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Sample records for detecting evolutionary selection

  1. Evolutionary Theories of Detection

    SciTech Connect

    Fitch, J P

    2005-04-29

    Current, mid-term and long range technologies for detection of pathogens and toxins are briefly described in the context of performance metrics and operational scenarios. Predictive (evolutionary) and speculative (revolutionary) assessments are given with trade-offs identified, where possible, among competing performance goals.

  2. Soft Selective Sweeps in Evolutionary Rescue

    PubMed Central

    Wilson, Benjamin A.; Pennings, Pleuni S.; Petrov, Dmitri A.

    2017-01-01

    Evolutionary rescue occurs when a population that is declining in size because of an environmental change is rescued from extinction by genetic adaptation. Evolutionary rescue is an important phenomenon at the intersection of ecology and population genetics, and the study of evolutionary rescue is critical to understanding processes ranging from species conservation to the evolution of drug and pesticide resistance. While most population-genetic models of evolutionary rescue focus on estimating the probability of rescue, we focus on whether one or more adaptive lineages contribute to evolutionary rescue. We find that when evolutionary rescue is likely, it is often driven by soft selective sweeps where multiple adaptive mutations spread through the population simultaneously. We give full analytic results for the probability of evolutionary rescue and the probability that evolutionary rescue occurs via soft selective sweeps. We expect that these results will find utility in understanding the genetic signatures associated with various evolutionary rescue scenarios in large populations, such as the evolution of drug resistance in viral, bacterial, or eukaryotic pathogens. PMID:28213477

  3. Evolutionary games on cycles with strong selection.

    PubMed

    Altrock, P M; Traulsen, A; Nowak, M A

    2017-02-01

    Evolutionary games on graphs describe how strategic interactions and population structure determine evolutionary success, quantified by the probability that a single mutant takes over a population. Graph structures, compared to the well-mixed case, can act as amplifiers or suppressors of selection by increasing or decreasing the fixation probability of a beneficial mutant. Properties of the associated mean fixation times can be more intricate, especially when selection is strong. The intuition is that fixation of a beneficial mutant happens fast in a dominance game, that fixation takes very long in a coexistence game, and that strong selection eliminates demographic noise. Here we show that these intuitions can be misleading in structured populations. We analyze mean fixation times on the cycle graph under strong frequency-dependent selection for two different microscopic evolutionary update rules (death-birth and birth-death). We establish exact analytical results for fixation times under strong selection and show that there are coexistence games in which fixation occurs in time polynomial in population size. Depending on the underlying game, we observe inherence of demographic noise even under strong selection if the process is driven by random death before selection for birth of an offspring (death-birth update). In contrast, if selection for an offspring occurs before random removal (birth-death update), then strong selection can remove demographic noise almost entirely.

  4. Evolutionary games on cycles with strong selection

    NASA Astrophysics Data System (ADS)

    Altrock, P. M.; Traulsen, A.; Nowak, M. A.

    2017-02-01

    Evolutionary games on graphs describe how strategic interactions and population structure determine evolutionary success, quantified by the probability that a single mutant takes over a population. Graph structures, compared to the well-mixed case, can act as amplifiers or suppressors of selection by increasing or decreasing the fixation probability of a beneficial mutant. Properties of the associated mean fixation times can be more intricate, especially when selection is strong. The intuition is that fixation of a beneficial mutant happens fast in a dominance game, that fixation takes very long in a coexistence game, and that strong selection eliminates demographic noise. Here we show that these intuitions can be misleading in structured populations. We analyze mean fixation times on the cycle graph under strong frequency-dependent selection for two different microscopic evolutionary update rules (death-birth and birth-death). We establish exact analytical results for fixation times under strong selection and show that there are coexistence games in which fixation occurs in time polynomial in population size. Depending on the underlying game, we observe inherence of demographic noise even under strong selection if the process is driven by random death before selection for birth of an offspring (death-birth update). In contrast, if selection for an offspring occurs before random removal (birth-death update), then strong selection can remove demographic noise almost entirely.

  5. Molecular selection in a unified evolutionary sequence

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1986-01-01

    With guidance from experiments and observations that indicate internally limited phenomena, an outline of unified evolutionary sequence is inferred. Such unification is not visible for a context of random matrix and random mutation. The sequence proceeds from Big Bang through prebiotic matter, protocells, through the evolving cell via molecular and natural selection, to mind, behavior, and society.

  6. Extrapolating Weak Selection in Evolutionary Games

    PubMed Central

    Wu, Bin; García, Julián; Hauert, Christoph; Traulsen, Arne

    2013-01-01

    In evolutionary games, reproductive success is determined by payoffs. Weak selection means that even large differences in game outcomes translate into small fitness differences. Many results have been derived using weak selection approximations, in which perturbation analysis facilitates the derivation of analytical results. Here, we ask whether results derived under weak selection are also qualitatively valid for intermediate and strong selection. By “qualitatively valid” we mean that the ranking of strategies induced by an evolutionary process does not change when the intensity of selection increases. For two-strategy games, we show that the ranking obtained under weak selection cannot be carried over to higher selection intensity if the number of players exceeds two. For games with three (or more) strategies, previous examples for multiplayer games have shown that the ranking of strategies can change with the intensity of selection. In particular, rank changes imply that the most abundant strategy at one intensity of selection can become the least abundant for another. We show that this applies already to pairwise interactions for a broad class of evolutionary processes. Even when both weak and strong selection limits lead to consistent predictions, rank changes can occur for intermediate intensities of selection. To analyze how common such games are, we show numerically that for randomly drawn two-player games with three or more strategies, rank changes frequently occur and their likelihood increases rapidly with the number of strategies . In particular, rank changes are almost certain for , which jeopardizes the predictive power of results derived for weak selection. PMID:24339769

  7. Product Mix Selection Using AN Evolutionary Technique

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Vasant, Pandian

    2009-08-01

    This paper proposes an evolutionary technique for the solution of a real—life industrial problem and particular for the product mix selection problem. The evolutionary technique is a combination of a genetic algorithm that preserves the feasibility of the trial solutions with penalties and some local optimization method. The goal of this paper has been achieved in finding the best near optimal solution for the profit fitness function respect to vagueness factor and level of satisfaction. The findings of the profit values will be very useful for the decision makers in the industrial engineering sector for the implementation purpose. It's possible to improve the solutions obtained in this study by employing other meta-heuristic methods such as simulated annealing, tabu Search, ant colony optimization, particle swarm optimization and artificial immune systems.

  8. Selective evolutionary generation systems: Theory and applications

    NASA Astrophysics Data System (ADS)

    Menezes, Amor A.

    This dissertation is devoted to the problem of behavior design, which is a generalization of the standard global optimization problem: instead of generating the optimizer, the generalization produces, on the space of candidate optimizers, a probability density function referred to as the behavior. The generalization depends on a parameter, the level of selectivity, such that as this parameter tends to infinity, the behavior becomes a delta function at the location of the global optimizer. The motivation for this generalization is that traditional off-line global optimization is non-resilient and non-opportunistic. That is, traditional global optimization is unresponsive to perturbations of the objective function. On-line optimization methods that are more resilient and opportunistic than their off-line counterparts typically consist of the computationally expensive sequential repetition of off-line techniques. A novel approach to inexpensive resilience and opportunism is to utilize the theory of Selective Evolutionary Generation Systems (SECS), which sequentially and probabilistically selects a candidate optimizer based on the ratio of the fitness values of two candidates and the level of selectivity. Using time-homogeneous, irreducible, ergodic Markov chains to model a sequence of local, and hence inexpensive, dynamic transitions, this dissertation proves that such transitions result in behavior that is called rational; such behavior is desirable because it can lead to both efficient search for an optimizer as well as resilient and opportunistic behavior. The dissertation also identifies system-theoretic properties of the proposed scheme, including equilibria, their stability and their optimality. Moreover, this dissertation demonstrates that the canonical genetic algorithm with fitness proportional selection and the (1+1) evolutionary strategy are particular cases of the scheme. Applications in three areas illustrate the versatility of the SECS theory: flight

  9. Tracing evolutionary relicts of positive selection on eight malaria-related immune genes in mammals.

    PubMed

    Huang, Bing-Hong; Liao, Pei-Chun

    2015-07-01

    Plasmodium-induced malaria widely infects primates and other mammals. Multiple past studies have revealed that positive selection could be the main evolutionary force triggering the genetic diversity of anti-malaria resistance-associated genes in human or primates. However, researchers focused most of their attention on the infra-generic and intra-specific genome evolution rather than analyzing the complete evolutionary history of mammals. Here we extend previous research by testing the evolutionary link of natural selection on eight candidate genes associated with malaria resistance in mammals. Three of the eight genes were detected to be affected by recombination, including TNF-α, iNOS and DARC. Positive selection was detected in the rest five immunogenes multiple times in different ancestral lineages of extant species throughout the mammalian evolution. Signals of positive selection were exposed in four malaria-related immunogenes in primates: CCL2, IL-10, HO1 and CD36. However, selection signals of G6PD have only been detected in non-primate eutherians. Significantly higher evolutionary rates and more radical amino acid replacement were also detected in primate CD36, suggesting its functional divergence from other eutherians. Prevalent positive selection throughout the evolutionary trajectory of mammalian malaria-related genes supports the arms race evolutionary hypothesis of host genetic response of mammalian immunogenes to infectious pathogens.

  10. Adaptation and habitat selection in the eco-evolutionary process.

    PubMed

    Morris, Douglas W

    2011-08-22

    The struggle for existence occurs through the vital rates of population growth. This basic fact demonstrates the tight connection between ecology and evolution that defines the emerging field of eco-evolutionary dynamics. An effective synthesis of the interdependencies between ecology and evolution is grounded in six principles. The mechanics of evolution specifies the origin and rules governing traits and evolutionary strategies. Traits and evolutionary strategies achieve their selective value through their functional relationships with fitness. Function depends on the underlying structure of variation and the temporal, spatial and organizational scales of evolution. An understanding of how changes in traits and strategies occur requires conjoining ecological and evolutionary dynamics. Adaptation merges these five pillars to achieve a comprehensive understanding of ecological and evolutionary change. I demonstrate the value of this world-view with reference to the theory and practice of habitat selection. The theory allows us to assess evolutionarily stable strategies and states of habitat selection, and to draw the adaptive landscapes for habitat-selecting species. The landscapes can then be used to forecast future evolution under a variety of climate change and other scenarios.

  11. Sexual selection: an evolutionary force in plants?

    PubMed

    Skogsmyr, Io; Lankinen, Asa

    2002-11-01

    Sexual selection has traditionally been used to explain exaggerated sexual traits in male animals. Today the concept has been developed and various other sexually related traits have been suggested to evolve in the same manner. In nearly all new areas where the theory of sexual selection has been applied, there has been an intense debate as to whether the application is justified. Is it the case that some scientists are all too ready to employ fashionable ideas? Or are there too many dogmatic researchers refusing to accept that science develops and old ideas are transformed? Maybe the controversies are simply a reflection of the difficulty of defining a theory under constant re-evaluation. Thus, we begin by summarizing the theory of sexual selection in order to assess the influence of sexual selection on the evolution of plant morphology. We discuss empirical findings concerning potentially affected traits. Although we have tried to address criticisms fairly, we still conclude that sexual selection can be a useful tool when studying the evolution of reproductive traits in plants. Furthermore, by including the evidence from an additional kingdom, a fuller understanding of the processes involved in sexual selection can be gained.

  12. Evolutionary Design of a Robotic Material Defect Detection System

    NASA Technical Reports Server (NTRS)

    Ballard, Gary; Howsman, Tom; Craft, Mike; ONeil, Daniel; Steincamp, Jim; Howell, Joe T. (Technical Monitor)

    2002-01-01

    During the post-flight inspection of SSME engines, several inaccessible regions must be disassembled to inspect for defects such as cracks, scratches, gouges, etc. An improvement to the inspection process would be the design and development of very small robots capable of penetrating these inaccessible regions and detecting the defects. The goal of this research was to utilize an evolutionary design approach for the robotic detection of these types of defects. A simulation and visualization tool was developed prior to receiving the hardware as a development test bed. A small, commercial off-the-shelf (COTS) robot was selected from several candidates as the proof of concept robot. The basic approach to detect the defects was to utilize Cadmium Sulfide (CdS) sensors to detect changes in contrast of an illuminated surface. A neural network, optimally designed utilizing a genetic algorithm, was employed to detect the presence of the defects (cracks). By utilization of the COTS robot and US sensors, the research successfully demonstrated that an evolutionarily designed neural network can detect the presence of surface defects.

  13. Efficient and scalable Pareto optimization by evolutionary local selection algorithms.

    PubMed

    Menczer, F; Degeratu, M; Street, W N

    2000-01-01

    Local selection is a simple selection scheme in evolutionary computation. Individual fitnesses are accumulated over time and compared to a fixed threshold, rather than to each other, to decide who gets to reproduce. Local selection, coupled with fitness functions stemming from the consumption of finite shared environmental resources, maintains diversity in a way similar to fitness sharing. However, it is more efficient than fitness sharing and lends itself to parallel implementations for distributed tasks. While local selection is not prone to premature convergence, it applies minimal selection pressure to the population. Local selection is, therefore, particularly suited to Pareto optimization or problem classes where diverse solutions must be covered. This paper introduces ELSA, an evolutionary algorithm employing local selection and outlines three experiments in which ELSA is applied to multiobjective problems: a multimodal graph search problem, and two Pareto optimization problems. In all these experiments, ELSA significantly outperforms other well-known evolutionary algorithms. The paper also discusses scalability, parameter dependence, and the potential distributed applications of the algorithm.

  14. Neuro-evolutionary event detection technique for downhole microseismic surveys

    NASA Astrophysics Data System (ADS)

    Maity, Debotyam; Salehi, Iraj

    2016-01-01

    Recent years have seen a significant increase in borehole microseismic data acquisition programs associated with unconventional reservoir developments such as hydraulic fracturing programs for shale oil and gas. The data so acquired is used for hydraulic fracture monitoring and diagnostics and therefore, the quality of the data in terms of resolution and accuracy has a significant impact on its value to the industry. Borehole microseismic data acquired in such environments typically suffer from propagation effects due to the presence of thin interbedded shale layers as well as noise and interference effects. Moreover, acquisition geometry has significant impact on detectability across portions of the sensor array. Our work focuses on developing robust first arrival detection and pick selection workflow for both P and S waves specifically designed for such environments. We introduce a novel workflow for refinement of picks with immunity towards significant noise artifacts and applicability over data with very low signal-to-noise ratio provided some accurate picks have already been made. This workflow utilizes multi-step hybrid detection and classification routine which makes use of a neural network based autopicker for initial picking and an evolutionary algorithm for pick refinement. We highlight the results from an actual field case study including multiple examples demonstrating immunity towards noise and compare the effectiveness of the workflow with two contemporary autopicking routines without the application of the shared detection/refinement procedure. Finally, we use a windowed waveform cross-correlation based uncertainty estimation method for potential quality control purposes. While the workflow was developed to work with the neural network based autopicker, it can be used with any other traditional autopicker and provides significant improvements in pick detection across seismic gathers.

  15. Evolutionary response when selection and genetic variation covary across environments.

    PubMed

    Wood, Corlett W; Brodie, Edmund D

    2016-10-01

    Although models of evolution usually assume that the strength of selection on a trait and the expression of genetic variation in that trait are independent, whenever the same ecological factor impacts both parameters, a correlation between the two may arise that accelerates trait evolution in some environments and slows it in others. Here, we address the evolutionary consequences and ecological causes of a correlation between selection and expressed genetic variation. Using a simple analytical model, we show that the correlation has a modest effect on the mean evolutionary response and a large effect on its variance, increasing among-population or among-generation variation in the response when positive, and diminishing variation when negative. We performed a literature review to identify the ecological factors that influence selection and expressed genetic variation across traits. We found that some factors - temperature and competition - are unlikely to generate the correlation because they affected one parameter more than the other, and identified others - most notably, environmental novelty - that merit further investigation because little is known about their impact on one of the two parameters. We argue that the correlation between selection and genetic variation deserves attention alongside other factors that promote or constrain evolution in heterogeneous landscapes.

  16. Evolutionary stasis in pollen morphogenesis due to natural selection.

    PubMed

    Matamoro-Vidal, Alexis; Prieu, Charlotte; Furness, Carol A; Albert, Béatrice; Gouyon, Pierre-Henri

    2016-01-01

    The contribution of developmental constraints and selective forces to the determination of evolutionary patterns is an important and unsolved question. We test whether the long-term evolutionary stasis observed for pollen morphogenesis (microsporogenesis) in eudicots is due to developmental constraints or to selection on a morphological trait shaped by microsporogenesis: the equatorial aperture pattern. Most eudicots have three equatorial apertures but several taxa have independently lost the equatorial pattern and have microsporogenesis decoupled from aperture pattern determination. If selection on the equatorial pattern limits variation, we expect to see increased variation in microsporogenesis in the nonequatorial clades. Variation of microsporogenesis was studied using phylogenetic comparative analyses in 83 species dispersed throughout eudicots including species with and without equatorial apertures. The species that have lost the equatorial pattern have highly variable microsporogenesis at the intra-individual and inter-specific levels regardless of their pollen morphology, whereas microsporogenesis remains stable in species with the equatorial pattern. The observed burst of variation upon loss of equatorial apertures shows that there are no strong developmental constraints precluding variation in microsporogenesis, and that the stasis is likely to be due principally to selective pressure acting on pollen morphogenesis because of its implication in the determination of the equatorial aperture pattern.

  17. Multiobjective Evolutionary Path Planning via Sugeno-Based Tournament Selection

    NASA Technical Reports Server (NTRS)

    Dozier, Gerry; McCullough, Shaun; Homaifar, Abdollah; Esterline, Albert

    1998-01-01

    This paper introduces a new tournament selection algorithm that can be used for evolutionary path planning systems. The fuzzy (Sugeno) tournament selection algorithm (STSA) described in this paper selects candidate paths (CPs) to be parents and undergo reproduction based on: (1) path feasibility, (2) the euclidean distance of a path from the origin to its destination, and (3) the average change in the slope of a path. In this paper, we provide a detailed description of the fuzzy inference system used in the STSA as well as some examples of its usefulness. We then use 12 instances of our STSA to rank a population of CPs based on the above criteria. We also show how the STSA can obviate the need for the development of an explicit (lexicographic multiobjective) evaluation function and use it to develop multiobjective motion paths.

  18. Detection of signatures of selection using Fst.

    PubMed

    Porto-Neto, Laercio R; Lee, Seung Hwan; Lee, Hak Kyo; Gondro, Cedric

    2013-01-01

    Natural selection has molded the evolution of species across all taxa. Much more recently, on an evolutionary scale, human-oriented selection started to play an important role in shaping organisms, markedly so after the domestication of animals and plants. These selection processes have left traceable marks in the genome. Following from the recent advances in molecular genetics technologies, a number of methods have been developed to detect such signals, termed genomic signatures of selection. In this chapter we discuss a straightforward protocol based on the F ST statistic to identify genomic regions that exhibit high variation in allelic frequency between groups, which is a characteristic of genomic regions that have gone through differential selection. How to define the borders of these regions and further explore its genetic content is then discussed.

