes, postoperative pain and complication rates could be improved with use of single site surgery. This study describes introduction of the method in a private hospital in Denmark, in which 40 patients have been treated for benign gynecologic conditions......LESS, or laparo-endoscopic single site surgery, is a promising new method in minimally invasive surgery. An increasing number of surgical procedures are being performed using this technique, however, its large-scale adoption awaits results of prospective randomized controlled studies confirming...

  13. How Massive Single Stars End Their Life

    Science.gov (United States)

    Heger, A.; Fryer, C. L.; Woosley, S. E.; Langer, N.; Hartmann, D. H.

    2003-01-01

    How massive stars die-what sort of explosion and remnant each produces-depends chiefly on the masses of their helium cores and hydrogen envelopes at death. For single stars, stellar winds are the only means of mass loss, and these are a function of the metallicity of the star. We discuss how metallicity, and a simplified prescription for its effect on mass loss, affects the evolution and final fate of massive stars. We map, as a function of mass and metallicity, where black holes and neutron stars are likely to form and where different types of supernovae are produced. Integrating over an initial mass function, we derive the relative populations as a function of metallicity. Provided that single stars rotate rapidly enough at death, we speculate on stellar populations that might produce gamma-ray bursts and jet-driven supernovae.

  14. Origin of Boundary Populations in Medaka (Oryzias latipes Species Complex).

    Science.gov (United States)

    Takehana, Yusuke; Sakai, Masato; Narita, Takanori; Sato, Tadashi; Naruse, Kiyoshi; Sakaizumi, Mitsuru

    2016-04-01

    The Japanese wild population of the medaka fish (Oryzias latipes species complex) comprises two genetically distinct groups, the Northern and the Southern Populations, with boundary populations having a unique genotype. It is thought that the boundary populations have been formed through introgressive hybridization between the two groups, because they are fixed with the Northern alleles at two allozymic loci, with the Southern alleles at two other loci, and have a unique allele at one locus. In this study, we examined the genetic population structure of the boundary populations using genome-wide single nucleotide polymorphism (SNP) data. Most SNPs of the Toyooka population, a typical boundary population, were shared with the Northern Population, some were shared with the Southern Population, and the remaining SNPs were unique to this population, suggesting that the boundary populations originated and diverged from the Northern Population. Further analyses of different populations using SNPs at eight genomic loci indicated that the boundary populations at different locations share similar genomic constitutions, and can be genetically distinguished from typical Northern Populations by unique SNPs. In addition, the boundary populations in the Maruyama River Basin had Northern mitochondrial DNA (mtDNA), while others, from the Fukuda and Kishida River Basins and from the Kumihama Bay area, had Southern mtDNA. These findings suggested that the boundary populations originated from the Northern Population, and then their genomes diverged as a result of geographical isolation, followed by mtDNA introgression from the Southern Population that occurred independently in some populations.

  15. A new axiomatic approach to the evaluation of population health

    DEFF Research Database (Denmark)

    Hougaard, Jens Leth; Moreno-Ternero, Juan D.; Østerdal, Lars Peter Raahave

    We explore in this paper the implications of ethical and operational principles for the evaluation of population health. We formalize those principles as axioms for social preferences over distributions of health for a given population. We single out several focal population health evaluation...

  16. Mass spectrometry-based metabolomics of single yeast cells.

    Science.gov (United States)

    Ibáñez, Alfredo J; Fagerer, Stephan R; Schmidt, Anna Mareike; Urban, Pawel L; Jefimovs, Konstantins; Geiger, Philipp; Dechant, Reinhard; Heinemann, Matthias; Zenobi, Renato

    2013-05-28

    Single-cell level measurements are necessary to characterize the intrinsic biological variability in a population of cells. In this study, we demonstrate that, with the microarrays for mass spectrometry platform, we are able to observe this variability. We monitor environmentally (2-deoxy-D-glucose) and genetically (ΔPFK2) perturbed Saccharomyces cerevisiae cells at the single-cell, few-cell, and population levels. Correlation plots between metabolites from the glycolytic pathway, as well as with the observed ATP/ADP ratio as a measure of cellular energy charge, give biological insight that is not accessible from population-level metabolomic data.

  17. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 2. Single-Molecule Spectroscopy: Every Molecule is Different! Kankan Bhattacharyya. General Article Volume 20 Issue 2 February 2015 pp 151-164. Fulltext. Click here to view fulltext PDF. Permanent link:

  18. Single Item Inventory Models

    NARCIS (Netherlands)

    E.M. Bazsa-Oldenkamp; P. den Iseger

    2001-01-01

    textabstractThis paper extends a fundamental result about single-item inventory systems. This approach allows more general performance measures, demand processes and order policies, and leads to easier analysis and implementation, than prior research. We obtain closed form expressions for the

  19. Single Nucleotide Polymorphism

    DEFF Research Database (Denmark)

    Børsting, Claus; Pereira, Vania; Andersen, Jeppe Dyrberg

    2014-01-01

    Single nucleotide polymorphisms (SNPs) are the most frequent DNA sequence variations in the genome. They have been studied extensively in the last decade with various purposes in mind. In this chapter, we will discuss the advantages and disadvantages of using SNPs for human identification...

  20. Single Value Devices

    NARCIS (Netherlands)

    Mader, Angelika H.; Dertien, Edwin Christian; Reidsma, Dennis

    2011-01-01

    We live in a world of continuous information overflow, but the quality of information and communication is suffering. Single value devices contribute to the information and communication quality by fo- cussing on one explicit, relevant piece of information. The information is decoupled from a

  1. Single Value Devices

    NARCIS (Netherlands)

    Mader, Angelika H.; Dertien, Edwin Christian; Reidsma, Dennis; Camurri, Antonio; Costa, Cristina

    We live in a world of continuous information overflow, but the quality of information and communication is suffering. Single value devices contribute to information and communication quality by focussing on one explicit, relevant piece of information. The information is decoupled from a computer and

  2. Single Value Devices

    NARCIS (Netherlands)

    Mader, Angelika H.; Reidsma, Dennis; Dertien, Edwin Christian; Volpe, G; Kolkmeier, Jan; Camurri, A.; Kolkmeier, Jan; Nijholt, Antinus

    2015-01-01

    We live in a world of continuous information overflow, but the quality of information and communication is suffering. Single value devices contribute to the information and communication quality by focussing on one explicit, relevant piece of information. The information is decoupled from a computer

  3. Beware the single hit!

    CERN Multimedia

    2008-01-01

    The first time that single particle effects from cosmic rays on electronics were observed was in 1991, when one of the instruments aboard an ESA satellite broke down after only five days in space. On 5 July, the TS-LEA group will have completed the installation of monitors that will help to reduce similar dangerous effects on LHC electronics.

  4. Single reusable spacecraft

    Data.gov (United States)

    National Aeronautics and Space Administration — Design of a my single person reusable spacecraft. It can carry one person and it has to be dropped from an aircraft at an altitude of 40,000 - 45,000 feet. Can be...

  5. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 2. Single-Molecule Spectroscopy: Every Molecule is Different! ... Author Affiliations. Kankan Bhattacharyya1. Department of Physical Chemistry, Indian Association for the Cultivation of Science Jadavpur, Kolkata 700 032 India.

  6. Single photon and nonlocality

    Indian Academy of Sciences (India)

    In a paper by Home and Agarwal [1], it is claimed that quantum nonlocality can be revealed in a simple interferometry experiment using only single particles. A critical analysis of the concept of hidden variable used by the authors of [1] shows that the reasoning is not correct.

  7. Beyond the Single Story

    Science.gov (United States)

    McKenney, Yekaterina

    2016-01-01

    Teachers of world literature have the opportunity to help students explore the more complex reality behind the stereotypes that they often see in the media. If we don't encourage students to challenge one-dimensional "single stories" that characterize an entire people--whether Muslims, Russians, Mexicans, African Americans, Chinese,…

  8. Watching single protein molecules in action

    DEFF Research Database (Denmark)

    Heiðarsson, Pétur Orri

    . This knowledge-gap is partly due to our inability to unveil the details of folding mechanisms that can be buried in the ensemble-averaged output of traditional bulk methods. Single-molecule techniques have provided a perspective beyond the ensemble average and enable studying the folding trajectories of protein...... molecules in unprecedented detail. These methods can, in principle, detect rare folding or misfolding events, and ultimately lead to a reconstruction of the free energy landscape. In this thesis, the folding mechanism of both single- and double-domain proteins is unraveled using single-molecule optical......, with transition states located almost halfway between the native and unfolded states. When pulled from the N- and C-termini, both experiments and simulations suggested that the molecule populates a transition state that resembles that observed during chemical denaturation, with respect to structure and position...

  9. Autonomous calibration of single spin qubit operations

    Science.gov (United States)

    Frank, Florian; Unden, Thomas; Zoller, Jonathan; Said, Ressa S.; Calarco, Tommaso; Montangero, Simone; Naydenov, Boris; Jelezko, Fedor

    2017-12-01

    Fully autonomous precise control of qubits is crucial for quantum information processing, quantum communication, and quantum sensing applications. It requires minimal human intervention on the ability to model, to predict, and to anticipate the quantum dynamics, as well as to precisely control and calibrate single qubit operations. Here, we demonstrate single qubit autonomous calibrations via closed-loop optimisations of electron spin quantum operations in diamond. The operations are examined by quantum state and process tomographic measurements at room temperature, and their performances against systematic errors are iteratively rectified by an optimal pulse engineering algorithm. We achieve an autonomous calibrated fidelity up to 1.00 on a time scale of minutes for a spin population inversion and up to 0.98 on a time scale of hours for a single qubit π/2 -rotation within the experimental error of 2%. These results manifest a full potential for versatile quantum technologies.

  10. On detecting selective sweeps using single genomes

    Directory of Open Access Journals (Sweden)

    Priyanka eSinha

    2011-12-01

    Full Text Available Identifying the genetic basis of human adaptation has remained a central focal point of modern population genetics. One major area of interest has been the use of polymorphism data to detect so-called 'footprints' of selective sweeps - patterns produced as a beneficial mutation arises and rapidly fixes in the population. Based on numerous simulation studies and power analyses, the necessary sample size for achieving appreciable power has been shown to vary from a few individuals to a few dozen, depending on the test statistic. And yet, the sequencing of multiple copies of a single region, or of multiple genomes as is now often the case, incurs considerable cost. Enard et al. (2010 have recently proposed a method to identify patterns of selective sweeps using a single genome - and apply this approach to human and non¬human primates (chimpanzee, orangutan and macaque. They employ essentially a modification of the Hudson, Kreitman and Aguade (HKA test - using heterozygous single nucleotide poly¬morphisms (SNPs from single individuals, and divergence data from two closely related spe¬cies (human-chimpanzee, human-orangutan and human-macaque. Given the potential importance of this finding, we here investigate the properties of this statistic. We demonstrate through simulation that this approach is neither robust to demography nor background selection; nor is it robust to variable recombination rates.

