WorldWideScience

Sample records for cooperation molecular population

  1. Variation, sex, and social cooperation: molecular population genetics of the social amoeba Dictyostelium discoideum.

    Directory of Open Access Journals (Sweden)

    Jonathan M Flowers

    2010-07-01

    Full Text Available Dictyostelium discoideum is a eukaryotic microbial model system for multicellular development, cell-cell signaling, and social behavior. Key models of social evolution require an understanding of genetic relationships between individuals across the genome or possibly at specific genes, but the nature of variation within D. discoideum is largely unknown. We re-sequenced 137 gene fragments in wild North American strains of D. discoideum and examined the levels and patterns of nucleotide variation in this social microbial species. We observe surprisingly low levels of nucleotide variation in D. discoideum across these strains, with a mean nucleotide diversity (pi of 0.08%, and no strong population stratification among North American strains. We also do not find any clear relationship between nucleotide divergence between strains and levels of social dominance and kin discrimination. Kin discrimination experiments, however, show that strains collected from the same location show greater ability to distinguish self from non-self than do strains from different geographic areas. This suggests that a greater ability to recognize self versus non-self may arise among strains that are more likely to encounter each other in nature, which would lead to preferential formation of fruiting bodies with clonemates and may prevent the evolution of cheating behaviors within D. discoideum populations. Finally, despite the fact that sex has rarely been observed in this species, we document a rapid decay of linkage disequilibrium between SNPs, the presence of recombinant genotypes among natural strains, and high estimates of the population recombination parameter rho. The SNP data indicate that recombination is widespread within D. discoideum and that sex as a form of social interaction is likely to be an important aspect of the life cycle.

  2. Population bottlenecks promote cooperation in bacterial biofilms.

    Directory of Open Access Journals (Sweden)

    Michael A Brockhurst

    Full Text Available Population bottlenecks are assumed to play a key role in the maintenance of social traits in microbes. Ecological parameters such as colonisation or disturbances can favour cooperation through causing population bottlenecks that enhance genetic structuring (relatedness. However, the size of the population bottleneck is likely to play a crucial role in determining the success of cooperation. Relatedness is likely to increase with decreasing bottleneck size thus favouring the evolution of cooperation. I used an experimental evolution approach to test this prediction with biofilm formation by the bacterium Pseudomonas fluorescens as the cooperative trait. Replicate populations were exposed to disturbance events every four days under one of six population bottleneck treatments (from 10(3 to 10(8 bacterial cells. In line with predictions, the frequency of evolved cheats within the populations increased with increasing bottleneck size. This result highlights the importance of ecologically mediated population bottlenecks in the maintenance of social traits in microbes.

  3. 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

  4. 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.

  5. Selection of Cooperation in Spatially Structured Populations

    Science.gov (United States)

    Yang, Hyunmo; Ghim, Cheol-Min

    The social dilemma games give rise to an emergence of cooperation in which altruistic individuals survive the natural selection at higher rate than random chance. We try to extend our understanding of this spatial reciprocity by including the impact of degree-degree correlation on the propensity toward prosocial behaviour in an otherwise well-mixed population. In a stochastic death-birth process with weak selection, we find that the disassortative degree mixing, or negative correlation between the degrees of neighbouring nodes significantly promotes the fixation of cooperators whereas the assortative mixing acts to suppress it. This is consistent with the fact that the spatial heterogeneity weakens the average tendency of a population to cooperate, which we describe in a unified scheme of the effective isothermality in coarse-grained networks. We also discuss the individual-level incentives that indirectly foster restructuring the social networks toward the more cooperative topologies.

  6. Duty ratio of cooperative molecular motors.

    Science.gov (United States)

    Dharan, Nadiv; Farago, Oded

    2012-02-01

    Molecular motors are found throughout the cells of the human body and have many different and important roles. These micromachines move along filament tracks and have the ability to convert chemical energy into mechanical work that powers cellular motility. Different types of motors are characterized by different duty ratios, which is the fraction of time that a motor is attached to its filament. In the case of myosin II (a nonprocessive molecular machine with a low duty ratio), cooperativity between several motors is essential to induce motion along its actin filament track. In this work we use statistical mechanical tools to calculate the duty ratio of cooperative molecular motors. The model suggests that the effective duty ratio of nonprocessive motors that work in cooperation is lower than the duty ratio of the individual motors. The origin of this effect is the elastic tension that develops in the filament which is relieved when motors detach from the track.

  7. The population genetics of cooperative gene regulation

    Directory of Open Access Journals (Sweden)

    Stewart Alexander J

    2012-09-01

    Full Text Available Abstract Background Changes in gene regulatory networks drive the evolution of phenotypic diversity both within and between species. Rewiring of transcriptional networks is achieved either by changes to transcription factor binding sites or by changes to the physical interactions among transcription factor proteins. It has been suggested that the evolution of cooperative binding among factors can facilitate the adaptive rewiring of a regulatory network. Results We use a population-genetic model to explore when cooperative binding of transcription factors is favored by evolution, and what effects cooperativity then has on the adaptive re-writing of regulatory networks. We consider a pair of transcription factors that regulate multiple targets and overlap in the sets of target genes they regulate. We show that, under stabilising selection, cooperative binding between the transcription factors is favoured provided the amount of overlap between their target genes exceeds a threshold. The value of this threshold depends on several population-genetic factors: strength of selection on binding sites, cost of pleiotropy associated with protein-protein interactions, rates of mutation and population size. Once it is established, we find that cooperative binding of transcription factors significantly accelerates the adaptive rewiring of transcriptional networks under positive selection. We compare our qualitative predictions to systematic data on Saccharomyces cerevisiae transcription factors, their binding sites, and their protein-protein interactions. Conclusions Our study reveals a rich set of evolutionary dynamics driven by a tradeoff between the beneficial effects of cooperative binding at targets shared by a pair of factors, and the detrimental effects of cooperative binding for non-shared targets. We find that cooperative regulation will evolve when transcription factors share a sufficient proportion of their target genes. These findings help to

  8. Evolution of cooperation in spatially structured populations

    Science.gov (United States)

    Brauchli; Killingback; Doebeli

    1999-10-21

    Using a spatial lattice model of the Iterated Prisoner's Dilemma we studied the evolution of cooperation within the strategy space of all stochastic strategies with a memory of one round. Comparing the spatial model with a randomly mixed model showed that (1) there is more cooperative behaviour in a spatially structured population, (2) PAVLOV and generous variants of it are very successful strategies in the spatial context and (3) in spatially structured populations evolution is much less chaotic than in unstructured populations. In spatially structured populations, generous variants of PAVLOV are found to be very successful strategies in playing the Iterated Prisoner's Dilemma. The main weakness of PAVLOV is that it is exploitable by defective strategies. In a spatial context this disadvantage is much less important than the good error correction of PAVLOV, and especially of generous PAVLOV, because in a spatially structured population successful strategies always build clusters. Copyright 1999 Academic Press.

  9. Duty-ratio of cooperative molecular motors

    CERN Document Server

    Dharan, Nadiv

    2012-01-01

    Molecular motors are found throughout the cells of the human body, and have many different and important roles. These micro-machines move along filament tracks, and have the ability to convert chemical energy into mechanical work that powers cellular motility. Different types of motors are characterized by different duty-ratios, which is the fraction of time that a motor is attached to its filament. In the case of myosin II - a non-processive molecular machine with a low duty ratio - cooperativity between several motors is essential to induce motion along its actin filament track. In this work we use statistical mechanical tools to calculate the duty ratio of cooperative molecular motors. The model suggests that the effective duty ratio of non-processive motors that work in cooperation is lower than the duty ratio of the individual motors. The origin of this effect is the elastic tension that develops in the filament which is relieved when motors detach from the track.

  10. Understanding cooperative behavior in structurally disordered populations

    Science.gov (United States)

    Xu, C.; Zhang, W.; Du, P.; Choi, C. W.; Hui, P. M.

    2016-06-01

    The effects of an inhomogeneous competing environment on the extent of cooperation are studied within the context of a site-diluted evolutionary snowdrift game on a square lattice, with the occupied sites representing the players, both numerically and analytically. The frequency of cooperation ℱ C generally shows a non-monotonic dependence on the fraction of occupied sites ρ, for different values of the payoff parameter r. Slightly diluting a lattice leads to a lower cooperation for small and high values of r. For a range of r, however, dilution leads to an enhanced cooperation. An analytic treatment is developed for ℱC I + ℱC II, with ℱC I emphasizing the importance of the small clusters of players especially for ℱC II from the other players is shown to be inadequate. A local configuration approximation (LCA) that treats the local competing configurations as the variables and amounts to include spatial correlation up to the neighborhood of a player's neighbors is developed. Results of ℱ C ( ρ) and the number of different local configurations from LCA are in good agreement with simulation results. A transparent physical picture of the dynamics stemming from LCA is also presented. The theoretical approach provides a framework that can be readily applied to competing agent-based models in structurally ordered and disordered populations.

  11. Cooperative transport by small teams of molecular motors

    OpenAIRE

    Klumpp, Stefan; Muller, Melanie J. I.; Lipowsky, Reinhard

    2006-01-01

    Molecular motors power directed transport of cargoes within cells. Even if a single motor is sufficient to transport a cargo, motors often cooperate in small teams. We discuss the cooperative cargo transport by several motors theoretically and explore some of its properties. In particular we emphasize how motor teams can drag cargoes through a viscous environment.

  12. Asymmetric evaluation promotes cooperation in network population

    Science.gov (United States)

    Shen, Chen; Li, Xiaoping; Shi, Lei; Deng, Zhenghong

    2017-05-01

    The evolution of cooperation remains a fundamental challenge in human society. Many previous studies investigated these questions via spatial reciprocity, where players obtain their payoffs by interacting with their direct neighbors. It has also been verified that environmental factors can influence the evolution of cooperation theoretically and empirically. In reality, however, individuals may have the limit knowledge about their indirect neighbors. Inspired by this fact, we consider an asymmetric fitness calculation mechanism, which only integrates the environment factors into the focal player, to explore the evolution of cooperation. Here, the environmental factor is defined as the average payoff of all individual neighbors, which is regulated by a tunable parameter u. Through numerical simulation, we find that, compared with the traditional version (u = 0), that the cooperation level can be greatly enhanced when u is positive. Interestingly, the larger the value of u, the higher the level of cooperation. Finally, to explore the generality of this finding, we have tested the results on different topologies.

  13. Demography and ecology drive variation in cooperation across human populations.

    Science.gov (United States)

    Lamba, Shakti; Mace, Ruth

    2011-08-30

    Recent studies argue that cross-cultural variation in human cooperation supports cultural group selection models of the evolution of large-scale cooperation. However, these studies confound cultural and environmental differences between populations by predominantly sampling one population per society. Here, we test the hypothesis that behavioral variation between populations is driven by environmental differences in demography and ecology. We use a public goods game played with money and a naturalistic measure of behavior involving the distribution of salt, an essential and locally valued resource, to demonstrate significant variation in levels of cooperation across 16 discrete populations of the same small-scale society, the Pahari Korwa of central India. Variation between these populations of the same cultural group is comparable to that found between different cultural groups in previous studies. Demographic factors partly explain this variation; age and a measure of social network size are associated with contributions in the public goods game, while population size and the number of adult sisters residing in the population are associated with decisions regarding salt. That behavioral variation is at least partly contingent on environmental differences between populations questions the existence of stable norms of cooperation. Hence, our findings call for reinterpretation of cross-cultural data on cooperation. Although cultural group selection could theoretically explain the evolution of large-scale cooperation, our results make clear that existing cross-cultural data cannot be taken as empirical support for this hypothesis.

  14. Complex transition to cooperative behavior in a structured population model.

    Directory of Open Access Journals (Sweden)

    Luciano Miranda

    Full Text Available Cooperation plays an important role in the evolution of species and human societies. The understanding of the emergence and persistence of cooperation in those systems is a fascinating and fundamental question. Many mechanisms were extensively studied and proposed as supporting cooperation. The current work addresses the role of migration for the maintenance of cooperation in structured populations. This problem is investigated in an evolutionary perspective through the prisoner's dilemma game paradigm. It is found that migration and structure play an essential role in the evolution of the cooperative behavior. The possible outcomes of the model are extinction of the entire population, dominance of the cooperative strategy and coexistence between cooperators and defectors. The coexistence phase is obtained in the range of large migration rates. It is also verified the existence of a critical level of structuring beyond that cooperation is always likely. In resume, we conclude that the increase in the number of demes as well as in the migration rate favor the fixation of the cooperative behavior.

  15. Special agents can promote cooperation in the population.

    Directory of Open Access Journals (Sweden)

    Xin Wang

    Full Text Available Cooperation is ubiquitous in our real life but everyone would like to maximize her own profits. How does cooperation occur in the group of self-interested agents without centralized control? Furthermore, in a hostile scenario, for example, cooperation is unlikely to emerge. Is there any mechanism to promote cooperation if populations are given and play rules are not allowed to change? In this paper, numerical experiments show that complete population interaction is unfriendly to cooperation in the finite but end-unknown Repeated Prisoner's Dilemma (RPD. Then a mechanism called soft control is proposed to promote cooperation. According to the basic idea of soft control, a number of special agents are introduced to intervene in the evolution of cooperation. They comply with play rules in the original group so that they are always treated as normal agents. For our purpose, these special agents have their own strategies and share knowledge. The capability of the mechanism is studied under different settings. We find that soft control can promote cooperation and is robust to noise. Meanwhile simulation results demonstrate the applicability of the mechanism in other scenarios. Besides, the analytical proof also illustrates the effectiveness of soft control and validates simulation results. As a way of intervention in collective behaviors, soft control provides a possible direction for the study of reciprocal behaviors.

  16. Moderate intra-group bias maximizes cooperation on interdependent populations.

    Directory of Open Access Journals (Sweden)

    Changbing Tang

    Full Text Available Evolutionary game theory on spatial structures has received increasing attention during the past decades. However, the majority of these achievements focuses on single and static population structures, which is not fully consistent with the fact that real structures are composed of many interactive groups. These groups are interdependent on each other and present dynamical features, in which individuals mimic the strategy of neighbors and switch their partnerships continually. It is however unclear how the dynamical and interdependent interactions among groups affect the evolution of collective behaviors. In this work, we employ the prisoner's dilemma game to investigate how the dynamics of structure influences cooperation on interdependent populations, where populations are represented by group structures. It is found that the more robust the links between cooperators (or the more fragile the links between cooperators and defectors, the more prevalent of cooperation. Furthermore, theoretical analysis shows that the intra-group bias can favor cooperation, which is only possible when individuals are likely to attach neighbors within the same group. Yet, interestingly, cooperation can be even inhibited for large intra-group bias, allowing the moderate intra-group bias maximizes the cooperation level.

  17. Scarcity may promote cooperation in populations of simple agents

    CERN Document Server

    Requejo, R J

    2013-01-01

    In the study of the evolution of cooperation, resource limitations are usually assumed just to provide a finite population size. Recently, however, it has been pointed out that resource limitation may also generate dynamical payoffs able to modify the original structure of the games. Here we study analytically a phase transition from a homogeneous population of defectors when resources are abundant to the survival of unconditional cooperators when resources reduce below a threshold. To this end, we introduce a model of simple agents, with no memory or ability of recognition, interacting in well-mixed populations. The result might shed light on the role played by resource constraints on the origin of multicellularity.

  18. Cooperation in the Mixed Population Minority Game with Imitation

    Institute of Scientific and Technical Information of China (English)

    全宏俊; 汪秉宏; 许伯铭; 罗晓曙

    2001-01-01

    After studying the effects of imitation on the mixed population of adaptive agents with different memories competing in a minority game, we have found that when the pure population lies in a crowded regime, the introduction of imitation can considerably improve cooperation among agents in a money market.

  19. Optimal migration promotes the outbreak of cooperation in heterogeneous populations

    CERN Document Server

    Schweitzer, Frank

    2012-01-01

    We consider a population of agents that are heterogeneous with respect to (i) their strategy when interacting $n_{g}$ times with other agents in an iterated prisoners dilemma game, (ii) their spatial location on $K$ different islands. After each generation, agents adopt strategies proportional to their average payoff received. Assuming a mix of two cooperating and two defecting strategies, we first investigate for isolated islands the conditions for an exclusive domination of each of these strategies and their possible coexistence. This allows to define a threshold frequency for cooperation that, dependent on $n_{g}$ and the initial mix of strategies, describes the outbreak of cooperation in the absense of migration. We then allow migration of a fixed fraction of the population after each generation. Assuming a worst case scenario where all islands are occupied by defecting strategies, whereas only one island is occupied by cooperators at the threshold frequency, we determine the optimal migration rate that a...

  20. Interactive diversity promotes the evolution of cooperation in structured populations

    Science.gov (United States)

    Su, Qi; Li, Aming; Zhou, Lei; Wang, Long

    2016-10-01

    Evolutionary games on networks traditionally assume that each individual adopts an identical strategy to interact with all its neighbors in each generation. Considering the prevalent diversity of individual interactions in the real society, here we propose the concept of interactive diversity, which allows individuals to adopt different strategies against different neighbors in each generation. We investigate the evolution of cooperation based on the edge dynamics rather than the traditional nodal dynamics in networked systems. The results show that, without invoking any other mechanisms, interactive diversity drives the frequency of cooperation to a high level for a wide range of parameters in both well-mixed and structured populations. Even in highly connected populations, cooperation still thrives. When interactive diversity and large topological heterogeneity are combined together, however, in the relaxed social dilemma, cooperation level is lower than that with just one of them, implying that the combination of many promotive factors may make a worse outcome. By an analytical approximation, we get the condition under which interactive diversity provides more advantages for cooperation than traditional evolutionary dynamics does. Numerical simulations validating the approximation are also presented. Our work provides a new line to explore the latent relation between the ubiquitous cooperation and individuals’ distinct responses in different interactions. The presented results suggest that interactive diversity should receive more attention in pursuing mechanisms fostering cooperation.

  1. Percolation threshold determines the optimal population density for public cooperation

    CERN Document Server

    Wang, Zhen; Perc, Matjaz; 10.1103/PhysRevE.85.037101

    2012-01-01

    While worldwide census data provide statistical evidence that firmly link the population density with several indicators of social welfare, the precise mechanisms underlying these observations are largely unknown. Here we study the impact of population density on the evolution of public cooperation in structured populations and find that the optimal density is uniquely related to the percolation threshold of the host graph irrespective of its topological details. We explain our observations by showing that spatial reciprocity peaks in the vicinity of the percolation threshold, when the emergence of a giant cooperative cluster is hindered neither by vacancy nor by invading defectors, thus discovering an intuitive yet universal law that links the population density with social prosperity.

  2. Growth dynamics and the evolution of cooperation in microbial populations

    OpenAIRE

    Jonas Cremer; Anna Melbinger; Erwin Frey

    2012-01-01

    Microbes providing public goods are widespread in nature despite running the risk of being exploited by free-riders. However, the precise ecological factors supporting cooperation are still puzzling. Following recent experiments, we consider the role of population growth and the repetitive fragmentation of populations into new colonies mimicking simple microbial life-cycles. Individual-based modeling reveals that demographic fluctuations, which lead to a large variance in the composition of c...

  3. Eco-evolutionary feedbacks can rescue cooperation in microbial populations

    Science.gov (United States)

    Moreno-Fenoll, Clara; Cavaliere, Matteo; Martínez-García, Esteban; Poyatos, Juan F.

    2017-01-01

    Bacterial populations whose growth depends on the cooperative production of public goods are usually threatened by the rise of cheaters that do not contribute but just consume the common resource. Minimizing cheater invasions appears then as a necessary mechanism to maintain these populations. However, that invasions result instead in the persistence of cooperation is a prospect that has yet remained largely unexplored. Here, we show that the demographic collapse induced by cheaters in the population can actually contribute to the rescue of cooperation, in a clear illustration of how ecology and evolution can influence each other. The effect is made possible by the interplay between spatial constraints and the essentiality of the shared resource. We validate this result by carefully combining theory and experiments, with the engineering of a synthetic bacterial community in which the public compound allows survival to a lethal stress. The characterization of the experimental system identifies additional factors that can matter, like the impact of the lag phase on the tolerance to stress, or the appearance of spontaneous mutants. Our work explains the unanticipated dynamics that eco-evolutionary feedbacks can generate in microbial communities, feedbacks that reveal fundamental for the adaptive change of ecosystems at all scales. PMID:28211914

  4. Population heterogeneity promotes a preference for blind cooperation

    Science.gov (United States)

    Perez-Escudero, Alfonso; Friedman, Jonathan; Gore, Jeff

    Game theory--and common sense--recommend to carefully weigh costs and benefits before deciding on a course of action. Yet we often disapprove of people who do so, even when their actual decision benefits us. For example, we prefer people who directly agree to do us a favor over those who agree only after securing enough information to ensure that the favor will not be too costly. Why should we care about how people make their decisions, rather than just focus on the decisions themselves? Hoffman et al. (2015) have shown that such aversion to information gathering may be beneficial when it is strong enough to increase the level of cooperation. Here we show that the same type of aversion arises in heterogeneous populations, but for a different reason: individuals who seek additional information may reveal themselves to be undesirable partners, since they are less likely to cooperate in the future when conditions change. Aversion to information gathering thus facilitates preferential interactions with blind cooperators, who are more favorable partners. Due to this new mechanism the prevalence of such aversion rapidly increases with population diversity, because partner discrimination is more useful in populations which harbor partners of a more varied quality. We gratefully acknowledge funding from the Paul G. Allen Family Foundation, EMBO and Human Frontier Science Program.

  5. Coarse-grained molecular simulations of allosteric cooperativity

    Science.gov (United States)

    Nandigrami, Prithviraj; Portman, John J.

    2016-03-01

    Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein's functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two Ca2+ ions to each domain of Calmodulin (CaM) through simulations of a simple coarse-grained model. In this model, the protein's conformational transitions between open and closed conformational ensembles are simulated explicitly and ligand binding and unbinding are treated implicitly within the grand canonical ensemble. Ligand binding is cooperative because the binding sites are coupled through a shift in the dominant conformational ensemble upon binding. The classic Monod-Wyman-Changeux model of allostery with appropriate binding free energies to the open and closed ensembles accurately describes the simulated binding thermodynamics. The simulations predict that the two domains of CaM have distinct binding affinity and cooperativity. In particular, the C-terminal domain binds Ca2+ with higher affinity and greater cooperativity than the N-terminal domain. From a structural point of view, the affinity of an individual binding loop depends sensitively on the loop's structural compatibility with the ligand in the bound ensemble, as well as the conformational flexibility of the binding site in the unbound ensemble.

  6. Effects of Degree on Cooperation in Evolutionary Prisoner's Dilemma Games on Structured Populations

    Institute of Scientific and Technical Information of China (English)

    DAI Qiong-Lin; CHENG Hong-Yan; LI Hai-Hong; YANG Jun-Zhong

    2010-01-01

    @@ We focus on the effects of individuals' degrees on spontaneous cooperation.By investigating evolutionary PDGs on random networks with two distinct degrees,we find some resonance-type behaviors of the cooperator frequency with the variation of degree.We also find that increasing hub's degree actually disfavors the cooperation though the heterogeneity in degree can enhance cooperation in the population.

  7. Coarse-Grained Molecular Simulations of Allosteric Cooperativity

    CERN Document Server

    Nandigrami, Prithviraj

    2015-01-01

    Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein's functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two calcium ions to each domain of calmodulin (CaM) through simulations of a simple coarse-grained model. In this model, the protein's conformational transitions between open and closed conformational ensembles are simulated explicitly and ligand binding and unbinding is treated implicitly at the mean field level. Ligand binding is cooperative because the binding sites are coupled through a shift in the dominant conformational ensemble upon binding. The classic Monod-Wyman-Changeux model of allostery with appropriate binding free energy to the open and closed ensembles accurately describe...

  8. Cooperation is related to dispersal patterns in Sino-Tibetan populations

    Science.gov (United States)

    Wu, Jia-Jia; Ji, Ting; He, Qiao-Qiao; Du, Juan; Mace, Ruth

    2015-01-01

    There is growing recognition in both evolutionary biology and anthropology that dispersal is key to establishing patterns of cooperation. However, some models predict that cooperation is more likely to evolve in low dispersal (viscous) populations, while others predict that local competition for resources inhibits cooperation. Sex-biased dispersal and extra-pair mating may also have an effect. Using economic games in Sino-Tibetan populations with strikingly different dispersal patterns, we measure cooperation in 36 villages in southwestern China; we test whether social structure is associated with cooperative behaviour toward those in the neighbourhood. We find that social organization is associated with levels of cooperation in public goods and dictator games and a resource dilemma; people are less cooperative towards other villagers in communities where dispersal by both sexes is low. This supports the view that dispersal for marriage played an important role in the evolution of large-scale cooperation in human society. PMID:26478534

  9. Cooperative behavior of molecular motors: Cargo transport and traffic phenomena

    Science.gov (United States)

    Lipowsky, Reinhard; Beeg, Janina; Dimova, Rumiana; Klumpp, Stefan; Müller, Melanie J. I.

    2010-01-01

    All eukaryotic cells including those of our own body contain complex transport systems based on molecular motors which walk along cytoskeletal filaments. These motors are rather small and make discrete mechanical steps with a step size of the order of 10 nm but are able to pull cargo particles over much larger distances, from micrometers up to meters. In vivo, the intracellular cargos include large membrane-bounded organelles, smaller vesicles, a subset of mRNAs, cytoskeletal filaments, and various protein building blocks, which are transported between different cell compartments. This cargo transport is usually performed by teams of motors. If all motors belong to the same molecular species, the cooperative action of the motors leads to uni-directional transport with a strongly increased run length and with a characteristic force dependence of the velocity distributions. If two antagonistic teams of motors pull on the same cargo particle, they perform a stochastic tug-of-war, which is characterized by a subtle force balance between the two motor teams and leads to several distinct patterns of bi-directional transport. So far, all experimental observations on bi-directional transport are consistent with such a tug-of-war. If many motors and/or cargo particles are transported along the filaments, one encounters various traffic phenomena. Depending on their mutual interactions and the compartment geometry, the motors form various spatio-temporal patterns such as traffic jams, and undergo nonequilibrium phase transitions between different patterns of transport.

  10. Evolutionary games and population dynamics: maintenance of cooperation in public goods games

    OpenAIRE

    Hauert, Christoph; Holmes, Miranda; Doebeli, Michael

    2006-01-01

    The emergence and abundance of cooperation in nature poses a tenacious and challenging puzzle to evolutionary biology. Cooperative behaviour seems to contradict Darwinian evolution because altruistic individuals increase the fitness of other members of the population at a cost to themselves. Thus, in the absence of supporting mechanisms, cooperation should decrease and vanish, as predicted by classical models for cooperation in evolutionary game theory, such as the Prisoner's Dilemma and publ...

  11. Spatial population expansion promotes the evolution of cooperation in an experimental Prisoner's Dilemma.

    Science.gov (United States)

    Van Dyken, J David; Müller, Melanie J I; Mack, Keenan M L; Desai, Michael M

    2013-05-20

    Cooperation is ubiquitous in nature, but explaining its existence remains a central interdisciplinary challenge. Cooperation is most difficult to explain in the Prisoner's Dilemma game, where cooperators always lose in direct competition with defectors despite increasing mean fitness. Here we demonstrate how spatial population expansion, a widespread natural phenomenon, promotes the evolution of cooperation. We engineer an experimental Prisoner's Dilemma game in the budding yeast Saccharomyces cerevisiae to show that, despite losing to defectors in nonexpanding conditions, cooperators increase in frequency in spatially expanding populations. Fluorescently labeled colonies show genetic demixing of cooperators and defectors, followed by increase in cooperator frequency as cooperator sectors overtake neighboring defector sectors. Together with lattice-based spatial simulations, our results suggest that spatial population expansion drives the evolution of cooperation by (1) increasing positive genetic assortment at population frontiers and (2) selecting for phenotypes maximizing local deme productivity. Spatial expansion thus creates a selective force whereby cooperator-enriched demes overtake neighboring defector-enriched demes in a "survival of the fastest." We conclude that colony growth alone can promote cooperation and prevent defection in microbes. Our results extend to other species with spatially restricted dispersal undergoing range expansion, including pathogens, invasive species, and humans.

  12. Stability and robustness analysis of cooperation cycles driven by destructive agents in finite populations

    CERN Document Server

    Requejo, Rubén J; Cuesta, José A; Arenas, Alex; 10.1103/PhysRevE.86.026105

    2012-01-01

    The emergence and promotion of cooperation are two of the main issues in evolutionary game theory, as cooperation is amenable to exploitation by defectors, which take advantage of cooperative individuals at no cost, dooming them to extinction. It has been recently shown that the existence of purely destructive agents (termed jokers) acting on the common enterprises (public goods games) can induce stable limit cycles among cooperation, defection, and destruction when infinite populations are considered. These cycles allow for time lapses in which cooperators represent a relevant fraction of the population, providing a mechanism for the emergence of cooperative states in nature and human societies. Here we study analytically and through agent-based simulations the dynamics generated by jokers in finite populations for several selection rules. Cycles appear in all cases studied, thus showing that the joker dynamics generically yields a robust cyclic behavior not restricted to infinite populations. We also comput...

  13. Molecular Cooperativity Governs Diverse and Monoallelic Olfactory Receptor Expression

    Science.gov (United States)

    Xing, Jianhua; Tian, Xiaojun; Zhang, Hang; Sannerud, Jens

    Multiple-objective optimization is common in biological systems. In the mammalian olfactory system, each sensory neuron stochastically expresses only one out of up to thousands of olfactory receptor (OR) gene alleles; at organism level the types of expressed ORs need to be maximized. The molecular mechanism of this Nobel-Prize winning puzzle remains unresolved after decades of extensive studies. Existing models focus only on monoallele activation, and cannot explain recent observations in mutants, especially the reduced global diversity of expressed ORs in G9a/GLP knockouts. In this work we integrated existing information on OR expression, and proposed an evolutionarily optimized three-layer regulation mechanism, which includes zonal segregation, epigenetic and enhancer competition coupled to a negative feedback loop. This model not only recapitulates monoallelic OR expression, but also elucidates how the olfactory system maximizes and maintains the diversity of OR expression. The model is validated by several experimental results, and particularly underscores cooperativity and synergy as a general design principle of multi-objective optimization in biology. The work is supported by the NIGMS/DMS Mathematical Biology program.

  14. Extortion provides alternative routes to the evolution of cooperation in structured populations

    Science.gov (United States)

    Xu, Xiongrui; Rong, Zhihai; Wu, Zhi-Xi; Zhou, Tao; Tse, Chi Kong

    2017-05-01

    In this paper, we study the evolution of cooperation in structured populations (individuals are located on either a regular lattice or a scale-free network) in the context of repeated games by involving three types of strategies, namely, unconditional cooperation, unconditional defection, and extortion. The strategy updating of the players is ruled by the replicator-like dynamics. We find that extortion strategies can act as catalysts to promote the emergence of cooperation in structured populations via different mechanisms. Specifically, on regular lattice, extortioners behave as both a shield, which can enwrap cooperators inside and keep them away from defectors, and a spear, which can defeat those surrounding defectors with the help of the neighboring cooperators. Particularly, the enhancement of cooperation displays a resonance-like behavior, suggesting the existence of optimal extortion strength mostly favoring the evolution of cooperation, which is in good agreement with the predictions from the generalized mean-field approximation theory. On scale-free network, the hubs, who are likely occupied by extortioners or defectors at the very beginning, are then prone to be conquered by cooperators on small-degree nodes as time elapses, thus establishing a bottom-up mechanism for the emergence and maintenance of cooperation.

  15. How Suspicion Grows: Effects of Population Size on Cooperation

    Science.gov (United States)

    2014-09-01

    joint crime . Both suspects are under pressure from police investigators to confess, since they cannot produce enough evidence to convict the two of...the crime . Should no one confess, they both can expect to receive short prison sentences for some reduced crime . Should one confess, while the other...Evolution of cooperation by reciprocation within structured demes. Journal of Genetics , 66(1), 69–84. Karau, S. J., & Williams, K. D. (1993). Social

  16. Cooperative Catalysis for Selective Alcohol Oxidation with Molecular Oxygen

    NARCIS (Netherlands)

    Slot, T.K.; Eisenberg, D.; van Noordenne, D.; Jungbacker, P.; Rothenberg, G.

    2016-01-01

    The activation of dioxygen for selective oxidation of organic molecules is a major catalytic challenge. Inspired by the activity of nitrogen-doped carbons in electrocatalytic oxygen reduction, we combined such a carbon with metal-oxide catalysts to yield cooperative catalysts. These simple materials

  17. Cooperative effects enhance the transport properties of molecular spider teams

    CERN Document Server

    Rank, Matthias; Frey, Erwin

    2013-01-01

    Molecular spiders are synthetic molecular motors based on DNA nanotechnology. While natural molecular motors have evolved towards very high efficiency, it remains a major challenge to develop efficient designs for man-made molecular motors. Inspired by biological motor proteins like kinesin and myosin, molecular spiders comprise a body and several legs. The legs walk on a lattice that is coated with substrate which can be cleaved catalytically. We propose a novel molecular spider design in which n spiders form a team. Our theoretical considerations show that coupling several spiders together alters the dynamics of the resulting team significantly. Although spiders operate at a scale where diffusion is dominant, spider teams can be tuned to behave nearly ballistic, which results in fast and predictable motion. Based on the separation of time scales of substrate and product dwell times, we develop a theory which utilises equivalence classes to coarse-grain the micro-state space. In addition, we calculate diffus...

  18. The concurrent evolution of cooperation and the population structures that support it.

    Science.gov (United States)

    Powers, Simon T; Penn, Alexandra S; Watson, Richard A

    2011-06-01

    The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits that affect their population structure to some degree. These traits, such as a group size preference, affect the relatedness of interacting individuals and hence the opportunity for kin or group selection. We argue that models that do not explicitly consider their evolution cannot provide a satisfactory account of the origin of cooperation, because they cannot explain how the prerequisite population structures arise. Here, we consider the concurrent evolution of genetic traits that affect population structure, with those that affect social behavior. We show that not only does population structure drive social evolution, as in previous models, but that the opportunity for cooperation can in turn drive the creation of population structures that support it. This occurs through the generation of linkage disequilibrium between socio-behavioral and population-structuring traits, such that direct kin selection on social behavior creates indirect selection pressure on population structure. We illustrate our argument with a model of the concurrent evolution of group size preference and social behavior.

  19. Molecular approaches to diversity of populations of apicomplexan parasites.

    Science.gov (United States)

    Beck, Hans-Peter; Blake, Damer; Dardé, Marie-Laure; Felger, Ingrid; Pedraza-Díaz, Susana; Regidor-Cerrillo, Javier; Gómez-Bautista, Mercedes; Ortega-Mora, Luis Miguel; Putignani, Lorenza; Shiels, Brian; Tait, Andrew; Weir, Willie

    2009-01-01

    Apicomplexan parasites include many parasites of importance either for livestock or as causative agents of human diseases. The importance of these parasites has been recognised by the European Commission and resulted in support of the COST (Cooperation in Science and Technology) Action 857 'Apicomplexan Biology in the Post-Genomic Era'. In this review we discuss the current understanding in 'Biodiversity and Population Genetics' of the major apicomplexan parasites, namely the Eimeria spp., Cryptosporidium spp., Toxoplasma gondii, Neospora caninum, Theileria spp. and Plasmodium spp. During the past decade molecular tools for characterizing and monitoring parasite populations have been firmly established as an integral part of field studies and intervention trials. Analyses have been conducted for most apicomplexan pathogens to describe the extent of genetic diversity, infection dynamics or population structure. The underlying key question for all parasites is to understand how genetic diversity influences epidemiology and pathogenicity and its implication in therapeutic and vaccination strategies as well as disease control. Similarities in the basic biology and disease or transmission patterns among this order of parasites promote multifaceted discussions and comparison of epidemiological approaches and methodological tools. This fosters mutual learning and has the potential for cross-fertilisation of ideas and technical approaches.

  20. Cooperation in the two-population snowdrift game with punishment enforced through different mechanisms

    OpenAIRE

    Rocha, André Barreira da Silva

    2016-01-01

    I study two mechanisms based on punishment to promote cooperation in the two-population snowdrift game. The first mechanism follows the traditional approach in the literature and is based on the inclusion of a third additional strategy in the payoff matrix of the stage-game. The second mechanism consists of letting cooperators to punish defectors with a given exogenous frequency. While both mechanisms share the same result regarding the minimum required level of punishment in order to elimina...

  1. South Asian co-operation in population programmes.

    Science.gov (United States)

    Iqbal, M A

    1989-12-01

    Efforts by governments of South Asian countries to improve the economic growth and welfare of the people are being negated by high fertility. In some countries, the expenditures on health programs have increased and the programs have expanded rapidly without any concomitant improvement in efficiency or cost-effectiveness. This highlights the urgency of tackling the problems of not only population growth but also of managing population programs. There are similarities as well as differences in the management of population programs in the South Asian countries. Bangladesh has a population policy with a strong political will behind it. It also has a sound administrative structure and organization. Some areas that need attention are building up the operational relationship between health and family planning personnel, improved infrastructure development, more community involvement, and better evaluation. Some states in India have shown outstanding success in population programs, and some have successfully experimented with beyond family planning methods. A greater awareness of family planning among health staff, a solid information base for decision making, and management training for medical officers and staff are also needed. Pakistan's population program has had uneven results in the past, but it has now developed multi-sectoral components in decentralized field activities, involvement of local organizations and leaders, and better information, education, and social marketing, but it still needs to plan for evaluation and strengthen management training. Of the South Asian countries, Sri Lanka, with a high level of literacy and health care, has shown the best achievement in its social sector. The coverage through the maternal and child health service delivery system has been commendable with 94% of deliveries through institutions. Regional meetings have identified program management problem areas in 1) planning, control, and coordination of program implementation, 2

  2. Comparative morphology among northern populations of breeding Cooper's Hawks

    Science.gov (United States)

    Rosenfield, Robert N.; Rosenfield, Laura J.; Bielefeldt, John; Murphy, Robert K.; Stewart, Andrew C.; Stout, William E.; Driscoll, Timothy G.; Bozek, Michael A.

    2010-01-01

    Few studies at a broad geographical scale have characterized intraspecific variation in morphology of woodland hawks in the genus Accipiter. From 1999 to 2007 we investigated morphological variation in large samples of live Cooper's Hawks (A. cooperii) nesting in four study areas: coniferous woodland around Victoria, British Columbia, Canada, isolated deciduous woodlands in short-grass prairies of northwestern North Dakota, towns and rural deciduous woodlands along the border of North Dakota and Minnesota, and urban and rural mixed deciduous and coniferous landscapes of Wisconsin. These sites span 2660 km across the northern part of the species' breeding range. We measured body mass (i.e., size), wing chord, tail length, tarsus diameter, hallux length, and culmen length of breeding adults, finding significant and clinal variation in body mass (or size). The smallest and most similar-sized birds occurred in British Columbia and western North Dakota, larger birds along the border between North Dakota and Minnesota, and the largest birds in Wisconsin. Several other characters varied significantly when mass was used as a covariate. Variation by study site in mean indices of sexual size dimorphism was negligible and not significant. We speculate that the morphological differences we found, in part, are the result of geographic isolation, where diets, migratory behavior, and structural characteristics of nesting habitats vary across landscape types.

  3. Population structure induces a symmetry breaking favoring the emergence of cooperation.

    Directory of Open Access Journals (Sweden)

    Jorge M Pacheco

    2009-12-01

    Full Text Available The evolution of cooperation described in terms of simple two-person interactions has received considerable attention in recent years, where several key results were obtained. Among those, it is now well established that the web of social interaction networks promotes the emergence of cooperation when modeled in terms of symmetric two-person games. Up until now, however, the impacts of the heterogeneity of social interactions into the emergence of cooperation have not been fully explored, as other aspects remain to be investigated. Here we carry out a study employing the simplest example of a prisoner's dilemma game in which the benefits collected by the participants may be proportional to the costs expended. We show that the heterogeneous nature of the social network naturally induces a symmetry breaking of the game, as contributions made by cooperators may become contingent on the social context in which the individual is embedded. A new, numerical, mean-field analysis reveals that prisoner's dilemmas on networks no longer constitute a defector dominance dilemma--instead, individuals engage effectively in a general coordination game. We find that the symmetry breaking induced by population structure profoundly affects the evolutionary dynamics of cooperation, dramatically enhancing the feasibility of cooperators: cooperation blooms when each cooperator contributes the same cost, equally shared among the plethora of games in which she participates. This work provides clear evidence that, while individual rational reasoning may hinder cooperative actions, the intricate nature of social interactions may effectively transform a local dilemma of cooperation into a global coordination problem.

  4. Range expansions transition from pulled to pushed waves with increasing cooperativity in an experimental microbial population

    Science.gov (United States)

    Gandhi, Saurabh; Yurtsev, Eugene; Korolev, Kirill; Gore, Jeff

    Range expansions are becoming more frequent due to environmental changes and rare long distance dispersal, often facilitated by anthropogenic activities. Simple models in theoretical ecology explain many emergent properties of range expansions, such as a constant expansion velocity, in terms of organism-level properties such as growth and dispersal rates. Testing these quantitative predictions in natural populations is difficult because of large environmental variability. Here, we used a controlled microbial model system to study range expansions of populations with and without intra-specific cooperativity. For non-cooperative growth, the expansion dynamics were dominated by population growth at the low-density front, which pulled the expansion forward. We found these expansions to be in close quantitative agreement with the classical theory of pulled waves by Fisher and Skellam, suitably adapted to our experimental system. However, as cooperativity increased, the expansions transitioned to being pushed, i.e. controlled by growth in the bulk as well as in the front. Although both pulled and pushed waves expand at a constant velocity and appear otherwise similar, their distinct dynamics leads to very different evolutionary consequences. Given the prevalence of cooperative growth in nature, understanding the effects of cooperativity is essential to managing invading species and understanding their evolution.

  5. Cooperative Jahn–Teller phase transition of icosahedral molecular units

    Science.gov (United States)

    Nasrollahi, Seyed H.; Vvedensky, Dimitri D.

    2017-02-01

    Non-linear molecules undergo distortions when the orbital degeneracy of the highest occupied level is lifted by the Jahn–Teller effect. If such molecules or clusters of atoms are coupled to one another, the system may experience a cooperative Jahn–Teller effect (CJTE). In this paper, we describe a model of how the CJTE leads to the crystallization of the disordered phase. The model Hamiltonian is based on a normal mode decomposition of the clusters in order to maintain the symmetry labels. We take account of the electron-strain and the electron-phonon couplings and, by displacing the coordinates of the oscillators, obtain a term that explicitly couples the Jahn–Teller centers, enabling us to perform a mean-field analysis. The calculation of the free energy then becomes straightforward, and obtaining phase diagrams in various regimes follows from the minimization of this free energy. The results show that the character of the phase transition may change from strong to weak first order and even to second-order, depending on the coupling to the vibrational modes. Taken together, these results may serve as a paradigm for crystallization near the transition temperature, where the atoms tend to form clusters of icosahedral symmetry.

  6. Analytical models for well-mixed populations of cooperators and defectors under limiting resources

    CERN Document Server

    Requejo, Rubén J; 10.1103/PhysRevE.85.066112

    2012-01-01

    In the study of the evolution of cooperation, resource limitations are usually assumed just to provide a finite population size. Recently, however, agent-based models have pointed out that resource limitation may modify the original structure of the interactions and allow for the survival of unconditional cooperators in well-mixed populations. Here, we present analytical simplified versions of two types of agent-based models recently published: one in which the limiting resource constrains the ability of reproduction of individuals but not their survival, and a second one where the limiting resource is necessary for both reproduction and survival. One finds that the analytical models display, with a few differences, the same qualitative behavior of the more complex agent-based models. In addition, the analytical models allow us to expand the study and identify the dimensionless parameters governing the final fate of the system, such as coexistence of cooperators and defectors, or dominance of defectors or of ...

  7. Does breeding population trajectory and age of nesting females influence disparate nestling sex ratios in two populations of Cooper's hawks?

    Science.gov (United States)

    Rosenfield, Robert N; Stout, William E; Giovanni, Matthew D; Levine, Noah H; Cava, Jenna A; Hardin, Madeline G; Haynes, Taylor G

    2015-09-01

    Offspring sex ratios at the termination of parental care should theoretically be skewed toward the less expensive sex, which in most avian species would be females, the smaller gender. Among birds, however, raptors offer an unusual dynamic because they exhibit reversed size dimorphism with females being larger than males. And thus theory would predict a preponderance of male offspring. Results for raptors and birds in general have been varied although population-level estimates of sex ratios in avian offspring are generally at unity. Adaptive adjustment of sex ratios in avian offspring is difficult to predict perhaps in part due to a lack of life-history details and short-term investigations that cannot account for precision or repeatability of sex ratios across time. We conducted a novel comparative study of sex ratios in nestling Cooper's hawks (Accipiter cooperii) in two study populations across breeding generations during 11 years in Wisconsin, 2001-2011. One breeding population recently colonized metropolitan Milwaukee and exhibited rapidly increasing population growth, while the ex-Milwaukee breeding population was stable. Following life-history trade-off theory and our prediction regarding this socially monogamous species in which reversed sexual size dimorphism is extreme, first-time breeding one-year-old, second-year females in both study populations produced a preponderance of the smaller and cheaper sex, males, whereas ASY (after-second-year), ≥2-year-old females in Milwaukee produced a nestling sex ratio near unity and predictably therefore a greater proportion of females compared to ASY females in ex-Milwaukee who produced a preponderance of males. Adjustment of sex ratios in both study populations occurred at conception. Life histories and selective pressures related to breeding population trajectory in two age cohorts of nesting female Cooper's hawk likely vary, and it is possible that these differences influenced the sex ratios we documented for

  8. Emotional decisions in structured populations for the evolution of public cooperation

    Science.gov (United States)

    Wang, Yongjie; Chen, Tong; Chen, Qiao; Si, Guangrun

    2017-02-01

    The behaviors of humans are not always profit-driven in public goods games (PGG). In addition, social preference and decision-making might be influenced, even changed by heuristics and conformity in the real life. Motivated by the facts, we would like to investigate the role of emotional system in cooperative behaviors of structured population in PGG. Meantime, the effects of diffusion of influence are studied in structured population. Numerical simulation results are indicated that emotions play very significant role indeed in emergence and maintenance of cooperation in structured populations in PGG. However, the influences of emotions on others are limited due to diminishing of influence diffusion and the existence of pure defectors. What is more, conformity, to some extent, could drive potentially more people to accept cooperative strategy with higher probability. Higher-level cooperation could be promoted as increasing values of synergy factors, but while the effects might diminish gradually as increasing number of positive heuristic players and conformist. Our work may be beneficial to address the social dilemmas in PGG.

  9. Evolutionary mixed games in structured populations: Cooperation and the benefits of heterogeneity

    Science.gov (United States)

    Amaral, Marco A.; Wardil, Lucas; Perc, Matjaž; da Silva, Jafferson K. L.

    2016-04-01

    Evolutionary games on networks traditionally involve the same game at each interaction. Here we depart from this assumption by considering mixed games, where the game played at each interaction is drawn uniformly at random from a set of two different games. While in well-mixed populations the random mixture of the two games is always equivalent to the average single game, in structured populations this is not always the case. We show that the outcome is, in fact, strongly dependent on the distance of separation of the two games in the parameter space. Effectively, this distance introduces payoff heterogeneity, and the average game is returned only if the heterogeneity is small. For higher levels of heterogeneity the distance to the average game grows, which often involves the promotion of cooperation. The presented results support preceding research that highlights the favorable role of heterogeneity regardless of its origin, and they also emphasize the importance of the population structure in amplifying facilitators of cooperation.

  10. Analytical models for well-mixed populations of cooperators and defectors under limiting resources

    Science.gov (United States)

    Requejo, R. J.; Camacho, J.

    2012-06-01

    In the study of the evolution of cooperation, resource limitations are usually assumed just to provide a finite population size. Recently, however, agent-based models have pointed out that resource limitation may modify the original structure of the interactions and allow for the survival of unconditional cooperators in well-mixed populations. Here, we present analytical simplified versions of two types of agent-based models recently published: one in which the limiting resource constrains the ability of reproduction of individuals but not their survival, and a second one where the limiting resource is necessary for both reproduction and survival. One finds that the analytical models display, with a few differences, the same qualitative behavior of the more complex agent-based models. In addition, the analytical models allow us to expand the study and identify the dimensionless parameters governing the final fate of the system, such as coexistence of cooperators and defectors, or dominance of defectors or of cooperators. We provide a detailed analysis of the occurring phase transitions as these parameters are varied.

  11. Molecular basis of cooperativity in pH-triggered supramolecular self-assembly

    Science.gov (United States)

    Li, Yang; Zhao, Tian; Wang, Chensu; Lin, Zhiqiang; Huang, Gang; Sumer, Baran D.; Gao, Jinming

    2016-10-01

    Supramolecular self-assembly offers a powerful strategy to produce high-performance, stimuli-responsive nanomaterials. However, lack of molecular understanding of stimulated responses frequently hampers our ability to rationally design nanomaterials with sharp responses. Here we elucidated the molecular pathway of pH-triggered supramolecular self-assembly of a series of ultra-pH sensitive (UPS) block copolymers. Hydrophobic micellization drove divergent proton distribution in either highly protonated unimer or neutral micelle states along the majority of the titration coordinate unlike conventional small molecular or polymeric bases. This all-or-nothing two-state solution is a hallmark of positive cooperativity. Integrated modelling and experimental validation yielded a Hill coefficient of 51 in pH cooperativity for a representative UPS block copolymer, by far the largest reported in the literature. These data suggest hydrophobic micellization and resulting positive cooperativity offer a versatile strategy to convert responsive nanomaterials into binary on/off switchable systems for chemical and biological sensing, as demonstrated in an additional anion sensing model.

  12. Three "quantum" models of competition and cooperation in interacting biological populations and social groups

    CERN Document Server

    Vol, E D

    2012-01-01

    In present paper we propose the consistent statistical approach which appropriate for a number of models describing both behavior of biological populations and various social groups interacting with each other.The approach proposed based on the ideas of quantum theory of open systems (QTOS) and allows one to account explicitly both discreteness of a system variables and their fluctuations near mean values.Therefore this approach can be applied also for the description of small populations where standard dynamical methods are failed. We study in detail three typical models of interaction between populations and groups: 1) antagonistic struggle between two populations 2) cooperation (or, more precisely, obligatory mutualism) between two species 3) the formation of coalition between two feeble groups in their conflict with third one that is more powerful . The models considered in a sense are mutually complementary and include the most types of interaction between populations and groups. Besides this method can ...

  13. Co-operative groups in their environments : a population-ecological model for co-operative membership and performance

    OpenAIRE

    Lasowski, Ophir

    2010-01-01

    The aim of this work is to develop an alternative evolutionary approach to assessing the performance of co-operative organizations. The focus of investigation is turned to the co-operative organization as a group of members in a market environment containing non-members. Significant unique features of the co-operative organization is illustrated at first. After reviewing historical aspects of evolution theories and their positioning in biology, economic and social sciences, alternative notion...

  14. Dynamics of cooperative emissions in a cascade three-level molecular system driven by an ultrashort laser pulse

    Institute of Scientific and Technical Information of China (English)

    Liu Ji-Cai; Wang Chun-Xin; Gel'mukhanov Faris; Wang Chuan-Kui

    2008-01-01

    This paper investigates the dynamics of cooperative emissions in a cascade three-level system driven by an ultrashort laser pulse by solving numerically the full-wave Maxwell-Bloeh equations.The 4,4'-bis(dimethylamino) stilbene molecule is used as the model molecule because of its strong two-photon absorption property.The two-colour cooperative emissions are studied as functions of molecular number density and dephasing rate of the dipole coherence.The propagation effects on the evolution of the cooperative radiations are also taken into account.The cooperative radiations are enhanced for large number density of the molecule,while the fast dephasing of the dipole coherence reduces the intensity of the cooperative radiations and delays the emission times or even inhibits the formation of the emissions.The delay time of the radiation decreases with the increase of the molecular number density and the propagation distance.

  15. Expansion of cooperatively growing populations: Optimal migration rates and habitat network structures

    Science.gov (United States)

    Yang, Kai-Cheng; Wu, Zhi-Xi; Holme, Petter; Nonaka, Etsuko

    2017-01-01

    Range expansion of species is driven by the interactions among individual- and population-level processes and the spatial pattern of habitats. In this work we study how cooperatively growing populations spread on networks representing the skeleton of complex landscapes. By separating the slow and fast variables of the expansion process, we are able to give analytical predictions for the critical conditions that divide the dynamic behaviors into different phases (extinction, localized survival, and global expansion). We observe a resonance phenomenon in how the critical condition depends on the expansion rate, indicating the existence of an optimal strategy for global expansion. We derive the conditions for such optimal migration in locally treelike graphs and numerically study other structured networks. Our results highlight the importance of both the underlying interaction pattern and migration rate of the expanding populations for range expansion. We also discuss potential applications of the results to biological control and conservation.

  16. Evolutionary mixed games in structured populations: Cooperation and the benefits of heterogeneity

    CERN Document Server

    Amaral, Marco A; Perc, Matjaz; da Silva, Jafferson K L

    2016-01-01

    Evolutionary games on networks traditionally involve the same game at each interaction. Here we depart from this assumption by considering mixed games, where the game played at each interaction is drawn uniformly at random from a set of two different games. While in well-mixed populations the random mixture of the two games is always equivalent to the average single game, in structured populations this is not always the case. We show that the outcome is in fact strongly dependent on the distance of separation of the two games in the parameter space. Effectively, this distance introduces payoff heterogeneity, and the average game is returned only if the heterogeneity is small. For higher levels of heterogeneity the distance to the average game grows, which often involves the promotion of cooperation. The presented results support preceding research that highlights the favorable role of heterogeneity regardless of its origin, and they also emphasize the importance of the population structure in amplifying facil...

  17. High frequency of extra-pair paternity in an urban population of Cooper's Hawks

    Science.gov (United States)

    Rosenfield, Robert N.; Sonsthagen, Sarah A.; Stout, William C.; Talbot, Sandra

    2015-01-01

    Raptors exhibit some of the highest rates of intra-pair copulations among birds, perhaps in an attempt by males to reduce the risk of being cuckolded. Indeed, the frequency of extra-pair fertilizations reported in studies of raptors to date is relatively low (0-11.2%). Socially monogamous Cooper's Hawks (Accipiter cooperii) exhibit one of the highest copulation rates among birds, yet there are no published accounts of extra-pair copulations (or paternity). We studied a population of Cooper's Hawks in Milwaukee, Wisconsin, during three breeding seasons (2003, 2004, and 2007), examining the possible effects of age (1 yr old vs. ≥ 2 yr old), adult mass, and brood size on the frequency of extra-pair paternity (EPP). We found that 19.3% of nestlings (N = 27/140) were extra-pair young (EPY), and 34% of all broods (N = 15/44) had at least one EPY. The sires of the EPY in our study were identified for only two broods, suggesting that floater males may have engaged in extra-pair copulations with territorial females. We found that brood size was a good predictor of the occurrence of EPP (EPP) in nests, but adult mass and female age were not. To our knowledge, these possible correlates of the occurrence of EPP in raptors had not previously been investigated. Male Cooper's Hawks provide food for females during the pre-nesting period, and delivery of food is, in contrast to other raptor species, typically followed by copulation. Thus, one possible explanation of the relatively high rates of EPP in our study is that females might accept or even solicit extra-pair copulations from males other than their mates as a means of maximizing energy intake for egg production. Such behavior might be particularly likely in our study area, i.e., a food-rich urban setting with a high breeding density of Cooper's Hawks.

  18. Collective effects in intra-cellular molecular motor transport: coordination, cooperation and competetion

    CERN Document Server

    Chowdhury, D

    2006-01-01

    Molecular motors do not work in isolation {\\it in-vivo}. We highlight some of the coordinations, cooperations and competitions that determine the collective properties of molecular motors in eukaryotic cells. In the context of traffic-like movement of motors on a track, we emphasize the importance of single-motor bio-chemical cycle and enzymatic activity on their collective spatio-temporal organisation. Our modelling strategy is based on a synthesis- the same model describes the single-motor mechano-chemistry at sufficiently low densities whereas at higher densities it accounts for the collective flow properties and the density profiles of the motors. We consider two specific examples, namely, traffic of single-headed kinesin motors KIF1A on a microtubule track and ribosome traffic on a messenger RNA track.

  19. Microscopic theory of cooperative spin crossover: Interaction of molecular modes with phonons

    Energy Technology Data Exchange (ETDEWEB)

    Palii, Andrew, E-mail: andrew.palii@uv.es, E-mail: klokishner@yahoo.com; Ostrovsky, Serghei; Reu, Oleg; Klokishner, Sophia, E-mail: andrew.palii@uv.es, E-mail: klokishner@yahoo.com [Institute of Applied Physics, Academy of Sciences of Moldova, Academy Str. 5, MD-2028 Kishinev (Moldova, Republic of); Tsukerblat, Boris [Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105 (Israel); Decurtins, Silvio; Liu, Shi-Xia [Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern (Switzerland)

    2015-08-28

    In this article, we present a new microscopic theoretical approach to the description of spin crossover in molecular crystals. The spin crossover crystals under consideration are composed of molecular fragments formed by the spin-crossover metal ion and its nearest ligand surrounding and exhibiting well defined localized (molecular) vibrations. As distinguished from the previous models of this phenomenon, the developed approach takes into account the interaction of spin-crossover ions not only with the phonons but also a strong coupling of the electronic shells with molecular modes. This leads to an effective coupling of the local modes with phonons which is shown to be responsible for the cooperative spin transition accompanied by the structural reorganization. The transition is characterized by the two order parameters representing the mean values of the products of electronic diagonal matrices and the coordinates of the local modes for the high- and low-spin states of the spin crossover complex. Finally, we demonstrate that the approach provides a reasonable explanation of the observed spin transition in the [Fe(ptz){sub 6}](BF{sub 4}){sub 2} crystal. The theory well reproduces the observed abrupt low-spin → high-spin transition and the temperature dependence of the high-spin fraction in a wide temperature range as well as the pronounced hysteresis loop. At the same time within the limiting approximations adopted in the developed model, the evaluated high-spin fraction vs. T shows that the cooperative spin-lattice transition proves to be incomplete in the sense that the high-spin fraction does not reach its maximum value at high temperature.

  20. Microscopic theory of cooperative spin crossover: Interaction of molecular modes with phonons.

    Science.gov (United States)

    Palii, Andrew; Ostrovsky, Serghei; Reu, Oleg; Tsukerblat, Boris; Decurtins, Silvio; Liu, Shi-Xia; Klokishner, Sophia

    2015-08-28

    In this article, we present a new microscopic theoretical approach to the description of spin crossover in molecular crystals. The spin crossover crystals under consideration are composed of molecular fragments formed by the spin-crossover metal ion and its nearest ligand surrounding and exhibiting well defined localized (molecular) vibrations. As distinguished from the previous models of this phenomenon, the developed approach takes into account the interaction of spin-crossover ions not only with the phonons but also a strong coupling of the electronic shells with molecular modes. This leads to an effective coupling of the local modes with phonons which is shown to be responsible for the cooperative spin transition accompanied by the structural reorganization. The transition is characterized by the two order parameters representing the mean values of the products of electronic diagonal matrices and the coordinates of the local modes for the high- and low-spin states of the spin crossover complex. Finally, we demonstrate that the approach provides a reasonable explanation of the observed spin transition in the [Fe(ptz)6](BF4)2 crystal. The theory well reproduces the observed abrupt low-spin → high-spin transition and the temperature dependence of the high-spin fraction in a wide temperature range as well as the pronounced hysteresis loop. At the same time within the limiting approximations adopted in the developed model, the evaluated high-spin fraction vs. T shows that the cooperative spin-lattice transition proves to be incomplete in the sense that the high-spin fraction does not reach its maximum value at high temperature.

  1. Post-fragmentation population structure in a cooperative breeding Afrotropical cloud forest bird: emergence of a source-sink population network.

    Science.gov (United States)

    Husemann, M; Cousseau, L; Callens, T; Matthysen, E; Vangestel, C; Hallmann, C; Lens, L

    2015-03-01

    The impact of demographic parameters on the genetic population structure and viability of organisms is a long-standing issue in the study of fragmented populations. Demographic and genetic tools are now readily available to estimate census and effective population sizes and migration and gene flow rates with increasing precision. Here we analysed the demography and genetic population structure over a recent 15-year time span in five remnant populations of Cabanis's greenbul (Phyllastrephus cabanisi), a cooperative breeding bird in a severely fragmented cloud forest habitat. Contrary to our expectation, genetic admixture and effective population sizes slightly increased, rather than decreased between our two sampling periods. In spite of small effective population sizes in tiny forest remnants, none of the populations showed evidence of a recent population bottleneck. Approximate Bayesian modelling, however, suggested that differentiation of the populations coincided at least partially with an episode of habitat fragmentation. The ratio of meta-Ne to meta-Nc was relatively low for birds, which is expected for cooperative breeding species, while Ne /Nc ratios strongly varied among local populations. While the overall trend of increasing population sizes and genetic admixture may suggest that Cabanis's greenbuls increasingly cope with fragmentation, the time period over which these trends were documented is rather short relative to the average longevity of tropical species. Furthermore, the critically low Nc in the small forest remnants keep the species prone to demographic and environmental stochasticity, and it remains open if, and to what extent, its cooperative breeding behaviour helps to buffer such effects.

  2. Are life history events of a northern breeding population of Cooper's Hawks influenced by changing climate?

    Science.gov (United States)

    Rosenfield, Robert N; Hardin, Madeline G; Bielefeldt, John; Keyel, Edward R

    2017-01-01

    Numerous studies have demonstrated earlier timing of spring migration and egg-laying in small passerines, but documentation of such responses to recent climate change in the life histories of higher trophic feeding birds such as raptors is relatively scarce. Raptors may be particularly susceptible to possible adverse effects of climate change due to their longer generation turnover times and lower reproductive capacity, which could lead to population declines because of an inability to match reproductive timing with optimal brood rearing conditions. Conversely adaptively favorable outcomes due to the influence of changing climate may occur. In general, birds that seasonally nest earlier typically have higher reproductive output compared to conspecifics that nest later in the season. Given the strong seasonal decline in reproductive output, and the heritability of nesting phenology, it is possible that nesting seasons would (adaptively) advance over time. Recent climate warming may release prior ecological constraints on birds that depend on food availability at the time of egg production, as do various raptors including Cooper's Hawks (Accipiter cooperii). Under this scenario, productivity, especially clutch size, might increase because it is likely that this reproductive demographic may be the most immediate response to the earlier seasonal presence of food resources. We demonstrated a statistically significant shift of about 4-5 days to an earlier timing of egg-hatching in spring across 36 years during 1980-2015 for a partially migratory population of Cooper's Hawks in Wisconsin, United States, which is consistent with a recent study that showed that Cooper's Hawks had advanced their timing of spring migration during 1979-2012. Both studies occurred in the Great Lakes region, an area that compared to global averages is experiencing earlier and increased warming particularly in the spring in Wisconsin. The nesting period did not lengthen. We suggest that the

  3. Stochastic noncooperative and cooperative evolutionary game strategies of a population of biological networks under natural selection.

    Science.gov (United States)

    Chen, Bor-Sen; Yeh, Chin-Hsun

    2017-09-05

    We review current static and dynamic evolutionary game strategies of biological networks and discuss the lack of random genetic variations and stochastic environmental disturbances in these models. To include these factors, a population of evolving biological networks is modeled as a nonlinear stochastic biological system with Poisson-driven genetic variations and random environmental fluctuations (stimuli). To gain insight into the evolutionary game theory of stochastic biological networks under natural selection, the phenotypic robustness and network evolvability of noncooperative and cooperative evolutionary game strategies are discussed from a stochastic Nash game perspective. The noncooperative strategy can be transformed into an equivalent multi-objective optimization problem and is shown to display significantly improved network robustness to tolerate genetic variations and buffer environmental disturbances, maintaining phenotypic traits for longer than the cooperative strategy. However, the noncooperative case requires greater effort and more compromises between partly conflicting players. Global linearization is used to simplify the problem of solving nonlinear stochastic evolutionary games. Finally, a simple stochastic evolutionary model of a metabolic pathway is simulated to illustrate the procedure of solving for two evolutionary game strategies and to confirm and compare their respective characteristics in the evolutionary process. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Molecular approaches to bivalve population studies: a review

    Directory of Open Access Journals (Sweden)

    Dragomir-Cosmin David

    2011-12-01

    Full Text Available This paper presents a literature review concerning the importance of molecular approaches in bivalve’s population study. The class Bivalvia counts more than 20,000 species with a wide distribution both in freshwater and marine environment. Given their importance especially in aquaculture as a source of food, they have also a strong economic impact upon human society. This review encompasses best practices in bivalve studies from field sampling to laboratory analyses, addressing questions about molecular methods and tools commonly used by specialized researchers. Molecular tools specifically deals with phylogeography, population genetics, biology, ecology and taxonomy. In all these fields, molecular markers play an important role by completing some unanswered questions such as the role of the bivalves in the ecosystems in relation to anthropogenic and global change issues. Numerous genetic markers were developed for specific problems, thereferore we identify as a major issue the absence of uniform and universally recognized methods. The various sections of the paper emphasize from peer reviewed literature literature which are considered the most useful markers, costs and benefits of different methodology, major gaps of knowledge.in bivalve population studies. By reviewing virtually all genetic markers employed during nearly half a century of bivalve molecular research, in our opinion two are the best option “tools: the mitochondrial COI (cytochrome oxidase subunit I and nuclear ITS2 (internal transcribed spacer 2.

  5. Molecular epidemiology and population structure of bovine Streptococcus uberis

    DEFF Research Database (Denmark)

    Rato, M G; Bexiga, R; Nunes, S F

    2008-01-01

    The molecular epidemiology and population structure of 30 bovine subclinical mastitis field isolates of Streptococcus uberis, collected from 6 Portuguese herds (among 12 farms screened) during 2002 and 2003, were examined by using pulsed-field gel electrophoresis (PFGE) for clustering of the isol...

  6. Genetic and morphological divergence among Cooper's Hawk (Accipiter cooperii) populations breeding in north-central and western North America

    Science.gov (United States)

    Sonsthagen, Sarah A.; Rosenfield, Robert N.; Bielefeldt, John; Murphy, Robert K.; Stewart, Andrew C.; Stout, William C.; Driscoll, Timothy G.; Bozek, Michael A.; Sloss, Brian L.; Talbot, Sandra L.

    2012-01-01

    Cooper's Hawk (Accipiter cooperii) populations breeding in the northern portion of the species' range exhibit variation in morphological traits that conforms to predictions based on differences in prey size, tree stand density, and migratory behavior. We examined genetic structure and gene flow and compared divergence at morphological traits (PST) and genetic markers (FST) to elucidate mechanisms (selection or genetic drift) that promote morphological diversification among Cooper's Hawk populations. Cooper's Hawks appear to conform to the genetic pattern of an east-west divide. Populations in British Columbia are genetically differentiated from north-central populations (Wisconsin, Minnesota, and North Dakota; pairwise microsatellite FST= 0.031-0.050; mitochondrial DNA ΦST = 0.177-0.204), which suggests that Cooper's Hawks were restricted to at least two Pleistocene glacial refugia. The strength of the Rocky Mountains—Great Plains area as a barrier to dispersal is further supported by restricted gene-flow rates between British Columbia and other sampled breeding populations. Divergence in morphological traits (PST) was also observed across study areas, but with British Columbia and North Dakota differentiated from Wisconsin and Minnesota, a pattern not predicted on the basis of FST and ΦST interpopulation estimates. Comparison of PSTand FSTestimates suggests that heterogeneous selection may be acting on Cooper's Hawks in the northern portion of their distribution, which is consistent with hypotheses that variation in prey mass and migratory behavior among populations may be influencing overall body size and wing chord. We were unable to distinguish between the effects of genetic drift and selection on tail length in the study populations.

  7. Invasion and expansion of cooperators in lattice populations: prisoner's dilemma vs. snowdrift games.

    Science.gov (United States)

    Fu, Feng; Nowak, Martin A; Hauert, Christoph

    2010-10-07

    The evolution of cooperation is an enduring conundrum in biology and the social sciences. Two social dilemmas, the prisoner's dilemma and the snowdrift game have emerged as the most promising mathematical metaphors to study cooperation. Spatial structure with limited local interactions has long been identified as a potent promoter of cooperation in the prisoner's dilemma but in the spatial snowdrift game, space may actually enhance or inhibit cooperation. Here we investigate and link the microscopic interaction between individuals to the characteristics of the emerging macroscopic patterns generated by the spatial invasion process of cooperators in a world of defectors. In our simulations, individuals are located on a square lattice with Moore neighborhood and update their strategies by probabilistically imitating the strategies of better performing neighbors. Under sufficiently benign conditions, cooperators can survive in both games. After rapid local equilibration, cooperators expand quadratically until global saturation is reached. Under favorable conditions, cooperators expand as a large contiguous cluster in both games with minor differences concerning the shape of embedded defectors. Under less favorable conditions, however, distinct differences arise. In the prisoner's dilemma, cooperators break up into isolated, compact clusters. The compact clustering reduces exploitation and leads to positive assortment, such that cooperators interact more frequently with other cooperators than with defectors. In contrast, in the snowdrift game, cooperators form small, dendritic clusters, which results in negative assortment and cooperators interact more frequently with defectors than with other cooperators. In order to characterize and quantify the emerging spatial patterns, we introduce a measure for the cluster shape and demonstrate that the macroscopic patterns can be used to determine the characteristics of the underlying microscopic interactions.