  19. Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements

    PubMed Central

    Brunet, Tyler D.P.; Doolittle, W. Ford

    2015-01-01

    One of several issues at play in the renewed debate over “junk DNA” is the organizational level at which genomic features might be seen as selected, and thus to exhibit function, as etiologically defined. The intuition frequently expressed by molecular geneticists that junk DNA is functional because it serves to “speed evolution” or as an “evolutionary repository” could be recast as a claim about selection between species (or clades) rather than within them, but this is not often done. Here, we review general arguments for the importance of selection at levels above that of organisms in evolution, and develop them further for a common genomic feature: the carriage of transposable elements (TEs). In many species, not least our own, TEs comprise a large fraction of all nuclear DNA, and whether they individually or collectively contribute to fitness—or are instead junk— is a subject of ongoing contestation. Even if TEs generally owe their origin to selfish selection at the lowest level (that of genomes), their prevalence in extant organisms and the prevalence of extant organisms bearing them must also respond to selection within species (on organismal fitness) and between species (on rates of speciation and extinction). At an even higher level, the persistence of clades may be affected (positively or negatively) by TE carriage. If indeed TEs speed evolution, it is at these higher levels of selection that such a function might best be attributed to them as a class. PMID:26253318

  20. Dwarfism in insular sloths: biogeography, selection, and evolutionary rate.

    PubMed

    Anderson, Robert P; Handley, Charles O

    2002-05-01

    The islands of Bocas del Toro, Panama, were sequentially separated from the adjacent mainland by rising sea levels during the past 10,000 years. Three-toed sloths (Bradypus) from five islands are smaller than their mainland counterparts, and the insular populations themselves vary in mean body size. We first examine relationships between body size and physical characteristics of the islands, testing hypotheses regarding optimal body size, evolutionary equilibria, and the presence of dispersal in this system. To do so, we conduct linear regressions of body size onto island area, distance from the mainland, and island age. Second, we retroactively calculate two measures of the evolutionary rate of change in body size (haldanes and darwins) and the standardized linear selection differential, or selection intensity (i). We also test the observed morphological changes against models of evolution by genetic drift. The results indicate that mean body size decreases linearly with island age, explaining up to 97% of the variation among population means. Neither island area nor distance from the mainland is significant in multiple regressions that include island age. Thus, we find no evidence for differential optimal body size among islands, or for dispersal in the system. In contrast, the dependence of body size on island age suggests uniform directional selection for small body size in the insular populations. Although genetic drift cannot be discounted as the cause for this evolution in body size, the probability is small given the consistent direction of evolution (repeated dwarfism). The insular sloths show a sustained rate of evolution similar to those measured in haldanes over tens of generations, appearing to unite micro- and macroevolutionary time scales. Furthermore, the magnitude and rate of this example of rapid differentiation fall within predictions of theoretical models from population genetics. However, the linearity of the relationship between body size and

  1. Evolutionary selection of enzymatically synthesized semiconductors from biomimetic mineralization vesicles.

    PubMed

    Bawazer, Lukmaan A; Izumi, Michi; Kolodin, Dmitriy; Neilson, James R; Schwenzer, Birgit; Morse, Daniel E

    2012-06-26

    The way nature evolves and sculpts materials using proteins inspires new approaches to materials engineering but is still not completely understood. Here, we present a cell-free synthetic biological platform to advance studies of biologically synthesized solid-state materials. This platform is capable of simultaneously exerting many of the hierarchical levels of control found in natural biomineralization, including genetic, chemical, spatial, structural, and morphological control, while supporting the evolutionary selection of new mineralizing proteins and the corresponding genetically encoded materials that they produce. DNA-directed protein expression and enzymatic mineralization occur on polystyrene microbeads in water-in-oil emulsions, yielding synthetic surrogates of biomineralizing cells that are then screened by flow sorting, with light-scattering signals used to sort the resulting mineralized composites differentially. We demonstrate the utility of this platform by evolutionarily selecting newly identified silicateins, biomineralizing enzymes previously identified from the silica skeleton of a marine sponge, for enzyme variants capable of synthesizing silicon dioxide (silica) or titanium dioxide (titania) composites. Mineral composites of intermediate strength are preferentially selected to remain intact for identification during cell sorting, and then to collapse postsorting to expose the encoding genes for enzymatic DNA amplification. Some of the newly selected silicatein variants catalyze the formation of crystalline silicates, whereas the parent silicateins lack this ability. The demonstrated bioengineered route to previously undescribed materials introduces in vitro enzyme selection as a viable strategy for mimicking genetic evolution of materials as it occurs in nature.

  2. Evolutionary selection of enzymatically synthesized semiconductors from biomimetic mineralization vesicles

    SciTech Connect

    Bawazer, Lukmaan A.; Izumi, Michi; Kolodin, Dmitriy; Neilson, James R.; Schwenzer, Birgit; Morse, Daniel E.

    2012-10-29

    The way nature evolves and sculpts materials using proteins inspires new approaches to materials engineering but is still not completely understood. Here, we present a cell-free synthetic biological platform to advance studies of biologically synthesized solid-state materials. This platform is capable of simultaneously exerting many of the hierarchical levels of control found in natural biomineralization, including genetic, chemical, spatial, structural, and morphological control, while supporting the evolutionary selection of new mineralizing proteins and the corresponding genetically encoded materials that they produce. DNA-directed protein expression and enzymatic mineralization occur on polystyrene microbeads in water-in-oil emulsions, yielding synthetic surrogates of biomineralizing cells that are then screened by flow sorting, with light-scattering signals used to sort the resulting mineralized composites differentially. We demonstrate the utility of this platform by evolutionarily selecting newly identified silicateins, biomineralizing enzymes previously identified from the silica skeleton of a marine sponge, for enzyme variants capable of synthesizing silicon dioxide (silica) or titanium dioxide (titania) composites. Mineral composites of intermediate strength are preferentially selected to remain intact for identification during cell sorting, and then to collapse postsorting to expose the encoding genes for enzymatic DNA amplification. Some of the newly selected silicatein variants catalyze the formation of crystalline silicates, whereas the parent silicateins lack this ability. The demonstrated bioengineered route to previously undescribed materials introduces in vitro enzyme selection as a viable strategy for mimicking genetic evolution of materials as it occurs in nature.

  3. Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus.

    PubMed

    Moncla, Louise H; Zhong, Gongxun; Nelson, Chase W; Dinis, Jorge M; Mutschler, James; Hughes, Austin L; Watanabe, Tokiko; Kawaoka, Yoshihiro; Friedrich, Thomas C

    2016-02-10

    Avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among mammals by acquiring mutations in hemagglutinin (HA) and polymerase. Using the ferret model, we trace the evolutionary pathway by which an avian-like virus evolves the capacity for mammalian replication and airborne transmission. During initial infection, within-host HA diversity increased drastically. Then, airborne transmission fixed two polymerase mutations that do not confer a detectable replication advantage. In later transmissions, selection fixed advantageous HA1 variants. Transmission initially involved a "loose" bottleneck, which became strongly selective after additional HA mutations emerged. The stringency and evolutionary forces governing between-host bottlenecks may therefore change throughout host adaptation. Mutations occurred in multiple combinations in transmitted viruses, suggesting that mammalian transmissibility can evolve through multiple genetic pathways despite phenotypic constraints. Our data provide a glimpse into avian influenza virus adaptation in mammals, with broad implications for surveillance on potentially zoonotic viruses.

  4. Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme

    PubMed Central

    Chen, Bor-Sen; Tsai, Kun-Wei; Li, Cheng-Wei

    2015-01-01

    Molecular biologists have long recognized carcinogenesis as an evolutionary process that involves natural selection. Cancer is driven by the somatic evolution of cell lineages. In this study, the evolution of somatic cancer cell lineages during carcinogenesis was modeled as an equilibrium point (ie, phenotype of attractor) shifting, the process of a nonlinear stochastic evolutionary biological network. This process is subject to intrinsic random fluctuations because of somatic genetic and epigenetic variations, as well as extrinsic disturbances because of carcinogens and stressors. In order to maintain the normal function (ie, phenotype) of an evolutionary biological network subjected to random intrinsic fluctuations and extrinsic disturbances, a network robustness scheme that incorporates natural selection needs to be developed. This can be accomplished by selecting certain genetic and epigenetic variations to modify the network structure to attenuate intrinsic fluctuations efficiently and to resist extrinsic disturbances in order to maintain the phenotype of the evolutionary biological network at an equilibrium point (attractor). However, during carcinogenesis, the remaining (or neutral) genetic and epigenetic variations accumulate, and the extrinsic disturbances become too large to maintain the normal phenotype at the desired equilibrium point for the nonlinear evolutionary biological network. Thus, the network is shifted to a cancer phenotype at a new equilibrium point that begins a new evolutionary process. In this study, the natural selection scheme of an evolutionary biological network of carcinogenesis was derived from a robust negative feedback scheme based on the nonlinear stochastic Nash game strategy. The evolvability and phenotypic robustness criteria of the evolutionary cancer network were also estimated by solving a Hamilton–Jacobi inequality – constrained optimization problem. The simulation revealed that the phenotypic shift of the lung cancer

  5. Design of an Evolutionary Approach for Intrusion Detection

    PubMed Central

    2013-01-01

    A novel evolutionary approach is proposed for effective intrusion detection based on benchmark datasets. The proposed approach can generate a pool of noninferior individual solutions and ensemble solutions thereof. The generated ensembles can be used to detect the intrusions accurately. For intrusion detection problem, the proposed approach could consider conflicting objectives simultaneously like detection rate of each attack class, error rate, accuracy, diversity, and so forth. The proposed approach can generate a pool of noninferior solutions and ensembles thereof having optimized trade-offs values of multiple conflicting objectives. In this paper, a three-phase, approach is proposed to generate solutions to a simple chromosome design in the first phase. In the first phase, a Pareto front of noninferior individual solutions is approximated. In the second phase of the proposed approach, the entire solution set is further refined to determine effective ensemble solutions considering solution interaction. In this phase, another improved Pareto front of ensemble solutions over that of individual solutions is approximated. The ensemble solutions in improved Pareto front reported improved detection results based on benchmark datasets for intrusion detection. In the third phase, a combination method like majority voting method is used to fuse the predictions of individual solutions for determining prediction of ensemble solution. Benchmark datasets, namely, KDD cup 1999 and ISCX 2012 dataset, are used to demonstrate and validate the performance of the proposed approach for intrusion detection. The proposed approach can discover individual solutions and ensemble solutions thereof with a good support and a detection rate from benchmark datasets (in comparison with well-known ensemble methods like bagging and boosting). In addition, the proposed approach is a generalized classification approach that is applicable to the problem of any field having multiple conflicting

  6. Variation and selection: The evolutionary analogy and the convergence of cognitive and behavioral psychology

    PubMed Central

    Morgan, David L.; Morgan, Robin K.; Toth, James M.

    1992-01-01

    The empirical and theoretical work of both operant and cognitive researchers has increasingly appealed to evolutionary concepts. In particular, both traditional operant studies of extinction-induced behavior and cognitive investigations of creativity and problem solving converge on the fundamental evolutionary principles of variation and selection. These contemporary developments and their implications for the alleged preparadigmatic status of psychology are discussed. PMID:22478123

  7. Evolutionary Psychology: A Natural Selection for Music Education?

    ERIC Educational Resources Information Center

    Graham, Rodger

    2006-01-01

    In this viewpoint it is suggested that recent research and authorship in the evolutionary psychology (EP) of music can provide musicians and educators with an enriched understanding of the adaptive role of music in human life. Within a climate of continual educational reform in which music is often marginalised from other mainstream curricular…

  8. Evolutionary Dynamics of MERS-CoV: Potential Recombination, Positive Selection and Transmission

    PubMed Central

    Zhang, Zhao; Shen, Libing; Gu, Xun

    2016-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) belongs to beta group of coronavirus and was first discovered in 2012. MERS-CoV can infect multiple host species and cause severe diseases in human. We conducted a series of phylogenetic and bioinformatic analyses to study the evolution dynamics of MERS-CoV among different host species with genomic data. Our analyses show: 1) 28 potential recombinant sequences were detected and they can be classified into seven potential recombinant types; 2) The spike (S) protein of MERS-CoV was under strong positive selection when MERS-CoV transmitted from their natural host to human; 3) Six out of nine positive selection sites detected in spike (S) protein are located in its receptor-binding domain which is in direct contact with host cells; 4) MERS-CoV frequently transmitted back and forth between human and camel after it had acquired the human-camel infection capability. Together, these results suggest that potential recombination events might have happened frequently during MERS-CoV’s evolutionary history and the positive selection sites in MERS-CoV’s S protein might enable it to infect human. PMID:27142087

  9. Analysis of C3 Suggests Three Periods of Positive Selection Events and Different Evolutionary Patterns between Fish and Mammals

    PubMed Central

    Meng, Fanxing; Sun, Yuena; Liu, Xuezhu; Wang, Jianxin; Xu, Tianjun; Wang, Rixin

    2012-01-01

    Background The third complement component (C3) is a central protein of the complement system conserved from fish to mammals. It also showed distinct characteristics in different animal groups. Striking features of the fish complement system were unveiled, including prominent levels of extrahepatic expression and isotypic diversity of the complement components. The evidences of the involvement of complement system in the enhancement of B and T cell responses found in mammals indicated that the complement system also serves as a bridge between the innate and adaptive responses. For the reasons mentioned above, it is interesting to explore the evolutionary process of C3 genes and to investigate whether the huge differences between aquatic and terrestrial environments affected the C3 evolution between fish and mammals. Methodology/Principal Findings Analysis revealed that these two groups of animals had experienced different evolution patterns. The mammalian C3 genes were under purifying selection pressure while the positive selection pressure was detected in fish C3 genes. Three periods of positive selection events of C3 genes were also detected. Two happened on the ancestral lineages to all vertebrates and mammals, respectively, one happened on early period of fish evolutionary history. Conclusions/Significance Three periods of positive selection events had happened on C3 genes during history and the fish and mammals C3 genes experience different evolutionary patterns for their distinct living environments. PMID:22624039

  10. Evolutionary model selection and parameter estimation for protein-protein interaction network based on differential evolution algorithm

    PubMed Central

    Huang, Lei; Liao, Li; Wu, Cathy H.

    2016-01-01

    Revealing the underlying evolutionary mechanism plays an important role in understanding protein interaction networks in the cell. While many evolutionary models have been proposed, the problem about applying these models to real network data, especially for differentiating which model can better describe evolutionary process for the observed network urgently remains as a challenge. The traditional way is to use a model with presumed parameters to generate a network, and then evaluate the fitness by summary statistics, which however cannot capture the complete network structures information and estimate parameter distribution. In this work we developed a novel method based on Approximate Bayesian Computation and modified Differential Evolution (ABC-DEP) that is capable of conducting model selection and parameter estimation simultaneously and detecting the underlying evolutionary mechanisms more accurately. We tested our method for its power in differentiating models and estimating parameters on the simulated data and found significant improvement in performance benchmark, as compared with a previous method. We further applied our method to real data of protein interaction networks in human and yeast. Our results show Duplication Attachment model as the predominant evolutionary mechanism for human PPI networks and Scale-Free model as the predominant mechanism for yeast PPI networks. PMID:26357273

  11. Using a two-phase evolutionary framework to select multiple network spreaders based on community structure

    NASA Astrophysics Data System (ADS)

    Fu, Yu-Hsiang; Huang, Chung-Yuan; Sun, Chuen-Tsai

    2016-11-01

    Using network community structures to identify multiple influential spreaders is an appropriate method for analyzing the dissemination of information, ideas and infectious diseases. For example, data on spreaders selected from groups of customers who make similar purchases may be used to advertise products and to optimize limited resource allocation. Other examples include community detection approaches aimed at identifying structures and groups in social or complex networks. However, determining the number of communities in a network remains a challenge. In this paper we describe our proposal for a two-phase evolutionary framework (TPEF) for determining community numbers and maximizing community modularity. Lancichinetti-Fortunato-Radicchi benchmark networks were used to test our proposed method and to analyze execution time, community structure quality, convergence, and the network spreading effect. Results indicate that our proposed TPEF generates satisfactory levels of community quality and convergence. They also suggest a need for an index, mechanism or sampling technique to determine whether a community detection approach should be used for selecting multiple network spreaders.

  12. An Evolutionary Algorithm to Generate Ellipsoid Detectors for Negative Selection

    DTIC Science & Technology

    2005-03-21

    Von Zuben [21] have both implemented an AIS using the network immune model. Timmis and Neal [91] applied the model to unsupervised machine learning...and de Castro and Von Zuben [21] applied the model to the problem of clustering and filtering unlabelled numerical data sets. Danger theory is young in...algorithm, clonal selection, is described in the next section. 2.6.1 Clonal Selection. De Castro and Von Zuben produced a clonal selection algorithm

  13. Trait Associations across Evolutionary Time within a Drosophila Phylogeny: Correlated Selection or Genetic Constraint?

    PubMed Central

    Kellermann, Vanessa; Overgaard, Johannes; Loeschcke, Volker; Kristensen, Torsten Nygaard; Hoffmann, Ary A.