  11. Reconstructing Native American population history.

    Science.gov (United States)

    Reich, David; Patterson, Nick; Campbell, Desmond; Tandon, Arti; Mazieres, Stéphane; Ray, Nicolas; Parra, Maria V; Rojas, Winston; Duque, Constanza; Mesa, Natalia; García, Luis F; Triana, Omar; Blair, Silvia; Maestre, Amanda; Dib, Juan C; Bravi, Claudio M; Bailliet, Graciela; Corach, Daniel; Hünemeier, Tábita; Bortolini, Maria Cátira; Salzano, Francisco M; Petzl-Erler, María Luiza; Acuña-Alonzo, Victor; Aguilar-Salinas, Carlos; Canizales-Quinteros, Samuel; Tusié-Luna, Teresa; Riba, Laura; Rodríguez-Cruz, Maricela; Lopez-Alarcón, Mardia; Coral-Vazquez, Ramón; Canto-Cetina, Thelma; Silva-Zolezzi, Irma; Fernandez-Lopez, Juan Carlos; Contreras, Alejandra V; Jimenez-Sanchez, Gerardo; Gómez-Vázquez, Maria José; Molina, Julio; Carracedo, Angel; Salas, Antonio; Gallo, Carla; Poletti, Giovanni; Witonsky, David B; Alkorta-Aranburu, Gorka; Sukernik, Rem I; Osipova, Ludmila; Fedorova, Sardana A; Vasquez, René; Villena, Mercedes; Moreau, Claudia; Barrantes, Ramiro; Pauls, David; Excoffier, Laurent; Bedoya, Gabriel; Rothhammer, Francisco; Dugoujon, Jean-Michel; Larrouy, Georges; Klitz, William; Labuda, Damian; Kidd, Judith; Kidd, Kenneth; Di Rienzo, Anna; Freimer, Nelson B; Price, Alkes L; Ruiz-Linares, Andrés

    2012-08-16

    The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

  12. Reconstructing Native American Population History

    Science.gov (United States)

    Reich, David; Patterson, Nick; Campbell, Desmond; Tandon, Arti; Mazieres, Stéphane; Ray, Nicolas; Parra, Maria V.; Rojas, Winston; Duque, Constanza; Mesa, Natalia; García, Luis F.; Triana, Omar; Blair, Silvia; Maestre, Amanda; Dib, Juan C.; Bravi, Claudio M.; Bailliet, Graciela; Corach, Daniel; Hünemeier, Tábita; Bortolini, Maria-Cátira; Salzano, Francisco M.; Petzl-Erler, María Luiza; Acuña-Alonzo, Victor; Aguilar-Salinas, Carlos; Canizales-Quinteros, Samuel; Tusié-Luna, Teresa; Riba, Laura; Rodríguez-Cruz, Maricela; Lopez-Alarcón, Mardia; Coral-Vazquez, Ramón; Canto-Cetina, Thelma; Silva-Zolezzi, Irma; Fernandez-Lopez, Juan Carlos; Contreras, Alejandra V.; Jimenez-Sanchez, Gerardo; Gómez-Vázquez, María José; Molina, Julio; Carracedo, Ángel; Salas, Antonio; Gallo, Carla; Poletti, Giovanni; Witonsky, David B.; Alkorta-Aranburu, Gorka; Sukernik, Rem I.; Osipova, Ludmila; Fedorova, Sardana; Vasquez, René; Villena, Mercedes; Moreau, Claudia; Barrantes, Ramiro; Pauls, David; Excoffier, Laurent; Bedoya, Gabriel; Rothhammer, Francisco; Dugoujon, Jean Michel; Larrouy, Georges; Klitz, William; Labuda, Damian; Kidd, Judith; Kidd, Kenneth; Rienzo, Anna Di; Freimer, Nelson B.; Price, Alkes L.; Ruiz-Linares, Andrés

    2013-01-01

    The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved1–5. One contentious issue is whether the settlement occurred via a single6–8 or multiple streams of migration from Siberia9–15. The pattern of dispersals within the Americas is also poorly understood. To address these questions at higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. We show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call “First American”. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan-speakers on both sides of the Panama Isthmus, who have ancestry from both North and South America. PMID:22801491

  13. Statistical Models of Adaptive Immune populations

    Science.gov (United States)

    Sethna, Zachary; Callan, Curtis; Walczak, Aleksandra; Mora, Thierry

    The availability of large (104-106 sequences) datasets of B or T cell populations from a single individual allows reliable fitting of complex statistical models for naïve generation, somatic selection, and hypermutation. It is crucial to utilize a probabilistic/informational approach when modeling these populations. The inferred probability distributions allow for population characterization, calculation of probability distributions of various hidden variables (e.g. number of insertions), as well as statistical properties of the distribution itself (e.g. entropy). In particular, the differences between the T cell populations of embryonic and mature mice will be examined as a case study. Comparing these populations, as well as proposed mixed populations, provides a concrete exercise in model creation, comparison, choice, and validation.

  14. Single sheet iron oxides

    DEFF Research Database (Denmark)

    Yin, Zhou

    activity. LDH single sheets have been reported to be effective sorbents, catalysts in electrochemical and photochemical reactions, and building thin films together with other nanomaterials for designing new functionalities. Here we focus on the delamination of FeII-FeIII LDHs into single sheet iron oxide...... was rapid compared to other iron oxides, reaching equilibrium within 60 minutes. Arsenic sorption and acid-base titration data could be successfully described with a 1pk Basic Stern Model (BSM). The point of zero charge was around 8. The intrinsic surface complexation equilibrium constants (log K...... became abundant at low pH. (3) Electrochemical reduction of chlorinated compounds using an SSI modified electrode. Here, the electrochemical reactivity of SSIs coated on indium tin oxide coated glass electrodes was investigated. Iron on the SSI modified electrode showed a typical Cyclic Voltammetry...

  15. Single frequency semiconductor lasers

    CERN Document Server

    Fang, Zujie; Chen, Gaoting; Qu, Ronghui

    2017-01-01

    This book systematically introduces the single frequency semiconductor laser, which is widely used in many vital advanced technologies, such as the laser cooling of atoms and atomic clock, high-precision measurements and spectroscopy, coherent optical communications, and advanced optical sensors. It presents both the fundamentals and characteristics of semiconductor lasers, including basic F-P structure and monolithic integrated structures; interprets laser noises and their measurements; and explains mechanisms and technologies relating to the main aspects of single frequency lasers, including external cavity lasers, frequency stabilization technologies, frequency sweeping, optical phase locked loops, and so on. It paints a clear, physical picture of related technologies and reviews new developments in the field as well. It will be a useful reference to graduate students, researchers, and engineers in the field.

  16. Metabolic variability in micro-populations.

    Science.gov (United States)

    Elhanati, Yuval; Brenner, Naama

    2012-01-01

    Biological cells in a population are variable in practically every property. Much is known about how variability of single cells is reflected in the statistical properties of infinitely large populations; however, many biologically relevant situations entail finite times and intermediate-sized populations. The statistical properties of an ensemble of finite populations then come into focus, raising questions concerning inter-population variability and dependence on initial conditions. Recent technologies of microfluidic and microdroplet-based population growth realize these situations and make them immediately relevant for experiments and biotechnological application. We here study the statistical properties, arising from metabolic variability of single cells, in an ensemble of micro-populations grown to saturation in a finite environment such as a micro-droplet. We develop a discrete stochastic model for this growth process, describing the possible histories as a random walk in a phenotypic space with an absorbing boundary. Using a mapping to Polya's Urn, a classic problem of probability theory, we find that distributions approach a limiting inoculum-dependent form after a large number of divisions. Thus, population size and structure are random variables whose mean, variance and in general their distribution can reflect initial conditions after many generations of growth. Implications of our results to experiments and to biotechnology are discussed.

  17. Metabolic variability in micro-populations.

    Directory of Open Access Journals (Sweden)

    Yuval Elhanati

    Full Text Available Biological cells in a population are variable in practically every property. Much is known about how variability of single cells is reflected in the statistical properties of infinitely large populations; however, many biologically relevant situations entail finite times and intermediate-sized populations. The statistical properties of an ensemble of finite populations then come into focus, raising questions concerning inter-population variability and dependence on initial conditions. Recent technologies of microfluidic and microdroplet-based population growth realize these situations and make them immediately relevant for experiments and biotechnological application. We here study the statistical properties, arising from metabolic variability of single cells, in an ensemble of micro-populations grown to saturation in a finite environment such as a micro-droplet. We develop a discrete stochastic model for this growth process, describing the possible histories as a random walk in a phenotypic space with an absorbing boundary. Using a mapping to Polya's Urn, a classic problem of probability theory, we find that distributions approach a limiting inoculum-dependent form after a large number of divisions. Thus, population size and structure are random variables whose mean, variance and in general their distribution can reflect initial conditions after many generations of growth. Implications of our results to experiments and to biotechnology are discussed.

  18. Watching single molecules dance

    Science.gov (United States)

    Mehta, Amit Dinesh

    Molecular motors convert chemical energy, from ATP hydrolysis or ion flow, into mechanical motion. A variety of increasingly precise mechanical probes have been developed to monitor and perturb these motors at the single molecule level. Several outstanding questions can be best approached at the single molecule level. These include: how far does a motor progress per energy quanta consumed? how does its reaction cycle respond to load? how many productive catalytic cycles can it undergo per diffusional encounter with its track? and what is the mechanical stiffness of a single molecule connection? A dual beam optical trap, in conjunction with in vitro ensemble motility assays, has been used to characterize two members of the myosin superfamily: muscle myosin II and chick brain myosin V. Both move the helical polymer actin, but myosin II acts in large ensembles to drive muscle contraction or cytokinesis, while myosin V acts in small numbers to transport vesicles. An optical trapping apparatus was rendered sufficiently precise to identify a myosin working stroke with 1nm or so, barring systematic errors such as those perhaps due to random protein orientations. This and other light microscopic motility assays were used to characterize myosin V: unlike myosin II this vesicle transport protein moves through many increments of travel while remaining strongly bound to a single actin filament. The step size, stall force, and travel distance of myosin V reveal a remarkably efficient motor capable of moving along a helical track for over a micrometer without significantly spiraling around it. Such properties are fully consistent with the putative role of an organelle transport motor, present in small numbers to maintain movement over long ranges relative to cellular size scales. The contrast between myosin II and myosin V resembles that between a human running on the moon and one walking on earth, where the former allows for faster motion when in larger ensembles but for less

  19. Single Purpose Satellite Systems

    OpenAIRE

    Watkins, Warren

    1989-01-01

    This paper examines the need for tactically responsive space systems capable of supporting battlefield and fleet commanders. Terminology used to describe this category of satellite system varies according to organization or agency. The Defense Advanced Research Projects Agency's Lightsat, the Naval Space Command's SPINSAT, and the Air Force Space Command s TACSAT, are reviewed. The United State Space Command's space support mission IS addressed and the role single-purpose satellites can play ...

  20. Single rotor turbine engine

    Science.gov (United States)

    Platts, David A.

    2002-01-01

    There has been invented a turbine engine with a single rotor which cools the engine, functions as a radial compressor, pushes air through the engine to the ignition point, and acts as an axial turbine for powering the compressor. The invention engine is designed to use a simple scheme of conventional passage shapes to provide both a radial and axial flow pattern through the single rotor, thereby allowing the radial intake air flow to cool the turbine blades and turbine exhaust gases in an axial flow to be used for energy transfer. In an alternative embodiment, an electric generator is incorporated in the engine to specifically adapt the invention for power generation. Magnets are embedded in the exhaust face of the single rotor proximate to a ring of stationary magnetic cores with windings to provide for the generation of electricity. In this alternative embodiment, the turbine is a radial inflow turbine rather than an axial turbine as used in the first embodiment. Radial inflow passages of conventional design are interleaved with radial compressor passages to allow the intake air to cool the turbine blades.

  1. Uniform Single Valued Neutrosophic Graphs

    Directory of Open Access Journals (Sweden)

    S. Broumi

    2017-09-01

    Full Text Available In this paper, we propose a new concept named the uniform single valued neutrosophic graph. An illustrative example and some properties are examined. Next, we develop an algorithmic approach for computing the complement of the single valued neutrosophic graph. A numerical example is demonstrated for computing the complement of single valued neutrosophic graphs and uniform single valued neutrosophic graph.

  2. Always single and single again women: a qualitative study.

    Science.gov (United States)

    Lewis, K G; Moon, S

    1997-04-01

    What is it like to be a single woman today? Are the experiences of women who have always been single different from those who find themselves single again after having been married? How can family therapists promote the development of single women both individually and relationally? The purpose of this phenomenological, multiple-case study was to investigate perceptions of being single among heterosexual single women between the ages of 30 and 65. Nine focus group interviews and a semistructured, mailed questionnaire were used to collect the data. Constant comparative analyses were used to develop the findings. The findings were organized around the most salient theme that emerged from the analyses: single women have unresolved or unrecognized ambivalences about being single. This overarching theme was supported by three subassertions: (a) single women are aware of both the advantages and the drawbacks of being single; (b) single women are ambivalent about the reasons for their singleness; (c) although content with being single, many women simultaneously experience feelings of loss and grief. Implications for the clinical practice of family therapy and future research on single women are discussed.