  8. Intramolecular hydrogen bonding and cooperative interactions in carbohydrates via the molecular tailoring approach.

    Science.gov (United States)

    Deshmukh, Milind M; Bartolotti, Libero J; Gadre, Shridhar R

    2008-01-17

    In spite of many theoretical and experimental attempts for understanding intramolecular hydrogen bonding (H-bonding) in carbohydrates, a direct quantification of individual intramolecular H-bond energies and the cooperativity among the H-bonded networks has not been reported in the literature. The present work attempts, for the first time, a direct estimation of individual intramolecular O-H...O interaction energies in sugar molecules using the recently developed molecular tailoring approach (MTA). The estimated H-bond energies are in the range of 1.2-4.1 kcal mol(-1). It is seen that the OH...O equatorial-equatorial interaction energies lie between 1.8 and 2.5 kcal mol(-1), with axial-equatorial ones being stronger (2.0-3.5 kcal mol(-1)). The strongest bonds are nonvicinal axial-axial H-bonds (3.0-4.1 kcal mol(-1)). This trend in H-bond energies is in agreement with the earlier reports based on the water-water H-bond angle, solvent-accessible surface area (SASA), and (1)H NMR analysis. The contribution to the H-bond energy from the cooperativity is also estimated using MTA. This contribution is seen to be typically between 0.1 and 0.6 kcal mol(-1) when H-bonds are a part of a relatively weak equatorial-equatorial H-bond network and is much higher (0.5-1.1 kcal mol(-1)) when H-bonds participate in an axial-axial H-bond network.

  9. Networking with noise at the molecular, cellular, and population level

    Science.gov (United States)

    Vilar, Jose

    2002-03-01

    The intrinsic stochastic nature of biochemical reactions affects enzymatic and transcriptional networks at different levels. Yet, cells are able to function effectively and consistently amidst such random fluctuations. I will discuss some molecular mechanisms that are able to reduce the intrinsic noise of chemical reactions, how suitable designs can make networks resistant to noise, and what strategies can be used by populations to achieve precise functions.

  10. Molecular mechanisms of cooperative binding of transcription factors Runx1-CBFβ-Ets1 on the TCRα gene enhancer.

    Science.gov (United States)

    Kasahara, Kota; Shiina, Masaaki; Fukuda, Ikuo; Ogata, Kazuhiro; Nakamura, Haruki

    2017-01-01

    Ets1 is an essential transcription factor (TF) for several important physiological processes, including cell proliferation and differentiation. Its recognition of the enhancer region of the TCRα gene is enhanced by the cooperative binding of the Runx1-CBFβ heterodimer, with the cancelation of phosphorylation-dependent autoinhibition. The detailed mechanism of this interesting cooperativity between Ets1 and the Runx1-CBFβ heterodimer is still largely unclear. Here, we investigated the molecular mechanisms of this cooperativity, by using molecular dynamics simulations. Consequently, we detected high flexibility of the loop region between the HI2 and H1 helices of Ets1. Upon Runx1-CBFβ heterodimer binding, this loop transiently adopts various sub-stable conformations in its interactions with the DNA. In addition, a network analysis suggested an allosteric pathway in the molecular assembly and identified some key residues that coincide with previous experimental studies. Our simulations suggest that the cooperative binding of Ets1 and the Runx1-CBFβ heterodimer alters the DNA conformation and induces sub-stable conformations of the HI2-H1 loop of Ets1. This phenomenon increases the flexibility of the regulatory module, including the HI2 helix, and destabilizes the inhibitory form of this module. Thus, we hypothesize that this effect facilitates Ets1-DNA binding and prevents the phosphorylation-dependent DNA binding autoinhibition.

  11. Molecular Data for the Sea Turtle Population in Brazil

    Directory of Open Access Journals (Sweden)

    Sibelle Torres Vilaça

    2013-01-01

    Full Text Available We report here a dataset comprising nine nuclear markers for the Brazilian population of Cheloniidae turtles: hawksbills (Eretmochelys imbricata, loggerheads (Caretta caretta, olive ridleys (Lepidochelys olivacea, and green turtles (Chelonia mydas. Because hybridization is a common phenomenon between the four Cheloniidae species nesting on the Brazilian coast, we also report molecular markers for the hybrids E. imbricata × C. caretta, C. caretta × L. olivacea, and E. imbricata × L. olivacea and for one hybrid E. imbricata × C. mydas and one between three species C. mydas × E. imbricata × C. caretta. The data was used in previous studies concerning (1 the description of frequent hybrids C. caretta × E. imbricata in Brazil, (2 the report of introgression in some of these hybrids, and (3 population genetics. As a next step for the study of these hybrids and their evolution, genome-wide studies will be performed in the Brazilian population of E. imbricata, C. caretta, and their hybrids.

  12. From the Cover: Cooperative extraction of membrane nanotubes by molecular motors

    Science.gov (United States)

    Leduc, Cécile; Campàs, Otger; Zeldovich, Konstantin B.; Roux, Aurélien; Jolimaitre, Pascale; Bourel-Bonnet, Line; Goud, Bruno; Joanny, Jean-François; Bassereau, Patricia; Prost, Jacques

    2004-12-01

    In eukaryotic cells, nanotubes represent a substantial fraction of transport intermediates between organelles. They are extracted from membranes by molecular motors walking along microtubules. We previously showed that kinesins fixed on giant unilamellar vesicles in contact with microtubules are sufficient to form nanotubes in vitro. Motors were attached to the membrane through beads, thus facilitating cooperative effects. Koster et al. [Koster, G., VanDuijn, M., Hofs, B. & Dogterom, M. (2003) Proc. Natl. Acad. Sci. USA 100, 15583-15588] proposed that motors could dynamically cluster at the tip of tubes when they are individually attached to the membrane. We demonstrate, in a recently designed experimental system, the existence of an accumulation of motors allowing tube extraction. We determine the motor density along a tube by using fluorescence intensity measurements. We also perform a theoretical analysis describing the dynamics of motors and tube growth. The only adjustable parameter is the motor binding rate onto microtubules, which we measure to be 4.7 ± 2.4 s-1. In addition, we quantitatively determine, for a given membrane tension, the existence of a threshold in motor density on the vesicle above which nanotubes can be formed. We find that the number of motors pulling a tube can range from four at threshold to a few tens away from it. The threshold in motor density (or in membrane tension at constant motor density) could be important for the understanding of membrane traffic regulation in cells. giant unilamellar vesicle | intracellular transport | kinesin | membrane tubule | traffic jam

  13. Two Populations of Molecular Clouds in the Antennae Galaxies

    CERN Document Server

    Wei, Lisa H; Ho, Luis C

    2012-01-01

    Super star clusters --- extremely massive clusters found predominately in starburst environments --- are essential building blocks in the formation of galaxies and thought to dominate star formation in the high-redshift universe. However, the transformation from molecular gas into these ultra-compact star clusters is not well understood. To study this process, we used the Submillimeter Array and the Plateau de Bure Interferometer to obtain high angular resolution (~1.5" or 160 pc) images of the Antennae overlap region in CO(2--1) to search for the molecular progenitors of the super star clusters. We resolve the molecular gas distribution into a large number of clouds, extending the differential cloud mass function down to a 5\\sigma completeness limit of 3.8x10^5 M_sun. We identify a distinct break in the mass function around log M_mol/M_sun ~ 6.5, which separates the molecular clouds into two distinct populations. The smaller, less massive clouds reside in more quiescent areas in the region, while the larger,...

  14. Mechanism of cooperative behaviour in systems of slow and fast molecular motors.

    Science.gov (United States)

    Larson, Adam G; Landahl, Eric C; Rice, Sarah E

    2009-06-28

    Two recent theoretical advances have described cargo transport by multiple identical motors and by multiple oppositely directed, but otherwise identical motors [M. J. Muller, S. Klumpp and R. Lipowsky, Proc. Natl. Acad. Sci. U. S. A., 2008, 105(12), 4609-4614; S. Klumpp and R. Lipowsky, Proc. Natl. Acad. Sci. U. S. A., 2005, 102(48), 17284-17289]. Here, we combine a similar theoretical approach with a simple experiment to describe the behaviour of a system comprised of slow and fast molecular motors having the same directionality. We observed the movement of microtubules by mixtures of slow and fast kinesin motors attached to a glass coverslip in a classic sliding filament assay. The motors are identical, except that the slow ones contain five point mutations that collectively reduce their velocity approximately 15-fold without compromising maximal ATPase activity. Our results indicate that a small fraction of fast motors are able to accelerate the dissociation of slow motors from microtubules. Because of this, a sharp, highly cooperative transition occurs from slow to fast microtubule movement as the relative number of fast motors in the assay is increased. Microtubules move at half-maximal velocity when only 15% of the motors in the assay are fast. Our model indicates that this behaviour depends primarily on the relative motor velocities and the asymmetry between their forward and backward dissociation forces. It weakly depends on the number of motors and their processivity. We predict that movement of cargoes bound to two types of motors having very different velocities will be dominated by one or the other motor. Therefore, cargoes can potentially undergo abrupt changes in movement in response to regulatory mechanisms acting on only a small fraction of motors.

  15. Molecular Genetic Variation in a Clonal Plant Population of Leymus chinensis (Trin.) Tzvel.

    Institute of Scientific and Technical Information of China (English)

    Yu-Sheng WANG; Li-Ming ZHAO; Hua WANG; Jie WANG; Da-Ming HUANG; Rui-Min HONG; Xiao-Hua TENG; Nakamura MIKI

    2005-01-01

    Randomly amplified polymorphic DNA (RAPD) analysis was used to investigate the genetic variation among populations, between populations, and within populations, relationships between genetic distance and geographic distance, and the molecular variation and population size. The effects of geographic and genetic distances, as well as of genetic differentiation and population size, on genetic variations of Leymus chinensis (Trin.) Tzvel. are discussed. The present study showed that there was significant RAPD variation between the Baicheng region population and the Daqing region population, with a molecular variance of 6.35% (P < 0.04), and for differentiation among area populations of the Daqing region, with a molecular variance of 8.78% (P < 0.002). A 21.06% RAPD variation among all 16 populations among two regions was found (P < 0.001), as well as 72.59% variation within populations (P < 0.001). Molecular variation within populations was significantly different among 16 populations.

  16. Effect of self-organized interdependence between populations on the evolution of cooperation

    Science.gov (United States)

    Luo, Chao; Zhang, Xiaolin

    2017-01-01

    In this article, based on interdependent networks, the effect of self-organized interdependence on the evolution of cooperation is studied. Different from the previous works, the interdependent strength, which can effectively improve the fitness of players, is taken as a kind of limited resources and co-evolves with players' strategy. We show that the self-organization of interdependent strength would spontaneously lead to power law distribution at the stationary state, where the level of cooperation in system can be significantly promoted. Furthermore, when intermediate quantity of interdependence resources existing in system, the power law distribution is most evident with the power β ≈ 1.72, meanwhile the level of cooperation also reaches the maximum value. We discuss the related microscopic system properties which are responsible for the observed results and also demonstrate that the power law distribution of interdependence resources is an elementary property which is robust against the governing repeated games and the initial resources allocation patterns.

  17. The molecular population genetics of shoot development in Arabidopsis thaliana.

    Science.gov (United States)

    Shepard, Kristen A

    2007-01-01

    Studies in Arabidopsis thaliana have provided us with a wealth of information about the genetic pathways that regulate plant morphogenesis. This developmental genetic treasure trove represents a fantastic resource for researchers interested in the microevolution of development. Several laboratories have begun using molecular population genetic analyses to investigate the evolutionary forces that act upon loci that regulate shoot morphogenesis. Much of this work has focused on coding sequence variation in transcription factors; however, recent studies have explored sequence variation in other types of proteins and in promoter regions. Several genes that regulate shoot development contain signatures of selective sweeps associated with positive selection or harbor putative balanced polymorphisms in coding and noncoding sequences. Other regulatory genes appear to be evolving neutrally, but have accumulated potentially deleterious replacement polymorphisms.

  18. A negative cooperativity mechanism of human CYP2E1 inferred from molecular dynamics simulations and free energy calculations.

    Science.gov (United States)

    Li, Jue; Wei, Dong-Qing; Wang, Jing-Fang; Li, Yi-Xue

    2011-12-27

    Human cytochrome P450 2E1 (CYP2E1) participates in the metabolism of over 2% of all the oral drugs. A hallmark peculiar feature of this enzyme is that it exhibits a pronounced negative cooperativity in substrate binding. However the mechanism by which the negative cooperativity occurs is unclear. Here, we performed molecular dynamics simulations and free energy calculations on human CYP2E1 to examine the structural differences between the substrate-free and the enzymes with one and two aniline molecules bound. Our results indicate that although the effector substrate does not bind in the active site cavity, it still can directly interact with the active site residues of human CYP2E1. The interaction of the effector substrate with the active site leads to a reorientation of active site residues, which thereby weakens the interactions of the active substrate with this site. We also identify a conserved residue T303 that plays a crucial role in the negative cooperative binding on the short-range effects. This residue is a key factor in the positioning of substrates and in proton delivery to the active site. Additionally, a long-range effect of the effector substrate is identified in which F478 is proposed to play a key role. As located in the interface between the active and effector sites, this residue structurally links the active and effector sites and is found to play a significant role in affecting substrate access and ligand positioning within the active site. In the negative cooperative binding, this residue can decrease the interactions of the active substrate with the active site by π-π stacking which then lowers the hydroxylation activity for the active substrate. These findings are in agreement with previous experimental observations and thus provide detailed atomistic insight into the poorly understood mechanism of the negative cooperativity in human CYP2E1.

  19. Behavioural types and ecological effects in a natural population of the cooperative cichlid Neolamprologus pulcher

    NARCIS (Netherlands)

    Witsenburg, Fardo; Schuerch, Roger; Otti, Oliver; Heg, Dik

    2010-01-01

    The ecological relevance of behavioural syndromes is little studied in cooperative breeding systems where it is assumed that the behavioural type might influence individual decisions on helping and dispersal (e.g. shy, nonaggressive and nonexplorative individuals remain philopatric and helpful, wher

  20. Development and implementation of algorithms in a population of cooperative autonomous mobile robots

    CSIR Research Space (South Africa)

    Namoshe, M

    2007-10-01

    Full Text Available An increase in the number of mobile robot users has lead to the design and implementation of cooperative autonomous mobile robots. Autonomous robots require the ability to build maps of an unknown environment while simultaneously using these maps...

  1. MOLECULAR STRUCTURE OF AMYOTROPHIC LATERAL SCLEROSIS IN RUSSIAN POPULATION

    Directory of Open Access Journals (Sweden)

    N. Yu. Abramycheva

    2016-01-01

    Full Text Available Materials and methods. 285 Russian patients with amyotrophic lateral sclerosis (ALS including 260 patients with a sporadic form and 25 with a familial form were examined for mutations in SOD1, C9orf72, TARDBP,  ANG and other genes and the presence of associations among polymorphic sites in ATXN2 (polyCAG and VEGF (-2578С/А genes.Molecular genetic analysis was performed using direct sequencing, fragment analysis and real-time polymerase chain reaction. On the last stage, rare ALS candidate genes were evaluated using a next generation sequencing (NGS panel.Results. Total rate of the identified mutations in the examined ALS cohort was 9.5 %. The most frequently observed defects were mutations in the SOD1 (24.0 % in familial ALS and 4.6 % in sporadic ALS and C9orf72 (pathological hexanucleotide repeat expansion was identified in 1.8 % cases of ALS, all sporadic genes. The TARDBP gene didn’t contain any mutations, though in the ALS group deletion c.715-126delG located in intron 5 of the TARDBP gene was significantly over-represented – 38.0 % vs. 26.6 % (χ2 = 13.17; р = 0.002. Mutations in the ANG gene were identified in 1.05 % of ALS patients (all cases were sporadic. In 1 (0.35 % sporadic case a G1082A mutation in the DCTN1 gene was identified. The examined group significantly more frequently carried a risk allele of the ATXN2 gene with an “intermediate” (28–33  number of CAG repeats – 5.0 % vs. 1.7 % in the control group (χ2 = 3.89; р = 0.0486. In Russian ALS patients, an association between the disease and the presence of a risk А-allele and homozygote genotype А/А of -2578С/А polymorphism in the VEGF gene was identified (χ2 = 7.14; р = 0.008 and χ2 = 13.46; р = 0.001 for the rates in the ALS population and in the control population, respectively, which is confirmed by the odds ratio.Conclusion. In the current article, molecular structure of ALS in the Russian population was examined, rates of individual genetic forms

  2. The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations

    OpenAIRE

    Fengjiao Liu; Zhang, John Z. H.; Ye Mei

    2016-01-01

    Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The re...

  3. Using Jigsaw-Style Spectroscopy Problem-Solving to Elucidate Molecular Structure through Online Cooperative Learning

    Science.gov (United States)

    Winschel, Grace A.; Everett, Renata K.; Coppola, Brian P.; Shultz, Ginger V.

    2015-01-01

    Cooperative learning was employed as an instructional approach to facilitate student development of spectroscopy problem solving skills. An interactive online environment was used as a framework to structure weekly discussions around spectroscopy problems outside of class. Weekly discussions consisted of modified jigsaw-style problem solving…

  4. Using Jigsaw-Style Spectroscopy Problem-Solving to Elucidate Molecular Structure through Online Cooperative Learning

    Science.gov (United States)

    Winschel, Grace A.; Everett, Renata K.; Coppola, Brian P.; Shultz, Ginger V.

    2015-01-01

    Cooperative learning was employed as an instructional approach to facilitate student development of spectroscopy problem solving skills. An interactive online environment was used as a framework to structure weekly discussions around spectroscopy problems outside of class. Weekly discussions consisted of modified jigsaw-style problem solving…

  5. Cellular cooperation: insights from microbes.

    Science.gov (United States)

    Celiker, Hasan; Gore, Jeff

    2013-01-01

    Cooperation between cells is a widespread phenomenon in nature, found across diverse systems ranging from microbial populations to multicellular organisms. For cooperation to evolve and be maintained within a population of cells, costs due to competition have to be outweighed by the benefits gained through cooperative actions. Because cooperation generally confers a cost to the cooperating cells, defector cells that do not cooperate but reap the benefits of cooperation can thrive and eventually drive the cooperating phenotypes to extinction. Here we summarize recent advances made in understanding how cooperation and multicellularity can evolve in microbial populations in the face of such conflicts and discuss parallels with cell populations within multicellular organisms.

  6. An assessment of exposure and effects of persistent organic pollutants in an urban Cooper's hawk (Accipiter cooperii) population.

    Science.gov (United States)

    Brogan, Jason M; Green, David J; Maisonneuve, France; Elliott, John E

    2017-01-01

    Among the stressors confronting urban wildlife, chemical contaminants pose a particular problem for high trophic feeding species. Previous data from fortuitous carcass collections revealed surprisingly high levels of persistent organic pollutants in raptor species, including the Cooper's hawk (Accipiter cooperii), from urbanized areas of southwestern British Columbia, Canada. Thus, in 2012 and 2013, we followed up on that finding by measuring POPs in blood samples from 21 adult and 15 nestling Cooper's hawks in Vancouver, a large urban area in southwestern Canada. Reproductive success and circulating thyroid hormones were measured to assess possible toxicological effects. Model comparisons showed concentrations of polychlorinated biphenyls (ΣPCBs) were positively influenced by the level of urbanization. Total thyroxin (TT4) was negatively associated with increases in ΣPCBs. Total triiodothyronine (TT3) was negatively associated with ΣPCBs and polybrominated diphenyl ethers (ΣPBDEs). The legacy insecticide, dieldrin, appeared to have some negative influence on reproductive success. There is some evidence of biochemical perturbation by PBDEs and lingering impact of legacy POPs which have not been used for at least 40 years, but overall Cooper's hawks have successfully populated this urban environment.

  7. The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations.

    Science.gov (United States)

    Liu, Fengjiao; Zhang, John Z H; Mei, Ye

    2016-06-01

    Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The results show that this cooperativity comes from both the enthalpy and entropy contributions. The former contribution mainly comes from the alternations of solvation free energy. Decomposition analysis shows that the mutated residues nearly have no contributions to the cooperativity. Instead, N49 and S88, which are located at the entry of the binding pocket and interact with the carboxyl group of biotin, make the dominant contribution among all the residues in the first binding shell around biotin.

  8. The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations

    Science.gov (United States)

    Liu, Fengjiao; Zhang, John Z. H.; Mei, Ye

    2016-06-01

    Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The results show that this cooperativity comes from both the enthalpy and entropy contributions. The former contribution mainly comes from the alternations of solvation free energy. Decomposition analysis shows that the mutated residues nearly have no contributions to the cooperativity. Instead, N49 and S88, which are located at the entry of the binding pocket and interact with the carboxyl group of biotin, make the dominant contribution among all the residues in the first binding shell around biotin.

  9. Quorum Sensing Coordinates Cooperative Expression of Pyruvate Metabolism Genes To Maintain a Sustainable Environment for Population Stability

    Science.gov (United States)

    Hawver, Lisa A.; Giulietti, Jennifer M.; Baleja, James D.

    2016-01-01

    ABSTRACT Quorum sensing (QS) is a microbial cell-cell communication system that regulates gene expression in response to population density to coordinate collective behaviors. Yet, the role of QS in resolving the stresses caused by the accumulation of toxic metabolic by-products at high cell density is not well defined. In response to cell density, QS could be involved in reprogramming of the metabolic network to maintain population stability. Using unbiased metabolomics, we discovered that Vibrio cholerae mutants genetically locked in a low cell density (LCD) QS state are unable to alter the pyruvate flux to convert fermentable carbon sources into neutral acetoin and 2,3-butanediol molecules to offset organic acid production. As a consequence, LCD-locked QS mutants rapidly lose viability when grown with fermentable carbon sources. This key metabolic switch relies on the QS-regulated small RNAs Qrr1-4 but is independent of known QS regulators AphA and HapR. Qrr1-4 dictate pyruvate flux by translational repression of the enzyme AlsS, which carries out the first step in acetoin and 2,3-butanediol biosynthesis. Consistent with the idea that QS facilitates the expression of a common trait in the population, AlsS needs to be expressed cooperatively in a group of cells. Heterogeneous populations with high percentages of cells not expressing AlsS are unstable. All of the cells, regardless of their respective QS states, succumb to stresses caused by toxic by-product accumulation. Our results indicate that the ability of the bacteria to cooperatively control metabolic flux through QS is critical in maintaining a sustainable environment and overall population stability. PMID:27923919

  10. Molecular insights into seed dispersal mutualisms driving plant population recruitment

    Science.gov (United States)

    García, Cristina; Grivet, Delphine

    2011-11-01

    Most plant species require mutualistic interactions with animals to fulfil their demographic cycle. In this regard frugivory (i.e., the intake of fruits by animals) enhances natural regeneration by mobilizing a large amount of seeds from source trees to deposition sites across the landscape. By doing so, frugivores move propagules, and the genotypes they harbour creating the spatial, ecological, and genetic environment under which subsequent recruitment proceeds. Recruitment patterns can be envisioned as the result of two density- and distance-dependent processes: seed dispersal and seed/seedling survival (the Janzen-Connell model). Population genetic studies add another layer of complexity for understanding the fate of dispersed propagules: the genetic relatedness among neighbouring seeds within a seed clump, a major outcome of frugivore activity, modifies their chances of germinating and surviving. Yet, we virtually ignore how the spatial distribution of maternal progenies and recruitment patterns relate with each other in frugivore-generated seed rains. Here we focus on the critical role of frugivore-mediated seed dispersal in shaping the spatial distribution of maternal progenies in the seed rain. We first examine which genetic mechanisms underlying recruitment are influenced by the spatial distribution of maternal progenies. Next, we examine those studies depicting the spatial distribution of maternal progenies in a frugivore-generated seed rain. In doing so, we briefly review the most suitable analytical approaches applied to track the contribution of fruiting trees to the seed rain based on molecular data. Then we look more specifically at the role of distinct frugivore guilds in determining maternal genetic correlations and their expected consequences for recruitment patterns. Finally we posit some general conclusions and suggest future research directions that would provide a more comprehensive understanding of the ecological and evolutionary consequences

  11. First molecular screening of deafness in the Altai Republic population

    Directory of Open Access Journals (Sweden)

    Claustres Mireille

    2005-03-01

    Full Text Available Abstract Background We studied the molecular basis of NSHL in Republic of Altai (South Siberia, Russia. The Altaians are the indigenous Asian population of the Altai Mountain region considered as a melting-pot and a dispersion center for world-wide human expansions in the past. Methods A total of 76 patients of Altaian, Russian or mixed ethnicity and 130 Altaian controls were analyzed by PCR-DHPLC and sequencing in the GJB2 gene. The GJB6 deletion and the common non-syndromic deafness-causing mitochondrial mutations were also tested when appropriate. Results 8.3% of the Altaian chromosomes were carrying GJB2 mutations versus 46.9% of the Russian chromosomes. The 235delC mutation was predominant among Altaians, whereas the 35delG mutation was most prevalent among Russian patients. Conclusion We found an Asian-specific GJB2 diversity among Altaians, and different GJB2 contribution for deafness in the Altaian and Russian patients. The high carrier frequency of 235delC in Altaians (4.6% is probably defined by gene drift/founder effect in a particular group. The question whether the Altai region could be one of founder sources for the 235delC mutation widespread in Asia is open.

  12. The YSO Population in the Vela-D Molecular Cloud

    CERN Document Server

    Strafella, F; Giannini, T; Elia, D; Maruccia, Y; Maiolo, B; Massi, F; Olmi, L; Molinari, S; Pezzuto, S

    2014-01-01

    We investigate the young stellar population in the Vela Molecular Ridge, Cloud-D (VMR-D), a star forming (SF) region observed by both Spitzer/NASA and Herschel/ESA space telescope. The point source, band-merged, Spitzer-IRAC catalog complemented with MIPS photometry previously obtained is used to search for candidate young stellar objects (YSO), also including sources detected in less than four IRAC bands. Bona fide YSO are selected by using appropriate color-color and color-magnitude criteria aimed to exclude both Galatic and extragalactic contaminants. The derived star formation rate and efficiency are compared with the same quantities characterizing other SF clouds. Additional photometric data, spanning from the near-IR to the submillimeter, are used to evaluate both bolometric luminosity and temperature for 33 YSOs located in a region of the cloud observed by both Spitzer and Herschel. The luminosity-temperature diagram suggests that some of these sources are representative of Class 0 objects with bolomet...

  13. Structural Basis for Cooperative Binding of Azoles to CYP2E1 as Interpreted through Guided Molecular Dynamics Simulations

    Science.gov (United States)

    Levy, Joseph W.; Hartman, Jessica H.; Perry, Martin D.; Miller, Grover P.

    2015-01-01

    CYP2E1 metabolizes a wide array of small, hydrophobic molecules, resulting in their detoxification or activation into carcinogens through Michaelis-Menten as well as cooperative mechanisms. Nevertheless, the molecular determinants for CYP2E1 specificity and metabolic efficiency toward these compounds are still unknown. Herein, we employed computational docking studies coupled to Molecular Dynamics simulations to provide a critical perspective for understanding a structural basis for cooperativity observed for an array of azoles from our previous binding and catalytic studies (Hartman, JH et al (2014) Biochem Pharmacol 87, 523-33). The resulting 28 CYP2E1 complexes in this study revealed a common passageway for azoles that included a hydrophobic steric barrier causing a pause in movement toward the active site. The entrance to the active site acted like a second sieve to restrict access to the inner chamber. Collectively, these interactions impacted the final orientation of azoles reaching the active site and hence could explain differences in their biochemical properties observed in our previous studies, such as the consequences of methylation at position 5 of the azole ring. The association of a second azole demonstrated significant differences in interactions stabilizing the bound complex than observed for the first binding event. Intermolecular interactions occurred between the two azoles as well as CYP2E1 residue side chains and backbone and involved both hydrophobic contacts and hydrogen bonds. The relative importance of these interactions depended on the structure of the respective azoles indicating the absence of specific defining criteria for binding unlike the well-characterized dominant role of hydrophobicity in active site binding. Consequently, the structure activity relationships described here and elsewhere are necessary to more accurately identify factors impacting the observation and significance of cooperativity in CYP2E1 binding and catalysis

  14. ILO standard setting, policy studies and technical cooperation relating to population issues and women.

    OpenAIRE

    Oppong C

    1993-01-01

    Examines the ILO's constitution, mandates and International Labour Standards in the areas of female worker protection, and promotion of equality and population. Highlights some current labour problems specific to women, including 'invisible' labour and its lack of documentation, the lack of equality, and the need for protection. Also highlights nine gender issues, both of labour and population. Bibliography, statistical tables and abstract in French.

  15. Molecular interactions of ribosomal components. IV: Cooperative interactions during assembly in vitro.

    Science.gov (United States)

    Green, M; Kurland, C G

    1973-08-01

    Cooperative interactions between different 30S ribosomal proteins during assembly in vitro are described. The site specific binding of S7 to 16S RNA is enhanced by S20; that of S16 requires S4 and S20; and S7 is required for the maximum binding of S9, S13 and S19. Some of these interactions are reflected in the protein neighborhoods of the functional ribosome, but this may not be a general rule. Finally, we suggest that the assembly cooperativety observed may not be a consequence of direct-protein interactions.

  16. Deer Population Health Evaluation for Pocosin Lakes National Wildlife Refuge from Southeastern Cooperative Wildlife Disease Study

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The letter and enclosed report discusses the health evaluation of 5 deer taken randomly from Pocosin Lakes National Wildlife Refuge population. Herd health appears...

  17. Living bacteria rheology: population growth, aggregation patterns and cooperative behaviour under different shear flows

    CERN Document Server

    Patricio, P; Portela, R; Sobral, R G; Grilo, I R; Cidade, T; Leal, C R

    2014-01-01

    The activity of growing living bacteria was investigated using real-time and in situ rheology -- in stationary and oscillatory shear. Two different strains of the human pathogen Staphylococcus aureus -- strain COL and its isogenic cell wall autolysis mutant -- were considered in this work. For low bacteria density, strain COL forms small clusters, while the mutant, presenting deficient cell separation, forms irregular larger aggregates. In the early stages of growth, when subjected to a stationary shear, the viscosity of both strains increases with the population of cells. As the bacteria reach the exponential phase of growth, the viscosity of the two strains follow different and rich behaviours, with no counterpart in the optical density or in the population's colony forming units measurements. While the viscosity of strain COL keeps increasing during the exponential phase and returns close to its initial value for the late phase of growth, where the population stabilizes, the viscosity of the mutant strain ...

  18. Recent Trends and Developments: Regional Co-operation in Population Education.

    Science.gov (United States)

    Population Education in Asia and the Pacific Newsletter and Forum, 1990

    1990-01-01

    Presented is an outline of objectives and outcomes specific to curriculum development, materials development, professional training, research and assessment, management and monitoring, and an agenda for future consultative seminars, all formulated at the UNESCO-sponsored regional consultative seminar on population education during May 1990, in…

  19. Inference of population history and patterns from molecular data

    DEFF Research Database (Denmark)

    Tataru, Paula

    , the existing mathematical models and computational methods need to be reformulated. I address this from an inference perspective in two areas of bioinformatics. Population genetics studies the influence exerted by various factors on the dynamics of a population's genetic variation. These factors cover...... evolutionary forces, such as mutation and selection, but also changes in population size. The aim in population genetics is to untangle the history of a population from observed genetic variation. This subject is dominated by two dual models, the Wright-Fisher and coalescent. I first introduce a new...... how standard algorithms can be improved by including pattern occurrence in the hidden structure of observed sequences. Such a hidden structure could be the localization and composition of genes within a DNA sequence. The second problem I target is the computational prediction of the pattern...

  20. Molecular genetic diversity study of Lepidium sativum population ...

    African Journals Online (AJOL)

    Vostro 2520

    (NJ) and PCO analysis showed very weak grouping among individuals collected from the same regions. .... compare the population and generate phenogram using NTSYS- pc ..... with 85 L. sativum accessions showed four distinct clusters.

  1. Minimum Population Search, an Application to Molecular Docking

    Directory of Open Access Journals (Sweden)

    Antonio Bolufé-Röhler

    2014-08-01

    Full Text Available Computer modeling of protein-ligand interactions is one of the most important phases in a drug design process. Part of the process involves the optimization of highly multi-modal objective (scoring functions. This research presents the Minimum Population Search heuristic as an alternative for solving these global unconstrained optimization problems. To determine the effectiveness of Minimum Population Search, a comparison with seven state-of-the-art search heuristics is performed. Being specifically designed for the optimization of large scale multi-modal problems, Minimum Population Search achieves excellent results on all of the tested complexes, especially when the amount of available function evaluations is strongly reduced. A first step is also made toward the design of hybrid algorithms based on the exploratory power of Minimum Population Search. Computational results show that hybridization leads to a further improvement in performance.

  2. Large scale molecular analysis of traditional European maize populations. Relationships with morphological variation.

    Science.gov (United States)

    Rebourg, C; Gouesnard, B; Charcosset, A

    2001-05-01

    A representative sample of 130 European traditional maize populations was analysed for both their morphological and molecular variation. The morphological analysis of 19 variables revealed a significant variability. Correlation analysis allowed us to distinguish between traits affected by earliness (plant and ear height) and structural traits (plant architecture, grain structure). Two main morphological types could be distinguished. Molecular analyses were performed for 29 RFLP loci on DNA bulks. The number of alleles detected was high when compared to previous studies (9.59 alleles per locus). Genetic diversity was also high (0.55), with a strong differentiation between populations (GST value of 35.6%). A clear relationship between the genetic diversity of the populations and their agronomic performances was highlighted. Morphological and molecular distances showed a tendency towards a triangular relationship. We therefore considered a two-phase process to be the most efficient approach for the classification of genetic resources: firstly, a molecular study to define groups of genetically close populations, and secondly a morphological description of populations from each group. In our European collection, this approach allowed us to separate the populations from Northern and Southern Europe and to define six groups of genetically close populations, comparable to European races. This study opens new prospects concerning the molecular analysis of very large collections of genetic resources, hitherto limited by the necessity of individual analyses, and proposes a first molecular classification of European maize germplasm.

  3. The Germans revisiting Gakovo: Encounters, cooperation and reconciliation of the former and present local populations

    Directory of Open Access Journals (Sweden)

    Krel Aleksandar

    2015-01-01

    Full Text Available This paper presents a case study about a reunion of the evicted members of the German national minority in Vojvodina, who after almost five decades came to visit their homeland, and the local population in Gakovo. The case study attests about lengthy and very complicated process in resolving post-conflict situations. The process’ launch is dependent on the willingness of the individuals involved to face not only one’s own pain caused by the enemy, but also on ability to comprehend, during an encounter with “the dark side of one’s past”, sufferings and humiliation experienced by the adversary. Awareness and acceptance of one’s own responsibility in the conflict are a prerequisite for forgiveness and reconciliation of the opposing parties. The outcome of this process is uncertain to the very end and conditioned upon the entire network of interlocking political, economic and cultural factors.

  4. Molecular genotyping of ABO blood groups in some population groups from India

    OpenAIRE

    Sabita Ray; Ajit C Gorakshakar; Vasantha, K.; Anita Nadkarni; Yazdi Italia; Kanjaksha Ghosh

    2014-01-01

    Background & objectives: Indian population is characterized by the presence of various castes and tribal groups. Various genetic polymorphisms have been used to differentiate among these groups. Amongst these, the ABO blood group system has been extensively studied. There is no information on molecular genotyping of ABO blood groups from India. Therefore, the main objective of this study was to characterize the common A, B and O alleles by molecular analysis in some Indian population groups. ...

  5. Phylogeography, population dynamics, and molecular evolution of European bat lyssaviruses

    DEFF Research Database (Denmark)

    Davis, P.L.; Holmes, E.C.; Larrous, F.

    2005-01-01

    origin, and population growth rates of EBLV-1. Our study encompassed data from 12 countries collected over a time span of 35 years and focused on the glycoprotein (G) and nucleoprotein (N) genes. We show that although the two subtypes of EBLV-1-EBLV-1a and EBLV-lb-have both grown at a low exponential...... rate since their introduction into Europe, they have differing population structures and dispersal patterns. Furthermore, there were strong constraints against amino acid change in both EBLV-1 and EBLV-2, as reflected in a low ratio of nonsynonymous to synonymous substitutions per site, particularly...

  6. Molecular mechanisms of cooperative binding of transcription factors Runx1–CBFβ–Ets1 on the TCRα gene enhancer

    Science.gov (United States)

    Kasahara, Kota; Shiina, Masaaki; Fukuda, Ikuo; Ogata, Kazuhiro; Nakamura, Haruki

    2017-01-01

    Ets1 is an essential transcription factor (TF) for several important physiological processes, including cell proliferation and differentiation. Its recognition of the enhancer region of the TCRα gene is enhanced by the cooperative binding of the Runx1–CBFβ heterodimer, with the cancelation of phosphorylation-dependent autoinhibition. The detailed mechanism of this interesting cooperativity between Ets1 and the Runx1–CBFβ heterodimer is still largely unclear. Here, we investigated the molecular mechanisms of this cooperativity, by using molecular dynamics simulations. Consequently, we detected high flexibility of the loop region between the HI2 and H1 helices of Ets1. Upon Runx1–CBFβ heterodimer binding, this loop transiently adopts various sub-stable conformations in its interactions with the DNA. In addition, a network analysis suggested an allosteric pathway in the molecular assembly and identified some key residues that coincide with previous experimental studies. Our simulations suggest that the cooperative binding of Ets1 and the Runx1–CBFβ heterodimer alters the DNA conformation and induces sub-stable conformations of the HI2–H1 loop of Ets1. This phenomenon increases the flexibility of the regulatory module, including the HI2 helix, and destabilizes the inhibitory form of this module. Thus, we hypothesize that this effect facilitates Ets1–DNA binding and prevents the phosphorylation-dependent DNA binding autoinhibition. PMID:28231333

  7. A Comparison of Three Molecular Markers for the Identification of Populations of Globodera pallida

    OpenAIRE

    Hoolahan, Angelique H.; Blok, Vivian C.; Gibson, Tracey; Dowton, Mark

    2012-01-01

    Potato cyst nematodes cost the potato industry substantial financial losses annually. Through the use of molecular markers, the distribution and infestation routes of these nematodes can be better elucidated, permitting the development of more effective preventative methods. Here we assess the ability of three molecular markers to resolve multiple representatives of five Globodera pallida populations as monophyletic groups. Molecular markers included a region of the rbp-1 gene (an effector), ...

  8. Thermodynamic study of simple molecular glasses: universal features in their heat capacity and the size of the cooperatively rearranging regions.

    Science.gov (United States)

    Tatsumi, Soichi; Aso, Shintaro; Yamamuro, Osamu

    2012-07-27

    We have obtained some universal thermodynamic properties on glass transitions of molecular liquids. The heat capacity C(p) of glassy propene, which was vitrified by using a vapor-deposition technique, was measured with a newly developed adiabatic calorimeter. Propene has the lowest glass transition temperature (T(g)=56 K), the largest C(p) jump at T(g) (C(p)(lq)/C(p)(gl)~2.5), and the lowest residual entropy (S(res)~Rln2) compared with glass-forming molecules measured before. We have analyzed the present data with other hydrocarbon molecules vitrified by liquid quenching and obtained the following results: (1) The excess heat capacities are scaled well by using a Kauzmann temperature T(K), (2) The size of the cooperative rearrangement region (CRR) frozen at T(g) increases with decreasing the temperature difference between T(g) and T(K) (Kauzmann temperature), and (3) The simpler the molecule is, the larger the frozen CRR becomes. These are all supporting the validity of the Adam-Gibbs theory.

  9. [Molecular characterization of Sigmodon hirsutus (Rodentia: Cricetidae) populations in Venezuela].

    Science.gov (United States)

    Lessmann, Janeth; Arrivillaga, Jazzmín; Aguilera, Marisol

    2011-06-01

    Recent phylogenetic studies based on cytochrome b gene sequence, have determined that the species historically known as Sigmodon hispidus (Rodentia) from South America comprises a species S. hirsutus of paraphyletic origin. The aim of this study was to test the hypothesis that populations from Venezuela, represent the sensu strict form, ancestral haplotypes, and monophyletic subspecieS. For this, 12 individual sequences from three localities of different biogeographic regions in Venezuela were evaluated and sequenced based on cyto b. Additionally, the sequences were used to develop a cladistic analysis and genetic distance calculations, and to compare this information with two individual sequences of Sigmodon specimens available in Genbank. Phylogenetic analyses show that the three populations of S. hirsutus of Venezuela form an ancestral and monophyletic subclade supported by high bootstrap values and significant genetic distance between subclade within the S. hirsutus. Besides, the existence of two lineages suggests two subspecies, S. hirsutus hirsutus from Venezuela, and S. hirsutus mexicanus from Mexico-Central America, but, both species need formal description.

  10. Molecular analysis of skeletal tuberculosis in an ancient Egyptian population.

    Science.gov (United States)

    Zink, A; Haas, C J; Reischl, U; Szeimies, U; Nerlich, A G

    2001-04-01

    A paleomicrobiological study was performed on 37 skeletal tissue specimens from cadavers in the necropolis of Thebes-West, Upper Egypt, (2120-500 BC) and four from the necropolis of Abydos (3000 BC). The subjects had typical macromorphological evidence of osseous tuberculosis (n = 3), morphological alterations that were not specific, but probably resulted from tuberculosis (n = 17), or were without morphological osseous changes (n = 21). DNA was extracted from these bone samples and amplified by PCR with a primer pair that recognised the Mycobacterium tuberculosis complex insertion sequence IS6110. To confirm specificity of the analysis, the amplification products of several samples were subjected to restriction enzyme digestion, or direct sequencing, or both. In 30 of the 41 cases analysed, ancient DNA was demonstrated by amplification by the presence of the human beta-actin or the amelogenin gene and nine of these cases were positive for M. tuberculosis DNA. The results were confirmed by restriction endonuclease digestion and sequencing. A positive result for M. tuberculosis DNA was seen in two of the three cases with typical morphological signs of tuberculosis and amplifiable DNA, in five of 13 non-specific, but probable cases (including two cases from c. 3000 BC), but also in two of 14 cases without pathological bone changes. These observations confirm that tuberculosis may be diagnosed unequivocally in skeletal material from ancient Egypt, even dating back to c. 3000 BC. As a positive molecular reaction was observed in most of the typical cases of skeletal tuberculosis, in about one-third of non-specific, but probable tuberculous osseous changes and, surprisingly, in about one-seventh of unremarkable samples, this suggests that infection with M. tuberculosis was relatively frequent in ancient Egypt.

  11. HLA DNA sequence variation among human populations: molecular signatures of demographic and selective events.

    Directory of Open Access Journals (Sweden)

    Stéphane Buhler

    Full Text Available Molecular differences between HLA alleles vary up to 57 nucleotides within the peptide binding coding region of human Major Histocompatibility Complex (MHC genes, but it is still unclear whether this variation results from a stochastic process or from selective constraints related to functional differences among HLA molecules. Although HLA alleles are generally treated as equidistant molecular units in population genetic studies, DNA sequence diversity among populations is also crucial to interpret the observed HLA polymorphism. In this study, we used a large dataset of 2,062 DNA sequences defined for the different HLA alleles to analyze nucleotide diversity of seven HLA genes in 23,500 individuals of about 200 populations spread worldwide. We first analyzed the HLA molecular structure and diversity of these populations in relation to geographic variation and we further investigated possible departures from selective neutrality through Tajima's tests and mismatch distributions. All results were compared to those obtained by classical approaches applied to HLA allele frequencies.Our study shows that the global patterns of HLA nucleotide diversity among populations are significantly correlated to geography, although in some specific cases the molecular information reveals unexpected genetic relationships. At all loci except HLA-DPB1, populations have accumulated a high proportion of very divergent alleles, suggesting an advantage of heterozygotes expressing molecularly distant HLA molecules (asymmetric overdominant selection model. However, both different intensities of selection and unequal levels of gene conversion may explain the heterogeneous mismatch distributions observed among the loci. Also, distinctive patterns of sequence divergence observed at the HLA-DPB1 locus suggest current neutrality but old selective pressures on this gene. We conclude that HLA DNA sequences advantageously complement HLA allele frequencies as a source of data used

  12. Molecular and morphometric variation in chromosomally differentiated populations of the grasshopper Sinipta dalmani (Orthopthera: Acrididae).

    Science.gov (United States)

    Sesarini, Carla; Remis, Maria I

    2008-07-01

    Sinipta dalmani is an Argentine grasshopper whose chromosome polymorphisms have been widely studied through cytogenetic, morphometric, and fitness component analyses. The present work analysed molecular and morphometric variation in seven chromosomally differentiated populations from Entre Rios and Buenos Aires provinces to analyse population structure. Molecular studies were performed studying RAPD loci and morphometric analyses were carried out measuring five morphometric traits. Genetic variability was high in all studied populations and was characterized by a decrease in H as a function of latitude and temperature. Both conventional F(ST) analysis and Bayesian approach for dominant marker showed that there were significant genetic differences among all populations, between provinces, and among populations within provinces. Entre Rios populations showed higher mean numbers of migrants per generation as well as low genetic differentiation and high gene flow with almost all populations whereas Buenos Aires populations may be considered as a result of a more recently colonization. There is considerable morphometric variation between populations and this variation correlates with latitude and temperature. Our results suggest that selection contributes to phenotypic differentiation among populations by moulding the differences in trait means whereas genetic drift is responsible for differences in the matrix of variance-covariance. The gene flow detected is insufficient to prevent phenotypic and chromosome divergences.

  13. Molecular biomonitoring of a population of nurses handling antineoplastic drugs

    Energy Technology Data Exchange (ETDEWEB)

    Cornetta, Tommaso [Department of Biology, ' Roma Tre' University, Viale Guglielmo Marconi, 446-00146 Rome (Italy); ' Don Carlo Gnocchi' Foundation, Rome (Italy); Padua, Luca [' Don Carlo Gnocchi' Foundation, Rome (Italy); Department of Neuroscience, Neurology Institute, Catholic University, Rome (Italy); Testa, Antonella; Ievoli, Elena [Toxicology and Biomedical Sciences Section, ENEA Research Center, Casaccia (Rome) (Italy); Festa, Fabiola [Department of Biology, ' Roma Tre' University, Viale Guglielmo Marconi, 446-00146 Rome (Italy); Tranfo, Giovanna [Department of Occupational Hygiene, Italian Institute for Occupational Prevention and Safety, Monteporzio Catone (Rome) (Italy); Baccelliere, Luigi [S. Martino Hospital, Genova (Italy); Cozzi, Renata [Department of Biology, ' Roma Tre' University, Viale Guglielmo Marconi, 446-00146 Rome (Italy)], E-mail: cozzi@bio.uniroma3.it

    2008-02-01

    Many antineoplastic drugs have been found to have carcinogenic, mutagenic and teratogenic activity and so hospital personnel handling these substances are potentially exposed to health risk. Understanding this risk derived from protracted occupational exposure has great relevance even if the workers normally adopt individual and environmental protective measures. To address this question we have studied the presence of DNA and chromosome damage in a population of nurses employed in Italian oncology units and in matched controls. We used the comet assay to evidence the presence of DNA strand breaks, due to both acute and chronic exposure, and the micronucleus (MN) test, which is a measure of clastogenic and aneugenic events. Furthermore, since the individual response to the exogenous insults may be genetically determined, we studied the possible influence of single nucleotide polymorphism in XRCC1 and XRCC3 DNA repair genes on induced genetic damage. We also considered the effects of confounding factors like smoking, age and gender. The results indicated that the exposed subjects had significantly high levels of genetic damage. Age and gender were associated with increased values in MN, both in control and in exposed groups; the smoking habit affects MN frequency in controls, but not in workers. Furthermore we found that exposed subjects bearing at least one XRCC1 variant allele (399Gln) show higher values of MN. The present data provide the evidence to show that occupational exposure to antineoplastic drugs, even if in safety controlled conditions, represents a serious health risk. Furthermore we have shown that the presence of XRCC1 genetic polymorphism could contribute to increase the genetic damage in susceptible individuals who are occupationally exposed to dangerous substances.

  14. Molecular and quantitative trait variation within and among populations of the intertidal copepod Tigriopus californicus.

    Science.gov (United States)

    Edmands, Suzanne; Harrison, J Scott

    2003-10-01

    While molecular and quantitative trait variation may be theoretically correlated, empirical studies using both approaches frequently reveal discordant patterns, and these discrepancies can contribute to our understanding of evolutionary processes. Here, we assessed genetic variation in six populations of the copepod Tigriopus californicus. Molecular variation was estimated using five polymorphic microsatellite loci, and quantitative variation was measured using 22-life history and morphometric characters. Within populations, no correlation was found between the levels of molecular variation (heterozygosity) and quantitative variation (heritability). Between populations, quantitative subdivision (Q(ST)) was correlated with molecular subdivision when measured as F(ST) but not when measured as R(ST). Unlike most taxa studied to date, the overall level of molecular subdivision exceeded the level of quantitative subdivision (F(ST) = 0.80, R(ST) = 0.89, Q(ST) = 0.30). Factors that could contribute to this pattern include stabilizing or fluctuating selection on quantitative traits or accelerated rates of molecular evolution.

  15. Molecular variability of Spodoptera frugiperda (Lepidoptera: Noctuidae) populations associated to maize and cotton crops in Brazil.

    Science.gov (United States)

    Martinelli, Samuel; Barata, Reinaldo Montrazi; Zucchi, Maria Imaculada; Silva-Filho, Marcio de Castro; Omoto, Celso

    2006-04-01

    The molecular variability among 10 populations of Spodoptera frugiperda (J.E. Smith), collected from maize, Zea mays L., or cotton Gossypium hirsutum L. crops located at distinctive geographical regions in Brazil, was assessed through random amplification of polymorphic DNA (RAPD)-polymerase chain reaction (PCR). In total, 208 RAPD markers were evaluated, and 98% of them were polymorphic. The mean genetic similarity was 0.6621 and 0.2499 by the Simple Matching and Jaccard matrices, respectively. In general, the unweighted pair-group method with arithmetic average dendrograms separated the populations into clusters related to the geographical origin of the samples. No branch of the dendrograms underpinning a molecular association of S. frugiperda has been identified to either of the two host plants. The molecular variance analysis showed that 18 and 82% of the genetic variation was distributed among and within the groups of populations, respectively. The principal coordinate analysis reinforced the pattern of population clustering found with the unweighted pair-group method with arithmetic average method. These results suggest the occurrence of considerable gene flow between S. frugiperda populations from maize and cotton fields located in the same region in Brazil. Therefore, for an effective management of this pest, there is an urgent need for a better understanding of the gene flow of S. frugiperda populations associated to different host plants along the distribution range of this pest over time in a specific cropping system.

  16. Seeing in the dark: molecular approaches to the study of bat populations.

    Science.gov (United States)

    Burland, T M; Wilmer, J W

    2001-08-01

    Whilst the use of molecular genetic techniques is widespread in the fields of population and evolutionary biology, their application within the mammalian order Chiroptera neither reflects the species richness nor the ecological and behavioural diversity of the order. This is despite the fact that the Chiroptera are problematic to study using more direct observational techniques. Here, we standardize and synthesise the current data, assess the contribution of molecular research to the study of bat species and highlight the importance of its continued and expanded use. At an inter-population level, molecular studies have demonstrated a great diversity of population genetic structure within the order. Among populations of migratory species, genetic structure appears universally low, and hence seasonal movement is likely to be the prevailing influence. However, for sedentary species an array of factors including dispersal ability, extrinsic barriers to gene flow and historical events may determine the extent of genetic partitioning among populations. Intrinsic factors such as wing morphology or roost requirements may also influence population genetic structure in sedentary bat species, a proposal which requires further research. Molecular studies have also made important contributions towards an understanding of social organisation in bats. Evidence indicates that in many polygynous species male mating success does not translate directly into reproductive success, perhaps as a result of multiple mating by females. Estimates of relatedness within and genetic structure among colonies are, in general, very low; a finding which has important implications regarding theories concerning the formation and persistence of bat social groups. Molecular studies have provided new and important insights into the ecology of bats, and have opened up exciting and previously unexplored avenues of research. The data from these studies suggest not only a predictive framework for future

  17. A morphological and molecular characterization of vine mealybug populations (Hemiptera, Pseudococcidae from Tunisia

    Directory of Open Access Journals (Sweden)

    Ramzi Mansour

    2012-05-01

    Full Text Available Some vine mealybug, Planococcus ficus (Signoret populations in Tunisian vineyards have been morphologically and genetically characterized. The morphological examination was based on the main distinctive characteristics of species of Planococcus, namely the number and distribution of the multilocular disc pores and tubular ducts on the adult female. This showed the existence of two different vine mealybug populations in Tunisia. Likewise, in the molecular analyses, two separate clades were revealed in the neighbour-joining phylogenetic tree, supporting the morphological studies and suggesting that there are two distinct populations of P. ficus on grapevine in Tunisia.

  18. Molecular and cultural assessment of chytrid and Spizellomyces populations in grassland soils.

    Science.gov (United States)

    Lozupone, C A; Klein, D A

    2002-01-01

    We developed a molecular method for the detection and quantification of members of the genus Spizellomyces in the environment and used this technique, together with traditional cultural techniques, to measure the effects of cultivation and nitrogen availability on Spizellomyces populations in grassland soils. Primer sets specific for Spizellomyces acuminatus and S. kniepii were developed by sequencing internal transcribed spacer 2 (ITS2) of the gene encoding ribosomal RNA for 9 isolates within the genus Spizellomyces, 5 representatives of different genera within the order Spizellomycetales and one member of the order Chytridiales. These primers were used with fungal-specific primers in a nested PCR approach to generate a specific molecular signal for S. acuminatus and S. kneipii in a soil from which S. acuminatus had previously been recovered. Using MPN-PCR (a quantitative molecular technique) and traditional cultural techniques, we found that chytridiomycetous fungi, including members of the genus Spizellomyces, are abundant in the grassland ecosystems studied. No significant differences in occurrence were observed between native and disturbed control soils but it appeared in 2 separate MPN assays and one MPN-PCR assay that chytrid populations increased in response to disturbance. No significant differences in chytrid or Spizellomyces populations were observed with variations in nitrogen availability. The primer sets and protocols developed in this study worked well to complement traditional cultural data to better assess Spizellomyces populations in the environment. These molecular approaches should provide a foundation for further work with these interesting and oft neglected fungi.

  19. 分子马达定向运动的合作机制%Cooperative Mechanism in Directed Motion of Molecular Motors

    Institute of Scientific and Technical Information of China (English)

    陈宏斌; 郑志刚

    2012-01-01

    Molecular motors are the frontier topic in biology and physics, and the dynamic mechanism of directed transport attracts much attention. In most cases,molecular motors operate in groups. The interaction and cooperation among motors play an important role in the collective behaviors of molecular motors. The behaviors and mechanism of collective transport of molecular motors are sketched out. Furthermore, two cases are detailedly discussed in which the cooperation among motors is needed for the implementation of directed transport. In the first case, the cooperation impels directed motion under overdamping condition. In the second case, through cooperation molecular motors can gain energy from driving in one direction and do work in the vertical direction,and then cause transversal drift.%分子马达是当前生物学和物理学的前沿课题,其定向运动的动力学机制一直是科学家关注的焦点之一.生物体内的分子马达一般是很多个一起协同工作.相互作用与合作在分子马达集体行为中起了很大作用.本文概述了分子马达合作运动的现象和机制.为进一步阐述合作的意义,本文详细讨论了分子马达必须依靠合作才能实现定向输运的两种情况.第一种,分子马达通过合作,在过阻尼条件下克服不停闪烁的棘齿势,实现了定向运动.第二种,分子马达通过合作,可以将一个方向上输入的驱动能量转化到垂直方向上做功,并产生定向输运.

  20. Population genetic structure of rare and endangered plants using molecular markers

    Science.gov (United States)

    Raji, Jennifer; Atkinson, Carter T.

    2013-01-01

    This study was initiated to assess the levels of genetic diversity and differentiation in the remaining populations of Phyllostegia stachyoides and Melicope zahlbruckneri in Hawai`i Volcanoes National Park and determine the extent of gene flow to identify genetically distinct individuals or groups for conservation purposes. Thirty-six Amplified Fragment Length Polymorphic (AFLP) primer combinations generated a total of 3,242 polymorphic deoxyribonucleic acid (DNA) fragments in the P. stachyoides population with a percentage of polymorphic bands (PPB) ranging from 39.3 to 65.7% and 2,780 for the M. zahlbruckneri population with a PPB of 18.8 to 64.6%. Population differentiation (Fst) of AFLP loci between subpopulations of P. stachyoides was low (0.043) across populations. Analysis of molecular variance of P. stachyoides showed that 4% of the observed genetic differentiation occurred between populations in different kīpuka and 96% when individuals were pooled from all kīpuka. Moderate genetic diversity was detected within the M. zahlbruckneri population. Bayesian and multivariate analyses both classified the P. stachyoides and M. zahlbruckneri populations into genetic groups with considerable sub-structuring detected in the P. stachyoides population. The proportion of genetic differentiation among populations explained by geographical distance was estimated by Mantel tests. No spatial correlation was found between genetic and geographic distances in both populations. Finally, a moderate but significant gene flow that could be attributed to insect or bird-mediated dispersal of pollen across the different kīpuka was observed. The results of this study highlight the utility of a multi-allelic DNA-based marker in screening a large number of polymorphic loci in small and closely related endangered populations and revealed the presence of genetically unique groups of individuals in both M. zahlbruckneri and P. stachyoides populations. Based on these findings

  1. Future Directions of Population Education. Report of a Regional Consultative Seminar organized by the Unesco Regional Office for Education in Asia and Oceania in co-operation with the Government of the Philippines (Manila, 14-21, August 1978).

    Science.gov (United States)

    United Nations Educational, Scientific, and Cultural Organization, Bangkok (Thailand). Regional Office for Education in Asia and Oceania.

    The document presents objectives and proceedings of a population education seminar involving representatives from 12 non Western nations. Major purposes of the seminar were to provide a forum where population experts from Asian and Oceanic nations could exchange ideas, cooperate in improving population education programs, and explore how to…

  2. Molecular and pedigree measures of relatedness provide similar estimates of inbreeding depression in a bottlenecked population.

    Science.gov (United States)

    Townsend, S M; Jamieson, I G

    2013-04-01

    Individual-based estimates of the degree of inbreeding or parental relatedness from pedigrees provide a critical starting point for studies of inbreeding depression, but in practice wild pedigrees are difficult to obtain. Because inbreeding increases the proportion of genomewide loci that are identical by descent, inbreeding variation within populations has the potential to generate observable correlations between heterozygosity measured using molecular markers and a variety of fitness related traits. Termed heterozygosity-fitness correlations (HFCs), these correlations have been observed in a wide variety of taxa. The difficulty of obtaining wild pedigree data, however, means that empirical investigations of how pedigree inbreeding influences HFCs are rare. Here, we assess evidence for inbreeding depression in three life-history traits (hatching and fledging success and juvenile survival) in an isolated population of Stewart Island robins using both pedigree- and molecular-derived measures of relatedness. We found results from the two measures were highly correlated and supported evidence for significant but weak inbreeding depression. However, standardized effect sizes for inbreeding depression based on the pedigree-based kin coefficients (k) were greater and had smaller standard errors than those based on molecular genetic measures of relatedness (RI), particularly for hatching and fledging success. Nevertheless, the results presented here support the use of molecular-based measures of relatedness in bottlenecked populations when information regarding inbreeding depression is desired but pedigree data on relatedness are unavailable. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  3. An overview of the utility of population simulation software in molecular ecology.

    Science.gov (United States)

    Hoban, Sean

    2014-05-01

    Stochastic simulation software that simultaneously model genetic, population and environmental processes can inform many topics in molecular ecology. These include forecasting species and community response to environmental change, inferring dispersal ecology, revealing cryptic mating, quantifying past population dynamics, assessing in situ management options and monitoring neutral and adaptive biodiversity change. Advances in population demographic-genetic simulation software, especially with respect to individual life history, landscapes and genetic processes, are transforming and expanding the ways that molecular data can be used. The aim of this review is to explain the roles that such software can play in molecular ecology studies (whether as a principal component or a supporting function) so that researchers can decide whether, when and precisely how simulations can be incorporated into their work. First, I use seven case studies to demonstrate how simulations are employed, their specific advantage/necessity and what alternative or complementary (nonsimulation) approaches are available. I also explain how simulations can be integrated with existing spatial, environmental, historical and genetic data sets. I next describe simulation features that may be of interest to molecular ecologists, such as spatial and behavioural considerations and species' interactions, to provide guidance on how particular simulation capabilities can serve particular needs. Lastly, I discuss the prospect of simulation software in emerging challenges (climate change, biodiversity monitoring, population exploitation) and opportunities (genomics, ancient DNA), in order to emphasize that the scope of simulation-based work is expanding. I also suggest practical considerations, priorities and elements of best practice. This should accelerate the uptake of simulation approaches and firmly embed them as a versatile tool in the molecular ecologist's toolbox. © 2014 John Wiley & Sons Ltd.

  4. Comprehensive genetic discrimination of Leonurus cardiaca populations by AFLP, ISSR, RAPD and IRAP molecular markers.

    Science.gov (United States)

    Khadivi-Khub, Abdollah; Soorni, Aboozar

    2014-06-01

    Leonurus cardiaca is well known for its medicinal importance. In this investigation, genotypic characterization of this species from six eco-geographical regions of Iran was evaluated by four molecular techniques (AFLP, RAPD, ISSR and IRAP). A total of 899 polymorphic fragments were detected by used molecular markers (AFLP = 356, RAPD = 325, ISSR = 113 and IRAP = 105) with an overall average polymorphism of 81.24%. Genetic variation calculated using Shannon's Information index (I) and Nei's gene diversity index (H) showed high genetic diversity in studied germplasm. Also, analysis of molecular variance showed high genetic variation among (55%) and within populations (45%). UPGMA dendrogram constructed from combined data of molecular markers distinguished studied populations in accordance with the results obtained by each marker which all individuals were clearly differentiated into two major clusters. The correlation coefficients were statistically significant for all marker systems with the highest correlation between similarity matrixes of RAPD and ISSR markers (r = 0.82). The present results have an important implication for L. cardiaca germplasm characterization, improvement, and conservation. Furthermore, the characterized individuals exhibited a great deal of molecular variation and they seem to have a rich gene pool for breeding programs.

  5. Diabatic Population Matrix Formalism for Performing Molecular Mechanics Style Simulations with Multiple Electronic States.

    Science.gov (United States)

    Park, Jae Woo; Rhee, Young Min

    2014-12-09

    An accurate description of nonbonded interactions is important in investigating dynamics of molecular systems. In many situations, fixed point charge models are successfully applied to explaining various chemical phenomena. However, these models with conventional formulations will not be appropriate in elucidating the detailed dynamics during nonadiabatic events. This is mainly because the chemical properties of any molecule, especially its electronic populations, significantly change with respect to molecular distortions in the vicinity of the surface crossing. To overcome this issue in molecular simulations yet within the framework of the fixed point charge model, we define a diabatic electronic population matrix and substitute it for the conventional adiabatic partial charges. We show that this matrix can be readily utilized toward attaining more reliable descriptions of Coulombic interactions, in combination with the interpolation formalism for obtaining the intramolecular interaction potential. We demonstrate how the mixed formalism with the diabatic charges and the interpolation can be applied to molecular simulations by conducting adiabatic and nonadiabatic molecular dynamics trajectory calculations of the green fluorescent protein chromophore anion in aqueous environment.

  6. Influence of molecular noise on the growth of single cells and bacterial populations.

    Directory of Open Access Journals (Sweden)

    Mischa Schmidt

    Full Text Available During the last decades experimental studies have revealed that single cells of a growing bacterial population are significantly exposed to molecular noise. Important sources for noise are low levels of metabolites and enzymes that cause significant statistical variations in the outcome of biochemical reactions. In this way molecular noise affects biological processes such as nutrient uptake, chemotactic tumbling behavior, or gene expression of genetically identical cells. These processes give rise to significant cell-to-cell variations of many directly observable quantities such as protein levels, cell sizes or individual doubling times. In this study we theoretically explore if there are evolutionary benefits of noise for a growing population of bacteria. We analyze different situations where noise is either suppressed or where it affects single cell behavior. We consider two specific examples that have been experimentally observed in wild-type Escherichia coli cells: (i the precision of division site placement (at which molecular noise is highly suppressed and (ii the occurrence of noise-induced phenotypic variations in fluctuating environments. Surprisingly, our analysis reveals that in these specific situations both regulatory schemes [i.e. suppression of noise in example (i and allowance of noise in example (ii] do not lead to an increased growth rate of the population. Assuming that the observed regulatory schemes are indeed caused by the presence of noise our findings indicate that the evolutionary benefits of noise are more subtle than a simple growth advantage for a bacterial population in nutrient rich conditions.

  7. Molecular evidence of the taxonomic status of western Mexican populations of Pliaethornis longirostris (Aves: Trochilidae).

    Science.gov (United States)

    Arbeláez-Cortés, Enrique; Navarro-Sigüenza, Adolfo G

    2013-01-01

    Species diversity is largely underestimated by current taxonomy, precluding a precise understanding of evolutionary processes. Genetic data have increased our understanding of that cryptic diversity, and multilocus studies are now desirable. In this study, we used mitochondrial and nuclear DNA sequences to evaluate the taxonomic status of the western Mexico's populations of Phaethornis longirostris. We found differences of 4.2 % in mtDNA and different alleles for one nDNA locus between western and eastern Mexican populations. Molecular and morphological evidence support the separation of these populations (P. 1. mexicanus and P. 1. griseoventer) as the species Phaethornis mexicanus Hartert 1897. Phaethornis mexicanus is endemic to western Mexico and sister to the remaining populations of P. longirostris. The speciation of P mexicanus probably occurred around 880,000 years ago by a vicariant event involving climatic-vegetational changes.

  8. The Properties of Bound and Unbound Molecular Cloud Populations Formed in Galactic Disc Simulations

    CERN Document Server

    Ward, Rachel L; Wadsley, James; Sills, Alison; Couchman, H M P

    2015-01-01

    We explore the effect of galactic environment on properties of molecular clouds. Using clouds formed in a large-scale galactic disc simulation, we measure the observable properties from synthetic column density maps. We confirm that a significant fraction of unbound clouds forms naturally in a galactic disc environment and that a mixed population of bound and unbound clouds can match observed scaling relations and distributions for extragalactic molecular clouds. By dividing the clouds into inner and outer disc populations, we compare their distributions of properties and test whether there are statistically significant differences between them. We find that clouds in the outer disc have lower masses, sizes, and velocity dispersions as compared to those in the inner disc for reasonable choices of the inner/outer boundary. We attribute the differences to the strong impact of galactic shear on the disc stability at large galactocentric radii. In particular, our Toomre analysis of the disc shows a narrowing enve...

  9. MORPHO-MOLECULAR STUDIES IN THE NATURAL POPULATIONS OF DIOSCOREA BULBIFERA LINN. IN NIGERIA

    Directory of Open Access Journals (Sweden)

    Adeniyi Jayeola

    2013-08-01

    Full Text Available Dioscorea bulbifera Linn. is a unique wild yam able to thrive in a wide range of ecological zones. Mopho-molecular studies were carried out with a view to relating the observed morphological variation to its genetics. For morphometric study,30 representative herbarium vouchers  were studied while recently expanded leaf tissue samples of 34 accessions of five natural populations were submitted for genomic DNA using sixteen SSR markers. Bulbil size and shape, petiole length, leaf colour and shape varied among populations. A low level of genetic variability characterized the two geographically closest of the five populations (with P=15.15 and 6.06%,; H=0.0646 and 0.0251 while the other populations showed higher values (P varied from 66.6 and 84.85%; H varied from 0.1992 and 0.1992. That the highest value of genetic distance (0.1964 occurred between Iwo and Polytechnic populations was unexpected. The highest value (0.9869 of genetic identity occurred between the Polytechnic and Pebble Road populations as expected. Clustering typically occurred at lower distance scale reflecting the proximity of their genetic distances and therefore low divergence. Conclusively, the use of microsatellite markers allowed the identification of genetic variability among the natural populations of D. bulbifera.

  10. Molecular basis of Rh blood group system in the Malaysian population.

    Science.gov (United States)

    Musa, Rozi Hanisa; Muhamad, Nor Asiah; Hassan, Afifah; Ayob, Yasmin; Yusoff, Narazah Mohd

    2015-01-01

    Rh molecular studies have been previously mainly conducted in Caucasians and African population. There is a limited data on the molecular basis for Rh genotypes among Asians. This study aims to characterize the Rh genes and frequency of the various RH genotypes among blood donors in National Blood Centre (NBC), Kuala Lumpur. A total of 1014 blood samples were obtained from blood donors from four different ethnic groups (360 Malays, 434 Chinese, 164 Indians and 56 others). Serological and molecular analysis of all 1014 blood samples were performed. An automated deoxyribonucleic acid sequencing analysis was performed. Rh phenotypes and RH genotypes showed heterogeneity and significant association with ethnicities. Discrepancies in allele D, C/c and E/e between phenotypes and genotypes results were observed. Discrepancy results in allele D showed significant association with the ethnic groups of the blood donors in NBC. There were multiple novel mutations (23) and published mutations (5) found in this study. Significant associations between discrepancy results and mutations were found in allele D and C/c. Performing RH molecular analysis in Malaysian population provided the basic database for the distribution of Rh genotypes of donors from major ethnic groups in Malaysia.

  11. A Comparison of Three Molecular Markers for the Identification of Populations of Globodera pallida.

    Science.gov (United States)

    Hoolahan, Angelique H; Blok, Vivian C; Gibson, Tracey; Dowton, Mark

    2012-03-01

    Potato cyst nematodes cost the potato industry substantial financial losses annually. Through the use of molecular markers, the distribution and infestation routes of these nematodes can be better elucidated, permitting the development of more effective preventative methods. Here we assess the ability of three molecular markers to resolve multiple representatives of five Globodera pallida populations as monophyletic groups. Molecular markers included a region of the rbp-1 gene (an effector), a non-coding nuclear DNA region (the ITS region), and a novel marker for G. pallida, a ∼3.4 kb non-coding mitochondrial DNA (mtDNA) region. Multiple phylogenetic analysis methods were performed on the three DNA regions separately, and on a data set of these three regions combined. The analyses of the combined data set were similar to that of the sole mtDNA marker; resolving more populations as monophyletic groups, relative to that of the ITS region and rbp-1 gene region. This suggests that individual markers may be inadequate for distinguishing populations of G. pallida. The use of this new non-coding mtDNA marker may provide further insights into the historical distribution of G. pallida, as well as enable the development of more sensitive diagnostic methods.