    2013-01-01

    Traits do not evolve independently. To understand how trait changes under selection might constrain adaptive changes, phenotypic and genetic correlations are typically considered within species, but these capture constraints across a few generations rather than evolutionary time. For longer-term constraints, comparisons are needed across species but associations may arise because of correlated selection pressures rather than genetic interactions. Implementing a unique approach, we use known patterns of selection to separate likely trait correlations arising due to correlated selection from those reflecting genetic constraints. We examined the evolution of stress resistance in >90 Drosophila species adapted to a range of environments, while controlling for phylogeny. Initially we examined the role of climate and phylogeny in shaping the evolution of starvation and body size, two traits previously not examined in this context. Following correction for phylogeny only a weak relationship between climate and starvation resistance was detected, while all of the variation in the relationship between body size and climate could be attributed to phylogeny. Species were divided into three environmental groups (hot and dry, hot and wet, cold) with the expectation that, if genetic correlations underpin trait correlations, these would persist irrespective of the environment, whereas selection-driven evolution should produce correlations dependent on the environment. We found positive associations between most traits in hot and dry environments coupled with high trait means. In contrast few trait correlations were observed in hot/wet and cold environments. These results suggest trait associations are primarily driven by correlated selection rather than genetic interactions, highlighting that such interactions are unlikely to limit evolution of stress resistance. PMID:24015206

  14. The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection

    PubMed Central

    Chen, Bor-Sen; Ho, Shih-Ju

    2014-01-01

    In this study, a population of evolutionary biological networks is described by a stochastic dynamic system with intrinsic random parameter fluctuations due to genetic variations and external disturbances caused by environmental changes in the evolutionary process. Since information on environmental changes is unavailable and their occurrence is unpredictable, they can be considered as a game player with the potential to destroy phenotypic stability. The biological network needs to develop an evolutionary strategy to improve phenotypic stability as much as possible, so it can be considered as another game player in the evolutionary process, ie, a stochastic Nash game of minimizing the maximum network evolution level caused by the worst environmental disturbances. Based on the nonlinear stochastic evolutionary game strategy, we find that some genetic variations can be used in natural selection to construct negative feedback loops, efficiently improving network robustness. This provides larger genetic robustness as a buffer against neutral genetic variations, as well as larger environmental robustness to resist environmental disturbances and maintain a network phenotypic traits in the evolutionary process. In this situation, the robust phenotypic traits of stochastic biological networks can be more frequently selected by natural selection in evolution. However, if the harbored neutral genetic variations are accumulated to a sufficiently large degree, and environmental disturbances are strong enough that the network robustness can no longer confer enough genetic robustness and environmental robustness, then the phenotype robustness might break down. In this case, a network phenotypic trait may be pushed from one equilibrium point to another, changing the phenotypic trait and starting a new phase of network evolution through the hidden neutral genetic variations harbored in network robustness by adaptive evolution. Further, the proposed evolutionary game is extended to

  15. Evolutionary stasis despite selection on a heritable trait in an invasive zooplankton.

    PubMed

    Miehls, A L J; Peacor, S D; Valliant, L; McAdam, A G

    2015-05-01

    Invasive species are one of the greatest threats to ecosystems, and there is evidence that evolution plays an important role in the success or failure of invasions. Yet, few studies have measured natural selection and evolutionary responses to selection in invasive species, particularly invasive animals. We quantified the strength of natural selection on the defensive morphology (distal spine) of an invasive zooplankton, Bythotrephes longimanus, in Lake Michigan across multiple months during three growing seasons. We used multiple lines of evidence, including historic and contemporary wild-captured individuals and palaeoecology of retrieved spines, to assess phenotypic change in distal spine length since invasion. We found evidence of temporally variable selection, with selection for decreased distal spine length early in the growing season and selection for increased distal spine length later in the season. This trend in natural selection is consistent with seasonal changes in the relative strength of non-gape-limited and gape-limited fish predation. Yet, despite net selection for increased distal spine length and a known genetic basis for distal spine length, we observed little evidence of an evolutionary response to selection. Multiple factors likely limit an evolutionary response to selection, including genetic correlations, trade-offs between components of fitness, and phenotypic plasticity.

  16. Detecting natural selection in genomic data.

    PubMed

    Vitti, Joseph J; Grossman, Sharon R; Sabeti, Pardis C

    2013-01-01

    The past fifty years have seen the development and application of numerous statistical methods to identify genomic regions that appear to be shaped by natural selection. These methods have been used to investigate the macro- and microevolution of a broad range of organisms, including humans. Here, we provide a comprehensive outline of these methods, explaining their conceptual motivations and statistical interpretations. We highlight areas of recent and future development in evolutionary genomics methods and discuss ongoing challenges for researchers employing such tests. In particular, we emphasize the importance of functional follow-up studies to characterize putative selected alleles and the use of selection scans as hypothesis-generating tools for investigating evolutionary histories.

  17. Random Drift versus Selection in Academic Vocabulary: An Evolutionary Analysis of Published Keywords

    PubMed Central

    Bentley, R. Alexander

    2008-01-01

    The evolution of vocabulary in academic publishing is characterized via keyword frequencies recorded in the ISI Web of Science citations database. In four distinct case-studies, evolutionary analysis of keyword frequency change through time is compared to a model of random copying used as the null hypothesis, such that selection may be identified against it. The case studies from the physical sciences indicate greater selection in keyword choice than in the social sciences. Similar evolutionary analyses can be applied to a wide range of phenomena; wherever the popularity of multiple items through time has been recorded, as with web searches, or sales of popular music and books, for example. PMID:18728786

  18. Evolutionary-Rough Feature Selection for Face Recognition

    NASA Astrophysics Data System (ADS)

    Mazumdar, Debasis; Mitra, Soma; Mitra, Sushmita

    Elastic Bunch Graph Matching is a feature-based face recognition algorithm which has been used to determine facial attributes from an image. However the dimension of the feature vectors, in case of EBGM, is quite high. Feature selection is a useful preprocessing step for reducing dimensionality, removing irrelevant data, improving learning accuracy and enhancing output comprehensibility.

  19. An evolutionary view of plant tissue culture: somaclonal variation and selection.

    PubMed

    Wang, Qin-Mei; Wang, Li

    2012-09-01

    Plants regenerated from in vitro cultures possess an array of genetic and epigenetic changes. This phenomenon is known as 'somaclonal variation' and the frequency of somaclonal variation (SV) is usually elevated far beyond that expected in nature. Initially, the relationship between time in culture and detected SV was found to support the widespread belief that SV accumulates with culture age. However, a few studies indicated that older cultures yielded regenerants with less SV. What leads to this seemed contradiction? In this article, we have proposed a novel in vitro callus selection hypothesis, differentiation bottleneck (D-bottleneck) and dedifferentiation bottleneck (Dd-bottleneck), which consider natural selection theory to be fit for cell population in vitro. The results of multiplication races between the cells with the true-to-type phenotype and the deleterious cells determine the increase/decrease of SV frequencies in calli or regenerants as in vitro culture time goes on. The possibility of interpreting the complex situation of time-related SV by the evolutionary theory is discussed in this paper. In addition, the SV threshold, space-determined hypothesis and D-bottleneck are proposed to interpret the loss of the regenerability through a long period of plant tissue culture (PTC).

  20. How can we estimate natural selection on endocrine traits? Lessons from evolutionary biology.

    PubMed

    Bonier, Frances; Martin, Paul R

    2016-11-30

    An evolutionary perspective can enrich almost any endeavour in biology, providing a deeper understanding of the variation we see in nature. To this end, evolutionary endocrinologists seek to describe the fitness consequences of variation in endocrine traits. Much of the recent work in our field, however, follows a flawed approach to the study of how selection shapes endocrine traits. Briefly, this approach relies on among-individual correlations between endocrine phenotypes (often circulating hormone levels) and fitness metrics to estimate selection on those endocrine traits. Adaptive plasticity in both endocrine and fitness-related traits can drive these correlations, generating patterns that do not accurately reflect natural selection. We illustrate why this approach to studying selection on endocrine traits is problematic, referring to work from evolutionary biologists who, decades ago, described this problem as it relates to a variety of other plastic traits. We extend these arguments to evolutionary endocrinology, where the likelihood that this flaw generates bias in estimates of selection is unusually high due to the exceptional responsiveness of hormones to environmental conditions, and their function to induce adaptive life-history responses to environmental variation. We end with a review of productive approaches for investigating the fitness consequences of variation in endocrine traits that we expect will generate exciting advances in our understanding of endocrine system evolution.

  1. Evolutionary rates for multivariate traits: the role of selection and genetic variation.

    PubMed

    Pitchers, William; Wolf, Jason B; Tregenza, Tom; Hunt, John; Dworkin, Ian

    2014-08-19

    A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders' equation (Δz(-)=Gβ), which predicts evolutionary change for a suite of phenotypic traits (Δz(-)) as a product of directional selection acting on them (β) and the genetic variance-covariance matrix for those traits (G ). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are, in part, due to genetic architecture. We find some evidence that sexually selected traits exhibit faster rates of evolution compared with life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G, we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates.

  2. How can we estimate natural selection on endocrine traits? Lessons from evolutionary biology

    PubMed Central

    2016-01-01

    An evolutionary perspective can enrich almost any endeavour in biology, providing a deeper understanding of the variation we see in nature. To this end, evolutionary endocrinologists seek to describe the fitness consequences of variation in endocrine traits. Much of the recent work in our field, however, follows a flawed approach to the study of how selection shapes endocrine traits. Briefly, this approach relies on among-individual correlations between endocrine phenotypes (often circulating hormone levels) and fitness metrics to estimate selection on those endocrine traits. Adaptive plasticity in both endocrine and fitness-related traits can drive these correlations, generating patterns that do not accurately reflect natural selection. We illustrate why this approach to studying selection on endocrine traits is problematic, referring to work from evolutionary biologists who, decades ago, described this problem as it relates to a variety of other plastic traits. We extend these arguments to evolutionary endocrinology, where the likelihood that this flaw generates bias in estimates of selection is unusually high due to the exceptional responsiveness of hormones to environmental conditions, and their function to induce adaptive life-history responses to environmental variation. We end with a review of productive approaches for investigating the fitness consequences of variation in endocrine traits that we expect will generate exciting advances in our understanding of endocrine system evolution. PMID:27881753

  3. Why don't zebras have machine guns? Adaptation, selection, and constraints in evolutionary theory.

    PubMed

    Shanahan, Timothy

    2008-03-01

    In an influential paper, Stephen Jay Gould and Richard Lewontin (1979) contrasted selection-driven adaptation with phylogenetic, architectural, and developmental constraints as distinct causes of phenotypic evolution. In subsequent publications Gould (e.g., 1997a,b, 2002) has elaborated this distinction into one between a narrow "Darwinian Fundamentalist" emphasis on "external functionalist" processes, and a more inclusive "pluralist" emphasis on "internal structuralist" principles. Although theoretical integration of functionalist and structuralist explanations is the ultimate aim, natural selection and internal constraints are treated as distinct causes of evolutionary change. This distinction is now routinely taken for granted in the literature in evolutionary biology. I argue that this distinction is problematic because the effects attributed to non-selective constraints are more parsimoniously explained as the ordinary effects of selection itself. Although it may still be a useful shorthand to speak of phylogenetic, architectural, and developmental constraints on phenotypic evolution, it is important to understand that such "constraints" do not constitute an alternative set of causes of evolutionary change. The result of this analysis is a clearer understanding of the relationship between adaptation, selection and constraints as explanatory concepts in evolutionary theory.

  4. Eco-evolutionary feedback promotes Red Queen dynamics and selects for sex in predator populations.

    PubMed

    Haafke, Julia; Abou Chakra, Maria; Becks, Lutz

    2016-03-01

    Although numerous hypotheses exist to explain the overwhelming presence of sexual reproduction across the tree of life, we still cannot explain its prevalence when considering all inherent costs involved. The Red Queen hypothesis states that sex is maintained because it can create novel genotypes with a selective advantage. This occurs when the interactions between species induce frequent environmental change. Here, we investigate whether coevolution and eco-evolutionary feedback dynamics in a predator-prey system allows for indirect selection and maintenance of sexual reproduction in the predator. Combining models and chemostat experiments of a rotifer-algae system we show a continuous feedback between population and trait change along with recurrent shifts from selection by predation and competition for a limited resource. We found that a high propensity for sex was indirectly selected and was maintained in rotifer populations within environments containing these eco-evolutionary dynamics; whereas within environments under constant conditions, predators evolved rapidly to lower levels of sex. Thus, our results indicate that the influence of eco-evolutionary feedback dynamics on the overall evolutionary change has been underestimated.

  5. Evolutionary entropy predicts the outcome of selection: Competition for resources that vary in abundance and diversity.

    PubMed

    Demetrius, Lloyd; Legendre, Stéphane

    2013-02-01

    Competition between individuals for resources which are limited and diverse in composition is the ultimate driving force of evolution. Classical studies of this event contend that the outcome is a deterministic process predicted by the growth rate of the competing types-a tenet called the Malthusian selection principle. Recent studies of competition indicate that the dynamics of selection is a stochastic process, regulated by the population size, the abundance and diversity of the resource, and predicted by evolutionary entropy-a statistical parameter which characterizes the rate at which the population returns to the steady state condition after a random endogenous or exogenous perturbation. This tenet, which we will call the entropic selection principle entails the following relations: This article delineates the analytic, computational and empirical support for this tenet. We show moreover that the Malthusian selection principle, a cornerstone of classical evolutionary genetics, is the limit, as population size and resource abundance tends to infinity of the entropic selection principle. The Malthusian tenet is an approximation to the entropic selection principle-an approximation whose validity increases with increasing population size and increasing resource abundance. Evolutionary entropy is a generic concept that characterizes the interaction dynamics of metabolic entities at several levels of biological organization: cellular, organismic and ecological. Accordingly, the entropic selection principle represents a general rule for explaining the processes of adaptation and evolution at each of these levels.

  6. Host plant selection by aphids: behavioral, evolutionary, and applied perspectives.

    PubMed

    Powell, Glen; Tosh, Colin R; Hardie, Jim

    2006-01-01

    As phloem feeders and major vectors of plant viruses, aphids are important pests of agricultural and horticultural crops worldwide. The processes of aphid settling and reproduction on plants therefore have a direct economic impact, and a better understanding of these events may lead to improved management strategies. Aphids are also important model organisms in the analysis of population differentiation and speciation in animals, and new ideas on plant utilization influence our understanding of the mechanisms generating biological diversity. Recent research suggests that the dominant cues controlling plant preference and initiation of reproduction are detected early during the stylet penetration process, well before the nutrient supply (phloem) is contacted. Aphids regularly puncture cells along the stylet pathway and ingest cytosolic samples, and the cues stimulating settling and parturition likely are metabolites present in peripheral (nonvascular) plant cells. We discuss these findings and their implications for aphid evolution and management.

  7. Combined evolutionary algorithm and minimum classification error training for DHMM-based land mine detection

    NASA Astrophysics Data System (ADS)

    Zhao, Yunxin; Chen, Ping; Gader, Paul D.; Zhang, Yue

    2002-08-01

    Minimum classification error (MCE) training is proposed to improve performance of a discrete hidden Markov model (DHMM) based landmine detection system. The system (baseline) was proposed previously for detection of both metal and nonmetal mines from ground penetrating radar signatures collected by moving vehicles. An initial DHMM model is trained by conventional methods of vector quantization and Baum-Welch algorithm. A sequential generalized probabilistic descent (GPD) algorithm that minimizes an empirical loss function is then used to estimate the landmine/background DHMM parameters, and an evolutionary algorithm based on fitness score of classification accuracy is used to generate and select codebooks. The landmine data of one geographical site was used for model training, and those of two different sites were used for evaluation of system performance. Three scenarios were studied: apply MCE/GPD alone to DHMM estimation, apply EA alone to codebook generation, first apply EA to codebook generation and then apply MCE/GPD to DHMM estimation. Overall, the combined EA and MCE/GPD training led to the best performance. At the same level of detection rate as the baseline DHMM system, the proposed training reduced false alarm rate by a factor of two, indicating significant performance improvement.

  8. Optimality and stability of symmetric evolutionary games with applications in genetic selection.

    PubMed

    Huang, Yuanyuan; Hao, Yiping; Wang, Min; Zhou, Wen; Wu, Zhijun

    2015-06-01

    Symmetric evolutionary games, i.e., evolutionary games with symmetric fitness matrices, have important applications in population genetics, where they can be used to model for example the selection and evolution of the genotypes of a given population. In this paper, we review the theory for obtaining optimal and stable strategies for symmetric evolutionary games, and provide some new proofs and computational methods. In particular, we review the relationship between the symmetric evolutionary game and the generalized knapsack problem, and discuss the first and second order necessary and sufficient conditions that can be derived from this relationship for testing the optimality and stability of the strategies. Some of the conditions are given in different forms from those in previous work and can be verified more efficiently. We also derive more efficient computational methods for the evaluation of the conditions than conventional approaches. We demonstrate how these conditions can be applied to justifying the strategies and their stabilities for a special class of genetic selection games including some in the study of genetic disorders.

  9. Comparative Genomic Analysis among Four Representative Isolates of Phytophthora sojae Reveals Genes under Evolutionary Selection

    PubMed Central

    Ye, Wenwu; Wang, Yang; Tyler, Brett M.; Wang, Yuanchao

    2016-01-01

    Comparative genomic analysis is useful for identifying genes affected by evolutionary selection and for studying adaptive variation in gene functions. In Phytophthora sojae, a model oomycete plant pathogen, the related study is lacking. We compared sequence data among four isolates of P. sojae, which represent its four major genotypes. These isolates exhibited >99.688%, >99.864%, and >98.981% sequence identities at genome, gene, and non-gene regions, respectively. One hundred and fifty-three positive selection and 139 negative selection candidate genes were identified. Between the two categories of genes, the positive selection genes were flanked by larger intergenic regions, poorly annotated in function, and less conserved; they had relatively lower transcription levels but many genes had increased transcripts during infection. Genes coding for predicted secreted proteins, particularly effectors, were overrepresented in positive selection. Several RxLR effector genes were identified as positive selection genes, exhibiting much stronger positive selection levels. In addition, candidate genes with presence/absence polymorphism were analyzed. This study provides a landscape of genomic variation among four representative P. sojae isolates and characterized several evolutionary selection-affected gene candidates. The results suggest a relatively covert two-speed genome evolution pattern in P. sojae and will provide clues for identification of new virulence factors in the oomycete plant pathogens. PMID:27746768

  10. The evolutionary forces maintaining a wild polymorphism of Littorina saxatilis: model selection by computer simulations.

    PubMed

    Pérez-Figueroa, A; Cruz, F; Carvajal-Rodríguez, A; Rolán-Alvarez, E; Caballero, A

    2005-01-01

    Two rocky shore ecotypes of Littorina saxatilis from north-west Spain live at different shore levels and habitats and have developed an incomplete reproductive isolation through size assortative mating. The system is regarded as an example of sympatric ecological speciation. Several experiments have indicated that different evolutionary forces (migration, assortative mating and habitat-dependent selection) play a role in maintaining the polymorphism. However, an assessment of the combined contributions of these forces supporting the observed pattern in the wild is absent. A model selection procedure using computer simulations was used to investigate the contribution of the different evolutionary forces towards the maintenance of the polymorphism. The agreement between alternative models and experimental estimates for a number of parameters was quantified by a least square method. The results of the analysis show that the fittest evolutionary model for the observed polymorphism is characterized by a high gene flow, intermediate-high reproductive isolation between ecotypes, and a moderate to strong selection against the nonresident ecotypes on each shore level. In addition, a substantial number of additive loci contributing to the selected trait and a narrow hybrid definition with respect to the phenotype are scenarios that better explain the polymorphism, whereas the ecotype fitnesses at the mid-shore, the level of phenotypic plasticity, and environmental effects are not key parameters.