  3. Bacterial computing with engineered populations.

    Science.gov (United States)

    Amos, Martyn; Axmann, Ilka Maria; Blüthgen, Nils; de la Cruz, Fernando; Jaramillo, Alfonso; Rodriguez-Paton, Alfonso; Simmel, Friedrich

    2015-07-28

    We describe strategies for the construction of bacterial computing platforms by describing a number of results from the recently completed bacterial computing with engineered populations project. In general, the implementation of such systems requires a framework containing various components such as intracellular circuits, single cell input/output and cell-cell interfacing, as well as extensive analysis. In this overview paper, we describe our approach to each of these, and suggest possible areas for future research. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  4. Human Population Problems

    Science.gov (United States)

    Emmel, Thomas C.; Sligh, Michael M.

    1970-01-01

    Asserts that overpopulation is the most pressing world problem. Topics discussed include population control in primitive societies, population growth and control in modern societies, methods of motivational population control, consequences of no population control, and mass famines during the 1970's in underdeveloped countries. Cities 33…

  5. Population Education Country Programmes.

    Science.gov (United States)

    Population Education in Asia and the Pacific Newsletter, 1983

    1983-01-01

    Describes population programs in Afghanistan (nonformal, population education literacy program), India (problems in planning/managing population education in higher education), Indonesia (training for secondary/out-of-school inspectors), and Pakistan (integration of population education into school curricula). Programs in China, Korea, Vietnam,…

  6. Why Population in 1974?

    Science.gov (United States)

    O'Connor, Marion

    1974-01-01

    Discusses the impact of world population growth leading to the establishment of the United Nations Fund for Population Activities and to the declaration of 1974 as World Population Year. Previews some of the parameters and interconnecting interests to be considered during this year of intensive population study. (JR)

  7. Accounting for Population Variation in Targeted Proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Fujimoto, Grant M.; Monroe, Matthew E.; Rodriguez, Larissa; Wu, Chaochao; MacLean, Brendan; Smith, Richard D.; MacCoss, Michael J.; Payne, Samuel H.

    2014-01-03

    Individual proteomes typically differ from the reference human proteome at ~10,000 single amino acid variants. When viewed at the population scale, this individual variation results in a wide variety of protein sequences. In targeted proteomics experiments, such variability would confound accurate protein quantification. To facilitate researchers in identifying target peptides with high variability within the human population we have created the Population Variation plug-in for Skyline, which provides easy access to the polymorphisms stored in dbSNP. Given a set of peptides, the tool reports minor allele frequency for common polymorphisms. We highlight the importance of considering genetic variation by applying the tool to public datasets.

  8. Single Electrode Heat Effects

    DEFF Research Database (Denmark)

    Jacobsen, Torben; Broers, G. H. J.

    1977-01-01

    The heat evolution at a single irreversibly working electrode is treated onthe basis of the Brønsted heat principle. The resulting equation is analogous to the expression for the total heat evolution in a galvanic cellwith the exception that –DeltaS is substituted by the Peltier entropy, Delta......SP, of theelectrode reaction. eta is the overvoltage at the electrode. This equation is appliedto a high temperature carbonate fuel cell. It is shown that the Peltier entropyterm by far exceeds the heat production due to the irreversible losses, and thatthe main part of heat evolved at the cathode is reabsorbed...

  9. Interval scanning photomicrography of microbial cell populations.

    Science.gov (United States)

    Casida, L. E., Jr.

    1972-01-01

    A single reproducible area of the preparation in a fixed focal plane is photographically scanned at intervals during incubation. The procedure can be used for evaluating the aerobic or anaerobic growth of many microbial cells simultaneously within a population. In addition, the microscope is not restricted to the viewing of any one microculture preparation, since the slide cultures are incubated separately from the microscope.

  10. Population structure of Staphylococcus aureus in China

    NARCIS (Netherlands)

    Yan, Xiaomei

    2015-01-01

    The present PhD research was aimed at analysing the population structure of Staphylococcus aureus in China. Between 2000 and 2005 we found that patients from a single Chinese hospital showed increasing trends in antimicrobial resistance. Among methicillin-resistant S. aureus (MRSA), resistance

  11. Single photons on demand

    International Nuclear Information System (INIS)

    Grangier, P.; Abram, I.

    2004-01-01

    Quantum cryptography and information processing are set to benefit from developments in novel light sources that can emit photons one by one. Quantum mechanics has gained a reputation for making counter-intuitive predictions. But we rarely get the chance to witness these effects directly because, being humans, we are simply too big. Take light, for example. The light sources that are familiar to us, such as those used in lighting and imaging or in CD and DVD players, are so huge that they emit billions and billions of photons. But what if there was a light source that emitted just one photon at a time? Over the past few years, new types of light source that are able to emit photons one by one have been emerging from laboratories around the world. Pulses of light composed of a single photon correspond to power flows in the femtowatt range - a million billion times less than that of a table lamp. The driving force behind the development of these single-photon sources is a range of novel applications that take advantage of the quantum nature of light. Quantum states of superposed and entangled photons could lead the way to guaranteed-secure communication, to information processing with unprecedented speed and efficiency, and to new schemes for quantum teleportation. (U.K.)

  12. Single-borehole techniques

    International Nuclear Information System (INIS)

    Klotz, D.; Moser, H.; Trimborn, P.

    1978-01-01

    Proceeding on the theoretical considerations and on the experience and practice derived from laboratory and field testing, a system consisting of tracer injection units, detector units, measuring probe units and packers is presented, from which the different borehole probes required can be combined. A couple of examples of recent applications shows the position of the Single-Borehole Techniques with respect to the traditional methods used for the measurement of the ground-water flow. A confrontation of the permeabilities of different aquifers consents, both on the basis of the Single-Borehole Techniques as by pumping experiments, the determination of the reliability of the Point-Dilution-Method. The Point-Dilution-Method is giving information about the vertical and horizontal distribution of the permeabilities in an aquifer. By measuring the vertical current in two karst wells, the tributary horizons of a well have been determined, which gave valuable information for the subsequent well construction. Local leakages could be detected by measuring the vertical flow rate through observation wells arranged along a grout curtain erected on both sides of the retaining barrage of the Keban dam. (orig.) [de

  13. Long-term panmixia in a cosmopolitan Indo-Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species

    KAUST Repository

    Horne, J. B.

    2013-01-11

    Phylogeographical studies have shown that some shallow-water marine organisms, such as certain coral reef fishes, lack spatial population structure at oceanic scales, despite vast distances of pelagic habitat between reefs and other dispersal barriers. However, whether these dispersive widespread taxa constitute long-term panmictic populations across their species ranges remains unknown. Conventional phylogeographical inferences frequently fail to distinguish between long-term panmixia and metapopulations connected by gene flow. Moreover, marine organisms have notoriously large effective population sizes that confound population structure detection. Therefore, at what spatial scale marine populations experience independent evolutionary trajectories and ultimately species divergence is still unclear. Here, we present a phylogeographical study of a cosmopolitan Indo-Pacific coral reef fish Naso hexacanthus and its sister species Naso caesius, using two mtDNA and two nDNA markers. The purpose of this study was two-fold: first, to test for broad-scale panmixia in N. hexacanthus by fitting the data to various phylogeographical models within a Bayesian statistical framework, and second, to explore patterns of genetic divergence between the two broadly sympatric species. We report that N. hexacanthus shows little population structure across the Indo-Pacific and a range-wide, long-term panmictic population model best fit the data. Hence, this species presently comprises a single evolutionary unit across much of the tropical Indian and Pacific Oceans. Naso hexacanthus and N. caesius were not reciprocally monophyletic in the mtDNA markers but showed varying degrees of population level divergence in the two nuclear introns. Overall, patterns are consistent with secondary introgression following a period of isolation, which may be attributed to oceanographic conditions of the mid to late Pleistocene, when these two species appear to have diverged. © 2013 The Authors. Journal

  14. Heralded single-photon absorption by a single atom

    Science.gov (United States)

    Piro, N.; Rohde, F.; Schuck, C.; Almendros, M.; Huwer, J.; Ghosh, J.; Haase, A.; Hennrich, M.; Dubin, F.; Eschner, J.

    2011-01-01

    Emission and absorption of single photons by single atoms is a fundamental limit of matter-light interaction, manifesting its quantum mechanical nature. As a controlled process, it is also a key tool in quantum optical information technology . Controlled single-photon emission is well advanced ; for controlled single-photon absorption by a single atom, proposals exist but only preliminary experimental steps have been taken . Here we report the absorption of single photons by a single trapped ion: employing a photon pair source, detection of the quantum-correlated partner photon heralds the presence of the resonant photon at the atom. We find clear correlations between the detection of the herald and the absorption process in the atom; we also demonstrate polarization control of this process. Our experiment evidences previously unexplored interaction between a single absorber and a quantum light source; with improved control over the coupling, it will open up new avenues in quantum technology.

  15. Ordering structured populations in multiplayer cooperation games

    Science.gov (United States)

    Peña, Jorge; Wu, Bin; Traulsen, Arne

    2016-01-01

    Spatial structure greatly affects the evolution of cooperation. While in two-player games the condition for cooperation to evolve depends on a single structure coefficient, in multiplayer games the condition might depend on several structure coefficients, making it difficult to compare different population structures. We propose a solution to this issue by introducing two simple ways of ordering population structures: the containment order and the volume order. If population structure is greater than population structure in the containment or the volume order, then can be considered a stronger promoter of cooperation. We provide conditions for establishing the containment order, give general results on the volume order, and illustrate our theory by comparing different models of spatial games and associated update rules. Our results hold for a large class of population structures and can be easily applied to specific cases once the structure coefficients have been calculated or estimated. PMID:26819335

  16. 75 FR 9247 - Single Family Mortgage Insurance Premium, Single Family

    Science.gov (United States)

    2010-03-01

    ... DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT [Docket No. FR-5376-N-13] Single Family Mortgage Insurance Premium, Single Family AGENCY: Office of the Chief Information Officer, HUD. ACTION: Notice... is soliciting public comments on the subject proposal. Lenders use the Single Family Premium...

  17. Periodic Solutions for a Delayed Population Model on Time Scales

    OpenAIRE

    Kejun Zhuang; Zhaohui Wen

    2010-01-01

    This paper deals with a delayed single population model on time scales. With the assistance of coincidence degree theory, sufficient conditions for existence of periodic solutions are obtained. Furthermore, the better estimations for bounds of periodic solutions are established.

  18. Minimum Wages and the Economic Well-Being of Single Mothers

    Science.gov (United States)

    Sabia, Joseph J.

    2008-01-01

    Using pooled cross-sectional data from the 1992 to 2005 March Current Population Survey (CPS), this study examines the relationship between minimum wage increases and the economic well-being of single mothers. Estimation results show that minimum wage increases were ineffective at reducing poverty among single mothers. Most working single mothers…

  19. Browsing Isolated Population Data

    Directory of Open Access Journals (Sweden)

    Manias Teresa

    2005-12-01

    Full Text Available Abstract Background In our studies of genetically isolated populations in a remote mountain area in the center of Sardinia (Italy, we found that 80–85% of the inhabitants of each village belong to a single huge pedigree with families strictly connected to each other through hundreds of loops. Moreover, intermarriages between villages join pedigrees of different villages through links that make family trees even more complicated. Unfortunately, none of the commonly used pedigree drawing tools are able to draw the complete pedigree, whereas it is commonly accepted that the visual representation of families is very important as it helps researchers in identifying clusters of inherited traits and genotypes. We had a representation issue that compels researchers to work with subsets extracted from the overall genealogy, causing a serious loss of information on familiar relationships. To visually explore such complex pedigrees, we developed PedNavigator, a browser for genealogical databases properly suited for genetic studies. Results The PedNavigator is useful for genealogical research due to its capacity to represent family relations between persons and to make a visual verification of the links during family history reconstruction. As for genetic studies, it is helpful to follow propagation of a specific set of genetic markers (haplotype, or to select people for linkage analysis, showing relations between various branch of a family tree of affected subjects. Availability PedNavigator is an application integrated into a Framework designed to handle data for human genetic studies based on the Oracle platform. To allow the use of PedNavigator also to people not owning the same required informatics infrastructure or systems, we developed PedNavigator Lite with mainly the same features of the integrated one, based on MySQL database server. This version is free for academic users, and it is available for download from our site http://www.shardna.com.