  12. Molecular insights of genetic variation in Erianthus arundinaceus populations native to China.

    Directory of Open Access Journals (Sweden)

    Jianbo Zhang

    Full Text Available BACKGROUND: E. arundinaceus (Retz. Jeswiet is a warm-season, tall-growing perennial species native to much southern portion in China. The grass has been extensively used in sugarcane breeding and is recently targeted as a bioenergy feedstock crop. However, information on the genetic structure of the Chinese wild germplasm is limited. Knowledge of genetic variation within and among populations is essential for breeding new cultivars in the species. The major objective of this study was to quantify the magnitude of genetic variation among and within natural populations in China. METHODOLOGY/PRINCIPAL FINDINGS: In this experiment, we analyzed genetic variation of 164 individuals of 18 populations collected from natural habitats in six Chinese provinces using 20 sequence-related amplified polymorphism (SRAP primer pairs generating 277 polymorphic bands. Among and within the populations, the percentage of polymorphic bands (PPB was 80.00% and 27.07%, genetic diversity (HE was 0.245 and 0.099, effective number of alleles (NE was 1.350 and 1.170, and Shannon's information index (I was 0.340 and 0.147, respectively. The populations were clustered into six groups exhibiting a high level of genetic differentiation, which was highly associated with geographic origins of respective germplasm populations, but was not significantly associated with geographic distances between the populations. CONCLUSIONS/SIGNIFICANCE: This is the first report indicating that large genetic variation exists in the Chinese E. arundinaceus germplasm based on the SRAP molecular marker analysis of native populations. The genetic structure of populations in the species has been substantially affected by geographic landforms and environments. The diverse collection will be highly valuable in genetic improvement in the species per se and likely in sugarcane.

  13. A diverse population of Cryptococcus gattii molecular type VGIII in southern Californian HIV/AIDS patients.

    Directory of Open Access Journals (Sweden)

    Edmond J Byrnes

    2011-09-01

    Full Text Available Cryptococcus gattii infections in southern California have been reported in patients with HIV/AIDS. In this study, we examined the molecular epidemiology, population structure, and virulence attributes of isolates collected from HIV/AIDS patients in Los Angeles County, California. We show that these isolates consist almost exclusively of VGIII molecular type, in contrast to the VGII molecular type isolates causing the North American Pacific Northwest outbreak. The global VGIII population structure can be divided into two molecular groups, VGIIIa and VGIIIb. Isolates from the Californian patients are virulent in murine and macrophage models of infection, with VGIIIa significantly more virulent than VGIIIb. Several VGIII isolates are highly fertile and produce abundant sexual spores that may serve as infectious propagules. The a and α VGIII MAT locus alleles are largely syntenic with limited rearrangements compared to the known VGI (a/α and VGII (α MAT loci, but each has unique characteristics including a distinct deletion flanking the 5' VGIII MATa alleles and the α allele is more heterogeneous than the a allele. Our studies indicate that C. gattii VGIII is endemic in southern California, with other isolates originating from the neighboring regions of Mexico, and in rarer cases from Oregon and Washington state. Given that >1,000,000 cases of cryptococcal infection and >620,000 attributable mortalities occur annually in the context of the global AIDS pandemic, our findings suggest a significant burden of C. gattii may be unrecognized, with potential prognostic and therapeutic implications. These results signify the need to classify pathogenic Cryptococcus cases and highlight possible host differences among the C. gattii molecular types influencing infection of immunocompetent (VGI/VGII vs. immunocompromised (VGIII/VGIV hosts.

  14. Implications of storing urinary DNA from different populations for molecular analyses.

    Directory of Open Access Journals (Sweden)

    Angela Cannas

    Full Text Available BACKGROUND: Molecular diagnosis using urine is established for many sexually transmitted diseases and is increasingly used to diagnose tumours and other infectious diseases. Storage of urine prior to analysis, whether due to home collection or bio-banking, is increasingly advocated yet no best practice has emerged. Here, we examined the stability of DNA in stored urine in two populations over 28 days. METHODOLOGY: Urine from 40 (20 male healthy volunteers from two populations, Italy and Zambia, was stored at four different temperatures (RT, 4 degrees C, -20 degrees C & -80 degrees C with and without EDTA preservative solution. Urines were extracted at days 0, 1, 3, 7 and 28 after storage. Human DNA content was measured using multi-copy (ALU J and single copy (TLR2 targets by quantitative real-time PCR. Zambian and Italian samples contained comparable DNA quantity at time zero. Generally, two trends were observed during storage; no degradation, or rapid degradation from days 0 to 7 followed by little further degradation to 28 days. The biphasic degradation was always observed in Zambia regardless of storage conditions, but only twice in Italy. CONCLUSION: Site-specific differences in urine composition significantly affect the stability of DNA during storage. Assessing the quality of stored urine for molecular analysis, by using the type of strategy described here, is paramount before these samples are used for molecular prognostic monitoring, genetic analyses and disease diagnosis.

  15. Interdisciplinary education to integrate pathology and epidemiology: towards molecular and population-level health science.

    Science.gov (United States)

    Ogino, Shuji; King, Emily E; Beck, Andrew H; Sherman, Mark E; Milner, Danny A; Giovannucci, Edward

    2012-10-15

    In recent decades, epidemiology, public health, and medical sciences have been increasingly compartmentalized into narrower disciplines. The authors recognize the value of integration of divergent scientific fields in order to create new methods, concepts, paradigms, and knowledge. Herein they describe the recent emergence of molecular pathological epidemiology (MPE), which represents an integration of population and molecular biologic science to gain insights into the etiologies, pathogenesis, evolution, and outcomes of complex multifactorial diseases. Most human diseases, including common cancers (such as breast, lung, prostate, and colorectal cancers, leukemia, and lymphoma) and other chronic diseases (such as diabetes mellitus, cardiovascular diseases, hypertension, autoimmune diseases, psychiatric diseases, and some infectious diseases), are caused by alterations in the genome, epigenome, transcriptome, proteome, metabolome, microbiome, and interactome of all of the above components. In this era of personalized medicine and personalized prevention, we need integrated science (such as MPE) which can decipher diseases at the molecular, genetic, cellular, and population levels simultaneously. The authors believe that convergence and integration of multiple disciplines should be commonplace in research and education. We need to be open-minded and flexible in designing integrated education curricula and training programs for future students, clinicians, practitioners, and investigators.

  16. Application of Molecular Cytogenetic Technique for Rapid Prenatal Diagnosis of Aneuploidies in Iranian Population

    Directory of Open Access Journals (Sweden)

    Habib Nasiri

    2009-06-01

    Full Text Available Objective: Classic cell culture and karyotyping is routinely used for prenatal detection of different chromosomal abnormalities. Molecular cytogenetic techniques have also recently been developed and used for this purpose. Quantitative florescence PCR using short tandem repeat (STR markers has more potential for high throughput diagnosis. Marker heterozygosity in short tandem repeats (STR is of critical importance in the clinical applicablity of this method. Materials and Methods: Different STR markers on chromosomes 13, 18, 21, X and Y  were analysed from  amniotic samples to detect related disorders such as Down, Edward, Patau,  Klinefelter sundromes , as well as sex chromosomes numerical abnormalities . Results: In our population some markers (D18S976, DXS6854, D21S11, and D21S1411 showed alleles with sizes out of expected ranges. But others occupied narrower range of predicted distribution. Most markers have enough heterozygosity (66.3-94.7 to be used for prenatal diagnosis. Furthermore, results obtained from full karyotype for all samples were in concordance with results of molecular cytogenetic testing. Conclusion: It is concluded that, in urgent situations, if proper markers used, molecular cytogenetic testing (QF-PCR could be a useful method for rapid prenatal diagnosis (PND in populations with high rate of consanguinity such as Iran.  

  17. Molecular Analysis of Dominant Microbial Populations in Heavily and Slightly Polluted Aquifers by a Seaside Landfill

    Institute of Scientific and Technical Information of China (English)

    TIAN Yangjie; YANG Hong; LI Daotang; WU Xiujuan

    2005-01-01

    The microbial populations were investigated in two groundwater samples, GW-H and GW-S, which represented heavily and slightly polluted aquifers by a seaside landfill. The concentrations of dissolved redox-relevant species suggested that iron-reduction/sulfate-reduction and denitrification were major redox processes for GW-H and GW-S. The dominant microbial populations were determined using restriction fragment length polymorphism analyses of 16S rRNA gene clone libraries. These microbes were then further studied by sequencing and phylogenetic analyses. The results indicate an obvious variation of the dominant populations between the two samples. The coexistence of sequences related to denitrifiers, sulfur-reducers, and methanotrophic bacteria was found in the GW-S sample, and a sequence associated with a sulfate-reducer was also found in the GW-H sample using molecular analyses. These results suggest that the molecular approach may be an important supplement to other approaches in characterizing the redox processes in polluted aquifers.

  18. Intersex in fishes and amphibians: population implications, prevalence, mechanisms and molecular biomarkers.

    Science.gov (United States)

    Abdel-Moneim, Ahmed; Coulter, David P; Mahapatra, Cecon T; Sepúlveda, Maria S

    2015-11-01

    Intersex is defined as the abnormal presence of both testicular and ovarian cells in gonads of gonochoristic animals. Its occurrence is widespread and reports on its presence in the gonads of vertebrates continues to increase. In this review, we use standardized terminology to summarize the current knowledge of intersex in gonochoristic fishes and amphibians. We describe the different indices that have been used to assess the severity of intersex and synthesize reports discussing the prevalence of intersex in relation to different types of pollutants. In addition, we evaluate the geographic distribution and chronology of the reported cases of intersex in fishes and amphibians, their pathological descriptions and severity and discuss species sensitivities. We also summarize molecular biomarkers that have been tested for early detection of intersex in wild populations and highlight additional biomarkers that target molecular pathways involved in gonadal development that require further investigation for use in the diagnosis of intersex. Finally, we discuss the needs for future research in this field.

  19. Principal Component Analysis and Molecular Characterization of Reniform Nematode Populations in Alabama

    Directory of Open Access Journals (Sweden)

    Seloame T. Nyaku

    2016-04-01

    Full Text Available U.S. cotton production is suffering from the yield loss caused by the reniform nematode (RN, Rotylenchulus reniformis. Management of this devastating pest is of utmost importance because, no upland cotton cultivar exhibits adequate resistance to RN. Nine populations of RN from distinct regions in Alabama and one population from Mississippi were studied and thirteen morphometric features were measured on 20 male and 20 female nematodes from each population. Highly correlated variables (positive in female and male RN morphometric parameters were observed for body length (L and distance of vulva from the lip region (V (r = 0.7 and tail length (TL and c′ (r = 0.8, respectively. The first and second principal components for the female and male populations showed distinct clustering into three groups. These results show pattern of sub-groups within the RN populations in Alabama. A one-way ANOVA on female and male RN populations showed significant differences (p ≤ 0.05 among the variables. Multiple sequence alignment (MSA of 18S rRNA sequences (421 showed lengths of 653 bp. Sites within the aligned sequences were conserved (53%, parsimony-informative (17%, singletons (28%, and indels (2%, respectively. Neighbor-Joining analysis showed intra and inter-nematodal variations within the populations as clone sequences from different nematodes irrespective of the sex of nematode isolate clustered together. Morphologically, the three groups (I, II and III could not be distinctly associated with the molecular data from the 18S rRNA sequences. The three groups may be identified as being non-geographically contiguous.

  20. Low-molecular-weight gelators: elucidating the principles of gelation based on gelator solubility and a cooperative self-assembly model.

    Science.gov (United States)

    Hirst, Andrew R; Coates, Ian A; Boucheteau, Thomas R; Miravet, Juan F; Escuder, Beatriu; Castelletto, Valeria; Hamley, Ian W; Smith, David K

    2008-07-16

    This paper highlights the key role played by solubility in influencing gelation and demonstrates that many facets of the gelation process depend on this vital parameter. In particular, we relate thermal stability ( T gel) and minimum gelation concentration (MGC) values of small-molecule gelation in terms of the solubility and cooperative self-assembly of gelator building blocks. By employing a van't Hoff analysis of solubility data, determined from simple NMR measurements, we are able to generate T calc values that reflect the calculated temperature for complete solubilization of the networked gelator. The concentration dependence of T calc allows the previously difficult to rationalize "plateau-region" thermal stability values to be elucidated in terms of gelator molecular design. This is demonstrated for a family of four gelators with lysine units attached to each end of an aliphatic diamine, with different peripheral groups (Z or Boc) in different locations on the periphery of the molecule. By tuning the peripheral protecting groups of the gelators, the solubility of the system is modified, which in turn controls the saturation point of the system and hence controls the concentration at which network formation takes place. We report that the critical concentration ( C crit) of gelator incorporated into the solid-phase sample-spanning network within the gel is invariant of gelator structural design. However, because some systems have higher solubilities, they are less effective gelators and require the application of higher total concentrations to achieve gelation, hence shedding light on the role of the MGC parameter in gelation. Furthermore, gelator structural design also modulates the level of cooperative self-assembly through solubility effects, as determined by applying a cooperative binding model to NMR data. Finally, the effect of gelator chemical design on the spatial organization of the networked gelator was probed by small-angle neutron and X

  1. Cooperative assembly of Co-Smad4 MH1 with R-Smad1/3 MH1 on DNA: a molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Guihong Wang

    Full Text Available BACKGROUND: Smads, the homologs of Sma and MAD proteins, play a key role in gene expression regulation in the transforming growth factor-β (TGF-β signaling pathway. Recent experimental studies have revealed that Smad4/R-Smad heterodimers bound on DNA are energetically more favorable than homodimeric R-Smad/R-Smad complexes bound on DNA, which indicates that Smad4 might act as binding vehicle to cooperatively assemble with activated R-Smads on DNA in the nucleus. However, the details of interaction mechanism for cooperative recruitment of Smad4 protein to R-Smad proteins on DNA, and allosteric communication between the Smad4-DNA and R-Smad-DNA interfaces via DNA mediating are not yet clear so far. METHODOLOGY: In the present work, we have constructed a series of Smadn+DNA+Smadn (n = 1, 3, 4 models and carried out molecular dynamics simulations, free energy calculations and DNA dynamics analysis for them to study the interaction properties of Smadn (n = 1, 3, 4 with DNA molecule. RESULTS: The results revealed that the binding of Smad4 protein to DNA molecule facilitates energetically the formation of the heteromeric Smad4+DNA+Smad1/3 complex by increasing the affinity of Smad1/3 with DNA molecule. Further investigations through the residue/base motion correlation and DNA dynamics analyses predicted that the binding of Smad4 protein to DNA molecule in the heteromeric Smad4+DNA+Smad1/3 model induces an allosteric communication from the Smad4-DNA interface to Smad1/Smad3-DNA interface via DNA base-pair helical motions, surface conformation changes and new hydrogen bond formations. The present work theoretically explains the mechanism of cooperative recruitment of Smad4 protein to Smad1/3 protein via DNA-mediated indirect readout mode in the nucleus.

  2. Prediction consistency and clinical presentations of breast cancer molecular subtypes for Han Chinese population

    Directory of Open Access Journals (Sweden)

    Huang Chi-Cheng

    2012-09-01

    Full Text Available Abstract Background Breast cancer is a heterogeneous disease in terms of transcriptional aberrations; moreover, microarray gene expression profiles had defined 5 molecular subtypes based on certain intrinsic genes. This study aimed to evaluate the prediction consistency of breast cancer molecular subtypes from 3 distinct intrinsic gene sets (Sørlie 500, Hu 306 and PAM50 as well as clinical presentations of each molecualr subtype in Han Chinese population. Methods In all, 169 breast cancer samples (44 from Taiwan and 125 from China of Han Chinese population were gathered, and the gene expression features corresponding to 3 distinct intrinsic gene sets (Sørlie 500, Hu 306 and PAM50 were retrieved for molecular subtype prediction. Results For Sørlie 500 and Hu 306 intrinsic gene set, mean-centring of genes and distance-weighted discrimination (DWD remarkably reduced the number of unclassified cases. Regarding pairwise agreement, the highest predictive consistency was found between Hu 306 and PAM50. In all, 150 and 126 samples were assigned into identical subtypes by both Hu 306 and PAM50 genes, under mean-centring and DWD. Luminal B tended to show a higher nuclear grade and have more HER2 over-expression status than luminal A did. No basal-like breast tumours were ER positive, and most HER2-enriched breast tumours showed HER2 over-expression, whereas, only two-thirds of ER negativity/HER2 over-expression tumros were predicted as HER2-enriched molecular subtype. For 44 Taiwanese breast cancers with survival data, a better prognosis of luminal A than luminal B subtype in ER-postive breast cancers and a better prognosis of basal-like than HER2-enriched subtype in ER-negative breast cancers was observed. Conclusions We suggest that the intrinsic signature Hu 306 or PAM50 be used for breast cancers in the Han Chinese population during molecular subtyping. For the prognostic value and decision making based on intrinsic subtypes, further prospective

  3. The molecular basis of the cooperation between EGF, FGF and eCB receptors in the regulation of neural stem cell function.

    Science.gov (United States)

    Sütterlin, Philipp; Williams, Emma J; Chambers, David; Saraf, Kathryn; von Schack, David; Reisenberg, Melina; Doherty, Patrick; Williams, Gareth

    2013-01-01

    Adult neurogenesis relies on EGF and FGF receptor (EGFR/FGFR) function and endocannabinoid (eCB) signalling. Here we have used a neural stem cell (NSC) line to determine how these systems cooperate to regulate neurogenesis. The results show the EGFR to be solely responsible for maintaining PI3K activation explaining its dominant role in promoting NSC survival. The EGFR and FGFR synergistically regulate the ERK/MAPK pathway, and this explains the requirement for both for optimal cell proliferation. The eCB receptors did not contribute to activation of the PI3K or ERK/MAPK pathways, highlighting the importance of another major proliferation pathway. The EGFR plays the dominant role in maintaining the transcriptome, with significant changes in the expression of over 3500 transcripts seen within hours of inhibition or activation of this receptor. The FGFR has a more modest effect on transcription with evidence for nodal integration with EGFR signalling at the level of the ERK/MAPK pathway. A common set of transcripts are regulated by the CB1 and CB2 receptors, with cooperation between these receptors and the EGFR apparent in the regulation of a pool of transcripts, most likely representing signal integration downstream from an as yet to be identified node. Finally, a first level molecular analysis of the transcriptional response shows regulation of a number of key growth factors, growth factor receptors and GPCRs to be under the control of the EGFR. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Population reversal driven by unrestrained interactions in molecular dynamics simulations: A dialanine model

    Directory of Open Access Journals (Sweden)

    Filippo Pullara

    2015-10-01

    Full Text Available Standard Molecular Dynamics simulations (MD are usually performed under periodic boundary conditions using the well-established “Ewald summation”. This implies that the distance among each element in a given lattice cell and its corresponding element in another cell, as well as their relative orientations, are constant. Consequently, protein-protein interactions between proteins in different cells—important in many biological activities, such as protein cooperativity and physiological/pathological aggregation—are severely restricted, and features driven by protein-protein interactions are lost. The consequences of these restrictions, although conceptually understood and mentioned in the literature, have not been quantitatively studied before. The effect of protein-protein interactions on the free energy landscape of a model system, dialanine, is presented. This simple system features a free energy diagram with well-separated minima. It is found that, in the case of absence of peptide-peptide (p-p interactions, the ψ = 150° dihedral angle determines the most energetically favored conformation (global free-energy minimum. When strong p-p interactions are induced, the global minimum switches to the ψ = 0° conformation. This shows that the free-energy landscape of an individual molecule is dramatically affected by the presence of other freely interacting molecules of its same type. Results of the study suggest how taking into account p-p interactions in MD allows having a more realistic picture of system activity and functional conformations.

  5. A new molecular diagnostic tool for surveying and monitoring Triops cancriformis populations

    Directory of Open Access Journals (Sweden)

    Graham S. Sellers

    2017-05-01

    Full Text Available The tadpole shrimp, Triops cancriformis, is a freshwater crustacean listed as endangered in the UK and Europe living in ephemeral pools. Populations are threatened by habitat destruction due to land development for agriculture and increased urbanisation. Despite this, there is a lack of efficient methods for discovering and monitoring populations. Established macroinvertebrate monitoring methods, such as net sampling, are unsuitable given the organism’s life history, that include long lived diapausing eggs, benthic habits and ephemerally active populations. Conventional hatching methods, such as sediment incubation, are both time consuming and potentially confounded by bet-hedging hatching strategies of diapausing eggs. Here we develop a new molecular diagnostic method to detect viable egg banks of T. cancriformis, and compare its performance to two conventional monitoring methods involving diapausing egg hatching. We apply this method to a collection of pond sediments from the Wildfowl & Wetlands Trust Caerlaverock National Nature Reserve, which holds one of the two remaining British populations of T. cancriformis. DNA barcoding of isolated eggs, using newly designed species-specific primers for a large region of mtDNA, was used to estimate egg viability. These estimates were compared to those obtained by the conventional methods of sediment and isolation hatching. Our method outperformed the conventional methods, revealing six ponds holding viable T. cancriformis diapausing egg banks in Caerlaverock. Additionally, designed species-specific primers for a short region of mtDNA identified degraded, inviable eggs and were used to ascertain the levels of recent mortality within an egg bank. Together with efficient sugar flotation techniques to extract eggs from sediment samples, our molecular method proved to be a faster and more powerful alternative for assessing the viability and condition of T. cancriformis diapausing egg banks.

  6. Population structure and genotypic variation of Crataegus pontica inferred by molecular markers.

    Science.gov (United States)

    Rahmani, Mohammad-Shafie; Shabanian, Naghi; Khadivi-Khub, Abdollah; Woeste, Keith E; Badakhshan, Hedieh; Alikhani, Leila

    2015-11-01

    Information about the natural patterns of genetic variability and their evolutionary bases are of fundamental practical importance for sustainable forest management and conservation. In the present study, the genetic diversity of 164 individuals from fourteen natural populations of Crataegus pontica K.Koch was assessed for the first time using three genome-based molecular techniques; inter-retrotransposon amplified polymorphism (IRAP); inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) polymorphism. IRAP, ISSR and SCoT analyses yielded 126, 254 and 199 scorable amplified bands, respectively, of which 90.48, 93.37 and 83.78% were polymorphic. ISSR revealed efficiency over IRAP and SCoT due to high effective multiplex ratio, marker index and resolving power. The dendrograms based on the markers used and combined data divided individuals into three major clusters. The correlation between the coefficient matrices for the IRAP, ISSR and SCoT data was significant. A higher level of genetic variation was observed within populations than among populations based on the markers used. The lower divergence levels depicted among the studied populations could be seen as evidence of gene flow. The promotion of gene exchange will be very beneficial to conserve and utilize the enormous genetic variability. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Comparison of algorithms to infer genetic population structure from unlinked molecular markers.

    Science.gov (United States)

    Peña-Malavera, Andrea; Bruno, Cecilia; Fernandez, Elmer; Balzarini, Monica

    2014-08-01

    Identifying population genetic structure (PGS) is crucial for breeding and conservation. Several clustering algorithms are available to identify the underlying PGS to be used with genetic data of maize genotypes. In this work, six methods to identify PGS from unlinked molecular marker data were compared using simulated and experimental data consisting of multilocus-biallelic genotypes. Datasets were delineated under different biological scenarios characterized by three levels of genetic divergence among populations (low, medium, and high FST) and two numbers of sub-populations (K=3 and K=5). The relative performance of hierarchical and non-hierarchical clustering, as well as model-based clustering (STRUCTURE) and clustering from neural networks (SOM-RP-Q). We use the clustering error rate of genotypes into discrete sub-populations as comparison criterion. In scenarios with great level of divergence among genotype groups all methods performed well. With moderate level of genetic divergence (FST=0.2), the algorithms SOM-RP-Q and STRUCTURE performed better than hierarchical and non-hierarchical clustering. In all simulated scenarios with low genetic divergence and in the experimental SNP maize panel (largely unlinked), SOM-RP-Q achieved the lowest clustering error rate. The SOM algorithm used here is more effective than other evaluated methods for sparse unlinked genetic data.

  8. Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers

    Directory of Open Access Journals (Sweden)

    Ilga Porth

    2014-04-01

    Full Text Available Molecular markers have proven to be invaluable tools for assessing plants’ genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of the genetic variation in an unprecedented way through increased coverage of the genome. Markers have diverse applications in plant sciences, but certain marker types, due to their inherent characteristics, have also shown their limitations. A combination of diverse marker types is usually recommended to provide an accurate assessment of the extent of intra- and inter-population genetic diversity of naturally distributed plant species on which proper conservation directives for species that are at risk of decline can be issued. Here, specifically, natural populations of forest trees are reviewed by summarizing published reports in terms of the status of genetic variation in the pure species. In general, for outbred forest tree species, the genetic diversity within populations is larger than among populations of the same species, indicative of a negligible local spatial structure. Additionally, as is the case for plants in general, the diversity at the phenotypic level is also much larger than at the marker level, as selectively neutral markers are commonly used to capture the extent of genetic variation. However, more and more, nucleotide diversity within candidate genes underlying adaptive traits are studied for signatures of selection at single sites. This adaptive genetic diversity constitutes important potential for future forest management and conservation purposes.

  9. Conflictual cooperation

    DEFF Research Database (Denmark)

    Axel, Erik

    2011-01-01

    , cooperation appeared as the continuous reworking of contradictions in the local arrangement of societal con- ditions. Subjects were distributed and distributed themselves according to social privileges, resources, and dilemmas in cooperation. Here, the subjects’ activities and understandings took form from...

  10. A Deuteration Survey of the Clump Population in the Gemini OB1 Molecular Cloud

    Science.gov (United States)

    Henrici, Andrew Scott; Shirley, Yancy L.; Svoboda, Brian E.

    2017-01-01

    Recent maps of dust continuum emission from entire molecular clouds at submillimeter wavelengths have made it possible to survey and study the chemistry of entire core and clump populations within a single cloud. One very strong chemical process in star-forming regions is the fractionation of deuterium in molecules, which results in an increase in the deuterium ratio many orders of magnitude over the ISM [D]/[H] ratio and provides a chemical probe of cold, dense regions. We present a survey of DCO+ 3-2 and N2D+ 3-2 toward the clump population in the high-mass, star-forming Gemini OB1 Molecular Cloud identified from 1.1 mm continuum imaging by the Bolocam Galactic Plane Survey. The peak 1.1 mm continuum positions of 52 clumps in the range 188°≤ l ≤194° were observed with the 10m Heinrich Hertz Submillimeter Telescope. We find that DCO+ emission is detected toward 90% of the clumps with a median deuterium ratio of 0.01 while N2D+ emission is detected toward only 25% of the clumps. The DCO+ fractionation anti-correlates with gas kinetic temperature and linewidth, a measure of the amount of turbulence within the clumps. We compare the deuteration ratios of with physical properties of the clumps and their evolutionary stage.

  11. Molecular markers for population genetic analyses in the family Psittacidae (Psittaciformes, Aves

    Directory of Open Access Journals (Sweden)

    Patrícia J. Faria

    2006-01-01

    Full Text Available The selection of molecular markers for population studies is an important tool for biodiversity conservation. The family Psittacidae contains many endangered and vulnerable species and we tested three kinds of molecular markers for their potential use in population studies of five psitacid species: 43 hyacinth macaws (Anodorhynchus hyacinthinus, 42 blue-and-yellow macaws (Ara ararauna, 23 red-and-green macaws (Ara chloroptera, 19 red-spectacled amazons (Amazona pretrei; and 18 red-tailed amazons (Amazona brasiliensis. We tested 21 clones from a genomic library of golden conure (Guarouba guarouba minisatellites and 12 pairs of microsatellite primers developed for the domestic chicken (Gallus gallus and A. hyacinthinus. We also tested seven tetranucleotide repeat primers for their ability to amplify regions between microsatellite loci (inter simple sequence repeats, ISSRs. We were able to select seven markers that were variable in different degrees for three species (A. hyacinthinus, A. chloroptera and A. ararauna. The mini and microsatellites produced more polymorphic patterns than the ISSRs. The genetic variability of the species studied seems to be correlated with their endangered status.

  12. Molecular tools for sterile sperm detection to monitor Ceratitis capitata populations under SIT programmes.

    Science.gov (United States)

    Juan-Blasco, María; Sabater-Muñoz, Beatriz; Argilés, Rafael; Jacas, Josep A; Castañera, Pedro; Urbaneja, Alberto

    2013-07-01

    The success of an area-wide sterile insect technique (SIT) programme against Ceratitis capitata (Wiedemann) (Diptera: Tephritidae) relies on the mating success of sterile males in the field. Limited information is available about the effectiveness of sterile males in achieving mates with wild females and how these matings contribute to reducing wild populations. To this end, firstly a mating competition test was performed in the laboratory with different release ratios (1:1:0, 1:1:1, 1:1:5, 1:1:10 and 1:1:20 for wild females:wild males:sterile VIENNA-8 males respectively) and different host fruit. Secondly, the same release ratios were evaluated under semi-natural conditions on caged trees and on sentinel host. By means of molecular markers, VIENNA-8 male sperm was positively detected in those females exposed to the male ratios 1:5, 1:10 and 1:20 in the laboratory. In the field test, sterile VIENNA-8 male matings and the C. capitata progeny on apples were positively correlated with the ratio of sterile males released and with the percentage of sterile matings respectively. These results confirm the validity of using the molecular detection of VIENNA-8 male sperm to predict the C. capitata population under semi-natural conditions. Implications of these results in measuring the efficacy of an SIT programme are discussed. © 2012 Society of Chemical Industry.

  13. Comparative Estimation of Genetic Diversity in Population Studies using Molecular Sampling and Traditional Sampling Methods.

    Science.gov (United States)

    Saeb, Amr Tm; David, Satish Kumar

    2014-01-01

    Entomopathogenic nematodes (EPN) are efficient biological pest control agents. Population genetics studies on EPN are seldom known. Therefore, it is of interest to evaluate the significance of molecular sampling method (MSM) for accuracy, time needed, and cost effectiveness over traditional sampling method (TSM). The study was conducted at the Mohican Hills golf course at the state of Ohio where the EPN H. bacteriophora has been monitored for 18 years. The nematode population occupies an area of approximately 3700 m(2) with density range from 0.25-2 per gram soil. Genetic diversity of EPN was studied by molecular sampling method (MSM) and traditional sampling method (TSM) using the mitochondrial gene pcox1. The MSM picked 88% in compared to TSM with only 30% of sequenced cox 1 gene. All studied genetic polymorphism measures (sequence and haplotype) showed high levels of genetic diversity of MSM over TSM. MSM minimizes the chance of mitochondrial genes amplification from non target organisms (insect or other contaminating microorganisms). Moreover, it allows the sampling of more individuals with a reliable and credible representative sample size. Thus, we show that MSM supersedes TSM in labour intensity, time consumption and requirement of no special experience and efficiency.

  14. The properties of bound and unbound molecular cloud populations formed in galactic disc simulations

    Science.gov (United States)

    Ward, Rachel L.; Benincasa, Samantha M.; Wadsley, James; Sills, Alison; Couchman, H. M. P.

    2016-01-01

    We explore the effect of galactic environment on properties of molecular clouds. Using clouds formed in a large-scale galactic disc simulation, we measure the observable properties from synthetic column density maps. We confirm that a significant fraction of unbound clouds forms naturally in a galactic disc environment and that a mixed population of bound and unbound clouds can match observed scaling relations and distributions for extragalactic molecular clouds. By dividing the clouds into inner and outer disc populations, we compare their distributions of properties and test whether there are statistically significant differences between them. We find that clouds in the outer disc have lower masses, sizes, and velocity dispersions as compared to those in the inner disc for reasonable choices of the inner/outer boundary. We attribute the differences to the strong impact of galactic shear on the disc stability at large galactocentric radii. In particular, our Toomre analysis of the disc shows a narrowing envelope of unstable masses as a function of radius, resulting in the formation of smaller, lower mass fragments in the outer disc. We also show that the star formation rate is affected by the environment of the parent cloud, and is particularly influenced by the underlying surface density profile of the gas throughout the disc. Our work highlights the strengths of using galaxy-scale simulations to understand the formation and evolution of cloud properties - and the star formation within them - in the context of their environment.

  15. Cooperative Learning

    Institute of Scientific and Technical Information of China (English)

    桑莹莹

    2015-01-01

    This paper is about the cooperative learning as a teaching method in a second language learning class. It mainly talks about the background, foundation, features, definitions, components, goals, advantages and disadvantages of cooperative learning. And as the encounter of the disadvantages in cooperative learning, this paper also proposes some strategies.

  16. Molecular basis of weak D and DEL in Han population in Anhui Province, China

    Institute of Scientific and Technical Information of China (English)

    CHEN Qing; LI Ming; LI Min; LU Xue-song; L(U) Rong; SUN Jun; LIU Zhong

    2012-01-01

    Background Rh blood group system is the most complex and immunogenetic blood group system.Prevalent RHD alleles varied in different populations.The purpose of this study is to determine the molecular basis of weak D and DEL phenotype in Anhui Chinese Han population.Methods The D antigen was determined with IgM monoclonal anti-D conformed to the guidelines for donor testing in China.Weak D samples were identified by an indirect antiglobulin test.DEL phenotype was determined by adsorption and elution test.All the RHD 10 exons were screened by PCR with sequence-specific priming or sequenced for the first-time donors who typed weak D,DEL or D negative by serologic test.Results Of all the 30 799 blood donors,155 blood samples were found D negative with IgM anti-D; 34 blood samples were found D positive by indirect antiglobulin test or absorption elution test.RHD alleles were identified by nucleotide sequencing.Total 4 RHD alleles were found including two new.One hundred and twenty of 155 (77.4%) of the serologically D negative samples lacked the RHD gene.One D negative was RHD(615de12).Thirty-two of 155 (20.6%)carried RHD(K409K) among them one carrying 1227G>A and 845G>A.Two of 155 (1.3%) was weak D type 15.Conclusions In this study at the molecular level,all DEL phenotype is RHD(K40gK); weak D type 15 is the prevalent weak D allele in Anhui Chinese Han population.Additionally,an improved more efficient method was adopted to amplify all the RHD exons in one PCR program.Our study added to the understanding of molecular mechanisms underlying D antigen expression in Anhui Han population and provided useful information for adopting suitable genotyping strategies in routine use.

  17. Approaches for cytogenetic and molecular analyses of small flow-sorted cell populations from childhood leukemia bone marrow samples

    DEFF Research Database (Denmark)

    Obro, Nina Friesgaard; Madsen, Hans O.; Ryder, Lars Peter;

    2011-01-01

    defined cell populations with subsequent analyses of leukemia-associated cytogenetic and molecular marker. The approaches described here optimize the use of the same tube of unfixed, antibody-stained BM cells for flow-sorting of small cell populations and subsequent exploratory FISH and PCR-based analyses....

  18. [The use of RAPD and ITE molecular markers to study genetical structure of the Crimean population of Triticum boeoticum Boiss].

    Science.gov (United States)

    Mallabaeva, D Sh; Ignatov, A N; Sheĭko, I A; Isikov, V P; Geliuta, V P; Boĭko, N G; Seriapin, A A; Dorokhov, D B

    2007-01-01

    Wild wheat Triticum boeoticum Boiss. is the rare species are included in the Red Book of Ukraine. This species are reducing the magnitude of population and the area of distribution under anthropogenic activity. We studied genetic structure of two populations of T. boeoticum, located on Sapun Mountain and in Baidar Valley in Crimea. According RAPD and ITE molecular analysis we have estimated that the population of T. boeoticum on Sapun Mountain is genetically more impoverished than a population from the Baidar Valley. For preservation of maximal natural genetic polymorphism of the rare species it is recommended to direct efforts to preservations of a population of T. boeoticum from the Baidar Valley.

  19. Contrasting results from molecular and pedigree-based population diversity measures in captive zebra highlight challenges facing genetic management of zoo populations.

    Science.gov (United States)

    Ito, Hideyuki; Ogden, Rob; Langenhorst, Tanya; Inoue-Murayama, Miho

    2017-01-01

    Zoo conservation breeding programs manage the retention of population genetic diversity through analysis of pedigree records. The range of demographic and genetic indices determined through pedigree analysis programs allows the conservation of diversity to be monitored relative to the particular founder population for a species. Such approaches are based on a number of well-documented founder assumptions, however without knowledge of actual molecular genetic diversity there is a risk that pedigree-based measures will be misinterpreted and population genetic diversity misunderstood. We examined the genetic diversity of the captive populations of Grevy's zebra, Hartmann's mountain zebra and plains zebra in Japan and the United Kingdom through analysis of mitochondrial DNA sequences. Very low nucleotide variability was observed in Grevy's zebra. The results were evaluated with respect to current and historic diversity in the wild, and indicate that low genetic diversity in the captive population is likely a result of low founder diversity, which in turn suggests relatively low wild genetic diversity prior to recent population declines. Comparison of molecular genetic diversity measures with analogous diversity indices generated from the studbook data for Grevy's zebra and Hartmann's mountain zebra show contrasting patterns, with Grevy's zebra displaying markedly less molecular diversity than mountain zebra, despite studbook analysis indicating that the Grevy's zebra population has substantially more founders, greater effective population size, lower mean kinship, and has suffered less loss of gene diversity. These findings emphasize the need to validate theoretical estimates of genetic diversity in captive breeding programs with empirical molecular genetic data. Zoo Biol. 36:87-94, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  20. Molecular and functional heterogeneity of early postnatal porcine satellite cell populations is associated with bioenergetic profile

    Science.gov (United States)

    Miersch, Claudia; Stange, Katja; Hering, Silvio; Kolisek, Martin; Viergutz, Torsten; Röntgen, Monika

    2017-01-01

    During postnatal development, hyperplastic and hypertrophic processes of skeletal muscle growth depend on the activation, proliferation, differentiation, and fusion of satellite cells (SC). Therefore, molecular and functional SC heterogeneity is an important component of muscle plasticity and will greatly affect long-term growth performance and muscle health. However, its regulation by cell intrinsic and extrinsic factors is far from clear. In particular, there is only minor information on the early postnatal period which is critical for muscle maturation and the establishment of adult SC pools. Here, we separated two SC subpopulations (P40/50, P50/70) from muscle of 4-day-old piglets. Our results characterize P40/50 as homogeneous population of committed (high expression of Myf5), fast-proliferating muscle progenitors. P50/70 constituted a slow-proliferating phenotype and contains high numbers of differentiated SC progeny. During culture, P50/70 is transformed to a population with lower differentiation potential that contains 40% Pax7-positive cells. A reversible state of low mitochondrial activity that results from active down-regulation of ATP-synthase is associated with the transition of some of the P50/70 cells to this more primitive fate typical for a reserve cell population. We assume that P40/50 and P50/70 subpopulations contribute unequally in the processes of myofiber growth and maintenance of the SC pool. PMID:28344332

  1. Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics

    Directory of Open Access Journals (Sweden)

    Galtier Nicolas

    2006-04-01

    Full Text Available Abstract Background A large number of bioinformatics applications in the fields of bio-sequence analysis, molecular evolution and population genetics typically share input/ouput methods, data storage requirements and data analysis algorithms. Such common features may be conveniently bundled into re-usable libraries, which enable the rapid development of new methods and robust applications. Results We present Bio++, a set of Object Oriented libraries written in C++. Available components include classes for data storage and handling (nucleotide/amino-acid/codon sequences, trees, distance matrices, population genetics datasets, various input/output formats, basic sequence manipulation (concatenation, transcription, translation, etc., phylogenetic analysis (maximum parsimony, markov models, distance methods, likelihood computation and maximization, population genetics/genomics (diversity statistics, neutrality tests, various multi-locus analyses and various algorithms for numerical calculus. Conclusion Implementation of methods aims at being both efficient and user-friendly. A special concern was given to the library design to enable easy extension and new methods development. We defined a general hierarchy of classes that allow the developer to implement its own algorithms while remaining compatible with the rest of the libraries. Bio++ source code is distributed free of charge under the CeCILL general public licence from its website http://kimura.univ-montp2.fr/BioPP.

  2. Pregnancy after treatment of breast cancer--a population-based study on behalf of Danish Breast Cancer Cooperative Group

    DEFF Research Database (Denmark)

    Kroman, N.; Jensen, M.B.; Wohlfahrt, J.;

    2008-01-01

    at diagnosis, tumour size, nodal status, or pregnancy history before diagnosis of breast cancer. Neither spontaneous abortions nor induced abortions subsequent to breast cancer treatment had a negative impact on prognosis. CONCLUSION: In line with our previous study, but based on more than twice the patient...... material, we found no evidence that a pregnancy after treatment of breast cancer has a negative influence the prognosis Udgivelsesdato: 2008......BACKGROUND: Estrogen is an established growth factor in breast cancer and it has been hypothesized that pregnancy associated estrogens may increase the risk of recurrence of breast cancer. In 1997 we published a population-based Danish study indicating no negative prognostic effect of pregnancy...

  3. Molecular basis for resistance to ACCase-inhibiting herbicides in Pseudosclerochloa kengiana populations.

    Science.gov (United States)

    Yuan, Guohui; Liu, Weitang; Bi, Yaling; Du, Long; Guo, Wenlei; Wang, Jinxin

    2015-03-01

    Pseudosclerochloa kengiana is a troublesome annual grass weed of wheat fields in the rice-wheat double cropping areas in China. Resistance has evolved in P. kengiana under continuously selective pressure of ACCase-inhibiting herbicides. Whole-plant experiments showed that two suspected resistant populations 12-SD-12 and 12-SD-13 were highly resistant to fenoxaprop-P-ethyl (69.9- and 57.2-fold); moderately resistant to clodinafop-propargyl (5.9- and 4.1-fold) and pinoxaden (4.4- and 3.5-fold); lowly resistant to fluazifop-P-butyl (2.2- and 2.0-fold) and sethoxydim (1.8- and 1.6-fold), but were sensitive to clethodim (1.0- and 0.9-fold) and mesosulfuron-methyl (1.1- and 0.9-fold). Molecular analyses confirmed that a Trp1999 to Ser mutation was present in the resistant populations. Two dCAPS markers were also developed to positively determine the wild type Trp and mutant Ser alleles at ACCase position 1999. All 350 individual plants of 12-SD-12 population analysed were heterozygous mutants. Meanwhile, 318 mutant heterozygotes and 32 wild types were detected from the 12-SD-13 population. In addition, the analysis of plant genotype and phenotype showed that all wild type plants were killed after treatment with any one of the ACCase-inhibiting herbicides used, while individual plants carrying the W1999S mutation survived except when treated with clethodim. To our knowledge, this is the first report of pinoxaden resistance and a Trp-1999-Ser mutation in the plastid ACCase for P. kengiana.

  4. Deeply Embedded Protostellar Population in the 20 km s-1 Cloud of the Central Molecular Zone

    CERN Document Server

    Lu, Xing; Kauffmann, Jens; Pillai, Thushara; Longmore, Steven N; Kruijssen, J M Diederik; Battersby, Cara; Gu, Qiusheng

    2015-01-01

    We report the discovery of a population of deeply embedded protostellar candidates in the 20 km s$^{-1}$ cloud, one of the massive molecular clouds in the Central Molecular Zone (CMZ) of the Milky Way, using interferometric submillimeter continuum and H$_2$O maser observations. The submillimeter continuum emission shows five 1-pc scale clumps, each of which further fragments into several 0.1-pc scale cores. We identify 17 dense cores, among which 12 are gravitationally bound. Among the 18 H$_2$O masers detected, 13 coincide with the cores and probably trace outflows emanating from the protostars. There are also 5 gravitationally bound dense cores without H$_2$O maser detection. In total the 13 masers and 5 cores may represent 18 protostars with spectral types later than B1 or potential growing more massive stars at earlier evolutionary stage, given the non-detection in the centimeter radio continuum. In combination with previous studies of CH$_3$OH masers, we conclude that the star formation in this cloud is ...

  5. PREFACE: Cooperative dynamics Cooperative dynamics

    Science.gov (United States)

    Gov, Nir

    2011-09-01

    The dynamics within living cells are dominated by non-equilibrium processes that consume chemical energy (usually in the form of ATP, adenosine triphosphate) and convert it into mechanical forces and motion. The mechanisms that allow this conversion process are mostly driven by the components of the cytoskeleton: (i) directed (polar) polymerization of filaments (either actin or microtubules) and (ii) molecular motors. The forces and motions produced by these two components of the cytoskeleton give rise to the formation of cellular shapes, and drive the intracellular transport and organization. It is clear that these systems present a multi-scale challenge, from the physics of the molecular processes to the organization of many interacting units. Understanding the physical nature of these systems will have a large impact on many fundamental problems in biology and break new grounds in the field of non-equilibrium physics. This field of research has seen a rapid development over the last ten years. Activities in this area range from theoretical and experimental work on the underlying fundamental (bio)physics at the single-molecule level, to investigations (in vivo and in vitro) of the dynamics and patterns of macroscopic pieces of 'living matter'. In this special issue we have gathered contributions that span the whole spectrum of length- and complexity-scales in this field. Some of the works demonstrate how active forces self-organize within the polymerizing cytoskeleton, on the level of cooperative cargo transport via motors or due to active fluxes at the cell membrane. On a larger scale, it is shown that polar filaments coupled to molecular motors give rise to a huge variety of surprising dynamics and patterns: spontaneously looping rings of gliding microtubules, and emergent phases of self-organized filaments and motors in different geometries. All of these articles share the common feature of being out-of-equilibrium, driven by metabolism. As demonstrated here

  6. Molecular study on human tuberculosis in three geographically distinct and time delineated populations from ancient Egypt.

    Science.gov (United States)

    Zink, A R; Grabner, W; Reischl, U; Wolf, H; Nerlich, A G

    2003-04-01

    We describe the molecular identification of human tuberculosis (TB) from vertebral bone tissue samples from three different populations of ancient Egypt. The specimens were obtained from the predynastic to early dynastic necropolis of Abydos (7 individuals, c. 3500-2650 B.C.), from a Middle Kingdom to Second Intermediate Period tomb of the necropolis of Thebes-West (37. c. 2100-1550 B.C.) and from five further Theban tombs used in the New Kingdom and the Late Period (39, c. 1450-500 B.C.). A total of 18 cases tested positive for the presence of ancient DNA (aDNA) of the M. tuberculosis complex. Out of the 9 cases with typical macromorphological signs of tuberculous spondylitis, 6 were positive for mycobacterial aDNA (66.7%). Of 24 cases with non-specific pathological alterations, 5 provided a positive result (20.8%). In 50 cases of normally appearing vertebral bones 7 tested positive (14.0%). There were only minor differences in the frequencies between the three populations. These data strongly support the notion that tuberculosis was present and prevalent in ancient Egypt since very early periods of this civilization. The unexpectedly high rate of mycobacterial aDNA in normal bone samples is presumably due to a pre- to perimortal systemic spread of the bacteria and indicates a generalized infection by M. tuberculosis.

  7. Genomic analysis reveals the molecular basis for capsule loss in the group B Streptococcus population.

    Science.gov (United States)

    Rosini, Roberto; Campisi, Edmondo; De Chiara, Matteo; Tettelin, Hervé; Rinaudo, Daniela; Toniolo, Chiara; Metruccio, Matteo; Guidotti, Silvia; Sørensen, Uffe B Skov; Kilian, Mogens; Ramirez, Mario; Janulczyk, Robert; Donati, Claudio; Grandi, Guido; Margarit, Immaculada

    2015-01-01

    The human and bovine bacterial pathogen Streptococcus agalactiae (Group B Streptococcus, GBS) expresses a thick polysaccharide capsule that constitutes a major virulence factor and vaccine target. GBS can be classified into ten distinct serotypes differing in the chemical composition of their capsular polysaccharide. However, non-typeable strains that do not react with anti-capsular sera are frequently isolated from colonized and infected humans and cattle. To gain a comprehensive insight into the molecular basis for the loss of capsule expression in GBS, a collection of well-characterized non-typeable strains was investigated by genome sequencing. Genome based phylogenetic analysis extended to a wide population of sequenced strains confirmed the recently observed high clonality among GBS lineages mainly containing human strains, and revealed a much higher degree of diversity in the bovine population. Remarkably, non-typeable strains were equally distributed in all lineages. A number of distinct mutations in the cps operon were identified that were apparently responsible for inactivation of capsule synthesis. The most frequent genetic alterations were point mutations leading to stop codons in the cps genes, and the main target was found to be cpsE encoding the portal glycosyl transferase of capsule biosynthesis. Complementation of strains carrying missense mutations in cpsE with a wild-type gene restored capsule expression allowing the identification of amino acid residues essential for enzyme activity.

  8. Genomic analysis reveals the molecular basis for capsule loss in the group B Streptococcus population.

    Directory of Open Access Journals (Sweden)

    Roberto Rosini

    Full Text Available The human and bovine bacterial pathogen Streptococcus agalactiae (Group B Streptococcus, GBS expresses a thick polysaccharide capsule that constitutes a major virulence factor and vaccine target. GBS can be classified into ten distinct serotypes differing in the chemical composition of their capsular polysaccharide. However, non-typeable strains that do not react with anti-capsular sera are frequently isolated from colonized and infected humans and cattle. To gain a comprehensive insight into the molecular basis for the loss of capsule expression in GBS, a collection of well-characterized non-typeable strains was investigated by genome sequencing. Genome based phylogenetic analysis extended to a wide population of sequenced strains confirmed the recently observed high clonality among GBS lineages mainly containing human strains, and revealed a much higher degree of diversity in the bovine population. Remarkably, non-typeable strains were equally distributed in all lineages. A number of distinct mutations in the cps operon were identified that were apparently responsible for inactivation of capsule synthesis. The most frequent genetic alterations were point mutations leading to stop codons in the cps genes, and the main target was found to be cpsE encoding the portal glycosyl transferase of capsule biosynthesis. Complementation of strains carrying missense mutations in cpsE with a wild-type gene restored capsule expression allowing the identification of amino acid residues essential for enzyme activity.

  9. Cytogenetic and molecular screening of the DAZ gene family in a population of infertile males

    Directory of Open Access Journals (Sweden)

    Nubia Amparo Ruiz Suárez

    2007-05-01

    Full Text Available The purpose of this study was to evalúate the frequency of Y chromosome structural, numerical, chromosomal and genetic abnormalities, as well as DAZ gene microdeletions in the Y chromosome in a population of infertile males. Genetic abnormalities have been established to date in up to 24% of males having severe abnormalities in their sperm (Dohle et al. 2002; deletion of the DAZ gene family (deleted in azoospermia is the most common cause. It has been found in 6% of the oligozoospermias and in 12% of the azoospermias (Van Landuyt et al. 2000. A popula­tion of 20 azoospermic and 10 oligozoospermic males was studied. Five males having normal sperm parameters were used as controls. Each sample was karyotyped (QFQ banding and underwent sY254, sY255 and sY257 mo­lecular amplification. Genetic study revealed alterations in 16.6% of the cases: 6.6% at chromosome level and 10% at molecule level. No chromosomal or molecular gene alterations were detected in control males. The frequencies found lead to a broader population-based study being recommended. They confirmed the need for performing judicious genetic counselling in infertile couples with male factor infertility to avoid or minimise the risks of trans-mitting these abnormalities to offspring and provide better prognosis for assisted reproductive techniques in such patients. Key words: azoospermia; oligozoospermia; microdeletions; ICSI

  10. At Baltic crossroads: a molecular snapshot of Mycobacterium tuberculosis population diversity in Kaliningrad, Russia.

    Science.gov (United States)

    Mokrousov, Igor; Otten, Tatiana; Zozio, Thierry; Turkin, Eugeni; Nazemtseva, Vera; Sheremet, Aleksandra; Vishnevsky, Boris; Narvskaya, Olga; Rastogi, Nalin

    2009-01-01

    The Kaliningrad region is the westernmost part of the Russian Federation; it includes an enclave on the Baltic Sea inside the European Union separated from mainland Russia by Lithuania and Poland. The incidence of tuberculosis in Kaliningrad has shown a steady and dramatic increase from 83/100,000 in 2000 to 134/100,000 in 2006; the rate of multidrug-resistant tuberculosis (MDR-tuberculosis) in the Kaliningrad region was reported to be 30.5% among newly diagnosed tuberculosis patients. This study presents a first molecular snapshot of the population diversity of Mycobacterium tuberculosis in this region. A total of 90 drug-resistant and susceptible M. tuberculosis strains from Kaliningrad were subjected to spoligotyping, 12-locus MIRU typing and mutation analysis of the drug resistance genes rpoB and katG. A comparison with international databases showed that the M. tuberculosis population in this region shares a joint pool of strains with the European part of Russia, and also exhibits a certain affinity with those of its northern European neighbours, such as Poland and Germany. Comparison of the genotyping and drug resistance data emphasized that the high prevalence of the MDR Beijing genotype strains is a major cause of the adverse epidemiological situation of MDR-tuberculosis in the Kaliningrad region.

  11. Network modularity promotes cooperation.

    Science.gov (United States)

    Marcoux, Marianne; Lusseau, David

    2013-05-01

    Cooperation in animals and humans is widely observed even if evolutionary biology theories predict the evolution of selfish individuals. Previous game theory models have shown that cooperation can evolve when the game takes place in a structured population such as a social network because it limits interactions between individuals. Modularity, the natural division of a network into groups, is a key characteristic of all social networks but the influence of this crucial social feature on the evolution of cooperation has never been investigated. Here, we provide novel pieces of evidence that network modularity promotes the evolution of cooperation in 2-person prisoner's dilemma games. By simulating games on social networks of different structures, we show that modularity shapes interactions between individuals favouring the evolution of cooperation. Modularity provides a simple mechanism for the evolution of cooperation without having to invoke complicated mechanisms such as reputation or punishment, or requiring genetic similarity among individuals. Thus, cooperation can evolve over wider social contexts than previously reported.

  12. Globalization and human cooperation.

    Science.gov (United States)

    Buchan, Nancy R; Grimalda, Gianluca; Wilson, Rick; Brewer, Marilynn; Fatas, Enrique; Foddy, Margaret

    2009-03-17

    Globalization magnifies the problems that affect all people and that require large-scale human cooperation, for example, the overharvesting of natural resources and human-induced global warming. However, what does globalization imply for the cooperation needed to address such global social dilemmas? Two competing hypotheses are offered. One hypothesis is that globalization prompts reactionary movements that reinforce parochial distinctions among people. Large-scale cooperation then focuses on favoring one's own ethnic, racial, or language group. The alternative hypothesis suggests that globalization strengthens cosmopolitan attitudes by weakening the relevance of ethnicity, locality, or nationhood as sources of identification. In essence, globalization, the increasing interconnectedness of people worldwide, broadens the group boundaries within which individuals perceive they belong. We test these hypotheses by measuring globalization at both the country and individual levels and analyzing the relationship between globalization and individual cooperation with distal others in multilevel sequential cooperation experiments in which players can contribute to individual, local, and/or global accounts. Our samples were drawn from the general populations of the United States, Italy, Russia, Argentina, South Africa, and Iran. We find that as country and individual levels of globalization increase, so too does individual cooperation at the global level vis-à-vis the local level. In essence, "globalized" individuals draw broader group boundaries than others, eschewing parochial motivations in favor of cosmopolitan ones. Globalization may thus be fundamental in shaping contemporary large-scale cooperation and may be a positive force toward the provision of global public goods.

  13. Molecular analysis of bacterial population structure and dynamics during cold storage of untreated and treated milk.

    Science.gov (United States)

    Rasolofo, Eric Andriamahery; St-Gelais, Daniel; LaPointe, Gisele; Roy, Denis

    2010-03-31

    Spoilage bacteria in milk are controlled by treatments such as thermization, microfiltration and addition of carbon dioxide. However, little information is known about the changes in microbial communities during subsequent cold storage of treated milk. Culture-dependent methods and a direct molecular approach combining 16S rRNA gene clone libraries and quantitative PCR (Q-PCR) were applied to obtain a better overview of the structure and the dynamics of milk microbiota. Raw milk samples were treated by the addition of carbon dioxide (CO(2)), thermization (TH) or microfiltration (MF) and stored at 4 degrees C or 8 degrees C up to 7d. Untreated milk (UT) was used as a control. Psychrotrophic and staphylococci bacteria were enumerated in the milk samples by culture methods. For the molecular approach, DNA was extracted from milk samples and 16S rRNA gene was amplified by PCR with universal primers prior to cloning. The Q-PCR method was used to evaluate the dynamics of dominant bacterial species revealed by clone library analysis of 16S rRNA gene. Comparison of the 16S rRNA gene sequence indicated that the two most abundant operational taxonomic units (OTU), determined at 97% identity, belonged to the class Gammaproteobacteria (40.3% of the 1415 sequences) and Bacilli (40%). Dominant bacterial species in UT, CO(2) and TH milk samples at day 3 were affiliated with Staphylococcus, Streptococcus, Clostridia, Aerococcus, Facklamia, Corynebacterium, Acinetobacter and Trichococcus. Dominant bacterial species detected in MF milk were Stenotrophomonas, Pseudomonas and Delftia, while Pseudomonas species dominated the bacterial population of UT, CO(2) and MF milk samples at day 7. Staphylococcus and Delftia were the dominant bacterial species in thermized milk. Q-PCR results showed that populations of S. aureus, A. viridans, A. calcoaceticus, C. variabile and S. uberis were stable during 7d of storage at 4 degrees C. Populations of P. fluorescens, S. uberis and total bacteria

  14. IN-SYNC. IV. The Young Stellar Population in the Orion A Molecular Cloud

    Science.gov (United States)

    Da Rio, Nicola; Tan, Jonathan C.; Covey, Kevin R.; Cottaar, Michiel; Foster, Jonathan B.; Cullen, Nicholas C.; Tobin, John J.; Kim, Jinyoung S.; Meyer, Michael R.; Nidever, David L.; Stassun, Keivan G.; Chojnowski, S. Drew; Flaherty, Kevin M.; Majewski, Steve; Skrutskie, Michael F.; Zasowski, Gail; Pan, Kaike

    2016-02-01

    We present the results of the Sloan Digital Sky Survey APOGEE INfrared Spectroscopy of Young Nebulous Clusters program (IN-SYNC) survey of the Orion A molecular cloud. This survey obtained high-resolution near-infrared spectroscopy of about 2700 young pre-main-sequence stars on a ˜ 6^\\circ field of view. We have measured accurate stellar parameters ({T}{{eff}}, {log}g, v{sin}i) and extinctions and placed the sources in the Hertzsprung-Russel diagram (HRD). We have also extracted radial velocities for the kinematic characterization of the population. We compare our measurements with literature results to assess the performance and accuracy of the survey. Source extinction shows evidence for dust grains that are larger than those in the diffuse interstellar medium: we estimate an average RV = 5.5 in the region. Importantly, we find a clear correlation between HRD inferred ages and spectroscopic surface-gravity-inferred ages and between extinction and disk presence; this strongly suggests a real spread of ages larger than a few Myr. Focusing on the young population around NGC 1980/ι Ori, which has previously been suggested to be a separate, foreground, older cluster, we confirm its older (˜5 Myr) age and low AV, but considering that its radial velocity distribution is indistinguishable from Orion A’s population, we suggest that NGC 1980 is part of Orion A’s star formation activity. Based on their stellar parameters and kinematic properties, we identify 383 new candidate members of Orion A, most of which are diskless sources in areas of the region poorly studied by previous works.

  15. The paradox of cooperation benefits.

    Science.gov (United States)

    Németh, A; Takács, K

    2010-05-21

    It seems obvious that as the benefits of cooperation increase, the share of cooperators in the population should also increase. It is well known that positive assortment between cooperative types, for instance in spatially structured populations, provide better conditions for the evolution of cooperation than complete mixing. This study demonstrates that, assuming positive assortment, under most conditions higher cooperation benefits also increase the share of cooperators. On the other hand, under a specified range of payoff values, when at least two payoff parameters are modified, the reverse is true. The conditions for this paradox are determined for two-person social dilemmas: the Prisoner's Dilemma, the Hawks and Doves game, and the Stag Hunt game, assuming global selection and positive assortment.

  16. Applications of single-strand conformation polymorphism (SSCP) to taxonomy, diagnosis, population genetics and molecular evolution of parasitic nematodes.

    Science.gov (United States)

    Gasser, R B; Chilton, N B

    2001-11-22

    The analysis of genetic variation in parasitic nematodes has important implications for studying aspects of taxonomy, diagnosis, population genetics, drug resistance and molecular evolution. This article highlights some applications of PCR-based single-strand conformation polymorphism (SSCP) for the analysis of sequence variation in individual parasites (and their populations) to address some of these areas. It also describes the principles and advantages of SSCP, and provides some examples for future applications in parasitology.

  17. From total suspended solids to molecular biology tools--a personal view of biological wastewater treatment process population dynamics.

    Science.gov (United States)

    Jenkins, David

    2008-08-01

    The development of the tools needed to study the population dynamics of biological wastewater treatment processes is traced from its beginnings in the early 1900s to today's use of molecular biology tools (Oerther and Love, 2003). Examples of the benefits of population dynamics research in improving the performance and aiding the design and operation of biological wastewater treatment processes are given. Some thoughts on future areas of study are presented.

  18. Analysis of molecular aberrations of Wnt pathway gladiators in colorectal cancer in the Kashmiri population

    Directory of Open Access Journals (Sweden)

    Sameer A

    2011-07-01

    Full Text Available Abstract The development and progression of colorectal cancer (CRC is a multi-step process, and the Wnt pathways with its two molecular gladiators adenomatous polyposis coli (APC and β-catenin plays an important role in transforming a normal tissue into a malignant one. In this study, we aimed to investigate the role of aberrations in the APC and β-catenin genes in the pathogenesis of CRC in the Kashmir valley, and to correlate it with various clinicopathological variables. We examined the paired tumour and normal-tissue specimens of 86 CRC patients for the occurrence of aberrations in the mutation cluster region (MCR of the APC gene and exon 3 of the β-catenin gene by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP and/or PCR-direct sequencing. Analysis of promoter hypermethylation of the APC gene was also carried out using methylation-specific PCR (MS-PCR. The overall mutation rate of the MCR of the APC gene among 86 CRC cases was 12.8 per cent (11 of 86. Promoter hypermethylation of APC was observed in 54.65 per cent (47 of 86 of cases. Furthermore, we found a significant association between tumour location, tumour grade and node status and the methylation status of the APC gene (p ≤ 0.05. Although the number of mutations in the APC and β-catenin genes in our CRC cases was very low, the study confirms the role of epigenetic gene silencing of the pivotal molecular gladiator, APC, of the Wnt pathway in the development of CRC in the Kashmiri population.

  19. THE YOUNG STELLAR OBJECT POPULATION IN THE VELA-D MOLECULAR CLOUD

    Energy Technology Data Exchange (ETDEWEB)

    Strafella, F.; Maruccia, Y.; Maiolo, B. [Dipartimento di Matematica e Fisica, Università del Salento, I-73100 Lecce (Italy); Lorenzetti, D.; Giannini, T. [INAF-Osservatorio Astronomico di Roma, Via Frascati 33, I-00040 Monte Porzio (Italy); Elia, D.; Molinari, S.; Pezzuto, S. [INAF-IAPS, Via Fosso del Cavaliere 100, I-00133 Roma (Italy); Massi, F.; Olmi, L., E-mail: francesco.strafella@le.infn.it [INAF-Osservatorio di Arcetri, Largo E. Fermi 5, I-50125 Firenze (Italy)

    2015-01-10

    We investigate the young stellar population in the Vela Molecular Ridge, Cloud-D, a star-forming region observed by both the Spitzer/NASA and Herschel/ESA space telescopes. The point-source, band-merged, Spitzer-IRAC catalog complemented with MIPS photometry previously obtained is used to search for candidate young stellar objects (YSOs), also including sources detected in less than four IRAC bands. Bona fide YSOs are selected by using appropriate color-color and color-magnitude criteria aimed at excluding both Galactic and extragalactic contaminants. The derived star formation rate and efficiency are compared with the same quantities characterizing other star-forming clouds. Additional photometric data, spanning from the near-IR to the submillimeter, are used to evaluate both bolometric luminosity and temperature for 33 YSOs located in a region of the cloud observed by both Spitzer and Herschel. The luminosity-temperature diagram suggests that some of these sources are representative of Class 0 objects with bolometric temperatures below 70 K and luminosities of the order of the solar luminosity. Far-IR observations from the Herschel/Hi-GAL key project for a survey of the Galactic plane are also used to obtain a band-merged photometric catalog of Herschel sources intended to independently search for protostars. We find 122 Herschel cores located on the molecular cloud, 30 of which are protostellar and 92 of which are starless. The global protostellar luminosity function is obtained by merging the Spitzer and Herschel protostars. Considering that 10 protostars are found in both the Spitzer and Herschel lists, it follows that in the investigated region we find 53 protostars and that the Spitzer-selected protostars account for approximately two-thirds of the total.

  20. Comparison of molecular linkage maps and QTLs for morphological traits in two reciprocal backcross populations of rice.

    Science.gov (United States)

    Qiao, Yongli; Jiang, Wenzhu; Rahman, Md Lutfor; Chu, Sang-Ho; Piao, Rihua; Han, Longzhi; Koh, Hee-Jong

    2008-05-31

    Comparison of maps and QTLs between populations may provide us with a better understanding of molecular maps and the inheritance of traits. We developed and used two reciprocal BC1F1 populations, IP/DS//IP and IP/DS//DS, for QTL analysis. DS (Dasanbyeo) is a Korean tongil-type cultivar (derived from an indica x japonica cross and similar to indica in its genetic make-up) and IP (Ilpumbyeo) is a Korean japonica cultivar. We constructed two molecular linkage maps corresponding to each backcross population using 196 markers for each map. The length of each chromosome was longer in the IP/DS//IP population than in the IP/DS//DS population, indicating that more recombinants were produced in the IP/DS//IP population. Distorted segregation was observed for 44 and 19 marker loci for the IP/DS//IP and IP/DS//DS populations, respectively; these were mostly skewed in favor of the indica alleles. A total of 36 main effect QTLs (M-QTLs) and 15 digenic epistatic interactions (E-QTLs) were detected for the seven traits investigated. The phenotypic variation explained (PVE) by M-QTLs ranged from 3.4% to 88.2%. Total PVE of the M-QTLs for each trait was significantly higher than that of the E-QTLs. The total number of M-QTLs identified in the IP/DS//IP population was higher than in the IP/DS//DS population. However, the total PVE by the M-QTLs and E-QTLs together for each trait was similar in the two populations, suggesting that the two BC1F1 populations are equally useful for QTL analysis. Maps and QTLs in the two populations were compared. Eleven new QTLs were identified for SN, SF, GL, and GW in this study, and they will be valuable in marker-assisted selection, particularly for improving grain traits in tongil-type varieties.

  1. Designing molecular dynamics simulations to shift populations of the conformational states of calmodulin.

    Directory of Open Access Journals (Sweden)

    Ayse Ozlem Aykut

    Full Text Available We elucidate the mechanisms that lead to population shifts in the conformational states of calcium-loaded calmodulin (Ca(2+-CaM. We design extensive molecular dynamics simulations to classify the effects that are responsible for adopting occupied conformations available in the ensemble of NMR structures. Electrostatic interactions amongst the different regions of the protein and with its vicinal water are herein mediated by lowering the ionic strength or the pH. Amino acid E31, which is one of the few charged residues whose ionization state is highly sensitive to pH differences in the physiological range, proves to be distinctive in its control of population shifts. E31A mutation at low ionic strength results in a distinct change from an extended to a compact Ca(2+-CaM conformation within tens of nanoseconds, that otherwise occur on the time scales of microseconds. The kinked linker found in this particular compact form is observed in many of the target-bound forms of Ca(2+-CaM, increasing the binding affinity. This mutation is unique in controlling C-lobe dynamics by affecting the fluctuations between the EF-hand motif helices. We also monitor the effect of the ionic strength on the conformational multiplicity of Ca(2+-CaM. By lowering the ionic strength, the tendency of nonspecific anions in water to accumulate near the protein surface increases, especially in the vicinity of the linker. The change in the distribution of ions in the vicinal layer of water allows N- and C- lobes to span a wide variety of relative orientations that are otherwise not observed at physiological ionic strength. E31 protonation restores the conformations associated with physiological environmental conditions even at low ionic strength.

  2. Molecular analysis of fungal populations in patients with oral candidiasis using internal transcribed spacer region.

    Science.gov (United States)

    Ieda, Shinsuke; Moriyama, Masafumi; Takeshita, Toru; Takashita, Toru; Maehara, Takashi; Imabayashi, Yumi; Shinozaki, Shoichi; Tanaka, Akihiko; Hayashida, Jun-Nosuke; Furukawa, Sachiko; Ohta, Miho; Yamashita, Yoshihisa; Nakamura, Seiji

    2014-01-01

    Oral candidiasis is closely associated with changes in the oral fungal flora and is caused primarily by Candida albicans. Conventional methods of fungal culture are time-consuming and not always conclusive. However, molecular genetic analysis of internal transcribed spacer (ITS) regions of fungal rRNA is rapid, reproducible and simple to perform. In this study we examined the fungal flora in patients with oral candidiasis and investigated changes in the flora after antifungal treatment using length heterogeneity-polymerization chain reaction (LH-PCR) analysis of ITS regions. Fifty-two patients with pseudomembranous oral candidiasis (POC) and 30 healthy controls were included in the study. Fungal DNA from oral rinse was examined for fungal species diversity by LH-PCR. Fungal populations were quantified by real-time PCR and previously-unidentified signals were confirmed by nucleotide sequencing. Relationships between the oral fungal flora and treatment-resistant factors were also examined. POC patients showed significantly more fungal species and a greater density of fungi than control individuals. Sixteen fungi were newly identified. The fungal populations from both groups were composed predominantly of C. albicans, though the ratio of C. dubliniensis was significantly higher in POC patients than in controls. The diversity and density of fungi were significantly reduced after treatment. Furthermore, fungal diversity and the proportion of C. dubliniensis were positively correlated with treatment duration. These results suggest that C. dubliniensis and high fungal flora diversity might be involved in the pathogenesis of oral candidiasis. We therefore conclude that LH-PCR is a useful technique for diagnosing and assessing the severity of oral candidal infection.