  11. The evolutionary legacy of size-selective harvesting extends from genes to populations

    PubMed Central

    Uusi-Heikkilä, Silva; Whiteley, Andrew R; Kuparinen, Anna; Matsumura, Shuichi; Venturelli, Paul A; Wolter, Christian; Slate, Jon; Primmer, Craig R; Meinelt, Thomas; Killen, Shaun S; Bierbach, David; Polverino, Giovanni; Ludwig, Arne; Arlinghaus, Robert

    2015-01-01

    Size-selective harvesting is assumed to alter life histories of exploited fish populations, thereby negatively affecting population productivity, recovery, and yield. However, demonstrating that fisheries-induced phenotypic changes in the wild are at least partly genetically determined has proved notoriously difficult. Moreover, the population-level consequences of fisheries-induced evolution are still being controversially discussed. Using an experimental approach, we found that five generations of size-selective harvesting altered the life histories and behavior, but not the metabolic rate, of wild-origin zebrafish (Danio rerio). Fish adapted to high positively size selective fishing pressure invested more in reproduction, reached a smaller adult body size, and were less explorative and bold. Phenotypic changes seemed subtle but were accompanied by genetic changes in functional loci. Thus, our results provided unambiguous evidence for rapid, harvest-induced phenotypic and evolutionary change when harvesting is intensive and size selective. According to a life-history model, the observed life-history changes elevated population growth rate in harvested conditions, but slowed population recovery under a simulated moratorium. Hence, the evolutionary legacy of size-selective harvesting includes populations that are productive under exploited conditions, but selectively disadvantaged to cope with natural selection pressures that often favor large body size. PMID:26136825

  12. Disruptive selection as a driver of evolutionary branching and caste evolution in social insects.

    PubMed

    Planqué, R; Powell, S; Franks, N R; van den Berg, J B

    2016-11-01

    Theory suggests that evolutionary branching via disruptive selection may be a relatively common and powerful force driving phenotypic divergence. Here, we extend this theory to social insects, which have novel social axes of phenotypic diversification. Our model, built around turtle ant (Cephalotes) biology, is used to explore whether disruptive selection can drive the evolutionary branching of divergent colony phenotypes that include a novel soldier caste. Soldier evolution is a recurrent theme in social insect diversification that is exemplified in the turtle ants. We show that phenotypic mutants can gain competitive advantages that induce disruptive selection and subsequent branching. A soldier caste does not generally appear before branching, but can evolve from subsequent competition. The soldier caste then evolves in association with specialized resource preferences that maximize defensive performance. Overall, our model indicates that resource specialization may occur in the absence of morphological specialization, but that when morphological specialization evolves, it is always in association with resource specialization. This evolutionary coupling of ecological and morphological specialization is consistent with recent empirical evidence, but contrary to predictions of classical caste theory. Our model provides a new theoretical understanding of the ecology of caste evolution that explicitly considers the process of adaptive phenotypic divergence and diversification.

  13. Eco-evolutionary dynamics in response to selection on life-history

    PubMed Central

    Cameron, Tom C; O'Sullivan, Daniel; Reynolds, Alan; Piertney, Stuart B; Benton, Tim G; Sorci, Gabriele

    2013-01-01

    Understanding the consequences of environmental change on ecological and evolutionary dynamics is inherently problematic because of the complex interplay between them. Using invertebrates in microcosms, we characterise phenotypic, population and evolutionary dynamics before, during and after exposure to a novel environment and harvesting over 20 generations. We demonstrate an evolved change in life-history traits (the age- and size-at-maturity, and survival to maturity) in response to selection caused by environmental change (wild to laboratory) and to harvesting (juvenile or adult). Life-history evolution, which drives changes in population growth rate and thus population dynamics, includes an increase in age-to-maturity of 76% (from 12.5 to 22 days) in the unharvested populations as they adapt to the new environment. Evolutionary responses to harvesting are outweighed by the response to environmental change (∼ 1.4 vs. 4% change in age-at-maturity per generation). The adaptive response to environmental change converts a negative population growth trajectory into a positive one: an example of evolutionary rescue. PMID:23565666

  14. Eco-evolutionary dynamics in response to selection on life-history.

    PubMed

    Cameron, Tom C; O'Sullivan, Daniel; Reynolds, Alan; Piertney, Stuart B; Benton, Tim G

    2013-06-01

    Understanding the consequences of environmental change on ecological and evolutionary dynamics is inherently problematic because of the complex interplay between them. Using invertebrates in microcosms, we characterise phenotypic, population and evolutionary dynamics before, during and after exposure to a novel environment and harvesting over 20 generations. We demonstrate an evolved change in life-history traits (the age- and size-at-maturity, and survival to maturity) in response to selection caused by environmental change (wild to laboratory) and to harvesting (juvenile or adult). Life-history evolution, which drives changes in population growth rate and thus population dynamics, includes an increase in age-to-maturity of 76% (from 12.5 to 22 days) in the unharvested populations as they adapt to the new environment. Evolutionary responses to harvesting are outweighed by the response to environmental change (~ 1.4 vs. 4% change in age-at-maturity per generation). The adaptive response to environmental change converts a negative population growth trajectory into a positive one: an example of evolutionary rescue.

  15. gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances

    PubMed Central

    Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav

    2016-01-01

    Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos). PMID:27846272

  16. gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances.

    PubMed

    Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav

    2016-01-01

    Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos).

  17. The limits of weak selection and large population size in evolutionary game theory.

    PubMed

    Sample, Christine; Allen, Benjamin

    2017-03-28

    Evolutionary game theory is a mathematical approach to studying how social behaviors evolve. In many recent works, evolutionary competition between strategies is modeled as a stochastic process in a finite population. In this context, two limits are both mathematically convenient and biologically relevant: weak selection and large population size. These limits can be combined in different ways, leading to potentially different results. We consider two orderings: the [Formula: see text] limit, in which weak selection is applied before the large population limit, and the [Formula: see text] limit, in which the order is reversed. Formal mathematical definitions of the [Formula: see text] and [Formula: see text] limits are provided. Applying these definitions to the Moran process of evolutionary game theory, we obtain asymptotic expressions for fixation probability and conditions for success in these limits. We find that the asymptotic expressions for fixation probability, and the conditions for a strategy to be favored over a neutral mutation, are different in the [Formula: see text] and [Formula: see text] limits. However, the ordering of limits does not affect the conditions for one strategy to be favored over another.

  18. Evolutionary signals of selection on cognition from the great tit genome and methylome

    PubMed Central

    Laine, Veronika N.; Gossmann, Toni I.; Schachtschneider, Kyle M.; Garroway, Colin J.; Madsen, Ole; Verhoeven, Koen J. F.; de Jager, Victor; Megens, Hendrik-Jan; Warren, Wesley C.; Minx, Patrick; Crooijmans, Richard P. M. A.; Corcoran, Pádraic; Adriaensen, Frank; Belda, Eduardo; Bushuev, Andrey; Cichon, Mariusz; Charmantier, Anne; Dingemanse, Niels; Doligez, Blandine; Eeva, Tapio; Erikstad, Kjell Einar; Fedorov, Slava; Hau, Michaela; Hille, Sabine; Hinde, Camilla; Kempenaers, Bart; Kerimov, Anvar; Krist, Milos; Mand, Raivo; Matthysen, Erik; Nager, Reudi; Norte, Claudia; Orell, Markku; Richner, Heinz; Slagsvold, Tore; Tilgar, Vallo; Tinbergen, Joost; Torok, Janos; Tschirren, Barbara; Yuta, Tera; Sheldon, Ben C.; Slate, Jon; Zeng, Kai; van Oers, Kees; Visser, Marcel E.; Groenen, Martien A. M.

    2016-01-01

    For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemble a great tit reference genome and whole-genome re-sequence another 29 individuals from across Europe. We show an overrepresentation of genes related to neuronal functions, learning and cognition in regions under positive selection, as well as increased CpG methylation in these regions. In addition, great tit neuronal non-CpG methylation patterns are very similar to those observed in mammals, suggesting a universal role in neuronal epigenetic regulation which can affect learning-, memory- and experience-induced plasticity. The high-quality great tit genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species. PMID:26805030

  19. Joint phenotypes, evolutionary conflict and the fundamental theorem of natural selection.

    PubMed

    Queller, David C

    2014-05-19

    Multiple organisms can sometimes affect a common phenotype. For example, the portion of a leaf eaten by an insect is a joint phenotype of the plant and insect and the amount of food obtained by an offspring can be a joint trait with its mother. Here, I describe the evolution of joint phenotypes in quantitative genetic terms. A joint phenotype for multiple species evolves as the sum of additive genetic variances in each species, weighted by the selection on each species. Selective conflict between the interactants occurs when selection takes opposite signs on the joint phenotype. The mean fitness of a population changes not just through its own genetic variance but also through the genetic variance for its fitness that resides in other species, an update of Fisher's fundamental theorem of natural selection. Some similar results, using inclusive fitness, apply to within-species interactions. The models provide a framework for understanding evolutionary conflicts at all levels.

  20. Applying an instance selection method to an evolutionary neural classifier design

    NASA Astrophysics Data System (ADS)

    Khritonenko, Dmitrii; Stanovov, Vladimir; Semenkin, Eugene

    2017-02-01

    In this paper the application of an instance selection algorithm to the design of a neural classifier is considered. A number of existing instance selection methods are presented. A new wrapper-method, whose main difference compared to other approaches is an iterative procedure for selecting training subsets from the dataset, is described. The approach is based on using training subsample selection probabilities for every instance. The value of these probabilities depends on the classification success for each measurement. An evolutionary algorithm for the design of a neural classifier is presented, which was used to test the efficiency of the presented approach. The described approach has been implemented and tested on a set of classification problems. The testing has shown that the presented algorithm allows the computational complexity to be decreased and the quality of the obtained classifiers to be increased. Compared to analogues found in scientific literature, it was shown that the presented algorithm is an effective tool for classification problem solving.

  1. How quickly do brains catch up with bodies? A comparative method for detecting evolutionary lag.

    PubMed Central

    Deaner, R O; Nunn, C L

    1999-01-01

    A trait may be at odds with theoretical expectation because it is still in the process of responding to a recent selective force. Such a situation can be termed evolutionary lag. Although many cases of evolutionary lag have been suggested, almost all of the arguments have focused on trait fitness. An alternative approach is to examine the prediction that trait expression is a function of the time over which the trait could evolve. Here we present a phylogenetic comparative method for using this 'time' approach and we apply the method to a long-standing lag hypothesis: evolutionary changes in brain size lag behind evolutionary changes in body size. We tested the prediction in primates that brain mass contrast residuals, calculated from a regression of pairwise brain mass contrasts on positive pairwise body mass contrasts, are correlated with the time since the paired species diverged. Contrary to the brain size lag hypothesis, time since divergence was not significantly correlated with brain mass contrast residuals. We found the same result when we accounted for socioecology, used alternative body mass estimates and used male rather than female values. These tests do not support the brain size lag hypothesis. Therefore, body mass need not be viewed as a suspect variable in comparative neuroanatomical studies and relative brain size should not be used to infer recent evolutionary changes in body size. PMID:10331289

  2. Optimal Wavelengths Selection Using Hierarchical Evolutionary Algorithm for Prediction of Firmness and Soluble Solids Content in Apples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hyperspectral scattering is a promising technique for rapid and noninvasive measurement of multiple quality attributes of apple fruit. A hierarchical evolutionary algorithm (HEA) approach, in combination with subspace decomposition and partial least squares (PLS) regression, was proposed to select o...

  3. Difference in evolutionary patterns of strongly or weakly selected characters among ant populations

    PubMed Central

    Imai, Shuichiro; Kobayashi, Kazuya; Ohkubo, Yusaku; Yagi, Norihiro; Hasegawa, Eisuke

    2016-01-01

    Despite being a central issue in evolutionary biology, few studies have examined the stasis of characters in populations with no gene flow. A possible mechanism of such stasis is stabilizing selection with similar peaks in each population. This study examined the evolutionary patterns of morphological characters with and without strong selection in ant populations. We show that compared to a character that seems to be less important, characters that are more important were less variable within and among populations. Microsatellite analyses showed significant genetic differences between populations, implying limited gene flow between them. The observed levels of genetic differentiation cannot be attributed to recent population separations. Thus, the observed differences in morphological variance seem to reflect the degree of selection on each character. The less important character changed proportionately with time, but such a pattern was not observed in more important characters. These results suggest that stabilizing selection maintains morphological stasis between populations of the same species with minimal gene flow independent of divergence times. PMID:27995972

  4. Charles Darwin's Origin of Species, directional selection, and the evolutionary sciences today.

    PubMed

    Kutschera, Ulrich

    2009-11-01

    The book On the Origin of Species, published in November 1859, is an "abstract" without references, compiled by Charles Darwin from a much longer manuscript entitled "Natural Selection." Here, I summarize the five theories that can be extracted from Darwin's monograph, explain the true meaning of the phrase "struggle for life" (i.e., competition and cooperation), and outline Darwin's original concept of natural selection in populations of animals and plants. Since neither Darwin nor Alfred R. Wallace distinguished between stabilizing and directional natural selection, the popular argument that "selection only eliminates but is not creative" is still alive today. However, I document that August Weismann (Die Bedeutung der sexuellen Fortpflanzung für die Selektions-Theorie. Gustav Fischer-Verlag, Jena, 1886) and Ivan Schmalhausen (Factors of evolution. The theory of stabilizing selection. The Blackiston Company, Philadelphia, 1949) provided precise definitions for directional (dynamic) selection in nature and illustrate this "Weismann-Schmalhausen principle" with respect to the evolutionary development of novel phenotypes. Then, the modern (synthetic) theory of biological evolution that is based on the work of Theodosius Dobzhansky (Genetics and the origin of species. Columbia University Press, New York, 1937) and others, and the expanded version of this system of theories, are outlined. Finally, I document that symbiogenesis (i.e., primary endosymbiosis, a process that gave rise to the first eukaryotic cells), ongoing directional natural selection, and the dynamic Earth (plate tectonics, i.e., geological events that both created and destroyed terrestrial and aquatic habitats) were the key processes responsible for the documented macroevolutionary patterns in all five kingdoms of life. Since the evolutionary development of the earliest archaic bacteria more than 3,500 mya, the biosphere of our dynamic planet has been dominated by prokaryotic microbes. Eubacteria

  5. Homosexual mating preferences from an evolutionary perspective: sexual selection theory revisited.

    PubMed

    Gobrogge, Kyle L; Perkins, Patrick S; Baker, Jessica H; Balcer, Kristen D; Breedlove, S Marc; Klump, Kelly L

    2007-10-01

    Studies in evolutionary psychology and sexual selection theory show that heterosexual men prefer younger mating partners than heterosexual women in order to ensure reproductive success. However, previous research has generally not examined differences in mating preferences as a function of sexual orientation or the type of relationship sought in naturalistic settings. Given that homosexual men seek partners for reasons other than procreation, they may exhibit different mating preferences than their heterosexual counterparts. Moreover, mating preferences may show important differences depending on whether an individual is seeking a long-term versus a short-term relationship. The purpose of the present study was to examine these issues by comparing partner preferences in terms of age and relationship type between homosexual and heterosexual men placing internet personal advertisements. Participants included 439 homosexual and 365 heterosexual men who placed internet ads in the U.S. or Canada. Ads were coded for the participant's age, relationship type (longer-term or short-term sexual encounter) sought, and partner age preferences. Significantly more homosexual than heterosexual men sought sexual encounters, although men (regardless of sexual orientation) seeking sexual encounters preferred a significantly wider age range of partners than men seeking longer-term relationships. These findings suggest that partner preferences are independent of evolutionary drives to procreate, since both types of men preferred similar ages in their partners. In addition, they highlight the importance of examining relationship type in evolutionary studies of mating preferences, as men's partner preferences show important differences depending upon the type of relationship sought.

  6. Unintentional selection, unanticipated insights: introductions, stocking and the evolutionary ecology of fishes.

    PubMed

    Hutchings, J A

    2014-12-01

    Natural environmental change has produced countless opportunities for species to disperse into and persist in habitats where they previously did not exist. Introduction and stocking programmes have facilitated similar sorts of colonization opportunities across considerably greater geographical scales and often in much shorter periods of time. Even though the mechanism of colonization differs, the result can be the same: evolutionary change in the colonizing population in response to novel selection pressures. As a consequence, some human-mediated fish transfers have unintentionally yielded novel research opportunities to study how phenotypes and genes interact with their environment and affect ecological and evolutionary change. The primary purpose here is to explore how work, directly or indirectly involved with human-mediated transfers, has unintentionally yielded novel research and research opportunities in fish ecology and evolution. Insights have produced new knowledge or altered previously held perceptions on topics such as local adaptation, rate of evolutionary change, phenotypic plasticity, alternative reproductive strategies, population structure and colonization probability. Well-documented stocking programmes, especially in terms of history, numbers and original population sources, can provide highly fertile ground for generating further insights on the ecology and evolution of fishes and of the factors likely to influence the success of conservation-based, restoration programmes.

  7. Mutation-selection dynamics and error threshold in an evolutionary model for Turing machines.

    PubMed

    Musso, Fabio; Feverati, Giovanni

    2012-01-01

    We investigate the mutation-selection dynamics for an evolutionary computation model based on Turing machines. The use of Turing machines allows for very simple mechanisms of code growth and code activation/inactivation through point mutations. To any value of the point mutation probability corresponds a maximum amount of active code that can be maintained by selection and the Turing machines that reach it are said to be at the error threshold. Simulations with our model show that the Turing machines population evolve toward the error threshold. Mathematical descriptions of the model point out that this behaviour is due more to the mutation-selection dynamics than to the intrinsic nature of the Turing machines. This indicates that this result is much more general than the model considered here and could play a role also in biological evolution.