  20. Isotropic Single Negative Metamaterials

    Directory of Open Access Journals (Sweden)

    P. Protiva

    2008-09-01

    Full Text Available This paper presents the application of simple, and therefore cheap, planar resonators for building 3D isotropic metamaterials. These resonators are: a broadside-coupled split ring resonator with a magnetic response providing negative permeability; an electric dipole terminated by a loop inductor together with a double H-shaped resonator with an electric response providing negative permittivity. Two kinds of 3D isotropic single negative metamaterials are reported. The first material consists of unit cells in the form of a cube bearing on its faces six equal planar resonators with tetrahedral symmetry. In the second material, the planar resonators boxed into spherical plastic shells and randomly distributed in a hosting material compose a real 3D volumetric metamaterial with an isotropic response. In both cases the metamaterial shows negative permittivity or permeability, according to the type of resonators that are used. The experiments prove the isotropic behavior of the cells and of the metamaterial specimens.

  1. Lanthanide single molecule magnets

    CERN Document Server

    Tang, Jinkui

    2015-01-01

    This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs, and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures – an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and...

  2. Coronary single vessel disease

    International Nuclear Information System (INIS)

    Kaltenbach, M.; Kober, G.; Satter, P.; Gruentzig, A.; Myler, R.; Sterzer, S.

    1980-01-01

    The seven-years-survival rate is about 80 percent with respect to the most favourable long-time prognosis for coronary single vessel diseases under conservative therapy. In this contribution the control angiography of 76 patients after aorto-coronary bypass operation or transluminal angioplastic is reported. Only two patients subjected to a bypass operation. The recidivity rate is 10 percent after an operation, whereby it is not possible to make a recidivity prognosis. If a recidivity shows up it is being developped during the first three months. If the control angiography three months after the operation shows a good result, then a favourable steady state result can be expected. A comparison of the result with four different centers is given. (APR) [de

  3. Single-Molecule Nanomagnets

    Science.gov (United States)

    Friedman, Jonathan R.; Sarachik, Myriam P.

    2010-04-01

    Single-molecule magnets straddle the classical and quantum mechanical worlds, displaying many fascinating phenomena. They may have important technological applications in information storage and quantum computation. We review the physical properties of two prototypical molecular nanomagnets, Mn12-acetate and Fe8: Each behaves as a rigid, spin-10 object and exhibits tunneling between up and down directions. As temperature is lowered, the spin-reversal process evolves from thermal activation to pure quantum tunneling. At low temperatures, magnetic avalanches occur in which the magnetization of an entire sample rapidly reverses. We discuss the important role that symmetry-breaking fields play in driving tunneling and in producing Berry-phase interference. Recent experimental advances indicate that quantum coherence can be maintained on timescales sufficient to allow a meaningful number of quantum computing operations to be performed. Efforts are under way to create monolayers and to address and manipulate individual molecules.

  4. Single Nucleotide Polymorphism

    DEFF Research Database (Denmark)

    Børsting, Claus; Pereira, Vania; Andersen, Jeppe Dyrberg

    2014-01-01

    and briefly describe the methods that are preferred for SNP typing in forensic genetics. In addition, we will illustrate how SNPs can be used as investigative leads in the police investigation by discussing the use of ancestry informative markers and forensic DNA phenotyping. Modern DNA sequencing......Single nucleotide polymorphisms (SNPs) are the most frequent DNA sequence variations in the genome. They have been studied extensively in the last decade with various purposes in mind. In this chapter, we will discuss the advantages and disadvantages of using SNPs for human identification...... technologies (also called next generation sequencing or NGS) have the potential to completely transform forensic genetic investigations as we know them today. Here, we will make a short introduction to NGS and explain how NGS may combine analysis of the traditional forensic genetic markers with analysis...

  5. Lanthanide single molecule magnets

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Jinkui; Zhang, Peng [Chinese Academy of Sciences, Changchun (China). Changchun Inst. of Applied Chemistry

    2015-10-01

    This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures - an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and explore new directions.

  6. Population and population policy in Pakistan.

    Science.gov (United States)

    Mauldin, W P

    1963-02-01

    Pakistan is a divided country with different religious groups represented. Since independence in 1941, the Muslim population has increased more rapidly than the Hindu population, the West Pakistan population more rapidly and steadily than the East Pakistan population. In the late 1950s the Pakistan government initiated a family planning program. The program has trained medical and paramedical personnel in family planning, added family planning services to existing medical centers, planned for a National Research Institute of Family Planning, employed mobile units to reach outlying areas, conducted limited clinical studies on some contraceptives, and used mass media advertising. Only India and Japan are doing more with government-sponsored family planning. A weak organizational structure and an inadequate number of trained personnel are the main weakness of the program. It is too early to assess the success of the program. A 10-point reduction in annual birth rates will be considered successful.

  7. Population and prehistory II: space-limited human populations in constant environments.

    Science.gov (United States)

    Puleston, Cedric O; Tuljapurkar, Shripad

    2008-09-01

    We present a population model to examine the forces that determined the quality and quantity of human life in early agricultural societies where cultivable area is limited. The model is driven by the non-linear and interdependent relationships between the age distribution of a population, its behavior and technology, and the nature of its environment. The common currency in the model is the production of food, on which age-specific rates of birth and death depend. There is a single non-trivial equilibrium population at which productivity balances caloric needs. One of the most powerful controls on equilibrium hunger level is fertility control. Gains against hunger are accompanied by decreases in population size. Increasing worker productivity does increase equilibrium population size but does not improve welfare at equilibrium. As a case study we apply the model to the population of a Polynesian valley before European contact.

  8. Health, drugs and service use among deprived single men: comparing (subgroups) of single male welfare recipients against employed single men in Amsterdam

    NARCIS (Netherlands)

    Kamann, T.C.; de Wit, M.A.S.; Cremer, S.; Beekman, A.T.F.

    2014-01-01

    Objectives: To aid public health policy in preventing severe social exclusion (like homelessness) and promoting social inclusion (like labour market participation), we aimed to quantify (unmet) health needs of an expectedly vulnerable population on which little was known about: single male welfare

  9. The Affects of a Single Bout of Exercise on Mood and Self-Esteem in Clinically Diagnosed Mental Health Patients

    OpenAIRE

    ELLIS, Naomi; RANDALL, Jason; PUNNETT, Grant

    2013-01-01

    Research has highlighted the importance of regular exercise within the general population and mental health groups in regard to mood and self-esteem, as well as single bout exercise within the general population. However, research into single bout exercise in mental health population is lacking. This study investigated the impact of a single bout of exercise, on mood and self-esteem, in patients with a wider clinical mental health diagnosis. Design: A quantitative questionnaire was completed ...

  10. Patterns of admixture and population structure in native populations of Northwest North America.

    Science.gov (United States)

    Verdu, Paul; Pemberton, Trevor J; Laurent, Romain; Kemp, Brian M; Gonzalez-Oliver, Angelica; Gorodezky, Clara; Hughes, Cris E; Shattuck, Milena R; Petzelt, Barbara; Mitchell, Joycelynn; Harry, Harold; William, Theresa; Worl, Rosita; Cybulski, Jerome S; Rosenberg, Noah A; Malhi, Ripan S

    2014-08-01

    The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

  11. Patterns of admixture and population structure in native populations of Northwest North America.

    Directory of Open Access Journals (Sweden)

    Paul Verdu

    2014-08-01

    Full Text Available The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

  12. Population and Environment

    OpenAIRE

    de Sherbinin, Alex; Carr, David; Cassels, Susan; Jiang, Leiwen

    2007-01-01

    The interactions between human population dynamics and the environment have often been viewed mechanistically. This review elucidates the complexities and contextual specificities of population-environment relationships in a number of domains. It explores the ways in which demographers and other social scientists have sought to understand the relationships among a full range of population dynamics (e.g., population size, growth, density, age and sex composition, migration, urbanization, vital...

  13. Genomewide predictions from maize single-cross data.

    Science.gov (United States)

    Massman, Jon M; Gordillo, Andres; Lorenzana, Robenzon E; Bernardo, Rex

    2013-01-01

    Maize (Zea mays L.) breeders evaluate many single-cross hybrids each year in multiple environments. Our objective was to determine the usefulness of genomewide predictions, based on marker effects from maize single-cross data, for identifying the best untested single crosses and the best inbreds within a biparental cross. We considered 479 experimental maize single crosses between 59 Iowa Stiff Stalk Synthetic (BSSS) inbreds and 44 non-BSSS inbreds. The single crosses were evaluated in multilocation experiments from 2001 to 2009 and the BSSS and non-BSSS inbreds had genotypic data for 669 single nucleotide polymorphism (SNP) markers. Single-cross performance was predicted by a previous best linear unbiased prediction (BLUP) approach that utilized marker-based relatedness and information on relatives, and from genomewide marker effects calculated by ridge-regression BLUP (RR-BLUP). With BLUP, the mean prediction accuracy (r(MG)) of single-cross performance was 0.87 for grain yield, 0.90 for grain moisture, 0.69 for stalk lodging, and 0.84 for root lodging. The BLUP and RR-BLUP models did not lead to r(MG) values that differed significantly. We then used the RR-BLUP model, developed from single-cross data, to predict the performance of testcrosses within 14 biparental populations. The r(MG) values within each testcross population were generally low and were often negative. These results were obtained despite the above-average level of linkage disequilibrium, i.e., r(2) between adjacent markers of 0.35 in the BSSS inbreds and 0.26 in the non-BSSS inbreds. Overall, our results suggested that genomewide marker effects estimated from maize single crosses are not advantageous (cofmpared with BLUP) for predicting single-cross performance and have erratic usefulness for predicting testcross performance within a biparental cross.

  14. Iowa Population Trends.

    Science.gov (United States)

    Tait, John L.; Johnson, Arthur H.

    The trends in population distribution and the composition of Iowa's population are reported in this document in order to provide the leaders and citizens of Iowa with information to assist them in making decisions relating to growth and development. Birth and death rates, rural and urban residence, population by race, and age structure are…

  15. [Population Growth and Development].

    Science.gov (United States)

    Clausen, A. W.

    Rapid population growth as a central development problem, the proper domain of government in reducing population growth, and effective measures which can be taken to reduce fertility are examined. Rapid population growth puts a brake on development because it exacerbates the difficult choice between higher consumption now and the investment needed…

  16. Controlling Population with Pollution

    Science.gov (United States)

    Browne, Joseph

    2010-01-01

    Population models are often discussed in algebra, calculus, and differential equations courses. In this article we will use the human population of the world as our application. After quick looks at two common models we'll investigate more deeply a model which incorporates the negative effect that accumulated pollution may have on population.

  17. Single atom spintronics

    International Nuclear Information System (INIS)

    Sullivan, M. R.; Armstrong, J. N.; Hua, S. Z.; Chopra, H. D.