  3. Physicality and Cooperative Design

    NARCIS (Netherlands)

    Vyas, Dhaval; Heylen, Dirk K.J.; Nijholt, Antinus; Popescu-Belis, Andrei; Stiefelhagen, Rainer

    2008-01-01

    CSCW researchers have increasingly come to realize that material work setting and its population of artefacts play a crucial part in coordination of distributed or co-located work. This paper uses the notion of physicality as a basis to understand cooperative work. Using examples from an ongoing

  4. Molecular and morphological characterization of Xiphinema chambersi population from live oak in Jekyll Island, Georgia, with comments on morphometric variations

    Science.gov (United States)

    Zafar A. Handoo; Lynn K. Carta; Andrea M. Skantar; Sergei A. Subbotin; Stephen Fraedrich

    2016-01-01

    A population of Xiphinema chambersi from the root zone around live oak (Quercus virginiana Mill.) trees on Jekyll Island, GA, is described using both morphological and molecular tools and compared with descriptions of type specimens. Initially, because of a few morphological differences, this nematode was thought to represent an undescribed species. However, on further...

  5. Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework.

    Science.gov (United States)

    Kijima, T E; Innan, Hideki

    2013-11-01

    A population genetic simulation framework is developed to understand the behavior and molecular evolution of DNA sequences of transposable elements. Our model incorporates random transposition and excision of transposable element (TE) copies, two modes of selection against TEs, and degeneration of transpositional activity by point mutations. We first investigated the relationships between the behavior of the copy number of TEs and these parameters. Our results show that when selection is weak, the genome can maintain a relatively large number of TEs, but most of them are less active. In contrast, with strong selection, the genome can maintain only a limited number of TEs but the proportion of active copies is large. In such a case, there could be substantial fluctuations of the copy number over generations. We also explored how DNA sequences of TEs evolve through the simulations. In general, active copies form clusters around the original sequence, while less active copies have long branches specific to themselves, exhibiting a star-shaped phylogeny. It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution.

  6. Iron and molecular opacities and the evolution of Population I stars

    Science.gov (United States)

    Stothers, Richard B.; Chin, Chao-Wen

    1993-01-01

    Effects of recent opacity revisions on the evolution of Population I stars are explored over the range 1.5-60 solar masses. Opacity parameters considered include the angular momentum coupling scheme for iron, the relative iron abundance, the total metal abundance, and diatomic and triatomic molecular sources. Only the total metal abundance exerts an important control over the evolutionary tracks. Blue loops on the H-R diagram during core helium burning can be very sensitive to opacity, but only insofar as the simple formation or suppression of a blue loop is concerned. The blue loops are most robust for stellar masses around 10 solar masses. We confirm, from a comparison of stellar models with observational data, that the total metal abundance is close to solar and that convective core overshooting is likely to be very slight. The new models predict the existence of an iron convection zone in the envelope and a great widening of the main-sequence band in the H-R diagram at luminosities brighter than 100,000 solar luminosities.

  7. IN-SYNC IV - The Young Stellar Population in the Orion A Molecular Cloud

    CERN Document Server

    Da Rio, Nicola; Covey, Kevin R; Cottaar, Michiel; Foster, Jonathan B; Cullen, Nicholas C; Tobin, John; Kim, Jinyoung S; Meyer, Michael R; Nidever, David L; Stassun, Keivan G; Chojnowski, S Drew; Flaherty, Kevin M; Majewski, Steve; Skrutskie, Michael F; Zasowski, Gail; Pan, Kaike

    2015-01-01

    We present the results of the SDSS APOGEE INfrared Spectroscopy of Young Nebulous Clusters program (IN-SYNC) survey of the Orion A molecular cloud. This survey obtained high resolution near infrared (NIR) spectroscopy of about 2700 young pre-main sequence stars throughout the region, acquired across five distinct fields spanning 6deg field of view (FOV). With these spectra, we have measured accurate stellar parameters (T_eff, log g, v sin i) and extinctions, and placed the sources in the Hertzsprung-Russel Diagram (HRD). We have also extracted radial velocities for the kinematic characterization of the population. We compare our measurements with literature results for a sub-sample of targets in order to assess the performances and accuracy of the survey. Source extinction shows evidence for dust grains that are larger than those in the diffuse interstellar medium (ISM): we estimate an average R_V=5.5 in the region. Importantly, we find a clear correlation between HRD inferred ages and spectroscopic surface-g...

  8. Cooperation and depressive symptoms.

    Science.gov (United States)

    Brendan Clark, C; Thorne, Christopher B; Hardy, Sonya; Cropsey, Karen L

    2013-09-25

    Deficits in pro-social cooperation are common in many individuals with mental illnesses such as depression. For decades, researchers have used economic game paradigms to compare cross-cultural cooperative behavior. However, research using economic games to assess cooperative behavior in clinical populations is in the early stages. We hypothesized that individuals with greater depressive symptoms would struggle to maintain reciprocity in iterative games, but not in single-iteration games measuring personal values. Participants (n=41) played four computer-based economic games (prisoner's dilemma, the public goods game, the ultimatum game, and the trust game) measuring different aspects of cooperation. Participants completed the Depression Anxiety and Stress Scale (DASS) and other measures of personality and demographics. Analyses assessed the relationships between game performance and psychological distress as measured by the DASS. Significant correlations were found between game performance and depressive symptoms, but not symptoms of anxiety or stress. Performance in the prisoner's dilemma and public goods game was significantly related to depression in a linear regression even when known associations with depressive affect such as age, gender, race, education, marital status, and neuroticism were controlled for. Depressive symptoms were associated with an inability to sustain reciprocal cooperation. Participants showed the predicted deficits in cooperation in these economic games. Economic games show the potential for assessing the social deficits associated with depressive symptoms. © 2013 Elsevier B.V. All rights reserved.

  9. Estimating genetic diversity and sampling strategy for a wild soybean (Glycine soja) population based on different molecular markers

    Institute of Scientific and Technical Information of China (English)

    CHEN Zhong; ZHAO Ru; GU Senchang; YAN Wen; CHENG Zhou; CHEN Muhong; LU Weifeng; WANG Shuhong; LU Baorong; LU Jun; ZHANG Fan; XIANG Rong; XIAO Shangbin; YAN Pin

    2006-01-01

    Genetic diversity is the basic and most important component of biodiversity. It is essential for the effective conservation and utilization of genetic resources to accurately estimate genetic diversity of the targeted species and populations. This paper reports analyses of genetic diversity of a wild soybean population using three molecular marker technologies (AFLP, ISSR and SSR), and computer simulation studies of randomly selected subsets with different sample size (5-90 individuals) drawn 50 times from a total of 100 wild soybean individuals. The variation patterns of genetic diversity indices, including expected heterozygosity (He), Shannon diversity index (/), and percentage of polymorphic loci (P), were analyzed to evaluate changes of genetic diversity associated with the increase of individuals in each subset. The results demonstrated that (1) values of genetic diversity indices of the same wild soybean population were considerably different when estimated by different molecular marker techniques; (2) genetic diversity indices obtained from subsets with different sample sizes also diverged considerably; (3) P values were relatively more reliable for comparing genetic diversity detected by different molecular marker techniques; and (4) different diversity indices reached 90% of the total genetic diversity of the soybean population quite differently in terms of the sample size (number of individuals) analyzed.When using the P value as a determinator, 30-40individuals could capture over 90% of the total genetic diversity of the wild soybean population. Results from this study provide a strong scientific basis for estimating genetic diversity and for strategic conservation of plant species.

  10. Concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations.

    Science.gov (United States)

    Müller, Christian S; Knehans, Tim; Davydov, Dmitri R; Bounds, Patricia L; von Mandach, Ursula; Halpert, James R; Caflisch, Amedeo; Koppenol, Willem H

    2015-01-27

    Cytochrome P450 3A4 (CYP3A4) is the major human P450 responsible for the metabolism of carbamazepine (CBZ). To explore the mechanisms of interactions of CYP3A4 with this anticonvulsive drug, we carried out multiple molecular dynamics (MD) simulations, starting with the complex of CYP3A4 manually docked with CBZ. On the basis of these simulations, we engineered CYP3A4 mutants I369F, I369L, A370V, and A370L, in which the productive binding orientation was expected to be stabilized, thus leading to increased turnover of CBZ to the 10,11-epoxide product. In addition, we generated CYP3A4 mutant S119A as a control construct with putative destabilization of the productive binding pose. Evaluation of the kinetics profiles of CBZ epoxidation demonstrate that CYP3A4-containing bacterial membranes (bactosomes) as well as purified CYP3A4 (wild-type and mutants I369L/F) exhibit substrate inhibition in reconstituted systems. In contrast, mutants S119A and A370V/L exhibit S-shaped profiles that are indicative of homotropic cooperativity. MD simulations with two to four CBZ molecules provide evidence that the substrate-binding pocket of CYP3A4 can accommodate more than one molecule of CBZ. Analysis of the kinetics profiles of CBZ metabolism with a model that combines the formalism of the Hill equation with an allowance for substrate inhibition demonstrates that the mechanism of interactions of CBZ with CYP3A4 involves multiple substrate-binding events (most likely three). Despite the retention of the multisite binding mechanism in the mutants, functional manifestations reveal an exquisite sensitivity to even minor structural changes in the binding pocket that are introduced by conservative substitutions such as I369F, I369L, and A370V.

  11. Molecular Epidemiology of Amoebiasis: A Cross-Sectional Study among North East Indian Population.

    Directory of Open Access Journals (Sweden)

    Joyobrato Nath

    2015-12-01

    Full Text Available Epidemiological studies carried out using culture or microscopy in most of the amoebiasis endemic developing countries, yielded confusing results since none of these could differentiate the pathogenic Entamoeba histolytica from the non-pathogenic Entamoeba dispar and Entamoeba moshkovskii. The Northeastern part of India is a hot spot of infection since the climatic conditions are most conducive for the infection and so far no systemic study has been carried out in this region.Following a cross-sectional study designed during the period 2011-2014, a total of 1260 fecal samples collected from the Northeast Indian population were subjected to microscopy, fecal culture and a sensitive and specific DNA dot blot screening assay developed in our laboratory targeting the Entamoeba spp. Further species discrimination using PCR assay performed in microscopy, culture and DNA dot blot screening positive samples showed E. histolytica an overall prevalence rate of 11.1%, 8.0% and 13.7% respectively. In addition, infection rates of nonpathogenic E. dispar and E. moshkovskii were 11.8% (95% CI = 10.2, 13.8 and 7.8% (95% CI = 6.4, 9.4 respectively. The spatial distributions of infection were 18.2% (107/588 of Assam, 11.7% (23/197 of Manipur, 10.2% (21/207 of Meghalaya, and 8.2% (22/268 of Tripura states. Association study of the disease with demographic features suggested poor living condition (OR = 3.21; 95% CI = 1.83, 5.63, previous history of infection in family member (OR = 3.18; 95% CI = 2.09, 4.82 and unhygienic toilet facility (OR = 1.79; 95% CI = 1.28, 2.49 as significant risk factors for amoebiasis. Children in age group <15 yr, participants having lower levels of education, and daily laborers exhibited a higher infection rate.Despite the importance of molecular diagnosis of amoebiasis, molecular epidemiological data based on a large sample size from endemic countries are rarely reported in the literature. Improved and faster method of diagnosis

  12. Molecular Epidemiology of Amoebiasis: A Cross-Sectional Study among North East Indian Population

    Science.gov (United States)

    Nath, Joyobrato; Ghosh, Sankar Kumar; Singha, Baby; Paul, Jaishree

    2015-01-01

    Background Epidemiological studies carried out using culture or microscopy in most of the amoebiasis endemic developing countries, yielded confusing results since none of these could differentiate the pathogenic Entamoeba histolytica from the non-pathogenic Entamoeba dispar and Entamoeba moshkovskii. The Northeastern part of India is a hot spot of infection since the climatic conditions are most conducive for the infection and so far no systemic study has been carried out in this region. Methodology/Principal Findings Following a cross-sectional study designed during the period 2011–2014, a total of 1260 fecal samples collected from the Northeast Indian population were subjected to microscopy, fecal culture and a sensitive and specific DNA dot blot screening assay developed in our laboratory targeting the Entamoeba spp. Further species discrimination using PCR assay performed in microscopy, culture and DNA dot blot screening positive samples showed E. histolytica an overall prevalence rate of 11.1%, 8.0% and 13.7% respectively. In addition, infection rates of nonpathogenic E. dispar and E. moshkovskii were 11.8% (95% CI = 10.2, 13.8) and 7.8% (95% CI = 6.4, 9.4) respectively. The spatial distributions of infection were 18.2% (107/588) of Assam, 11.7% (23/197) of Manipur, 10.2% (21/207) of Meghalaya, and 8.2% (22/268) of Tripura states. Association study of the disease with demographic features suggested poor living condition (OR = 3.21; 95% CI = 1.83, 5.63), previous history of infection in family member (OR = 3.18; 95% CI = 2.09, 4.82) and unhygienic toilet facility (OR = 1.79; 95% CI = 1.28, 2.49) as significant risk factors for amoebiasis. Children in age group <15 yr, participants having lower levels of education, and daily laborers exhibited a higher infection rate. Conclusions/Significance Despite the importance of molecular diagnosis of amoebiasis, molecular epidemiological data based on a large sample size from endemic countries are rarely reported in the

  13. How feeling betrayed affects cooperation.

    Directory of Open Access Journals (Sweden)

    Pouria Ramazi

    Full Text Available For a population of interacting self-interested agents, we study how the average cooperation level is affected by some individuals' feelings of being betrayed and guilt. We quantify these feelings as adjusted payoffs in asymmetric games, where for different emotions, the payoff matrix takes the structure of that of either a prisoner's dilemma or a snowdrift game. Then we analyze the evolution of cooperation in a well-mixed population of agents, each of whom is associated with such a payoff matrix. At each time-step, an agent is randomly chosen from the population to update her strategy based on the myopic best-response update rule. According to the simulations, decreasing the feeling of being betrayed in a portion of agents does not necessarily increase the level of cooperation in the population. However, this resistance of the population against low-betrayal-level agents is effective only up to some extend that is explicitly determined by the payoff matrices and the number of agents associated with these matrices. Two other models are also considered where the betrayal factor of an agent fluctuates as a function of the number of cooperators and defectors that she encounters. Unstable behaviors are observed for the level of cooperation in these cases; however, we show that one can tune the parameters in the function to make the whole population become cooperative or defective.

  14. Signatures of Hot Molecular Hydrogen Absorption from Protoplanetary Disks. I. Non-thermal Populations

    Science.gov (United States)

    Hoadley, Keri; France, Kevin; Arulanantham, Nicole; Parke Loyd, R. O.; Kruczek, Nicholas

    2017-09-01

    The environment around protoplanetary disks (PPDs) regulates processes that drive the chemical and structural evolution of circumstellar material. We perform a detailed empirical survey of warm molecular hydrogen (H2) absorption observed against H i-Lyα (Lyα: λ1215.67) emission profiles for 22 PPDs, using archival Hubble Space Telescope ultraviolet (UV) spectra to identify H2 absorption signatures and quantify the column densities of H2 ground states in each sightline. We compare thermal equilibrium models of H2 to the observed H2 rovibrational level distributions. We find that, for the majority of targets, there is a clear deviation in high-energy states (T exc ≳ 20,000 K) away from thermal equilibrium populations (T(H2) ≳ 3500 K). We create a metric to estimate the total column density of non-thermal H2 (N(H2)nLTE) and find that the total column densities of thermal (N(H2)) and N(H2)nLTE correlate for transition disks and targets with detectable C iv-pumped H2 fluorescence. We compare N(H2) and N(H2)nLTE to circumstellar observables and find that N(H2)nLTE correlates with X-ray and far-UV luminosities, but no correlations are observed with the luminosities of discrete emission features (e.g., Lyα, C iv). Additionally, N(H2) and N(H2)nLTE are too low to account for the H2 fluorescence observed in PPDs, so we speculate that this H2 may instead be associated with a diffuse, hot, atomic halo surrounding the planet-forming disk. We create a simple photon-pumping model for each target to test this hypothesis and find that Lyα efficiently pumps H2 levels with T exc ≥ 10,000 K out of thermal equilibrium.

  15. Molecular identification and population dynamics of two species of Pemphigus (Homoptera: Pemphidae) on cabbage

    Institute of Scientific and Technical Information of China (English)

    Naiqi Chen; Tong-Xian Liu; Mamoudou Sétamou; J. Victor French; Eliezer S. Louzada

    2009-01-01

    The poplar petiole gall aphid, Pemphiguspopulitransversus Riley, has been one of the major pests on cruciferous vegetable in the Rio Grande Valley (LRGV) of Texas since the late 1940s. It normally migrates from poplar trees to cruciferous vegetables in the fall, and migrates back to the trees in early spring of the coming year. Some root-feeding aphids were found on cruciferous vegetables in late spring and early summer in 1998 and the following years. Those aphids have been identified as Pemphigus obesinymphae Moran. This discovery completely changed the current knowledge about the root-feeding aphids on cruciferous vegetables in the LRGV. Due to their small size, morphological and feeding similarities between P. populitransversus and P. obesinymphae, their identification and distinction are difficult. In this study, random amplification ofpolymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) were used to distinguish these two species over a period of time when the two species occurred together, or separately, in cabbage fields. The two species occurred on cabbage at different times of the year, and overlapped from October to June. From May to October, both species migrated to their primary hosts. The apterous aphids found on cabbage in winter contained mainly P. obesinymphae, whereas in early spring more apterous P. populitransversus were recovered. The root-feeding aphids would feed on cabbage plants as long as this host was available even during the hot, dry summer in the LRGV, although their populations were generally low. Both RAPD and AFLP techniques were efficient in discriminating the two species that showed obviously genetic variability. These molecular techniques confirmed the existence of the two aphid species in apterous samples collected from the soil in cabbage fields in the LRGV, and the results performed by RAPD were confirmed by AFLP. Furthermore, the results suggest that RAPD technique was a better choice despite its

  16. Molecular profile and clinical variables in BRCA1-positive breast cancers. A population-based study.

    Science.gov (United States)

    Musolino, Antonino; Michiara, Maria; Bella, Maria A; Naldi, Nadia; Zanelli, Paola; Bortesi, Beatrice; Capelletti, Marzia; Soldani, Linda; Camisa, Roberta; Martella, Eugenia; Franciosi, Vittorio; Savi, Mario; Neri, Tauro M; Ardizzoni, Andrea; Cascinu, Stefano

    2005-01-01

    To evaluate the clinical features of breast cancer patients with genetic susceptibility to this disease and to investigate the contribution of BRCA1 germline mutations to the phenotype of these tumors. We reviewed the clinical and pathological records of 102 women with suspected inherited susceptibility to breast cancer consecutively seen at the Genetic Oncology Service of Parma, Italy. Sixty-two patients with a high probability of harboring a germline, cancer-predisposing mutation were tested for BRCA1 mutations. Exon 11 was screened using the protein truncation test and detected mutations were confirmed by direct sequencing (DS). All other exons were analyzed by DS. Among the 62 patients with a completed mutation analysis, 48 (77.4%) had wild-type BRCA1, six (9.6%) had variants of unclear significance, eight (13%) had deleterious mutations. BRCA1-associated breast cancers (BABC) were significantly less likely to be diagnosed at stage I than breast cancers in women without mutations (12.5% vs 51%; P = 0.045), more likely to have a high proliferation rate (100% vs 24%, P < 0.001), and more likely to be histological grade 3 (100% vs 14%, P < 0.001), estrogen and progesterone receptor negative (87.5% vs 13%, P < 0.001; 75% vs 23%, P = 0.004), and p53 positive (87.5% vs 30%, P = 0.023). All tumors with BRCA1 mutations were HER-2/neu negative compared with 57% of the non-BRCA1 tumors (P = 0.04). There were no significant differences between BABC and non-BABC in 20-year relapse-free survival, 20-year event-free survival, and 20-year overall survival. In this population-based study, BABC seems to present with adverse molecular features when compared with non-BABC, although the prognosis appears to be similar.

  17. Mycobacterium tuberculosis population structure and molecular epidemiological analysis in Sucre municipality, Miranda state, Venezuela.

    Science.gov (United States)

    Patiño, Margareth A; Abadía, Edgar; Solalba Gómez; Maes, Mailis; Muñoz, Mariana; Gómez, Daniela; Guzmán, Patricia; Méndez, María Victoria; Ramirez, Carmen; Mercedes, España; de Waard, Jacobus; Takiff, Howard

    2014-12-01

    Sucre municipality is a large, densely populated marginal area in the eastern part of Caracas, Venezuela that consistently has more cases of tuberculosis than other municipalities in the country. To identify the neighborhoods in the municipality with the highest prevalence of tuberculosis, and determine whether the Mycobacterium tuberculosis strain distribution in this municipality is different from that previously found in the western part of Caracas and the rest of Venezuela, we collected data on all tuberculosis cases in the municipality diagnosed in 2005-6. We performed two separate molecular epidemiological studies, spoligotyping 44 strains in a first study, and spoligotyping 131 strains, followed by MIRU-VNTR 15 on 21 clustered isolates in the second. With spoligotyping, the most common patterns were Shared International Type SIT17 (21%); SIT42 (15%); SIT93 (11%); SIT20 (7%); SIT53 (6%), a distribution similar to other parts of Venezuela, except that SIT42 and SIT20 were more common. MIRU-VNTR 15 showed that six of seven SIT17 strains examined belonged to a large cluster previously found circulating in Venezuela, but all of the SIT42 strains were related to a cluster centered in the neighborhoods of Unión and Maca, with a MIRU-VNTR pattern not previously seen in Venezuela. It appears that a large percentage of the tuberculosis in the Sucre municipality is caused by the active transmission of two strain families centered within distinct neighborhoods, one reflecting communication with the rest of the country, and the other suggesting the insular, isolated nature of some sectors.

  18. Transfer of genetic therapy across human populations: molecular targets for increasing patient coverage in repeat expansion diseases.

    Science.gov (United States)

    Varela, Miguel A; Curtis, Helen J; Douglas, Andrew G L; Hammond, Suzan M; O'Loughlin, Aisling J; Sobrido, Maria J; Scholefield, Janine; Wood, Matthew J A

    2016-02-01

    Allele-specific gene therapy aims to silence expression of mutant alleles through targeting of disease-linked single-nucleotide polymorphisms (SNPs). However, SNP linkage to disease varies between populations, making such molecular therapies applicable only to a subset of patients. Moreover, not all SNPs have the molecular features necessary for potent gene silencing. Here we provide knowledge to allow the maximisation of patient coverage by building a comprehensive understanding of SNPs ranked according to their predicted suitability toward allele-specific silencing in 14 repeat expansion diseases: amyotrophic lateral sclerosis and frontotemporal dementia, dentatorubral-pallidoluysian atrophy, myotonic dystrophy 1, myotonic dystrophy 2, Huntington's disease and several spinocerebellar ataxias. Our systematic analysis of DNA sequence variation shows that most annotated SNPs are not suitable for potent allele-specific silencing across populations because of suboptimal sequence features and low variability (>97% in HD). We suggest maximising patient coverage by selecting SNPs with high heterozygosity across populations, and preferentially targeting SNPs that lead to purine:purine mismatches in wild-type alleles to obtain potent allele-specific silencing. We therefore provide fundamental knowledge on strategies for optimising patient coverage of therapeutics for microsatellite expansion disorders by linking analysis of population genetic variation to the selection of molecular targets.

  19. Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.

    2014-01-01

    The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers...... eight populations into four groups including Yorkshire, two wild populations, Mong Cai population and a group of four other indigenous populations. The Bayesian clustering with the admixture model implemented in Structure 2.1 indicated seven possible homogenous clusters among eight populations. From 79......% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations....

  20. Cooperative response of keratinocytes and melanocytes to UV radiation during PUVA therapy

    Science.gov (United States)

    Stolnitz, Mikhail M.; Baskakov, Pavel V.; Peshkova, Anna Y.

    1999-03-01

    The mathematical model of processes in UV-irradiated furocoumarin-sensitized epidermis is presented taking into account the mutual influence of keratinocytes and melanocytes populations. The model describes epidermis as a hierarchical structure on tissue (keratinocytes-melanocytes cooperation, melanin screen formation), cellular (proliferation and differentiation, transitions between subpopulations), subcellular (cell movement on mitotic cycle, generation, maturing and migration of melanosomes), and molecular (melanin synthesis, processes of DNA damage and repair, molecular signal transduction) levels.

  1. A molecular epidemiologic study of thalassemia using newborns' cord blood in a multiracial Asian population in Singapore: results and recommendations for a population screening program.

    Science.gov (United States)

    Kham, S K; Yin, Shirley Kham Kow; Quah, Thuan Chong; Loong, Ai Mei; Tan, Poh Lin; Fraser, Angus; Chong, S S; Chuan, Samuel Chong Siong; Yeoh, A E; Eng-Juh, Allen Yeoh

    2004-12-01

    DNA technology provides a new avenue to perform neonatal screening tests for single-gene diseases in populations of high frequency. Thalassemia is one of the high-frequency single-gene disorders affecting Singapore and many countries in the malaria belt. The authors explored the feasibility of using PCR-based diagnostic screening on 1,116 unselected sequential cord blood samples for neonatal screening. The cord blood samples were screened for the most common reported alpha- and beta-thalassemia mutations in each ethnic group (Chinese, Malays, and Indians) in a multiracial population. The carrier frequency for alpha-thalassemia mutations was about 6.4% in the Chinese (alpha deletions = 3.9%, alpha deletions = 2.5%), 4.8% in Malays, and 5.2% in Indians. Only alpha deletions were observed in the Chinese. The carrier frequency for beta-thalassemia mutations was 2.7% in the Chinese, 6.3% in Malays, and 0.7% in Indians. Extrapolating to the population distribution of Singapore, the authors found a higher overall expected carrier frequency for alpha- and beta-thalassemia mutations of 9% compared with a previous population study of 6% by phenotype. The highly accurate results make this molecular epidemiologic screening an ideal method to screen for and prevent severe thalassemia in high-risk populations.

  2. Conformational gel analysis and graphics: Measurement of side chain rotational isomer populations by NMR and molecular mechanics

    CERN Document Server

    Haydock, Christopher

    2007-01-01

    Conformational gel analysis and graphics systematically identifies and evaluates plausible alternatives to the side chain conformations found by conventional peptide or protein structure determination methods. The proposed analysis determines the populations of side chain rotational isomers and the probability distribution of these populations. The following steps are repeated for each side chain of a peptide or protein: first, extract the local molecular mechanics of side chain rotational isomerization from a single representative global conformation; second, expand the predominant set of rotational isomers to include all probable rotational isomers down to those that constitute just a small percentage of the population; and third, evaluate the constraints vicinal coupling constants and NOESY cross relaxation rates place on rotational isomer populations. In this article we apply conformational gel analysis to the cobalt glycyl-leucine dipeptide and detail the steps necessary to generalize the analysis to oth...

  3. ISSR markers for analysis of molecular diversity and genetic structure of Indian teak (Tectona grandis L.f. populations

    Directory of Open Access Journals (Sweden)

    Shamin Akhtar Ansari

    2012-06-01

    Full Text Available Inter simple sequence repeats (ISSR constitute a powerful dominant DNA molecular marker system used for diversity analysis, which is indispensable for making estimates of genetic base and demarcation of populations for undertaking conservation and improvement program offorest tree species. Twenty nine populations of teak (Tectona grandis L.f. were collected from central and peninsular India for analysis of genetic diversity and structure. Genomic DNA from ten randomly selected individuals of each population was extracted and amplified using five ISSR primers (UBC-801, 834, 880, 899 and 900. The primers showed 100% polymorphism. UBC-900 recorded the highest Nei's genetic diversity (0.32 to 0.40 and UBC-899 had the highest Shannon's Information Index (0.49 to 0.59. AMOVA revealed a very high intra-population genetic diversity (91%, in comparison to inter-population genetic diversity among states (6.17% and within states (2.77%, were also indirectly confirmed by large standard deviations associated with genetic diversity estimates for individual population, as well as poor bootstrapping values for most of the cluster nodes. However, UPGMA dendrogram revealed several clusters, with populations from central India being present almost in each cluster, making groups with populations of adjoining states and distant states. Nevertheless, the cluster analysis distinguished the drier teak populations of central India from the moist teak populations of south India, which was also confirmed by Principle Coordinate Analysis. The findings advocates the need not only for enhancing selection intensity for large number of plus trees, but also for laying out more number of in situ conservation plots within natural populations of each cluster for germplasm conservation of teak aimed at improving the teak productivity and quality in future. 

  4. Genetic Dissection of Sympatric Populations of Brown Planthopper, Nilaparvata lugens (Stål, Using DALP-PCR Molecular Markers

    Directory of Open Access Journals (Sweden)

    M. A. Latif

    2012-01-01

    Full Text Available Direct amplified length polymorphism (DALP combines the advantages of a high-resolution fingerprint method and also characterizing the genetic polymorphisms. This molecular method was also found to be useful in brown planthopper, Nilaparvata lugens species complex for the analysis of genetic polymorphisms. A total of 11 populations of Nilaparvata spp. were collected from 6 locations from Malaysia. Two sympatric populations of brown planthopper, N. lugens, one from rice and the other from a weed grass (Leersia hexandra, were collected from each of five locations. N. bakeri was used as an out group. Three oligonucleotide primer pairs, DALP231/DALPR′5, DALP234/DALPR′5, and DALP235/DALPR′5 were applied in this study. The unweighted pair group method with arithmetic mean (UPGMA dendrogram based on genetic distances for the 11 populations of Nilaparvata spp. revealed that populations belonging to the same species and the same host type clustered together irrespective of their geographical localities of capture. The populations of N. lugens formed into two distinct clusters, one was insects with high esterase activities usually captured from rice and the other was with low esterase activities usually captured from L. hexandra. N. bakeri, an out group, was the most isolated group. Analyses of principal components, molecular variance, and robustness also supported greatly to the findings of cluster analysis.

  5. Molecular epidemiology of hepatitis C infection in Cyprus within the general population and high-risk cohorts

    Directory of Open Access Journals (Sweden)

    Kostrikis Leondios G

    2011-10-01

    Full Text Available Abstract Background Initial data on the molecular epidemiology of HCV infection in Cyprus showed a highly polyphyletic infection and multiple points of introduction into the general population. The continuation and expansion of this investigation is presented here including high risk groups. Findings The samples include additional subjects from the general population, a group of inmates and HIV/HCV coinfected individuals, whose strains were amplified by RT-PCR and sequenced in partial Core-E1 and NS5B regions. The results confirm the broad genotype distribution and polyphyletic infection on the island, and no new subtypes were found. Monophyletic clusters between strains of the prisoners and the injecting drug users imply sharing of infected equipment, and highlight the risk of widespread transmission in these cohorts, although no spill-over to the general population was observed. Conclusions The results of this study underline the impact of population movements and high-risk population groups on the changing molecular epidemiology of HCV, with strains moving to Europe from Asia, Africa and Eastern Europe by means of immigration and modern transmission routes.

  6. Approaches for cytogenetic and molecular analyses of small flow-sorted cell populations from childhood leukemia bone marrow samples

    DEFF Research Database (Denmark)

    Obro, Nina Friesgaard; Madsen, Hans Ole; Ryder, Lars Peter

    2011-01-01

    defined cell populations with subsequent analyses of leukemia-associated cytogenetic and molecular marker. The approaches described here optimize the use of the same tube of unfixed, antibody-stained BM cells for flow-sorting of small cell populations and subsequent exploratory FISH and PCR-based analyses.......Discordances between minimal residual disease estimates obtained by different methods are a problem in childhood acute lymphoblastic leukemia. We aimed to optimize methods allowing the biological exploration of such discrepancies, i.e. the combination of flow-sorting of small immunophenotypically...

  7. Molecular ecology meets remote sensing: environmental drivers to population structure of humpback dolphins in the Western Indian Ocean.

    Science.gov (United States)

    Mendez, M; Subramaniam, A; Collins, T; Minton, G; Baldwin, R; Berggren, P; Särnblad, A; Amir, O A; Peddemors, V M; Karczmarski, L; Guissamulo, A; Rosenbaum, H C

    2011-10-01

    Genetic analyses of population structure can be placed in explicit environmental contexts if appropriate environmental data are available. Here, we use high-coverage and high-resolution oceanographic and genetic sequence data to assess population structure patterns and their potential environmental influences for humpback dolphins in the Western Indian Ocean. We analyzed mitochondrial DNA data from 94 dolphins from the coasts of South Africa, Mozambique, Tanzania and Oman, employing frequency-based and maximum-likelihood algorithms to assess population structure and migration patterns. The genetic data were combined with 13 years of remote sensing oceanographic data of variables known to influence cetacean dispersal and population structure. Our analyses show strong and highly significant genetic structure between all putative populations, except for those in South Africa and Mozambique. Interestingly, the oceanographic data display marked environmental heterogeneity between all sampling areas and a degree of overlap between South Africa and Mozambique. Our combined analyses therefore suggest the occurrence of genetically isolated populations of humpback dolphins in areas that are environmentally distinct. This study highlights the utility of molecular tools in combination with high-resolution and high-coverage environmental data to address questions not only pertaining to genetic population structure, but also to relevant ecological processes in marine species.

  8. The species flocks of East African cichlid fishes: recent advances in molecular phylogenetics and population genetics

    Science.gov (United States)

    Salzburger, Walter; Meyer, Axel

    With more than 3,000 species, the fish family Cichlidae is one of the most species-rich families of vertebrates. Cichlids occur in southern and central America, Africa, Madagascar, and India. The hotspot of their biodiversity is East Africa, where they form adaptive radiations composed of hundreds of endemic species in several lakes of various sizes and ages. The unparalleled species richness of East African cichlids has been something of a conundrum for evolutionary biologists and ecologists, since it has been in doubt whether these hundreds of species arose by allopatric speciation or whether it is necessary to invoke somewhat less traditional models of speciation, such as micro-allopatric, peripatric, or even sympatric speciation or evolution through sexual selection mediated by female choice. Ernst Mayr's analyses of these evolutionary uniquely diverse species assemblages have contributed to a more direct approach to this problem and have led to a deeper understanding of the patterns and processes that caused the formation of these huge groups of species. We review here recent molecular data on population differentiation and phylogenetics, which have helped to unravel, to some extent, the patterns and processes that led to the formation and ecological maintenance of cichlid species flocks. It is becoming apparent that sexually selected traits do play an important role in speciation in micro-allopatric or even sympatric settings. Species richness seems to be roughly correlated with the surface area, but not the age, of the lakes. We observe that the oldest lineages of a species flock of cichlids are often less species-rich and live in the open water or deepwater habitats. While the species flocks of the Lake Malawai and the Lake Victoria areas were shown to be monophyletic, the cichlid assemblage of Lake Tanganyika seems to consist of several independent species flocks. Cichlids emerge as an evolutionary model system in which many fundamental questions in

  9. Molecular genetic analysis of populations of Wohlfahrt's wound myiasis fly, Wohlfahrtia magnifica, in outbreak populations from Greece and Morocco.

    Science.gov (United States)

    Hall, M J R; Testa, J M; Smith, L; Adams, Z J O; Khallaayoune, K; Sotiraki, S; Stefanakis, A; Farkas, R; Ready, P D

    2009-06-01

    Wohlfahrt's wound myiasis fly, Wohlfahrtia magnifica (Schiner) (Diptera: Sarcophagidae), is the most important cause of traumatic myiasis in the southern Palaearctic region. Larval stages are obligate parasites and the wounds caused by infestations are very similar to those caused by Old and New World screwworm flies. During the last decade, W. magnifica appears to have expanded its range to parts of northern and central Morocco, and to Crete, Greece. Specimens of W. magnifica were collected in Morocco and Crete either as larvae (preserved in 80% ethanol) or as adults (dry-pinned). Comparison specimens were collected in Spain, Hungary and mainland Greece. A DNA fragment containing the 3' 715 base pairs of the mitochondrial cytochrome b gene was amplified by polymerase chain reaction from each of 132 larvae or adults of W. magnifica and the amplicons were directly sequenced and analysed phylogeographically. Twelve cytochrome b haplotypes were detected. All haplotypes from Morocco belonged to a lineage that included specimens from the Iberian peninsula, and restricted mixing of central and northern populations in Morocco was demonstrated. Cytochrome b haplotyping combined with an analysis of larval size provided clear evidence of multiple infestations of hosts in all geographical areas, with one quarter of wounds containing larvae from two to at least four females. More than 80% of specimens from Crete contained a haplotype predominating in mainland Greece and Hungary. Our survey indicated that wohlfahrtiosis was more widespread in northern and central Morocco than previously recorded by government veterinarians. However, the prevalence of wohlfahrtiosis was low (< 1%). The high genetic diversity of Moroccan populations is consistent with longterm endemicity, rather than recent introduction. Crete showed a higher prevalence of wohlfahrtiosis (< or = 15%) and less genetic diversity of W. magnifica, which is consistent with a recent introduction. The western and

  10. Mechanisms for similarity based cooperation

    Science.gov (United States)

    Traulsen, A.

    2008-06-01

    Cooperation based on similarity has been discussed since Richard Dawkins introduced the term “green beard” effect. In these models, individuals cooperate based on an aribtrary signal (or tag) such as the famous green beard. Here, two different models for such tag based cooperation are analysed. As neutral drift is important in both models, a finite population framework is applied. The first model, which we term “cooperative tags” considers a situation in which groups of cooperators are formed by some joint signal. Defectors adopting the signal and exploiting the group can lead to a breakdown of cooperation. In this case, conditions are derived under which the average abundance of the more cooperative strategy exceeds 50%. The second model considers a situation in which individuals start defecting towards others that are not similar to them. This situation is termed “defective tags”. It is shown that in this case, individuals using tags to cooperate exclusively with their own kind dominate over unconditional cooperators.

  11. ISSR markers for analysis of molecular diversity and genetic structure of Indian teak (Tectona grandis L.f. populations

    Directory of Open Access Journals (Sweden)

    S.A. Ansari

    2012-05-01

    Full Text Available Inter simple sequence repeats (ISSR constitute a powerful dominantDNA molecular marker system used for diversity analysis, which isindispensable for making estimates of genetic base and demarcation of populations for undertaking conservation and improvement program of forest tree species. Twenty nine populations of teak (Tectona grandis L.f. were collected from central and peninsular India for analysis of genetic diversity and structure. Genomic DNA from ten randomly selected individuals of each population was extracted and amplified using five ISSR primers(UBC-801, 834, 880, 899 and 900. The primers showed 100% polymorphism. UBC-900 recorded the highest Nei’s genetic diversity (0.32 to 0.40and UBC-899 had the highest Shannon’s Information Index (0.49 to 0.59. AMOVA revealed a very high intra-population genetic diversity (91%, in comparison to inter-population genetic diversity among states (6.17% and within states (2.77% which were also indirectly confirmed by large standard deviations associated with genetic diversity estimates for individual population, as well as poor bootstrapping values for most of the cluster nodes. However, UPGMA dendrogram revealed several clusters, with populationsfrom central India being present almost in each cluster, makinggroups with populations of adjoining states and distant states. Nevertheless,the cluster analysis distinguished the drier teak populations of central India from the moist teak populations of south India, which was also confirmed by Principle Coordinate Analysis. The findings advocates the need not only for enhancing selection intensity for large number of plus trees, but also for laying out more number of in situ conservation plots within natural populations of each cluster for germplasm conservation of teak aimed at improving the teak productivity and quality in future.

  12. ENHANCING COOPERATION

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    China and Japan can cooperate on a wide scope of issues, such as the organization of the Beijing Olympic Games next year and aid to Africa,said Ide Keiji, Minister of Public Relations, Press, Culture, Education and Sports and Spokesperson of the Embassy

  13. Comparison of Mutation Profiles in the Duchenne Muscular Dystrophy Gene among Populations: Implications for Potential Molecular Therapies

    Directory of Open Access Journals (Sweden)

    Luz Berenice López-Hernández

    2015-03-01

    Full Text Available Novel therapeutic approaches are emerging to restore dystrophin function in Duchenne Muscular Dystrophy (DMD, a severe neuromuscular disease characterized by progressive muscle wasting and weakness. Some of the molecular therapies, such as exon skipping, stop codon read-through and internal ribosome entry site-mediated translation rely on the type and location of mutations. Hence, their potential applicability worldwide depends on mutation frequencies within populations. In view of this, we compared the mutation profiles of the populations represented in the DMD Leiden Open-source Variation Database with original data from Mexican patients (n = 162 with clinical diagnosis of the disease. Our data confirm that applicability of exon 51 is high in most populations, but also show that differences in theoretical applicability of exon skipping may exist among populations; Mexico has the highest frequency of potential candidates for the skipping of exons 44 and 46, which is different from other populations (p < 0.001. To our knowledge, this is the first comprehensive comparison of theoretical applicability of exon skipping targets among specific populations.

  14. Comparison of mutation profiles in the Duchenne muscular dystrophy gene among populations: implications for potential molecular therapies.

    Science.gov (United States)

    López-Hernández, Luz Berenice; Gómez-Díaz, Benjamín; Luna-Angulo, Alexandra Berenice; Anaya-Segura, Mónica; Bunyan, David John; Zúñiga-Guzman, Carolina; Escobar-Cedillo, Rosa Elena; Roque-Ramírez, Bladimir; Ruano-Calderón, Luis Angel; Rangel-Villalobos, Héctor; López-Hernández, Julia Angélica; Estrada-Mena, Francisco Javier; García, Silvia; Coral-Vázquez, Ramón Mauricio

    2015-03-09

    Novel therapeutic approaches are emerging to restore dystrophin function in Duchenne Muscular Dystrophy (DMD), a severe neuromuscular disease characterized by progressive muscle wasting and weakness. Some of the molecular therapies, such as exon skipping, stop codon read-through and internal ribosome entry site-mediated translation rely on the type and location of mutations. Hence, their potential applicability worldwide depends on mutation frequencies within populations. In view of this, we compared the mutation profiles of the populations represented in the DMD Leiden Open-source Variation Database with original data from Mexican patients (n = 162) with clinical diagnosis of the disease. Our data confirm that applicability of exon 51 is high in most populations, but also show that differences in theoretical applicability of exon skipping may exist among populations; Mexico has the highest frequency of potential candidates for the skipping of exons 44 and 46, which is different from other populations (p < 0.001). To our knowledge, this is the first comprehensive comparison of theoretical applicability of exon skipping targets among specific populations.

  15. The Dose Makes The Cooperation

    CERN Document Server

    Cetin, Uzay

    2016-01-01

    Explaining cooperation is one of the greatest challenges for basic scientific research. We proposed an agent-based model to study co-evolution of memory and cooperation. In our model, reciprocal agents with limited memory size play Prisoner's Dilemma Game iteratively. The characteristic of the environment, whether it is threatening or not, is embedded in the payoff matrix. Our findings are as follows. (i) Memory plays a critical role in the protection of cooperation. (ii) In the absence of threat, subsequent generations loose their memory and are consequently invaded by defectors. (iii) In contrast, the presence of an appropriate level of threat triggers the emergence of a self-protection mechanism for cooperation within subsequent generations. On the evolutionary level, memory size acts like an immune response of the population against aggressive defection. (iv) Even more extreme threat results again in defection. Our findings boil down to the following: The dose of the threat makes the cooperation.

  16. Applications of Multiple Nuclear Genes to the Molecular Phylogeny, Population Genetics and Hybrid Identification in the Mangrove Genus Rhizophora.

    Directory of Open Access Journals (Sweden)

    Yongmei Chen

    Full Text Available The genus Rhizophora is one of the most important components of mangrove forests. It is an ideal system for studying biogeography, molecular evolution, population genetics, hybridization and conservation genetics of mangroves. However, there are no sufficient molecular markers to address these topics. Here, we developed 77 pairs of nuclear gene primers, which showed successful PCR amplifications across all five Rhizophora species and sequencing in R. apiculata. Here, we present three tentative applications using a subset of the developed nuclear genes to (I reconstruct the phylogeny, (II examine the genetic structure and (III identify natural hybridization in Rhizophora. Phylogenetic analyses support the hypothesis that Rhizophora had disappeared in the Atlantic-East Pacific (AEP region and was re-colonized from the IWP region approximately 12.7 Mya. Population genetics analyses in four natural populations of R. apiculata in Hainan, China, revealed extremely low genetic diversity, strong population differentiation and extensive admixture, suggesting that the Pleistocene glaciations, particularly the last glacial maximum, greatly influenced the population dynamics of R. apiculata in Hainan. We also verified the hybrid status of a morphologically intermediate individual between R. apiculata and R. stylosa in Hainan. Based on the sequences of five nuclear genes and one chloroplast intergenic spacer, this individual is likely to be an F1 hybrid, with R. stylosa as its maternal parent. The nuclear gene markers developed in this study should be of great value for characterizing the hybridization and introgression patterns in other cases of this genus and testing the role of natural selection using population genomics approaches.

  17. Molecular structure of Mycobacterium tuberculosis population in Russia and its interaction with neighboring countries

    Directory of Open Access Journals (Sweden)

    I Mokrousov

    2015-01-01

    Large-scale SNP or WGS population-based studies targeting strains from indigenous populations and, eventually, analysis of ancient DNA will better test these hypotheses. Host genetics factors likely play the most prominent role in the differential dissemination of particular M. tuberculosis genotypes.

  18. Molecular markers reveal limited population genetic structure in a North American corvid, Clark's nutcracker (Nucifraga columbiana).

    Science.gov (United States)

    Dohms, Kimberly M; Burg, Theresa M

    2013-01-01

    The genetic impact of barriers and Pleistocene glaciations on high latitude resident species has not been widely investigated. The Clark's nutcracker is an endemic North American corvid closely associated with Pinus-dominated forests. The nutcracker's encompasses known barriers to dispersal for other species, and glaciated and unglaciated areas. Clark's nutcrackers also irruptively disperse long distances in search of pine seed crops, creating the potential for gene flow among populations. Using the highly variable mitochondrial DNA control region, seven microsatellite loci, and species distribution modeling, we examined the effects of glaciations and dispersal barriers on population genetic patterns and population structure of nutcrackers. We sequenced 900 bp of mitochondrial control region for 169 individuals from 15 populations and analysed seven polymorphic microsatellite loci for 13 populations across the Clark's nutcracker range. We used species distribution modeling and a range of phylogeographic analyses to examine evolutionary history. Clark's nutcracker populations are not highly differentiated throughout their range, suggesting high levels of gene flow among populations, though we did find some evidence of isolation by distance and peripheral isolation. Our analyses suggested expansion from a single refugium after the last glacial maximum, but patterns of genetic diversity and paleodistribution modeling of suitable habitat were inconclusive as to the location of this refugium. Potential barriers to dispersal (e.g. mountain ranges) do not appear to restrict gene flow in Clark's nutcracker, and postglacial expansion likely occurred quickly from a single refugium located south of the ice sheets.

  19. Molecular markers reveal limited population genetic structure in a North American corvid, Clark's nutcracker (Nucifraga columbiana.

    Directory of Open Access Journals (Sweden)

    Kimberly M Dohms

    Full Text Available The genetic impact of barriers and Pleistocene glaciations on high latitude resident species has not been widely investigated. The Clark's nutcracker is an endemic North American corvid closely associated with Pinus-dominated forests. The nutcracker's encompasses known barriers to dispersal for other species, and glaciated and unglaciated areas. Clark's nutcrackers also irruptively disperse long distances in search of pine seed crops, creating the potential for gene flow among populations. Using the highly variable mitochondrial DNA control region, seven microsatellite loci, and species distribution modeling, we examined the effects of glaciations and dispersal barriers on population genetic patterns and population structure of nutcrackers. We sequenced 900 bp of mitochondrial control region for 169 individuals from 15 populations and analysed seven polymorphic microsatellite loci for 13 populations across the Clark's nutcracker range. We used species distribution modeling and a range of phylogeographic analyses to examine evolutionary history. Clark's nutcracker populations are not highly differentiated throughout their range, suggesting high levels of gene flow among populations, though we did find some evidence of isolation by distance and peripheral isolation. Our analyses suggested expansion from a single refugium after the last glacial maximum, but patterns of genetic diversity and paleodistribution modeling of suitable habitat were inconclusive as to the location of this refugium. Potential barriers to dispersal (e.g. mountain ranges do not appear to restrict gene flow in Clark's nutcracker, and postglacial expansion likely occurred quickly from a single refugium located south of the ice sheets.

  20. The nearly neutral and selection theories of molecular evolution under the fisher geometrical framework: substitution rate, population size, and complexity.

    Science.gov (United States)

    Razeto-Barry, Pablo; Díaz, Javier; Vásquez, Rodrigo A

    2012-06-01

    The general theories of molecular evolution depend on relatively arbitrary assumptions about the relative distribution and rate of advantageous, deleterious, neutral, and nearly neutral mutations. The Fisher geometrical model (FGM) has been used to make distributions of mutations biologically interpretable. We explored an FGM-based molecular model to represent molecular evolutionary processes typically studied by nearly neutral and selection models, but in which distributions and relative rates of mutations with different selection coefficients are a consequence of biologically interpretable parameters, such as the average size of the phenotypic effect of mutations and the number of traits (complexity) of organisms. A variant of the FGM-based model that we called the static regime (SR) represents evolution as a nearly neutral process in which substitution rates are determined by a dynamic substitution process in which the population's phenotype remains around a suboptimum equilibrium fitness produced by a balance between slightly deleterious and slightly advantageous compensatory substitutions. As in previous nearly neutral models, the SR predicts a negative relationship between molecular evolutionary rate and population size; however, SR does not have the unrealistic properties of previous nearly neutral models such as the narrow window of selection strengths in which they work. In addition, the SR suggests that compensatory mutations cannot explain the high rate of fixations driven by positive selection currently found in DNA sequences, contrary to what has been previously suggested. We also developed a generalization of SR in which the optimum phenotype can change stochastically due to environmental or physiological shifts, which we called the variable regime (VR). VR models evolution as an interplay between adaptive processes and nearly neutral steady-state processes. When strong environmental fluctuations are incorporated, the process becomes a selection model

  1. Social learning in cooperative dilemmas.

    Science.gov (United States)

    Lamba, Shakti

    2014-07-22

    Helping is a cornerstone of social organization and commonplace in human societies. A major challenge for the evolutionary sciences is to explain how cooperation is maintained in large populations with high levels of migration, conditions under which cooperators can be exploited by selfish individuals. Cultural group selection models posit that such large-scale cooperation evolves via selection acting on populations among which behavioural variation is maintained by the cultural transmission of cooperative norms. These models assume that individuals acquire cooperative strategies via social learning. This assumption remains empirically untested. Here, I test this by investigating whether individuals employ conformist or payoff-biased learning in public goods games conducted in 14 villages of a forager-horticulturist society, the Pahari Korwa of India. Individuals did not show a clear tendency to conform or to be payoff-biased and are highly variable in their use of social learning. This variation is partly explained by both individual and village characteristics. The tendency to conform decreases and to be payoff-biased increases as the value of the modal contribution increases. These findings suggest that the use of social learning in cooperative dilemmas is contingent on individuals' circumstances and environments, and question the existence of stably transmitted cultural norms of cooperation.

  2. Polyfunctional and IFN-γ monofunctional human CD4+ T cell populations are molecularly distinct

    Science.gov (United States)

    Burel, Julie G.; Apte, Simon H.; Groves, Penny L.; McCarthy, James S.; Doolan, Denise L.

    2017-01-01

    Pathogen-specific polyfunctional T cell responses have been associated with favorable clinical outcomes, but it is not known whether molecular differences exist between polyfunctional and monofunctional cytokine-producing T cells. Here, we report that polyfunctional CD4+ T cells induced during Plasmodium falciparum (P. falciparum) blood-stage infection in humans have a unique transcriptomic profile compared with IFN-γ monofunctional CD4+ T cells and, thus, are molecularly distinct. The 14-gene signature revealed in P. falciparum–reactive polyfunctional T cells is associated with cytokine signaling and lymphocyte chemotaxis, and systems biology analysis identified IL-27 as an upstream regulator of the polyfunctional gene signature. Importantly, the polyfunctional gene signature is largely conserved in Influenza-reactive polyfunctional CD4+ T cells, suggesting that polyfunctional T cells have core characteristics independent of pathogen specificity. This study provides the first evidence to our knowledge that consistent molecular differences exist between polyfunctional and monofunctional CD4+ T cells. PMID:28194431

  3. The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts.

    Science.gov (United States)

    MacLean, R Craig; Hall, Alex R; Perron, Gabriel G; Buckling, Angus

    2010-06-01

    Despite efforts from a range of disciplines, our ability to predict and combat the evolution of antibiotic resistance in pathogenic bacteria is limited. This is because resistance evolution involves a complex interplay between the specific drug, bacterial genetics and both natural and treatment ecology. Incorporating details of the molecular mechanisms of drug resistance and ecology into evolutionary models has proved useful in predicting the dynamics of resistance evolution. However, putting these models to practical use will require extensive collaboration between mathematicians, molecular biologists, evolutionary ecologists and clinicians.

  4. Excited cooper pairs

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Arrietea, M. G.; Solis, M. A.; De Llano, M. [Universidad Nacional Autonoma de Mexico, Mexico, D.F (Mexico)

    2001-02-01

    Excited cooper pairs formed in a many-fermion system are those with nonzero total center-of mass momentum (CMM). They are normally neglected in the standard Bardeen-Cooper-Schrieffer (BCS) theory of superconductivity for being too few compared with zero CMM pairs. However, a Bose-Einstein condensation picture requires both zero and nonzero CMM pairs. Assuming a BCS model interaction between fermions we determine the populations for all CMM values of Cooper pairs by actually calculating the number of nonzero-CMM pairs relative to that of zero-CMM ones in both 2D and 3D. Although this ratio decreases rapidly with CMM, the number of Cooper pairs for any specific CMM less than the maximum (or breakup of the pair) momentum turns out to be typically larger than about 95% of those with zero-CMM at zero temperature T. Even at T {approx}100 K this fraction en 2D is still as large as about 70% for typical quasi-2D cuprate superconductor parameters. [Spanish] Los pares de cooper excitados formados en un sistema de muchos electrones, son aquellos con momentos de centro de masa (CMM) diferente de cero. Normalmente estos no son tomados en cuenta en la teoria estandar de la superconductividad de Bardeen-Cooper-Schrieffer (BCS) al suponer que su numero es muy pequeno comparados con los pares de centro de masa igual a cero. Sin embargo, un esquema de condensacion Bose-Einstein requiere de ambos pares, con CMM cero y diferente de cero. Asumiendo una interaccion modelo BCS entre los fermiones, determinamos la poblacion de pares cooper con cada uno de todos los posibles valores del CMM calculando el numero de pares con momentos de centro de masa diferente de cero relativo a los pares de CMM igual a cero, en 2D y 3D. Aunque esta razon decrece rapidamente con el CMM, el numero de pares de cooper para cualquier CMM especifico menor que el momento maximo (o rompimiento de par) es tipicamente mas grande que el 95% de aquellos con CMM cero. Aun a T {approx}100 K esta fraccion en 2D es

  5. Molecular characterization and population structure of the macaw palm, Acrocomia aculeata (Arecaceae), ex situ germplasm collection using microsatellites markers.

    Science.gov (United States)

    Lanes, Éder C M; Motoike, Sérgio Y; Kuki, Kacilda N; Nick, Carlos; Freitas, Renata D

    2015-01-01

    The Acrocomia aculeata is one of the most promising plants for sustainable production of renewable energy. In order to understand patterns of the distribution of the allelic diversity of A. aculeata ex situ germplasm collection, the present study investigated the hypothesis that the genetic variability of the accessions may match their geographical origin. A genotypic analysis of 77 A. aculeata accessions was conducted with 6 simple sequence repeat markers. A high degree of molecular diversity among the accessions was found, with an average of 9 alleles per locus and a polymorphic information content with a mean of 0.76. A total of 4 clusters was identified by the Bayesian analysis of population structure. The highest subpopulation diversity was identified in Pop1, mainly formed by accessions from State of Mato Grosso do Sul. The populations Pop2A, Pop2B, and Pop2C, all from the State of Minas Gerais, showed high genetic variability as determined by a higher F st, and a wide genetic variance, which were identified within and among the population by analysis of molecular variance. Based on our results and on Vavilov's theory on crop origins, one possible diversity center for A. aculeata is proposed to be in a region in southeast Brazil.

  6. Molecular population genetics of the NADPH cytochrome P450 reductase (CPR) gene in Anopheles minimus.

    Science.gov (United States)

    Srivastava, Hemlata; Huong, Ngo Thi; Arunyawat, Uraiwan; Das, Aparup

    2014-08-01

    Development of insecticide resistance (IR) in mosquito vectors is a primary huddle to malaria control program. Since IR has genetic basis, and genes constantly evolve with response to environment for adaptation to organisms, it is important to know evolutionary pattern of genes conferring IR in malaria vectors. The mosquito Anopheles minimus is a major malaria vector of the Southeast (SE) Asia and India and is susceptible to all insecticides, and thus of interest to know if natural selection has shaped variations in the gene conferring IR. If not, the DNA fragment of such a gene could be used to infer population structure and demography of this species of malaria vector. We have therefore sequenced a ~569 bp DNA segment of the NADPH cytochrome P450 reductase (CPR) gene (widely known to confer IR) in 123 individuals of An. minimus collected in 10 different locations (eight Indian, one Thai and one Vietnamese). Two Indian population samples were completely mono-morphic in the CPR gene. In general, low genetic diversity was found with no evidence of natural selection in this gene. The data were therefore analyzed to infer population structure and demography of this species. The 10 populations could be genetically differentiated into four different groups; the samples from Thailand and Vietnam contained high nucleotide diversity. All the 10 populations conform to demographic equilibrium model with signature of past population expansion in four populations. The results in general indicate that the An. minimus mosquitoes sampled in the two SE Asian localities contain several genetic characteristics of being parts of the ancestral population.

  7. Comparative evaluation of the FilmArray meningitis/encephalitis molecular panel in a pediatric population.

    Science.gov (United States)

    Graf, Erin H; Farquharson, Maria Victoria; Cárdenas, Ana María

    2017-01-01

    We compared an FDA cleared molecular meningitis/encephalitis panel to lab developed viral PCRs and bacterial culture. Of the 67 viral PCR or bacterial culture-positive samples, 92.5% were positive for the same target by the panel. Of the 66 negative samples tested, no targets were detected by the panel, for an agreement of 96.2%.

  8. Sharing the sandbox: Evolutionary mechanisms that maintain bacterial cooperation.

    Science.gov (United States)

    Bruger, Eric; Waters, Christopher

    2015-01-01

    Microbes are now known to participate in an extensive repertoire of cooperative behaviors such as biofilm formation, production of extracellular public-goods, group motility, and higher-ordered multicellular structures. A fundamental question is how these cooperative tasks are maintained in the face of non-cooperating defector cells. Recently, a number of molecular mechanisms including facultative participation, spatial sorting, and policing have been discovered to stabilize cooperation. Often these different mechanisms work in concert to reinforce cooperation. In this review, we describe bacterial cooperation and the current understanding of the molecular mechanisms that maintain it.

  9. Morphology and molecular phylogeny of an Antarctic population of Paraholosticha muscicola (Kahl, 1932) Wenzel, 1953 (Ciliophora, Hypotricha)

    Science.gov (United States)

    Jung, Jae-Ho; Park, Kyung-Min; Min, Gi-Sik; Berger, Helmut; Kim, Sanghee

    2015-12-01

    The morphology of an Antarctic soil population of Paraholosticha muscicola, type species of Paraholosticha, is described from life and after protargol preparation. The data agree rather well with that of relevant descriptions, but the total variability of several features is relatively high in this species. Paraholosticha ovata and P. lichenicola are very likely junior synonyms. In addition, we sequenced the SSU rRNA gene of P. muscicola and thus we can estimate for the first time the phylogenetic position of a member of the Keronopsidae, the sole hypotrichs that divide in cysts. The molecular data basically support the position derived from morphological concepts, that is, P. muscicola branches off outside the Dorsomarginalia because kinety fragmentation and dorsomarginal rows are lacking. However, as in many other molecular analyses, discrepancies with morphology-based hypothesis are present. The misclassification of Paraholosticha and its sister-group Keronopsis in the Keronidae, with Kerona pediculus as type species, is discussed.

  10. Cooperative strings and glassy interfaces.

    Science.gov (United States)

    Salez, Thomas; Salez, Justin; Dalnoki-Veress, Kari; Raphaël, Elie; Forrest, James A

    2015-07-07

    We introduce a minimal theory of glass formation based on the ideas of molecular crowding and resultant string-like cooperative rearrangement, and address the effects of free interfaces. In the bulk case, we obtain a scaling expression for the number of particles taking part in cooperative strings, and we recover the Adam-Gibbs description of glassy dynamics. Then, by including thermal dilatation, the Vogel-Fulcher-Tammann relation is derived. Moreover, the random and string-like characters of the cooperative rearrangement allow us to predict a temperature-dependent expression for the cooperative length ξ of bulk relaxation. Finally, we explore the influence of sample boundaries when the system size becomes comparable to ξ. The theory is in agreement with measurements of the glass-transition temperature of thin polymer films, and allows quantification of the temperature-dependent thickness hm of the interfacial mobile layer.

  11. Population Redistribution among Multiple Electronic States of Molecular Nitrogen Ions in Strong Laser Fields

    CERN Document Server

    Yao, Jinping; Chu, Wei; Zeng, Bin; Wu, Chengyin; Lu, Ruifeng; Li, Ziting; Xie, Hongqiang; Li, Guihua; Yu, Chao; Wang, Zhanshan; Jiang, Hongbing; Gong, Qihuang; Cheng, Ya

    2015-01-01

    We carry out a combined theoretical and experimental investigation on the population distributions in the ground and excited states of tunnel ionized N2 molecules at various driver wavelengths in the near- and mid-infrared range. Our results reveal that efficient couplings (i.e., population exchanges) between the ground state and the excited states occur in strong laser fields. The couplings result in the population inversion between the ground and the excited states at the wavelengths near 800 nm, which is verified by our experiment by observing the amplification of a seed at ~391 nm. The result provides insight into the mechanism of free-space nitrogen ion lasers generated in remote air with strong femtosecond laser pulses.

  12. [Social cooperatives in Italy].

    Science.gov (United States)

    Villotti, P; Zaniboni, S; Fraccaroli, F

    2014-06-01

    This paper describes the role of social cooperatives in Italy as a type of economic, non-profit organization and their role in contributing to the economic and social growth of the country. The purpose of this paper is to learn more about the experience of the Italian social cooperatives in promoting the work integration process of disadvantaged workers, especially those suffering from mental disorders, from a theoretical and an empirical point of view. Social enterprise is the most popular and consolidated legal and organizational model for social enterprises in Italy, introduced by Law 381/91. Developed during the early 1980s, and formally recognized by law in the early 1990s, social cooperatives aim at pursuing the general interest of the community to promote the human needs and social inclusion of citizens. They are orientated towards aims that go beyond the interest of the business owners, the primary beneficiary of their activities is the community, or groups of disadvantaged people. In Italy, Law 381/91 distinguishes between two categories of social cooperatives, those producing goods of social utility, such as culture, welfare and educational services (A-type), and those providing economic activities for the integration of disadvantaged people into employment (B-type). The main purpose of B-type social cooperatives is to integrate disadvantaged people into the open labour market. This goal is reached after a period of training and working experience inside the firm, during which the staff works to improve both the social and professional abilities of disadvantaged people. During the years, B-type social co-ops acquired a particular relevance in the care of people with mental disorders by offering them with job opportunities. Having a job is central in the recovery process of people suffering from mental diseases, meaning that B-type social co-ops in Italy play an important rehabilitative and integrative role for this vulnerable population of workers. The

  13. Molecular analysis of the metabolic rates of discrete subsurface populations of sulfate reducers

    Energy Technology Data Exchange (ETDEWEB)

    Miletto, M.; Williams, K.H.; N' Guessan, A.L.; Lovley, D.R.

    2011-04-01

    Elucidating the in situ metabolic activity of phylogenetically diverse populations of sulfate-reducing microorganisms that populate anoxic sedimentary environments is key to understanding subsurface ecology. Previous pure culture studies have demonstrated that transcript abundance of dissimilatory (bi)sulfite reductase genes is correlated with the sulfate reducing activity of individual cells. To evaluate whether expression of these genes was diagnostic for subsurface communities, dissimilatory (bi)sulfite reductase gene transcript abundance in phylogenetically distinct sulfate-reducing populations was quantified during a field experiment in which acetate was added to uranium-contaminated groundwater. Analysis of dsrAB sequences prior to the addition of acetate indicated that Desulfobacteraceae, Desulfobulbaceae, and Syntrophaceae-related sulfate reducers were the most abundant. Quantifying dsrB transcripts of the individual populations suggested that Desulfobacteraceae initially had higher dsrB transcripts per cell than Desulfobulbaceae or Syntrophaceae populations, and that the activity of Desulfobacteraceae increased further when the metabolism of dissimilatory metal reducers competing for the added acetate declined. In contrast, dsrB transcript abundance in Desulfobulbaceae and Syntrophaceae remained relatively constant, suggesting a lack of stimulation by added acetate. The indication of higher sulfate-reducing activity in the Desulfobacteraceae was consistent with the finding that Desulfobacteraceae became the predominant component of the sulfate-reducing community. Discontinuing acetate additions resulted in a decline in dsrB transcript abundance in the Desulfobacteraceae. These results suggest that monitoring transcripts of dissimilatory (bi)sulfite reductase genes in distinct populations of sulfate reducers can provide insight into the relative rates of metabolism of different components of the sulfate-reducing community and their ability to respond to

  14. Molecular evidence of Wolbachia infection in natural populations of tropical odonates.

    Science.gov (United States)

    Thipaksorn, Apisit; Jamnongluk, Wanwisa; Kittayapong, Pattamaporn

    2003-10-01

    Wolbachia are endosymbiotic bacteria that cause reproductive alterations in numerous arthropod species. Using a PCR-based method, we found that, out of 33 odonate species, four species were infected with Wolbachia. This finding represents the first record of Wolbachia infection in tropical odonates. Identical wsp gene sequences were found in the Wolbachia-infected common odonate species, Agriocnemis f. femina, collected from different locations in Thailand. The infection frequencies in several natural populations suggest that replacement of uninfected populations by Wolbachia-infected ones has recently occurred in this damselfly species.

  15. Cooperation on Social Networks and Its Robustness

    CERN Document Server

    Antonioni, Alberto

    2012-01-01

    In this work we have used computer models of social-like networks to show by extensive numerical simulations that cooperation in evolutionary games can emerge and be stable on this class of networks. The amounts of cooperation reached are at least as much as in scale-free networks but here the population model is more realistic. Cooperation is robust with respect to different strategy update rules, population dynamics, and payoff computation. Only when straight average payoff is used or there is high strategy or network noise does cooperation decrease in all games and disappear in the Prisoner's Dilemma.

  16. Molecular anthropology meets genetic medicine to treat blindness in the North African Jewish population: human gene therapy initiated in Israel.

    Science.gov (United States)

    Banin, Eyal; Bandah-Rozenfeld, Dikla; Obolensky, Alexey; Cideciyan, Artur V; Aleman, Tomas S; Marks-Ohana, Devora; Sela, Malka; Boye, Sanford; Sumaroka, Alexander; Roman, Alejandro J; Schwartz, Sharon B; Hauswirth, William W; Jacobson, Samuel G; Hemo, Itzhak; Sharon, Dror

    2010-12-01

    The history of the North African Jewish community is ancient and complicated with a number of immigration waves and persecutions dramatically affecting its population size. A decade-long process in Israel of clinical-molecular screening of North African Jews with incurable autosomal recessive blindness led to the identification of a homozygous splicing mutation (c.95-2A > T; IVS2-2A > T) in RPE65, the gene encoding the isomerase that catalyzes a key step in the retinoid-visual cycle, in patients from 10 unrelated families. A total of 33 patients (four now deceased) had the severe childhood blindness known as Leber congenital amaurosis (LCA), making it the most common cause of retinal degeneration in this population. Haplotype analysis in seven of the patients revealed a shared homozygous region, indicating a population-specific founder mutation. The age of the RPE65 founder mutation was estimated to have emerged 100-230 (mean, 153) generations ago, suggesting it originated before the establishment of the Jewish community in North Africa. Individuals with this RPE65 mutation were characterized with retinal studies to determine if they were candidates for gene replacement, the recent and only therapy to date for this otherwise incurable blindness. The step from molecular anthropological studies to application of genetic medicine was then taken, and a representative of this patient subgroup was treated with subretinal rAAV2-RPE65 gene therapy. An increase in vision was present in the treated area as early as 15 days after the intervention. This process of genetically analyzing affected isolated populations as a screen for gene-based therapy suggests a new paradigm for disease diagnosis and treatment.

  17. Molecular and Population Analysis of Natural Selection on the Human Haptoglobin Duplication

    OpenAIRE

    Rodriguez, Santiago; Williams, Dylan M; Guthrie, Philip AI; McArdle, Wendy L.; Smith, George Davey; Evans, David M.; Gaunt, Tom R.; Day, Ian NM

    2012-01-01

    Haptoglobin binds free haemoglobin that prevents oxidative damage produced by haemolysis. There is a copy number variant (CNV) in the haptoglobin gene (HP) consisting of two alleles, Hp1 (no duplication), and Hp2 (1.7kb duplication involving two exons). The spread of the Hp2 allele is believed to have taken place under selective pressures conferred by malaria resistance. However, molecular evidence is lacking and Hp did not emerge in genomewide SNPs surveys for evidence of selection. In Europ...