  8. Detection Progress of Selected Drugs in TLC

    PubMed Central

    Pyka, Alina

    2014-01-01

    This entry describes applications of known indicators and dyes as new visualizing reagents and various visualizing systems as well as photocatalytic reactions and bioautography method for the detection of bioactive compounds including drugs and compounds isolated from herbal extracts. Broadening index, detection index, characteristics of densitometric band, modified contrast index, limit of detection, densitometric visualizing index, and linearity range of detected compounds were used for the evaluation of visualizing effects of applied visualizing reagents. It was shown that visualizing effect depends on the chemical structure of the visualizing reagent, the structure of the substance detected, and the chromatographic adsorbent applied. The usefulness of densitometry to direct detection of some drugs was also shown. Quoted papers indicate the detection progress of selected drugs investigated by thin-layer chromatography (TLC). PMID:24551853

  9. Differential Evolutionary Selection and Natural Evolvability Observed in ALT Proteins of Human Filarial Parasites.

    PubMed

    Devoe, Neil C; Corbett, Ian J; Barker, Linsey; Chang, Robert; Gudis, Polyxeni; Mullen, Nathan; Perez, Kailey; Raposo, Hugo; Scholz, John; May, Meghan

    2016-01-01

    The abundant larval transcript (ALT-2) protein is present in all members of the Filarioidea, and has been reported as a potential candidate antigen for a subunit vaccine against lymphatic filariasis. To assess the potential for vaccine escape or heterologous protection, we examined the evolutionary selection acting on ALT-2. The ratios of nonsynonymous (K(a)) to synonymous (K(s)) mutation frequencies (ω) were calculated for the alt-2 genes of the lymphatic filariasis agents Brugia malayi and Wuchereria bancrofti and the agents of river blindness and African eyeworm disease Onchocerca volvulus and Loa loa. Two distinct Bayesian models of sequence evolution showed that ALT-2 of W. bancrofti and L. loa were under significant (P<0.05; P < 0.001) diversifying selection, while ALT-2 of B. malayi and O. volvulus were under neutral to stabilizing selection. Diversifying selection as measured by ω values was notably strongest on the region of ALT-2 encoding the signal peptide of L. loa and was elevated in the variable acidic domain of L. loa and W. bancrofti. Phylogenetic analysis indicated that the ALT-2 consensus sequences formed three clades: the first consisting of B. malayi, the second consisting of W. bancrofti, and the third containing both O. volvulus and L. loa. ALT-2 selection was therefore not predictable by phylogeny or pathology, as the two species parasitizing the eye were selected differently, as were the two species parasitizing the lymphatic system. The most immunogenic regions of L. loa and W. bancrofti ALT-2 sequence as modeled by antigenicity prediction analysis did not correspond with elevated levels of diversifying selection, and were not selected differently than predicted antigenic epitopes in B. malayi and O. volvulus. Measurements of ALT-2 evolvability made by χ2 analysis between alleles that were stable (O. volvulus and B. malayi) and those that were under diversifying selection (W. bancrofti and L. loa) indicated significant (P<0

  10. Differential Evolutionary Selection and Natural Evolvability Observed in ALT Proteins of Human Filarial Parasites

    PubMed Central

    Devoe, Neil C.; Corbett, Ian J.; Barker, Linsey; Chang, Robert; Gudis, Polyxeni; Mullen, Nathan; Perez, Kailey; Raposo, Hugo; Scholz, John; May, Meghan

    2016-01-01

    The abundant larval transcript (ALT-2) protein is present in all members of the Filarioidea, and has been reported as a potential candidate antigen for a subunit vaccine against lymphatic filariasis. To assess the potential for vaccine escape or heterologous protection, we examined the evolutionary selection acting on ALT-2. The ratios of nonsynonymous (K(a)) to synonymous (K(s)) mutation frequencies (ω) were calculated for the alt-2 genes of the lymphatic filariasis agents Brugia malayi and Wuchereria bancrofti and the agents of river blindness and African eyeworm disease Onchocerca volvulus and Loa loa. Two distinct Bayesian models of sequence evolution showed that ALT-2 of W. bancrofti and L. loa were under significant (P<0.05; P < 0.001) diversifying selection, while ALT-2 of B. malayi and O. volvulus were under neutral to stabilizing selection. Diversifying selection as measured by ω values was notably strongest on the region of ALT-2 encoding the signal peptide of L. loa and was elevated in the variable acidic domain of L. loa and W. bancrofti. Phylogenetic analysis indicated that the ALT-2 consensus sequences formed three clades: the first consisting of B. malayi, the second consisting of W. bancrofti, and the third containing both O. volvulus and L. loa. ALT-2 selection was therefore not predictable by phylogeny or pathology, as the two species parasitizing the eye were selected differently, as were the two species parasitizing the lymphatic system. The most immunogenic regions of L. loa and W. bancrofti ALT-2 sequence as modeled by antigenicity prediction analysis did not correspond with elevated levels of diversifying selection, and were not selected differently than predicted antigenic epitopes in B. malayi and O. volvulus. Measurements of ALT-2 evolvability made by χ2 analysis between alleles that were stable (O. volvulus and B. malayi) and those that were under diversifying selection (W. bancrofti and L. loa) indicated significant (P<0

  11. A standard deviation selection in evolutionary algorithm for grouper fish feed formulation

    NASA Astrophysics Data System (ADS)

    Cai-Juan, Soong; Ramli, Razamin; Rahman, Rosshairy Abdul

    2016-10-01

    Malaysia is one of the major producer countries for fishery production due to its location in the equatorial environment. Grouper fish is one of the potential markets in contributing to the income of the country due to its desirable taste, high demand and high price. However, the demand of grouper fish is still insufficient from the wild catch. Therefore, there is a need to farm grouper fish to cater to the market demand. In order to farm grouper fish, there is a need to have prior knowledge of the proper nutrients needed because there is no exact data available. Therefore, in this study, primary data and secondary data are collected even though there is a limitation of related papers and 30 samples are investigated by using standard deviation selection in Evolutionary algorithm. Thus, this study would unlock frontiers for an extensive research in respect of grouper fish feed formulation. Results shown that the fitness of standard deviation selection in evolutionary algorithm is applicable. The feasible and low fitness, quick solution can be obtained. These fitness can be further predicted to minimize cost in farming grouper fish.

  12. Gene selection for microarray cancer classification using a new evolutionary method employing artificial intelligence concepts.

    PubMed

    Dashtban, M; Balafar, Mohammadali

    2017-03-01

    Gene selection is a demanding task for microarray data analysis. The diverse complexity of different cancers makes this issue still challenging. In this study, a novel evolutionary method based on genetic algorithms and artificial intelligence is proposed to identify predictive genes for cancer classification. A filter method was first applied to reduce the dimensionality of feature space followed by employing an integer-coded genetic algorithm with dynamic-length genotype, intelligent parameter settings, and modified operators. The algorithmic behaviors including convergence trends, mutation and crossover rate changes, and running time were studied, conceptually discussed, and shown to be coherent with literature findings. Two well-known filter methods, Laplacian and Fisher score, were examined considering similarities, the quality of selected genes, and their influences on the evolutionary approach. Several statistical tests concerning choice of classifier, choice of dataset, and choice of filter method were performed, and they revealed some significant differences between the performance of different classifiers and filter methods over datasets. The proposed method was benchmarked upon five popular high-dimensional cancer datasets; for each, top explored genes were reported. Comparing the experimental results with several state-of-the-art methods revealed that the proposed method outperforms previous methods in DLBCL dataset.

  13. Selection of relevant input variables in storm water quality modeling by multiobjective evolutionary polynomial regression paradigm

    NASA Astrophysics Data System (ADS)

    Creaco, E.; Berardi, L.; Sun, Siao; Giustolisi, O.; Savic, D.

    2016-04-01

    The growing availability of field data, from information and communication technologies (ICTs) in "smart" urban infrastructures, allows data modeling to understand complex phenomena and to support management decisions. Among the analyzed phenomena, those related to storm water quality modeling have recently been gaining interest in the scientific literature. Nonetheless, the large amount of available data poses the problem of selecting relevant variables to describe a phenomenon and enable robust data modeling. This paper presents a procedure for the selection of relevant input variables using the multiobjective evolutionary polynomial regression (EPR-MOGA) paradigm. The procedure is based on scrutinizing the explanatory variables that appear inside the set of EPR-MOGA symbolic model expressions of increasing complexity and goodness of fit to target output. The strategy also enables the selection to be validated by engineering judgement. In such context, the multiple case study extension of EPR-MOGA, called MCS-EPR-MOGA, is adopted. The application of the proposed procedure to modeling storm water quality parameters in two French catchments shows that it was able to significantly reduce the number of explanatory variables for successive analyses. Finally, the EPR-MOGA models obtained after the input selection are compared with those obtained by using the same technique without benefitting from input selection and with those obtained in previous works where other data-modeling techniques were used on the same data. The comparison highlights the effectiveness of both EPR-MOGA and the input selection procedure.

  14. Evolutionary switches between two serine codon sets are driven by selection

    PubMed Central

    Rogozin, Igor B.; Belinky, Frida; Pavlenko, Vladimir; Shabalina, Svetlana A.; Kristensen, David M.; Koonin, Eugene V.

    2016-01-01

    Serine is the only amino acid that is encoded by two disjoint codon sets so that a tandem substitution of two nucleotides is required to switch between the two sets. Previously published evidence suggests that, for the most evolutionarily conserved serines, the codon set switch occurs by simultaneous substitution of two nucleotides. Here we report a genome-wide reconstruction of the evolution of serine codons in triplets of closely related species from diverse prokaryotes and eukaryotes. The results indicate that the great majority of codon set switches proceed by two consecutive nucleotide substitutions, via a threonine or cysteine intermediate, and are driven by selection. These findings imply a strong pressure of purifying selection in protein evolution, which in the case of serine codon set switches occurs via an initial deleterious substitution quickly followed by a second, compensatory substitution. The result is frequent reversal of amino acid replacements and, at short evolutionary distances, pervasive homoplasy. PMID:27799560

  15. Negative Selection Algorithm for Aircraft Fault Detection

    NASA Technical Reports Server (NTRS)

    Dasgupta, D.; KrishnaKumar, K.; Wong, D.; Berry, M.

    2004-01-01

    We investigated a real-valued Negative Selection Algorithm (NSA) for fault detection in man-in-the-loop aircraft operation. The detection algorithm uses body-axes angular rate sensory data exhibiting the normal flight behavior patterns, to generate probabilistically a set of fault detectors that can detect any abnormalities (including faults and damages) in the behavior pattern of the aircraft flight. We performed experiments with datasets (collected under normal and various simulated failure conditions) using the NASA Ames man-in-the-loop high-fidelity C-17 flight simulator. The paper provides results of experiments with different datasets representing various failure conditions.

  16. Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials

    PubMed Central

    Meyer-Lucht, Yvonne; Otten, Celine; Püttker, Thomas; Sommer, Simone

    2008-01-01

    Background Research on the genetic architecture and diversity of the MHC has focused mainly on eutherian mammals, birds and fish. So far, studies on model marsupials used in laboratory investigations indicated very little or even no variation in MHC class II genes. However, natural levels of diversity and selection are unknown in marsupials as studies on wild populations are virtually absent. We used two endemic South American mouse opossums, Gracilinanus microtarsus and Marmosops incanus, to investigate characteristic features of MHC selection. This study is the first investigation of MHC selection in free-ranging Neotropical marsupials. In addition, the evolutionary history of MHC lineages within the group of marsupials was examined. Results G. microtarsus showed extensive levels of MHC diversity within and among individuals as 47 MHC-DAB alleles and high levels of sequence divergence were detected at a minimum of four loci. Positively selected codon sites were identified, of which most were congruent with human antigen binding sites. The diversity in M. incanus was rather low with only eight observed alleles at presumably two loci. However, these alleles also revealed high sequence divergence. Again, positive selection was identified on specific codon sites, all congruent with human ABS and with positively selected sites observed in G. microtarsus. In a phylogenetic comparison alleles of M. incanus interspersed widely within alleles of G. microtarsus with four alleles being present in both species. Conclusion Our investigations revealed extensive MHC class II polymorphism in a natural marsupial population, contrary to previous assumptions. Furthermore, our study confirms for the first time in marsupials the presence of three characteristic features common at MHC loci of eutherian mammals, birds and fish: large allelic sequence divergence, positive selection on specific sites and trans-specific polymorphism. PMID:18534008

  17. Detection Limits and Selectivity in Electrochemical Detectors.

    ERIC Educational Resources Information Center

    Weber, Stephen G.; Long, John T.

    1988-01-01

    Discusses three aspects of electrochemical detectors: (1) signal and noise generation and signal-to-noise ratio, (2) improvement of qualitative information content, and (3) control of selectivity of the detector. Explains electronic principles of detectors and detection limits. Lists current applications and research. (ML)

  18. Evolutionary tradeoffs can select against nitrogen fixation and thereby maintain nitrogen limitation.

    PubMed

    Menge, Duncan N L; Levin, Simon A; Hedin, Lars O

    2008-02-05

    Symbiotic nitrogen (N) fixing trees are absent from old-growth temperate and boreal ecosystems, even though many of these are N-limited. To explore mechanisms that could select against N fixation in N-limited, old-growth ecosystems, we developed a simple resource-based evolutionary model of N fixation. When there are no costs of N fixation, increasing amounts of N fixation will be selected for until N no longer limits production. However, tradeoffs between N fixation and plant mortality or turnover, plant uptake of available soil N, or N use efficiency (NUE) can select against N fixation in N-limited ecosystems and can thereby maintain N limitation indefinitely (provided that there are losses of plant-unavailable N). Three key traits influence the threshold that determines how large these tradeoffs must be to select against N fixation. A low NUE, high mortality (or turnover) rate and low losses of plant-unavailable N all increase the likelihood that N fixation will be selected against, and a preliminary examination of published data on these parameters shows that these mechanisms, particularly the tradeoff with NUE, are quite feasible in some systems. Although these results are promising, a better characterization of these parameters in multiple ecosystems is necessary to determine whether these mechanisms explain the lack of symbiotic N fixers-and thus the maintenance of N limitation-in old-growth forests.

  19. Evolutionary tradeoffs can select against nitrogen fixation and thereby maintain nitrogen limitation

    PubMed Central

    Menge, Duncan N. L.; Levin, Simon A.; Hedin, Lars O.

    2008-01-01

    Symbiotic nitrogen (N) fixing trees are absent from old-growth temperate and boreal ecosystems, even though many of these are N-limited. To explore mechanisms that could select against N fixation in N-limited, old-growth ecosystems, we developed a simple resource-based evolutionary model of N fixation. When there are no costs of N fixation, increasing amounts of N fixation will be selected for until N no longer limits production. However, tradeoffs between N fixation and plant mortality or turnover, plant uptake of available soil N, or N use efficiency (NUE) can select against N fixation in N-limited ecosystems and can thereby maintain N limitation indefinitely (provided that there are losses of plant-unavailable N). Three key traits influence the threshold that determines how large these tradeoffs must be to select against N fixation. A low NUE, high mortality (or turnover) rate and low losses of plant-unavailable N all increase the likelihood that N fixation will be selected against, and a preliminary examination of published data on these parameters shows that these mechanisms, particularly the tradeoff with NUE, are quite feasible in some systems. Although these results are promising, a better characterization of these parameters in multiple ecosystems is necessary to determine whether these mechanisms explain the lack of symbiotic N fixers—and thus the maintenance of N limitation—in old-growth forests. PMID:18223153

  20. Evolutionary vestigialization of sex in a clonal plant: selection versus neutral mutation in geographically peripheral populations.

    PubMed Central

    Dorken, Marcel E.; Neville, Kathryn J.; Eckert, Christopher G.

    2004-01-01

    The loss of traits that no longer contribute to fitness is widespread; however, the causative evolutionary mechanisms are poorly understood. Vestigialization could proceed through the fixation of selectively neutral degenerative mutations via genetic drift. Alternatively, selection may facilitate vestigialization if trait loss results in enhanced fitness. We tested these hypotheses using Decodon verticillatus, a clonal plant in which sexual sterility has arisen repeatedly in populations across the northern geographical range limit. We compared growth and survival of replicated genotypes from 7 sexually fertile and 18 sterile populations, over 3 years in a common environment. Survival of sterile genotypes was 53% greater than for fertile genotypes, but there was no difference in biomass accumulation. Almost all mortality, and hence increased performance of sterile genotypes, occurred during simulated overwinter dormancy. These observations suggest that selection has facilitated the vestigialization of sex, and thus do not support the neutral mutation hypothesis. The selective mechanism probably involves the relaxation of a genetic trade-off between sexual reproduction and survival: alleles that increase vegetative performance at the expense of sexual fertility are selected in geographically peripheral populations where sexual reproduction is suppressed by adverse environmental conditions. PMID:15556890

  1. Charles Darwin's Origin of Species, directional selection, and the evolutionary sciences today

    NASA Astrophysics Data System (ADS)

    Kutschera, Ulrich

    2009-11-01

    The book On the Origin of Species, published in November 1859, is an “abstract” without references, compiled by Charles Darwin from a much longer manuscript entitled “Natural Selection.” Here, I summarize the five theories that can be extracted from Darwin’s monograph, explain the true meaning of the phrase “struggle for life” (i.e., competition and cooperation), and outline Darwin’s original concept of natural selection in populations of animals and plants. Since neither Darwin nor Alfred R. Wallace distinguished between stabilizing and directional natural selection, the popular argument that “selection only eliminates but is not creative” is still alive today. However, I document that August Weismann ( Die Bedeutung der sexuellen Fortpflanzung für die Selektions-Theorie. Gustav Fischer-Verlag, Jena, 1886) and Ivan Schmalhausen ( Factors of evolution. The theory of stabilizing selection. The Blackiston Company, Philadelphia, 1949) provided precise definitions for directional (dynamic) selection in nature and illustrate this “Weismann-Schmalhausen principle” with respect to the evolutionary development of novel phenotypes. Then, the modern (synthetic) theory of biological evolution that is based on the work of Theodosius Dobzhansky ( Genetics and the origin of species. Columbia University Press, New York, 1937) and others, and the expanded version of this system of theories, are outlined. Finally, I document that symbiogenesis (i.e., primary endosymbiosis, a process that gave rise to the first eukaryotic cells), ongoing directional natural selection, and the dynamic Earth (plate tectonics, i.e., geological events that both created and destroyed terrestrial and aquatic habitats) were the key processes responsible for the documented macroevolutionary patterns in all five kingdoms of life. Since the evolutionary development of the earliest archaic bacteria more than 3,500 mya, the biosphere of our dynamic planet has been dominated by

  2. Opportunity for natural selection in a Basque population and its secular trend: evolutionary implications of epidemic mortality.

    PubMed

    Alfonso-Sánchez, Miguel A; Calderón, Rosario; Peña, José A

    2004-06-01

    Analysis of the interaction between mortality patterns and opportunity for natural selection could help to elucidate potential evolutionary implications of epidemic mortality. In this paper secular trends are studied in relation to Crow's index (It) and its components of mortality (Im) and fertility (If), using parish records for family reconstitution in a Basque population. A principal components analysis (91% of the variance accounted for) showed marked quantitative and qualitative variations of Im and If depending on the stage of demographic transition of the population analyzed: In pretransitional societies the opportunity for natural selection is determined mainly by differential prereproductive mortality, whereas in posttransitional societies selection resulting from differential fertility plays a key role. The highest values for the mortality component (range 0.81-1.26) and for the relative contribution of Im, to It (range 47.1-57.2%) were observed in periods with a high incidence of infectious diseases and when the most severe mortality crises were detected (1830-1859, 1860-1889, and 1890-1919). A differential incidence of epidemic mortality was also found at prereproductive ages (before 16 years) and at reproductive ages (16-45 years), which provides strong support for the idea of the long-term genetic consequences of mortality crises.

  3. An evolutionary theory of large-scale human warfare: Group-structured cultural selection.

    PubMed

    Zefferman, Matthew R; Mathew, Sarah

    2015-01-01

    When humans wage war, it is not unusual for battlefields to be strewn with dead warriors. These warriors typically were men in their reproductive prime who, had they not died in battle, might have gone on to father more children. Typically, they are also genetically unrelated to one another. We know of no other animal species in which reproductively capable, genetically unrelated individuals risk their lives in this manner. Because the immense private costs borne by individual warriors create benefits that are shared widely by others in their group, warfare is a stark evolutionary puzzle that is difficult to explain. Although several scholars have posited models of the evolution of human warfare, these models do not adequately explain how humans solve the problem of collective action in warfare at the evolutionarily novel scale of hundreds of genetically unrelated individuals. We propose that group-structured cultural selection explains this phenomenon.