    2005-01-01

    Full text: Single atom spintronics (SASS) represents the ultimate physical limit in device miniaturization. SASS is characterized by ballistic electron transport, and is a fertile ground for exploring new phenomena. In addition to the 'stationary' (field independent) scattering centers that have a small and fixed contribution to total transmission probability of electron waves, domain walls constitute an additional and enhanced source of scattering in these magnetic quantum point contacts (QPCs), the latter being both field and spin-dependent. Through the measurement of complete hysteresis loops as a function of quantized conductance, we present definitive evidence of enhanced backscattering of electron waves by atomically sharp domain walls in QPCs formed between microfabricated thin films [1]. Since domain walls move in a magnetic field, the magnitude of spin-dependent scattering changes as the QPC is cycled along its hysteresis loop. For example, as shown in the inset in Fig. 1, from zero towards saturation in a given field direction, the resistance varies as the wall is being swept away, whereas the resistance is constant upon returning from saturation towards zero, since in this segment of the hysteresis loop no domain wall is present across the contact. The observed spin-valve like behavior is realized by control over wall width and shape anisotropy. This behavior also unmistakably sets itself apart from any mechanical artifacts; additionally, measurements made on single atom contacts provide an artifact-free environment [2]. Intuitively, it is simpler to organize the observed BMR data according to all possible transitions between different conductance plateaus, as shown by the dotted line in Fig. 1; the solid circles show experimental data for Co, which follows the predicted scheme. Requisite elements for the observation of the effect will be discussed in detail along with a review of state of research in this field. Practically, the challenge lies in making

  18. A single particle energies

    Energy Technology Data Exchange (ETDEWEB)

    Bodmer, A.R. [Illinois Univ., Chicago, IL (United States). Dept. of Physics]|[Argonne National Lab., IL (United States); Usmani, Q.N.; Sami, M. [Jamia Millia Islamia, New Delhi (India). Dept. of Physics

    1993-09-01

    We consider the binding energies of {Lambda} hypernuclei (HN), in particular the single-particle (s.p.) energy data, which have been obtained for a wide range of HN with mass numbers A {le} 89 and for orbital angular momenta {ell}{sub {Lambda}} {le} 4. We briefly review some of the relevant properties of A hypernuclei. These are nuclei {sub {Lambda}}{sup A}Z with baryon number A in which a single {Lambda} hyperon (baryon number = 1) is bound to an ordinary nucleus {sup A}Z consisting of A - 1 nucleons = Z protons + N neutrons. The {Lambda} hyperon is neutral, has spin 1/2, strangeness S = {minus}1, isospin I = O and a mass M{sub {Lambda}} = 1116 MeV/c{sup 2}. Although the {Lambda} interacts with a nucleon, its interaction is only about half as strong as that between two nucleons, and thus very roughly V{sub {Lambda}N} {approx} 0.5 V{sub NN}. As a result, the two-body {Lambda}N system is unbound, and the lightest bound HN is the three-body hypertriton {sub {Lambda}}{sup 3}H in which the {Lambda} is bound to a deuteron with the {Lambda}-d separation energy being only {approx} 0.1 MeV corresponding to an exponential tail of radius {approx} 15 fm! In strong interactions the strangeness S is of course conserved, and the {Lambda} is distinct from the nucleons. In a HN strangeness changes only in the weak decays of the {Lambda} which can decay either via ``free`` pionic decay {Lambda} {yields} N + {pi} or via induced decay {Lambda} + N {yields} N + N which is only possible in the presence of nucleons. Because of the small energy release the pionic decay is strongly suppressed in all but the lightest HN and the induced decay dominates. However, the weak decay lifetime {approx} 10{sup {minus}10}s is in fact close to the lifetime of a free {Lambda}. Since this is much longer than the strong interaction time {approx} 10{sup {minus}22}s we can ignore the weak interactions when considering the binding of HN, just as for ordinary nuclei.

  19. A single particle energies

    International Nuclear Information System (INIS)

    Bodmer, A.R.; Usmani, Q.N.; Sami, M.

    1993-01-01

    We consider the binding energies of Λ hypernuclei (HN), in particular the single-particle (s.p.) energy data, which have been obtained for a wide range of HN with mass numbers A ≤ 89 and for orbital angular momenta ell Λ ≤ 4. We briefly review some of the relevant properties of A hypernuclei. These are nuclei Λ A Z with baryon number A in which a single Λ hyperon (baryon number = 1) is bound to an ordinary nucleus A Z consisting of A - 1 nucleons = Z protons + N neutrons. The Λ hyperon is neutral, has spin 1/2, strangeness S = -1, isospin I = O and a mass M Λ = 1116 MeV/c 2 . Although the Λ interacts with a nucleon, its interaction is only about half as strong as that between two nucleons, and thus very roughly V ΛN ∼ 0.5 V NN . As a result, the two-body ΛN system is unbound, and the lightest bound HN is the three-body hypertriton Λ 3 H in which the Λ is bound to a deuteron with the Λ-d separation energy being only ∼ 0.1 MeV corresponding to an exponential tail of radius ∼ 15 fm exclamation point In strong interactions the strangeness S is of course conserved, and the Λ is distinct from the nucleons. In a HN strangeness changes only in the weak decays of the Λ which can decay either via ''free'' pionic decay Λ → N + π or via induced decay Λ + N → N + N which is only possible in the presence of nucleons. Because of the small energy release the pionic decay is strongly suppressed in all but the lightest HN and the induced decay dominates. However, the weak decay lifetime ∼ 10 -10 s is in fact close to the lifetime of a free Λ. Since this is much longer than the strong interaction time ∼ 10 -22 s we can ignore the weak interactions when considering the binding of HN, just as for ordinary nuclei

  20. The single entity option

    International Nuclear Information System (INIS)

    Friedlander, M.C.; Roberts, K.M.

    1997-01-01

    Traditionally, an owner hires an engineer to design a power facility or other project and then circulates the completed plans to several contractors for competitive bidding. Although there are many variations on this theme, there is an alternative method which is growing in popularity--the design-build concept. In this construction method, the same entity designs and constructs the facility. The design builder may be a single firm with both design and construction capacity in-house, or it may be a combination of two or more firms with complementary abilities. If there are multiple firms, they may be structured as a joint venture or with one of the firms prime and the others in a subcontracting role. The critical aspect is that the owner contracts with one entity which has the responsibility for both designing and constructing the facility. According to statistics compiled by the Design-Build Institute of America and F.W. Dodge DATALINE2, a national reporter of construction statistics and information, from April 1995 to April 1996 the number of design-build contracts increased 103 percent over the previous year. Of a total $212 billion construction market, about $37.2 billion--18 percent--was design build. The strongest growth was in the category of industrial--plants, refineries, factories and warehouses--in which the concept use was up more than 300 percent from the previous year

  1. Microfluidics-Enabled Enzyme Activity Measurement in Single Cells.

    Science.gov (United States)

    Tesauro, Cinzia; Frøhlich, Rikke; Stougaard, Magnus; Ho, Yi-Ping; Knudsen, Birgitta R

    2015-01-01

    Cellular heterogeneity has presented a significant challenge in the studies of biology. While most of our understanding is based on the analysis of ensemble average, individual cells may process information and respond to perturbations very differently. Presented here is a highly sensitive platform capable of measuring enzymatic activity at the single-cell level. The strategy innovatively combines a rolling circle-enhanced enzyme activity detection (REEAD) assay with droplet microfluidics. The single-molecule sensitivity of REEAD allows highly sensitive detection of enzymatic activities, i.e. at the single catalytic event level, whereas the microfluidics enables isolation of single cells. Further, confined reactions in picoliter-sized droplets significantly improve enzyme extraction from human cells or microorganisms and result in faster reaction kinetics. Taken together, the described protocol is expected to open up new possibilities in the single-cell research, particularly for the elucidation of heterogeneity in a population of cells.

  2. Clinical Outcome Prediction Using Single-Cell Data.

    Science.gov (United States)

    Pouyan, Maziyar Baran; Jindal, Vasu; Nourani, Mehrdad

    2016-10-01

    Single-cell technologies like flow cytometry (FCM) provide valuable biological data for knowledge discovery in complex cellular systems like tissues and organs. FCM data contains multi-dimensional information about the cellular heterogeneity of intricate cellular systems. It is possible to correlate single-cell markers with phenotypic properties of those systems. Cell population identification and clinical outcome prediction from single-cell measurements are challenging problems in the field of single cell analysis. In this paper, we propose a hybrid learning approach to predict clinical outcome using samples' single-cell FCM data. The proposed method is efficient in both i) identification of cellular clusters in each sample's FCM data and ii) predict clinical outcome (healthy versus unhealthy) for each subject. Our method is robust and the experimental results indicate promising performance.

  3. [Population policies and population trends in China].

    Science.gov (United States)

    Pressat, R

    1983-04-01

    Although relatively little has been known about the Chinese population in recent centuries, figures are available for more remote times. In the year 2 the Chinese population was recorded at 60 million. In 1928, when the last pre-Revolution census was conducted, China had a population of 475 million. The population was not believed to have grown very much due to internal disorders, war, and foreigh invasion, but the 1953 census counted 582 million to which were added 18 million to include Taiwan and overseas Chinese. The figure of 600 million appears to mark the beginning of concern over demographic problems. The crude birth rate was estimated at 37/1000 and the death rate at 17/1000. The 1953 census was conducted with Soviet aid and was given some publicity. The period 1953-58 was marked by a mortality decline and a steady fertility rate, but the population is believed to have declined from 647 million in 1958 to 643 million in 1962, the end of the Great Leap Forward. A census suppressed until recently gave a total of 694 million for 1964. Population growth was considerable from 1961-66. In the 1st part of the Cultural Revolution from 1966-70, no effort was made to control population growth; in 1971, the crude birth rate was estimated at 30-35/1000, the mortality rate was 8/1000, and the growth rate was 2.6%. 1971-79 marked the 1st phase of birth limitation, which became more pressing with time. The population was counted at 1 billion 8 million in 1982, with a birth rate of 21/1000, a death rate of 6/1000, and a growth rate of 1.5%. Because of China's comprehensive system of population registration, the results of the 1982 census were not completely unexpected. Wide differences in growth rates were noted between provinces, and the minorities grew at a faster rate than the Han majority. Immediately after the Revolution, population was relatively neglected in China in favor of greater attention to economic growth. The 1st warnings about the consequences of overly

  4. Single-dopant resonance in a single-electron transistor

    OpenAIRE

    Golovach, V. N.; Jehl, X.; Houzet, M.; Pierre, M.; Roche, B.; Sanquer, M.; Glazman, L. I.

    2011-01-01

    Single dopants in semiconductor nanostructures have been studied in great details recently as they are good candidates for quantum bits, provided they are coupled to a detector. Here we report coupling of a single As donor atom to a single-electron transistor (SET) in a silicon nanowire field-effect transistor. Both capacitive and tunnel coupling are achieved, the latter resulting in a dramatic increase of the conductance through the SET, by up to one order of magnitude. The experimental resu...

  5. Subcellular western blotting of single cells.

    Science.gov (United States)

    Yamauchi, Kevin A; Herr, Amy E

    2017-01-01

    Although immunoassays are the de facto standard for determining subcellular protein localization in individual cells, antibody probe cross-reactivity and fixation artifacts remain confounding factors. To enhance selectivity while providing single-cell resolution, we introduce a subcellular western blotting technique capable of separately assaying proteins in the 14 pL cytoplasm and 2 pL nucleus of individual cells. To confer precision fluidic control, we describe a passive multilayer microdevice that leverages the rapid transport times afforded by miniaturization. After isolating single cells in microwells, we apply single-cell differential detergent fractionation to lyse and western blot the cytoplasmic lysate, whereas the nucleus remains intact in the microwell. Subsequently, we lyse the intact nucleus and western blot the nuclear lysate. To index each protein analysis to the originating subcellular compartment, we utilize bi-directional electrophoresis, a multidimensional separation that assays the lysate from each compartment in a distinct region of the separation axis. Single-cell bi-directional electrophoresis eliminates the need for semi-subjective image segmentation algorithms required in immunocytochemistry. The subcellular, single-cell western blot is demonstrated for six targets per cell, and successfully localizes spliceosome-associated proteins solubilized from large protein and RNA complexes, even for closely sized proteins (a 7 kDa difference). Measurement of NF-κB translocation dynamics in unfixed cells at 15-min intervals demonstrates reduced technical variance compared with immunofluorescence. This chemical cytometry assay directly measures the nucleocytoplasmic protein distribution in individual unfixed cells, thus providing insight into protein signaling in heterogeneous cell populations.