  18. Efficacy and tolerance of an injectable medical device containing stable hybrid cooperative complexes of high- and low-molecular-weight hyaluronic acid: a monocentric 16 weeks open-label evaluation

    Directory of Open Access Journals (Sweden)

    Sparavigna A

    2016-09-01

    Full Text Available Adele Sparavigna, Beatrice Tenconi DermIng srl, Clinical Research and Bioengineering Institute, Monza, MB, Italy Background: An injectable medical device containing stable hybrid cooperative complexes of high- and low-molecular-weight hyaluronic acid (HA has been developed with characteristics suited for a global improvement of facial esthetics. Objective: To evaluate the HA product performance in improving some key facial esthetic features. The study employed clinical scales, subjective evaluations, and facial skin objective measurements. Methods: A single Italian site treated 64 female subjects aged 38–60 years, with injections at five predetermined points, on each side of the face, with a 4-week time lapse between the first and the second product administration. Subjects were evaluated after 4, 8, 12, and 16 weeks, using validated clinical scales, subjective evaluation, and objective quantitative outcome measures. Assessment of esthetic results included photographic documentation. Results: Both the clinical and subjective assessments, and the majority of objective instrumental parameters indicated an improvement throughout the study and were already significant at week 4 or 8 and were still significant at week 16 (3 months after the second treatment. Minor and temporary local skin reactions were observed in 23% of subjects at the site of the injections, and the global judgment on tolerability was good or excellent, both in the investigators’ opinion and volunteers’ self-evaluation. Conclusion: Both subjective and objective improvement of the facial parameters was consistent with the bio-remodeling purpose, and persistent and still statistically significant at the end of the study. The tolerability and safety profile of the product were judged good or excellent both by investigators and volunteers. This study supports the claim for bio-remodeling of these stable hybrid cooperative complexes of low- and high-molecular-weight HA. Keywords

  19. Morphometric and molecular analyses for populations of Palaemon longirostris and Palaemon garciacidi (Crustacea, Palaemonidae): Evidence for a single species

    Science.gov (United States)

    Cartaxana, Alexandra

    2015-03-01

    Authors have disagreed on the taxonomic status of the white prawns along the coasts of the Northeast Atlantic Ocean and the Mediterranean Sea. The present study compares variation in morphology and mtDNA in populations of white prawns, identified as Palaemon longirostris and P. garciacidi, from the United Kingdom, The Netherlands, France, Spain, Portugal, Morocco and Tunisia. Differences in morphology among populations were tested using a multiple discriminant analyses (DA) on morphometric data. In order to resolve variation in mtDNA, 16S and COI mitochondrial (mt) genes were used. The morphometric analyses do not support their separation into distinct species, since individual prawns could not be assigned unequivocally to one of the various studied populations and a geographic pattern could be detected only in females. Molecular data corroborate the morphological analyses, since no geographic structure was found and the levels of sequence divergence observed among haplotypes from distinct populations (0.1-0.8%) are consistent with other 16S and COI intraspecific divergences of decapod crustaceans. Therefore, findings from this study do not support the distinction of P. longirostris and P. garciacidi as different species.

  20. Anatomical and molecular consequences of Unilateral Naris Closure on two populations of olfactory sensory neurons expressing defined odorant receptors.

    Science.gov (United States)

    Molinas, Adrien; Aoudé, Imad; Soubeyre, Vanessa; Tazir, Bassim; Cadiou, Hervé; Grosmaitre, Xavier

    2016-07-28

    Mammalian olfactory sensory neurons (OSNs), the primary elements of the olfactory system, are located in the olfactory epithelium lining the nasal cavity. Exposed to the environment, their lifespan is short. Consequently, OSNs are regularly regenerated and several reports show that activity strongly modulates their development and regeneration: the peripheral olfactory system can adjust to the amount of stimulus through compensatory mechanisms. Unilateral naris occlusion (UNO) was frequently used to investigate this mechanism at the entire epithelium level. However, there is little data regarding the effects of UNO at the cellular level, especially on individual neuronal populations expressing a defined odorant receptor. Here, using UNO during the first three postnatal weeks, we analyzed the anatomical and molecular consequences of sensory deprivation in OSNs populations expressing the MOR23 and M71 receptors. The density of MOR23-expressing neurons is decreased in the closed side while UNO does not affect the density of M71-expressing neurons. Using Real Time qPCR on isolated neurons, we observed that UNO modulates the transcript levels for transduction pathway proteins (odorant receptors, CNGA2, PDE1c). The transcripts modulated by UNO will differ between populations depending on the receptor expressed. These results suggest that sensory deprivation will have different effects on different OSNs' populations. As a consequence, early experience will shape the functional properties of OSNs differently depending on the type of odorant receptor they express.

  1. Molecular analysis of the human faecal archaea in a southern Indian population

    Indian Academy of Sciences (India)

    SANDYA B RANI; RAMADASS BALAMURUGAN; BALAKRISHNAN S RAMAKRISHNA

    2017-03-01

    Archaea are an important constituent of the human gut microbiota, but there is no information on human gut archaea inan Indian population. In this study, faecal samples were obtained from different age groups (neonatal babies, preschoolchildren, school-going children, adolescents, adults and elderly) of a southern Indian population, and from atribal population also resident in southern India). 16S rRNA gene sequences specific to Archaea were amplified frompooled faecal DNA in each group, sequenced, and aligned against the NCBI database. Of the 806 adequate sequencesin the study, most aligned with 22 known sequences. There were 9 novel sequences in the present study. All sequenceswere deposited in the GenBank nucleotide sequence database with the following accession numbers: KF607113 -KF607918. Methanobrevibacter was the most prevalent genus among all the age groups accounting for 98% inneonates, 96% in post-weaning, and 100% each in preschool, school and adult population. In the elderly, Methanobrevibacteraccounted for 96% and in tribal adults, 99% of the clones belonged to Methanobrevibacter genus. Othergenera detected included Caldisphaera, Halobaculum, Methanosphaeraand Thermogymnomonas. Methanobrevibactersmithii predominated in all age groups, accounting for 749 (92.9%) of the 806 sequences. Archaea can befound in the faeces of southern Indian residents immediately after birth. Methanobrevibacter smithii was the dominantfaecal archeon in all age groups, with other genera being found at the extremes of age.

  2. Molecular Characterization of a Xiphinema hunaniense Population with Morphometric Data of all Four Juvenile Stages.

    Science.gov (United States)

    Wu, Y; Zheng, J; Robbins, R T

    2007-03-01

    A population of Xiphinema hunanienseWang and Wu, 1992 with all four juvenile stages was found in the rhizosphere of Pinus sp. in Hangzhou, Zhejiang, China. Morphometrics of 18 females and 35 juveniles of this population are given herein. Detailed morphology and morphometrics of the four juvenile stages are provided. Further comparisons based on morphometrics of the population with previous studies of the females and the first-stage juveniles of X. hunaniense with X. radicicola are given, and morphological variation in X. hunaniense populations are discussed. A revised polytomous key code of Loof and Luc (1990) for X. hunaniense identification is provided, i.e., A1- B4- C4- D4/5- E1- F2(3)- G2- H2-I3- J4- K2- L1. In addition, the sequence of the D2 and D3 expansion region of the 28S rRNA gene was analyzed and compared with sequences of closely related species downloaded from the NCBI database. Cluster analysis of sequences confirmed and supported the species identifications.

  3. Where are the polyps? Molecular identification, distribution and population differentiation of

    NARCIS (Netherlands)

    van Walraven, L.; Driessen, F.; van Bleijswijk, J.; Bol, A.; Luttikhuizen, P.C.; Coolen, J.; Bos, O.G.; Gittenberger, A.; Schrieken, N.; Langenberg, V.T.; van der Veer, H.W.

    2016-01-01

    For many species of metagenic jellyfish the location of the benthic polyps is unknown. To gain insight in the distribution, species composition and population structure of scyphozoan jellyfish polyps in the southern North Sea area, polyp samples were collected from natural and artificial substrates

  4. Where are the polyps? Molecular identification, distribution and population differentiation of

    NARCIS (Netherlands)

    van Walraven, L.; Driessen, F.; van Bleijswijk, J.; Bol, A.; Luttikhuizen, P.C.; Coolen, J.; Bos, O.G.; Gittenberger, A.; Schrieken, N.; Langenberg, V.T.; van der Veer, H.W.

    2016-01-01

    For many species of metagenic jellyfish the location of the benthic polyps is unknown. To gain insight in the distribution, species composition and population structure of scyphozoan jellyfish polyps in the southern North Sea area, polyp samples were collected from natural and artificial substrates

  5. Cooperativity in beryllium bonds.

    Science.gov (United States)

    Alkorta, Ibon; Elguero, José; Yáñez, Manuel; Mó, Otilia

    2014-03-07

    A theoretical study of the beryllium bonded clusters of the (iminomethyl)beryllium hydride and (iminomethyl)beryllium fluoride [HC(BeX)=NH, X = H, F] molecules has been carried out at the B3LYP/6-311++G(3df,2p) level of theory. Linear and cyclic clusters have been characterized up to the decamer. The geometric, energetic, electronic and NMR properties of the clusters clearly indicate positive cooperativity. The evolution of the molecular properties, as the size of the cluster increases, is similar to those reported in polymers held together by hydrogen bonds.

  6. Asymptomatic bacteriuria: prevalence rates of causal microorganisms, etiology of infection in different patient populations, and recent advances in molecular detection.

    Science.gov (United States)

    Ipe, Deepak S; Sundac, Lana; Benjamin, William H; Moore, Kate H; Ulett, Glen C

    2013-09-01

    Bacteriuria, or the presence of bacteria in urine, is associated with both asymptomatic and symptomatic urinary tract infection and underpins much of the dynamic of microbial colonization of the urinary tract. The prevalence of bacteriuria in dissimilar patient groups such as healthy adults, institutionalized elderly, pregnant women, and immune-compromised patients varies widely. In addition, assessing the importance of 'significant bacteriuria' in infected individuals represents a diagnostic challenge, partly due to various causal microorganisms, and requires careful consideration of the distinct etiologies of bacteriuria in different populations and circumstances. Recent molecular discoveries have revealed how some bacterial traits can enable organisms to grow in human urine, which, as a fitness adaptation, is likely to influence the progression of bacteriuria in some individuals. In this review, we comprehensively analyze currently available data on the prevalence of causal organisms with a focus on asymptomatic bacteriuria in dissimilar populations. We evaluate recent advances in the molecular detection of bacteriuria from a diagnostic viewpoint and briefly discuss the potential benefits and some of the challenges of these approaches. Overall, this review provides an update on the comparative prevalence and etiology of bacteriuria from both microbiological and clinical perspectives. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  7. Multilocus sequence typing as a tool for studying the molecular epidemiology and population structure of Brachyspira hyodysenteriae.

    Science.gov (United States)

    La, Tom; Phillips, Nyree D; Harland, Belinda L; Wanchanthuek, Phatthanaphong; Bellgard, Matthew I; Hampson, David J

    2009-09-18

    The purpose of this study was to develop and apply a multilocus sequence typing (MLST) scheme to study the molecular epidemiology of Brachyspira hyodysenteriae, the aetiological agent of swine dysentery. Sequences of seven conserved genomic loci were examined in 111 B. hyodysenteriae strains. Fifty-eight of these previously had been analysed by multilocus enzyme electrophoresis (MLEE), and for some the results of pulsed field gel electrophoresis (PFGE), restriction endonuclease analysis (REA) and/or serotyping also were available. The discriminatory power of these methods was compared. The strains were divided into 67 sequence types (STs) and 46 amino acid types (AATs) by MLST. The Index of Association value was significantly different from zero, indication that the population was clonal. Eleven clonal complexes (Cc) comprising between 2 and 10 STs were recognised. A population snapshot based on AATs placed 77.5% of the isolates from 30 of the AATs into one major cluster. The founder type AAT9 included 13 strains from nine STs that were isolated in Australia, Sweden, Germany and Belgium, including one from a mallard. The MLST results were generally comparable to those produced by MLEE. The MLST system had a similar discriminatory power to PFGE, but was more discriminatory than REA, MLEE or serotyping. MLST data provided evidence for likely transmission of strains between farms, but also for the occurrence of temporal "micro-evolution" of strains on individual farms. Overall, the MLST system proved to be a useful new tool for investigating the molecular epidemiology and diversity of B. hyodysenteriae.

  8. Could molecular effects of Caulerpa racemosa metabolites modulate the impact on fish populations of Diplodus sargus?

    Science.gov (United States)

    Gorbi, S; Giuliani, M E; Pittura, L; d'Errico, G; Terlizzi, A; Felline, S; Grauso, L; Mollo, E; Cutignano, A; Regoli, F

    2014-05-01

    The green alga Caulerpa racemosa is a non-native, invasive species in the Mediterranean, and an important stressor for several native organisms. The algal capacity to produce secondary metabolites has been suggested to modulate success of the C. racemosa invasion, although many of potentially involved biological pathways still remain unexplored. In this respect, the aim of the present study was to investigate some molecular and cellular effects in the white seabream Diplodus sargus, an ecologically key species, which included the alien C. racemosa in its diet. Organisms were sampled in 2 seasonal periods from 3 locations of Southern Italy, each characterized by different levels of algal abundance. The level of caulerpin, one of the main secondary algal metabolites, in fish tissues has been used as an indicator of the trophic exposure to the seaweed and related with molecular and cellular responses. Chemical analyses indicated that fish from invaded sites can accumulate caulerpin, with liver concentrations ranging from a few up to hundreds of μg/g. Biomarkers analyses revealed only limited alterations of the main antioxidant defences, such as glutathione reductase and levels of glutathione; on the other hand, increased enzymatic activities of cytochrome P450, glutathione S-transferases and acyl CoA oxidase, as well as enhanced gene transcription for peroxisome proliferator-activated receptor alpha, cytochrome P4501A and vitellogenin 1 were observed in fish more exposed to C. racemosa as indicated by liver concentrations of caulerpin higher than 50 μg/g. Despite a direct molecular relationship with this algal metabolite could not be established, our results suggest that a C. racemosa enriched diet can modulate biotransformation and fatty acids metabolism of D. sargus. Assessing whether similar effects represent short- or long-term effects will be of crucial importance to understand consequences on the general health status and reproductive performance of

  9. THE MAGELLANIC MOPRA ASSESSMENT (MAGMA). I. THE MOLECULAR CLOUD POPULATION OF THE LARGE MAGELLANIC CLOUD

    Energy Technology Data Exchange (ETDEWEB)

    Wong, Tony; Chu, You-Hua; Gruendl, Robert A.; Looney, Leslie W.; Seale, Jonathan; Welty, Daniel E. [Astronomy Department, University of Illinois, Urbana, IL 61801 (United States); Hughes, Annie; Maddison, Sarah [Centre for Astrophysics and Supercomputing, Swinburne University of Technology, Hawthorn, VIC 3122 (Australia); Ott, Juergen [National Radio Astronomy Observatory, P.O. Box O, 1003 Lopezville Road, Socorro, NM 87801 (United States); Muller, Erik; Fukui, Yasuo; Kawamura, Akiko; Mizuno, Yoji [Department of Astrophysics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Pineda, Jorge L. [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109-8099 (United States); Bernard, Jean-Philippe; Paradis, Deborah [CNRS, IRAP, 9 Av. Colonel Roche, BP 44346, F-31028 Toulouse cedex 4 (France); Henkel, Christian [Max-Planck-Institut fuer Radioastronomie, Auf dem Huegel 69, D-53121 Bonn (Germany); Klein, Ulrich, E-mail: wongt@astro.illinois.edu [Argelander Institut fuer Astronomie, Universitaet Bonn, Auf dem Huegel 71, D-53121 Bonn (Germany)

    2011-12-01

    We present the properties of an extensive sample of molecular clouds in the Large Magellanic Cloud (LMC) mapped at 11 pc resolution in the CO(1-0) line. Targets were chosen based on a limiting CO flux and peak brightness as measured by the NANTEN survey. The observations were conducted with the ATNF Mopra Telescope as part of the Magellanic Mopra Assessment. We identify clouds as regions of connected CO emission and find that the distributions of cloud sizes, fluxes, and masses are sensitive to the choice of decomposition parameters. In all cases, however, the luminosity function of CO clouds is steeper than dN/dL{proportional_to}L{sup -2}, suggesting that a substantial fraction of mass is in low-mass clouds. A correlation between size and linewidth, while apparent for the largest emission structures, breaks down when those structures are decomposed into smaller structures. We argue that the correlation between virial mass and CO luminosity is the result of comparing two covariant quantities, with the correlation appearing tighter on larger scales where a size-linewidth relation holds. The virial parameter (the ratio of a cloud's kinetic to self-gravitational energy) shows a wide range of values and exhibits no clear trends with the CO luminosity or the likelihood of hosting young stellar object (YSO) candidates, casting further doubt on the assumption of virialization for molecular clouds in the LMC. Higher CO luminosity increases the likelihood of a cloud harboring a YSO candidate, and more luminous YSOs are more likely to be coincident with detectable CO emission, confirming the close link between giant molecular clouds and massive star formation.

  10. Molecular crowding causes narrowing of population heterogeneity and restricts internal dynamics in a protein

    Science.gov (United States)

    Mondal, Samsuzzoha; Kallianpur, Mamata V.; Udgaonkar, Jayant B.; Krishnamoorthy, G.

    2016-03-01

    Macromolecular crowding is a distinguishing property of intracellular media. Knowledge on the structure and dynamics of a protein in a crowded environment is essential for a complete understanding of its function. Reduction in intermolecular space could cause structural and functional alterations. Here, we have studied a model protein barstar to see how polyethylene glycol (PEG)-induced crowding affects its various structural states (native, unfolded and molten-globule-like) with different extents of change in conformational heterogeneity. Intramolecular distances and distance distributions were determined by time-resolved Förster resonance energy transfer from Trp53 to several acceptor sites by analysis of fluorescence decay kinetics using the Maximum Entropy Method. We observed PEG-induced narrowing of population distributions along with shifting of populations towards more compact states. Structural compactness also resulted in the slowing down of internal dynamics of the protein as revealed by fluorescence anisotropy decay kinetics of the fluorophore IAEDANS attached at several sites.

  11. Molecular typing of HLA class II antigens in a São Paulo population

    Directory of Open Access Journals (Sweden)

    Goldberg A.C.

    1998-01-01

    Full Text Available In the present paper we show data obtained from a normal population with a racially mixed profile typical of the city of São Paulo, State of São Paulo. Data were generated with polymerase chain reaction using sequence specific primers (PCR-SSP for HLA-DRB and polymerase chain reaction followed by hybridization with sequence specific oligonucleotide probes (PCR-SSO for HLA-DQA1 and HLA-DQB1 loci. HLA-DRB, DQA1, DQB1 and haplotype frequencies as well as common linkage disequilibria were found. This population was also shown to be in genetic equilibrium according to the Hardy-Weinberg law. HLA-DR typing of a normal sample from the city of Porto Velho, State of Rondonia, highlighted the importance of different sets of HLA profiles found in other regions of the country. This database provides essential information for screening studies of disease associations, forensic analyses and transplants.

  12. Introduction of HIV type 1 into an isolated population: molecular epidemiologic study from Greenland

    DEFF Research Database (Denmark)

    Madsen, Tina V; Leitner, Thomas; Lohse, Nicolai

    2007-01-01

    Introduction of HIV-1 into a population may not always give rise to a subsequent epidemic. Greenland is an isolated and sparsely populated island in The Danish Kingdom. We aimed to estimate the number of introductions of HIV-1 into Greenland, the number of subsequent epidemics, and the countries...... from which the virus was introduced. Phylogenetic analyses were performed on three regions of HIV-1 (gag, pol, and env) in samples from 70 Greenlandic patients. Furthermore, we included gene sequences from contemporary Danish HIV-1-infected patients and sequences from the Los Alamos HIV Sequence...... Database. All Greenlandic sequences were subtype B except one sequence found to be a recombinant (probably CRF13). Sequence clusters in the phylogenetic trees indicated that there had been at least nine introductions of HIV-1 into Greenland. One cluster, supported by bootstrap values of 81, 76, and 96...

  13. Prevalence and molecular characterization of Glucose-6-Phosphate dehydrogenase deficient variants among the Kurdish population of Northern Iraq

    Directory of Open Access Journals (Sweden)

    Jamal Shakir AR

    2010-07-01

    Full Text Available Abstract Background Glucose-6-Phosphate dehydrogenase (G6PD is a key enzyme of the pentose monophosphate pathway, and its deficiency is the most common inherited enzymopathy worldwide. G6PD deficiency is common among Iraqis, including those of the Kurdish ethnic group, however no study of significance has ever addressed the molecular basis of this disorder in this population. The aim of this study is to determine the prevalence of this enzymopathy and its molecular basis among Iraqi Kurds. Methods A total of 580 healthy male Kurdish Iraqis randomly selected from a main regional premarital screening center in Northern Iraq were screened for G6PD deficiency using methemoglobin reduction test. The results were confirmed by quantitative enzyme assay for the cases that showed G6PD deficiency. DNA analysis was performed on 115 G6PD deficient subjects, 50 from the premarital screening group and 65 unrelated Kurdish male patients with documented acute hemolytic episodes due to G6PD deficiency. Analysis was performed using polymerase chain reaction/restriction fragment length polymorphism for five deficient molecular variants, namely G6PD Mediterranean (563 C→T, G6PD Chatham (1003 G→A, G6PD A- (202 G→A, G6PD Aures (143 T→C and G6PD Cosenza (1376 G→C, as well as the silent 1311 (C→T mutation. Results Among 580 random Iraqi male Kurds, 63 (10.9% had documented G6PD deficiency. Molecular studies performed on a total of 115 G6PD deficient males revealed that 101 (87.8% had the G6PD Mediterranean variant and 10 (8.7% had the G6PD Chatham variant. No cases of G6PD A-, G6PD Aures or G6PD Cosenza were identified, leaving 4 cases (3.5% uncharacterized. Further molecular screening revealed that the silent mutation 1311 was present in 93/95 of the Mediterranean and 1/10 of the Chatham cases. Conclusions The current study revealed a high prevalence of G6PD deficiency among Iraqi Kurdish population of Northern Iraq with most cases being due to the G6PD

  14. Molecular Studies of HTLV-1 in a Newly Recognized High Risk Population (AIDS).

    Science.gov (United States)

    1992-06-16

    have identified a high risk of HTLV-I infection in Iranian Jews originating from the city of Mashad in Khurusan, northeastern Iran. This group seems...Iranian Jews seems to be substantially lower than that among Mashadis. The explanation may be geographic, and Mashad may be within a previously...this population unless USAMRD, or any other federal agency, may 13 - help us with a proper connection with the Mashad University or any other

  15. Molecular genetic variability, population structure and mating system in tropical forages

    Directory of Open Access Journals (Sweden)

    Melissa Garcia

    2013-09-01

    Full Text Available Microsatellite (SSR markers were developed for the following tropical forage species, using accessions available from the plant genetic resources (PGR collections held by EMBRAPA (Brazilian Agricultural Research Corporation: Brachiaria brizantha, B. humidicola, Panicum maximum, Paspalum spp., Stylosanthes capitata, S. guianensis, S. macrocephala, Calopogonium mucunoides and Centrosema spp. The markers were used to analyze population structure and genetic diversity, evolution and origin of the genetic variability in the center of origin, mating systems and genetic resources in EMBRAPA’s germplasm bank. The results shed light on the amount of genetic variation within and between populations, revealed the need in some cases for further plant collection to adequately represent the species in PGR collections, allowed us to assemble core collections (subsets of the total collections that should contain most of the available diversity and (in the case of the legumes showed the need to avoid unwanted outcrossing when regenerating conserved material. The data will allow plant breeders to better select accessions for hybrid production, discriminate between genotypes and use marker-assisted selection in breeding programs. Our results will also underpin the construction of genetic maps, mapping of genes of agronomic interest and numerous other studies on genetic variability, population structure, gene flow and reproductive systems for the tropical forage species studied in this work.

  16. Molecular Population Structure of Junonia Butterflies from French Guiana, Guadeloupe, and Martinique

    Directory of Open Access Journals (Sweden)

    Amber P. Gemmell

    2014-01-01

    Full Text Available Up to 9 described species of Junonia butterflies occur in the Americas, but authorities disagree due to species similarities, geographical and seasonal variability, and possible hybridization. In dispute is whether Caribbean Junonia are conspecific with South American species. Cytochrome oxidase I (COI barcodes, wingless (wg sequences, and Randomly Amplified Fingerprints (RAF were studied to reveal Junonia population structure in French Guiana, Guadeloupe, Martinique, and Argentina. Phylogenetic analysis of COI recovered 2 haplotype groups, but most Junonia species can have either haplotype, so COI barcodes are ambiguous. Analysis of nuclear wingless alleles revealed geographic patterns but did not identify Junonia species. Nuclear RAF genotyping distinguished 11 populations of Junonia arranged into 3 clusters. Gene flow occurs within clusters but is limited between clusters. One cluster included all Argentinian samples. Two clusters included samples from French Guiana, Martinique, and Guadeloupe and appear to be divided by larval host plant use (Lamiales versus Scrophulariales. Many Junonia taxa were distributed across populations, possibly reflecting patterns of genetic exchange. We had difficulty distinguishing between the Caribbean forms J. zonalis and J. neildi, but we demonstrate that Caribbean Junonia are genetically distinct from South American J. evarete and J. genoveva, supporting the taxonomic hypothesis that they are heterospecific.

  17. Molecular Pathology and Haplotype Analysis of Wilson Disease in Mediterranean Populations

    Science.gov (United States)

    Figus, Annalena; Angius, Andrea; Loudianos, Georgios; Bertini, Chiara; Dessì, Valeria; Loi, Angela; Deiana, Manila; Lovicu, Mario; Olla, Nazario; Sole, Gabriella; De Virgiliis, Stefano; Lilliu, Franco; Farci, Anna Maria Giulia; Nurchi, Annamaria; Giacchino, Raffaella; Barabino, Arrigo; Marazzi, Maria; Zancan, Lucia; Greggio, Nella A.; Marcellini, Matilde; Solinas, Antonello; Deplano, Angelo; Barbera, Cristiana; Devoto, Marcella; Ozsoylu, Sinasi; Kocak, Nurten; Akar, Nejat; Karayalcin, Selin; Mokini, Vahe; Cullufi, Paskal; Balestrieri, Angelo; Cao, Antonio; Pirastu, Mario

    1995-01-01

    We analyzed mutations and defined the chromosomal haplotype in 127 patients of Mediterranean descent who were affected by Wilson disease (WD), 39 Sardinians, 49 Italians, 33 Turks, and 6 Albanians. Haplotypes were derived by use of the microsatellite markers D13S301, D13S296, D13S297, and D13S298, which are linked to the WD locus. There were five common haplotypes in Sardinians, three in Italians, and two in Turks, which accounted for 85%, 32%, and 30% of the WD chromosomes, respectively. We identified 16 novel mutations: 8 frameshifts, 7 missense mutations, and 1 splicing defect. In addition, we detected the previously described mutations: 2302insC, 3404delC, Argl320ter, Gly944-Ser, and Hisl070Gin. Of the new mutations detected, two, the 1515insT on haplotype I and 2464delC on haplotype XVI, accounted for 6% and 13%, respectively, of the mutations in WD chromosomes in the Sardinian population. Mutations H1070Q, 2302insC, and 2533delA represented 13%, 8%, and 8%, respectively, of the mutations in WD chromosomes in other Mediterranean populations. The remaining mutations were rare and limited to one or two patients from different populations. Thus, WD results from some frequent mutations and many rare defects. ImagesFigure 1 PMID:8533760

  18. Molecular pathology and haplotype analysis of Wilson disease in Mediterranean populations

    Energy Technology Data Exchange (ETDEWEB)

    Figus, A.; Farcia, A.M.G.; Nurchi, A. [Universita degli Studi di Cagliari (Italy)] [and others

    1995-12-01

    We analyzed mutations and defined the chromosomal haplotype in 127 patients of Mediterranean descent who were affected in Wilson disease (WD): 39 Sardinians, 49 Italians, 33 Turks, and 6 Albanians. Haplotypes were derived by use of the microsatellite markers D13S301, D13S296, D13S297, and D13S298, which are linked to the WD locus. There were five common haplotypes in Sardinians, three in Italians, and two in Turks, which accounted for 85%, 32%, and 30% of the WD chromosomes, respectively. We identified 16 novel mutations: 8 frameshifts, 7 missense mutations, and 1 splicing defect. In addition, we detected the previously described mutations: 2302insC, 3404delC, Arg1320ter, Gly944Ser, and His1070Gin. Of the new mutations detected, two, the 1515insT on haplotype I and 2464delC on haplotype XVI, accounted for 6% and 13%, respectively, of the mutations in WD chromsomes in the Sardinian populations. Mutations H1070Q, 2302insC, and 2533delA represented 13%, 8%, and 8%, respectively, of the mutations in WD chromsomes in other Mediterranean populations. The remaining mutations were rare and limited to one or two patients from different populations. Thus, WD results from some frequent mutations and many rare defects. 28 refs., 1 fig., 3 tabs.

  19. Assessment of molecular testing in fine-needle aspiration biopsy samples: an experience in a Chinese population.

    Science.gov (United States)

    Liu, Shu; Gao, Aibo; Zhang, Bingfei; Zhang, Zhaoxia; Zhao, Yanru; Chen, Pu; Ji, Meiju; Hou, Peng; Shi, Bingyin

    2014-10-01

    Fine-needle aspiration biopsy remains the mainstay for preoperative examination of thyroid nodules; however, it does not provide a definite diagnosis in up to 25% of nodules. Considerable studies have been performed to identify molecular markers to resolve this diagnostic dilemma. The aim of this study was to establish the distribution and frequency of common genetic alterations in a comprehensive set of benign and malignant thyroid nodules, and to determine the feasibility and role of testing for a panel of genetic alterations in improving the accuracy of cytology diagnosis in a Chinese population. This study was conducted in 314 thyroid nodules comprising 104 papillary thyroid carcinomas, 13 suspicious nodules, 52 indeterminate nodules, and 145 benign nodules. Point mutations and RET/PTC rearrangements, were evaluated by pyrosequencing and TaqMan real-time PCR, respectively. After surgery, 115 nodules were confirmed as conventional papillary thyroid carcinoma and 102 (88.70%) of these nodules harbored either the BRAF(V600E) mutation (76.52%) or RET/PTC rearrangements (12.17%). RAS mutation was found in 1 (33.33%) follicular thyroid carcinoma, 1 (14.29%) follicular thyroid adenoma and 4 (10%) goiter nodules. With cytology and molecular testing, the diagnostic accuracy was further increased to 98.82% in papillary thyroid carcinoma diagnosis, and was preoperatively increased to 76.92% and 84.00%, respectively, in nodules with suspicious and indeterminate cytology. In conclusion, molecular testing of a panel of genetic alterations in fine-needle aspiration biopsy can be effectively performed in clinical practice. It enhances the accuracy of cytology and is of particular value for indeterminate nodules in the Chinese population. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. Metabolite toxicity determines the pace of molecular evolution within microbial populations.

    Science.gov (United States)

    Lilja, Elin E; Johnson, David R

    2017-02-14

    The production of toxic metabolites has shaped the spatial and temporal arrangement of metabolic processes within microbial cells. While diverse solutions to mitigate metabolite toxicity have evolved, less is known about how evolution itself is affected by metabolite toxicity. We hypothesized that the pace of molecular evolution should increase as metabolite toxicity increases. At least two mechanisms could cause this. First, metabolite toxicity could increase the mutation rate. Second, metabolite toxicity could increase the number of available mutations with large beneficial effects that selection could act upon (e.g., mutations that provide tolerance to toxicity), which consequently would increase the rate at which those mutations increase in frequency. We tested this hypothesis by experimentally evolving the bacterium Pseudomonas stutzeri under denitrifying conditions. The metabolite nitrite accumulates during denitrification and has pH-dependent toxic effects, which allowed us to evolve P. stutzeri at different magnitudes of nitrite toxicity. We demonstrate that increased nitrite toxicity results in an increased pace of molecular evolution. We further demonstrate that this increase is generally due to an increased number of available mutations with large beneficial effects and not to an increased mutation rate. Our results demonstrate that the production of toxic metabolites can have important impacts on the evolutionary processes of microbial cells. Given the ubiquity of toxic metabolites, they could also have implications for understanding the evolutionary histories of biological organisms.

  1. Prenatal molecular diagnosis of β-thalassemia and sickle cell anemia in the Syrian population.

    Science.gov (United States)

    Murad, Hossam; Moassas, Faten; Jarjour, Rami; Mukhalalaty, Yasser; Al-Achkar, Walid

    2014-01-01

    Our objective was to evaluate the prenatal diagnosis (PND) of β-thalassemia (β-thal) and sickle cell anemia in Syria. Mutations detected from blood of at-risk couples and 55 amniotic fluid samples collected at the second trimester of pregnancy (14-22 weeks' gestation) were characterized. Molecular screening and direct DNA sequencing of the HBB gene was carried out. DNA analyses showed 14 affected fetuses (25.45%), 32 (58.18%) carriers and eight (14.54%) normal fetuses. It appears that 20.0% of individuals carried the sickle cell anemia mutation and 80.0% carried the β-thal mutation. Thirteen different known mutations were detected in the fetuses. The most common mutations were: IVS-II-1 (G > A), codon 39 (C > T)], IVS-I-110 (G > A), IVS-I-1 (G > A) and IVS-I-5 (G > C). The Hb S [β6(A3)Glu → Val; HBB: c.20A > T] mutation was the only abnormal hemoglobin (Hb) that was found. The results point to a successful future for PND of β-thal and sickle cell anemia in Syria, using a rapid and accurate molecular method. We hope that this method will be used as a common application approach to decrease the incidence of β-thal major (β-TM).

  2. Simulating a base population in honey bee for molecular genetic studies

    Directory of Open Access Journals (Sweden)

    Gupta Pooja

    2012-06-01

    Full Text Available Abstract Background Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding value estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has a distinct genetic and reproductive biology. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee. Results Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1 the position of markers on each chromosome, (2 allele frequency, (3 χ2 statistics for Hardy-Weinberg equilibrium, (4 a sorted list of markers with a minor allele frequency less than or equal to the input value, (5 average r2 values of linkage disequilibrium between all simulated marker loci pair for all generations and (6 average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. Conclusion We developed a software program that takes into account the genetic and reproductive biology specific to the honey bee

  3. Molecular diversity, population structure, and linkage disequilibrium in a worldwide collection of tobacco (Nicotiana tabacum L. germplasm

    Directory of Open Access Journals (Sweden)

    Fricano Agostino

    2012-03-01

    Full Text Available Abstract Background The goals of our study were to assess the phylogeny and the population structure of tobacco accessions representing a wide range of genetic diversity; identify a subset of accessions as a core collection capturing most of the existing genetic diversity; and estimate, in the tobacco core collection, the extent of linkage disequilibrium (LD in seven genomic regions using simple sequence repeat (SSR markers. To this end, a collection of accessions were genotyped with SSR markers. Molecular diversity was evaluated and LD was analyzed across seven regions of the genome. Results A genotyping database for 312 tobacco accessions was profiled with 49 SSR markers. Principal Coordinate Analysis (PCoA and Bayesian cluster analysis revealed structuring of the tobacco population with regard to commercial classes and six main clades were identified, which correspond to "Oriental", Flue-Cured", "Burley", "Dark", "Primitive", and "Other" classes. Pairwise kinship was calculated between accessions, and an overall low level of co-ancestry was observed. A set of 89 genotypes was identified that captured the whole genetic diversity detected at the 49 loci. LD was evaluated on these genotypes, using 422 SSR markers mapping on seven linkage groups. LD was estimated as squared correlation of allele frequencies (r2. The pattern of intrachromosomal LD revealed that in tobacco LD extended up to distances as great as 75 cM with r2 > 0.05 or up to 1 cM with r2 > 0.2. The pattern of LD was clearly dependent on the population structure. Conclusions A global population of tobacco is highly structured. Clustering highlights the accessions with the same market class. LD in tobacco extends up to 75 cM and is strongly dependent on the population structure.

  4. New Insights into the Molecular Epidemiology and Population Genetics of Schistosoma mansoni in Ugandan Pre-school Children and Mothers

    Science.gov (United States)

    Betson, Martha; Sousa-Figueiredo, Jose C.; Kabatereine, Narcis B.; Stothard, J. Russell

    2013-01-01

    Significant numbers of pre-school children are infected with Schistosoma mansoni in sub-Saharan Africa and are likely to play a role in parasite transmission. However, they are currently excluded from control programmes. Molecular phylogenetic studies have provided insights into the evolutionary origins and transmission dynamics of S. mansoni, but there has been no research into schistosome molecular epidemiology in pre-school children. Here, we investigated the genetic diversity and population structure of S. mansoni in pre-school children and mothers living in lakeshore communities in Uganda and monitored for changes over time after praziquantel treatment. Parasites were sampled from children (<6 years) and mothers enrolled in the longitudinal Schistosomiasis Mothers and Infants Study at baseline and at 6-, 12- and 18-month follow-up surveys. 1347 parasites from 35 mothers and 45 children were genotyped by direct sequencing of the cytochrome c oxidase (cox1) gene. The cox1 region was highly diverse with over 230 unique sequences identified. Parasite populations were genetically differentiated between lakes and non-synonymous mutations were more diverse at Lake Victoria than Lake Albert. Surprisingly, parasite populations sampled from children showed a similar genetic diversity to those sampled from mothers, pointing towards a non-linear relationship between duration of exposure and accumulation of parasite diversity. The genetic diversity six months after praziquantel treatment was similar to pre-treatment diversity. Our results confirm the substantial genetic diversity of S. mansoni in East Africa and provide significant insights into transmission dynamics within young children and mothers, important information for schistosomiasis control programmes. PMID:24349589

  5. New insights into the molecular epidemiology and population genetics of Schistosoma mansoni in Ugandan pre-school children and mothers.

    Directory of Open Access Journals (Sweden)

    Martha Betson

    Full Text Available Significant numbers of pre-school children are infected with Schistosoma mansoni in sub-Saharan Africa and are likely to play a role in parasite transmission. However, they are currently excluded from control programmes. Molecular phylogenetic studies have provided insights into the evolutionary origins and transmission dynamics of S. mansoni, but there has been no research into schistosome molecular epidemiology in pre-school children. Here, we investigated the genetic diversity and population structure of S. mansoni in pre-school children and mothers living in lakeshore communities in Uganda and monitored for changes over time after praziquantel treatment. Parasites were sampled from children (<6 years and mothers enrolled in the longitudinal Schistosomiasis Mothers and Infants Study at baseline and at 6-, 12- and 18-month follow-up surveys. 1347 parasites from 35 mothers and 45 children were genotyped by direct sequencing of the cytochrome c oxidase (cox1 gene. The cox1 region was highly diverse with over 230 unique sequences identified. Parasite populations were genetically differentiated between lakes and non-synonymous mutations were more diverse at Lake Victoria than Lake Albert. Surprisingly, parasite populations sampled from children showed a similar genetic diversity to those sampled from mothers, pointing towards a non-linear relationship between duration of exposure and accumulation of parasite diversity. The genetic diversity six months after praziquantel treatment was similar to pre-treatment diversity. Our results confirm the substantial genetic diversity of S. mansoni in East Africa and provide significant insights into transmission dynamics within young children and mothers, important information for schistosomiasis control programmes.

  6. Evolutionary molecular medicine.

    Science.gov (United States)

    Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

    2012-05-01

    Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

  7. Frequency of common HFE variants in the Saudi population: a high throughput molecular beacon-based study

    Directory of Open Access Journals (Sweden)

    Al-Hamed Mohamed

    2006-05-01

    Full Text Available Abstract Background Hereditary Hemochromatosis (HH is an autosomal recessive disorder highlighted byiron-overload. Two popular mutations in HFE, p.C282Y and p.H63D, have been discovered and found to associate with HH in different ethnic backgrounds. p.C282Y and p.H63D diagnosis is usually made byrestriction enzyme analysis. However, the use of this technique is largelylimited to research laboratories because they are relativelyexpensive, time-consuming, and difficult to transform into a high throughput format. Methods Single nucleotide variations in target DNA sequences can be readily identified using molecular beacon fluorescent probes. These are quenched probes with loop and hairpin structure, and they become fluorescent upon specific target recognition. We developed high throughput homogeneous real-time PCR assays using molecular beacon technology, to genotype p.C282Y and p.H63D variants. Representative samples of different genotypes for these variants were assayed by restriction enzyme analysis and direct sequencing as bench mark methods for comparison with the newly developed molecular beacon-based real-time PCR assay. Results Complete concordance was achieved by all three assay formats. Homozygotes (mutant and wildtype and heterozygotes were readily differentiated by the allele specific molecular beacons as reported by the associated fluorophore in the real-time assay developed in this study. Additionally, these assays were used in a high throughput format to establish the allele frequency of C282Y and H63D in Saudis for the first time. Conclusion These assays may be reliably applied as a diagnostic test or large scale method for population screening.

  8. Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

    Directory of Open Access Journals (Sweden)

    Rangel-Figueiredo Teresa

    2010-06-01

    Full Text Available Abstract Background Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95. With breed information, 30 cows and three bulls were identified (q > 0.95 that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10 relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P st = 0.028, P > 0.05. Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50 to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions Molecular analyses complemented previous morphological findings to identify 33 animals that

  9. Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

    Science.gov (United States)

    2010-01-01

    Background Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA) were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95). With breed information, 30 cows and three bulls were identified (q > 0.95) that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10) relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P 0.05). Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50) to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions Molecular analyses complemented previous morphological findings to identify 33 animals that can be considered remnants of the

  10. Facing the estimation of effective population size based on molecular markers: comparison of estimators

    DEFF Research Database (Denmark)

    Jimenez Mena, Belen; Verrier, Etienne; Hospital, Frederic

    We performed a simulation study of several estimators of the effective population size (Ne): NeH = estimator based on the rate of decrease in heterozygosity; NeT = estimator based on the temporal method; NeLD = linkage disequilibrium-based method. We first focused on NeH, which presented...... under scenarios of 3 and 20 bi-allelic loci. Increasing the number of loci largely improved the performance of NeT and NeLD. We highlight the value of NeT and NeLD when large numbers of bi-allelic loci are available, which is nowadays the case for SNPs markers....

  11. Molecular taxonomic analysis of the plant associations of adult pollen beetles (Nitidulidae: Meligethinae), and the population structure of Brassicogethes aeneus.

    Science.gov (United States)

    Ouvrard, Pierre; Hicks, Damien M; Mouland, Molly; Nicholls, James A; Baldock, Katherine C R; Goddard, Mark A; Kunin, William E; Potts, Simon G; Thieme, Thomas; Veromann, Eve; Stone, Graham N

    2016-12-01

    Pollen beetles (Nitidulidae: Meligethinae) are among the most abundant flower-visiting insects in Europe. While some species damage millions of hectares of crops annually, the biology of many species is little known. We assessed the utility of a 797 base pair fragment of the cytochrome oxidase 1 gene to resolve molecular operational taxonomic units (MOTUs) in 750 adult pollen beetles sampled from flowers of 63 plant species sampled across the UK and continental Europe. We used the same locus to analyse region-scale patterns in population structure and demography in an economically important pest, Brassicogethes aeneus. We identified 44 Meligethinae at ∼2% divergence, 35 of which contained published sequences. A few specimens could not be identified because the MOTUs containing them included published sequences for multiple Linnaean species, suggesting either retention of ancestral haplotype polymorphism or identification errors in published sequences. Over 90% of UK specimens were identifiable as B. aeneus. Plant associations of adult B. aeneus were found to be far wider taxonomically than for their larvae. UK B. aeneus populations showed contrasting affiliations between the north (most similar to Scandinavia and the Baltic) and south (most similar to western continental Europe), with strong signatures of population growth in the south.

  12. Futile attempts to differentiate provide molecular evidence for individual differences within a population of cells during cellular reprogramming.

    Science.gov (United States)

    Hoffmann, Xenia-Katharina; Tesmer, Jens; Souquet, Manfred; Marwan, Wolfgang

    2012-04-01

    The heterogeneity of cell populations and the influence of stochastic noise might be important issues for the molecular analysis of cellular reprogramming at the system level. Here, we show that in Physarum polycephalum, the expression patterns of marker genes correlate with the fate decision of individual multinucleate plasmodial cells that had been exposed to a differentiation-inducing photostimulus. For several hours after stimulation, the expression kinetics of PI-3-kinase, piwi, and pumilio orthologs and other marker genes were qualitatively similar in all stimulated cells but quantitatively different in those cells that subsequently maintained their proliferative potential and failed to differentiate accordingly. The results suggest that the population of nuclei in an individual plasmodium behaves synchronously in terms of gene regulation to an extent that the plasmodium provides a source for macroscopic amounts of homogeneous single-cell material for analysing the dynamic processes of cellular reprogramming. Based on the experimental findings, we predict that circuits with switch-like behaviour that control the cell fate decision of a multinucleate plasmodium operate through continuous changes in the concentration of cellular regulators because the nuclear population suspended in a large cytoplasmic volume damps stochastic noise.

  13. The microgeographical patterns of morphological and molecular variation of a mixed ploidy population in the species complex Actinidia chinensis.

    Science.gov (United States)

    Liu, Yifei; Li, Dawei; Yan, Ling; Huang, Hongwen

    2015-01-01

    Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%). Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches.

  14. The microgeographical patterns of morphological and molecular variation of a mixed ploidy population in the species complex Actinidia chinensis.

    Directory of Open Access Journals (Sweden)

    Yifei Liu

    Full Text Available Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%. Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches.

  15. Molecular characterization of microbial populations in groundwater sources and sand filters for drinking water production.

    Science.gov (United States)

    de Vet, W W J M; Dinkla, I J T; Muyzer, G; Rietveld, L C; van Loosdrecht, M C M

    2009-01-01

    In full-scale drinking water production from groundwater, subsurface aeration is an effective means of enhancing the often troublesome process of nitrification. Until now the exact mechanism, however, has been unknown. By studying the microbial population we can improve the understanding of this process. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments of bacteria, archaea and ammonia-oxidizing bacteria was used to characterize the microbial populations in raw groundwater and trickling filters of an active nitrifying surface aerated system and an inactive non-surface aerated system. Only in the active filter were nitrifying microorganisms found above the detection limit of the method. In ammonia oxidation in this groundwater filter both bacteria and archaea played a role, while members belonging to the genus Nitrospira were the only nitrite-oxidizing species found. The subsurface aerated groundwater did not contain any of the nitrifying organisms active in the filter above the detection limit, but did contain Gallionella species that might play a major role in iron oxidation in the filter.

  16. Cytogenetic and molecular biomonitoring of a Portuguese population exposed to pesticides.

    Science.gov (United States)

    Costa, Carla; Teixeira, João P; Silva, Susana; Roma-Torres, Joana; Coelho, Patrícia; Gaspar, Jorge; Alves, Maria; Laffon, Blanca; Rueff, José; Mayan, Olga

    2006-09-01

    Widespread use of pesticides in agriculture represents a threat not only to the environment but also to human populations exposed to them. Many of these compounds are capable of inducing mutations in DNA and lead to several diseases including cancer. In the present study, cytogenetic damage in peripheral lymphocytes from 33 farmers of Oporto district (Portugal) exposed to pesticides was evaluated by means of micronuclei (MN), sister chromatid exchange (SCE) and chromosomal aberrations (CA). In addition, effect of polymorphic genes of xenobiotic metabolizing enzymes (GSTM1, GSTT1, GSTP1, CYP2E1 and EPHX1) was also evaluated. A non-exposed group from the same area and with same demographic characteristics without exposure to genotoxic compounds was studied and data obtained from both groups was compared. MN and SCE frequencies were significantly higher in the exposed group (P environment (greenhouses) with higher levels of genetic damage. Use of personal protective equipment revealed to be important to prevent exposure and diminish genetic damage inflicted by pesticides. Allele frequencies of studied polymorphic genes obtained in this study are similar to the ones described by other authors for Caucasian populations. Despite the low number of subjects, results suggest that low mEH (microsomal epoxide hydrolase) activity as well as GSTT1 positive genotype are associated with increased cytogenetic damage.

  17. Molecular Characterization of TP53 Gene in Human Populations Exposed to Low-Dose Ionizing Radiation

    Directory of Open Access Journals (Sweden)

    Igor Brasil-Costa

    2013-01-01

    Full Text Available Ionizing radiation, such as that emitted by uranium, may cause mutations and consequently lead to neoplasia in human cells. The TP53 gene acts to maintain genomic integrity and constitutes an important biomarker of susceptibility. The present study investigated the main alterations observed in exons 4, 5, 6, 7, and 8 of the TP53 gene and adjacent introns in Amazonian populations exposed to radioactivity. Samples were collected from 163 individuals. Occurrence of the following alterations was observed: (i a missense exchange in exon 4 (Arg72Pro; (ii 2 synonymous exchanges, 1 in exon 5 (His179His, and another in exon 6 (Arg213Arg; (iii 4 intronic exchanges, 3 in intron 7 (C → T at position 13.436; C → T at position 13.491; T → G at position 13.511 and 1 in intron 8 (T → G at position 13.958. Alteration of codon 72 was found to be an important risk factor for cancer development (P=0.024; OR=6.48; CI: 1.29–32.64 when adjusted for age and smoking. Thus, TP53 gene may be an important biomarker for carcinogenesis susceptibility in human populations exposed to ionizing radiation.

  18. Environmental effects on molecular and phenotypic variation in populations of Eruca sativa across a steep climatic gradient.

    Science.gov (United States)

    Westberg, Erik; Ohali, Shachar; Shevelevich, Anatoly; Fine, Pinchas; Barazani, Oz

    2013-08-01

    In Israel Eruca sativa has a geographically narrow distribution across a steep climatic gradient that ranges from mesic Mediterranean to hot desert environments. These conditions offer an opportunity to study the influence of the environment on intraspecific genetic variation. For this, we combined an analysis of neutral genetic markers with a phenotypic evaluation in common-garden experiments, and environmental characterization of populations that included climatic and edaphic parameters, as well as geographic distribution. A Bayesian clustering of individuals from nine representative populations based on amplified fragment length polymorphism (AFLP) divided the populations into a southern and a northern geographic cluster, with one admixed population at the geographic border between them. Linear mixed models, with cluster added as a grouping factor, revealed no clear effects of environment or geography on genetic distances, but this may be due to a strong association of geography and environment with genetic clusters. However, environmental factors accounted for part of the phenotypic variation observed in the common-garden experiments. In addition, candidate loci for selection were identified by association with environmental parameters and by two outlier methods. One locus, identified by all three methods, also showed an association with trichome density and herbivore damage, in net-house and field experiments, respectively. Accordingly, we propose that because trichomes are directly linked to defense against both herbivores and excess radiation, they could potentially be related to adaptive variation in these populations. These results demonstrate the value of combining environmental and phenotypic data with a detailed genetic survey when studying adaptation in plant populations. This article describes the use of several types of data to estimate the influence of the environment on intraspecific genetic variation in populations originating from a steep

  19. Collapse of cooperation in evolving games.

    Science.gov (United States)

    Stewart, Alexander J; Plotkin, Joshua B

    2014-12-09

    Game theory provides a quantitative framework for analyzing the behavior of rational agents. The Iterated Prisoner's Dilemma in particular has become a standard model for studying cooperation and cheating, with cooperation often emerging as a robust outcome in evolving populations. Here we extend evolutionary game theory by allowing players' payoffs as well as their strategies to evolve in response to selection on heritable mutations. In nature, many organisms engage in mutually beneficial interactions and individuals may seek to change the ratio of risk to reward for cooperation by altering the resources they commit to cooperative interactions. To study this, we construct a general framework for the coevolution of strategies and payoffs in arbitrary iterated games. We show that, when there is a tradeoff between the benefits and costs of cooperation, coevolution often leads to a dramatic loss of cooperation in the Iterated Prisoner's Dilemma. The collapse of cooperation is so extreme that the average payoff in a population can decline even as the potential reward for mutual cooperation increases. Depending upon the form of tradeoffs, evolution may even move away from the Iterated Prisoner's Dilemma game altogether. Our work offers a new perspective on the Prisoner's Dilemma and its predictions for cooperation in natural populations; and it provides a general framework to understand the coevolution of strategies and payoffs in iterated interactions.

  20. Cooperation, framing and political attitudes

    DEFF Research Database (Denmark)

    Fosgaard, Toke Reinholt; Hansen, Lars Gårn; Wengström, Erik Roland

    This paper shows that political attitudes are linked to cooperative behavior in an incentivized experiment with a large sample randomly drawn from the Danish population. However, this relationship depends on the way the experiment is framed. In the standard game in which subjects give to a public...... that this difference in the framing effect across political point of views is to some extent explained by differences in beliefs and basic cooperation preferences.......This paper shows that political attitudes are linked to cooperative behavior in an incentivized experiment with a large sample randomly drawn from the Danish population. However, this relationship depends on the way the experiment is framed. In the standard game in which subjects give to a public...

  1. NOD-like receptor cooperativity in effector-triggered immunity.

    Science.gov (United States)

    Griebel, Thomas; Maekawa, Takaki; Parker, Jane E

    2014-11-01

    Intracellular nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) are basic elements of innate immunity in plants and animals. Whereas animal NLRs react to conserved microbe- or damage-associated molecular patterns, plant NLRs intercept the actions of diverse pathogen virulence factors (effectors). In this review, we discuss recent genetic and molecular evidence for functional NLR pairs, and discuss the significance of NLR self-association and heteromeric NLR assemblies in the triggering of downstream signaling pathways. We highlight the versatility and impact of cooperating NLR pairs that combine pathogen sensing with the initiation of defense signaling in both plant and animal immunity. We propose that different NLR receptor molecular configurations provide opportunities for fine-tuning resistance pathways and enhancing the host's pathogen recognition spectrum to keep pace with rapidly evolving microbial populations. Copyright © 2014. Published by Elsevier Ltd.

  2. Mutation analysis of β-thalassemia in East-Western Indian population: a recent molecular approach

    Directory of Open Access Journals (Sweden)

    Shah PS

    2017-05-01

    Full Text Available Parth S Shah,1 Nidhi D Shah,2 Hari Shankar P Ray,3 Nikunj B Khatri,3 Ketan K Vaghasia,3 Rutvik J Raval,4 Sandip C Shah,3 Mandava V Rao5 1Department of Medicine, Lahey Hospital and Medical Center, Boston, MA, 2Department of Pediatrics, Nassau University Medical Centre, New York, NY, USA; 3Supratech Micropath Laboratory and Research Institute, 4Department of Zoology, 5School of Sciences, Gujarat University, Ahmedabad, Gujarat, India Background: β-Thalassemia is the most prevalent genetic disorder in India. Its traits and coinheritance vary from mild to severe conditions, resulting in thalassemia minor, intermediate, and major, depending upon many factors.Purpose: The objective of this study was to identify the incidence of β-thalassemia traits, their coinheritance, and mutations, as well as to support the patients already diagnosed with β-thalassemia in East-Western Indian population for better management.Patients and methods: Seventy-five referral cases for β-thalassemia were analyzed for various β-thalassemia traits, heterozygosity, and homozygosity conditions. Blood phenotypic parameters using cell counter and capillary electrophoresis were investigated. Analyses of eight common mutations of thalassemia in India were carried out using polymerase chain reaction-amplification refractory mutation system, end point polymerase chain reaction, and DNA sequencing methods.Results: Of these (75 referral cases from East-Western Indian region, 68 were positive for β-thalassemia (90.67%. The majority of case types were of β-thalassemia minor (49, 65.33%, followed by HbE traits (6, 8.0% and β-thalassemia major, including heterozygous and homozygous (5, 6.66%; 4, 5.33% types and then HbE homozygous (2, 2.66%, as well as one each of the HbE/β-thalassemia and HbD/β-thalassemia (1, 1.34% combination. Mutation analysis also revealed that the highest frequency of mutation was c.92+5G>C (41, 60.29% followed by deletion 619bp (9, 13.23% and c.79G>A (8, 11

  3. Mutation analysis of β-thalassemia in East-Western Indian population: a recent molecular approach

    Science.gov (United States)

    Shah, Parth S; Shah, Nidhi D; Ray, Hari Shankar P; Khatri, Nikunj B; Vaghasia, Ketan K; Raval, Rutvik J; Shah, Sandip C; Rao, Mandava V

    2017-01-01

    Background β-Thalassemia is the most prevalent genetic disorder in India. Its traits and coinheritance vary from mild to severe conditions, resulting in thalassemia minor, intermediate, and major, depending upon many factors. Purpose The objective of this study was to identify the incidence of β-thalassemia traits, their coinheritance, and mutations, as well as to support the patients already diagnosed with β-thalassemia in East-Western Indian population for better management. Patients and methods Seventy-five referral cases for β-thalassemia were analyzed for various β-thalassemia traits, heterozygosity, and homozygosity conditions. Blood phenotypic parameters using cell counter and capillary electrophoresis were investigated. Analyses of eight common mutations of thalassemia in India were carried out using polymerase chain reaction-amplification refractory mutation system, end point polymerase chain reaction, and DNA sequencing methods. Results Of these (75) referral cases from East-Western Indian region, 68 were positive for β-thalassemia (90.67%). The majority of case types were of β-thalassemia minor (49, 65.33%), followed by HbE traits (6, 8.0%) and β-thalassemia major, including heterozygous and homozygous (5, 6.66%; 4, 5.33%) types and then HbE homozygous (2, 2.66%), as well as one each of the HbE/β-thalassemia and HbD/β-thalassemia (1, 1.34%) combination. Mutation analysis also revealed that the highest frequency of mutation was c.92+5G>C (41, 60.29%) followed by deletion 619bp (9, 13.23%) and c.79G>A (8, 11.76%) in our study group. Five cases (nos. 24, 27, 33, 58, and 71) exhibited coinheritance between β0/β+ (2), β0/β D (1), and c.124_127delTTCT/β+ or β0(2) affecting the Rajasthani and Gujarati populations in our study of the Western region of India. Conclusion We strongly recommend these Western populations for genetic screening before adopting reproductive technologies and interracial marital relations. PMID:28546763

  4. Molecular analysis of RNF213 gene for moyamoya disease in the Chinese Han population.

    Directory of Open Access Journals (Sweden)

    Zhiyuan Wu

    Full Text Available BACKGROUND: Moyamoya disease (MMD is an uncommon cerebrovascular disorder characterized by progressive occlusion of the internal carotid artery causing cerebral ischemia and hemorrhage. Genetic factors in the etiology and pathogenesis of MMD are being increasingly recognized. Previous studies have shown that the RNF213 gene was related to MMD susceptibility in the Japanese population. However, there is no large scale study of the association between this gene and MMD in the Chinese Han population. Thus we designed this case-control study to validate the R4810K mutation and to define the further spectrum of RNF213 mutations in Han Chinese. METHODOLOGY/PRINCIPAL FINDINGS: Genotyping of the R4810K mutation in the RNF213 gene was performed in 170 MMD cases and 507 controls from a Chinese Han population. The R4810K mutation was identified in 22 of 170 MMD cases (13%, including 21 heterozygotes and a single familial homozygote. Two of the 507 controls (0.4% were heterozygous R4810K carriers. The R4810K mutation greatly increased the risk for MMD (OR = 36.7, 95% CI: 8.6~156.6, P = 6.1 E-15. The allele frequency of R4810K was significantly different between patients with ischemia and hemorrhage (OR = 5.4, 95% CI: 1.8~16.1, P = 0.001. Genomic sequencing covering RNF213 exon 40 to exon 68 also identified eight other non-R4810K variants; P4007R, Q4367L, A4399T, T4586P, L4631V, E4950D, A5021V and M5136I. Among them A4399T polymorphism was found in 28/170 cases (16.5% and 45/507 controls (8.9% and was associated with MMD (OR = 2.0, 95% CI: 1.2~3.3, P = 0.004, especially with hemorrhage (OR = 2.8, 95% CI: 1.2~6.5, P = 0.014. CONCLUSIONS: RNF213 mutations are associated with MMD susceptibility in Han Chinese. The ischemic type MMD is particularly related to the R4810K mutation. However, A4399T is also a susceptible variant for MMD, primarily associated with hemorrhage. Identification of novel variants in the RNF213 gene further highlights the genetic

  5. Implementing conventional logic unconventionally: photochromic molecular populations as registers and logic gates.

    Science.gov (United States)

    Chaplin, J C; Russell, N A; Krasnogor, N

    2012-07-01

    In this paper we detail experimental methods to implement registers, logic gates and logic circuits using populations of photochromic molecules exposed to sequences of light pulses. Photochromic molecules are molecules with two or more stable states that can be switched reversibly between states by illuminating with appropriate wavelengths of radiation. Registers are implemented by using the concentration of molecules in each state in a given sample to represent an integer value. The register's value can then be read using the intensity of a fluorescence signal from the sample. Logic gates have been implemented using a register with inputs in the form of light pulses to implement 1-input/1-output and 2-input/1-output logic gates. A proof of concept logic circuit is also demonstrated; coupled with the software workflow describe the transition from a circuit design to the corresponding sequence of light pulses. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  6. [Molecular-genetic analysis of DNA pol and TK of HSV-1 population using NGS technology].

    Science.gov (United States)

    Gus'kova, A A; Skoblov, M Iu; Lavrov, A V; Zubtsov, D A; Andronova, V L; Gol'dshteĭn, D V; Galegov, G A; Skoblov, Iu S

    2013-01-01

    It was determined the ratio of viral DNA and DNA from Vero cells using the polymerase chain reaction in real time in Vero cell lysate, infected with L2 strain of the herpes simplex virus type 1. Copy number of the virus reached a maximum after 24 hours of incubation of infection. Total DNA was isolated and sequenced using NGS technology by Ion Torrent device. Nucleotide sequences of the thymidine kinase gene (UL23) and DNA polymerase (UL30) were determined for a population of HSV-1 strain L2. Comparison of the primary structure of these genes with the corresponding nucleotide sequences of known strains of HSV-1 KOS and 17 was conducted. Differences in the structure of genes UL23 and UL30 between strain L2 and reference strains KOS and 17 are not important, because changes are found in non-conservative regions.

  7. Molecular population genetics of the -esterase gene cluster of Drosophila melanogaster

    Indian Academy of Sciences (India)

    Evgeniy S. Balakirev; Francisco J. Ayala

    2003-12-01

    We have investigated nucleotide polymorphism at the -esterase gene cluster including the Est-6 gene and Est-6 putative pseudogene in four samples of Drosophila melanogaster derived from natural populations of southern Africa (Zimbabwe), Europe (Spain), North America (USA: California), and South America (Venezuela). A complex haplo-type structure is revealed in both Est-6 and Est-6. Total nucleotide diversity is twice in Est-6 as in Est-6; diversity is higher in the African sample than in the non-African ones. Strong linkage disequilibrium occurs within the -esterase gene cluster in non-African samples, but not in the African one. Intragenic gene conversion events are detected within Est-6 and, to a much greater extent, within Est-6; intergenic gene conversion events are rare. Tests of neutrality with recombination are significant for the -esterase gene cluster in the non-African samples but not significant in the African one. We suggest that the demographic history (bottleneck and admixture of genetically differentiated populations) is the major factor shaping the pattern of nucleotide polymorphism in the -esterase gene cluster. However there are some ‘footprints’ of directional and balancing selection shaping specific distribution of nucleotide polymorphism within the cluster. Intergenic epistatic selection between Est-6 and Est-6 may play an important role in the evolution of the -esterase gene cluster preserving the putative pseudogene from degenerative destruction and reflecting possible functional interaction between the functional gene and the putative pseudogene. Est-6 and Est-6 may represent an indivisible intergenic complex (‘intergene’) in which each single component (Est-6 or Est-6) cannot separately carry out the full functional role.

  8. Molecular Signature and In Vivo Behavior of Bone Marrow Endosteal and Subendosteal Stromal Cell Populations and their Relevance to Hematopoiesis

    Science.gov (United States)

    Balduino, Alex; Coelho, Valeria Mello; Wang, Zhou; Taichman, Russell S.; Krebsbach, Paul H.; Weeraratna, Ashani T.; Becker, Kevin G.; de Mello, Wallace; Taub, Dennis D.; Borojevic, Radovan

    2012-01-01

    In the bone marrow cavity, hematopoietic stem cells (HSC) have been shown to reside in the endosteal and subendosteal perivascular niches, which play specific roles on HSC maintenance. Although cells with long-term ability to reconstitute full hematopoietic system can be isolated from both niches, several data support a heterogenous distribution regarding the cycling behavior of HSC. Whether this distinct behavior depends upon the role played by the stromal populations which distinctly create these two niches is a question that remains open. In the present report, we used our previously described in vivo assay to demonstrate that endosteal and subendosteal stromal populations are very distinct regarding skeletal lineage differentiation potential. This was further supported by a microarray-based analysis, which also demonstrated that these two stromal populations play distinct, albeit complementary, roles in HSC niche. Both stromal populations were preferentially isolated from the trabecular region and behave distinctly in vitro, as previously reported. Even though these two niches are organized in a very close range, in vivo assays and molecular analyses allowed us to identify endosteal stroma (F-OST) cells as fully committed osteoblasts and subendosteal stroma (F-RET) cells as uncommitted mesenchymal cells mainly represented by perivascular reticular cells expressing high levels of chemokine ligand, CXCL12. Interestingly, a number of cytokines and growth factors including interleukin-6 (IL-6), IL-7, IL-15, Hepatocyte growth factor (HGF) and stem cell factor (SCF) matrix metalloproteases (MMPs) were also found to be differentially expressed by F-OST and F-RET cells. Further microarray analyses indicated important mechanisms used by the two stromal compartments in order to create and coordinate the “quiescent” and “proliferative” niches in which hematopoietic stem cells and progenitors reside. PMID:22841688

  9. Molecular signature and in vivo behavior of bone marrow endosteal and subendosteal stromal cell populations and their relevance to hematopoiesis

    Energy Technology Data Exchange (ETDEWEB)

    Balduino, Alex, E-mail: balduino@uva.edu.br [School of Dentistry, Veiga de Almeida University, Rio de Janeiro, RJ (Brazil); Mello-Coelho, Valeria [Biomedical Science Institute, Federal University of Rio de Janeiro, Rio de Janeiro, RJ (Brazil); National Institute on Aging, National Institute of Health, Baltimore, MD (United States); Wang, Zhou; Taichman, Russell S.; Krebsbach, Paul H. [Department of Periodontics, Prevention and Geriatrics, University of Michigan School of Dentistry, Ann Arbor, MI (United States); Weeraratna, Ashani T.; Becker, Kevin G. [National Institute on Aging, National Institute of Health, Baltimore, MD (United States); Mello, Wallace de [Instituto Oswaldo Cruz, Rio de Janeiro, RJ (Brazil); Taub, Dennis D. [National Institute on Aging, National Institute of Health, Baltimore, MD (United States); Borojevic, Radovan [Biomedical Science Institute, Federal University of Rio de Janeiro, Rio de Janeiro, RJ (Brazil)

    2012-11-15

    In the bone marrow cavity, hematopoietic stem cells (HSC) have been shown to reside in the endosteal and subendosteal perivascular niches, which play specific roles on HSC maintenance. Although cells with long-term ability to reconstitute full hematopoietic system can be isolated from both niches, several data support a heterogenous distribution regarding the cycling behavior of HSC. Whether this distinct behavior depends upon the role played by the stromal populations which distinctly create these two niches is a question that remains open. In the present report, we used our previously described in vivo assay to demonstrate that endosteal and subendosteal stromal populations are very distinct regarding skeletal lineage differentiation potential. This was further supported by a microarray-based analysis, which also demonstrated that these two stromal populations play distinct, albeit complementary, roles in HSC niche. Both stromal populations were preferentially isolated from the trabecular region and behave distinctly in vitro, as previously reported. Even though these two niches are organized in a very close range, in vivo assays and molecular analyses allowed us to identify endosteal stroma (F-OST) cells as fully committed osteoblasts and subendosteal stroma (F-RET) cells as uncommitted mesenchymal cells mainly represented by perivascular reticular cells expressing high levels of chemokine ligand, CXCL12. Interestingly, a number of cytokines and growth factors including interleukin-6 (IL-6), IL-7, IL-15, Hepatocyte growth factor (HGF) and stem cell factor (SCF) matrix metalloproteases (MMPs) were also found to be differentially expressed by F-OST and F-RET cells. Further microarray analyses indicated important mechanisms used by the two stromal compartments in order to create and coordinate the 'quiescent' and 'proliferative' niches in which hematopoietic stem cells and progenitors reside.

  10. Molecular characterisation of stromal populations derived from human embryonic stem cells

    DEFF Research Database (Denmark)

    Harkness, L.; Twine, N. A.; Abu Dawud, R.;

    2015-01-01

    Human bone marrow-derived stromal (skeletal) stem cells (BM-hMSC) are being employed in an increasing number of clinical trials for tissue regeneration. A limiting factor for their clinical use is the inability to obtain sufficient cell numbers. Human embryonic stem cells (hESC) can provide an un......ESC-stromal cells can thus be considered as a possible alternative candidate cells for hMSC, to be employed in regenerative medicine protocols.......Human bone marrow-derived stromal (skeletal) stem cells (BM-hMSC) are being employed in an increasing number of clinical trials for tissue regeneration. A limiting factor for their clinical use is the inability to obtain sufficient cell numbers. Human embryonic stem cells (hESC) can provide...... an unlimited source of clinical grade cells for therapy. We have generated MSC-like cells from hESC (called here hESC-stromal) that exhibit surface markers and differentiate to osteoblasts and adipocytes, similar to BM-hMSC. In the present study, we used microarray analysis to compare the molecular phenotype...