  4. Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria

    PubMed Central

    2013-01-01

    Background Actinobacteria have adapted to contrasted ecological niches such as the soil, and among others to plants or animals as pathogens or symbionts. Mycobacterium genus contains mostly pathogens that cause a variety of mammalian diseases, among which the well-known leprosy and tuberculosis, it also has saprophytic relatives. Streptomyces genus is mostly a soil microbe known for its secondary metabolites, it contains also plant pathogens, animal pathogens and symbionts. Frankia, a nitrogen-fixing actinobacterium establishes a root symbiosis with dicotyledonous pionneer plants. Pathogens and symbionts live inside eukaryotic cells and tissues and interact with their cellular environment through secreted proteins and effectors transported through transmembrane systems; nevertheless they also need to avoid triggering host defense reactions. A comparative genome analysis of the secretomes of symbionts and pathogens allows a thorough investigation of selective pressures shaping their evolution. In the present study, the rates of silent mutations to non-silent mutations in secretory proteins were assessed in different strains of Frankia, Streptomyces and Mycobacterium, of which several genomes have recently become publicly available. Results It was found that secreted proteins as a whole have a stronger purifying evolutionary rate (non-synonymous to synonymous substitutions or Ka/Ks ratio) than the non-secretory proteins in most of the studied genomes. This difference becomes statistically significant in cases involving obligate symbionts and pathogens. Amongst the Frankia, secretomes of symbiotic strains were found to have undergone evolutionary trends different from those of the mainly saprophytic strains. Even within the secretory proteins, the signal peptide part has a higher Ka/Ks ratio than the mature part. Two contrasting trends were noticed amongst the Frankia genomes regarding the relation between selection strength (i.e. Ka/Ks ratio) and the codon adaptation

  5. Novel approach to evolutionary neural network based descriptor selection and QSAR model development

    NASA Astrophysics Data System (ADS)

    Debeljak, Željko; Marohnić, Viktor; Srečnik, Goran; Medić-Šarić, Marica

    2005-12-01

    Capability of evolutionary neural network (ENN) based QSAR approach to direct the descriptor selection process towards stable descriptor subset (DS) composition characterized by acceptable generalization, as well as the influence of description stability on QSAR model interpretation have been examined. In order to analyze the DS stability and QSAR model generalization properties multiple random dataset partitions into training and test set were made. Acceptability criteria proposed by Golbraikh et al. [J. Comput.-Aided Mol. Des., 17 (2003) 241] have been chosen for selection of highly predictive QSAR models from a set of all models produced by ENN for each dataset splitting. All QSAR models that pass Golbraikh's filter generated by ENN for each dataset partition were collected. Two final DS forming principles were compared. Standard principle is based on selection of descriptors characterized by highest frequencies among all descriptors that appear in the pool [J. Chem. Inf. Comput. Sci., 43 (2003) 949]. Search across the model pool for DS that are stable against multiple dataset subsampling i.e. universal DS solutions is the basis of novel approach. Based on described principles benzodiazepine QSAR has been proposed and evaluated against results reported by others in terms of final DS composition and model predictive performance.

  6. PROTECTED POLYMORPHISMS AND EVOLUTIONARY STABILITY OF PATCH-SELECTION STRATEGIES IN STOCHASTIC ENVIRONMENTS

    PubMed Central

    EVANS, STEVEN N.; HENING, ALEXANDRU; SCHREIBER, SEBASTIAN J.

    2015-01-01

    We consider a population living in a patchy environment that varies stochastically in space and time. The population is composed of two morphs (that is, individuals of the same species with different genotypes). In terms of survival and reproductive success, the associated phenotypes differ only in their habitat selection strategies. We compute invasion rates corresponding to the rates at which the abundance of an initially rare morph increases in the presence of the other morph established at equilibrium. If both morphs have positive invasion rates when rare, then there is an equilibrium distribution such that the two morphs coexist; that is, there is a protected polymorphism for habitat selection. Alternatively, if one morph has a negative invasion rate when rare, then it is asymptotically displaced by the other morph under all initial conditions where both morphs are present. We refine the characterization of an evolutionary stable strategy for habitat selection from [Schreiber, 2012] in a mathematically rigorous manner. We provide a necessary and sufficient condition for the existence of an ESS that uses all patches and determine when using a single patch is an ESS. We also provide an explicit formula for the ESS when there are two habitat types. We show that adding environmental stochasticity results in an ESS that, when compared to the ESS for the corresponding model without stochasticity, spends less time in patches with larger carrying capacities and possibly makes use of sink patches, thereby practicing a spatial form of bet hedging. PMID:25151369

  7. Across-environment genetic correlations and the frequency of selective environments shape the evolutionary dynamics of growth rate in Impatiens capensis.

    PubMed

    Stinchcombe, John R; Izem, Rima; Heschel, M Shane; McGoey, Brechann V; Schmitt, Johanna

    2010-10-01

    Trade-offs can exist within and across environments, and constrain evolutionary trajectories. To examine the effects of competition and resource availability on trade-offs, we grew individuals of recombinant inbred lines of Impatiens capensis in a factorial combination of five densities with two light environments (full light and neutral shade) and used a Bayesian logistic growth analysis to estimate intrinsic growth rates. To estimate across-environment constraints, we developed a variance decomposition approach to principal components analysis, which accounted for sample size, model-fitting, and within-RIL variation prior to eigenanalysis. We detected negative across-environment genetic covariances in intrinsic growth rates, although only under full-light. To evaluate the potential importance of these covariances, we surveyed natural populations of I. capensis to measure the frequency of different density environments across space and time. We combined our empirical estimates of across-environment genetic variance-covariance matrices and frequency of selective environments with hypothetical (yet realistic) selection gradients to project evolutionary responses in multiple density environments. Selection in common environments can lead to correlated responses to selection in rare environments that oppose and counteract direct selection in those rare environments. Our results highlight the importance of considering both the frequency of selective environments and the across-environment genetic covariances in traits simultaneously.

  8. A unifying evolutionary framework for infrared-selected obscured and unobscured quasar host haloes

    NASA Astrophysics Data System (ADS)

    DiPompeo, M. A.; Hickox, R. C.; Myers, A. D.; Geach, J. E.

    2017-01-01

    Recent measurements of the dark matter halo masses of infrared-selected obscured quasars are in tension - some indicate that obscured quasars have a higher halo mass compared to their unobscured counterparts, while others find no difference. The former result is inconsistent with the simplest models of quasar unification which rely solely on the viewing angle, while the latter may support such models. Here, using empirical relationships between dark matter halo and supermassive black hole (BH) masses, we provide a simple evolutionary picture which naturally explains these findings and is motivated by more sophisticated merger-driven quasar-fuelling models. The model tracks the growth rate of haloes, with the BH growing in spurts of quasar activity in order to `catch up' with the Mbh-Mstellar-Mhalo relationship. The first part of the quasar phase is obscured and is followed by an unobscured phase. Depending on the luminosity limit of the sample, driven by observational selection effects, a difference in halo masses may or may not be significant. For high-luminosity samples, the difference can be large (a few to 10 times higher masses in obscured quasars), while for lower luminosity samples, the halo mass difference is very small, much smaller than current observational constraints. Such a simple model provides a qualitative explanation for the higher mass haloes of obscured quasars, as well as a rough quantitative agreement with seemingly disparate results.

  9. Natural selection. V. How to read the fundamental equations of evolutionary change in terms of information theory.

    PubMed

    Frank, S A

    2012-12-01

    The equations of evolutionary change by natural selection are commonly expressed in statistical terms. Fisher's fundamental theorem emphasizes the variance in fitness. Quantitative genetics expresses selection with covariances and regressions. Population genetic equations depend on genetic variances. How can we read those statistical expressions with respect to the meaning of natural selection? One possibility is to relate the statistical expressions to the amount of information that populations accumulate by selection. However, the connection between selection and information theory has never been compelling. Here, I show the correct relations between statistical expressions for selection and information theory expressions for selection. Those relations link selection to the fundamental concepts of entropy and information in the theories of physics, statistics and communication. We can now read the equations of selection in terms of their natural meaning. Selection causes populations to accumulate information about the environment.

  10. Covariance based outlier detection with feature selection.

    PubMed

    Zwilling, Chris E; Wang, Michelle Y

    2016-08-01

    The present covariance based outlier detection algorithm selects from a candidate set of feature vectors that are best at identifying outliers. Features extracted from biomedical and health informatics data can be more informative in disease assessment and there are no restrictions on the nature and number of features that can be tested. But an important challenge for an algorithm operating on a set of features is for it to winnow the effective features from the ineffective ones. The powerful algorithm described in this paper leverages covariance information from the time series data to identify features with the highest sensitivity for outlier identification. Empirical results demonstrate the efficacy of the method.

  11. Phylogenetic analysis and positive-selection site detecting of vascular endothelial growth factor family in vertebrates.

    PubMed

    He, Wenwu; Tang, Yanyan; Qi, Bin; Lu, Chuansen; Qin, Chao; Wei, Yunfei; Yi, Jiachao; Chen, Mingwu

    2014-02-10

    Vascular endothelial growth factor (VEGF), known to play an important role in vascular homeostasis, vascular integrity and angiogenesis, is little known about the evolutionary relationship of its five members especially the role of gene duplication and natural selection in the evolution of the VEGF family. In this study, seventy-five full-length cDNA sequences from 33 vertebrate species were extracted from the NCBI's GenBank, UniProt protein database and the Ensembl database. By phylogenetic analyses, we investigated the origin, conservation, and evolution of the VEGFs. Five VEGF family members in vertebrates might be formed by gene duplication. The inferred evolutionary transitions that separate members which belong to different gene clusters correlated with changes in functional properties. Selection analysis and protein structure analysis were combined to explain the relationship of the site-specific evolution in the vertebrate VEGF family. Eleven positive selection sites, one transmembrane region and the active sites were detected in this process.

  12. Chaos Enhanced Differential Evolution in the Task of Evolutionary Control of Selected Set of Discrete Chaotic Systems

    PubMed Central

    Pluhacek, Michal; Davendra, Donald; Oplatková Kominkova, Zuzana

    2014-01-01

    Evolutionary technique differential evolution (DE) is used for the evolutionary tuning of controller parameters for the stabilization of set of different chaotic systems. The novelty of the approach is that the selected controlled discrete dissipative chaotic system is used also as the chaotic pseudorandom number generator to drive the mutation and crossover process in the DE. The idea was to utilize the hidden chaotic dynamics in pseudorandom sequences given by chaotic map to help differential evolution algorithm search for the best controller settings for the very same chaotic system. The optimizations were performed for three different chaotic systems, two types of case studies and developed cost functions. PMID:25243230

  13. Evolutionary neural networks for anomaly detection based on the behavior of a program.

    PubMed

    Han, Sang-Jun; Cho, Sung-Bae

    2006-06-01

    The process of learning the behavior of a given program by using machine-learning techniques (based on system-call audit data) is effective to detect intrusions. Rule learning, neural networks, statistics, and hidden Markov models (HMMs) are some of the kinds of representative methods for intrusion detection. Among them, neural networks are known for good performance in learning system-call sequences. In order to apply this knowledge to real-world problems successfully, it is important to determine the structures and weights of these call sequences. However, finding the appropriate structures requires very long time periods because there are no suitable analytical solutions. In this paper, a novel intrusion-detection technique based on evolutionary neural networks (ENNs) is proposed. One advantage of using ENNs is that it takes less time to obtain superior neural networks than when using conventional approaches. This is because they discover the structures and weights of the neural networks simultaneously. Experimental results with the 1999 Defense Advanced Research Projects Agency (DARPA) Intrusion Detection Evaluation (IDEVAL) data confirm that ENNs are promising tools for intrusion detection.

  14. Detecting signatures of positive selection associated with musical aptitude in the human genome.

    PubMed

    Liu, Xuanyao; Kanduri, Chakravarthi; Oikkonen, Jaana; Karma, Kai; Raijas, Pirre; Ukkola-Vuoti, Liisa; Teo, Yik-Ying; Järvelä, Irma

    2016-02-16

    Abilities related to musical aptitude appear to have a long history in human evolution. To elucidate the molecular and evolutionary background of musical aptitude, we compared genome-wide genotyping data (641 K SNPs) of 148 Finnish individuals characterized for musical aptitude. We assigned signatures of positive selection in a case-control setting using three selection methods: haploPS, XP-EHH and FST. Gene ontology classification revealed that the positive selection regions contained genes affecting inner-ear development. Additionally, literature survey has shown that several of the identified genes were known to be involved in auditory perception (e.g. GPR98, USH2A), cognition and memory (e.g. GRIN2B, IL1A, IL1B, RAPGEF5), reward mechanisms (RGS9), and song perception and production of songbirds (e.g. FOXP1, RGS9, GPR98, GRIN2B). Interestingly, genes related to inner-ear development and cognition were also detected in a previous genome-wide association study of musical aptitude. However, the candidate genes detected in this study were not reported earlier in studies of musical abilities. Identification of genes related to language development (FOXP1 and VLDLR) support the popular hypothesis that music and language share a common genetic and evolutionary background. The findings are consistent with the evolutionary conservation of genes related to auditory processes in other species and provide first empirical evidence for signatures of positive selection for abilities that contribute to musical aptitude.

  15. Detecting signatures of positive selection associated with musical aptitude in the human genome

    PubMed Central

    Liu, Xuanyao; Kanduri, Chakravarthi; Oikkonen, Jaana; Karma, Kai; Raijas, Pirre; Ukkola-Vuoti, Liisa; Teo, Yik-Ying; Järvelä, Irma

    2016-01-01

    Abilities related to musical aptitude appear to have a long history in human evolution. To elucidate the molecular and evolutionary background of musical aptitude, we compared genome-wide genotyping data (641 K SNPs) of 148 Finnish individuals characterized for musical aptitude. We assigned signatures of positive selection in a case-control setting using three selection methods: haploPS, XP-EHH and FST. Gene ontology classification revealed that the positive selection regions contained genes affecting inner-ear development. Additionally, literature survey has shown that several of the identified genes were known to be involved in auditory perception (e.g. GPR98, USH2A), cognition and memory (e.g. GRIN2B, IL1A, IL1B, RAPGEF5), reward mechanisms (RGS9), and song perception and production of songbirds (e.g. FOXP1, RGS9, GPR98, GRIN2B). Interestingly, genes related to inner-ear development and cognition were also detected in a previous genome-wide association study of musical aptitude. However, the candidate genes detected in this study were not reported earlier in studies of musical abilities. Identification of genes related to language development (FOXP1 and VLDLR) support the popular hypothesis that music and language share a common genetic and evolutionary background. The findings are consistent with the evolutionary conservation of genes related to auditory processes in other species and provide first empirical evidence for signatures of positive selection for abilities that contribute to musical aptitude. PMID:26879527

  16. A multiobjective evolutionary algorithm based on similarity for community detection from signed social networks.

    PubMed

    Liu, Chenlong; Liu, Jing; Jiang, Zhongzhou

    2014-12-01

    Various types of social relationships, such as friends and foes, can be represented as signed social networks (SNs) that contain both positive and negative links. Although many community detection (CD) algorithms have been proposed, most of them were designed primarily for networks containing only positive links. Thus, it is important to design CD algorithms which can handle large-scale SNs. To this purpose, we first extend the original similarity to the signed similarity based on the social balance theory. Then, based on the signed similarity and the natural contradiction between positive and negative links, two objective functions are designed to model the problem of detecting communities in SNs as a multiobjective problem. Afterward, we propose a multiobjective evolutionary algorithm, called MEAs-SN. In MEAs-SN, to overcome the defects of direct and indirect representations for communities, a direct and indirect combined representation is designed. Attributing to this representation, MEAs-SN can switch between different representations during the evolutionary process. As a result, MEAs-SN can benefit from both representations. Moreover, owing to this representation, MEAs-SN can also detect overlapping communities directly. In the experiments, both benchmark problems and large-scale synthetic networks generated by various parameter settings are used to validate the performance of MEAs-SN. The experimental results show the effectiveness and efficacy of MEAs-SN on networks with 1000, 5000, and 10,000 nodes and also in various noisy situations. A thorough comparison is also made between MEAs-SN and three existing algorithms, and the results show that MEAs-SN outperforms other algorithms.

  17. Cannabimimetic phytochemicals in the diet - an evolutionary link to food selection and metabolic stress adaptation?

    PubMed

    Gertsch, Jürg

    2016-11-27

    The endocannabinoid system (ECS) is a major lipid signalling network that plays important pro-homeostatic (allostatic) roles not only in the nervous system but also in peripheral organs. There is increasing evidence that there is a dietary component in the modulation of the ECS. Cannabinoid receptors in hominids co-evolved with diet, and the ECS constitutes a feedback loop for food selection and energy metabolism. Here, it is postulated that the mismatch of ancient lipid genes of hunter-gatherers and pastoralists with the high-carbohydrate diet introduced by agriculture could be compensated for via dietary modulation of the ECS. In addition to the fatty acid precursors of endocannabinoids, the potential role of dietary cannabimimetic phytochemicals in agriculturist nutrition is discussed. Dietary secondary metabolites from vegetables and spices able to enhance the activity of cannabinoid-type 2 (CB2 ) receptors may provide adaptive metabolic advantages and counteract inflammation. In contrast, chronic CB1 receptor activation in hedonic obese individuals may enhance pathophysiological processes related to hyperlipidaemia, diabetes, hepatorenal inflammation and cardiometabolic risk. Food able to modulate the CB1 /CB2 receptor activation ratio may thus play a role in the nutrition transition of Western high-calorie diets. In this review, the interplay between diet and the ECS is highlighted from an evolutionary perspective. The emerging potential of cannabimimetic food as a nutraceutical strategy is critically discussed.

  18. Delayed life history effects, multilevel selection, and evolutionary trade-offs in the California tiger salamander.

    PubMed

    Searcy, Christopher A; Gray, Levi N; Trenham, Peter C; Shaffer, H Bradley

    2014-01-01

    Delayed life history effects (DLHEs) occur when fitness in one life stage affects fitness in subsequent life stages. Given their biphasic life cycle, pond-breeding amphibians provide a natural system for studying DLHEs, although these effects are not restricted to species with biphasic life histories. In this study, we used multiple mark-recapture techniques enabled by a large trapping array to monitor components of fitness and resulting DLHEs in a population of the endangered California tiger salamander (Ambystoma californiense). We found that DLHEs are prominent across all life stage transitions and that there is variation in whether selection acts primarily at the individual or cohort level. We also demonstrated that there is more than an order of magnitude variation in mean cohort fitness, providing tremendous variation for DLHEs to act upon. We documented an evolutionary trade-off between mass at emergence and date of emergence, which may play a role in maintaining the variation in mass (fitness) at emergence. A literature review revealed that such high levels of intercohort variation occur in many other pond-breeding amphibians, and that appropriately documenting the magnitude of intercohort variation requires long-term studies (roughly two population turnovers). Given the profound effect that DLHEs can have on population dynamics, quantifying intercohort variation in mean fitness and the level(s) at which selection acts will be very important for developing accurate models of population dynamics. In general, when developing models of population dynamics, more attention should be paid to variation in mean fitness and not just variation in total numbers.