  6. A study on meme propagation in multimemetic algorithms

    Directory of Open Access Journals (Sweden)

    Nogueras Rafael

    2015-09-01

    Full Text Available Multimemetic algorithms (MMAs are a subclass of memetic algorithms in which memes are explicitly attached to genotypes and evolve alongside them. We analyze the propagation of memes in MMAs with a spatial structure. For this purpose we propose an idealized selecto-Lamarckian model that only features selection and local improvement, and study under which conditions good, high-potential memes can proliferate. We compare population models with panmictic and toroidal grid topologies. We show that the increased takeover time induced by the latter is essential for improving the chances for good memes to express themselves in the population by improving their hosts, hence enhancing their survival rates. Experiments realized with an actual MMA on three different complex pseudo-Boolean functions are consistent with these findings, indicating that memes are more successful in a spatially structured MMA, rather than in a panmictic MMA, and that the performance of the former is significantly better than that of its panmictic counterpart

  7. Peru: population and policy.

    Science.gov (United States)

    Sobrevilla, L A

    1987-06-01

    Peru's 1985 Population Policy Law states as its second objective that individuals and couples should be well informed and provided with the education and health services that will assist them in making responsible decisions about the number and spacing of their children. Thus, the law establishes a firm basis for IEC programs. With regard to population education, the purpose of the law is to create awareness through all educational channels of the reciprocal influence of population dynamics and socioeconomic development and to promote positive attitudes toward small family size. The law promotes the use of the communications media to educate and inform about population issues. The National Population Council, which coordinates and supervises the IEC activities of public sector agencies, has issued publications and audiovisual materials, conducted meetings with government officials and opinion leaders, and promoted awareness of population policy as a key part of development planning. In 1984, the Council organized the First National Seminar on Communication and Population to review activities, set the basis for intersectoral coordination, unify criteria, and review population policy concepts and language. The Ministry of Health carries out IEC activities as part of its family planning services program. In addition, the Ministry of Education has organized a national population education program that aims to revise school curricula to include a greater emphasis on population dynamics and family life education. The activities of a number of private institutions complement the IEC work public sector organizations.

  8. Molecular Population Genetics.

    Science.gov (United States)

    Casillas, Sònia; Barbadilla, Antonio

    2017-03-01

    Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. Copyright © 2017 Casillas and Barbadilla.

  9. Molecular Population Genetics

    Science.gov (United States)

    Casillas, Sònia; Barbadilla, Antonio

    2017-01-01

    Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. PMID:28270526

  10. Advances in single chain technology.

    Science.gov (United States)

    Gonzalez-Burgos, Marina; Latorre-Sanchez, Alejandro; Pomposo, José A

    2015-10-07

    The recent ability to manipulate and visualize single atoms at atomic level has given rise to modern bottom-up nanotechnology. Similar exquisite degree of control at the individual polymeric chain level for producing functional soft nanoentities is expected to become a reality in the next few years through the full development of so-called "single chain technology". Ultra-small unimolecular soft nano-objects endowed with useful, autonomous and smart functions are the expected, long-term valuable output of single chain technology. This review covers the recent advances in single chain technology for the construction of soft nano-objects via chain compaction, with an emphasis in dynamic, letter-shaped and compositionally unsymmetrical single rings, complex multi-ring systems, single chain nanoparticles, tadpoles, dumbbells and hairpins, as well as the potential end-use applications of individual soft nano-objects endowed with useful functions in catalysis, sensing, drug delivery and other uses.

  11. Nanodiamond Emitters of Single Photons

    Directory of Open Access Journals (Sweden)

    Vlasov I.I.

    2015-01-01

    Full Text Available Luminescence properties of single color centers were studied in nanodiamonds of different origin. It was found that single photon emitters could be realized even in molecularsized diamond (less than 2 nm capable of housing stable luminescent center “silicon-vacancy.” First results on incorporation of single-photon emitters based on luminescent nanodiamonds in plasmonic nanoantennas to enhance the photon count rate and directionality, diminish the fluorescence decay time, and provide polarization selectivity are presented.

  12. GPU accelerated population annealing algorithm

    Science.gov (United States)

    Barash, Lev Yu.; Weigel, Martin; Borovský, Michal; Janke, Wolfhard; Shchur, Lev N.

    2017-11-01

    steps and multi-histogram reweighting. Additional comments: Code repository at https://github.com/LevBarash/PAising. The system size and size of the population of replicas are limited depending on the memory of the GPU device used. For the default parameter values used in the sample programs, L = 64, θ = 100, β0 = 0, βf = 1, Δβ = 0 . 005, R = 20 000, a typical run time on an NVIDIA Tesla K80 GPU is 151 seconds for the single spin coded (SSC) and 17 seconds for the multi-spin coded (MSC) program (see Section 2 for a description of these parameters).

  13. Population and Environment

    OpenAIRE

    Theodore Panayotou

    2000-01-01

    The past fifty years have witnessed two simultaneous and accelerating trends: an explosive growth in population and a steep increase in resource depletion and environmental degradation. These trends have fueled the debate on the link between population and environment that began 150 years earlier, when Malthus voiced his concern about the ability of the earth and its finite resources to feed an exponentially growing population. The purpose of this study is to review the literature on populati...

  14. Leptin gene polymorphism in Indian Sahiwal cattle by single strand ...

    African Journals Online (AJOL)

    These leptin gene variants can be sequenced and screened in the entire population to develop single nucleotide polymorphisms (SNPs) for association studies with different productive and reproductive performances and marker assisted selection. Keywords: Leptin gene, PCR-SSCP, genetic variability, dairy cattle

  15. Comparative study of analgesic effectiveness of single doses of ...

    African Journals Online (AJOL)

    Method: This study employed the visual analogue scale to measure the effectiveness of single doses of ibuprofen and paracetamol over a six-hour period, following a third molar surgery in a homogenous study population, matched for age, body mass index (BMI) and gender. Alarms were set to remind patients to score pain ...

  16. Prospects for inferring pairwise relationships with single nucleotide polymorphisms

    Science.gov (United States)

    Jeffery C. Glaubitz; O. Eugene, Jr. Rhodes; J. Andrew DeWoody

    2003-01-01

    An extraordinarily large number of single nucleotide polymorphisms (SNPs) are now available in humans as well as in other model organisms. Technological advancements may soon make it feasible to assay hundreds of SNPs in virtually any organism of interest. One potential application of SNPs is the determination of pairwise genetic relationships in populations without...

  17. Gender Differences in Communication Patterns of Females in Single ...

    African Journals Online (AJOL)

    This study examined gender differences in communication patterns of females in single-sex and mixed-sex schools. The design of the study was an ex-post facto design. Two research questions and one hypothesis guided the study. All the population of 218 senior secondary II female students was used for the study which ...

  18. Control of Single-Stage Single-Phase PV inverter

    DEFF Research Database (Denmark)

    Ciobotaru, Mihai; Teodorescu, Remus; Blaabjerg, Frede

    2005-01-01

    In this paper the issue of control strategies for single-stage photovoltaic (PV) inverter is addressed. Two different current controllers have been implemented and an experimental comparison between them has been made. A complete control structure for the single-phase PV system is also presented...

  19. On population in a polluted patchy environment

    International Nuclear Information System (INIS)

    He, J; Wang, K

    2008-01-01

    In this paper, the effect of diffusion on the permanence of a species in a polluted patchy environment is studied. We set up a single species diffusive system on a region composed of two patches, one of which is contaminated and the other is clear. When there is no diffusion and the exogenous toxicant concentration exceeds some a value, the population in the polluted patch will go to extinction. When the diffusion exists, we give suitable conditions for the permanence or extinction of the population in the system

  20. Targeting population heterogeneity for optimal cell factories

    DEFF Research Database (Denmark)

    Heins, Anna-Lena; Carlqvist, Magnus; Helmark, S.

    the heterogeneity level of the population. To further investigate these phenomena and gain a deeper understanding of population heterogeneity, Saccharomyces cerevisiae growth reporter strains based on the expression of green fluorescent protein (GFP) were constructed which enabled us to perform single cell level......, substrates, and pH are typically observed in many industrial scale fermentation processes. Consequently, the microbial cells experience rapid changes in environmental conditions as they circulate throughout the reactor, which might pose stress on the cells and affect their metabolism and consequently affect...

  1. Measurably evolving populations

    DEFF Research Database (Denmark)

    Drummond, Alexei James; Pybus, Oliver George; Rambaut, Andrew

    2003-01-01

    processes through time. Populations for which such studies are possible � measurably evolving populations (MEPs) � are characterized by sufficiently long or numerous sampled sequences and a fast mutation rate relative to the available range of sequence sampling times. The impact of sequences sampled through...... time has been most apparent in the disciplines of RNA viral evolution and ancient DNA, where they enable us to estimate divergence times without paleontological calibrations, and to analyze temporal changes in population size, population structure and substitution rates. Thus, MEPs could increase our...

  2. Do single women value early retirement more than single men?

    DEFF Research Database (Denmark)

    Danø, Anne Møller; Ejrnæs, Mette; Husted, Leif

    2005-01-01

    The focus of this paper is to analyse why a large fraction of single elderly people choose to retire early. A structural model directly based on the individual decision of labour supply is estimated on a sample of singles, where singles are defined as those who are living alone. We find that inco...... are willing to reduce the income to 81%. Men's retirement decision is mainly influenced by income and health, whereas women's retirement decision is also affected by education and unemployment experience...... and health are important determinants of the retirement decision. Furthermore, we find substantial gender differences in the retirement pattern. Healthy single women value retirement more than healthy single men and are willing to reduce their disposable income to 74% of their previous income while men...

  3. Single cell transcriptional analysis reveals novel innate immune cell types

    Directory of Open Access Journals (Sweden)

    Linda E. Kippner

    2014-06-01

    Full Text Available Single-cell analysis has the potential to provide us with a host of new knowledge about biological systems, but it comes with the challenge of correctly interpreting the biological information. While emerging techniques have made it possible to measure inter-cellular variability at the transcriptome level, no consensus yet exists on the most appropriate method of data analysis of such single cell data. Methods for analysis of transcriptional data at the population level are well established but are not well suited to single cell analysis due to their dependence on population averages. In order to address this question, we have systematically tested combinations of methods for primary data analysis on single cell transcription data generated from two types of primary immune cells, neutrophils and T lymphocytes. Cells were obtained from healthy individuals, and single cell transcript expression data was obtained by a combination of single cell sorting and nanoscale quantitative real time PCR (qRT-PCR for markers of cell type, intracellular signaling, and immune functionality. Gene expression analysis was focused on hierarchical clustering to determine the existence of cellular subgroups within the populations. Nine combinations of criteria for data exclusion and normalization were tested and evaluated. Bimodality in gene expression indicated the presence of cellular subgroups which were also revealed by data clustering. We observed evidence for two clearly defined cellular subtypes in the neutrophil populations and at least two in the T lymphocyte populations. When normalizing the data by different methods, we observed varying outcomes with corresponding interpretations of the biological characteristics of the cell populations. Normalization of the data by linear standardization taking into account technical effects such as plate effects, resulted in interpretations that most closely matched biological expectations. Single cell transcription

  4. Single-cell sequencing in stem cell biology.

    Science.gov (United States)

    Wen, Lu; Tang, Fuchou

    2016-04-15

    Cell-to-cell variation and heterogeneity are fundamental and intrinsic characteristics of stem cell populations, but these differences are masked when bulk cells are used for omic analysis. Single-cell sequencing technologies serve as powerful tools to dissect cellular heterogeneity comprehensively and to identify distinct phenotypic cell types, even within a 'homogeneous' stem cell population. These technologies, including single-cell genome, epigenome, and transcriptome sequencing technologies, have been developing rapidly in recent years. The application of these methods to different types of stem cells, including pluripotent stem cells and tissue-specific stem cells, has led to exciting new findings in the stem cell field. In this review, we discuss the recent progress as well as future perspectives in the methodologies and applications of single-cell omic sequencing technologies.