  11. Molecular characterisation of stromal populations derived from human embryonic stem cells

    DEFF Research Database (Denmark)

    Harkness, L.; Twine, N. A.; Abu Dawud, R.;

    2015-01-01

    of hESC-stromal and immortalised BM-hMSC cells (hMSC-TERT). Of the 7379 genes expressed above baseline, only 9.3% of genes were differentially expressed between undifferentiated hESC-stromal and BM-hMSC. Following ex vivo osteoblast induction, 665 and 695 genes exhibited >. 2-fold change (FC) in h......ESC-stromal and BM-hMSC, respectively with 172 genes common to both cell types. Functional annotation of significantly changing genes revealed similarities in gene ontology between the two cell types. Interestingly, genes in categories of cell adhesion/motility and epithelial-mesenchymal transition (EMT) were highly...... enriched in hESC-stromal whereas genes associated with cell cycle processes were enriched in hMSC-TERT. This data suggests that while hESC-stromal cells exhibit a similar molecular phenotype to hMSC-TERT, differences exist that can be explained by ontological differences between these two cell types. h...

  12. Incidence of respiratory viruses in a pediatric population: molecular and epidemiological aspects

    Directory of Open Access Journals (Sweden)

    Anna Di Taranto

    2012-09-01

    Full Text Available Introduction: Respiratory infections are not well defined and the etiology is often unknown. Material and method: four hundred fortynine subjectrs were enrolled in the study; in all patientes there was a suspect of inflammatory diseases of the respiratory tract. At admission, a nasopharyngeal swab was made. A multiplex PCR was performed after extraction and reverse transcription of viral RNA. The amplified fragments were revealed by using an electrophoresis separation. Results: Two hundred and four patients (45.4% were hospitalized for infection of the upper respiratory tract, 141 (31.4% for lower respiratory infection and the remaining (23% for other symptoms. One hundred fiftyseven (35% patients were positive for human influenza A (H1N1 subtype and 184 for other respiratory viruses,of which 59 (32% gave a positive for respiratory syncytial virus, 42 (23% for rhinovirus, 31 (17% for parainfluenza virus, 12 (6.5% for coronavirus, 28 (15% for adenovirus and 6 (3% for influenza B (3% and 6 (3% for metapneumovirus. The M1 gene sequence of influenza A H1N1 strains from 12 patients had a high identity with that of the reference virus. Conclusion: Furthermore H1N1 and RSV were the main causative agents of acute respiratory infection. A molecular approach provides an accurate and rapid aetiological diagnosis of viral respiratory infections. The molecolar features in the M1 gene suggested that the H1N1 influenza strains circulating in Apulia region had a conserved genetic make up.

  13. The Magellanic Mopra Assessment (MAGMA). I. The Molecular Cloud Population of the Large Magellanic Cloud

    CERN Document Server

    Wong, Tony; Ott, Jürgen; Muller, Erik; Pineda, Jorge L; Bernard, Jean-Philippe; Chu, You-Hua; Fukui, Yasuo; Gruendl, Robert A; Henkel, Christian; Kawamura, Akiko; Klein, Ulrich; Looney, Leslie W; Maddison, Sarah; Mizuno, Yoji; Paradis, Deborah; Seale, Jonathan; Welty, Daniel E

    2011-01-01

    We present the properties of an extensive sample of molecular clouds in the Large Magellanic Cloud (LMC) mapped at 11 pc resolution in the CO(1-0) line. We identify clouds as regions of connected CO emission, and find that the distributions of cloud sizes, fluxes and masses are sensitive to the choice of decomposition parameters. In all cases, however, the luminosity function of CO clouds is steeper than dN/dL \\propto L^{-2}, suggesting that a substantial fraction of mass is in low-mass clouds. A correlation between size and linewidth, while apparent for the largest emission structures, breaks down when those structures are decomposed into smaller structures. We argue that the correlation between virial mass and CO luminosity is the result of comparing two covariant quantities, with the correlation appearing tighter on larger scales where a size-linewidth relation holds. The virial parameter (the ratio of a cloud's kinetic to self-gravitational energy) shows a wide range of values and exhibits no clear trends...

  14. [History of biological anthropology of the Basque population: empiricism with molecular genetics].

    Science.gov (United States)

    Bauduer, Frédéric

    2008-01-01

    For decades, biological and cultural pecularities of the Basques represent major points of interest for scholars. Studies on biological anthropology began in the mid XIXth century with anthropometry and craniology. From the 1930's, hemotypology revealed characteristics (ABO and Rhesus groups) existing also within the surrounding zones of the North-Western Pyrenees (Gascony) which seem to share the same toponymic elements or successoral rights anterior to the Romanization. Current molecular biology techniques exploring mitochondrial DNA or Y chromosome have strengthened the scenario which considers the present Basques as the most direct descendants of a preneolithic Pyrenean people. During the last glacial maximum, the aquitanocantabric area would have served as a refuge for human groups who contributed thereafter to the repopulation of Western Europe. The genetic profile argues in favour of a strong degree of endogamy and drift. These two elements explain the presence of numerous cases of inherited disorders related to founding effects. The origin of the genetic heterogeneity is not yet established.

  15. Asymptotic behavior of a rotational population distribution in a molecular quantum-kicked rotor with ideal quantum resonance

    Energy Technology Data Exchange (ETDEWEB)

    Matsuoka, Leo, E-mail: leo-matsuoka@hiroshima-u.ac.jp [Graduate School of Engineering, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8527 (Japan); Segawa, Etsuo [Graduate School of Information Sciences, Tohoku University, Aoba, Sendai 980-8579 (Japan); Yuki, Kenta [Graduate School of Engineering, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8527 (Japan); Konno, Norio [Department of Applied Mathematics, Faculty of Engineering, Yokohama National University, Hodogaya, Yokohama 240-8501 (Japan); Obata, Nobuaki [Graduate School of Information Sciences, Tohoku University, Aoba, Sendai 980-8579 (Japan)

    2017-06-09

    We performed a mathematical analysis of the time-dependent dynamics of a quantum-kicked rotor implemented in a diatomic molecule under the condition of ideal quantum resonance. We examined a model system featuring a diatomic molecule in a periodic train of terahertz pulses, regarding the molecule as a rigid rotor with the state-dependent transition moment and including the effect of the magnetic quantum number M. We derived the explicit expression for the asymptotic distribution of a rotational population by making the transition matrix correspondent with a sequence of ultraspherical polynomials. The mathematical results obtained were validated by numerical simulations. - Highlights: • The behavior of the molecular quantum-kicked rotor was mathematically investigated. • The matrix elements were made correspondent with the ultraspherical polynomials. • The explicit formula for asymptotic distribution was obtained. • Complete agreement with the numerical simulation was verified.

  16. Curl flux, coherence, and population landscape of molecular systems: Nonequilibrium quantum steady state, energy (charge) transport, and thermodynamics

    CERN Document Server

    Zhang, Zhedong

    2015-01-01

    We established a theoretical framework in terms of the curl flux, population landscape, and coherence for non-equilibrium quantum systems at steady state, through exploring the energy and charge transport in molecular processes. The curl quantum flux plays the key role in determining transport properties and the system reaches equilibrium when flux vanishes. The novel curl quantum flux reflects the degree of non-equilibriumness and the time-irreversibility. We found an analytical expression for the quantum flux and its relationship to the environmental pumping (non-equilibriumness quantified by the voltage away from the equilibrium) and the quantum tunneling. Furthermore, we investigated another quantum signature, the coherence, quantitatively measured by the non-zero off diagonal element of the density matrix. Besides the environment-assistance which can give dramatic enhancement of coherence and quantum flux with high voltage at a fixed tunneling strength, the quantum flux is promoted by the coherence in th...

  17. Use of microsatellite markers in molecular analysis of segregating populations of papaya (Carica papaya L.) derived from backcrossing.

    Science.gov (United States)

    Pinto, F O; Pereira, M G; Luz, L N; Cardozo, D L; Ramos, H C C; Macedo, C M P

    2013-07-08

    Brazil is the world leader in papaya production. However, only a small number of cultivars are registered for commercial planting, mainly owing to delays in obtaining cultivars and the high costs of the field phase of breeding programs. These costs can be reduced when molecular tools are combined with conventional breeding methods. In the present study, we conducted a molecular analysis of a self-fertilized population of a first backcrossing generation of BC1S1 papaya plants via microsatellite markers both to monitor the level of homozygosity and the gene/allele transfer that confers the Golden trait (fruit color) and to assess the parental genomic proportion in the genotypes studied. Based on the analysis of 20 polymorphic microsatellite loci, 19 genotypes with the Golden trait belonging to BC1S1 were evaluated in addition to the parental genotypes. Genetic distance was estimated through weighted index. The genotypes were then grouped using the hierarchical nearest neighbor method, and the analysis of principal coordinates was used to measure the proportion of parental genomes in the segregating genotypes. The mean value of the inbreeding coefficient was 0.36. The analysis of the principal coordinates revealed that on average, 64% of the recurrent parent genome was present in the population. Together, the analyses allowed the selection of 3 individuals for the next backcross cycle (33BC1S1-18, 34BC1S1-16, and 37BC1S1-10). These individuals had a higher proportion of the recurrent parent and were grouped close to the recurrent parent in the cluster analysis.

  18. Globular cluster formation with multiple stellar populations: self-enrichment in fractal massive molecular clouds

    Science.gov (United States)

    Bekki, Kenji

    2017-08-01

    Internal chemical abundance spreads are one of fundamental properties of globular clusters (GCs) in the Galaxy. In order to understand the origin of such abundance spreads, we numerically investigate GC formation from massive molecular clouds (MCs) with fractal structures using our new hydrodynamical simulations with star formation and feedback effects of core-collapse supernovae (SNe) and asymptotic giant branch (AGB) stars. We particularly investigate star formation from gas chemically contaminated by SNe and AGB stars ('self-enrichment') in forming GCs within MCs with different initial conditions and environments. The principal results are as follows. GCs with multiple generations of stars can be formed from merging of hierarchical star cluster complexes that are developed from high-density regions of fractal MCs. Feedback effects of SNe and AGB stars can control the formation efficiencies of stars formed from original gas of MCs and from gas ejected from AGB stars. The simulated GCs have strong radial gradients of helium abundances within the central 3 pc. The original MC masses need to be as large as 107 M⊙ for a canonical initial stellar mass function (IMF) so that the final masses of stars formed from AGB ejecta can be ∼105 M⊙. Since star formation from AGB ejecta is rather prolonged (∼108 yr), their formation can be strongly suppressed by SNe of the stars themselves. This result implies that the so-called mass budget problem is much more severe than ever thought in the self-enrichment scenario of GC formation and thus that IMF for the second generation of stars should be 'top-light'.

  19. Deeply Embedded Protostellar Population in the Central Molecular Zone Suggested by H$_2$O Masers and Dense Cores

    CERN Document Server

    Lu, Xing; Kauffmann, Jens; Pillai, Thushara; Longmore, Steven N; Kruijssen, J M Diederik; Battersby, Cara

    2016-01-01

    The Central Molecular Zone (CMZ), usually referring to the inner 500 pc of the Galaxy, contains a dozen of massive ($\\sim10^5$ $M_\\odot$) molecular clouds. Are these clouds going to actively form stars like Sgr B2? How are they affected by the extreme physical conditions in the CMZ, such as strong turbulence? Here we present a first step towards answering these questions. Using high-sensitivity, high angular resolution radio and (sub)millimeter observations, we studied deeply embedded star formation in six massive clouds in the CMZ, including the 20 and 50 km s$^{-1}$ clouds, Sgr B1 off (as known as dust ridge clouds e/f), Sgr C, Sgr D, and G0.253-0.016. The VLA water maser observations suggest a population of deeply embedded protostellar candidates, many of which are new detections. The SMA 1.3 mm continuum observations reveal peaks in dust emission associated with the masers, suggesting the existence of dense cores. While our findings confirm that clouds such as G0.253-0.016 lack internal compact substructu...

  20. DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms.

    Science.gov (United States)

    Frías-López, Cristina; Sánchez-Herrero, José F; Guirao-Rico, Sara; Mora, Elisa; Arnedo, Miquel A; Sánchez-Gracia, Alejandro; Rozas, Julio

    2016-12-15

    The development of molecular markers is one of the most important challenges in phylogenetic and genome wide population genetics studies, especially in studies with non-model organisms. A highly promising approach for obtaining suitable markers is the utilization of genomic partitioning strategies for the simultaneous discovery and genotyping of a large number of markers. Unfortunately, not all markers obtained from these strategies provide enough information for solving multiple evolutionary questions at a reasonable taxonomic resolution. We have developed Development Of Molecular markers In Non-model Organisms (DOMINO), a bioinformatics tool for informative marker development from both next generation sequencing (NGS) data and pre-computed sequence alignments. The application implements popular NGS tools with new utilities in a highly versatile pipeline specifically designed to discover or select personalized markers at different levels of taxonomic resolution. These markers can be directly used to study the taxa surveyed for their design, utilized for further downstream PCR amplification in a broader set taxonomic scope, or exploited as suitable templates to bait design for target DNA enrichment techniques. We conducted an exhaustive evaluation of the performance of DOMINO via computer simulations and illustrate its utility to find informative markers in an empirical dataset. DOMINO is freely available from www.ub.edu/softevol/domino CONTACT: elsanchez@ub.edu or jrozas@ub.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  1. Tuning the transition temperature and cooperativity of bapbpy-based mononuclear spin-crossover compounds: interplay between molecular and crystal engineering.

    Science.gov (United States)

    Arcis-Castíllo, Zulema; Zheng, Sipeng; Siegler, Maxime A; Roubeau, Olivier; Bedoui, Salma; Bonnet, Sylvestre

    2011-12-23

    In this study, we show that 1) different isomers of the same mononuclear iron(II) complex give materials with different spin-crossover (hereafter SCO) properties, and 2) minor modifications of the bapbpy (bapbpy=N6,N6'-di(pyridin-2-yl)-2,2'-bipyridine-6,6'-diamine) ligand allows SCO to be obtained near room temperature. We also provide a qualitative model to understand the link between the structure of bapbpy-based ligands and the SCO properties of their iron(II) compounds. Thus, seven new trans-[Fe{R(2)(bapbpy)}(NCS)(2)] compounds were prepared, in which the R(2)bapbpy ligand bears picoline (9-12), quin-2-oline (13), isoquin-3-oline (14), or isoquin-1-oline (15) substituents. From this series, three compounds (12, 14, and 15) have SCO properties, one of which (15) occurs at 288 K. The crystal structures of compounds 11, 12, and 15 show that the intermolecular interactions in these materials are similar to those found in the parent compound [Fe(bapbpy)(NCS)(2)] (1), in which each iron complex interacts with its neighbors through weak N-H···S hydrogen bonding and π-π stacking. For compounds 12 and 15, hindering groups located near the N-H bridges weaken the N-S intermolecular interactions, which is correlated to non-cooperative SCO. For compound 14, the substitution is further away from the N-H bridges, and the SCO remains cooperative as in 1 with a hysteresis cycle. Optical microscopy photographs show the strikingly different spatio-temporal evolution of the phase transition in the noncooperative SCO compound 12 relative to that found in 1. Heat-capacity measurements were made for compounds 1, 12, 14, and 15 and fitted to the Sorai domain model. The number n of like-spin SCO centers per interacting domain, which is related to the cooperativity of the spin transition, was found high for compounds 1 and 14 and low for compounds 12 and 15. Finally, we found that although both pairs of compounds 11/12 and 14/15 are pairs of isomers their SCO properties are

  2. Two-dimensional electronic spectroscopy can fully characterize the population transfer in molecular systems

    Science.gov (United States)

    Dostál, Jakub; Benešová, Barbora; Brixner, Tobias

    2016-09-01

    Excitation energy transfer in complex systems often proceeds through series of intermediate states. One of the goals of time-resolved spectroscopy is to identify the spectral signatures of all of them in the acquired experimental data and to characterize the energy transfer scheme between them. It is well known that in the case of transient absorption spectra such decomposition is ambiguous even if many simplifying considerations are taken. In contrast to transient absorption, absorptive 2D spectra intuitively resemble population transfer matrices. Therefore, it seems possible to decompose the 2D spectra unambiguously. Here we show that all necessary information is encoded in the combination of absorptive 2D and linear absorption spectra. We set up a simple model describing a broad class of absorptive 2D spectra and prove analytically that they can be inverted uniquely towards physical parameters fully determining the species-associated spectra of individual constituents together with all connecting intrinsic rate constants. Due to the matrix formulation of the model, it is suitable for fast computer calculation necessary to efficiently perform the inversion numerically by fitting the combination of experimental 2D and absorption spectra. Moreover, the model allows for decomposition of the 2D spectrum into its stimulated emission, ground-state bleach, and excited-state absorption components almost unambiguously. The numerical procedure is illustrated exemplarily.

  3. The New Genomics: What Molecular Databases Can Tell Us About Human Population Variation and Endocrine Disease.

    Science.gov (United States)

    Rotwein, Peter

    2017-07-01

    Major recent advances in genetics and genomics present unique opportunities for enhancing our understanding of human physiology and disease predisposition. Here I demonstrate how analysis of genomic information can provide new insights into endocrine systems, using the human growth hormone (GH) signaling pathway as an illustrative example. GH is essential for normal postnatal growth in children, and plays important roles in other biological processes throughout life. GH actions are mediated by the GH receptor, primarily via the JAK2 protein tyrosine kinase and the STAT5B transcription factor, and inactivating mutations in this pathway all lead to impaired somatic growth. Variation in GH signaling genes has been evaluated using DNA sequence data from the Exome Aggregation Consortium, a compendium of information from >60,000 individuals. Results reveal many potential missense and other alterations in the coding regions of GH1, GHR, JAK2, and STAT5B, with most changes being uncommon. The total number of different alleles per gene varied by ~threefold, from 101 for GH1 to 338 for JAK2. Several known disease-linked mutations in GH1, GHR, and JAK2 were present but infrequent in the population; however, three amino acid changes in GHR were sufficiently prevalent (~4% to 44% of chromosomes) to suggest that they are not disease causing. Collectively, these data provide new opportunities to understand how genetically driven variability in GH signaling and action may modify human physiology and disease. Copyright © 2017 Endocrine Society.

  4. Molecular genetic studies and delineation of the oculocutaneous albinism phenotype in the Pakistani population

    Directory of Open Access Journals (Sweden)

    Jaworek Thomas J

    2012-06-01

    Full Text Available Abstract Background Oculocutaneous albinism (OCA is caused by a group of genetically heterogeneous inherited defects that result in the loss of pigmentation in the eyes, skin and hair. Mutations in the TYR, OCA2, TYRP1 and SLC45A2 genes have been shown to cause isolated OCA. No comprehensive analysis has been conducted to study the spectrum of OCA alleles prevailing in Pakistani albino populations. Methods We enrolled 40 large Pakistani families and screened them for OCA genes and a candidate gene, SLC24A5. Protein function effects were evaluated using in silico prediction algorithms and ex vivo studies in human melanocytes. The effects of splice-site mutations were determined using an exon-trapping assay. Results Screening of the TYR gene revealed four known (p.Arg299His, p.Pro406Leu, p.Gly419Arg, p.Arg278* and three novel mutations (p.Pro21Leu, p.Cys35Arg, p.Tyr411His in ten families. Ex vivo studies revealed the retention of an EGFP-tagged mutant (p.Pro21Leu, p.Cys35Arg or p.Tyr411His tyrosinase in the endoplasmic reticulum (ER at 37°C, but a significant fraction of p.Cys35Arg and p.Tyr411His left the ER in cells grown at a permissive temperature (31°C. Three novel (p.Asp486Tyr, p.Leu527Arg, c.1045-15 T > G and two known mutations (p.Pro743Leu, p.Ala787Thr of OCA2 were found in fourteen families. Exon-trapping assays with a construct containing a novel c.1045-15 T > G mutation revealed an error in splicing. No mutation in TYRP1, SLC45A2, and SLC24A5 was found in the remaining 16 families. Clinical evaluation of the families segregating either TYR or OCA2 mutations showed nystagmus, photophobia, and loss of pigmentation in the skin or hair follicles. Most of the affected individuals had grayish-blue colored eyes. Conclusions Our results show that ten and fourteen families harbored mutations in the TYR and OCA2 genes, respectively. Our findings, along with the results of previous studies, indicate that the p.Cys35Arg, p.Arg278

  5. Efficacy and tolerance of an injectable medical device containing stable hybrid cooperative complexes of high- and low-molecular-weight hyaluronic acid: a monocentric 16 weeks open-label evaluation

    Science.gov (United States)

    Sparavigna, Adele; Tenconi, Beatrice

    2016-01-01

    Background An injectable medical device containing stable hybrid cooperative complexes of high- and low-molecular-weight hyaluronic acid (HA) has been developed with characteristics suited for a global improvement of facial esthetics. Objective To evaluate the HA product performance in improving some key facial esthetic features. The study employed clinical scales, subjective evaluations, and facial skin objective measurements. Methods A single Italian site treated 64 female subjects aged 38–60 years, with injections at five predetermined points, on each side of the face, with a 4-week time lapse between the first and the second product administration. Subjects were evaluated after 4, 8, 12, and 16 weeks, using validated clinical scales, subjective evaluation, and objective quantitative outcome measures. Assessment of esthetic results included photographic documentation. Results Both the clinical and subjective assessments, and the majority of objective instrumental parameters indicated an improvement throughout the study and were already significant at week 4 or 8 and were still significant at week 16 (3 months after the second treatment). Minor and temporary local skin reactions were observed in 23% of subjects at the site of the injections, and the global judgment on tolerability was good or excellent, both in the investigators’ opinion and volunteers’ self-evaluation. Conclusion Both subjective and objective improvement of the facial parameters was consistent with the bio-remodeling purpose, and persistent and still statistically significant at the end of the study. The tolerability and safety profile of the product were judged good or excellent both by investigators and volunteers. This study supports the claim for bio-remodeling of these stable hybrid cooperative complexes of low- and high-molecular-weight HA. PMID:27713647

  6. Ecological public goods games: cooperation and bifurcation.

    Science.gov (United States)

    Hauert, Christoph; Wakano, Joe Yuichiro; Doebeli, Michael

    2008-03-01

    The Public Goods Game is one of the most popular models for studying the origin and maintenance of cooperation. In its simplest form, this evolutionary game has two regimes: defection goes to fixation if the multiplication factor r is smaller than the interaction group size N, whereas cooperation goes to fixation if the multiplication factor r is larger than the interaction group size N. Hauert et al. [Hauert, C., Holmes, M., Doebeli, M., 2006a. Evolutionary games and population dynamics: Maintenance of cooperation in public goods games. Proc. R. Soc. Lond. B 273, 2565-2570] have introduced the Ecological Public Goods Game by viewing the payoffs from the evolutionary game as birth rates in a population dynamic model. This results in a feedback between ecological and evolutionary dynamics: if defectors are prevalent, birth rates are low and population densities decline, which leads to smaller interaction groups for the Public Goods game, and hence to dominance of cooperators, with a concomitant increase in birth rates and population densities. This feedback can lead to stable co-existence between cooperators and defectors. Here we provide a detailed analysis of the dynamics of the Ecological Public Goods Game, showing that the model exhibits various types of bifurcations, including supercritical Hopf bifurcations, which result in stable limit cycles, and hence in oscillatory co-existence of cooperators and defectors. These results show that including population dynamics in evolutionary games can have important consequences for the evolutionary dynamics of cooperation.

  7. Molecular virology of hepatitis B virus, sub-genotype C4 in northern Australian Indigenous populations.

    Science.gov (United States)

    Littlejohn, M; Davies, J; Yuen, L; Edwards, R; Sozzi, T; Jackson, K; Cowie, B; Tong, S; Davis, J; Locarnini, S

    2014-04-01

    Indigenous Australians experience a significant health burden from chronic hepatitis B infection; however, the strain of hepatitis B virus (HBV) found among Indigenous Australians has not been well characterized. Blood samples were collected from 65 Indigenous Australians with chronic HBV infection from across the Top End of Australia's Northern Territory. Phylogenetic analysis of HBV from these samples revealed that 100% of the isolates were genotype C, sub-genotype C4, expressing the serotype ayw3. This strain is a divergent group within the HBV/C genotype, and has only been described in Indigenous Australians. Evidence of recombination was suggested by discordant phylogenetic clustering of the C4 sequences when comparing the full genome to the surface region and confirmed by recombination analysis which showed the surface gene region to be most closely related to genotype J, while the remaining regions of the genome were most similar to genotype C sequences. Mutational analysis revealed the presence of multiple mutations that have been linked with more rapid liver disease progression and an increased risk of hepatocellular carcinoma. These mutations were detected in the majority of sequences examined. Variants associated with vaccine failure were detected as the predominant viral quasi-species in 3/35 samples. In summary, the HBV C4 variant found in this population has a high potential to cause advanced liver disease and to escape vaccination programs. Further in vitro functional and natural history studies are warranted in order to determine the clinical and public health consequences of infection with the HBV C4 variant in these communities. © 2014 Wiley Periodicals, Inc.

  8. Molecular assessment of mating strategies in a population of Atlantic spotted dolphins.

    Directory of Open Access Journals (Sweden)

    Michelle L Green

    Full Text Available Similar to other small cetacean species, Atlantic spotted dolphins (Stenella frontalis have been the object of concentrated behavioral study. Although mating and courtship behaviors occur often and the social structure of the population is well-studied, the genetic mating system of the species is unknown. To assess the genetic mating system, we genotyped females and their progeny at ten microsatellite loci. Genotype analysis provided estimates of the minimum number of male sires necessary to account for the allelic diversity observed among the progeny. Using the estimates of male sires, we determined whether females mated with the same or different males during independent estrus events. Using Gerud2.0, a minimum of two males was necessary to account for the genetic variation seen among progeny arrays of all tested females. ML-Relate assigned the most likely relationship between offspring pairs; half or full sibling. Relationship analysis supported the conservative male estimates of Gerud2.0 but in some cases, half or full sibling relationships between offspring could not be fully resolved. Integrating the results from Gerud2.0, ML-Relate with previous observational and paternity data, we constructed two-, three-, and four-male pedigree models for each genotyped female. Because increased genetic diversity of offspring may explain multi-male mating, we assessed the internal genetic relatedness of each offspring's genotype to determine whether parent pairs of offspring were closely related. We found varying levels of internal relatedness ranging from unrelated to closely related (range -0.136-0.321. Because there are several hypothesized explanations for multi-male mating, we assessed our data to determine the most plausible explanation for multi-male mating in our study system. Our study indicated females may benefit from mating with multiple males by passing genes for long-term viability to their young.

  9. Molecular characterization of Cyclophilin (TcCyP19) in Trypanosoma cruzi populations susceptible and resistant to benznidazole.

    Science.gov (United States)

    Rêgo, Juciane Vaz; Duarte, Ana Paula; Liarte, Daniel Barbosa; de Carvalho Sousa, Francirlene; Barreto, Humberto Medeiros; Bua, Jacqueline; Romanha, Alvaro José; Rádis-Baptista, Gandhi; Murta, Silvane Maria Fonseca

    2015-01-01

    Cyclophilin (CyP), a peptidyl-prolyl cis/trans isomerase, is a key molecule with diverse biological functions that include roles in molecular chaperoning, stress response, immune modulation, and signal transduction. In this respect, CyP could serve as a potential drug target in disease-causing parasites. Previous studies employing proteomics techniques have shown that the TcCyP19 isoform was more abundant in a benznidazole (BZ)-resistant Trypanosoma cruzi population than in its susceptible counterpart. In this study, TcCyP19 has been characterized in BZ-susceptible and BZ-resistant T. cruzi populations. Phylogenetic analysis revealed a clear dichotomy between Cyphophilin A (CyPA) sequences from trypanosomatids and mammals. Sequencing analysis revealed that the amino acid sequences of TcCyP19 were identical among the T. cruzi samples analyzed. Southern blot analysis showed that TcCyP19 is a single-copy gene, located in chromosomal bands varying in size from 0.68 to 2.2 Mb, depending on the strain of T. cruzi. Northern blot and qPCR indicated that the levels of TcCyP19 mRNA were twofold higher in drug-resistant T. cruzi populations than in their drug-susceptible counterparts. Similarly, as determined by two-dimensional gel electrophoresis immunoblot, the expression of TcCyP19 protein was increased to the same degree in BZ-resistant T. cruzi populations. No differences in TcCyP19 mRNA and protein expression levels were observed between the susceptible and the naturally resistant T. cruzi strains analyzed. Taken together, these data indicate that cyclophilin TcCyP19 expression is up-regulated at both transcriptional and translational levels in T. cruzi populations that were in vitro-induced and in vivo-selected for resistance to BZ.

  10. Molecular and Morphological Characterization of Xiphinema chambersi Population from Live Oak in Jekyll Island, Georgia, with Comments on Morphometric Variations.

    Science.gov (United States)

    Handoo, Zafar A; Carta, Lynn K; Skantar, Andrea M; Subbotin, Sergei A; Fraedrich, Stephen W

    2016-03-01

    A population of Xiphinema chambersi from the root zone around live oak (Quercus virginiana Mill.) trees on Jekyll Island, GA, is described using both morphological and molecular tools and compared with descriptions of type specimens. Initially, because of a few morphological differences, this nematode was thought to represent an undescribed species. However, on further examination, the morphometrics of the nematodes from live oak tend to agree with most of the morphometrics in the original description and redescription of X. chambersi except for few minor differences in V% relative to body length, slightly shorter stylet length, different c value, and the number of caudal pores. We consider these differences to be part of the normal variation within this species and accordingly image this new population of X. chambersi and redescribe the species. The new population is characterized by having females with a body length of 2.1 to 2.5 mm; lip region slightly rounded and set off from head; total stylet length 170 to 193 µm; vulva at 20.4% to 21.8% of body length; a monodelphic, posterior reproductive system; elongate, conoid tail with a blunt terminus and four pairs of caudal pores, of which two pairs are subdorsal and two subventral. Sequence data from the D2-D3 region of the 28S rRNA molecule subjected to GenBank sequence comparison using BLAST showed that the sequence had 96% and 99% similarity with X. chambersi from Alabama and Florida, respectively. Phylogenetic relationships of X. chambersi with other xiphinematids based on analysis of this DNA fragment are presented. This finding represents a new location of X. chambersi in Georgia on live oak for this species.

  11. Fungicide-driven evolution and molecular basis of multidrug resistance in field populations of the grey mould fungus Botrytis cinerea.

    Directory of Open Access Journals (Sweden)

    Matthias Kretschmer

    2009-12-01

    Full Text Available The grey mould fungus Botrytis cinerea causes losses of commercially important fruits, vegetables and ornamentals worldwide. Fungicide treatments are effective for disease control, but bear the risk of resistance development. The major resistance mechanism in fungi is target protein modification resulting in reduced drug binding. Multiple drug resistance (MDR caused by increased efflux activity is common in human pathogenic microbes, but rarely described for plant pathogens. Annual monitoring for fungicide resistance in field isolates from fungicide-treated vineyards in France and Germany revealed a rapidly increasing appearance of B. cinerea field populations with three distinct MDR phenotypes. All MDR strains showed increased fungicide efflux activity and overexpression of efflux transporter genes. Similar to clinical MDR isolates of Candida yeasts that are due to transcription factor mutations, all MDR1 strains were shown to harbor activating mutations in a transcription factor (Mrr1 that controls the gene encoding ABC transporter AtrB. MDR2 strains had undergone a unique rearrangement in the promoter region of the major facilitator superfamily transporter gene mfsM2, induced by insertion of a retrotransposon-derived sequence. MDR2 strains carrying the same rearranged mfsM2 allele have probably migrated from French to German wine-growing regions. The roles of atrB, mrr1 and mfsM2 were proven by the phenotypes of knock-out and overexpression mutants. As confirmed by sexual crosses, combinations of mrr1 and mfsM2 mutations lead to MDR3 strains with higher broad-spectrum resistance. An MDR3 strain was shown in field experiments to be selected against sensitive strains by fungicide treatments. Our data document for the first time the rising prevalence, spread and molecular basis of MDR populations in a major plant pathogen in agricultural environments. These populations will increase the risk of grey mould rot and hamper the effectiveness of

  12. Fungicide-driven evolution and molecular basis of multidrug resistance in field populations of the grey mould fungus Botrytis cinerea.

    Directory of Open Access Journals (Sweden)

    Matthias Kretschmer

    2009-12-01

    Full Text Available The grey mould fungus Botrytis cinerea causes losses of commercially important fruits, vegetables and ornamentals worldwide. Fungicide treatments are effective for disease control, but bear the risk of resistance development. The major resistance mechanism in fungi is target protein modification resulting in reduced drug binding. Multiple drug resistance (MDR caused by increased efflux activity is common in human pathogenic microbes, but rarely described for plant pathogens. Annual monitoring for fungicide resistance in field isolates from fungicide-treated vineyards in France and Germany revealed a rapidly increasing appearance of B. cinerea field populations with three distinct MDR phenotypes. All MDR strains showed increased fungicide efflux activity and overexpression of efflux transporter genes. Similar to clinical MDR isolates of Candida yeasts that are due to transcription factor mutations, all MDR1 strains were shown to harbor activating mutations in a transcription factor (Mrr1 that controls the gene encoding ABC transporter AtrB. MDR2 strains had undergone a unique rearrangement in the promoter region of the major facilitator superfamily transporter gene mfsM2, induced by insertion of a retrotransposon-derived sequence. MDR2 strains carrying the same rearranged mfsM2 allele have probably migrated from French to German wine-growing regions. The roles of atrB, mrr1 and mfsM2 were proven by the phenotypes of knock-out and overexpression mutants. As confirmed by sexual crosses, combinations of mrr1 and mfsM2 mutations lead to MDR3 strains with higher broad-spectrum resistance. An MDR3 strain was shown in field experiments to be selected against sensitive strains by fungicide treatments. Our data document for the first time the rising prevalence, spread and molecular basis of MDR populations in a major plant pathogen in agricultural environments. These populations will increase the risk of grey mould rot and hamper the effectiveness of

  13. Population Genetic Structure and Marker Trait Associations Using Morphological, Phytochemical and Molecular Parameters in Habenaria edgeworthii-a Threatened Medicinal Orchid of West Himalaya, India.

    Science.gov (United States)

    Giri, Lalit; Jugran, Arun Kumar; Bahukhandi, Amit; Dhyani, Praveen; Bhatt, Indra D; Rawal, Ranbeer Singh; Nandi, Shyamal Kumar; Dhar, Uppeandra

    2017-01-01

    Habenaria edgeworthii Hook. f. ex Collett is an important terrestrial orchid used in different Ayurvedic formulations. In the present study, variations among morphological, phytochemical and molecular markers were assessed. A significant difference was observed among populations using morphological traits. Inter-simple sequence repeat (ISSR) data revealed lower genetic diversity at population level (He = 0.207) as compared to species level (He = 0.334). Analysis of molecular variance (AMOVA) indicates 74 % variation among populations and 26 % within population. Tuber extracts showed significantly (p morphological and phytochemical attributes were studied using multiple regression analysis (MRA). Several ISSR fragments were associated with some morphological and phytochemical traits. These ISSR fragments can be useful for breeding programme of the species when no other genetic information, such as linkage maps and quantitative trait loci, is available.

  14. Cooperative gating between ion channels.

    Science.gov (United States)

    Choi, Kee-Hyun

    2014-01-01

    Cooperative gating between ion channels, i.e. the gating of one channel directly coupled to the gating of neighboring channels, has been observed in diverse channel types at the single-channel level. Positively coupled gating could enhance channel-mediated signaling while negative coupling may effectively reduce channel gating noise. Indeed, the physiological significance of cooperative channel gating in signal transduction has been recognized in several in vivo studies. Moreover, coupled gating of ion channels was reported to be associated with some human disease states. In this review, physiological roles for channel cooperativity and channel clustering observed in vitro and in vivo are introduced, and stimulation-induced channel clustering and direct channel cross linking are suggested as the physical mechanisms of channel assembly. Along with physical clustering, several molecular mechanisms proposed as the molecular basis for functional coupling of neighboring channels are covered: permeant ions as a channel coupling mediator, concerted channel activation through the membrane, and allosteric mechanisms. Also, single-channel analysis methods for cooperative gating such as the binomial analysis, the variance analysis, the conditional dwell time density analysis, and the maximum likelihood fitting analysis are reviewed and discussed.

  15. Evolution of cooperation in multiplex networks.

    Science.gov (United States)

    Gómez-Gardeñes, Jesús; Reinares, Irene; Arenas, Alex; Floría, Luis Mario

    2012-01-01

    We study evolutionary game dynamics on structured populations in which individuals take part in several layers of networks of interactions simultaneously. This multiplex of interdependent networks accounts for the different kind of social ties each individual has. By coupling the evolutionary dynamics of a Prisoner's Dilemma game in each of the networks, we show that the resilience of cooperative behaviors for extremely large values of the temptation to defect is enhanced by the multiplex structure. Furthermore, this resilience is intrinsically related to a non-trivial organization of cooperation across the network layers, thus providing a new way out for cooperation to survive in structured populations.

  16. Curl flux, coherence, and population landscape of molecular systems: Nonequilibrium quantum steady state, energy (charge) transport, and thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Z. D. [Department of Physics and Astronomy, SUNY Stony Brook, New York 11794 (United States); Wang, J. [Department of Physics and Astronomy, SUNY Stony Brook, New York 11794 (United States); Department of Chemistry, SUNY Stony Brook, New York 11794 (United States); State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022 (China)

    2014-06-28

    We established a theoretical framework in terms of the curl flux, population landscape, and coherence for non-equilibrium quantum systems at steady state, through exploring the energy and charge transport in molecular processes. The curl quantum flux plays the key role in determining transport properties and the system reaches equilibrium when flux vanishes. The novel curl quantum flux reflects the degree of non-equilibriumness and the time-irreversibility. We found an analytical expression for the quantum flux and its relationship to the environmental pumping (non-equilibriumness quantified by the voltage away from the equilibrium) and the quantum tunneling. Furthermore, we investigated another quantum signature, the coherence, quantitatively measured by the non-zero off diagonal element of the density matrix. Populations of states give the probabilities of individual states and therefore quantify the population landscape. Both curl flux and coherence depend on steady state population landscape. Besides the environment-assistance which can give dramatic enhancement of coherence and quantum flux with high voltage at a fixed tunneling strength, the quantum flux is promoted by the coherence in the regime of small tunneling while reduced by the coherence in the regime of large tunneling, due to the non-monotonic relationship between the coherence and tunneling. This is in contrast to the previously found linear relationship. For the systems coupled to bosonic (photonic and phononic) reservoirs the flux is significantly promoted at large voltage while for fermionic (electronic) reservoirs the flux reaches a saturation after a significant enhancement at large voltage due to the Pauli exclusion principle. In view of the system as a quantum heat engine, we studied the non-equilibrium thermodynamics and established the analytical connections of curl quantum flux to the transport quantities such as energy (charge) transfer efficiency, chemical reaction efficiency, energy

  17. Chinese Journal of Population, Resources and Environment announces cooperation with Thomson Reuters —— Adopts world leading online peer review system ScholarOne Manuscripts

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The Chinese Journal of Population, Resources and Environment, (ISSN 1004-2857, CN 37-1202/N), recently adopted ScholarOne Manuscripts to manage its submissions and peer review process. The comprehensive online platform will help further promote academic exchange by streamlining the editorial and publication process: authors enjoy ease of submission and ability to track manuscript review status while editors can manage review tasks in a dynamic, fully-integrated interface that enables the most informed decision-making.

  18. Signed Networks, Triadic Interactions and the Evolution of Cooperation

    Directory of Open Access Journals (Sweden)

    Károly Takács

    2013-09-01

    Full Text Available We outline a model to study the evolution of cooperation in a population of agents playing the prisoner's dilemma in signed networks. We highlight that if only dyadic interactions are taken into account, cooperation never evolves. However, when triadic considerations are introduced, a window of opportunity for emergence of cooperation as a stable behaviour emerges.

  19. DEEPLY EMBEDDED PROTOSTELLAR POPULATION IN THE 20 km s{sup −1} CLOUD OF THE CENTRAL MOLECULAR ZONE

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Xing; Gu, Qiusheng [School of Astronomy and Space Science, Nanjing University, Nanjing 210093 (China); Zhang, Qizhou; Battersby, Cara [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Kauffmann, Jens; Pillai, Thushara [Max Planck Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany); Longmore, Steven N. [Astrophysics Research Institute, Liverpool John Moores University, 146 Brownlow Hill, Liverpool L3 5RF (United Kingdom); Kruijssen, J. M. Diederik, E-mail: xinglv.nju@gmail.com [Zentrum für Astronomie der Universität Heidelberg, Astronomisches Rechen-Institut, Mönchhofstraße 12-14, D-69120 Heidelberg (Germany)

    2015-12-01

    We report the discovery of a population of deeply embedded protostellar candidates in the 20 km s{sup −1} cloud, one of the massive molecular clouds in the Central Molecular Zone (CMZ) of the Milky Way, using interferometric submillimeter continuum and H{sub 2}O maser observations. The submillimeter continuum emission shows five 1 pc scale clumps, each of which further fragments into several 0.1 pc scale cores. We identify 17 dense cores, among which 12 are gravitationally bound. Among the 18 H{sub 2}O masers detected, 13 coincide with the cores and probably trace outflows emanating from the protostars. There are also 5 gravitationally bound dense cores without H{sub 2}O maser detection. In total, the 13 masers and 5 cores may represent 18 protostars with spectral types later than B1 or potentially growing more massive stars at earlier evolutionary stages, given the non-detection in the centimeter radio continuum. In combination with previous studies of CH{sub 3}OH masers, we conclude that the star formation in this cloud is at an early evolutionary phase, before the presence of any significant ionizing or heating sources. Our findings indicate that star formation in this cloud may be triggered by a tidal compression as it approaches pericenter, similar to the case of G0.253+0.016 but with a higher star formation rate, and demonstrate that high angular resolution, high-sensitivity maser, and submillimeter observations are promising techniques to unveil deeply embedded star formation in the CMZ.

  20. Molecular heterogeneity in a patient-derived glioblastoma xenoline is regulated by different cancer stem cell populations.

    Directory of Open Access Journals (Sweden)

    Jo Meagan Garner

    Full Text Available Malignant glioblastoma (GBM is a highly aggressive brain tumor with a dismal prognosis and limited therapeutic options. Genomic profiling of GBM samples has identified four molecular subtypes (Proneural, Neural, Classical and Mesenchymal, which may arise from different glioblastoma stem-like cell (GSC populations. We previously showed that adherent cultures of GSCs grown on laminin-coated plates (Ad-GSCs and spheroid cultures of GSCs (Sp-GSCs had high expression of stem cell markers (CD133, Sox2 and Nestin, but low expression of differentiation markers (βIII-tubulin and glial fibrillary acid protein. In the present study, we characterized GBM tumors produced by subcutaneous and intracranial injection of Ad-GSCs and Sp-GSCs isolated from a patient-derived xenoline. Although they formed tumors with identical histological features, gene expression analysis revealed that xenografts of Sp-GSCs had a Classical molecular subtype similar to that of bulk tumor cells. In contrast xenografts of Ad-GSCs expressed a Mesenchymal gene signature. Adherent GSC-derived xenografts had high STAT3 and ANGPTL4 expression, and enrichment for stem cell markers, transcriptional networks and pro-angiogenic markers characteristic of the Mesenchymal subtype. Examination of clinical samples from GBM patients showed that STAT3 expression was directly correlated with ANGPTL4 expression, and that increased expression of these genes correlated with poor patient survival and performance. A pharmacological STAT3 inhibitor abrogated STAT3 binding to the ANGPTL4 promoter and exhibited anticancer activity in vivo. Therefore, Ad-GSCs and Sp-GSCs produced histologically identical tumors with different gene expression patterns, and a STAT3/ANGPTL4 pathway is identified in glioblastoma that may serve as a target for therapeutic intervention.

  1. Supply and Marketing Cooperatives

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ China Supply and Marketing Cooperatives Council of CCPIT was established in March 1996. It is an institution under direct leadership of China Supply and Market-ing Cooperatives and at the same time a branch of China Council for Promotion of International Trade, with its major task to promoting and facilitating export-oriented economic trade and technological cooper-ation of the national supply and marketing cooperative system.

  2. Population genetic analysis of Serpulina pilosicoli and its molecular epidemiology in villages in the eastern Highlands of Papua New Guinea.

    Science.gov (United States)

    Trott, D J; Mikosza, A S; Combs, B G; Oxberry, S L; Hampson, D J

    1998-07-01

    The population genetics of Serpulina pilosicoli and its molecular epidemiology in villages in the Eastern Highlands province of Papua New Guinea were investigated. Multilocus enzyme electrophoresis (MLEE) was used to analyse 164 isolates from humans and animals. These were divided into 33 electrophoretic types (ETs), four of which contained 65% of the isolates. The mean genetic diversity (n = number of ETs) for 145 human isolates was 0.18, and the mean number of alleles at five polymorphic loci was 2.6. The species appeared to be recombinant, as there was a lack of linkage disequilibrium, and 25% of all the possible combinations of alleles was present in the population. PFGE analysis using the enzymes M/ul and Sa/l divided 157 of the isolates into 99 PFGE types, demonstrating the existence of considerable strain diversity in a geographically restricted area. The two techniques were in excellent agreement; however, PFGE was more discriminatory for strain typing than was MLEE. Nine out of 19 (47.4%) culture-positive individuals were colonized by the same PFGE type of S. pilosicoli when retested after 6 weeks. For three individuals, the PFGE profiles of the second isolate differed from the first in only one or two DNA bands, while the other seven individuals were colonized with distinct PFGE types on each occasion. In two cases, strains with the same PFGE pattern were isolated from humans and dogs, suggesting that cross-species transmission of S. pilosicoli may occur naturally and that the infection can be zoonotic.

  3. Gredos San Diego Cooperative. Cooperate to undertake

    Directory of Open Access Journals (Sweden)

    Carlos de la Higuera

    2012-12-01

    Full Text Available This paper analyzes the cooperative experience through Gredos San Diego model, its institutional approaches and its history from the point of view of management, focusing on the variables that enable the success of a collective ownership institution. First, the author makes a brief analysis of the principles that guide the cooperative, its origins and its current situation, including the development of GSD Cooperative Group. It continues exploring the evolution of management, dividing it into four distinct stages, and concludes with a summary with the findings of the previous president of the cooperative.Received: 23.07.2012Accepted: 10.09.2012

  4. Molecular and morphological characterization of Xiphinema chambersi population from live oak in Jekyll Island, Georgia, with comments on morphometric variations

    Science.gov (United States)

    Zafar A Handoo; Lynn K. Carta; Andrea M. Skantar; Sergei A. Subbotin; Stephen W. Fraedrich

    2016-01-01

    A population of Xiphinema chambersi from the root zone around live oak (Quercus virginiana Mill.) trees on Jekyll Island, GA, is described using both morphological and molecular tools and compared with descriptions of type specimens. Initially, because of a few morphological differences, this nematode was thought to represent...

  5. Circulation of HIV-1 CRF02_AG among MSM Population in Central Italy: A Molecular Epidemiology-Based Study

    Directory of Open Access Journals (Sweden)

    Massimo Giuliani

    2013-01-01

    Full Text Available Introduction. The evolutionary and demographic history of the circular recombinant form CRF02_AG in a selected retrospective group of HIV-1 infected men who have sex with men (MSM resident in Central Italy was investigated. Methods. A total of 55 HIV-1 subtype CRF02_AG pol sequences were analyzed using Bayesian methods and a relaxed molecular clock to reconstruct their dated phylogeny and estimate population dynamics. Results. Dated phylogeny indicated that the HIV-1 CRF02_AG strains currently circulating in Central Italy originated in the early 90's. Bayesian phylogenetic analysis revealed the existence of a main HIV-1 CRF02_AG clade, introduced in the area of Rome before 2000 and subsequently differentiated in two different subclades with a different date of introduction (2000 versus 2005. All the sequences within clusters were interspersed, indicating that the MSM analyzed form a close and restricted network where the individuals, also moving within different clinical centers, attend the same places to meet and exchange sex. Conclusions. It was suggested that the HIV-1 CRF02_AG epidemic entered central Italy in the early 1990s, with a similar trend observed in western Europe.

  6. Crystal chemistry and photomechanical behavior of 3,4-dimethoxycinnamic acid: correlation between maximum yield in the solid-state topochemical reaction and cooperative molecular motion.

    Science.gov (United States)

    Mishra, Manish Kumar; Mukherjee, Arijit; Ramamurty, Upadrasta; Desiraju, Gautam R

    2015-11-01

    A new monoclinic polymorph, form II (P21/c, Z = 4), has been isolated for 3,4-dimethoxycinnamic acid (DMCA). Its solid-state 2 + 2 photoreaction to the corresponding α-truxillic acid is different from that of the first polymorph, the triclinic form I ([Formula: see text], Z = 4) that was reported in 1984. The crystal structures of the two forms are rather different. The two polymorphs also exhibit different photomechanical properties. Form I exhibits photosalient behavior but this effect is absent in form II. These properties can be explained on the basis of the crystal packing in the two forms. The nanoindentation technique is used to shed further insights into these structure-property relationships. A faster photoreaction in form I and a higher yield in form II are rationalized on the basis of the mechanical properties of the individual crystal forms. It is suggested that both Schmidt-type and Kaupp-type topochemistry are applicable for the solid-state trans-cinnamic acid photodimerization reaction. Form I of DMCA is more plastic and seems to react under Kaupp-type conditions with maximum molecular movements. Form II is more brittle, and its interlocked structure seems to favor Schmidt-type topochemistry with minimum molecular movement.

  7. Cooperation under indirect reciprocity and imitative trust.

    Directory of Open Access Journals (Sweden)

    Serguei Saavedra

    Full Text Available Indirect reciprocity, a key concept in behavioral experiments and evolutionary game theory, provides a mechanism that allows reciprocal altruism to emerge in a population of self-regarding individuals even when repeated interactions between pairs of actors are unlikely. Recent empirical evidence show that humans typically follow complex assessment strategies involving both reciprocity and social imitation when making cooperative decisions. However, currently, we have no systematic understanding of how imitation, a mechanism that may also generate negative effects via a process of cumulative advantage, affects cooperation when repeated interactions are unlikely or information about a recipient's reputation is unavailable. Here we extend existing evolutionary models, which use an image score for reputation to track how individuals cooperate by contributing resources, by introducing a new imitative-trust score, which tracks whether actors have been the recipients of cooperation in the past. We show that imitative trust can co-exist with indirect reciprocity mechanisms up to a threshold and then cooperation reverses -revealing the elusive nature of cooperation. Moreover, we find that when information about a recipient's reputation is limited, trusting the action of third parties towards her (i.e. imitating does favor a higher collective cooperation compared to random-trusting and share-alike mechanisms. We believe these results shed new light on the factors favoring social imitation as an adaptive mechanism in populations of cooperating social actors.

  8. Cooperation under indirect reciprocity and imitative trust.

    Science.gov (United States)

    Saavedra, Serguei; Smith, David; Reed-Tsochas, Felix

    2010-10-27

    Indirect reciprocity, a key concept in behavioral experiments and evolutionary game theory, provides a mechanism that allows reciprocal altruism to emerge in a population of self-regarding individuals even when repeated interactions between pairs of actors are unlikely. Recent empirical evidence show that humans typically follow complex assessment strategies involving both reciprocity and social imitation when making cooperative decisions. However, currently, we have no systematic understanding of how imitation, a mechanism that may also generate negative effects via a process of cumulative advantage, affects cooperation when repeated interactions are unlikely or information about a recipient's reputation is unavailable. Here we extend existing evolutionary models, which use an image score for reputation to track how individuals cooperate by contributing resources, by introducing a new imitative-trust score, which tracks whether actors have been the recipients of cooperation in the past. We show that imitative trust can co-exist with indirect reciprocity mechanisms up to a threshold and then cooperation reverses -revealing the elusive nature of cooperation. Moreover, we find that when information about a recipient's reputation is limited, trusting the action of third parties towards her (i.e. imitating) does favor a higher collective cooperation compared to random-trusting and share-alike mechanisms. We believe these results shed new light on the factors favoring social imitation as an adaptive mechanism in populations of cooperating social actors.

  9. Evolution of cooperation on stochastic dynamical networks.

    Directory of Open Access Journals (Sweden)

    Bin Wu

    Full Text Available Cooperative behavior that increases the fitness of others at a cost to oneself can be promoted by natural selection only in the presence of an additional mechanism. One such mechanism is based on population structure, which can lead to clustering of cooperating agents. Recently, the focus has turned to complex dynamical population structures such as social networks, where the nodes represent individuals and links represent social relationships. We investigate how the dynamics of a social network can change the level of cooperation in the network. Individuals either update their strategies by imitating their partners or adjust their social ties. For the dynamics of the network structure, a random link is selected and breaks with a probability determined by the adjacent individuals. Once it is broken, a new one is established. This linking dynamics can be conveniently characterized by a Markov chain in the configuration space of an ever-changing network of interacting agents. Our model can be analytically solved provided the dynamics of links proceeds much faster than the dynamics of strategies. This leads to a simple rule for the evolution of cooperation: The more fragile links between cooperating players and non-cooperating players are (or the more robust links between cooperators are, the more likely cooperation prevails. Our approach may pave the way for analytically investigating coevolution of strategy and structure.

  10. Cooperation, framing and political attitudes

    DEFF Research Database (Denmark)

    Fosgaard, Toke Reinholt; Hansen, Lars Gårn; Wengström, Erik Roland

    This paper shows that political attitudes are linked to cooperative behavior in an incentivized experiment with a large sample randomly drawn from the Danish population. However, this relationship depends on the way the experiment is framed. In the standard game in which subjects give to a public...... that this difference in the framing effect across political point of views is to some extent explained by differences in beliefs and basic cooperation preferences.......This paper shows that political attitudes are linked to cooperative behavior in an incentivized experiment with a large sample randomly drawn from the Danish population. However, this relationship depends on the way the experiment is framed. In the standard game in which subjects give to a public...... good, contributions are the same regardless of political attitudes. In an economically equivalent version, in which subjects take from a public good, left-wingers cooperate significantly more than subjects in the middle or to the right of the political spectrum. Through simulation techniques we find...

  11. 植物自然群体适应逆境的分子机理%Molecular Mechanisms of Stress Adaptation in Plant Natural Populations

    Institute of Scientific and Technical Information of China (English)

    胡志昂; 王洪新

    2001-01-01

    Recent advances in studies of genetic variation at protein andDNA levels in plant natural populations and its relationship with environmental changes were reviewed with special reference to the works on the wild barley (Hordeum spontaneum C. Koch.). On one side, adaptation was shown in statistic data, on the other side, the fact that a considerable part of genetic variation does exist within populations (subpopulations) under same ecological condition indicated its maintainability of neutral or near-neutral mutations in natural populations. The researches on adaptive populations of plants, especially on wild soybean (Glycine soja Sieb. et Zucc.) mainly conducted in author's laboratory, have shown that the most part of molecular variation within and among populations can not be explained by selection particularly as far as the individual uniqueness was concerned. There are some data shown that adaptation may be caused by accumulation of a few near-neutral mutations. Recent publications on molecular mechanisms of morphological evolution has been received special attention to elucidate the discrepancy between molecular evolution and morphological adaptive evolution. A frame on the unified evolution theory has been built. Finally some related viewpoints of philosophy were discussed.

  12. China-Africa: New Directions of Cooperation

    Directory of Open Access Journals (Sweden)

    L V Ponomarenko

    2015-12-01

    Full Text Available This article analyzes the policy of fifth generation of Chinese leadership with regard to African states. The article deals with the concept of “Chinese Dream”, which was first declared in Africa, an innovative model of international cooperation in the framework of the formation of “economic zone of the Silk Road”. The authors reveal three basic directions of cooperation - political, economic and humanitarian cooperation. Political cooperation is characterized by the activation of mutual visits at the highest level, the interaction in the framework of the UN General Assembly, participation in UN peacekeeping operations. Economic cooperation is characterized by the activation of bilateral trade, the transition to a “modernized version of” investment cooperation, implementation of the strategy of “going abroad” of Chinese products, imports of natural resources from Africa, creating jobs for the local population, financing of infrastructure projects, the transfer of labor-intensive industries in Africa. Humanitarian cooperation includes training program for Africa, the implementation of the Sino-African programs, technology partnerships, research and exchange, and the China-Africa Forum “Think Tank”. Cooperation in health care also plays an important role. The authors note that the new Chinese leadership declares transition to an upgraded version of the Sino-African cooperation.

  13. Cooperative Online Education

    Directory of Open Access Journals (Sweden)

    Morten Flate Paulsen

    2008-07-01

    Full Text Available Cooperative learning seeks to develop virtual learning environments that allow students to have optimal individual freedom within online learning communities. The pedagogical and administrative challenges with regard to accommodating both individual freedom and cooperation are explained in the Theory of Cooperative Freedom. This article shows that cooperative learning can be implemented successfully through a set of instruments or means. To illustrate this with current examples, the article presents NKI Distance Education’s surveys and experiences with cooperative learning. The article also discusses how issues such as web 2.0, transparency, learning partners and individual progression plans relate to cooperative online education.

  14. [Molecular genetic analysis of wild soybean (Glycine soja Sieb. & Zucc.) population structure in anthropogenic and natural landscapes of Primorskii krai].

    Science.gov (United States)

    Nedoluzhko, A V; Tikhonov, A V; Dorokhov, D B

    2008-08-01

    The data are presented on genetic population structure of wild soybean growing in natural and anthropogenically disturbed landscapes of Primorskii krai of the Russian Federation. Comparative analysis showed that wild soybean populations exposed to anthropogenic influence exhibited lower genetic diversity than natural populations. Recommendations on conservation of the wild plant gene pools using comparative data on population genetic structures are made.

  15. Cooperative Tagging Center (CTC)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Cooperative Tagging Center (CTC) began as the Cooperative Game Fish Tagging Program (GTP) at Woods Hole Oceanographic Institute (WHOI) in 1954. The GTP was...

  16. Social diversity promotes cooperation in spatial multigames

    Science.gov (United States)

    Qin, Jiahu; Chen, Yaming; Kang, Yu; Perc, Matjaž

    2017-04-01

    Social diversity is omnipresent in the modern world. Here we introduce this diversity into spatial multigames and study its impact on the evolution of cooperation. Multigames are characterized by two or more different social dilemmas being contested among players in the population. When a fraction of players plays the prisoner's dilemma game while the remainder plays the snowdrift game cooperation becomes a difficult proposition. We show that social diversity, determined by the payoff scaling factors from the uniform, exponential or power-law distribution, significantly promotes cooperation. In particular, the stronger the social diversity, the more widespread cooperative behavior becomes. Monte Carlo simulations on the square lattice reveal that a power-law distribution of social diversity is in fact optimal for socially favorable states, thus resonating with findings previously reported for single social dilemmas. We also show that the same promotion mechanism works in time-varying environments, thus further generalizing the important role of social diversity for cooperation in social dilemmas.

  17. Inequity aversion and the evolution of cooperation

    Science.gov (United States)

    Ahmed, Asrar; Karlapalem, Kamalakar

    2014-02-01

    Evolution of cooperation is a widely studied problem in biology, social science, economics, and artificial intelligence. Most of the existing approaches that explain cooperation rely on some notion of direct or indirect reciprocity. These reciprocity based models assume agents recognize their partner and know their previous interactions, which requires advanced cognitive abilities. In this paper we are interested in developing a model that produces cooperation without requiring any explicit memory of previous game plays. Our model is based on the notion of inequity aversion, a concept introduced within behavioral economics, whereby individuals care about payoff equality in outcomes. Here we explore the effect of using income inequality to guide partner selection and interaction. We study our model by considering both the well-mixed and the spatially structured population and present the conditions under which cooperation becomes dominant. Our results support the hypothesis that inequity aversion promotes cooperative relationship among nonkin.

  18. Molecular phylogenetics and biogeography of the Neotropical skink genus Mabuya Fitzinger (Squamata: Scincidae) with emphasis on Colombian populations.

    Science.gov (United States)

    Pinto-Sánchez, Nelsy Rocío; Calderón-Espinosa, Martha L; Miralles, Aurélien; Crawford, Andrew J; Ramírez-Pinilla, Martha Patricia

    2015-12-01

    Understanding the phylogenetic and geographical history of Neotropical lineages requires having adequate geographic and taxonomic sampling across the region. However, Colombia has remained a geographical gap in many studies of Neotropical diversity. Here we present a study of Neotropical skinks of the genus Mabuya, reptiles that are difficult to identify or delimit due to their conservative morphology. The goal of the present study is to propose phylogenetic and biogeographic hypotheses of Mabuya including samples from the previously under-studied territory of Colombia, and address relevant biogeographic and taxonomic issues. We combined molecular and morphological data sampled densely by us within Colombia with published data representing broad sampling across the Neotropical realm, including DNA sequence data from two mitochondrial (12S rRNA and cytochrome b) and three nuclear genes (Rag2, NGFB and R35). To evaluate species boundaries we employed a general mixed Yule-coalescent (GMYC) model applied to the mitochondrial data set. Our results suggest that the diversity of Mabuya within Colombia is higher than previously recognized, and includes lineages from Central America and from eastern and southern South America. The genus appears to have originated in eastern South America in the Early Miocene, with subsequent expansions into Central America and the Caribbean in the Late Miocene, including at least six oceanic dispersal events to Caribbean Islands. We identified at least four new candidate species for Colombia and two species that were not previously reported in Colombia. The populations of northeastern Colombia can be assigned to M. zuliae, while specimens from Orinoquia and the eastern foothills of the Cordillera Oriental of Colombia correspond to M. altamazonica. The validity of seven species of Mabuya sensu lato was not supported due to a combination of three factors: (1) non-monophyly, (2) <75% likelihood bootstrap support and <0.95 Bayesian posterior

  19. BRCA mutations, molecular markers, and clinical variables in early-onset breast cancer: a population-based study.

    Science.gov (United States)

    Musolino, Antonino; Bella, Maria A; Bortesi, Beatrice; Michiara, Maria; Naldi, Nadia; Zanelli, Paola; Capelletti, Marzia; Pezzuolo, Debora; Camisa, Roberta; Savi, Mario; Neri, Tauro M; Ardizzoni, Andrea

    2007-06-01

    Early age at onset is generally considered an indicator of genetic susceptibility to breast cancer. To address both the proportion of early-onset breast cancer associated with BRCA-1 or BRCA-2 germline mutation and the contribution of germline mutations to the clinical features and outcome of these tumors, we analyzed molecular status and clinical variables of a population-based sample of 66 Italian women diagnosed with breast cancer before the age of 40 who were unselected for family history. BRCA mutations were screened by automated sequencing of the entire BRCA-1 and BRCA-2 coding regions and splice junctions. Twenty-eight late-onset (over 45 years), sporadic, breast cancers were designated as "control group" for comparisons with early-onset cases. BRCA mutations (10 BRCA-1 and 6 BRCA-2) were detected in 15 (22.7%) out of 66 tested patients. The combination of ER, PR, HER-2/neu negativity and p53 positivity was significantly more frequent in BRCA-1 positive tumors than in BRCA-2 positive and non-BRCA tumors (P=0.03). Taken collectively, BRCA-positive tumors correlated with high histologic grade and ER negativity compared with non-BRCA and sporadic tumors (P=0.05 and 0.003, respectively). There were no significant differences between BRCA-associated breast cancers (BABC) and non-BABC in relapse-free, event-free, and overall survival. Our data confirm that the combination of age at onset and tumor phenotype can provide an efficient model for identifying individuals with a high probability of carrying BRCA mutations and support the hypothesis that breast cancer in BRCA carriers is qualitatively distinct from other early-onset breast cancers and from late-onset, sporadic, breast carcinomas. Further studies on incident cases are necessary to define the independent prognostic significance of germline BRCA mutations.

  20. Molecular population genetics of human CYP3A locus: signatures of positive selection and implications for evolutionary environmental medicine.

    Science.gov (United States)

    Chen, Xiaoping; Wang, Haijian; Zhou, Gangqiao; Zhang, Xiumei; Dong, Xiaojia; Zhi, Lianteng; Jin, Li; He, Fuchu

    2009-10-01

    The human CYP3A gene cluster codes for cytochrome P450 (CYP) subfamily enzymes that catalyze the metabolism of various exogenous and endogenous chemicals and is an obvious candidate for evolutionary and environmental genomic study. Functional variants in the CYP3A locus may have undergone a selective sweep in response to various environmental conditions. The goal of this study was to profile the allelic structure across the human CYP3A locus and investigate natural selection on that locus. From the CYP3A locus spanning 231 kb, we resequenced 54 genomic DNA fragments (a total of 43,675 bases) spanning four genes (CYP3A4, CYP3A5, CYP3A7, and CYP3A43) and two pseudogenes (CYP3AP1 and CYP3AP2), and randomly selected intergenic regions at the CYP3A locus in Africans (24 individuals), Caucasians (24 individuals), and Chinese (29 individuals). We comprehensively investigated the nucleotide diversity and haplotype structure and examined the possible role of natural selection in shaping the sequence variation throughout the gene cluster. Neutrality tests with Tajima's D, Fu and Li's D* and F*, and Fay and Wu's H indicated possible roles of positive selection on the entire CYP3A locus in non-Africans. Sliding-window analyses of nucleotide diversity and frequency spectrum, as well as haplotype diversity and phylogenetically inferred haplotype structure, revealed that CYP3A4 and CYP3A7 had recently undergone or were undergoing a selective sweep in all three populations, whereas CYP3A43 and CYP3A5 were undergoing a selective sweep in non-Africans and Caucasians, respectively. The refined allelic architecture and selection spectrum for the human CYP3A locus highlight that evolutionary dynamics of molecular adaptation may underlie the phenotypic variation of the xenobiotic disposition system and varied predisposition to complex disorders in which xenobiotics play a role.

  1. Fashion, cooperation, and social interactions.

    Science.gov (United States)

    Cao, Zhigang; Gao, Haoyu; Qu, Xinglong; Yang, Mingmin; Yang, Xiaoguang

    2013-01-01

    Fashion plays such a crucial rule in the evolution of culture and society that it is regarded as a second nature to the human being. Also, its impact on economy is quite nontrivial. On what is fashionable, interestingly, there are two viewpoints that are both extremely widespread but almost opposite: conformists think that what is popular is fashionable, while rebels believe that being different is the essence. Fashion color is fashionable in the first sense, and Lady Gaga in the second. We investigate a model where the population consists of the afore-mentioned two groups of people that are located on social networks (a spatial cellular automata network and small-world networks). This model captures two fundamental kinds of social interactions (coordination and anti-coordination) simultaneously, and also has its own interest to game theory: it is a hybrid model of pure competition and pure cooperation. This is true because when a conformist meets a rebel, they play the zero sum matching pennies game, which is pure competition. When two conformists (rebels) meet, they play the (anti-) coordination game, which is pure cooperation. Simulation shows that simple social interactions greatly promote cooperation: in most cases people can reach an extraordinarily high level of cooperation, through a selfish, myopic, naive, and local interacting dynamic (the best response dynamic). We find that degree of synchronization also plays a critical role, but mostly on the negative side. Four indices, namely cooperation degree, average satisfaction degree, equilibrium ratio and complete ratio, are defined and applied to measure people's cooperation levels from various angles. Phase transition, as well as emergence of many interesting geographic patterns in the cellular automata network, is also observed.

  2. Fashion, cooperation, and social interactions.

    Directory of Open Access Journals (Sweden)

    Zhigang Cao

    Full Text Available Fashion plays such a crucial rule in the evolution of culture and society that it is regarded as a second nature to the human being. Also, its impact on economy is quite nontrivial. On what is fashionable, interestingly, there are two viewpoints that are both extremely widespread but almost opposite: conformists think that what is popular is fashionable, while rebels believe that being different is the essence. Fashion color is fashionable in the first sense, and Lady Gaga in the second. We investigate a model where the population consists of the afore-mentioned two groups of people that are located on social networks (a spatial cellular automata network and small-world networks. This model captures two fundamental kinds of social interactions (coordination and anti-coordination simultaneously, and also has its own interest to game theory: it is a hybrid model of pure competition and pure cooperation. This is true because when a conformist meets a rebel, they play the zero sum matching pennies game, which is pure competition. When two conformists (rebels meet, they play the (anti- coordination game, which is pure cooperation. Simulation shows that simple social interactions greatly promote cooperation: in most cases people can reach an extraordinarily high level of cooperation, through a selfish, myopic, naive, and local interacting dynamic (the best response dynamic. We find that degree of synchronization also plays a critical role, but mostly on the negative side. Four indices, namely cooperation degree, average satisfaction degree, equilibrium ratio and complete ratio, are defined and applied to measure people's cooperation levels from various angles. Phase transition, as well as emergence of many interesting geographic patterns in the cellular automata network, is also observed.

  3. Extensive Dialogues and Cooperation

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    @@ Chinese Taipei On March 23,Chairman Wan Jifei of the China Council for the Promotion of International Trade (CCPIT) and Board Chairman Wang Zhigang of the Taipei World Trade Center (TWTC) signed a cooperation agreement at the Taipei World Trade Tower,marking the new page of the development of cooperation and relations between the two organizations and the establishment of their cooperation mechanism.

  4. Sorting and sustaining cooperation

    DEFF Research Database (Denmark)

    Vikander, Nick

    2013-01-01

    This paper looks at cooperation in teams where some people are selfish and others are conditional cooperators, and where lay-offs will occur at a fixed future date. I show that the best way to sustain cooperation prior to the lay-offs is often in a sorting equilibrium, where conditional cooperato...

  5. Molecular dynamics simulation of the cooperative adsorption of barley lipid transfer protein and cis-isocohumulone at the vacuum-water interface.