  19. Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome

    PubMed Central

    Ma, Yan-Ping; Ke, Hao; Liang, Zhi-Ling; Liu, Zhen-Xing; Hao, Le; Ma, Jiang-Yao; Li, Yu-Gu

    2016-01-01

    Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine (T) compositional constraints might contribute an important role to the synonymous codon usage pattern. The GC3% against the effective number of codon (ENC) value suggested that translational selection was the important factor for codon bias in the microorganism. Principal component analysis (PCA) showed that (i) mutational pressure was the most important factor in shaping codon usage of all open reading frames (ORFs) in the S. agalactiae genome; (ii) strand specific mutational bias was not capable of influencing the codon usage bias in the leading and lagging strands; and (iii) gene length was not the important factor in synonymous codon usage pattern in this organism. Additionally, the high correlation between tRNA adaptation index (tAI) value and codon adaptation index (CAI), frequency of optimal codons (Fop) value, reinforced the role of natural selection for efficient translation in S. agalactiae. Comparison of synonymous codon usage pattern between S. agalactiae and susceptible hosts (human and tilapia) showed that synonymous codon usage of S. agalactiae was independent of the synonymous codon usage of susceptible hosts. The study of codon usage in S. agalactiae may provide evidence about the molecular evolution of the bacterium and a greater understanding of evolutionary relationships between S. agalactiae and its hosts. PMID:26927064

  20. Macroevolutionary patterns of bumblebee body size: detecting the interplay between natural and sexual selection

    PubMed Central

    del Castillo, Raúl Cueva; Fairbairn, Daphne J

    2012-01-01

    Bumblebees and other eusocial bees offer a unique opportunity to analyze the evolution of body size differences between sexes. The workers, being sterile females, are not subject to selection for reproductive function and thus provide a natural control for parsing the effects of selection on reproductive function (i.e., sexual and fecundity selection) from other natural selection. Using a phylogenetic comparative approach, we explored the allometric relationships among queens, males, and workers in 70 species of bumblebees (Bombus sp.). We found hyperallometry in thorax width for males relative to workers, indicating greater evolutionary divergence of body size in males than in sterile females. This is consistent with the hypothesis that selection for reproductive function, most probably sexual selection, has caused divergence in male size among species. The slope for males on workers was significantly steeper than that for queens on workers and the latter did not depart from isometry, providing further evidence of greater evolutionary divergence in male size than female size, and no evidence that reproductive selection has accelerated divergence of females. We did not detect significant hyperallometry when male size was regressed directly on queen size and our results thus add the genus Bombus to the increasing list of clades that have female-larger sexual size dimorphism and do not conform to Rensch's rule when analyzed according to standard methodology. Nevertheless, by using worker size as a common control, we were able to demonstrate that bumblee species do show the evolutionary pattern underlying Rensch's rule, that being correlated evolution of body size in males and females, but with greater evolutionary divergence in males. PMID:22408725

  1. Hyperspectral Anomaly Detection by Graph Pixel Selection.

    PubMed

    Yuan, Yuan; Ma, Dandan; Wang, Qi

    2016-12-01

    Hyperspectral anomaly detection (AD) is an important problem in remote sensing field. It can make full use of the spectral differences to discover certain potential interesting regions without any target priors. Traditional Mahalanobis-distance-based anomaly detectors assume the background spectrum distribution conforms to a Gaussian distribution. However, this and other similar distributions may not be satisfied for the real hyperspectral images. Moreover, the background statistics are susceptible to contamination of anomaly targets which will lead to a high false-positive rate. To address these intrinsic problems, this paper proposes a novel AD method based on the graph theory. We first construct a vertex- and edge-weighted graph and then utilize a pixel selection process to locate the anomaly targets. Two contributions are claimed in this paper: 1) no background distributions are required which makes the method more adaptive and 2) both the vertex and edge weights are considered which enables a more accurate detection performance and better robustness to noise. Intensive experiments on the simulated and real hyperspectral images demonstrate that the proposed method outperforms other benchmark competitors. In addition, the robustness of the proposed method has been validated by using various window sizes. This experimental result also demonstrates the valuable characteristic of less computational complexity and less parameter tuning for real applications.

  2. Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes.

    PubMed

    Ganu, Radhika S; Ishida, Yasuko; Koutmos, Markos; Kolokotronis, Sergios-Orestis; Roca, Alfred L; Garrow, Timothy A; Schook, Lawrence B

    2015-01-01

    Betaine-homocysteine S-methyltransferase (BHMT) and BHMT2 convert homocysteine to methionine using betaine and S-methylmethionine, respectively, as methyl donor substrates. Increased levels of homocysteine in blood are associated with cardiovascular disease. Given their role in human health and nutrition, we identified BHMT and BHMT2 genes and proteins from 38 species of deuterostomes including human and non-human primates. We aligned the genes to look for signatures of selection, to infer evolutionary rates and events across lineages, and to identify the evolutionary timing of a gene duplication event that gave rise to two genes, BHMT and BHMT2. We found that BHMT was present in the genomes of the sea urchin, amphibians, reptiles, birds and mammals; BHMT2 was present only across mammals. BHMT and BHMT2 were present in tandem in the genomes of all monotreme, marsupial and placental species examined. Evolutionary rates were accelerated for BHMT2 relative to BHMT. Selective pressure varied across lineages, with the highest dN/dS ratios for BHMT and BHMT2 occurring immediately following the gene duplication event, as determined using GA Branch analysis. Nine codons were found to display signatures suggestive of positive selection; these contribute to the enzymatic or oligomerization domains, suggesting involvement in enzyme function. Gene duplication likely occurred after the divergence of mammals from other vertebrates but prior to the divergence of extant mammalian subclasses, followed by two deletions in BHMT2 that affect oligomerization and methyl donor specificity. The faster evolutionary rate of BHMT2 overall suggests that selective constraints were reduced relative to BHMT. The dN/dS ratios in both BHMT and BHMT2 was highest following the gene duplication, suggesting that purifying selection played a lesser role as the two paralogs diverged in function.

  3. Evolutionary and Experimental Assessment of Novel Markers for Detection of Xanthomonas euvesicatoria in Plant Samples

    PubMed Central

    Albuquerque, Pedro; Caridade, Cristina M. R.; Rodrigues, Arlete S.; Marcal, Andre R. S.; Cruz, Joana; Cruz, Leonor; Santos, Catarina L.; Mendes, Marta V.; Tavares, Fernando

    2012-01-01

    Background Bacterial spot-causing xanthomonads (BSX) are quarantine phytopathogenic bacteria responsible for heavy losses in tomato and pepper production. Despite the research on improved plant spraying methods and resistant cultivars, the use of healthy plant material is still considered as the most effective bacterial spot control measure. Therefore, rapid and efficient detection methods are crucial for an early detection of these phytopathogens. Methodology In this work, we selected and validated novel DNA markers for reliable detection of the BSX Xanthomonas euvesicatoria (Xeu). Xeu-specific DNA regions were selected using two online applications, CUPID and Insignia. Furthermore, to facilitate the selection of putative DNA markers, a customized C program was designed to retrieve the regions outputted by both databases. The in silico validation was further extended in order to provide an insight on the origin of these Xeu-specific regions by assessing chromosomal location, GC content, codon usage and synteny analyses. Primer-pairs were designed for amplification of those regions and the PCR validation assays showed that most primers allowed for positive amplification with different Xeu strains. The obtained amplicons were labeled and used as probes in dot blot assays, which allowed testing the probes against a collection of 12 non-BSX Xanthomonas and 23 other phytopathogenic bacteria. These assays confirmed the specificity of the selected DNA markers. Finally, we designed and tested a duplex PCR assay and an inverted dot blot platform for culture-independent detection of Xeu in infected plants. Significance This study details a selection strategy able to provide a large number of Xeu-specific DNA markers. As demonstrated, the selected markers can detect Xeu in infected plants both by PCR and by hybridization-based assays coupled with automatic data analysis. Furthermore, this work is a contribution to implement more efficient DNA-based methods of bacterial

  4. Evidence of Positive Selection of Aquaporins Genes from Pontoporia blainvillei during the Evolutionary Process of Cetaceans

    PubMed Central

    São Pedro, Simone Lima; Alves, João Marcelo Pereira; Barreto, André Silva; Lima, André Oliveira de Souza

    2015-01-01

    Background Marine mammals are well adapted to their hyperosmotic environment. Several morphological and physiological adaptations for water conservation and salt excretion are known to be present in cetaceans, being responsible for regulating salt balance. However, most previous studies have focused on the unique renal physiology of marine mammals, but the molecular bases of these mechanisms remain poorly explored. Many genes have been identified to be involved in osmotic regulation, including the aquaporins. Considering that aquaporin genes were potentially subject to strong selective pressure, the aim of this study was to analyze the molecular evolution of seven aquaporin genes (AQP1, AQP2, AQP3, AQP4, AQP6, AQP7, and AQP9) comparing the lineages of cetaceans and terrestrial mammals. Results Our results demonstrated strong positive selection in cetacean-specific lineages acting only in the gene for AQP2 (amino acids 23, 83, 107,179, 180, 181, 182), whereas no selection was observed in terrestrial mammalian lineages. We also analyzed the changes in the 3D structure of the aquaporin 2 protein. Signs of strong positive selection in AQP2 sites 179, 180, 181, and 182 were unexpectedly identified only in the baiji lineage, which was the only river dolphin examined in this study. Positive selection in aquaporins AQP1 (45), AQP4 (74), AQP7 (342, 343, 356) was detected in cetaceans and artiodactyls, suggesting that these events are not related to maintaining water and electrolyte homeostasis in seawater. Conclusions Our results suggest that the AQP2 gene might reflect different selective pressures in maintaining water balance in cetaceans, contributing to the passage from the terrestrial environment to the aquatic. Further studies are necessary, especially those including other freshwater dolphins, who exhibit osmoregulatory mechanisms different from those of marine cetaceans for the same essential task of maintaining serum electrolyte balance. PMID:26226365

  5. A Composite-Likelihood Method for Detecting Incomplete Selective Sweep from Population Genomic Data.

    PubMed

    Vy, Ha My T; Kim, Yuseob

    2015-06-01

    Adaptive evolution occurs as beneficial mutations arise and then increase in frequency by positive natural selection. How, when, and where in the genome such evolutionary events occur is a fundamental question in evolutionary biology. It is possible to detect ongoing positive selection or an incomplete selective sweep in species with sexual reproduction because, when a beneficial mutation is on the way to fixation, homologous chromosomes in the population are divided into two groups: one carrying the beneficial allele with very low polymorphism at nearby linked loci and the other carrying the ancestral allele with a normal pattern of sequence variation. Previous studies developed long-range haplotype tests to capture this difference between two groups as the signal of an incomplete selective sweep. In this study, we propose a composite-likelihood-ratio (CLR) test for detecting incomplete selective sweeps based on the joint sampling probabilities for allele frequencies of two groups as a function of strength of selection and recombination rate. Tested against simulated data, this method yielded statistical power and accuracy in parameter estimation that are higher than the iHS test and comparable to the more recently developed nSL test. This procedure was also applied to African Drosophila melanogaster population genomic data to detect candidate genes under ongoing positive selection. Upon visual inspection of sequence polymorphism, candidates detected by our CLR method exhibited clear haplotype structures predicted under incomplete selective sweeps. Our results suggest that different methods capture different aspects of genetic information regarding incomplete sweeps and thus are partially complementary to each other.

  6. Evolutionary analysis of TLR9 genes reveals the positive selection of extant teleosts in Perciformes.

    PubMed

    Zhu, Zhihuang; Sun, Yuena; Wang, Rixin; Xu, Tianjun

    2013-08-01

    The innate immune system can recognize non-self through pattern recognition receptors. Toll-like receptors were the best-known members of these receptors, and they could sense, recognize, and bind pathogen-associated molecular patterns. TLRs played an important role in innate immune system and were conserved in both invertebrate and vertebrate lineages. Thereinto, TLR9 could detect unmethylated CpG motifs in dsDNA and was expected to undergo coevolution with its microbial ligands. It was known that aquatic and terrestrial organisms dwelled in different environments which contained different pathogens, and they had to adapt to their local environmental conditions. Therefore, we collected TLR9 genes from invertebrate to vertebrate to further explore whether the huge differences between aquatic and terrestrial environments affected the TLR9s evolution between aquatic and terrestrial organisms. Molecular evolution analysis detected positively selected sites in the ancestral lineages of vertebrates, teleosts, and Perciformes but not in the ancestral lineage of mammals. In PAML, site model revealed that extant mammalian TLR9 genes underwent positive selection. However, the positive selection of extant teleosts appeared primarily in Perciformes in which there were 14 positively selected sites. Among these sites, two of them were located on the amino acid insertions of the leucine-rich repeats which could create DNA binding sites, three were found on the convex surface which might possibly affect the flexibility of the TLR solenoids, and six were located on the β-face of concave surface which contained the ligand-binding sites of the TLR solenoids. In other ML methods, we also found three sites under selection that coincided with the codons identified by M8 and these sites were all located in LRRs. The diverse aquatic and terrestrial environments might possess different pathogens to make the living organisms adapt to their local environmental conditions. The positive

  7. Capability of the Maximax&Maximin selection operator in the evolutionary algorithm for a nurse scheduling problem

    NASA Astrophysics Data System (ADS)

    Ramli, Razamin; Tein, Lim Huai

    2016-08-01

    A good work schedule can improve hospital operations by providing better coverage with appropriate staffing levels in managing nurse personnel. Hence, constructing the best nurse work schedule is the appropriate effort. In doing so, an improved selection operator in the Evolutionary Algorithm (EA) strategy for a nurse scheduling problem (NSP) is proposed. The smart and efficient scheduling procedures were considered. Computation of the performance of each potential solution or schedule was done through fitness evaluation. The best so far solution was obtained via special Maximax&Maximin (MM) parent selection operator embedded in the EA, which fulfilled all constraints considered in the NSP.

  8. On the evolutionary status of X-ray selected weak-line T Tauri star candidates in Taurus-Auriga

    NASA Astrophysics Data System (ADS)

    Martín, E. L.; Magazzù, A.

    1999-02-01

    We present lithium observations of 35 stars previously reported by Wichmann et al. (1996) to be possible new weak T Tauri stars (WTTS) discovered by ROSAT in the Taurus-Auriga star-forming region. These stars were identified on the basis of low-resolution optical spectra. We have used our higher resolution spectra for measuring the equivalent widths of the Li i 670.8 nm resonance line, and for revisiting the evolutionary status of these stars. Most ( ~ 85%) of the stars in our sample coming from ROSAT pointed observations are indeed confirmed to be new WTTS, but only a minority ( ~ 22%) of the stars coming from the ROSAT all-sky survey are confirmed as WTTS. There are two reasons why we reject some stars as WTTS. One is that seven of the stars do not have a detectable lithium line at all. The other is that we use a definition different from that Wichmann et al. (1996) for classifying stars as WTTS. In particular, we identify eight stars as post T Tauri stars (PTTS) on the basis of their moderate lithium depletion. Our results confirm that the widely dispersed RASS-selected candidate WTTS tend to be older than the T Tauri stars associated with dark molecular clouds. The presence of PTTS around central Taurus suggests that the clouds may have been forming stars for more than ~ 10 Myr, although at a very low rate. On the basis of the PTTS identified in this work we discuss possible differences between them and the WTTS. We find that PTTS seem to have slightly lower Hα emission equivalent width than WTTS, but the small number of known PTTS prevent us from making a strong conclusion. Based on observations made with the Isaac Newton and the William Herschel telescopes operated on the island of La~Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrof\\'\\i sica de Canarias

  9. Decomposition-Based Multiobjective Evolutionary Algorithm for Community Detection in Dynamic Social Networks

    PubMed Central

    Ma, Jingjing; Liu, Jie; Ma, Wenping; Gong, Maoguo; Jiao, Licheng

    2014-01-01

    Community structure is one of the most important properties in social networks. In dynamic networks, there are two conflicting criteria that need to be considered. One is the snapshot quality, which evaluates the quality of the community partitions at the current time step. The other is the temporal cost, which evaluates the difference between communities at different time steps. In this paper, we propose a decomposition-based multiobjective community detection algorithm to simultaneously optimize these two objectives to reveal community structure and its evolution in dynamic networks. It employs the framework of multiobjective evolutionary algorithm based on decomposition to simultaneously optimize the modularity and normalized mutual information, which quantitatively measure the quality of the community partitions and temporal cost, respectively. A local search strategy dealing with the problem-specific knowledge is incorporated to improve the effectiveness of the new algorithm. Experiments on computer-generated and real-world networks demonstrate that the proposed algorithm can not only find community structure and capture community evolution more accurately, but also be steadier than the two compared algorithms. PMID:24723806

  10. Pulvinar neurons reveal neurobiological evidence of past selection for rapid detection of snakes

    PubMed Central

    Van Le, Quan; Isbell, Lynne A.; Matsumoto, Jumpei; Nguyen, Minh; Hori, Etsuro; Maior, Rafael S.; Tomaz, Carlos; Tran, Anh Hai; Ono, Taketoshi; Nishijo, Hisao

    2013-01-01

    Snakes and their relationships with humans and other primates have attracted broad attention from multiple fields of study, but not, surprisingly, from neuroscience, despite the involvement of the visual system and strong behavioral and physiological evidence that humans and other primates can detect snakes faster than innocuous objects. Here, we report the existence of neurons in the primate medial and dorsolateral pulvinar that respond selectively to visual images of snakes. Compared with three other categories of stimuli (monkey faces, monkey hands, and geometrical shapes), snakes elicited the strongest, fastest responses, and the responses were not reduced by low spatial filtering. These findings integrate neuroscience with evolutionary biology, anthropology, psychology, herpetology, and primatology by identifying a neurobiological basis for primates’ heightened visual sensitivity to snakes, and adding a crucial component to the growing evolutionary perspective that snakes have long shaped our primate lineage. PMID:24167268

  11. Pulvinar neurons reveal neurobiological evidence of past selection for rapid detection of snakes.

    PubMed

    Van Le, Quan; Isbell, Lynne A; Matsumoto, Jumpei; Nguyen, Minh; Hori, Etsuro; Maior, Rafael S; Tomaz, Carlos; Tran, Anh Hai; Ono, Taketoshi; Nishijo, Hisao

    2013-11-19

    Snakes and their relationships with humans and other primates have attracted broad attention from multiple fields of study, but not, surprisingly, from neuroscience, despite the involvement of the visual system and strong behavioral and physiological evidence that humans and other primates can detect snakes faster than innocuous objects. Here, we report the existence of neurons in the primate medial and dorsolateral pulvinar that respond selectively to visual images of snakes. Compared with three other categories of stimuli (monkey faces, monkey hands, and geometrical shapes), snakes elicited the strongest, fastest responses, and the responses were not reduced by low spatial filtering. These findings integrate neuroscience with evolutionary biology, anthropology, psychology, herpetology, and primatology by identifying a neurobiological basis for primates' heightened visual sensitivity to snakes, and adding a crucial component to the growing evolutionary perspective that snakes have long shaped our primate lineage.

  12. Selection of energy source and evolutionary stable strategies for power plants under financial intervention of government

    NASA Astrophysics Data System (ADS)

    Hafezalkotob, Ashkan; Mahmoudi, Reza

    2017-03-01

    Currently, many socially responsible governments adopt economic incentives and deterrents to manage environmental impacts of electricity suppliers. Considering the Stackelberg leadership of the government, the government's role in the competition of power plants in an electricity market is investigated. A one-population evolutionary game model of power plants is developed to study how their production strategy depends on tariffs levied by the government. We establish that a unique evolutionary stable strategy (ESS) for the population exists. Numerical examples demonstrate that revenue maximization and environment protection policies of the government significantly affect the production ESS of competitive power plants. The results reveal that the government can introduce a green energy source as an ESS of the competitive power plants by imposing appropriate tariffs.