  5. Quantum optics with single quantum dot devices

    International Nuclear Information System (INIS)

    Zwiller, Valery; Aichele, Thomas; Benson, Oliver

    2004-01-01

    A single radiative transition in a single-quantum emitter results in the emission of a single photon. Single quantum dots are single-quantum emitters with all the requirements to generate single photons at visible and near-infrared wavelengths. It is also possible to generate more than single photons with single quantum dots. In this paper we show that single quantum dots can be used to generate non-classical states of light, from single photons to photon triplets. Advanced solid state structures can be fabricated with single quantum dots as their active region. We also show results obtained on devices based on single quantum dots

  6. Single-cavity SLED device

    International Nuclear Information System (INIS)

    Lippmann, B.A.

    1984-09-01

    The conventional SLED device used at SLAC requires two cavities. However, the same effect can be obtained with a single cavity; the theory and operation of the device is the same, only the hardware is changed. The single-cavity device is described here

  7. Single top t-channel

    CERN Document Server

    Faltermann, Nils

    2017-01-01

    The production of single top quarks allows to study the interplay of top quark physics and the electroweak sector of the standard model. Deviations from predictions can be a hint for physics beyond the standard model. The t-channel is the dominant production mode for single top quarks at the LHC. This talk presents the latest measurements from the ATLAS and CMS collaborations.

  8. Quantum transport through single molecules

    NARCIS (Netherlands)

    Osorio Oliveros, E.A.

    2009-01-01

    This thesis describes three-terminal transport measurements through single molecules. The interest in this field stems from the dream that single molecules will form the building blocks for future nanoscale electronic devices. The advantages are their small size -nanometers-, and their synthetic

  9. Population and development.

    Science.gov (United States)

    1999-04-01

    This article highlights improvements in China's population development, particularly in its family planning programs. China first realized the importance of family planning in 1962. 2 years later, a Family Planning Office was established under the State Council, which was upgraded into a Leading Group in 1973, and population began to be incorporated into national planning. In 1981, the State Family Planning Commission was established as a ministry-level organization directly under the State Council. In 1982, the government further defined its population policy as "controlling population growth and improving population quality.¿ Moreover, in the wake of the International Conference on Population Development in 1994 and the Fourth World Conference on Women in 1995, China has called for reorientations in family planning programs and in social regulations. This article also presents the efforts of the Chinese government to protect the country's environment and the employment of certain measures to facilitate population migration in response to the needs of the migrant population for family planning and health care.

  10. The Population Activist's Handbook.

    Science.gov (United States)

    Population Inst., Washington, DC.

    This handbook is a guide to effective action strategies on dealing with overpopulation. Divided into five sections, the book outlines programs, suggests references, and lists resources that are helpful for thinking and for planning action on population issues. Section one focuses on strategies to change the current population policy choices made…

  11. The World Population Dilemma.

    Science.gov (United States)

    Population Reference Bureau, Inc., Washington, DC.

    This book is the third in a series published by the Population Reference Bureau aimed at illuminating the facts and consequences of human population dynamics for secondary and college-age students. Many illustrations, charts and graphs are included in this volume to help the reader grasp a number of the current ideas and concepts that are used in…

  12. Glaucoma in Asian Populations

    Science.gov (United States)

    ... is expected to become an even more serious problem as the world population and longevity increases. The other major glaucoma type ... of all cases of blindness from glaucoma in China. There is great racial diversity among Asian populations, and these differences are represented in the presentation ...

  13. Population. Headline Series.

    Science.gov (United States)

    Oppenheimer, Valerie K.

    Useful as background reading or secondary classroom material, this pamphlet reviews several dimensions of world population growth and control. The first of seven chapters, World Population Growth: Past, Present and Future, discusses some of the reasons for the greatly accelerated growth since 1950, and points out that even significantly rapid…

  14. Regional Population Dynamics

    Science.gov (United States)

    Andrew Birt

    2011-01-01

    The population dynamics of the southern pine beetle (SPB) exhibit characteristic fluctuations between relatively long endemic and shorter outbreak periods. Populations exhibit complex and hierarchical spatial structure with beetles and larvae aggregating within individual trees, infestations with multiple infested trees, and regional outbreaks that comprise a large...

  15. Negative Drift in Populations

    DEFF Research Database (Denmark)

    Lehre, Per Kristian

    2011-01-01

    An important step in gaining a better understanding of the stochastic dynamics of evolving populations, is the development of appropriate analytical tools. We present a new drift theorem for populations that allows properties of their long-term behaviour, e.g. the runtime of evolutionary algorithms...

  16. Population structure of Staphylococcus aureus in China

    OpenAIRE

    Yan, Xiaomei

    2015-01-01

    The present PhD research was aimed at analysing the population structure of Staphylococcus aureus in China. Between 2000 and 2005 we found that patients from a single Chinese hospital showed increasing trends in antimicrobial resistance. Among methicillin-resistant S. aureus (MRSA), resistance against rifampicin doubled to 68%. Staphylococcal food poisoning (SFP) is frequent in China. Two predominant S. aureus lineages, ST6 and ST943, were identified causing outbreaks of SFP in Southern China...

  17. Single-dopant resonance in a single-electron transistor

    Science.gov (United States)

    Golovach, V. N.; Jehl, X.; Houzet, M.; Pierre, M.; Roche, B.; Sanquer, M.; Glazman, L. I.

    2011-02-01

    Single dopants in semiconductor nanostructures have been studied in great detail recently as they are good candidates for quantum bits, provided they are coupled to a detector. Here we report the coupling of a single As donor atom to a single-electron transistor (SET) in a silicon nanowire field-effect transistor. Both capacitive and tunnel coupling are achieved, the latter resulting in a dramatic increase of the conductance through the SET, by up to one order of magnitude. The experimental results are well explained by the rate-equation theory developed in parallel with the experiment.

  18. Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: insights from genome-wide SNPs and microsatellites.

    Science.gov (United States)

    Antoniou, Aglaia; Kasapidis, Panagiotis; Kotoulas, Georgios; Mylonas, Constantinos C; Magoulas, Antonios

    2017-12-01

    Elucidating the patterns of the Atlantic Bluefin tuna [ABFT, Thunnus thynnus (Linnaeus, 1758)] population structure constitutes a challenging task of great importance. Most of the unique challenges stem from its biology, as well as the attributes of the marine realm in which it disperses. Accurate information is urgently needed for stock assessment, and the identification of critical features to the persistence and adaptation of populations in order to formulate and adopt effective strategies for ABFT conservation and management. Conclusions of a great number of ABFT genetic studies on the Mediterranean Sea stock structure are rather controversial and not yet conclusive. In this study, ABFT genomic diversity was investigated in the Mediterranean Sea, which is the most important area for the species' reproduction. Analyzing genome-wide SNPs and microsatellites from ABFT samples collected throughout the Mediterranean Sea did not provide strong evidence of genetic structure, pointing towards the existence of a single panmictic unit. An alternative view would recognize a failure to reject the null hypothesis of a panmictic unit as an effect of the study's sampling design, the type of markers used, and the effectiveness/suitability of analysis methods in respect to the species biological characteristics or any combination of the above. Unravelling the drivers of ABFT population diversity would require the consideration of important aspects of the species spawning behavior for the determination of the appropriate sampling design. Novel approaches and methods of analysis that will bring together experts in genetics/-omics, ecology and oceanography are deemed necessary. Analyzing ABFT genetic data under the discipline of seascape genetics could provide the analysis framework under which major abiotic and biotic forces controlling ABFT recruitment could be identified, elucidating the complicated population dynamics of the species, while multiple and continuous fisheries

  19. Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level

    Directory of Open Access Journals (Sweden)

    Zixi Chen

    2017-09-01

    Full Text Available Microbiologists traditionally study population rather than individual cells, as it is generally assumed that the status of individual cells will be similar to that observed in the population. However, the recent studies have shown that the individual behavior of each single cell could be quite different from that of the whole population, suggesting the importance of extending traditional microbiology studies to single-cell level. With recent technological advances, such as flow cytometry, next-generation sequencing (NGS, and microspectroscopy, single-cell microbiology has greatly enhanced the understanding of individuality and heterogeneity of microbes in many biological systems. Notably, the application of multiple ‘omics’ in single-cell analysis has shed light on how individual cells perceive, respond, and adapt to the environment, how heterogeneity arises under external stress and finally determines the fate of the whole population, and how microbes survive under natural conditions. As single-cell analysis involves no axenic cultivation of target microorganism, it has also been demonstrated as a valuable tool for dissecting the microbial ‘dark matter.’ In this review, current state-of-the-art tools and methods for genomic and transcriptomic analysis of microbes at single-cell level were critically summarized, including single-cell isolation methods and experimental strategies of single-cell analysis with NGS. In addition, perspectives on the future trends of technology development in the field of single-cell analysis was also presented.

  20. Stockholm sidesteps population issue.

    Science.gov (United States)

    1972-08-01

    Population policies were discussed during a U.N. Conference on the Human Environment held in Stockholm in June 1972. Although it was acknowledged that people in developed countries have a much more detrimental impact on the environment due to their high levels of consumption, various positions were taken on the importance of family planning in developing countries. Both the Chinese delegate and Indira Ghandi of India remarked that one cannot blame overpopulation for ecological problems. Other speakers agreed that technology would solve ecological problems and that population growth rates would take care of themselves when development occurred. Other speakers, such as Dr. Paul Ehrlich believe that worldwide stabilization of population is necessary to maintain life-support systems of this planet. The majority of delegates to the Conference did not consider the reduction of population growth to be a priority, although it was recommended that national governments develop population policies, and that WHO give increased support to family planning activities. It was also recommended that adequate attention be given to the relationship between population and environment at the World Population Conference in 1974.

  1. Single banking supervision and the single supervisory mechanism

    Directory of Open Access Journals (Sweden)

    Gheorghe, C. A.

    2013-06-01

    Full Text Available A resolution seems to have been found for the banking crisis. The first steps have been made towards the construction of the Economic and Monetary Union, steps involving the single supervision of banks, in order to avoid the discount of a new financial crisis on the expense of the EU state members. The Single Supervisory Mechanism – SSM is to become effective as of March 1, 2014, at the earliest.