    Science.gov (United States)

    Euston, S R; Hughes, P; Naser, Md A; Westacott, R E

    2008-11-01

    Molecular dynamic simulations have been carried out on systems containing a mixture of barley lipid transfer protein (LTP) and cis-isocohumulone (a hop derived iso-alpha-acid) in one of its enol forms, in bulk water and at the vacuum-water interface. In solution, the cis-isocohumulone molecules bind to the surface of the LTP molecule. The mechanism of binding appears to be purely hydrophobic in nature via desolvation of the protein surface. Binding of hop acids to the LTP leads to a small change in the 3-D conformation of the protein, but no change in the proportion of secondary structure present in helices, even though there is a significant degree of hop acid binding to the helical regions. At the vacuum-water interface, cis-isocohumulone shows a high surface activity and adsorbs rapidly at the interface. LTP then shows a preference to bind to the preadsorbed hop acid layer at the interface rather than to the bare water-vacuum interface. The free energy of adsorption of LTP at the hop-vacuum-water interface is more favorable than for adsorption at the vacuum-water interface. Our results support the view that hop iso-alpha-acids promote beer foam stability by forming bridges between separate adsorbed protein molecules, thus strengthening the adsorbed protein layer and reducing foam breakdown by lamellar phase drainage. The results also suggest a second mechanism may also occur, whereby the concentration of protein at the interface is increased via enhanced protein adsorption to adsorbed hop acid layers. This too would increase foam stability through its effect on the stabilizing protein layer around the foam bubbles.

  6. Overexpression of PDGFRA cooperates with loss of NF1 and p53 to accelerate the molecular pathogenesis of malignant peripheral nerve sheath tumors

    Science.gov (United States)

    Ki, D H; He, S; Rodig, S; Look, A T

    2017-01-01

    Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive, frequently metastatic sarcomas that are associated with neurofibromatosis type 1 (NF1), a prominent inherited genetic disease in humans. Although loss of the NF1 gene predisposes to MPNST induction, relatively long tumor latency in NF1 patients suggests that additional genetic or epigenetic abnormalities are needed for the development of these nerve sheath malignancies. To study the molecular pathways contributing to the formation of MPNSTs in NF1 patients, we used a zebrafish tumor model defined by nf1 loss in a p53-deficient background together with the overexpression of either wild-type or constitutively activated PDGFRA (platelet-derived growth factor receptor-α) under control of the sox10 neural crest-specific promoter. Here we demonstrate the accelerated onset and increased penetrance of MPNST formation in fish overexpressing both the wild-type and the mutant PDGFRA transgenes in cells of neural crest origin. Interestingly, overexpression of the wild-type PDGFRA was even more potent in promoting transformation than the mutant PDGFRA, which is important because ~78% of human MPNSTs have expression of wild-type PDGFRA, whereas only 5% harbor activating mutations of the gene encoding this receptor. Further analysis revealed the induction of cellular senescence in zebrafish embryos overexpressing mutant, but not wild-type, PDGFRA, suggesting a mechanism through which the oncogenic activity of the mutant receptor is tempered by the activation of premature cellular senescence in an NF1-deficient background. Taken together, our study suggests a model in which overexpression of wild-type PDGFRA associated with NF1 deficiency leads to aberrant activation of downstream RAS signaling and thus contributes importantly to MPNST development—a prediction supported by the ability of the kinase inhibitor sunitinib alone and in combination with the MEK inhibitor trametinib to retard MPNST progression in

  7. Overexpression of PDGFRA cooperates with loss of NF1 and p53 to accelerate the molecular pathogenesis of malignant peripheral nerve sheath tumors.

    Science.gov (United States)

    Ki, D H; He, S; Rodig, S; Look, A T

    2017-02-23

    Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive, frequently metastatic sarcomas that are associated with neurofibromatosis type 1 (NF1), a prominent inherited genetic disease in humans. Although loss of the NF1 gene predisposes to MPNST induction, relatively long tumor latency in NF1 patients suggests that additional genetic or epigenetic abnormalities are needed for the development of these nerve sheath malignancies. To study the molecular pathways contributing to the formation of MPNSTs in NF1 patients, we used a zebrafish tumor model defined by nf1 loss in a p53-deficient background together with the overexpression of either wild-type or constitutively activated PDGFRA (platelet-derived growth factor receptor-α) under control of the sox10 neural crest-specific promoter. Here we demonstrate the accelerated onset and increased penetrance of MPNST formation in fish overexpressing both the wild-type and the mutant PDGFRA transgenes in cells of neural crest origin. Interestingly, overexpression of the wild-type PDGFRA was even more potent in promoting transformation than the mutant PDGFRA, which is important because ~78% of human MPNSTs have expression of wild-type PDGFRA, whereas only 5% harbor activating mutations of the gene encoding this receptor. Further analysis revealed the induction of cellular senescence in zebrafish embryos overexpressing mutant, but not wild-type, PDGFRA, suggesting a mechanism through which the oncogenic activity of the mutant receptor is tempered by the activation of premature cellular senescence in an NF1-deficient background. Taken together, our study suggests a model in which overexpression of wild-type PDGFRA associated with NF1 deficiency leads to aberrant activation of downstream RAS signaling and thus contributes importantly to MPNST development-a prediction supported by the ability of the kinase inhibitor sunitinib alone and in combination with the MEK inhibitor trametinib to retard MPNST progression in

  8. Caracterização molecular de populações de Butia capitata (Arecaceae do Sul do Brasil através de marcadores AFLP Molecular characterization of Butia capitata populations (Arecaceae in Southern Brazil estimated by AFLP analysis

    Directory of Open Access Journals (Sweden)

    Miriam Valli Buttow

    2010-03-01

    Full Text Available O gênero Butia (Arecaceae é um pequeno gênero subtropical com espécies no sul da América do Sul, considerado ornamental. Além disso, seus frutos são apreciados pelo sabor e aroma peculiares. Porém, no Rio Grande do Sul, as populações naturais sofrem com o avanço das atividades rurais e da construção imobiliária. O objetivo deste trabalho foi caracterizar oito populações de Butia capitata ocorrentes no Rio Grande do Sul através de marcadores moleculares do tipo AFLP. Pela análise molecular da variância, foi possível verificar que 83,68% da variabilidade genética são atribuídos à variação entre populações e 13,67% são atribuídos a diferenças entre populações dentro de regiões. A análise comparativa entre as oito populações feita de duas a duas demonstrou que são significativas as diferenças entre 15 populações, com média de 14,72% da variação molecular atribuída às diferenças entre populações. Este resultado indica a presença de variabilidade genética distribuída entre todas as populações, sem subdivisão decorrente de isolamento geográfico.The Butia genus (Arecaceae is a small genus with subtropical species distributed in South America widely used as an ornamental plant. Besides, its fruits are appreciated for its unique flavor and aroma. But in some regions in Rio Grande do Sul State natural populations suffer with progress of building and rural activities. The aim of this study, therefore, was characterizing eight populations of Butia capitata through AFLP markers. By analysis of molecular variance was possible to verify that 83.68% of genetic variability is attributed to variation among populations and 13.67% is attributed to differences among populations within regions. In the pair-wise analysis, differences between 15 populations were significant, with an average of 14.72% of molecular variation attributed to differences between populations. This result indicates the presence of genetic

  9. Costly advertising and the evolution of cooperation.

    Directory of Open Access Journals (Sweden)

    Markus Brede

    Full Text Available In this paper, I investigate the co-evolution of fast and slow strategy spread and game strategies in populations of spatially distributed agents engaged in a one off evolutionary dilemma game. Agents are characterized by a pair of traits, a game strategy (cooperate or defect and a binary 'advertising' strategy (advertise or don't advertise. Advertising, which comes at a cost [Formula: see text], allows investment into faster propagation of the agents' traits to adjacent individuals. Importantly, game strategy and advertising strategy are subject to the same evolutionary mechanism. Via analytical reasoning and numerical simulations I demonstrate that a range of advertising costs exists, such that the prevalence of cooperation is significantly enhanced through co-evolution. Linking costly replication to the success of cooperators exposes a novel co-evolutionary mechanism that might contribute towards a better understanding of the origins of cooperation-supporting heterogeneity in agent populations.

  10. Cooperative credit systems: defence of the model

    Directory of Open Access Journals (Sweden)

    Roxana Sánchez Boza

    2015-11-01

    Full Text Available This study analyses the role carried out by saving and credit cooperatives in Central America where they have gained momentum, mainly in the past ten years. Cooperatives of this type are called financial intermediation cooperatives due to the influence of various legislative regulations that have placed them in the context of international control, the type of economic activity they perform and the fact that they make profits from both public and private international entities which enable their growth.Many of these organisations can be commended. They are highly competitive on financial markets and strive to extend their profits to increasingly larger parts of the population while also searching for new products to benefit the sector of the population that has chosen the cooperative model as a means to progress in a sphere of equity and respect for the rights of their fellow men.Received: 31.05.2015Accepted: 17.07.2015

  11. Spatial prisoner's dilemma games with zealous cooperators

    Science.gov (United States)

    Matsuzawa, Ryo; Tanimoto, Jun; Fukuda, Eriko

    2016-08-01

    The existence of a zealot who stays a cooperator irrespective of the result of an interaction has been reported to add "social viscosity" to a population and thereby helps increase the cooperation level in prisoner's dilemma games, which premises the so-called well-mixed situation of a population. We found that this is not always true when a spatial structure, i.e., connecting agent, is introduced. Deploying zealots is counterproductive, especially when the underlying topology is homogenous, similar to that of a lattice. Our simulation reveals how the existence of never-converting cooperators destroys rather than boosts cooperation. We explain detailed mechanisms behind this interesting finding by referring to our previously presented concepts with respect to evolutionary dynamic processes for spatial games under the names enduring and expanding periods.

  12. Costly Advertising and the Evolution of Cooperation

    Science.gov (United States)

    Brede, Markus

    2013-01-01

    In this paper, I investigate the co-evolution of fast and slow strategy spread and game strategies in populations of spatially distributed agents engaged in a one off evolutionary dilemma game. Agents are characterized by a pair of traits, a game strategy (cooperate or defect) and a binary ‘advertising’ strategy (advertise or don’t advertise). Advertising, which comes at a cost , allows investment into faster propagation of the agents’ traits to adjacent individuals. Importantly, game strategy and advertising strategy are subject to the same evolutionary mechanism. Via analytical reasoning and numerical simulations I demonstrate that a range of advertising costs exists, such that the prevalence of cooperation is significantly enhanced through co-evolution. Linking costly replication to the success of cooperators exposes a novel co-evolutionary mechanism that might contribute towards a better understanding of the origins of cooperation-supporting heterogeneity in agent populations. PMID:23861752

  13. Costly advertising and the evolution of cooperation.

    Science.gov (United States)

    Brede, Markus

    2013-01-01

    In this paper, I investigate the co-evolution of fast and slow strategy spread and game strategies in populations of spatially distributed agents engaged in a one off evolutionary dilemma game. Agents are characterized by a pair of traits, a game strategy (cooperate or defect) and a binary 'advertising' strategy (advertise or don't advertise). Advertising, which comes at a cost [Formula: see text], allows investment into faster propagation of the agents' traits to adjacent individuals. Importantly, game strategy and advertising strategy are subject to the same evolutionary mechanism. Via analytical reasoning and numerical simulations I demonstrate that a range of advertising costs exists, such that the prevalence of cooperation is significantly enhanced through co-evolution. Linking costly replication to the success of cooperators exposes a novel co-evolutionary mechanism that might contribute towards a better understanding of the origins of cooperation-supporting heterogeneity in agent populations.

  14. Evolution of Cooperation in Public Goods Games

    Institute of Scientific and Technical Information of China (English)

    夏承遗; 张娟娟; 王祎玲; 王劲松

    2011-01-01

    We investigate the evolution of cooperation with evolutionary public goods games based on finite populations, where four pure strategies: cooperators, defectors, punishers and loners who are unwilling to participate are considered. By adopting approximate best response dynamics, we show that the magnitude of rationality not only quantitatively explains the experiment results in [Nature (London) 425 (2003) 390], but also it will heavily influence the evolution of cooperation. Compared with previous results of infinite populations, which result in two equilibriums, we show that there merely exists a special equilibrium cooperation. In addition, we characterize that loner's and the relevant high value of bounded rationality will sustain payoff plays an active role in the maintenance of cooperation, which will only be warranted for the low and moderate values of loner's payoff. It thus indicates the effects of rationality and loner's payoff will influence the cooperation. Finally, we highlight the important result that the introduction of voluntary participation and punishment will facilitate cooperation greatly.

  15. Assortment of encounters and evolution of cooperativeness.

    Science.gov (United States)

    Eshel, I; Cavalli-Sforza, L L

    1982-02-01

    The method of evolutionary stable strategies (ESS), in its current form, is confronted with a difficulty when it tries to explain how some social behaviors initiate their evolution. We show that this difficulty may be removed by changing the assumption made tacitly in game theory (and in ESS) of randomness of meetings or encounters. In reality, such randomness seems to be rare in nature. Family, population and social structure, customs, and habits impose various types of deviation from randomness. Introducing nonrandomness of meeting in a way formally similar to assortative mating, we show that the bar to initial increase of inherited cooperative or altruistic behaviors can be removed, provided there is sufficient assortment of meetings. Family structure may cause contacts predominantly between certain types of relatives, and one can reconstruct some results of classical kin selection in terms of evolutionary stable strategy with assortative meetings. Neighbor effects and group selection might be similarly treated. Assortment need not be a passive consequence of population and social structure, but it can also be actively pursued. Behaviors favoring the choice of cooperative companions will have the effect of favoring the evolution of cooperativeness. It can be shown that discrimination in the choice of companions, especially if combined with assortment, can favor the development of cooperativeness, making initial increase of cooperative behavior possible even at levels of assortment passively imposed which would not be adequate, per se, to guarantee the increase of cooperativeness. It is possible that, in some cases, cooperativeness and behavior favoring some type of assortment are coselected.

  16. Designing for cooperation - cooperating in design

    DEFF Research Database (Denmark)

    Kyng, Morten

    1991-01-01

    This article will discuss how to design computer applications that enhance the quality of work and products, and will relate the discussion to current themes in the field of Computer-Supported Cooperative Work (CSCW). Cooperation is a key element of computer use and work practice, yet here...... a specific "CSCW approach is not taken." Instead the focus is cooperation as an important aspect of work that should be integrated into most computer support efforts in order to develop successful computer support, however, other aspects such as power, conflict and control must also be considered....

  17. Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools.

    Science.gov (United States)

    Dufresne, France; Stift, Marc; Vergilino, Roland; Mable, Barbara K

    2014-01-01

    Despite the importance of polyploidy and the increasing availability of new genomic data, there remain important gaps in our knowledge of polyploid population genetics. These gaps arise from the complex nature of polyploid data (e.g. multiple alleles and loci, mixed inheritance patterns, association between ploidy and mating system variation). Furthermore, many of the standard tools for population genetics that have been developed for diploids are often not feasible for polyploids. This review aims to provide an overview of the state-of-the-art in polyploid population genetics and to identify the main areas where further development of molecular techniques and statistical theory is required. We review commonly used molecular tools (amplified fragment length polymorphism, microsatellites, Sanger sequencing, next-generation sequencing and derived technologies) and their challenges associated with their use in polyploid populations: that is, allele dosage determination, null alleles, difficulty of distinguishing orthologues from paralogues and copy number variation. In addition, we review the approaches that have been used for population genetic analysis in polyploids and their specific problems. These problems are in most cases directly associated with dosage uncertainty and the problem of inferring allele frequencies and assumptions regarding inheritance. This leads us to conclude that for advancing the field of polyploid population genetics, most priority should be given to development of new molecular approaches that allow efficient dosage determination, and to further development of analytical approaches to circumvent dosage uncertainty and to accommodate 'flexible' modes of inheritance. In addition, there is a need for more simulation-based studies that test what kinds of biases could result from both existing and novel approaches. © 2013 John Wiley & Sons Ltd.

  18. Estimating Breeding Values With Molecular Relatedness and Reconstructed Pedigrees in Natural Mating Populations of Common Sole, Solea Solea

    NARCIS (Netherlands)

    Blonk, R.J.W.; Komen, J.; Kamstra, A.; Arendonk, van J.A.M.

    2010-01-01

    Captive populations where natural mating in groups is used to obtain offspring typically yield unbalanced population structures with highly skewed parental contributions and unknown pedigrees. Consequently, for genetic parameter estimation, relationships need to be reconstructed or estimated using D

  19. Cooperative strategies European perspectives

    CERN Document Server

    Killing, J Peter

    1997-01-01

    Cooperative Strategies: European Perspectives is one of three geographically targeted volumes in which the contributors present the most current research on topics such as advances in theories of cooperative strategies, the formation of cooperative alliances, the dynamics of partner relationships, and the role of information and knowledge in cooperative alliances. Blending conceptual insights with empirical analyses, the contributors highlight commonalities and differences across national, cultural, and trade zones. The chapters in this volume are anchored in a wide set of theoretical approaches, conceptual frameworks, and models, illustrating how rich the area of cooperative strategies is for scholarly inquiry.

  20. Dilemmas of partial cooperation.

    Science.gov (United States)

    Stark, Hans-Ulrich

    2010-08-01

    Related to the often applied cooperation models of social dilemmas, we deal with scenarios in which defection dominates cooperation, but an intermediate fraction of cooperators, that is, "partial cooperation," would maximize the overall performance of a group of individuals. Of course, such a solution comes at the expense of cooperators that do not profit from the overall maximum. However, because there are mechanisms accounting for mutual benefits after repeated interactions or through evolutionary mechanisms, such situations can constitute "dilemmas" of partial cooperation. Among the 12 ordinally distinct, symmetrical 2 x 2 games, three (barely considered) variants are correspondents of such dilemmas. Whereas some previous studies investigated particular instances of such games, we here provide the unifying framework and concisely relate it to the broad literature on cooperation in social dilemmas. Complementing our argumentation, we study the evolution of partial cooperation by deriving the respective conditions under which coexistence of cooperators and defectors, that is, partial cooperation, can be a stable outcome of evolutionary dynamics in these scenarios. Finally, we discuss the relevance of such models for research on the large biodiversity and variation in cooperative efforts both in biological and social systems.

  1. Molecular phylogeny of an Indian population of Kleinstyla dorsicirrata (Foissner, 1982) Foissner et al., 2002. comb. nov. (Hypotrichia, Oxytrichidae): an oxytrichid with incomplete dorsal kinety fragmentation.

    Science.gov (United States)

    Singh, Jasbir; Kamra, Komal

    2014-01-01

    Kleinstyla dorsicirrata (Foissner, 1982) Foissner et al., 2002. comb. nov. (basionym: Gastrostyla dorsicirrata) is a slightly flexible oxytrichid, measuring about 88-115 × 27-46 μm in life and possesses cortical granules. Kleinstyla dorsicirrata is the only oxytrichid known so far with incompletely fragmented dorsal kinety. Morphological and morphogenetic data recognise K. dorsicirrata as nonstylonychine oxytrichid. Molecular phylogeny of an Indian population was inferred using 18S rRNA gene sequences and was examined with respect to oxytrichids exhibiting variation in dorsal kinety fragmentation. Kleinstyla dorsicirrata clusters with Oxytricha lanceolata; this proximity is quite significant as both show deviation from typical oxytrichid fragmentation of dorsal kinety. Molecular phylogeny of Indian population confirms its nonstylonychine oxytrichid status. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

  2. Sharing the sandbox: Evolutionary mechanisms that maintain bacterial cooperation [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Eric Bruger

    2015-12-01

    Full Text Available Microbes are now known to participate in an extensive repertoire of cooperative behaviors such as biofilm formation, production of extracellular public-goods, group motility, and higher-ordered multicellular structures. A fundamental question is how these cooperative tasks are maintained in the face of non-cooperating defector cells. Recently, a number of molecular mechanisms including facultative participation, spatial sorting, and policing have been discovered to stabilize cooperation. Often these different mechanisms work in concert to reinforce cooperation. In this review, we describe bacterial cooperation and the current understanding of the molecular mechanisms that maintain it.

  3. Role of aspiration-induced migration in cooperation

    CERN Document Server

    Yang, Han-Xin; Wang, Bing-Hong

    2011-01-01

    Both cooperation and migration are ubiquitous in human society and animal world. In this Rapid Communication, we propose an aspiration-induced migration in which individuals will migrate to new sites provided that their payoffs are below some aspiration level. It is found that moderate aspiration level can best favor cooperative behavior. In particular, moderate aspiration level enables cooperator clusters to maintain and expand whereas induces defector clusters to disintegrate, thus promoting the diffusion of cooperation among population. Our results provide insights into understanding the role played by migration in the emergence of cooperative behavior.

  4. Sequence Analysis of mtDNA COIGene and Molecular Phylogeny of Different Geographical Populations of Bemisia tabaci (Gennadius)

    Institute of Scientific and Technical Information of China (English)

    CHU Dong; ZHANG You-jun; CONG Bin; XU Bao-yun; WU Qing-jun; ZHU Guo-ren

    2005-01-01

    Bemisia tabaci(Gennadius) is a serious pest in many cropping systems worldwide and occurs in different biotypes. The mtDNA COI gene of the 12 Bemisia tabaci (Gennadius) populations from different regions and countries were analyzed.Based on mtDNA COI sequences, their biotypes were characterized and phylogenetic relationships among these populations were established with the method of UPGMA. The results indicated the genetic similarity between those populations from Beijing, Zhengzhou, Zaozhuang, Nanjing, Shanghai, Haikou, and the B-biotype populations from California, Texas, Arizona reached 99.8-100%, which meant the nation-wide infested populations of B. tabaci in China in recent years were B-biotypes. Another population collected from Kunming of Yunnan Province showed very high similarity with Q-biotype B. tabaci from Spain and Morocco, which meant the Kunming population was Q-biotype. This is the first report on the invasion of Q-biotype into China.

  5. To cooperate or not to cooperate

    DEFF Research Database (Denmark)

    Wessels, Josepha Ivanka

    To Cooperate or not to Cooperate...? discusses results of a research project to study the rehabilitation of 1500-year old water tunnels, so called "qanats", in Syria. Communities all over the world are using traditional technologies to extract drinkingwater, irrigate their lands and feed their li......To Cooperate or not to Cooperate...? discusses results of a research project to study the rehabilitation of 1500-year old water tunnels, so called "qanats", in Syria. Communities all over the world are using traditional technologies to extract drinkingwater, irrigate their lands and feed...... their livestock. But these often sustainable and ancient ways to make use of groundwater are in rapid decline worldwide. A research project started in 1999 to study the rehabilitation of 1500-year old water tunnels called "qanats"in Syria. To Cooperate or not to Cooperate...? discusses results and outcomes...... of this research project. The main objective of this research is to better understand the proces of collective maintenance of these ancient water tunnels. The study evaluates the social, cultural, political and environmental factors that have driven abandonment and decay of qanats in Syria. It tries to reconcile...

  6. Studies of Resurgent Bed Bugs: Population Genetic Structure, Impact of Aggregation on Development and Molecular Screening for Bartonella

    Science.gov (United States)

    Saenz, Virna Lisa

    The recent resurgence of bed bugs (Cimex lectularius L.) has created an unprecedented demand for research on its biology. The main objectives of this dissertation research were to investigate several aspects of bed bug biology: infestation and dispersal dynamics at a large and small geographical scale using molecular markers, to determine the impact of aggregation on bed bug development and to screen bed bug populations for a re-emergent pathogen. First, we studied the infestation and dispersal dynamics of bed bugs at large geographical scale (e.g., across cities, states). Although bed bug infestations are on the rise, there is a poor understanding of their dispersal patterns and sources of infestation. We conducted a genetic study of 21 bed bug infestations from the eastern United States. We genotyped samples comprised of 8 - 10 individuals per infestation at nine polymorphic microsatellite loci. Despite high genetic diversity across all infestations, with 5 -- 17 alleles per locus (mean = 10.3), we found low genetic diversity (1 -- 4 alleles per locus) within all but one of the infestations. These results suggest that nearly all the studied infestations were started by a small propagule possibly consisting of a singly mated female and/or her progeny. All infestations were strongly genetically differentiated from each other (mean pairwise FST between populations = 0.68) and we did not find strong evidence of a geographic pattern of structuring. The high level of genetic diversity across infestations from the eastern United States together with the lack of geographically organized structure is consistent with multiple introductions into the United States from foreign sources. This work is described in Chapter 2 and was published in the Journal of Medical Entomology in 2012. Second, we investigated dispersal and infestation dynamics of bed bugs at a fine geographical scale within three multistory apartment buildings: one from Raleigh, NC and two from Jersey City, NJ

  7. Crowding-induced Cooperativity in DNA Surface Hybridization

    Science.gov (United States)

    Lei, Qun-li; Ren, Chun-lai; Su, Xiao-hang; Ma, Yu-qiang

    2015-01-01

    High density DNA brush is not only used to model cellular crowding, but also has a wide application in DNA-functionalized materials. Experiments have shown complicated cooperative hybridization/melting phenomena in these systems, raising the question that how molecular crowding influences DNA hybridization. In this work, a theoretical modeling including all possible inter and intramolecular interactions, as well as molecular details for different species, is proposed. We find that molecular crowding can lead to two distinct cooperative behaviours: negatively cooperative hybridization marked by a broader transition width, and positively cooperative hybridization with a sharper transition, well reconciling the experimental findings. Moreover, a phase transition as a result of positive cooperativity is also found. Our study provides new insights in crowding and compartmentation in cell, and has the potential value in controlling surface morphologies of DNA functionalized nano-particles. PMID:25875056

  8. Global network cooperation catalysed by a small prosocial migrant clique

    CERN Document Server

    Miller, Steve

    2016-01-01

    Much research has been carried out to understand the emergence of cooperation in simulated social networks of competing individuals. Such research typically implements a population as a single connected network. Here we adopt a more realistic premise; namely that populations consist of multiple networks, whose members migrate from one to another. Specifically, we isolate the key elements of the scenario where a minority of members from a cooperative network migrate to a network populated by defectors. Using the public goods game to model group-wise cooperation, we find that under certain circumstances, the concerted actions of a trivial number of such migrants will catalyse widespread behavioural change throughout an entire population. Such results support a wider argument: that the general presence of some form of disruption contributes to the emergence of cooperation in social networks, and consequently that simpler models may encode a determinism that precludes the emergence of cooperation.

  9. A unifying study of phenotypic and molecular genetic variability in natural populations of Anadenanthera colubrina var. cebil from Yungas and Paranaense biogeographic provinces in Argentina

    Indian Academy of Sciences (India)

    María Victoria García; Kathleen Prinz; María Eugenia Barrandeguy; Marcos Miretti; Reiner Finkeldey

    2014-04-01

    Anadenanthera colubrina var. cebil is a discontinuously distributed native tree species in South American subtropical forests. Thirteen quantitative traits and eight nuclear microsatellite loci were examined in individuals from two biogeographic provinces of Argentina to determine the number and composition of genetically distinguishable groups of individuals and explore possible spatial patterns of the phenotypic and genetic variability. Means of reproductive traits were higher in the Yungas than in the Paranaense biogeographic province, whereas five out of eight nonreproductive quantitative traits showed higher mean values in the latter. Variance coefficients were moderate, and there were significant differences between and within provinces. Three clusters were defined based on spatial model for cluster membership for quantitative traits. One cluster grouped the individuals from the Paranaense biogeographic province whereas the individuals from the Yungas biogeographic province grouped regarding its population of origin. Parameters of molecular genetic variability showed higher values in the Yungas than in the Paranaense biogeographic province. Observed heterozygosity was lower than expected heterozygosity in both biogeographic provinces, indicating an excess of homozygosity. The homozygosity test by Watterson and the exact test by Slatkin suggested diversifying selection for locus Ac41.1. Bayesian clustering spatial model for microsatellites loci data were performed for both all loci and for all loci excluding locus Ac41.1. In both analyses two clusters were inferred. Analysis of molecular variance revealed similar results for all genotypes and for all genotypes defined excluding locus Ac41.1. Most of the total variance is attributable to genetic variation within clusters. The presence of homogeneous clusters was detected for both the phenotypic and molecular genetic variability. Two Bayesian clustering analyses were performed according to molecular genetic data

  10. Cooperative effects in spherical spasers

    DEFF Research Database (Denmark)

    Bordo, Vladimir

    2017-01-01

    a shell/core contains an arbitrarily large number of active molecules in the vicinity of a metallic core/shell. An essential aspect of the theory is an ab initio account of the feedback from the core/shell boundaries which significantly modifies the molecular dynamics. The theory provides rigorous, albeit......A fully analytical semiclassical theory of cooperative optical processes which occur in an ensemble of molecules embedded in a spherical core-shell nanoparticle is developed from first principles. Both the plasmonic Dicke effect and spaser generation are investigated for the designs in which...

  11. Cooperative wireless communications

    CERN Document Server

    Zhang, Yan

    2009-01-01

    Cooperative devices and mechanisms are increasingly important to enhance the performance of wireless communications and networks, with their ability to decrease power consumption and packet loss rate and increase system capacity, computation, and network resilience. Considering the wide range of applications, strategies, and benefits associated with cooperative wireless communications, researchers and product developers need a succinct understanding of relevant theory, fundamentals, and techniques to navigate this challenging field. ""Cooperative Wireless Communications"" provides just that. I

  12. Molecular and morphological characterization of an unusual Meloidogyne arenaria population from traveler’s tree (Ravenala madagascariensis)

    Science.gov (United States)

    An unusual Meloidogyne arenaria population was discovered on roots of a traveler’s tree (Ravenala madagascariensis) intended for display at a public arboretum in Pennsylvania. The population aroused curiosity by the lack of visible galling on the roots of the infected plant, and the females were typ...

  13. MOLECULAR DETECTION OF CLARITHROMYCIN AND FLUOROQUINOLONES RESISTANCE IN HELICOBACTER PYLORI INFECTION, DIRECTLY APPLIED TO GASTRIC BIOPSIES, IN AN URBAN BRAZILIAN POPULATION.

    Science.gov (United States)

    Martins, Gustavo Miranda; Sanches, Bruno Squárcio Fernandes; Moretzsohn, Luciana Dias; Lima, Karine Sampaio; Cota, Bianca Della Croce V; Coelho, Luiz Gonzaga Vaz

    2016-01-01

    - Antimicrobial resistance is the major factor leading to eradication failure in H. pylori treatment. Molecular tests are useful to detect genetic mutations predictive of clarithromycin and fluoroquinolones resistance. Knowledge of the local prevalence rate of resistance is important to define the best recommended treatment. - To assess the prevalence of primary resistance of H. pylori to clarithromycin and fluoroquinolones, using a molecular test, in a Southeastern urban Brazilian population. - A total of 72 H. pylori seropositive patients [65% female, mean age 39 (19-73) years] never treated before for this infection were studied. All patients underwent gastroscopy in addition to antrum and corpus biopsies and molecular test GenoType HelicoDR (Hain Life Science, Germany) to detect H. pylori and point mutations in genes responsible for clarithromycin and fluoroquinolone resistance. The molecular procedure was divided into three steps: DNA extraction from biopsy samples, a multiplex amplification with biotinylated primers and a reverse hybridization. The most frequent point mutations involved in resistance to the two antibiotics were evaluated. - Resistance to clarithromycin was detected in nine (12.5%) patients and to fluoroquinolones in eight (11.1%) patients. The point mutation A2147G was the most common (77.8%) among resistant strains to clarithromycin. In 50% of the resistant strains to fluoroquinolones, the mutant codon couldn't be identified. - The resistance rates to clarithromycin and fluorquinolones in a large urban population in the Southeast of Brazil were acceptable, suggesting that these drugs remain appropriate options to first and second-line of H. pylori treatment. The molecular test represents an adequate diagnostic tool for monitoring H. pylori resistance.

  14. Emergence of cooperation in public goods games.

    Science.gov (United States)

    Kurokawa, Shun; Ihara, Yasuo

    2009-04-07

    Evolution of cooperation has been a major issue in evolutionary biology. Cooperation is observed not only in dyadic interactions, but also in social interactions involving more than two individuals. It has been argued that direct reciprocity cannot explain the emergence of cooperation in large groups because the basin of attraction for the 'cooperative' equilibrium state shrinks rapidly as the group size increases. However, this argument is based on the analysis of models that consider the deterministic process. More recently, stochastic models of two-player games have been developed and the conditions for natural selection to favour the emergence of cooperation in finite populations have been specified. These conditions have been given as a mathematically simple expression, which is called the one-third law. In this paper, we investigate a stochastic model of n-player games and show that natural selection can favour a reciprocator replacing a population of defectors in the n-player repeated Prisoner's Dilemma game. We also derive a generalized version of the one-third law (the {2/[n(n+1)]}1/(n-1) law). Additionally, contrary to previous studies, the model suggests that the evolution of cooperation in public goods game can be facilitated by larger group size under certain conditions.

  15. Cooperative Station History Forms

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Various forms, photographs and correspondence documenting the history of Cooperative station instrumentation, location changes, inspections, and...

  16. Futures for energy cooperatives

    Energy Technology Data Exchange (ETDEWEB)

    None

    1981-01-01

    A listing of Federal agencies and programs with potential funding for community-scale cooperatives using conservation measures and solar technologies is presented in Section 1. Section 2 presents profiles of existing community energy cooperatives describing their location, history, membership, services, sources of finance and technical assistance. A condensed summary from a recent conference on Energy Cooperatives featuring notes on co-op members' experiences, problems, and opportunities is presented in Section 3. Section 4 lists contacts for additional information. A National Consumer Cooperative Bank Load Application is shown in the appendix.

  17. Cooperation or Silent Rivalry?

    DEFF Research Database (Denmark)

    Zank, Wolfgang

    2010-01-01

    a gravitational pull which goes beyond economic problems. Furthermore, the EU has gradually built up a coherent policy on many fields. The EU has become the “reform anchor” and most important cooperation partner for Egypt. The progress towards increasing Egypt’s “Stake in the Internal Market” places cooperation...... on an increasingly institutionalized basis. In terms of military cooperation the US is still the partner for Egypt. But outside the military sphere institutionalized cooperation is comparatively week. In particular the failure of the US to conclude a free-trade agreement has been crucial. But it would be wrong...

  18. Population Genetics of Jaguars (Panthera onca) in the Brazilian Pantanal: Molecular Evidence for Demographic Connectivity on a Regional Scale.

    Science.gov (United States)

    Valdez, Fernanda Pedone; Haag, Taiana; Azevedo, Fernando C C; Silveira, Leandro; Cavalcanti, Sandra M C; Salzano, Francisco M; Eizirik, Eduardo

    2015-01-01

    Habitat loss and fragmentation are important threats to carnivores worldwide, and can be especially intense for large predators. Jaguars have already been extirpated from over half of their original area of distribution, and few regions still maintain large populations. For these, detailed understanding is crucial for setting appropriate recovery targets in impacted areas. The Pantanal is among the best examples of a region with a large jaguar population in a healthy environment. Here, we analyzed 12 microsatellite loci to characterize genetic diversity and population structure of 52 jaguars sampled in 4 localities of the southern Pantanal, and compared them with prior studies of heavily fragmented populations of the Atlantic Forest. Although we observed some internal structure among the Pantanal localities, our results indicated that this area comprises a single population with high genetic variability. Moreover, our comparative analyses supported the hypothesis that the strong population structure observed in the Atlantic Forest derives from recent, anthropogenic fragmentation. We also observed significant but low levels of genetic differentiation between the Pantanal and Atlantic Forest populations, indicating recent connectivity between jaguars occurring in these biomes. Evidence for admixture between the Pantanal and a population on the western boundary of the Atlantic Forest corroborates the transitional nature of the latter area, where the jaguar population has already been extirpated. Our results can be used to understand jaguar population dynamics in a region that is less disturbed than the Atlantic forest, and to support the design of conservation strategies that maintain and restore natural connectivity among currently isolated areas. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Determinants of public cooperation in multiplex networks

    Science.gov (United States)

    Battiston, Federico; Perc, Matjaž; Latora, Vito

    2017-07-01

    Synergies between evolutionary game theory and statistical physics have significantly improved our understanding of public cooperation in structured populations. Multiplex networks, in particular, provide the theoretical framework within network science that allows us to mathematically describe the rich structure of interactions characterizing human societies. While research has shown that multiplex networks may enhance the resilience of cooperation, the interplay between the overlap in the structure of the layers and the control parameters of the corresponding games has not yet been investigated. With this aim, we consider here the public goods game on a multiplex network, and we unveil the role of the number of layers and the overlap of links, as well as the impact of different synergy factors in different layers, on the onset of cooperation. We show that enhanced public cooperation emerges only when a significant edge overlap is combined with at least one layer being able to sustain some cooperation by means of a sufficiently high synergy factor. In the absence of either of these conditions, the evolution of cooperation in multiplex networks is determined by the bounds of traditional network reciprocity with no enhanced resilience. These results caution against overly optimistic predictions that the presence of multiple social domains may in itself promote cooperation, and they help us better understand the complexity behind prosocial behavior in layered social systems.

  20. Evolution of Cooperation among Mobile Agents

    CERN Document Server

    Chen, Zhuo; Cai, Yun-Ze; Xu, Xiao-Ming

    2010-01-01

    We study the effects of mobility on the evolution of cooperation among self-driven agents, which move at a constant speed v in a two-dimensional plane without boundary restrictions and average directions of neighbors within a radius R for collective motion. Adopting the the prisoner's dilemma game and the snowdrift game as metaphors, we find that cooperation can be maintained and even enhanced for small v and modest values of R, when compared with the case that all agents do not move. Depending on the payoff parameter and the game model, the cooperator frequency may show resonant behavior, or reach an absorbing state of all cooperators as the increase of R and the initial population density. These findings may help understanding the role of individual motion in social systems.

  1. The Joker effect: cooperation driven by destructive agents

    CERN Document Server

    Arenas, Alex; Cuesta, José A; Requejo, Rubén

    2011-01-01

    Understanding the emergence of cooperation is a central issue in evolutionary game theory. The hardest setup for the attainment of cooperation in a population of individuals is the Public Goods game in which cooperative agents generate a common good at their own expenses, while defectors "free-ride" this good. Eventually this causes the exhaustion of the good, a situation which is bad for everybody. Previous results have shown that introducing reputation, allowing for volunteer participation, punishing defectors, rewarding cooperators or structuring agents, can enhance cooperation. Here we present a model which shows how the introduction of rare, malicious agents -that we term jokers- performing just destructive actions on the other agents induce bursts of cooperation. The appearance of jokers promotes a rock-paper-scissors dynamics, where jokers outbeat defectors and cooperators outperform jokers, which are subsequently invaded by defectors. Thus, paradoxically, the existence of destructive agents acting ind...

  2. Emergence of cooperation with self-organized criticality

    CERN Document Server

    Jeong, Hyeong-Chai

    2010-01-01

    Cooperation and self-organized criticality are two main keywords in current studies of evolution. We propose a generalized Bak-Sneppen model and provide a natural mechanism which accounts for both phenomena simultaneously. We use the prisoner's dilemma games to mimic the interactions among the species. Each species is identified by its cooperation probability and its fitness is given by the payoffs from the neighbors. The species with the least payoff is replaced by a new species with a random cooperation probability. When the neighbors of the least fit one are also replaced with a non-zero probability, a strong cooperation emerges. Bak-Sneppen process builds a self-organized structure so that the cooperation can emerge even in the parameter region where a uniform or random population decreases the number of cooperators. The emergence of cooperation is due to the same dynamical correlation which leads to self-organized criticality in replacement activities.

  3. Diagnostic Molecular Markers for Phosphine Resistance in U.S. Populations of Tribolium castaneum and Rhyzopertha dominica

    Science.gov (United States)

    Chen, Zhaorigetu; Schlipalius, David; Opit, George; Subramanyam, Bhadriraju; Phillips, Thomas W.

    2015-01-01

    Stored product beetles that are resistant to the fumigant pesticide phosphine (hydrogen phosphide) gas have been reported for more than 40 years in many places worldwide. Traditionally, determination of phosphine resistance in stored product beetles is based on a discriminating dose bioassay that can take up to two weeks to evaluate. We developed a diagnostic cleaved amplified polymorphic sequence method, CAPS, to detect individuals with alleles for strong resistance to phosphine in populations of the red flour beetle, Tribolium castaneum, and the lesser grain borer, Rhyzopertha dominica, according to a single nucleotide mutation in the dihydrolipoamide dehydrogenase (DLD) gene. We initially isolated and sequenced the DLD genes from susceptible and strongly resistant populations of both species. The corresponding amino acid sequences were then deduced. A single amino acid mutation in DLD in populations of T. castaneum and R. dominica with strong resistance was identified as P45S in T. castaneum and P49S in R. dominica, both collected from northern Oklahoma, USA. PCR products containing these mutations were digested by the restriction enzymes MboI and BstNI, which revealed presence or absence, respectively of the resistant (R) allele and allowed inference of genotypes with that allele. Seven populations of T. castaneum from Kansas were subjected to discriminating dose bioassays for the weak and strong resistance phenotypes. Application of CAPS to these seven populations confirmed the R allele was in high frequency in the strongly resistant populations, and was absent or at a lower frequency in populations with weak resistance, which suggests that these populations with a low frequency of the R allele have the potential for selection of the strong resistance phenotype. CAPS markers for strong phosphine resistance will help to detect and confirm resistant beetles and can facilitate resistance management actions against a given pest population. PMID:25826251

  4. Diagnostic molecular markers for phosphine resistance in U.S. populations of Tribolium castaneum and Rhyzopertha dominica.

    Science.gov (United States)

    Chen, Zhaorigetu; Schlipalius, David; Opit, George; Subramanyam, Bhadriraju; Phillips, Thomas W

    2015-01-01

    Stored product beetles that are resistant to the fumigant pesticide phosphine (hydrogen phosphide) gas have been reported for more than 40 years in many places worldwide. Traditionally, determination of phosphine resistance in stored product beetles is based on a discriminating dose bioassay that can take up to two weeks to evaluate. We developed a diagnostic cleaved amplified polymorphic sequence method, CAPS, to detect individuals with alleles for strong resistance to phosphine in populations of the red flour beetle, Tribolium castaneum, and the lesser grain borer, Rhyzopertha dominica, according to a single nucleotide mutation in the dihydrolipoamide dehydrogenase (DLD) gene. We initially isolated and sequenced the DLD genes from susceptible and strongly resistant populations of both species. The corresponding amino acid sequences were then deduced. A single amino acid mutation in DLD in populations of T. castaneum and R. dominica with strong resistance was identified as P45S in T. castaneum and P49S in R. dominica, both collected from northern Oklahoma, USA. PCR products containing these mutations were digested by the restriction enzymes MboI and BstNI, which revealed presence or absence, respectively of the resistant (R) allele and allowed inference of genotypes with that allele. Seven populations of T. castaneum from Kansas were subjected to discriminating dose bioassays for the weak and strong resistance phenotypes. Application of CAPS to these seven populations confirmed the R allele was in high frequency in the strongly resistant populations, and was absent or at a lower frequency in populations with weak resistance, which suggests that these populations with a low frequency of the R allele have the potential for selection of the strong resistance phenotype. CAPS markers for strong phosphine resistance will help to detect and confirm resistant beetles and can facilitate resistance management actions against a given pest population.

  5. Diagnostic molecular markers for phosphine resistance in U.S. populations of Tribolium castaneum and Rhyzopertha dominica.

    Directory of Open Access Journals (Sweden)

    Zhaorigetu Chen

    Full Text Available Stored product beetles that are resistant to the fumigant pesticide phosphine (hydrogen phosphide gas have been reported for more than 40 years in many places worldwide. Traditionally, determination of phosphine resistance in stored product beetles is based on a discriminating dose bioassay that can take up to two weeks to evaluate. We developed a diagnostic cleaved amplified polymorphic sequence method, CAPS, to detect individuals with alleles for strong resistance to phosphine in populations of the red flour beetle, Tribolium castaneum, and the lesser grain borer, Rhyzopertha dominica, according to a single nucleotide mutation in the dihydrolipoamide dehydrogenase (DLD gene. We initially isolated and sequenced the DLD genes from susceptible and strongly resistant populations of both species. The corresponding amino acid sequences were then deduced. A single amino acid mutation in DLD in populations of T. castaneum and R. dominica with strong resistance was identified as P45S in T. castaneum and P49S in R. dominica, both collected from northern Oklahoma, USA. PCR products containing these mutations were digested by the restriction enzymes MboI and BstNI, which revealed presence or absence, respectively of the resistant (R allele and allowed inference of genotypes with that allele. Seven populations of T. castaneum from Kansas were subjected to discriminating dose bioassays for the weak and strong resistance phenotypes. Application of CAPS to these seven populations confirmed the R allele was in high frequency in the strongly resistant populations, and was absent or at a lower frequency in populations with weak resistance, which suggests that these populations with a low frequency of the R allele have the potential for selection of the strong resistance phenotype. CAPS markers for strong phosphine resistance will help to detect and confirm resistant beetles and can facilitate resistance management actions against a given pest population.

  6. Application of the first internal transcribed spacer (ITS-1) of ribosomal DNA as a molecular marker to population analysis in farrer's scallop Chlamys farreri

    Institute of Scientific and Technical Information of China (English)

    YU Ziniu; WEI Xiaohua; KONG Xiaoyu; YU Shanshan

    2007-01-01

    Sequence variation of the first internal transcribed spacer of ribosomal DNA (ITS-1) was examined and its application to the study of genetic variation was explored in four populations of farrer's scallop Chlamys farreri. ITS-1 fragments,with a length of about 300 bp,of 78 individuals collected from Dalian, Qingdao, Yantai in China and Korea respectively were amplified via PCR, cloned and sequenced. Intra-genomic variation was examined by sequencing several clones of single individuals. Alignment and polymorphism analysis detected 44 haplotypes and 50 polymorphic sites which consist of 30 substitutions and 20 indels, indicating a high level of polymorphisms. Sequence analysis also showed a very low level of intra-individual variation. All these features validated the feasibility of application of ITS-1 fragment to population analysis. Polymorphism analysis showed that the Korea sample has the richest genetic variation, followed by Yantai and Qingdao samples. AMOVA (analysis of molecular variance) showed that the majority (96.26%) of genetic variation was distributed within populations and 3.74% resulted from among populations, but with P<0.05 (= 0.042), indicating that the populations in this study have significant divergence. This output was basically concordant with the result arising from RAPD data and different from that from mitochondrial 16S rDNA sequence data. Discussion on this inconsistency was made accordingly.

  7. Molecular Variation of Adh and P6 Genes in an African Population of Drosophila Melanogaster and Its Relation to Chromosomal Inversions

    Science.gov (United States)

    Benassi, V.; Aulard, S.; Mazeau, S.; Veuille, M.

    1993-01-01

    Four-cutter molecular polymorphism of Adh and P6, and chromosome inversion polymorphism of chromosome II were investigated in 95 isogenic lines of an Ivory Coast population of Drosophila melanogaster, a species assumed to have recently spread throughout the world from a West African origin. The P6 gene showed little linkage disequilibrium with the In(2L)t inversion, although it is located within this inversion. This suggests that the inversion and the P6 locus have extensively exchanged genetic information through either double crossover or gene conversion. Allozymic variation in ADH was in linkage disequilibrium with In(2L)t and In(2R)NS inversions. Evidence suggests either that inversion linkage with the Fast allele is selectively maintained, or that this allele only recently appeared. Molecular polymorphism at the Adh locus in the Ivory Coast is not higher than in North American populations. New haplotypes specific to the African population were found, some of them connect the ``Wa(s)-like'' haplotypes found at high frequencies in the United States to the other slow haplotypes. Their relation with In(2L)t supports the hypothesis that Wa(s) recently recombined away from an In(2L)t chromosome which may be the cause of its divergence from the other haplotypes. PMID:8349110

  8. Morphometric and molecular characterization of Gyrodactylus teuchis Lautraite, Blanc, Thiery, Daniel & Vigneulle, 1999 (Monogenea: Gyrodactylidae) from an Austrian brown trout population.

    Science.gov (United States)

    Hahn, Christoph; Bakke, Tor A; Bachmann, Lutz; Weiss, Steven; Harris, Phil D

    2011-12-01

    Gyrodactylus teuchis is a widespread parasite of wild and farmed salmonids throughout Europe. It has been frequently confused with the notifiable pathogen G. salaris, to which it bears a striking morphological similarity. The species is frequently referred to as 'cryptic', and diagnoses are primarily based on molecular evidence. We provide the first comprehensive re-description of G. teuchis from a natural wild brown trout population in the Danube watershed, based on the state of the art morphometrics in addition to standard molecular markers. We demonstrate that despite the lack of uni-variate diagnostic character measurements, G. teuchis can be reliably distinguished from G. salaris using multivariate morphological approaches such as Principal Component Analysis or Canonical Variate Analysis, suggesting that automated diagnostic approaches for G. salaris can be modified to take account of potential G. teuchis in samples. This is the first record of G. teuchis from a host population unlikely to have been modified by human stocking efforts. The morphological variability observed in the samples collected from one site on 1 day reflects the overall level of variation reported for European G. teuchis. We also report new sequence variants of the internal transcribed spacer (ITS-1) of the nuclear ribosomal gene cluster with evidence for intra-individual heterogeneity of ITS-1 within this population of G. teuchis.

  9. [Individual identification of Amur leopards (Panthera pardus orientalis) using molecular-genetic methods and estimation of the population].

    Science.gov (United States)

    Rozhnov, V V; Sorokin, P A; Lukarevskiĭ, V S; Naĭdenko, S V; Ernandes-Blanko, Kh A; Lukarevskiĭ, S V

    2013-01-01

    For the first time, the genetic structure of a population of Amur leopards (Panthera pardus orientalis) in southwest Primorie was analyzed in detail. In 2010-2012, 23 individuals were identified individually. It was shown that the studied microsatellite markers are suitable for individual identification of leopards, monitoring the population numbers, and creating a unified database of genetic profiles of this species to solve research and nature-preserving tasks.

  10. Molecular ecology meets remote sensing: Environmental drivers to population structure of humpback dolphins in the Western Indian Ocean

    OpenAIRE

    2011-01-01

    Genetic analyses of population structure can be placed in explicit environmental contexts if appropriate environmental data are available. Here, we use high-coverage and high-resolution oceanographic and genetic sequence data to assess population structure patterns and their potential environmental influences for humpback dolphins in the Western Indian Ocean. We analyzed mitochondrial DNA data from 94 dolphins from the coasts of South Africa, Mozambique, Tanzania and Oman, employing frequency...

  11. Population structure of the Atlantic sand fiddler crab Uca pugilator along the eastern coast of US revealed by molecular data

    Directory of Open Access Journals (Sweden)

    David A. WEESE

    2009-04-01

    Full Text Available The Atlantic sand fiddler crab Uca pugilator, is an extremely abundant crab found along the eastern coast of the United States. Fiddler crabs have a life cycle with an obligatory planktonic larval phase of 30–90 days, which might be expected to lead to widespread larval dispersal and consequent genetic homogeneity over considerable distances. However, a large amount of morphological and behavioral variation is found between northern and southern populations along the eastern coast. This study was undertaken to determine the population genetic structure of U.pugilator and to determine whether these differences may have a genetic basis. The population structure of the fiddler crab was analyzed using 472 individuals collected from 12 sites along the eastern coast. PCR-based single stand conformation polymorphism (SSCP was used to investigate between-site variation in the mitochondrial 16S rRNA gene of these individuals. Analysis of genetic variation indicated frequent gene flow between nearby localities, but much reduced levels between populations separated by larger geographic distances. Thus, despite the potential for high dispersal by planktonic larvae, population differentiation and isolation by distance is evident between northern and southern populations of U.pugilator. A high amount of genetic differentiation (FST = 0.3468 was found between northern and southern regions suggesting that the morphological and behavioral differences between these two regions have a genetic basis and may represent subspecies.

  12. Population structure of the Atlantic sand fiddler crab Uca pugilator along the eastern coast of US revealed by molecular data

    Institute of Scientific and Technical Information of China (English)

    David A.WEESE; Denson K.MCLAIN; Ann E.PRATT; Quentin Q.FANG

    2009-01-01

    The Atlantic sand fiddler crab Uca pugilator is an extremely abundant crab found along the eastern coast of the United States. Fiddler crabs have a life cycle with an obligatory planktonic larval phase of 30-90 days, which might be expected to lead to widespread larval dispersal and consequent genetic homogeneity over considerable distances. However, a large amount of morphological and behavioral variation is found between northern and southern populations along the eastern coast. This study was undertaken to determine the population genetic structure of U.pugilator and to determine whether these differences may have a genetic basis. The population structure of the fiddler crab was analyzed using 472 individuals collected from 12 sites along the eastern coast. PCR-based single stand conformation polymorphism (SSCP) was used to investigate between-site variation in the mitochondrial 16S rRNA gene of these individuals. Analysis of genetic variation indicated frequent gene flow between nearby localities, but much reduced levels between populations separated by larger geographic distances. Thus, despite the potential for high dispersal by planktonic larvae, population differentiation and isolation by distance is evident between northern and southern populations of U.pugilator. A high amount of genetic differentiation (FST=0.3468) was found between northern and southern regions suggesting that the morphological and behavioral differences between these two regions have a genetic basis and may represent subspecies [Current Zoology 55(2):150-157,2009].

  13. Molecular Characterization of Lates niloticus (Perciformes, Latidae Populations from three Nigerian Waterbodies using Random Amplified Polymorphic DNA and Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Ogbuebunu K. E.

    2017-02-01

    Full Text Available Thirty Lates niloticus (Linnaeus, 1758 from three Nigerian waterbodies were genotyped on six RAPD primers and five microsatellites loci. RAPD revealed that effective number of alleles (AE at population level per locus was within the range of 1.641 ± 0.066 to 1.645 ± 0.041 while the mean number of alleles (AN across populations equals 2.000. Characterization on five microsatellites loci revealed genetic diversity within and among studied populations. Observed heterozygousity (HO was within the range of 0.317 ± 0.335 to 0.523 ± 0.315 while expected heterozygousity (HE was within the range of 0.414 ± 0.306 to 0.715 ± 0.097. Proportion of differentiation (FST within populations was 0.236. Overall gene flow (Nm among populations equals 0.806. This study established the successful use of RAPD and microsatellite as tools for studying population structure of fish species, especially L. niloticus. Thus, it can be concluded that L. niloticus in the three (3 sampled Nigerian waterbodies is undergoing evolution.

  14. Fragility and cooperativity concepts in hydrogen-bonded organic glasses

    Energy Technology Data Exchange (ETDEWEB)

    Delpouve, N., E-mail: delpouve.nicolas@gmail.com [AMME-LECAP EA 4528 International Laboratory, University of Rouen, Avenue de l' Universite BP 12, 76801 Saint Etienne du Rouvray (France); Vuillequez, A.; Saiter, A.; Youssef, B.; Saiter, J.M. [AMME-LECAP EA 4528 International Laboratory, University of Rouen, Avenue de l' Universite BP 12, 76801 Saint Etienne du Rouvray (France)

    2012-09-01

    Molecular dynamics at the glass transition of three lactose/oil glassy systems have been investigated according to the cooperativity and fragility approaches. From Donth's approach, the cooperativity length is estimated by modulated temperature calorimetric measurements. Results reveal that modification of the disaccharide by oil leads to increase the disorder degree in the lactose, the size of the cooperative domains and the fragility index. These particular hydrogen-bonded organic glasses follow the general tendency observed on organic and inorganic polymers: the higher the cooperativity length, the higher the value of the fragility index at T{sub g}.

  15. Cooperation or Silent Rivalry?

    DEFF Research Database (Denmark)

    Zank, Wolfgang

    2010-01-01

    on an increasingly institutionalized basis. In terms of military cooperation the US is still the partner for Egypt. But outside the military sphere institutionalized cooperation is comparatively week. In particular the failure of the US to conclude a free-trade agreement has been crucial. But it would be wrong...

  16. Readings in Cooperative Education.

    Science.gov (United States)

    Leventhal, Jerome I.

    Twenty-three journal articles on cooperative education were selected in a review of the literature by two Temple University graduate classes in the fall of 1975 and the spring of 1976 for those interested in the role of coordinating cooperative education programs. The journal readings consist of articles on theory/planning (6), implementation…

  17. Coordination and Cooperation

    OpenAIRE

    Janssen, Maarten

    2003-01-01

    textabstractThis comment makes four related points. First, explaining coordination is different from explaining cooperation. Second, solving the coordination problem is more important for the theory of games than solving the cooperation problem. Third, a version of the Principle of Coordination can be rationalized on individualistic grounds. Finally, psychological game theory should consider how players perceive their gaming situation. ---------------------------------------------------------...

  18. Cooperation, compensation and transition

    NARCIS (Netherlands)

    Ju, Y.

    2004-01-01

    Cooperation and compensation are two important and well-linked issues in economics. The central question in cooperation is how to share the joint gains among participating players. Compensation is a specific aspect of surplus sharing problems providing incentives for agents to sacrifice their own di

  19. Cooperative Science Lesson Plans.

    Science.gov (United States)

    Cooperative Learning, 1991

    1991-01-01

    Offers several elementary level cooperative science lesson plans. The article includes a recipe for cooperative class learning, instructions for making a compost pile, directions for finding evidence of energy, experiments in math and science using oranges to test density, and discussions of buoyancy using eggs. (SM)

  20. Cooperative Learning Strategies.

    Science.gov (United States)

    Barnes, Buckley; O'Farrell, Gail

    1990-01-01

    Presents essential characteristics and types of cooperative learning strategies for use in elementary social studies. Outlines exercises for forming teams and building team spirit. Points out such methods promote group interdependence and student responsibility for learning and teaching others. Highlights two cooperative group strategies, Jigsaw…

  1. Coordination and Cooperation

    NARCIS (Netherlands)

    M.C.W. Janssen (Maarten)

    2003-01-01

    textabstractThis comment makes four related points. First, explaining coordination is different from explaining cooperation. Second, solving the coordination problem is more important for the theory of games than solving the cooperation problem. Third, a version of the Principle of Coordination can

  2. International Cooperation Advances Internationalization

    Institute of Scientific and Technical Information of China (English)

    Ge Mingyi

    2004-01-01

    @@ Intemational scientific cooperation continues to successfully promote the development of research and the quality of researchers in China, and also the internationalization of China's research system and research organizations. An outstanding example of this is the 30 years of fruitful cooperation between the Chinese Academy of Sciences and the Max Planck Society.

  3. Coordination and Cooperation

    NARCIS (Netherlands)

    M.C.W. Janssen (Maarten)

    2003-01-01

    textabstractThis comment makes four related points. First, explaining coordination is different from explaining cooperation. Second, solving the coordination problem is more important for the theory of games than solving the cooperation problem. Third, a version of the Principle of Coordination can

  4. Cooperators Unite! Assortative linking promotes cooperation particularly for medium sized associations

    Directory of Open Access Journals (Sweden)

    Boza Gergely

    2010-06-01

    Full Text Available Abstract Background Evolution of cooperative behaviour is widely studied in different models where interaction is heterogeneous, although static among individuals. However, in nature individuals can often recognize each other and chose, besides to cooperate or not, to preferentially associate with or to avoid certain individuals. Here we consider a dynamical interaction graph, in contrast to a static one. We propose several rules of rejecting unwanted partners and seeking out new ones, and study the probability of emergence and maintenance of cooperation on these dynamic networks. Results Our simulations reveal that cooperation can evolve and be stable in the population if we introduce preferential linking, even if defectors can perform it too. The fixation of cooperation has higher probability than that of on static graphs, and this effect is more prevalent at high benefit to cost ratios. We also find an optimal number of partners, for which the fixation probability of cooperation shows a maximum. Conclusions The ability to recognize, seek out or avoid interaction partners based on the outcome of past interactions has an important effect on the emergence of cooperation. Observations about the number of partners in natural cooperating groups are in concordance with the result of our model.

  5. The increased risk of joint venture promotes social cooperation.

    Directory of Open Access Journals (Sweden)

    Te Wu

    Full Text Available The joint venture of many members is common both in animal world and human society. In these public enterprizes, highly cooperative groups are more likely to while low cooperative groups are still possible but not probable to succeed. Existent literature mostly focuses on the traditional public goods game, in which cooperators create public wealth unconditionally and benefit all group members unbiasedly. We here institute a model addressing this public goods dilemma with incorporating the public resource foraging failure risk. Risk-averse individuals tend to lead a autarkic life, while risk-preferential ones tend to participate in the risky public goods game. For participants, group's success relies on its cooperativeness, with increasing contribution leading to increasing success likelihood. We introduce a function with one tunable parameter to describe the risk removal pattern and study in detail three representative classes. Analytical results show that the widely replicated population dynamics of cyclical dominance of loner, cooperator and defector disappear, while most of the time loners act as savors while eventually they also disappear. Depending on the way that group's success relies on its cooperativeness, either cooperators pervade the entire population or they coexist with defectors. Even in the later case, cooperators still hold salient superiority in number as some defectors also survive by parasitizing. The harder the joint venture succeeds, the higher level of cooperation once cooperators can win the evolutionary race. Our work may enrich the literature concerning the risky public goods games.

  6. The increased risk of joint venture promotes social cooperation.

    Science.gov (United States)

    Wu, Te; Fu, Feng; Zhang, Yanling; Wang, Long

    2013-01-01

    The joint venture of many members is common both in animal world and human society. In these public enterprizes, highly cooperative groups are more likely to while low cooperative groups are still possible but not probable to succeed. Existent literature mostly focuses on the traditional public goods game, in which cooperators create public wealth unconditionally and benefit all group members unbiasedly. We here institute a model addressing this public goods dilemma with incorporating the public resource foraging failure risk. Risk-averse individuals tend to lead a autarkic life, while risk-preferential ones tend to participate in the risky public goods game. For participants, group's success relies on its cooperativeness, with increasing contribution leading to increasing success likelihood. We introduce a function with one tunable parameter to describe the risk removal pattern and study in detail three representative classes. Analytical results show that the widely replicated population dynamics of cyclical dominance of loner, cooperator and defector disappear, while most of the time loners act as savors while eventually they also disappear. Depending on the way that group's success relies on its cooperativeness, either cooperators pervade the entire population or they coexist with defectors. Even in the later case, cooperators still hold salient superiority in number as some defectors also survive by parasitizing. The harder the joint venture succeeds, the higher level of cooperation once cooperators can win the evolutionary race. Our work may enrich the literature concerning the risky public goods games.

  7. Efficiency in Microfinance Cooperatives

    Directory of Open Access Journals (Sweden)

    HARTARSKA, Valentina

    2012-12-01

    Full Text Available In recognition of cooperatives’ contribution to the socio-economic well-being of their participants, the United Nations has declared 2012 as the International Year of Cooperatives. Microfinance cooperatives make a large part of the microfinance industry. We study efficiency of microfinance cooperatives and provide estimates of the optimal size of such organizations. We employ the classical efficiency analysis consisting of estimating a system of equations and identify the optimal size of microfinance cooperatives in terms of their number of clients (outreach efficiency, as well as dollar value of lending and deposits (sustainability. We find that microfinance cooperatives have increasing returns to scale which means that the vast majority can lower cost if they become larger. We calculate that the optimal size is around $100 million in lending and half of that in deposits. We find less robust estimates in terms of reaching many clients with a range from 40,000 to 180,000 borrowers.

  8. Culture and cooperation.

    Science.gov (United States)

    Gächter, Simon; Herrmann, Benedikt; Thöni, Christian

    2010-09-12

    Does the cultural background influence the success with which genetically unrelated individuals cooperate in social dilemma situations? In this paper, we provide an answer by analysing the data of Herrmann et al. (2008a), who studied cooperation and punishment in 16 subject pools from six different world cultures (as classified by Inglehart & Baker (2000)). We use analysis of variance to disentangle the importance of cultural background relative to individual heterogeneity and group-level differences in cooperation. We find that culture has a substantial influence on the extent of cooperation, in addition to individual heterogeneity and group-level differences identified by previous research. The significance of this result is that cultural background has a substantial influence on cooperation in otherwise identical environments. This is particularly true in the presence of punishment opportunities.

  9. Evolution of Cooperation in Evolutionary Games for Heterogeneous Interactions

    Institute of Scientific and Technical Information of China (English)

    钱晓岚; 杨俊忠

    2012-01-01

    When a population structure is modelled as a square lattice,the cooperation may be improved for an evolutionary prisoner dilemma game or be inhibited for an evolutionary snowdrift game.In this work,we investigate cooperation in a population on a square lattice where the interaction among players contains both prisoner dilemma game and snowdrift game.The heterogeneity in interaction is introduced to the population in two different ways:the heterogenous character of interaction assigned to every player(HCP) or the heterogenous character of interaction assigned to every link between any two players(HCL).The resonant enhancement of cooperation in the case of HCP is observed while the resonant inhibition of cooperation in the case of HCL is prominent.The explanations on the enhancement or inhibition of cooperation are presented for these two cases.

  10. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach.

    Directory of Open Access Journals (Sweden)

    Simon Boitard

    2016-03-01

    Full Text Available Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey, PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles.

  11. Genetic diversity in a Poincianella pyramidalis (Tul.) L.P. Queiroz population assessed by RAPD molecular markers.

    Science.gov (United States)

    Belarmino, K S; Rêgo, M M; Bruno, R L A; Medeiros, G D A; Andrade, A P; Rêgo, E R

    2017-08-31

    Poincianella pyramidalis (Tul.) L.P. Queiroz is an endemic Caatinga (Brazilian savannah biome) species that has been exploited for different purposes, although information is necessary about still existing natural populations. The objective of this study was to evaluate the genetic diversity among 20 P. pyramidalis individuals occurring in a population localized in the Caatinga biome of Paraíba State, aiming at seed collection, using RAPD markers. For the DNA extraction, young shoots of the individuals were used, and amplification was carried out using 20 primers. The obtained markers were converted to a binary matrix, from which a genetic dissimilarity matrix was built using the arithmetic complement of Jaccard's coefficient, and the dendrogram was built by the UPGMA analysis. No amplified fragment was monomorphic, resulting in 100% polymorphism of the analyzed population. The mean genetic diversity among the matrices was 63.28%, ranging from 30.9 to 97.7%. Individuals 09 and 17 showed relevant genetic proximity, and thus planting their seedlings at close sites would not be indicated. The population evaluated in this study showed high genetic diversity, originating twelve groups from the UPGMA hierarchical cluster analysis. Based on the results, individuals 09 and 17 can provide plant material for the evaluation of the physiological performance of P. pyramidalis seeds, and the set of individuals of this population has a high genetic diversity that characterizes them as adequate matrices for projects of restoration and conservation of the seed species.

  12. Development of cooperative system bridges

    Institute of Scientific and Technical Information of China (English)

    ZHANG Zhe; WAN Qi-bai; SHI Lei

    2008-01-01

    Cooperative system bridges comprise several basic structures that act jointly to improve structural characteristics. We delved into the historical development of cooperative system bridges. Cooperative systems are classified as different-load cooperative systems and same-load cooperative systems by distinguishing the modes of load distribution. For different-load cooperation, individual basic structures are at different positions in the direction along bridge axis and carry the loads separately. While for same-load cooperation, all basic structures overlap in geometrical locations and support the entire loads conjointly. The choosing of span ratios between basic structures, the design of connections of different-load cooperative systems were discussed as well as optimizations of relative rigidity for same-load cooperative systems which greatly influence structural characteristics. The general situation and several structural measurements of several cooperative bridges were demonstrated. This information can assist engineers in developing their concepts in cooperative systems and can lead to more efficient and economical cooperative bridges.

  13. Resource abundance and the critical transition to cooperation.

    Science.gov (United States)

    Connelly, B D; Bruger, E L; McKinley, P K; Waters, C M

    2016-12-30

    Cooperation is abundant in nature, occurring at all levels of biological complexity. Yet cooperation is continually threatened by subversion from noncooperating cheaters. Previous studies have shown that cooperation can nevertheless be maintained when the benefits that cooperation provides to relatives outweigh the associated costs. These fitness costs and benefits are not fixed properties, but can be affected by the environment in which populations reside. Here, we describe how one environmental factor, resource abundance, decisively affects the evolution of cooperative public goods production in two independent evolving systems. In the Avida digital evolution platform, populations evolved in environments with different levels of a required resource, whereas populations of Vibrio cholerae evolved in the presence of different nutrient concentrations. In both systems, cooperators and cheaters co-existed stably in resource-rich environments, whereas cheaters dominated in resource-poor environments. These two outcomes were separated by a sharp transition that occurred at a critical level of resource. These results offer new insights into how the environment affects the evolution of cooperation and highlight the challenges that populations of cooperators face when they experience environmental change.

  14. Emergence and resilience of cooperation in the spatial Prisoner's Dilemma via a reward mechanism

    CERN Document Server

    Jimenez, Raul; Cuesta, Jose A; Sanchez, Angel

    2007-01-01

    We study the problem of the emergence of cooperation in the spatial Prisoner's Dilemma. The pioneering work by Nowak and May showed that large initial populations of cooperators can survive and sustain cooperation in a square lattice with imitate-the-best evolutionary dynamics. We revisit this problem in a cost-benefit formulation suitable for a number of biological applications. We show that if a fixed-amount reward is established for cooperators to share, a single cooperator can invade a population of defectors and form structures that are resilient to re-invasion even if the reward mechanism is turned off. We discuss analytically the case of the invasion by a single cooperator and present agent-based simulations for small initial fractions of cooperators. Large cooperation levels, in the sustainability range, are found. In the conclusions we discuss possible applications of this model as well as its connections with other mechanisms proposed to promote the emergence of cooperation.

  15. Invasion of cooperation in scale-free networks: Accumulated vs. average payoffs

    CERN Document Server

    Ichinose, Genki

    2014-01-01

    It is well known that cooperation cannot be an evolutionary stable strategy for a non-iterative game in a well-mixed population. In contrast, structured populations favor cooperation since cooperators can benefit each other by forming local clusters. Previous studies have shown that scale-free networks strongly promote cooperation. However, little is known about the invasion mechanism of cooperation in scale-free networks. To study microscopic and macroscopic behaviors of cooperators' invasion, we conducted computational experiments of the evolution of cooperation in scale-free networks where, starting from all defectors, cooperators can spontaneously emerge by mutation. Since the evolutionary dynamics are influenced by the definition of fitness, we tested two commonly adopted fitness functions: accumulated payoff and average payoff. Simulation results show that cooperation is strongly enhanced with the accumulated payoff fitness compared to the average payoff fitness. However, the difference between the two ...

  16. Improving Reading Comprehension through Cooperative Learning.

    Science.gov (United States)

    Caposey, Tracey; Heider, Barbara

    This report describes a program for improving reading comprehension through cooperative learning. The targeted population consisted of elementary and middle school students in growing middle class communities, located in northern Illinois. The problems of reading comprehension in content areas were documented through teacher observation and…

  17. Competition between species can stabilize public-goods cooperation within a species.

    Science.gov (United States)

    Celiker, Hasan; Gore, Jeff

    2012-01-01

    Competition between species is a major ecological force that can drive evolution. Here, we test the effect of this force on the evolution of cooperation within a species. We use sucrose metabolism of budding yeast, Saccharomyces cerevisiae, as a model cooperative system that is subject to social parasitism by cheater strategies. We find that when cocultured with a bacterial competitor, Escherichia coli, the frequency of cooperator phenotypes in yeast populations increases dramatically as compared with isolated yeast populations. Bacterial competition stabilizes cooperation within yeast by limiting the yeast population density and also by depleting the public goods produced by cooperating yeast cells. Both of these changes induced by bacterial competition increase the cooperator frequency because cooperator yeast cells have a small preferential access to the public goods they produce; this preferential access becomes more important when the public good is scarce. Our results indicate that a thorough understanding of species interactions is crucial for explaining the maintenance and evolution of cooperation in nature.

  18. Morphology, ontogenesis, and molecular phylogeny of an Indian population of Cyrtohymena (Cyrtohymenides) shii, including remarks on the subgenus.

    Science.gov (United States)

    Singh, Jasbir; Kamra, Komal; Sapra, Gulshan Rai

    2013-05-01

    The freshwater ciliate Cyrtohymena (Cyrtohymenides) shii (Shi et al., 1997) Shao et al., 2012 (Hypotricha, Oxytrichidae), isolated from Barsey Rhododendron Sanctuary of The Eastern Himalayas, is slightly flexible, measures about 150 μm × 50 μm in life and possesses citrine cortical granules randomly distributed singly and in small clusters. Cells of our Indian population have five or six dorsal kineties arising from multiple fragmentation of the third dorsal anlage. The subgenus Cyrtohymenides includes species with multiple dorsal kinety fragmentation namely C. (C.) aspoecki (type species), C. (C.) australis, and the present species. Ventral morphogenesis of the genus Cyrtohymena has been reported only for the type species C. muscorum. Notable features of the Indian population include formation of frontal anlagen from four parental cirri, two more parental cirri possibly contribute to these anlagen later, and the formation of primary primordia which later split transversely to form two sets, one for each daughter cell. 18S rDNA sequence of the Indian population matches with those of two populations of C. citrina; it also clusters with Afrokeronopsis aurea, a neokeronopsid, with which it interestingly shares some morphological features, supporting the CEUU hypothesis.

  19. Multinational investigation of cross-societal cooperation.

    Science.gov (United States)

    Dorrough, Angela Rachael; Glöckner, Andreas

    2016-09-27

    In a globalized world, establishing successful cooperation between people from different nations is becoming increasingly important. We present results from a comprehensive investigation of cross-societal cooperation in one-shot prisoner's dilemmas involving population-representative samples from six countries and identify crucial facilitators of and obstacles to cooperation. In interactions involving mutual knowledge about only the other players' nationalities, we demonstrate that people hold strong and transnationally shared expectations (i.e., stereotypes) concerning the cooperation level of interaction partners from other countries. These expectations are the strongest determinants of participant cooperation. Paradoxically, however, they turn out to be incorrect stereotypes that even correlate negatively with reality. In addition to erroneous expectations, participants' cooperation behavior is driven by (shared) social preferences that vary according to the interaction partner's nationality. In the cross-societal context, these social preferences are influenced by differences in wealth and ingroup favoritism, as well as effects of specific country combinations but not by spatial distance between nations.

  20. Multinational investigation of cross-societal cooperation

    Science.gov (United States)

    Dorrough, Angela Rachael

    2016-01-01

    In a globalized world, establishing successful cooperation between people from different nations is becoming increasingly important. We present results from a comprehensive investigation of cross-societal cooperation in one-shot prisoner’s dilemmas involving population-representative samples from six countries and identify crucial facilitators of and obstacles to cooperation. In interactions involving mutual knowledge about only the other players’ nationalities, we demonstrate that people hold strong and transnationally shared expectations (i.e., stereotypes) concerning the cooperation level of interaction partners from other countries. These expectations are the strongest determinants of participant cooperation. Paradoxically, however, they turn out to be incorrect stereotypes that even correlate negatively with reality. In addition to erroneous expectations, participants’ cooperation behavior is driven by (shared) social preferences that vary according to the interaction partner’s nationality. In the cross-societal context, these social preferences are influenced by differences in wealth and ingroup favoritism, as well as effects of specific country combinations but not by spatial distance between nations. PMID:27621437

  1. Scandinavian Cooperative Advantage

    DEFF Research Database (Denmark)

    Strand, Robert; Freeman, R. Edward

    2015-01-01

    . We conclude by endorsing the expression “Scandinavian cooperative advantage” in an effort to draw attention to the Scandinavian context and encourage the field of strategic management to shift its focus from achieving a competitive advantage toward achieving a cooperative advantage....... of relationships to these historical contributions. Thus, we propose that Scandinavia offers a particularly promising context from which to draw inspiration regarding effective company-stakeholder cooperation and where ample of examples of what is more recently referred to as “creating shared value” can be found...

  2. Evolution of cooperative imitators in social networks

    Science.gov (United States)

    Li, Yixiao

    2017-02-01

    Many evolutionary game models for network reciprocity are based on an imitation dynamics, yet how semirational imitators prevail has seldom been explained. Here we use a model to investigate the coevolutionary dynamics of cooperation and partnership adjustment in a polygenic population of semirational imitators and rational payoff maximizers. A rational individual chooses a strategy best responding to its neighbors when updating strategy and switches to a new partner who can bring it the maximal payoff from all candidates when adjusting the partnership. In contrast, a semirational individual imitates its neighbor's strategy directly and adjusts its partnership based upon a simple reputation rule. Individual-based simulations show that cooperation cannot evolve in a population of all best responders even if they can switch their partners to somebody who can reward them best in game playing. However, when imitators exist, a stable community that consists of cooperative imitators emerges. Further, we show that a birth-death selection mechanism can eliminate all best responders, cultivating a social regime of all cooperative imitators. Compared with parallel simulations that assume fixed networks, cooperative imitators are evolutionarily favored, provided they are able to adjust their partners.

  3. Kinetic Cooperativity, Loop Dynamics, and Allostery from NMR and MD simulations

    Science.gov (United States)

    Bruschweiler, Rafael

    The hallmark of glucokinase (GCK), which catalyzes the phosphorylation of glucose during glycolysis, is its kinetic cooperativity whose understanding at atomic detail has remained open since its discovery over 40 years ago. I will discuss how the origin of kinetic cooperativity is rooted in intramolecular protein dynamics using NMR relaxation data of 17 isoleucines distributed over all parts of GCK. Residues of glucose-free GCK located in the small domain display a distinct exchange behavior involving multiple conformers that are substantially populated, whereas in the glucose-bound form these dynamic processes are quenched. The conformational exchange process directly competes with the enzymatic turnover at physiological glucose concentrations, thereby generating the sigmoidal rate dependence that defines kinetic cooperativity. The flexible nature of protein loops and the timescales of their dynamics are critical for many biologically important events at the molecular level, such as protein interaction and recognition processes. Based on a library of proteins, rules about loop dynamics in terms of amplitude and timescales can be derived using molecular dynamics (MD) simulations and NMR data. These rules have been implemented in the new web server ToeLoop (for Timescales Of Every Loop) that permits the prediction of loop dynamics based on an average 3D protein structure (http://spin.ccic.ohio-state.edu/index.php/loop/index).

  4. Evaluation of copper-induced stress on eggplant (Solanum melongena L.) seedlings at the molecular and population levels by use of various biomarkers.

    Science.gov (United States)

    Körpe, Didem Aksoy; Aras, Sümer

    2011-02-03

    Heavy-metal contamination is an important environmental problem in the world. It is known that high concentrations of heavy metals cause toxic damage to cells and tissues. In this study the effects of copper (Cu(2+)) contamination were determined at the molecular and population levels in eggplant (Solanum melongena L.) seedlings exposed to various concentrations of the metal ion. Inhibition of root growth, reduction in dry weight and total soluble protein content in the roots of eggplant seedlings were observed with increasing Cu(2+) concentrations. In ecotoxicology, analysis by random amplification of polymorphic DNA (RAPD) has been applied as a suitable biomarker assay for plants. For the RAPD analyses, nine RAPD primers were found to produce unique polymorphic band patterns and were subsequently used to produce a total of 80 and 168 bands in the roots of untreated and treated eggplant seedlings, respectively. The changes in RAPD profiles after Cu(2+) contamination were considered as variations, i.e. as gain and/or loss of bands compared with control seedlings. These results suggest that changes in genomic template stability could be detected with RAPD profiles and this result could be compared with the growth, dry weight and total soluble protein content of the seedlings grown at various Cu(2+) concentrations. The measurements of parameters at the molecular and population levels are fundamental to accumulate valuable information and to understand clearly the effect of a contaminant on an organism in ecotoxicology.

  5. Transcriptomic Profiling of Diverse Aedes aegypti Strains Reveals Increased Basal-level Immune Activation in Dengue Virus-refractory Populations and Identifies Novel Virus-vector Molecular Interactions

    Science.gov (United States)

    Sim, Shuzhen; Jupatanakul, Natapong; Ramirez, José L.; Kang, Seokyoung; Romero-Vivas, Claudia M.; Mohammed, Hamish; Dimopoulos, George

    2013-01-01

    Genetic variation among Aedes aegypti populations can greatly influence their vector competence for human pathogens such as the dengue virus (DENV). While intra-species transcriptome differences remain relatively unstudied when compared to coding sequence polymorphisms, they also affect numerous aspects of mosquito biology. Comparative molecular profiling of mosquito strain transcriptomes can therefore provide valuable insight into the regulation of vector competence. We established a panel of A. aegypti strains with varying levels of susceptibility to DENV, comprising both laboratory-maintained strains and field-derived colonies collected from geographically distinct dengue-endemic regions spanning South America, the Caribbean, and Southeast Asia. A comparative genome-wide gene expression microarray-based analysis revealed higher basal levels of numerous immunity-related gene transcripts in DENV-refractory mosquito strains than in susceptible strains, and RNA interference assays further showed different degrees of immune pathway contribution to refractoriness in different strains. By correlating transcript abundance patterns with DENV susceptibility across our panel, we also identified new candidate modulators of DENV infection in the mosquito, and we provide functional evidence for two potential DENV host factors and one potential restriction factor. Our comparative transcriptome dataset thus not only provides valuable information about immune gene regulation and usage in natural refractoriness of mosquito populations to dengue virus but also allows us to identify new molecular interactions between the virus and its mosquito vector. PMID:23861987

  6. Threshold Games and Cooperation on Multiplayer Graphs.

    Directory of Open Access Journals (Sweden)

    Kaare B Mikkelsen

    Full Text Available The study investigates the effect on cooperation in multiplayer games, when the population from which all individuals are drawn is structured-i.e. when a given individual is only competing with a small subset of the entire population.To optimize the focus on multiplayer effects, a class of games were chosen for which the payoff depends nonlinearly on the number of cooperators-this ensures that the game cannot be represented as a sum of pair-wise interactions, and increases the likelihood of observing behaviour different from that seen in two-player games. The chosen class of games are named "threshold games", and are defined by a threshold, M > 0, which describes the minimal number of cooperators in a given match required for all the participants to receive a benefit. The model was studied primarily through numerical simulations of large populations of individuals, each with interaction neighbourhoods described by various classes of networks.When comparing the level of cooperation in a structured population to the mean-field model, we find that most types of structure lead to a decrease in cooperation. This is both interesting and novel, simply due to the generality and breadth of relevance of the model-it is likely that any model with similar payoff structure exhibits related behaviour. More importantly, we find that the details of the behaviour depends to a large extent on the size of the immediate neighbourhoods of the individuals, as dictated by the network structure. In effect, the players behave as if they are part of a much smaller, fully mixed, population, which we suggest an expression for.

  7. 75 FR 21307 - Injury Prevention Program; Announcement Type: Cooperative Agreement

    Science.gov (United States)

    2010-04-23

    ... information in their scope of work. Provide organizational structure (chart) Coalition/ Collaboration... HUMAN SERVICES Indian Health Service Injury Prevention Program; Announcement Type: Cooperative Agreement... strategies in 3-year projects with no population requirements. II. Award Information Type of Awards...

  8. Use of reverse transcriptase polymerase chain reaction (RT-PCR) in molecular screening of Newcastle disease virus in poultry and free-living bird populations.

    Science.gov (United States)

    Carrasco, Adriano de Oliveira Torres; Rodrigues, Juliana Nogueira Martins; Seki, Meire Christina; de Moraes, Fabricio Edgar; Silva, Jaqueline Raymondi; Durigon, Edison Luis; Pinto, Aramis Augusto

    2013-02-01

    The aim of this study was to evaluate a simple molecular method of reverse transcriptase polymerase chain reaction (RT-PCR) to differentiate Newcastle disease virus strains according to their pathogenicity, in order to use it in molecular screening of Newcastle disease virus in poultry and free-living bird populations. Specific primers were developed to differentiate LaSota--LS--(vaccine strain) and Sao Joao do Meriti--SJM--strain (highly pathogenic strain). Chickens and pigeons were experimentally vaccinated/infected for an in vivo study to determine virus shedding in feces. Validation of sensitivity and specificity of the primers (SJM and LS) by experimental models used in the present study and results obtained in the molecular analysis of the primers by BLAST made it possible to generalize results. The development of primers that differentiate the level of pathogenicity of NDV stains is very important, mainly in countries where real-time RT-PCR is still not used as a routine test. These primers were able to determine the presence of the agent and to differentiate it according to its pathogenicity.

  9. Molecular genetics of X chromosome-linked color vision among populations of African and Japanese ancestry: High frequency of a shortened red pigment gene among Afro-Americans

    Energy Technology Data Exchange (ETDEWEB)

    Joergensen, A.L.; Deeb, S.S.; Motulsky, A.G. (Univ. of Washington, Seattle (USA))

    1990-09-01

    Red-green color vision in humans is mediated by the X chromosome-linked highly homologous red and green pigment genes. Color vision defects are caused by deletions and fusions involving these genes. However, the authors found the frequency of molecular abnormalities among Caucasians to be twice as high as that of phenotypic color vision defects. Among Japanese the frequency of phenotypic and molecular color vision defects was similar. Among Afro-Americans, molecular defects were at least five times more frequent than phenotypic color vision defects. In addition, 35% of Afro-Americans, 2% of Japanese, and <1% of Caucasians had a shortened red pigment gene not associated with phenotpyic color vision defects. This gene lacked 1.9 kilobases in its first intron and had the identical size as the green pigment gene from which it presumably originated by gene conversion in an ancestral African population. This gene and the closely linked glucose-6-phosphate dehydrogenase A{sup +} variant were in linkage equilibrium. A model for the evolutionary origin of the color vision pigment genes in higher primates is portrayed.

  10. Chloroplast DNA analysis of Tunisian cork oak populations (Quercus suber L.): sequence variations and molecular evolution of the trnL (UAA)-trnF (GAA) region.

    Science.gov (United States)

    Abdessamad, A; Baraket, G; Sakka, H; Ammari, Y; Ksontini, M; Hannachi, A Salhi

    2016-10-24

    Sequences of the trnL-trnF spacer and combined trnL-trnF region in chloroplast DNA of cork oak (Quercus suber L.) were analyzed to detect polymorphisms and to elucidate molecular evolution and demographic history. The aligned sequences varied in length and nucleotide composition. The overall ratio of transition/transversion (ti/tv) of 0.724 for the intergenic spacer and 0.258 for the pooled sequences were estimated, and indicated that transversions are more frequent than transitions. The molecular evolution and demographic history of Q. suber were investigated. Neutrality tests (Tajima's D and Fu and Li) ruled out the null hypothesis of a strictly neutral model, and Fu's Fs and Ramos-Onsins and Rozas' R2 confirmed the recent expansion of cork oak trees, validating its persistency in North Africa since the last glaciation during the Quaternary. The observed uni-modal mismatch distribution and the Harpending's raggedness index confirmed the demographic history model for cork oak. A phylogenetic dendrogram showed that the distribution of Q. suber trees occurs independently of geographical origin, the relief of the population site, and the bioclimatic stages. The molecular history and cytoplasmic diversity suggest that in situ and ex situ conservation strategies can be recommended for preserving landscape value and facing predictable future climatic changes.

  11. Molecular Markers Reveal Limited Population Genetic Structure in a North American Corvid, Clark’s Nutcracker (Nucifraga columbiana)

    OpenAIRE

    Dohms, Kimberly M.; Theresa M Burg

    2013-01-01

    The genetic impact of barriers and Pleistocene glaciations on high latitude resident species has not been widely investigated. The Clark's nutcracker is an endemic North American corvid closely associated with Pinus-dominated forests. The nutcracker's encompasses known barriers to dispersal for other species, and glaciated and unglaciated areas. Clark's nutcrackers also irruptively disperse long distances in search of pine seed crops, creating the potential for gene flow among populations. Us...

  12. Molecular phylogeography and population genetic structure of O. longilobus and O. taihangensis (Opisthopappus on the Taihang mountains.

    Directory of Open Access Journals (Sweden)

    Yiling Wang

    Full Text Available Historic events such as the uplift of mountains and climatic oscillations in the Quaternary periods greatly affected the evolution and modern distribution of the flora. We sequenced the trnL-trnF, ndhJ-trnL and ITS from populations throughout the known distributions of O. longilobus and O. taihangensis to understand the evolutionary history and the divergence related to the past shifts of habitats in the Taihang Mountains regions. The results showed high genetic diversity and pronounced genetic differentiation among the populations of the two species with a significant phylogeographical pattern (NST>GST, P<0.05, which imply restricted gene flow among the populations and significant geographical or environmental isolation. Ten chloroplast DNA (cpDNA and eighteen nucleus ribosome DNA (nrDNA haplotypes were identified and clustered into two lineages. Two corresponding refuge areas were revealed across the entire distribution ranges of O. longilobus and at least three refuge areas for O. taihangensis. O. longilobus underwent an evolutionary historical process of long-distance dispersal and colonization, whereas O. taihangensis underwent a population expansion before the main uplift of Taihang Mountains. The differentiation time between O. longilobus and O. taihangensis is estimated to have occurred at the early Pleistocene. Physiographic complexity and paleovegetation transition of Taihang Mountains mainly shaped the specific formation and effected the present distribution of these two species. The results therefore support the inference that Quaternary refugial isolation promoted allopatric speciation in Taihang Mountains. This may help to explain the existence of high diversity and endemism of plant species in central/northern China.

  13. Molecular Signature and In Vivo Behavior of Bone Marrow Endosteal and Subendosteal Stromal Cell Populations and their Relevance to Hematopoiesis

    OpenAIRE

    Balduino, Alex; Coelho, Valeria Mello; Wang, Zhou; Taichman, Russell S; Krebsbach, Paul H; Weeraratna, Ashani T.; Becker, Kevin G.; de Mello, Wallace; Taub, Dennis D.; Borojevic, Radovan

    2012-01-01

    In the bone marrow cavity, hematopoietic stem cells (HSC) have been shown to reside in the endosteal and subendosteal perivascular niches, which play specific roles on HSC maintenance. Although cells with long-term ability to reconstitute full hematopoietic system can be isolated from both niches, several data support a heterogenous distribution regarding the cycling behavior of HSC. Whether this distinct behavior depends upon the role played by the stromal populations which distinctly create...

  14. Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing

    Directory of Open Access Journals (Sweden)

    Chen Bor-Sen

    2012-10-01

    Full Text Available Abstract Background Collective rhythms of gene regulatory networks have been a subject of considerable interest for biologists and theoreticians, in particular the synchronization of dynamic cells mediated by intercellular communication. Synchronization of a population of synthetic genetic oscillators is an important design in practical applications, because such a population distributed over different host cells needs to exploit molecular phenomena simultaneously in order to emerge a biological phenomenon. However, this synchronization may be corrupted by intrinsic kinetic parameter fluctuations and extrinsic environmental molecular noise. Therefore, robust synchronization is an important design topic in nonlinear stochastic coupled synthetic genetic oscillators with intrinsic kinetic parameter fluctuations and extrinsic molecular noise. Results Initially, the condition for robust synchronization of synthetic genetic oscillators was derived based on Hamilton Jacobi inequality (HJI. We found that if the synchronization robustness can confer enough intrinsic robustness to tolerate intrinsic parameter fluctuation and extrinsic robustness to filter the environmental noise, then robust synchronization of coupled synthetic genetic oscillators is guaranteed. If the synchronization robustness of a population of nonlinear stochastic coupled synthetic genetic oscillators distributed over different host cells could not be maintained, then robust synchronization could be enhanced by external control input through quorum sensing molecules. In order to simplify the analysis and design of robust synchronization of nonlinear stochastic synthetic genetic oscillators, the fuzzy interpolation method was employed to interpolate several local linear stochastic coupled systems to approximate the nonlinear stochastic coupled system so that the HJI-based synchronization design problem could be replaced by a simple linear matrix inequality (LMI-based design problem

  15. Cooperative processing data bases

    Science.gov (United States)

    Hasta, Juzar

    1991-01-01

    Cooperative processing for the 1990's using client-server technology is addressed. The main theme is concepts of downsizing from mainframes and minicomputers to workstations on a local area network (LAN). This document is presented in view graph form.

  16. Cooperative Hurricane Network Obs

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Observations from the Cooperative Hurricane Reporting Network (CHURN), a special network of stations that provided observations when tropical cyclones approached the...

  17. Cooperative Transport Planning

    NARCIS (Netherlands)

    Zutt, J.; De Weerdt, M.M.

    2000-01-01

    To test and compare different forms of cooperative planning algorithms developed in the CABS project we use a generic simulator called MARS. Examples in the transportation sector are implemented in this simulator.

  18. Solar cooperatives; Genosse Sonne

    Energy Technology Data Exchange (ETDEWEB)

    Jensen, Dierk

    2010-06-15

    Not a boom but a trend: Increasingly, solar power plants and other renewables-based systems are financed by cooperatives. This organizational structure requires long-term strategies and some idealism. (orig.)

  19. Cooperative Weather Observations

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Monthly logs include a daily account of temperature extremes and precipitation, along with snow data at some locations. U.S. Cooperative Observer Program (COOP)...

  20. Cooperative Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Hanning Chen

    2009-01-01

    Full Text Available Bacterial Foraging Optimization (BFO is a novel optimization algorithm based on the social foraging behavior of E. coli bacteria. This paper presents a variation on the original BFO algorithm, namely, the Cooperative Bacterial Foraging Optimization (CBFO, which significantly improve the original BFO in solving complex optimization problems. This significant improvement is achieved by applying two cooperative approaches to the original BFO, namely, the serial heterogeneous cooperation on the implicit space decomposition level and the serial heterogeneous cooperation on the hybrid space decomposition level. The experiments compare the performance of two CBFO variants with the original BFO, the standard PSO and a real-coded GA on four widely used benchmark functions. The new method shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

  1. Landscape Conservation Cooperatives

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Landscape Conservation Cooperatives (LCCs) are public-private partnerships composed of states, tribes, federal agencies, non-governmental organizations,...

  2. Regional National Cooperative Observer

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA publication dedicated to issues, news and recognition of observers in the National Weather Service Cooperative Observer program. Issues published regionally...

  3. Globalization and economic cooperation

    Directory of Open Access Journals (Sweden)

    Javier Divar

    2006-12-01

    Full Text Available Economic globalization is nothing, really, that the universality of capitalism. Not globalized culture, and economic participation, and human rights, ... has only globalized market. We must react by substituting those materialistic values with cooperative economy.

  4. Cooperative Purchasing Reduces Costs.

    Science.gov (United States)

    Kula, Edwin J.

    1981-01-01

    Several suburban Chicago (Illinois) school districts are members of the South Suburban School Purchasing Cooperative, which serves as a conduit for volume purchases of educational supplies. (Author/MLF)

  5. Cooperating and Prospering

    Institute of Scientific and Technical Information of China (English)

    ZHAO MINGWEN

    2010-01-01

    @@ Since its establish-ment in 2001, the Shanghai Cooperation Organization (SCO)-a re-gional organization grouping China, Russia, Kazakhstan, Kyrgyzstan, Tajikistan and Uzbekistan-has grown at a notable pace.

  6. Cooperative Fire Protection Agreement

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The purpose of this Agreement is to provide for cooperation in the prevention, detection and suppression of wildland fires within the protection areas designated in...

  7. Cooperation Beats Conflict

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    China and the Philippines agree to strengthen economic and trade cooperation while minimizing disputes Philippine President Benigno Aquino III recently completed a five-day visit to China, his first state visit to China since he took office last year.

  8. Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident

    Energy Technology Data Exchange (ETDEWEB)

    Kasai, Y.; Kishira, H.; Syutsubo, K.; Harayama, S.

    2001-04-01

    In January 1997, the tanker Nakhodka sank in the Japan Sea, and more than 5000 tons of heavy oil leaked. The released oil contaminated more than 500 km of the coastline, and some still remained even by June 1999. To investigate the long-term influence of the Nakhodka oil spill on marine bacterial populations, sea water and residual oil were sampled from the oil-contaminated zones 10, 18, 22 and 29 months after the accident, and the bacterial populations in these samples were analysed by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments. The dominant DGGE bands were sequenced, and the sequences were compared with those in DNA sequence libraries. Most of the bacteria in the sea water samples were classified as the Cytophaga-Flavobacterium-Bacteroides phylum, {alpha}-Proteobacteria or cyanobacteria. The bacteria detected in the oil paste samples were different from those detected in the sea water samples; they were types related to hydrocarbon degraders, exemplified by strains closely related to Sphingomonas subarctica and Alcanivorax borkumensis. The sizes of the major bacterial populations in the oil paste samples ranged from 3.4 x 10{sup 5} to 1.6 x 10{sup 6} bacteria per gram of oil paste, these low numbers explaining the slow rate of natural attenuation. (Author)

  9. Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident.

    Science.gov (United States)

    Kasai, Y; Kishira, H; Syutsubo, K; Harayama, S

    2001-04-01

    In January 1997, the tanker Nakhodka sank in the Japan Sea, and more than 5000 tons of heavy oil leaked. The released oil contaminated more than 500 km of the coastline, and some still remained even by June 1999. To investigate the long-term influence of the Nakhodka oil spill on marine bacterial populations, sea water and residual oil were sampled from the oil-contaminated zones 10, 18, 22 and 29 months after the accident, and the bacterial populations in these samples were analysed by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments. The dominant DGGE bands were sequenced, and the sequences were compared with those in DNA sequence libraries. Most of the bacteria in the sea water samples were classified as the Cytophaga-Flavobacterium-Bacteroides phylum, alpha-Proteobacteria or cyanobacteria. The bacteria detected in the oil paste samples were different from those detected in the sea water samples; they were types related to hydrocarbon degraders, exemplified by strains closely related to Sphingomonas subarctica and Alcanivorax borkumensis. The sizes of the major bacterial populations in the oil paste samples ranged from 3.4 x 10(5) to 1.6 x 10(6) bacteria per gram of oil paste, these low numbers explaining the slow rate of natural attenuation.

  10. Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues.

    Science.gov (United States)

    Vaca-Paniagua, Felipe; Alvarez-Gomez, Rosa María; Maldonado-Martínez, Hector Aquiles; Pérez-Plasencia, Carlos; Fragoso-Ontiveros, Veronica; Lasa-Gonsebatt, Federico; Herrera, Luis Alonso; Cantú, David; Bargallo-Rocha, Enrique; Mohar, Alejandro; Durand, Geoffroy; Forey, Nathalie; Voegele, Catherine; Vallée, Maxime; Le Calvez-Kelm, Florence; McKay, James; Ardin, Maude; Villar, Stéphanie; Zavadil, Jiri; Olivier, Magali

    2015-01-01

    Triple negative breast cancer (TNBC), defined by the lack of expression of the estrogen receptor, progesterone receptor and human epidermal receptor 2, is an aggressive form of breast cancer that is more prevalent in certain populations, in particular in low- and middle-income regions. The detailed molecular features of TNBC in these regions remain unexplored as samples are mostly accessible as formalin-fixed paraffin embedded (FFPE) archived tissues, a challenging material for advanced genomic and transcriptomic studies. Using dedicated reagents and analysis pipelines, we performed whole exome sequencing and miRNA and mRNA profiling of 12 FFPE tumor tissues collected from pathological archives in Mexico. Sequencing analyses of the tumor tissues and their blood pairs identified TP53 and RB1 genes as the most frequently mutated genes, with a somatic mutation load of 1.7 mutations/exome Mb on average. Transcriptional analyses revealed an overexpression of growth-promoting signals (EGFR, PDGFR, VEGF, PIK3CA, FOXM1), a repression of cell cycle control pathways (TP53, RB1), a deregulation of DNA-repair pathways, and alterations in epigenetic modifiers through miRNA:mRNA network de-regulation. The molecular programs identified were typical of those described in basal-like tumors in other populations. This work demonstrates the feasibility of using archived clinical samples for advanced integrated genomics analyses. It thus opens up opportunities for investigating molecular features of tumors from regions where only FFPE tissues are available, allowing retrospective studies on the search for treatment strategies or on the exploration of the geographic diversity of breast cancer.

  11. Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues

    Science.gov (United States)

    Vaca-Paniagua, Felipe; Alvarez-Gomez, Rosa María; Maldonado-Martínez, Hector Aquiles; Pérez-Plasencia, Carlos; Fragoso-Ontiveros, Veronica; Lasa-Gonsebatt, Federico; Herrera, Luis Alonso; Cantú, David; Bargallo-Rocha, Enrique; Mohar, Alejandro; Durand, Geoffroy; Forey, Nathalie; Voegele, Catherine; Vallée, Maxime; Le Calvez-Kelm, Florence; McKay, James; Ardin, Maude; Villar, Stéphanie; Zavadil, Jiri; Olivier, Magali

    2015-01-01

    Triple negative breast cancer (TNBC), defined by the lack of expression of the estrogen receptor, progesterone receptor and human epidermal receptor 2, is an aggressive form of breast cancer that is more prevalent in certain populations, in particular in low- and middle-income regions. The detailed molecular features of TNBC in these regions remain unexplored as samples are mostly accessible as formalin-fixed paraffin embedded (FFPE) archived tissues, a challenging material for advanced genomic and transcriptomic studies. Using dedicated reagents and analysis pipelines, we performed whole exome sequencing and miRNA and mRNA profiling of 12 FFPE tumor tissues collected from pathological archives in Mexico. Sequencing analyses of the tumor tissues and their blood pairs identified TP53 and RB1 genes as the most frequently mutated genes, with a somatic mutation load of 1.7 mutations/exome Mb on average. Transcriptional analyses revealed an overexpression of growth-promoting signals (EGFR, PDGFR, VEGF, PIK3CA, FOXM1), a repression of cell cycle control pathways (TP53, RB1), a deregulation of DNA-repair pathways, and alterations in epigenetic modifiers through miRNA:mRNA network de-regulation. The molecular programs identified were typical of those described in basal-like tumors in other populations. This work demonstrates the feasibility of using archived clinical samples for advanced integrated genomics analyses. It thus opens up opportunities for investigating molecular features of tumors from regions where only FFPE tissues are available, allowing retrospective studies on the search for treatment strategies or on the exploration of the geographic diversity of breast cancer. PMID:25961742

  12. Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues.

    Directory of Open Access Journals (Sweden)

    Felipe Vaca-Paniagua

    Full Text Available Triple negative breast cancer (TNBC, defined by the lack of expression of the estrogen receptor, progesterone receptor and human epidermal receptor 2, is an aggressive form of breast cancer that is more prevalent in certain populations, in particular in low- and middle-income regions. The detailed molecular features of TNBC in these regions remain unexplored as samples are mostly accessible as formalin-fixed paraffin embedded (FFPE archived tissues, a challenging material for advanced genomic and transcriptomic studies. Using dedicated reagents and analysis pipelines, we performed whole exome sequencing and miRNA and mRNA profiling of 12 FFPE tumor tissues collected from pathological archives in Mexico. Sequencing analyses of the tumor tissues and their blood pairs identified TP53 and RB1 genes as the most frequently mutated genes, with a somatic mutation load of 1.7 mutations/exome Mb on average. Transcriptional analyses revealed an overexpression of growth-promoting signals (EGFR, PDGFR, VEGF, PIK3CA, FOXM1, a repression of cell cycle control pathways (TP53, RB1, a deregulation of DNA-repair pathways, and alterations in epigenetic modifiers through miRNA:mRNA network de-regulation. The molecular programs identified were typical of those described in basal-like tumors in other populations. This work demonstrates the feasibility of using archived clinical samples for advanced integrated genomics analyses. It thus opens up opportunities for investigating molecular features of tumors from regions where only FFPE tissues are available, allowing retrospective studies on the search for treatment strategies or on the exploration of the geographic diversity of breast cancer.

  13. Cooperative effects for CYP2E1 differ between styrene and its metabolites

    OpenAIRE

    2013-01-01

    Cooperative interactions are frequently observed in the metabolism of drugs and pollutants by cytochrome P450s; nevertheless, the molecular determinants for cooperativity remain elusive. Previously, we demonstrated that steady-state styrene metabolism by CYP2E1 exhibits positive cooperativity.We hypothesized that styrene metabolites have lower affinity than styrene toward CYP2E1 and limited ability to induce cooperative effects during metabolism. To test the hypothesis, we determined the pote...

  14. Kinematic Results From a Systematic Search for Infall Signatures Towards the Starless Core Population in the Perseus Molecular Cloud

    Science.gov (United States)

    Walker-LaFollette, Amanda; Shirley, Y. L.; Amaya, H.; Becker, S. L.; Biddle, L. I.; Lichtenberger, M.; Nieberding, M. N.; Raphael, B. A.; Romine, J. M.; Small, L.; Stanford-Jones, C.; Smith, C.; Thompson, R.; Towner, A. P.; Turner, J.; Watson, Z.; Cates, I.; McGraw, A. M.; Pearson, K.; Robertson, A.; Tombleson, R.

    2014-01-01

    We present the results of a survey searching for infall signatures toward 72 starless cores in the Perseus molecular cloud. Observations of the ground state rotational transitions of HCN, HNC, and H13CN were carried out using the 12-m radio telescope on Kitt Peak operated by the Arizona Radio Observatory. All three molecules are tracers of dense molecular gas. HCN 1-0 is an excellent infall tracer, with its three hyperfine lines probing different optical depths. We examined the spectra for signs of infall by comparing observed line asymmetries with the velocity peak of the optically thin isotopologue H13CN. We find that there is an excess of blue asymmetries, but clearly self-absorbed profiles are rare (blue asymmetric and blue skewed profiles to the number of class II protostars, we find a range for the observable collapse lifetime of 6x10^4-2x10^5yrs, which is commensurate with the gravitational free-fall time (5x10^4yrs) for the observed central densities of Perseus starless cores. The best infall candidates all have observed masses that are above the Jeans mass. We calculate the infall speeds for the best collapse candidates and compare their dynamics to other known collapsing starless cores. This project was observed by The University of Arizona Undergraduate Astronomy Club.

  15. Cooperating mobile robots

    Energy Technology Data Exchange (ETDEWEB)

    Harrington, John J.; Eskridge, Steven E.; Hurtado, John E.; Byrne, Raymond H.

    2004-02-03

    A miniature mobile robot provides a relatively inexpensive mobile robot. A mobile robot for searching an area provides a way for multiple mobile robots in cooperating teams. A robotic system with a team of mobile robots communicating information among each other provides a way to locate a source in cooperation. A mobile robot with a sensor, a communication system, and a processor, provides a way to execute a strategy for searching an area.

  16. Extending Eurasia Security Cooperation

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    After 14 years of development, the Shanghai Cooperation Organization (SCO) , has set its sights on goals for the next de-cade at the 15th meeting of the Council of SCO Heads of State that was held in Ufa, the capital of Russia's Bashkortostan Republic, on July 9-10. The SCO, established in Shanghai in 2001, is committed to building fdendly neighbor rela- tions and maintaining security and stability in the Central Asian region through multilateral cooperation.

  17. Cooperation Without Intervention

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    In January, China announced its desire to increase cooperation with African countries by issuing China's African Policy, a paper intended to guide relations with the continent by continuing a non-interventionist and non-ideological strategy. Christopher Mutsvangwa, Zimbabwean Ambassador to China, shared his views of the policy with Beijing Review reporter Ni Yanshuo and answered criticisms of the China-Africa relationship by Western countries that tie cooperation to democracy and human rights.

  18. Cooperation in Construction:

    DEFF Research Database (Denmark)

    Vogelius, Peter; Storgaard, Kresten

    2016-01-01

    The study presents a building project executed by a major Danish construction company, where cooperation and its staging were essential for achieving high productivity and competitiveness. The form of this cooperation is the main theme for the article. The contractor actively changed....... The management logic of the main contractor is interpreted as based on a sociology-inspired understanding focusing on norms and social values rather than on contractual (law) and functional (engineering) logic, which had hitherto been prevalent in Danish construction management....

  19. Global Reserve Cooperation

    Science.gov (United States)

    2011-03-24

    St ra te gy R es ea rc h Pr oj ec t GLOBAL RESERVE COOPERATION BY LIEUTENANT COLONEL PAMELA L. MCGAHA United States Army National Guard...DATES COVERED (From - To) 4. TITLE AND SUBTITLE Global Reserve Cooperation 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM...decade, the United States, its allies, and partner nations have greatly increased their reliance on Reserve Component forces. This global

  20. Stochastic dynamics of the prisoner's dilemma with cooperation facilitators.

    Science.gov (United States)

    Mobilia, Mauro

    2012-07-01

    In the framework of the paradigmatic prisoner's dilemma game, we investigate the evolutionary dynamics of social dilemmas in the presence of "cooperation facilitators." In our model, cooperators and defectors interact as in the classical prisoner's dilemma, where selection favors defection. However, here the presence of a small number of cooperation facilitators enhances the fitness (reproductive potential) of cooperators, while it does not alter that of defectors. In a finite population of size N, the dynamics of the prisoner's dilemma with facilitators is characterized by the probability that cooperation takes over (fixation probability) by the mean times to reach the absorbing states. These quantities are computed exactly using Fokker-Planck equations. Our findings, corroborated by stochastic simulations, demonstrate that the influence of facilitators crucially depends on the difference between their density z and the game's cost-to-benefit ratio r. When z > r, the fixation of cooperators is likely in a large population and, under weak selection pressure, invasion and replacement of defection by cooperation is favored by selection if b(z - r)(1 - z) > N(-1), where 0cooperation payoff benefit. When z < r, the fixation probability of cooperators is exponentially enhanced by the presence of facilitators but defection is the dominating strategy.

  1. Phase transitions and hysteresis of cooperative contagion processes

    CERN Document Server

    Chen, Li; Brockmann, Dirk

    2016-01-01

    We investigate the effects of cooperation between two interacting infectious diseases that spread and stabilize in a host population. We propose a model in which individuals that are infected with one disease are more likely to acquire the second disease, both diseases following the susceptible-infected-susceptible reaction scheme. We analyze cooperative coinfection in stochastic network models as well as the idealized, well-mixed mean field system and show that cooperative mechanisms dramatically change the nature of phase transitions compared to single disease dynamics. We show that, generically, cooperative coinfection exhibits discontinuous transitions from the disease free to high prevalence state when a critical transmission rate is crossed. Furthermore, cooperative coinfection exhibits two distinct critical points, one for outbreaks the second one for eradication that can be substantially lower. This implies that cooperative coinfection exhibits hysteresis in its response to changing effective transmis...

  2. Parasites may help stabilize cooperative relationships

    Directory of Open Access Journals (Sweden)

    Little Ainslie EF

    2009-06-01

    Full Text Available Abstract Background The persistence of cooperative relationships is an evolutionary paradox; selection should favor those individuals that exploit their partners (cheating, resulting in the breakdown of cooperation over evolutionary time. Our current understanding of the evolutionary stability of mutualisms (cooperation between species is strongly shaped by the view that they are often maintained by partners having mechanisms to avoid or retaliate against exploitation by cheaters. In contrast, we empirically and theoretically examine how additional symbionts, specifically specialized parasites, potentially influence the stability of bipartite mutualistic associations. In our empirical work we focus on the obligate mutualism between fungus-growing ants and the fungi they cultivate for food. This mutualism is exploited by specialized microfungal parasites (genus Escovopsis that infect the ant's fungal gardens. Using sub-colonies of fungus-growing ants, we investigate the interactions between the fungus garden parasite and cooperative and experimentally-enforced uncooperative ("cheating" pairs of ants and fungi. To further examine if parasites have the potential to help stabilize some mutualisms we conduct Iterative Prisoner's Dilemma (IPD simulations, a common framework for predicting the outcomes of cooperative/non-cooperative interactions, which incorporate parasitism as an additional factor. Results In our empirical work employing sub-colonies of fungus-growing ants, we found that Escovopsis-infected sub-colonies composed of cheating populations of ants or fungi lost significantly more garden biomass than sub-colonies subjected to infection or cheating (ants or fungi alone. Since the loss of fungus garden compromises the fitness of both mutualists, our findings suggest that the potential benefit received by the ants or fungi for cheating is outweighed by the increased concomitant cost of parasitism engendered by non-cooperation (cheating. IPD

  3. EU-China cooperation on regional policy

    Directory of Open Access Journals (Sweden)

    Eva Minarčíková

    2016-03-01

    Full Text Available Although the European Union and China are different in terms of area, population, economic, social, political and cultural development, both of them have to face similar challenge – the significant regional disparities and unbalanced regional development. Based on this the EU-China cooperation on regional policy has been launched and there is huge potential to develop mutual learning initiatives to allow their regions developed. The main aim of this paper is to outline the trends in evolution and perspectives of EU-China cooperation on regional policy.

  4. Random diffusion and cooperation in continuous two-dimensional space.

    Science.gov (United States)

    Antonioni, Alberto; Tomassini, Marco; Buesser, Pierre

    2014-03-07

    This work presents a systematic study of population games of the Prisoner's Dilemma, Hawk-Dove, and Stag Hunt types in two-dimensional Euclidean space under two-person, one-shot game-theoretic interactions, and in the presence of agent random mobility. The goal is to investigate whether cooperation can evolve and be stable when agents can move randomly in continuous space. When the agents all have the same constant velocity cooperation may evolve if the agents update their strategies imitating the most successful neighbor. If a fitness difference proportional is used instead, cooperation does not improve with respect to the static random geometric graph case. When viscosity effects set-in and agent velocity becomes a quickly decreasing function of the number of neighbors they have, one observes the formation of monomorphic stable clusters of cooperators or defectors in the Prisoner's Dilemma. However, cooperation does not spread in the population as in the constant velocity case.

  5. Spatial self-organization favors heterotypic cooperation over cheating.

    Science.gov (United States)

    Momeni, Babak; Waite, Adam James; Shou, Wenying

    2013-11-12

    Heterotypic cooperation-two populations exchanging distinct benefits that are costly to produce-is widespread. Cheaters, exploiting benefits while evading contribution, can undermine cooperation. Two mechanisms can stabilize heterotypic cooperation. In 'partner choice', cooperators recognize and choose cooperating over cheating partners; in 'partner fidelity feedback', fitness-feedback from repeated interactions ensures that aiding your partner helps yourself. How might a spatial environment, which facilitates repeated interactions, promote fitness-feedback? We examined this process through mathematical models and engineered Saccharomyces cerevisiae strains incapable of recognition. Here, cooperators and their heterotypic cooperative partners (partners) exchanged distinct essential metabolites. Cheaters exploited partner-produced metabolites without reciprocating, and were competitively superior to cooperators. Despite initially random spatial distributions, cooperators gained more partner neighbors than cheaters did. The less a cheater contributed, the more it was excluded and disfavored. This self-organization, driven by asymmetric fitness effects of cooperators and cheaters on partners during cell growth into open space, achieves assortment. DOI: http://dx.doi.org/10.7554/eLife.00960.001.

  6. The evolution of cooperation by negotiation in a noisy world.

    Science.gov (United States)

    Ito, K; McNamara, J M; Yamauchi, A; Higginson, A D

    2017-03-01

    Cooperative interactions among individuals are ubiquitous despite the possibility of exploitation by selfish free riders. One mechanism that may promote cooperation is 'negotiation': individuals altering their behaviour in response to the behaviour of others. Negotiating individuals decide their actions through a recursive process of reciprocal observation, thereby reducing the possibility of free riding. Evolutionary games with response rules have shown that infinitely many forms of the rule can be evolutionarily stable simultaneously, unless there is variation in individual quality. This potentially restricts the conditions under which negotiation could maintain cooperation. Organisms interact with one another in a noisy world in which cooperative effort and the assessment of effort may be subject to error. Here, we show that such noise can make the number of evolutionarily stable rules finite, even without quality variation, and so noise could help maintain cooperative behaviour. We show that the curvature of the benefit function is the key factor determining whether individuals invest more or less as their partner's investment increases, investing less when the benefit to investment has diminishing returns. If the benefits of low investment are very small then behavioural flexibility tends to promote cooperation, because negotiation enables cooperators to reach large benefits. Under some conditions, this leads to a repeating cycle in which cooperative behaviour rises and falls over time, which may explain between-population differences in cooperative behaviour. In other conditions, negotiation leads to extremely high levels of cooperative behaviour, suggesting that behavioural flexibility could facilitate the evolution of eusociality in the absence of high relatedness.

  7. TRACING EMBEDDED STELLAR POPULATIONS IN CLUSTERS AND GALAXIES USING MOLECULAR EMISSION: METHANOL AS A SIGNATURE OF THE LOW-MASS END OF THE IMF

    Energy Technology Data Exchange (ETDEWEB)

    Kristensen, Lars E. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Bergin, Edwin A., E-mail: lkristensen@cfa.harvard.edu [Department of Astronomy, University of Michigan, 500 Church Street, Ann Arbor, MI 48109 (United States)

    2015-07-10

    Most low-mass protostars form in clusters, in particular high-mass clusters; however, how low-mass stars form in high-mass clusters and what the mass distribution is are still open questions both in our own Galaxy and elsewhere. To access the population of forming embedded low-mass protostars observationally, we propose using molecular outflows as tracers. Because the outflow emission scales with mass, the effective contrast between low-mass protostars and their high-mass cousins is greatly lowered. In particular, maps of methanol emission at 338.4 GHz (J = 7{sub 0}–6{sub 0} A{sup +}) in low-mass clusters illustrate that this transition is an excellent probe of the low-mass population. We present here a model of a forming cluster where methanol emission is assigned to every embedded low-mass protostar. The resulting model image of methanol emission is compared to recent ALMA observations toward a high-mass cluster and the similarity is striking: the toy model reproduces observations to better than a factor of two and suggests that approximately 50% of the total flux originates in low-mass outflows. Future fine-tuning of the model will eventually make it a tool for interpreting the embedded low-mass population of distant regions within our own Galaxy and ultimately higher-redshift starburst galaxies, not just for methanol emission but also water and high-J CO.

  8. Phenotypic and molecular characterization of a tomato (Solanum lycopersicum L.) F2 population segregation for improving shelf life.

    Science.gov (United States)

    Yogendra, K N; Ramanjini Gowda, P H

    2013-02-27

    Breeding for better quality fruits is a major focus for tomatoes, which are continuously subjected to post-harvest losses. Several methods have been used to improve the fruit shelf life of tomatoes, including the use of ripening gene mutants of Solanum lycopersicum. We developed extended shelf-life tomato hybrids with better quality fruits using ripening mutants. Nine tomato crosses were developed using 3 fruit ripening gene mutants of S. lycopersicum [alcobaca (alc), non-ripening, and ripening inhibitor] and 3 agronomically superior Indian cultivars ('Sankranti', 'Vaibhav', and 'Pusaruby') with short shelf life. The hybrid progenies developed from alc x 'Vaibhav' had the highest extended shelf life (up to 40 days) compared with that of other varieties and hybrids. Further, the F(2) progenies of alc x 'Vaibhav' were evaluated for fruit quality traits and yield parameters. A wide range of genetic variability was observed in shelf life (5-106 days) and fruit firmness (0.55-10.65 lbs/cm(2)). The potential polymorphic simple sequence repeat markers underlying shelf life traits were identified in an F(2) mapping population. The marker association with fruit quality traits and yield was confirmed with single-marker analysis and composite interval mapping. The genetic parameters analyzed in the parents and F(1) and F(2) populations indicated that the cross between the cultivar 'Vaibhav' and ripening gene mutant alc yielded fruit with long shelf life and good quality.

  9. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species.

    Science.gov (United States)

    Baroncelli, Riccardo; Zapparata, Antonio; Sarrocco, Sabrina; Sukno, Serenella A; Lane, Charles R; Thon, Michael R; Vannacci, Giovanni; Holub, Eric; Sreenivasaprasad, Surapareddy

    2015-01-01

    Fragaria × ananassa (common name: strawberry) is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l.) is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production.

  10. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species.

    Directory of Open Access Journals (Sweden)

    Riccardo Baroncelli

    Full Text Available Fragaria × ananassa (common name: strawberry is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l. is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production.

  11. Molecular phylogeography and population genetic structure of O. longilobus and O. taihangensis (Opisthopappus) on the Taihang mountains.

    Science.gov (United States)

    Wang, Yiling; Yan, Guiqin

    2014-01-01

    Historic events such as the uplift of mountains and climatic oscillations in the Quaternary periods greatly affected the evolution and modern distribution of the flora. We sequenced the trnL-trnF, ndhJ-trnL and ITS from populations throughout the known distributions of O. longilobus and O. taihangensis to understand the evolutionary history and the divergence related to the past shifts of habitats in the Taihang Mountains regions. The results showed high genetic diversity and pronounced genetic differentiation among the populations of the two species with a significant phylogeographical pattern (NST>GST, PMountains. The differentiation time between O. longilobus and O. taihangensis is estimated to have occurred at the early Pleistocene. Physiographic complexity and paleovegetation transition of Taihang Mountains mainly shaped the specific formation and effected the present distribution of these two species. The results therefore support the inference that Quaternary refugial isolation promoted allopatric speciation in Taihang Mountains. This may help to explain the existence of high diversity and endemism of plant species in central/northern China.

  12. Tay-Sachs Carrier Screening by Enzyme and Molecular Analyses in the New York City Minority Population.

    Science.gov (United States)

    Mehta, Nikita; Lazarin, Gabriel A; Spiegel, Erica; Berentsen, Kathleen; Brennan, Kelly; Giordano, Jessica; Haque, Imran S; Wapner, Ronald

    2016-09-01

    Carrier screening for Tay-Sachs disease is performed by sequence analysis of the HEXA gene and/or hexosaminidase A enzymatic activity testing. Enzymatic analysis (EA) has been suggested as the optimal carrier screening method, especially in non-Ashkenazi Jewish (non-AJ) individuals, but its utilization and efficacy have not been fully evaluated in the general population. This study assesses the reliability of EA in comparison with HEXA sequence analysis in non-AJ populations. Five hundred eight Hispanic and African American patients (516 samples) had EA of their leukocytes performed and 12 of these patients who tested positive by EA ("carriers") had subsequent HEXA gene sequencing performed. Of the 508 patients, 25 (4.9%) were EA positive and 40 (7.9%) were inconclusive. Of the 12 patients who were sequenced, 11 did not carry a pathogenic variant and one carried a likely deleterious mutation (NM_000520.4(HEXA):c.1510C>T). High inconclusive rates and poor correlation between positive/inconclusive enzyme results and identification of pathogenic mutations suggest that ethnic-specific recalibration of reference ranges for EA may be necessary. Alternatively, HEXA gene sequencing could be performed.

  13. Molecular evolution at the cytochrome oxidase subunit 2 gene among divergent populations of the intertidal copepod, Tigriopus californicus.

    Science.gov (United States)

    Rawson, Paul D; Burton, Ronald S

    2006-06-01

    The cytochrome c oxidase subunit 2 gene (COII) encodes a highly conserved protein that is directly responsible for the initial transfer of electrons from cytochrome c to cytochrome c oxidase (COX) crucial to the production of ATP during cellular respiration. Despite its integral role in electron transport, we have observed extensive intraspecific nucleotide and amino acid variation among 26 full-length COII sequences sampled from seven populations of the marine copepod, Tigriopus californicus. Although intrapopulation divergence was virtually nonexistent, interpopulation divergence at the COII locus was nearly 20% at the nucleotide level, including 38 nonsynonymous substitutions. Given the high degree of interaction between the cytochrome c oxidase subunit 2 protein (COX2) and the nuclear-encoded subunits of COX and cytochrome c (CYC), we hypothesized that some codons in the COII gene are likely to be under positive selection in order to compensate for amino acid substitutions in other subunits. Estimates of the ratio of nonsynonymous to synonymous substitution (omega), obtained using a series of maximum likelihood models of codon substitution, indicated that the majority of codons in T. californicus COII are under strong purifying selection (omega < 1), while approximately 4% of the sites in this gene appear to evolve under relaxed selective constraint (omega = 1). A branch-site maximum likelihood model identified three sites that may have experienced positive selection within the central California sequence clade in our COII phylogeny; these results are consistent with previous studies showing functional and fitness consequences among interpopulation hybrids between central and northern California populations.

  14. Globalisation and global trade influence molecular viral population genetics of Torque Teno Sus Viruses 1 and 2 in pigs.

    Science.gov (United States)

    Cortey, Martí; Pileri, Emanuela; Segalés, Joaquim; Kekarainen, Tuija

    2012-04-23

    Globalisation, in terms of the rapid and free movement of people, animals and food, has created a new paradigm, increasing the range and rate of distribution of many pathogens. In the present study, Torque teno sus viruses (TTSuVs) have been used as a model to evaluate the effects of global trade on viral heterogeneity, and how the movement of live pigs can affect the distribution and composition of virus populations. Seventeen countries from different parts of the world have been screened for TTSuV1 and TTSuvV2. High levels of genetic diversity have been found as well as two new TTSuV subtypes. A small fraction of this diversity (50%) was best explained by the exchange of live pigs among countries, pointing to the direct relationship between the movement of hosts and the diversity of their accompanying viruses. Taking TTSuVs as sentinels, this study revealed that the distribution and diversity of comensal microflora in live animals subjected to global trade is shaped by the commercial movements among countries. In the case of TTSuVs, it appears that commercial movements of animals are eroding the genetic composition of the virus populations that may have been present in pig herds since their domestication.

  15. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species

    Science.gov (United States)

    Baroncelli, Riccardo; Zapparata, Antonio; Sarrocco, Sabrina; Sukno, Serenella A.; Lane, Charles R.; Thon, Michael R.; Vannacci, Giovanni; Holub, Eric; Sreenivasaprasad, Surapareddy

    2015-01-01

    Fragaria × ananassa (common name: strawberry) is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l.) is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production. PMID:26086351

  16. Molecular characterization of microbial populations in full-scale biofilters treating iron, manganese and ammonia containing groundwater in Harbin, China.

    Science.gov (United States)

    Li, Xiang-kun; Chu, Zhao-rui; Liu, Ya-jun; Zhu, Meng-ting; Yang, Liu; Zhang, Jie

    2013-11-01

    In iron and manganese-containing groundwater treatment for drinking water production, biological filter is an effective process to remove such pollutants. Until now the exact microbial mechanism of iron and manganese removal, especially coupled with other pollutants, such as ammonia, has not been clearly understood. To assess this issue, the performance of a full-scale biofilter located in Harbin, China was monitored over four months. Microbial populations in the biofilter were investigated using T-RFLP and clone library technique. Results suggested that Gallionella, Leptothrix, Nitrospira, Hyphomicrobium and Pseudomonas are dominant in the biofilter and play major roles in the removal of iron, manganese and ammonia. The spatial distribution of microbial populations along the depth of the biofilter demonstrated the stratification of the removal of iron, manganese and ammonia. Additionally, the absence of ammonia-oxidizing bacteria in the biofilter implicated that ammonia-oxidizing archaea might be responsible for the oxidation of ammonia to nitrite. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  17. Cooperative Learning Instructional Methods for CS1: Design, Implementation, and Evaluation

    Science.gov (United States)

    Beck, Leland; Chizhik, Alexander

    2013-01-01

    Cooperative learning is a well-known instructional technique that has been applied with a wide variety of subject matter and a broad spectrum of populations. This article briefly reviews the principles of cooperative learning, and describes how these principles were incorporated into a comprehensive set of cooperative learning activities for a CS1…

  18. Cooperative Learning Instructional Methods for CS1: Design, Implementation, and Evaluation

    Science.gov (United States)

    Beck, Leland; Chizhik, Alexander

    2013-01-01

    Cooperative learning is a well-known instructional technique that has been applied with a wide variety of subject matter and a broad spectrum of populations. This article briefly reviews the principles of cooperative learning, and describes how these principles were incorporated into a comprehensive set of cooperative learning activities for a CS1…

  19. Epidemiological and Molecular Characterization of a Mexican Population Isolate with High Prevalence of Limb-Girdle Muscular Dystrophy Type 2A Due to a Novel Calpain-3 Mutation

    Science.gov (United States)

    Pantoja-Melendez, Carlos A.; Miranda-Duarte, Antonio; Roque-Ramirez, Bladimir; Zenteno, Juan C.

    2017-01-01

    Limb-Girdle Muscular Dystrophy type 2 (LGMD2) is a group of autosomally recessive inherited disorders defined by weakness and wasting of the shoulder and pelvic girdle muscles. In the past, several population isolates with high incidence of LGMD2 arising from founder mutation effects have been identified. The aim of this work is to describe the results of clinical, epidemiologic, and molecular studies performed in a Mexican village segregating numerous cases of LGMD2. A population census was conducted in the village to identify all LGMD affected patients. Molecular analysis included genome wide homozygosity mapping using a 250K SNP Affymetrix microarray followed by PCR amplification and direct nucleotide sequencing of the candidate gene. In addition, DNA from 401 randomly selected unaffected villagers was analyzed to establish the carrier frequency of the LGMD2 causal mutation. A total of 32 LGMD2 patients were identified in the village, rendering a disease prevalence of 4.3 (CI: 2.9–5.9) cases per 1,000 habitants (1 in 232). Genome wide homozygosity mapping revealed that affected individuals shared a 6.6 Mb region of homozygosity at chromosome 15q15. The identified homozygous interval contained CAPN3, the gene responsible for LGMD2 type A (LGMD2A). Direct sequencing of this gene revealed homozygosity for a novel c.348C>A mutation (p.Ala116Asp) in DNA from all 20 affected subjects available for genetic screening, except one which was heterozygous for the mutation. In such patient, a heterozygous c.2362AG>TCATCT deletion/insertion was recognized as the second CAPN3 mutation. Western blot and autocatalytic activity analyses in protein lysates from skeletal muscle biopsy obtained from a p.Ala116Asp homozygous patient suggested that this particular mutation increased the autocatalytic activity of CAPN3. Thirty eigth heterozygotes of the p.Ala116Asp mutation were identified among 401 genotyped unaffected villagers, yielding a population carrier frequency of 1 in 11

  20. Molecular gate keepers succumb to gene aberrations in colorectal cancer in Kashmiri population, revealing a high incidence area

    Directory of Open Access Journals (Sweden)

    Sameer A

    2009-01-01

    Full Text Available Background/Aim: Colorectal cancer (CRC is one of the leading malignancies worldwide and has been reported to show geographical variation in its incidence, even within areas of ethnic homogeneity. The aim of this study was to identify p53 and K-ras gene mutations in CRC patients in a Kashmiri population, and to assess whether these mutations are linked with clinicopathological parameters. Materials and Methods: Paired tumor and normal tissue samples from a consecutive series of 53 patients undergoing resective surgery for CRC were prospectively studied for p53 and K-ras gene mutations by PCR/single strand conformation polymorphism (SSCP. Results: Less than half (45%, 19/42 of the patients presented mutations in the p53 gene. Twenty eight mutations were found in the p53 gene, which comprised of 23 substitutions (17 transitions + 6 transversions, and five insertions. The 23 substitutions constituted 18 missense mutations, two nonsense mutations, and three silent mutations. Of the 28 mutations (7.14% observed in this study, 2 were not previously reported for CRC samples and were identified as novel p53 mutations. A few patients (22.64%, 12/53 presented with mutations in K-ras, constituting 13 missense mutations, out of which 11 were G→A transitions, one was a G→C transversion, and one a G→T transversion. More than half (61.5% of the mutations occurred in codon 12 whereas a few (38.5% occurred in codon 13. One tumor contained missense mutations in both codons. Comparison of the mutation profiles of our patients with those of other ethnic populations and regions reflected both differences and similarities, indicating co-exposure to a unique set of risk factors. Conclusion: Mutations of the p53 and K-ras genes are some of the most common genetic changes in the development of human CRC. The high frequency of p53 gene mutations implicates p53 as a predominant factor for CRC in the high-risk ethnic Kashmiri population.

  1. Reactive Strategies: The Establishment of Cooperation

    CERN Document Server

    Júnior, Elton J S; da Silva, Jafferson K L

    2014-01-01

    Cooperation is usually represented as a Prisoner's Dilemma game. Although individual self-interest may not favour cooperation, cooperation can evolve if, for example, players interact multiple times adjusting their behaviour accordingly to opponent's previous action. To analyze population dynamics, replicator equation has been widely used under several versions. Although it is usually stated that a strategy called Generous-tit-for-tat is the winner within the reactive strategies set, here we show that this result depends on replicator's version and on the number of available strategies, stemming from the fact that a dynamics system is also defined by the number of available strategies and not only by the model version. Using computer simulations and analytical arguments, we show that Generous-tit-for-tat victory is found only if the number of strategies available is not too large, with defection winning otherwise.

  2. Molecular detection of tick-borne protozoan parasites in a population of domestic cats in midwestern Brazil.

    Science.gov (United States)

    Braga, Ísis Assis; de Souza Ramos, Dirceu Guilherme; Marcili, Arlei; Melo, Andréia Lima Tomé; Taques, Isis Indaiara Gonçalves Granjeiro; Amude, Alexandre Mendes; Chitarra, Cristiane Silva; Nakazato, Luciano; Dutra, Valéria; de Campos Pacheco, Richard; Aguiar, Daniel Moura

    2016-07-01

    Some tick-borne pathogens that infect domestic cats have been considered emergent in veterinary medicine. Occurrences of Hepatozoon spp., Babesia spp. and Cytauxzoon spp. have been described in several regions of Brazil. This paper offers a comprehensive analysis of the 18S rRNA gene of a Hepatozoon sp. strain detected in domestic cats in the metropolitan area of Cuiabá, in Midwestern Brazil. Based on a molecular analysis, we detected the presence of Hepatozoon species circulating among cats in this region. The aforementioned strain is closely related to other isolates of H. felis detected in wild felids. Moreover, a phylogenetic analysis indicates that this genotype is grouped into a clade of 18S rRNA sequences previously described for the genus Hepatozoon in wild felids around the world. Hepatozoon felis strains detected in cats from Spain and Israel showed, respectively, 98% and 97% identity to our sequence and are clustered on a separate branch of the phylogenetic tree. This finding suggests a high diversity of Hepatozoon genotypes occurring in cats in Europe and South America. None of the analyzed cats were positive for Babesia spp. or Cytauxzoon spp. by PCR analysis.

  3. Molecular analysis using DHPLC of cystic fibrosis: increase of the mutation detection rate among the affected population in Central Italy

    Directory of Open Access Journals (Sweden)

    Nardone Anna

    2004-04-01

    Full Text Available Abstract Background Cystic fibrosis (CF is a multisystem disorder characterised by mutations of the CFTR gene, which encodes for an important component in the coordination of electrolyte movement across of epithelial cell membranes. Symptoms are pulmonary disease, pancreatic exocrine insufficiency, male infertility and elevated sweat concentrations. The CFTR gene has numerous mutations (>1000 and functionally important polymorphisms (>200. Early identification is important to provide appropriate therapeutic interventions, prognostic and genetic counselling and to ensure access to specialised medical services. However, molecular diagnosis by direct mutation screening has proved difficult in certain ethnic groups due to allelic heterogeneity and variable frequency of causative mutations. Methods We applied a gene scanning approach using DHPLC system for analysing specifically all CFTR exons and characterise sequence variations in a subgroup of CF Italian patients from the Lazio region (Central Italy characterised by an extensive allelic heterogeneity. Results We have identified a total of 36 different mutations representing 88% of the CF chromosomes. Among these are two novel CFTR mutations, including one missense (H199R and one microdeletion (4167delCTAAGCC. Conclusion Using this approach, we were able to increase our standard power rate of mutation detection of about 11% (77% vs. 88%.

  4. Fundamental Limits of Cooperation

    CERN Document Server

    Lozano, Angel; Andrews, Jeffrey G

    2012-01-01

    Cooperation is viewed as a key ingredient for interference management in wireless systems. This paper shows that cooperation has fundamental limitations. The main result is that even full cooperation between transmitters cannot in general change an interference-limited network to a noise-limited network. The key idea is that there exists a spectral efficiency upper bound that is independent of the transmit power. First, a spectral efficiency upper bound is established for systems that rely on pilot-assisted channel estimation; in this framework, cooperation is shown to be possible only within clusters of limited size, which are subject to out-of-cluster interference whose power scales with that of the in-cluster signals. Second, an upper bound is also shown to exist when cooperation is through noncoherent communication; thus, the spectral efficiency limitation is not a by-product of the reliance on pilot-assisted channel estimation. Consequently, existing literature that routinely assumes the high-power spect...

  5. Molecular Assessment and Taxonomic Status of the Rapid Racerunner (Eremias velox complex) with Particular Attention to the Populations in Northwestern China

    Institute of Scientific and Technical Information of China (English)

    Jinlong LIU; Natalia A.ANANJEVA; Marina A.CHIRIKOVA; Konstantin D.MILTO; Xianguang GUO

    2014-01-01

    The rapid racerunner, Eremias velox, is a widely distributed lizard from the northern Caucasus across entire Central Asia eastward to China. It is increasingly common to accept E. velox as a species complex in its entire range. To date, published morphological and molecular systematic hypotheses of this complex are only partially congruent, and its taxonomic status and evolutionary history are still far from clear. The mitochondrial cytochrome b gene and 12S rRNA sequences were used to evaluate the taxonomy of this complex, with particular attention to the phylogenetic placement of populations in northwestern China. Examination of the phylogenetic analyses recovers seven distinct,previously assigned to E. v. velox. Finally, each of the three independently evolving lineages from Iranian Plateau should be recognized as three species new to science under the general lineage concept.

  6. Molecular phylogeny of Vipera Laurenti, 1768 and the related genera Macrovipera (Reuss, 1927) and Daboia (Gray, 1842), with comments about neurotoxic Vipera aspis aspis populations.

    Science.gov (United States)

    Garrigues, Thomas; Dauga, Catherine; Ferquel, Elisabeth; Choumet, Valérie; Failloux, Anna-Bella

    2005-04-01

    We used mtDNA sequences (cytochrome b and NADH dehydrogenase subunit 2) to reconstruct molecular phylogenies of Vipera sensu lato, Vipera sensu stricto, and Vipera aspis. Three major clades were identified within the Vipera s.l. group: (1) the European vipers, (2) the oriental vipers, consisting of Montivipera (Vipera 2) plus Macrovipera lebetina, and (3) a group of Asian and North African vipers consisting of Daboia russelii, V. palaestinae, and Macrovipera mauritanica. We also distinguished three clades within the monophyletic European Vipera group: V. ammodytes, V. aspis, and V. latastei, and Pelias with monophyly of Vipera 1 uncertain. Within V. aspis, the specimens collected in France formed the sister group of an Italian clade. The "neurotoxic" French population of V. aspis, which has a specific venom profile, separated from other French V. aspis early in the history of this group.

  7. Cooperation, Norms, and Revolutions: A Unified Game-Theoretical Approach

    CERN Document Server

    Helbing, Dirk; 10.1371/journal.pone.0012530

    2010-01-01

    Cooperation is of utmost importance to society as a whole, but is often challenged by individual self-interests. While game theory has studied this problem extensively, there is little work on interactions within and across groups with different preferences or beliefs. Yet, people from different social or cultural backgrounds often meet and interact. This can yield conflict, since behavior that is considered cooperative by one population might be perceived as non-cooperative from the viewpoint of another. To understand the dynamics and outcome of the competitive interactions within and between groups, we study game-dynamical replicator equations for multiple populations with incompatible interests and different power (be this due to different population sizes, material resources, social capital, or other factors). These equations allow us to address various important questions: For example, can cooperation in the prisoner's dilemma be promoted, when two interacting groups have different preferences? Under wha...

  8. Molecular phylogeny and population structure of the codling moth (Cydia pomonella) in Central Europe: I. Ancient clade splitting revealed by mitochondrial haplotype markers.

    Science.gov (United States)

    Meraner, A; Brandstätter, A; Thaler, R; Aray, B; Unterlechner, M; Niederstätter, H; Parson, W; Zelger, R; Dalla Via, J; Dallinger, R

    2008-09-01

    The codling moth (Cydia pomonella L., Tortricidae, Lepidoptera) is an important pest of pome fruit with global distribution. It has adapted successfully to different habitats by forming various ecotypes and populations, often termed strains, which differ among each other in several morphological, developmental, and physiological features. Many strains of Cydia pomonella have developed resistance against a broad range of chemically different pesticides. Obviously, pesticide-resistant strains must have a genetic basis inherent to the gene pool of codling moth populations, and this deserves our particular attention. The primary intention of the present study was to contribute novel information regarding the evolutionary phylogeny and phylogeography of codling moth populations in Central Europe. In addition, we aimed at testing the hypothesis that differential biological traits