  2. Economics of population versus economic demography

    Directory of Open Access Journals (Sweden)

    A. A. Tkachenko

    2017-01-01

    Full Text Available The article specifies the correlation between economic demography and the economy of population as the most important scientific areas of modern research. It is concluded that the Russian scientific community lags in the development of these sciences from the world scientific thought. Special attention is paid to the works and ideas of S. Kuznets and Amartya Sen as outstanding researchers of the interrelationships between the population and the economy. It is emphasized that their contribution was not only theoretical but also of practical importance. The importance of G. Myrdal’s works for modern studies of the consequences of population aging is considered. The article examines foreign training courses on “Population Economics”, presented at the Universities of Wisconsin and McMaster, their analysis led to the conclusion that the preparation of textbooks on courses is less productive than the use of scientific articles in journals, containing more recent ideas and achievements of science. The author considers the system, proposed in the course Michel Grignon and Byron G. Spencer «The Economics of Population» more preferable. The article substantiates the opinion that the economic theory of well-being should be the core of the population economy. It is concluded that the differences between economic demography and the economy of population are not just differences between the micro- and macro levels, as some authors write, but the transition to large scales and entropy.The author identifies three most important areas of demo-economic research, which include research in the field of human capital, international economic migration, especially remittance, analysis of the stratification of the population and society by the income in the global and national economies. One can single out the general area of interests of the population economy and economic demography in which these sciences are almost impossible to divide and in which only

  3. The population threat.

    Science.gov (United States)

    Teitelbaum, M S

    1992-01-01

    Commentary is provided on the challenges faced by the new Clinton administration in formulating US key foreign policy initiatives. There is an urgent need to provide balanced and effective foreign aid for reducing high fertility rates in the developing world. There is also a need to effectively monitor the large migrations of populations. Over the past 10 years, the US has not been actively practicing world leadership on population issues. 3 changes in 1993 give impetus to redirect foreign policy: 1) the waning influence of fringe groups who controlled population issues; 2) the campaign promises to restore UN population stabilization programs; and 3) the evidence from the Persian Gulf and Yugoslavia that demographic issues require planning and assessment. Global population growth has been concentrated in the past 40 years, in part due to mortality declines and sustained high fertility. Of significance is the rapidness and momentum of growth. A high percentage are and will be children. Urban population is also growing rapidly in high fertility countries. Countries with high fertility and significant rural-to-urban migration also have large international migrations. The evolution of policy since the 1950s, which for the most part ignored population issues, is discussed. The American debates have been charged with emotionalism: about human sexuality, legitimacy of voluntary fertility control, the role and status of women and men, abortion, intergenerational transfer of obligations, ethnic solidarity and the sovereignty of national borders, and the proper roles of the state versus the marketplace. There have been over 200 years of ideological argument over population issues. The Malthusian argument was that large population size did not increase prosperity, and growth should be limited. The Marxist-Leninist position was that contraception was Malthusian, abortion was a woman's right, and population growth was neutral. By late 1970 the Chinese Maoists adopted the moral

  4. Predation and caribou populations

    Directory of Open Access Journals (Sweden)

    Dale R. Seip

    1991-10-01

    Full Text Available Predation, especially wolf (Canis lupus predation, limits many North American caribou (Rangifer tarandus populations below the density that food resources could sustain. The impact of predation depends on the parameters for the functional and numerical response of the wolves, relative to the potential annual increment of the caribou population. Differences in predator-avoidance strategies largely explain the major differences in caribou densities that occur naturally in North America. Caribou migrations that spatially separate caribou from wolves allow relatively high densities of caribou to survive. Non-migratory caribou that live in areas where wolf populations are sustained by alternate prey can be eliminated by wolf predation.

  5. Immunization in special populations.

    Science.gov (United States)

    Miller, Michael A; Rathore, Mobeen H

    2012-01-01

    In summary, immunizations in special populations require understanding the underlying disease and how it might affect the immune system's ability to mount an antibody response to vaccines or predispose certain patient populations to developing certain serious infections. There is still a great need for research on the optimal timing of vaccines after transplants, how to assess protection and development of a protective antibody response after immunization, and whether certain groups (eg, HIV) need to be revaccinated after a certain amount of time if their antibody levels decline. In addition, there are limited data on efficacy of the newer vaccines in these special patient populations, which also requires further investigation.

  6. Fluctuations in a coupled population model

    International Nuclear Information System (INIS)

    Jakeman, E; Hopcraft, K I; Matthews, J O

    2005-01-01

    We investigate a discrete Markov process in which the immigration of individuals into one population is controlled by the fluctuations in another. We examine the effect of coupling back the second population to the first through a similar mechanism and derive exact solutions for the generating functions of the population statistics. We show that a stationary state exists over a certain parameter range and obtain expressions for moments and correlation functions in this regime. When more than two populations are coupled, cyclically transient oscillations and periodic behaviour of correlation functions are predicted. We demonstrate that if the initial distribution of either population is stable, or more generally has a power-law tail that falls off like N -(1+α) (0 < α < 1), then for certain parameter values there exists a stationary state that is also power law but not stable. This stationary state cannot be accessed from a single multiple immigrant population model, but arises solely from the nonlinear interaction of the coupled system

  7. The population genetics of evolutionary rescue.

    Directory of Open Access Journals (Sweden)

    H Allen Orr

    2014-08-01

    Full Text Available Evolutionary rescue occurs when a population that is threatened with extinction by an environmental change adapts to the change sufficiently rapidly to survive. Here we extend the mathematical theory of evolutionary rescue. In particular, we model evolutionary rescue to a sudden environmental change when adaptation involves evolution at a single locus. We consider adaptation using either new mutations or alleles from the standing genetic variation that begin rare. We obtain several results: i the total probability of evolutionary rescue from either new mutation or standing variation; ii the conditions under which rescue is more likely to involve a new mutation versus an allele from the standing genetic variation; iii a mathematical description of the U-shaped curve of total population size through time, conditional on rescue; and iv the time until the average population size begins to rebound as well as the minimal expected population size experienced by a rescued population. Our analysis requires taking into account a subtle population-genetic effect (familiar from the theory of genetic hitchhiking that involves "oversampling" of those lucky alleles that ultimately sweep to high frequency. Our results are relevant to conservation biology, experimental microbial evolution, and medicine (e.g., the dynamics of antibiotic resistance.

  8. Article Molecular analysis of three FUT3 gene single nucleotide polymorphisms and their relationship with the lewis erythrocytary phenotype in a human population of japanese-ancestry living in Tomé Açu, a town in the Brazilian Amazon

    Directory of Open Access Journals (Sweden)

    Pablo Abdon da Costa Francez

    2007-03-01

    Full Text Available The Lewis blood group system involves two major antigens, Leª and Le b. Their antigenic determinants are not primary gene products but are synthesized by the transfer of sugar subunits to a precursory chain by a specific enzyme which is the product of the FUT3 gene (Lewis gene. The presence of three FUT3 gene single nucleotide polymorphisms (SNPs (59T > G; 508G > A and 1067T > A was related to the Lewis phenotype of erythrocytes from 185 individuals of Japanese ancestry living in the town of Tomé-Açu in the Brazilian Amazon region. This relationship was detected using a serological hemagglutination test and the Dot-ELISA assay along with the molecular technique PCR-RFLP. We found that the three SNPs investigated in this study only accounted for a proportion of the Lewis-negative phenotype of the erythrocytes.

  9. Populated Places of Iowa

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — This coverage contains points that represent populated places, ie. cities, towns, villages or any other named place where people live. The coverage was developed...

  10. Parallel grid population

    Science.gov (United States)

    Wald, Ingo; Ize, Santiago

    2015-07-28

    Parallel population of a grid with a plurality of objects using a plurality of processors. One example embodiment is a method for parallel population of a grid with a plurality of objects using a plurality of processors. The method includes a first act of dividing a grid into n distinct grid portions, where n is the number of processors available for populating the grid. The method also includes acts of dividing a plurality of objects into n distinct sets of objects, assigning a distinct set of objects to each processor such that each processor determines by which distinct grid portion(s) each object in its distinct set of objects is at least partially bounded, and assigning a distinct grid portion to each processor such that each processor populates its distinct grid portion with any objects that were previously determined to be at least partially bounded by its distinct grid portion.

  11. Fish population dynamics

    National Research Council Canada - National Science Library

    Gulland, J. A

    1977-01-01

    This book describes how the dynamics of fish populations can be analysed in terms of the factors affecting their rates of growth, mortality and reproduction, with particular emphasis on the effects of fishing...

  12. County Population Vulnerability

    Data.gov (United States)

    City and County of Durham, North Carolina — This layer summarizes the social vulnerability index for populations within each county in the United States at scales 1:3m and below. It answers the question...

  13. Market Squid Population Dynamics

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains population dynamics data on paralarvae, juvenile and adult market squid collected off California and the US Pacific Northwest. These data were...

  14. Stochastically sustained population oscillations in high-β nanolasers

    International Nuclear Information System (INIS)

    Lebreton, A; Abram, I; Robert-Philip, I; Beveratos, A; Takemura, N; Kuwata-Gonokami, M

    2013-01-01

    Nonlinear dynamical systems involving small populations of individuals may sustain oscillations in the population densities arising from discrete changes in population numbers due to random events. By applying these ideas to nanolasers operating with small numbers of emitting dipoles and photons at threshold, we show that such lasers should display photon and dipole population cycles above threshold, which should be observable as a periodic modulation in the second-order correlation function of the nanolaser output. Such a modulation was recently reported in a single-mode vertical-cavity surface-emitting semiconductor laser. (paper)

  15. Single-electron thermal noise.

    Science.gov (United States)

    Nishiguchi, Katsuhiko; Ono, Yukinori; Fujiwara, Akira

    2014-07-11

    We report the observation of thermal noise in the motion of single electrons in an ultimately small dynamic random access memory (DRAM). The nanometer-scale transistors that compose the DRAM resolve the thermal noise in single-electron motion. A complete set of fundamental tests conducted on this single-electron thermal noise shows that the noise perfectly follows all the aspects predicted by statistical mechanics, which include the occupation probability, the law of equipartition, a detailed balance, and the law of kT/C. In addition, the counting statistics on the directional motion (i.e., the current) of the single-electron thermal noise indicate that the individual electron motion follows the Poisson process, as it does in shot noise.

  16. Single-employer Pension Plans

    Data.gov (United States)

    Pension Benefit Guaranty Corporation — This spreadsheet lists the active single-employer pensions plans insured by PBGC. Plans are identified by name, employer identification number (EIN) and plan number...

  17. Microfluidics for single cell analysis

    DEFF Research Database (Denmark)

    Jensen, Marie Pødenphant

    Isolation and manipulation of single cells have gained an increasing interest from researchers because of the heterogeneity of cells from the same cell culture. Single cell analysis can ensure a better understanding of differences between individual cells and potentially solve a variety of clinical...... problems. In this thesis lab on a chip systems for rare single cell analysis are investigated. The focus was to develop a commercial, disposable device for circulating tumour cell (CTC) analysis. Such a device must be able to separate rare cells from blood samples and subsequently capture the specific...... cells, and simultaneously be fabricated and operated at low costs and be user-friendly. These challenges were addressed through development of two microfluidic devices, one for rare cell isolation based on pinched flow fractionation (PFF) and one for single cell capture based on hydrodynamic trapping...

  18. Single Sign On Internal (SSOi)

    Data.gov (United States)

    Department of Veterans Affairs — Provides single sign-on solution for internal facing VA applications. Allows internal users access to a variety of VA systems and applications using a reduced set of...

  19. Food for tomorrow's population.

    Science.gov (United States)

    Hugo, G

    1983-06-01

    This discussion outlines and clarifies the dimensions of the world's current food-population balance and examines likely future changes in this balance over the next 20 years. The 1st section summarizes the contemporary world demographic situation in the early 1980s, focusing on regional differences in patterns of population growth and the significant food shortages in the developing countries. A subsequent section considers the outlook for population growth up to the year 2000 with particular reference to the most recent UN population projects. The discussion of food production and supply includes some specific comments on the situation in Indonesia. The world's population in 1983 has been estimated at 4677 million. It will reach 5 billion in the next 5 years. The countries which can least afford it are growing the fastest. These countries will account for 79% of the world's population in 2000 and 83% by 2020. Fertility in the less developed countries (LDCs) is twice that of more developed countries, with women in the former group having an average of around 4.5 children and in the latter, 1.9. The substantial declines in fertility in many countries are not fully reflected in declines in population growth and natural increase rates. This is because of major improvements which have occurred in mortality. During recent decades there has been a marked increase in world food production. In the developed countries increases in food production have continued at more than twice those for population, but this was not the case in the less developed countries where the margin narrowed during the 1950s and 1960s until in the early 1970s population was increasing at a slightly faster rate overall than was food production. Food crisis situations continue to occur with disturbing frequency in several regions. Seasonal, regional, and national variations in food shortages are not the only dimensions to food-population imbalances. Within nations there is inequality in access to

  20. EDUCATION AND ROMA POPULATION

    Directory of Open Access Journals (Sweden)

    Ana Asensio Belenguer

    2016-07-01

    Full Text Available This article deals with Education and the Roma Population. It presents an approach to schooling of Romani children since its outset in the city of Zaragoza (Spain. It analyzes the current status as presented by the Strategy for Social Inclusion of this people 2012-2020, and collects, from various sources, the fact that education remains a pending challenge for Roma Population. Measures to be taken by the educational community from a gender and inclusive perspective are proposed.