  13. Novel and selective detection of Tabun mimics.

    PubMed

    Jang, Yoon Jeong; Tsay, Olga G; Murale, Dhiraj P; Jeong, Jeong A; Segev, Aviv; Churchill, David G

    2014-07-18

    Detection of nerve agent-related molecules based on BODIPY-salicylaldehyde oxime conjugation was studied. Fluorescence intensity of the B-SAL-OXIME species increases in the presence of DECP, whereas it decreases in the presence of DCP and DEMP (limit of detection = 997 nM). Benzonitrile formation in the novel fluorescent B-SAL-OXIME system was elucidated using model substrates.

  14. Evolutionary time-series analysis reveals the signature of frequency-dependent selection on a female mating polymorphism.

    PubMed

    Le Rouzic, Arnaud; Hansen, Thomas F; Gosden, Thomas P; Svensson, Erik I

    2015-06-01

    A major challenge in evolutionary biology is understanding how stochastic and deterministic factors interact and influence macroevolutionary dynamics in natural populations. One classical approach is to record frequency changes of heritable and visible genetic polymorphisms over multiple generations. Here, we combined this approach with a maximum likelihood-based population-genetic model with the aim of understanding and quantifying the evolutionary processes operating on a female mating polymorphism in the blue-tailed damselfly Ischnura elegans. Previous studies on this color-polymorphic species have suggested that males form a search image for females, which leads to excessive mating harassment of common female morphs. We analyzed a large temporally and spatially replicated data set of between-generation morph frequency changes in I. elegans. Morph frequencies were more stable than expected from genetic drift alone, suggesting the presence of selection toward a stable equilibrium that prevents local loss or fixation of morphs. This can be interpreted as the signature of negative frequency-dependent selection maintaining the phenotypic stasis and genetic diversity in these populations. Our novel analytical approach allows the estimation of the strength of frequency-dependent selection from the morph frequency fluctuations around their inferred long-term equilibria. This approach can be extended and applied to other polymorphic organisms for which time-series data across multiple generations are available.

  15. USING POPULATION GENOMICS TO DETECT SELECTION IN NATURAL POPULATIONS: KEY CONCEPTS AND METHODOLOGICAL CONSIDERATIONS

    PubMed Central

    Hohenlohe, Paul A.; Phillips, Patrick C.; Cresko, William A.

    2010-01-01

    Natural selection shapes patterns of genetic variation among individuals, populations, and species, and it does so differentially across genomes. The field of population genomics provides a comprehensive genome-scale view of the action of selection, even beyond traditional model organisms. However, even with nearly complete genomic sequence information, our ability to detect the signature of selection on specific genomic regions depends on choosing experimental and analytical tools appropriate to the biological situation. For example, processes that occur at different timescales, such as sorting of standing genetic variation, mutation-selection balance, or fixed interspecific divergence, have different consequences for genomic patterns of variation. Inappropriate experimental or analytical approaches may fail to detect even strong selection or falsely identify a signature of selection. Here we outline the conceptual framework of population genomics, relate genomic patterns of variation to evolutionary processes, and identify major biological factors to be considered in studies of selection. As data-gathering technology continues to advance, our ability to understand selection in natural populations will be limited more by conceptual and analytical weaknesses than by the amount of molecular data. Our aim is to bring critical biological considerations to the fore in population genomics research and to spur the development and application of analytical tools appropriate to diverse biological systems. PMID:21218185

  16. 46 CFR 108.404 - Selection of fire detection system.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Selection of fire detection system. 108.404 Section 108.404 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) A-MOBILE OFFSHORE DRILLING UNITS DESIGN AND EQUIPMENT Fire Extinguishing Systems § 108.404 Selection of fire detection system. (a) If...

  17. 46 CFR 108.404 - Selection of fire detection system.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 4 2013-10-01 2013-10-01 false Selection of fire detection system. 108.404 Section 108.404 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) A-MOBILE OFFSHORE DRILLING UNITS DESIGN AND EQUIPMENT Fire Extinguishing Systems § 108.404 Selection of fire detection system. (a) If...

  18. 46 CFR 108.404 - Selection of fire detection system.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 4 2012-10-01 2012-10-01 false Selection of fire detection system. 108.404 Section 108.404 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) A-MOBILE OFFSHORE DRILLING UNITS DESIGN AND EQUIPMENT Fire Extinguishing Systems § 108.404 Selection of fire detection system. (a) If...

  19. 46 CFR 108.404 - Selection of fire detection system.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 4 2014-10-01 2014-10-01 false Selection of fire detection system. 108.404 Section 108.404 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) A-MOBILE OFFSHORE DRILLING UNITS DESIGN AND EQUIPMENT Fire Extinguishing Systems § 108.404 Selection of fire detection system. (a) If...

  20. Three-dimensional window analysis for detecting positive selection at structural regions of proteins.

    PubMed

    Suzuki, Yoshiyuki

    2004-12-01

    Detection of natural selection operating at the amino acid sequence level is important in the study of molecular evolution. Single-site analysis and one-dimensional window analysis can be used to detect selection when the biological functions of amino acid sites are unknown. Single-site analysis is useful when selection operates more or less constantly over evolutionary time, but less so when selection operates temporarily. One-dimensional window analysis is more sensitive than single-site analysis when the functions of amino acid sites in close proximity in the linear sequence are similar, although this is not always the case. Here I present a three-dimensional window analysis method for detecting selection given the three-dimensional structure of the protein of interest. In the three-dimensional structure, the window is defined as the sphere centered on the alpha-carbon of an amino acid site. The window size is the radius of the sphere. The sites whose alpha-carbons are included in the window are grouped for the neutrality test. The window is moved within the three-dimensional structure by sequentially moving the central site along the primary amino acid sequence. To detect positive selection, it may also be useful to group the surface-exposed sites in the window separately. Three-dimensional window analysis appears not only to be more sensitive than single-site analysis and one-dimensional window analysis but also to provide similar specificity for inferring positive selection in the analyses of the hemagglutinin and neuraminidase genes of human influenza A viruses. This method, however, may fail to detect selection when it operates only on a particular site, in which case single-site analysis may be preferred, although a large number of sequences is required.

  1. Molecular sieve sensors for selective detection at the nanogram level

    DOEpatents

    Bein, Thomas; Brown, Kelly D.; Frye, Gregory C.; Brinker, Charles J.

    1992-01-01

    The invention relates to a selective chemical sensor for selective detection of chemical entities even at the nanogram level. The invention further relates to methods of using the sensor. The sensor comprises: (a) a piezoelectric substrate capable of detecting mass changes resulting from adsorption of material thereon; and (b) a coating applied to the substrate, which selectively sorbs chemical entities of a size smaller than a preselected magnitude.

  2. Microbial Biosensors for Selective Detection of Disaccharides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seven microbial strains were screened for their ability to detect disaccharides as components of Clark-type oxygen biosensors. Sensors responded to varying degrees to maltose, cellobiose, sucrose, and melibiose, but none responded strongly to lactose. Although microbial sensors are relatively nons...

  3. Evolutionary responses of tree phenology to the combined effects of assortative mating, gene flow and divergent selection

    PubMed Central

    Soularue, J-P; Kremer, A

    2014-01-01

    The timing of bud burst (TBB) in temperate trees is a key adaptive trait, the expression of which is triggered by temperature gradients across the landscape. TBB is strongly correlated with flowering time and is therefore probably mediated by assortative mating. We derived theoretical predictions and realized numerical simulations of evolutionary changes in TBB in response to divergent selection and gene flow in a metapopulation. We showed that the combination of the environmental gradient of TBB and assortative mating creates contrasting genetic clines, depending on the direction of divergent selection. If divergent selection acts in the same direction as the environmental gradient (cogradient settings), genetic clines are established and inflated by assortative mating. Conversely, under divergent selection of the same strength but acting in the opposite direction (countergradient selection), genetic clines are slightly constrained. We explored the consequences of these dynamics for population maladaptation, by monitoring pollen swamping. Depending on the direction of divergent selection with respect to the environmental gradient, pollen filtering owing to assortative mating either facilitates or impedes adaptation in peripheral populations. PMID:24924591

  4. Evolutionary responses of tree phenology to the combined effects of assortative mating, gene flow and divergent selection.

    PubMed

    Soularue, J-P; Kremer, A

    2014-12-01

    The timing of bud burst (TBB) in temperate trees is a key adaptive trait, the expression of which is triggered by temperature gradients across the landscape. TBB is strongly correlated with flowering time and is therefore probably mediated by assortative mating. We derived theoretical predictions and realized numerical simulations of evolutionary changes in TBB in response to divergent selection and gene flow in a metapopulation. We showed that the combination of the environmental gradient of TBB and assortative mating creates contrasting genetic clines, depending on the direction of divergent selection. If divergent selection acts in the same direction as the environmental gradient (cogradient settings), genetic clines are established and inflated by assortative mating. Conversely, under divergent selection of the same strength but acting in the opposite direction (countergradient selection), genetic clines are slightly constrained. We explored the consequences of these dynamics for population maladaptation, by monitoring pollen swamping. Depending on the direction of divergent selection with respect to the environmental gradient, pollen filtering owing to assortative mating either facilitates or impedes adaptation in peripheral populations.

  5. Evolutionary insights into T-type Ca(2+) channel structure, function, and ion selectivity from the Trichoplax adhaerens homologue.

    PubMed

    Smith, Carolyn L; Abdallah, Salsabil; Wong, Yuen Yan; Le, Phuong; Harracksingh, Alicia N; Artinian, Liana; Tamvacakis, Arianna N; Rehder, Vincent; Reese, Thomas S; Senatore, Adriano

    2017-04-03

    Four-domain voltage-gated Ca(2+) (Cav) channels play fundamental roles in the nervous system, but little is known about when or how their unique properties and cellular roles evolved. Of the three types of metazoan Cav channels, Cav1 (L-type), Cav2 (P/Q-, N- and R-type) and Cav3 (T-type), Cav3 channels are optimized for regulating cellular excitability because of their fast kinetics and low activation voltages. These same properties permit Cav3 channels to drive low-threshold exocytosis in select neurons and neurosecretory cells. Here, we characterize the single T-type calcium channel from Trichoplax adhaerens (TCav3), an early diverging animal that lacks muscle, neurons, and synapses. Co-immunolocalization using antibodies against TCav3 and neurosecretory cell marker complexin labeled gland cells, which are hypothesized to play roles in paracrine signaling. Cloning and in vitro expression of TCav3 reveals that, despite roughly 600 million years of divergence from other T-type channels, it bears the defining structural and biophysical features of the Cav3 family. We also characterize the channel's cation permeation properties and find that its pore is less selective for Ca(2+) over Na(+) compared with the human homologue Cav3.1, yet it exhibits a similar potent block of inward Na(+) current by low external Ca(2+) concentrations (i.e., the Ca(2+) block effect). A comparison of the permeability features of TCav3 with other cloned channels suggests that Ca(2+) block is a locus of evolutionary change in T-type channel cation permeation properties and that mammalian channels distinguish themselves from invertebrate ones by bearing both stronger Ca(2+) block and higher Ca(2+) selectivity. TCav3 is the most divergent metazoan T-type calcium channel and thus provides an evolutionary perspective on Cav3 channel structure-function properties, ion selectivity, and cellular physiology.

  6. Evolutionary analysis of classical HLA class I and II genes suggests that recent positive selection acted on DPB1*04:01 in Japanese population.

    PubMed

    Kawashima, Minae; Ohashi, Jun; Nishida, Nao; Tokunaga, Katsushi

    2012-01-01

    The human leukocyte antigen (HLA) genes exhibit the highest degree of polymorphism in the human genome. This high degree of variation at classical HLA class I and class II loci has been maintained by balancing selection for a long evolutionary time. However, little is known about recent positive selection acting on specific HLA alleles in a local population. To detect the signature of recent positive selection, we genotyped six HLA loci, HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQB1, and HLA-DPB1 in 418 Japanese subjects, and then assessed the haplotype homozygosity (HH) of each HLA allele. There were 120 HLA alleles across the six loci. Among the 80 HLA alleles with frequencies of more than 1%, DPB1*04∶01, which had a frequency of 6.1%, showed exceptionally high HH (0.53). This finding raises the possibility that recent positive selection has acted on DPB1*04∶01. The DPB1*04∶01 allele, which was present in the most common 6-locus HLA haplotype (4.4%), A*33∶03-C*14∶03-B*44∶03-DRB1*13∶02-DQB1*06∶04-DPB1*04∶01, seems to have flowed from the Korean peninsula to the Japanese archipelago in the Yayoi period. A stochastic simulation approach indicated that the strong linkage disequilibrium between DQB1*06∶04 and DPB1*04∶01 observed in Japanese cannot be explained without positive selection favoring DPB1*04∶01. The selection coefficient of DPB1*04∶01 was estimated as 0.041 (95% credible interval 0.021-0.077). Our results suggest that DPB1*04∶01 has recently undergone strong positive selection in Japanese population.

  7. Japanese monkeys (Macaca fuscata) quickly detect snakes but not spiders: Evolutionary origins of fear-relevant animals.

    PubMed

    Kawai, Nobuyuki; Koda, Hiroki

    2016-08-01

    Humans quickly detect the presence of evolutionary threats through visual perception. Many theorists have considered humans to be predisposed to respond to both snakes and spiders as evolutionarily fear-relevant stimuli. Evidence supports that human adults, children, and snake-naive monkeys all detect pictures of snakes among pictures of flowers more quickly than vice versa, but recent neurophysiological and behavioral studies suggest that spiders may, in fact, be processed similarly to nonthreat animals. The evidence of quick detection and rapid fear learning by primates is limited to snakes, and no such evidence exists for spiders, suggesting qualitative differences between fear of snakes and fear of spiders. Here, we show that snake-naive Japanese monkeys detect a single snake picture among 8 nonthreat animal pictures (koala) more quickly than vice versa; however, no such difference in detection was observed between spiders and pleasant animals. These robust differences between snakes and spiders are the most convincing evidence that the primate visual system is predisposed to pay attention to snakes but not spiders. These findings suggest that attentional bias toward snakes has an evolutionary basis but that bias toward spiders is more due to top-down, conceptually driven effects of emotion on attention capture. (PsycINFO Database Record

  8. Hidden evolution: progress and limitations in detecting multifarious natural selection.

    PubMed

    Johnson, Norman A; Kliman, Richard M

    2002-04-01

    From illustrative examples of research on the best-studied group of species to date, Drosophila melanogaster and its closest relatives, we argue that selection is multifarious, but often hidden. Selective fixation of new, highly advantageous alleles is the most parsimonious explanation for a typical pattern of molecular variation observed in genomic regions characterized by very low recombination: drastically reduced DNA sequence variation within species and typical levels of sequence divergence among species. At the same time, the identity of the gene (or genes) influenced by selection is not just difficult to discern; it may be impossible. Studies of the genetic basis of reproductive isolation demonstrate that, although the D. melanogaster complex species appear virtually identical, dozens of currently unidentified genes contribute to hybrid sterility. We argue that these findings are best explained by selectively-driven functional divergence and demonstrate the multifarious nature of selection. Although multifarious selection certainly occurs, the exact characters responsible for differences in survival and reproductive success are unknown. We do not see these inherent limits as a cause for despair or a problem for evolutionary biology. Instead, we hope to raise awareness of these complexities of evolution by highlighting both the progress and the limitations of characterizing multifarious natural selection.

  9. Detecting Selection on Temporal and Spatial Scales: A Genomic Time-Series Assessment of Selective Responses to Devil Facial Tumor Disease

    PubMed Central

    Brüniche-Olsen, Anna; Austin, Jeremy J.; Jones, Menna E.; Holland, Barbara R.; Burridge, Christopher P.

    2016-01-01

    Detecting loci under selection is an important task in evolutionary biology. In conservation genetics detecting selection is key to investigating adaptation to the spread of infectious disease. Loci under selection can be detected on a spatial scale, accounting for differences in demographic history among populations, or on a temporal scale, tracing changes in allele frequencies over time. Here we use these two approaches to investigate selective responses to the spread of an infectious cancer—devil facial tumor disease (DFTD)—that since 1996 has ravaged the Tasmanian devil (Sarcophilus harrisii). Using time-series ‘restriction site associated DNA’ (RAD) markers from populations pre- and post DFTD arrival, and DFTD free populations, we infer loci under selection due to DFTD and investigate signatures of selection that are incongruent among methods, populations, and times. The lack of congruence among populations influenced by DFTD with respect to inferred loci under selection, and the direction of that selection, fail to implicate a consistent selective role for DFTD. Instead genetic drift is more likely driving the observed allele frequency changes over time. Our study illustrates the importance of applying methods with different performance optima e.g. accounting for population structure and background selection, and assessing congruence of the results. PMID:26930198

  10. Detecting Selection on Temporal and Spatial Scales: A Genomic Time-Series Assessment of Selective Responses to Devil Facial Tumor Disease.

    PubMed

    Brüniche-Olsen, Anna; Austin, Jeremy J; Jones, Menna E; Holland, Barbara R; Burridge, Christopher P

    2016-01-01

    Detecting loci under selection is an important task in evolutionary biology. In conservation genetics detecting selection is key to investigating adaptation to the spread of infectious disease. Loci under selection can be detected on a spatial scale, accounting for differences in demographic history among populations, or on a temporal scale, tracing changes in allele frequencies over time. Here we use these two approaches to investigate selective responses to the spread of an infectious cancer--devil facial tumor disease (DFTD)--that since 1996 has ravaged the Tasmanian devil (Sarcophilus harrisii). Using time-series 'restriction site associated DNA' (RAD) markers from populations pre- and post DFTD arrival, and DFTD free populations, we infer loci under selection due to DFTD and investigate signatures of selection that are incongruent among methods, populations, and times. The lack of congruence among populations influenced by DFTD with respect to inferred loci under selection, and the direction of that selection, fail to implicate a consistent selective role for DFTD. Instead genetic drift is more likely driving the observed allele frequency changes over time. Our study illustrates the importance of applying methods with different performance optima e.g. accounting for population structure and background selection, and assessing congruence of the results.

  11. Selective detection of antibodies in microstructured polymer optical fibers.

    PubMed

    Jensen, Jesper; Hoiby, Poul; Emiliyanov, Grigoriy; Bang, Ole; Pedersen, Lars; Bjarklev, Anders

    2005-07-25

    We demonstrate selective detection of fluorophore labeled antibodies from minute samples probed by a sensor layer of complementary biomolecules immobilized inside the air holes of microstructured Polymer Optical Fiber (mPOF). The fiber core is defined by a ring of 6 air holes and a simple procedure was applied to selectively capture either alpha-streptavidin or alpha-CRP antibodies inside these air holes. A sensitive and easy-to-use fluorescence method was used for the optical detection. Our results show that mPOF based biosensors can provide reliable and selective antibody detection in ultra small sample volumes.

  12. Embryonic development of goldfish (Carassius auratus): A model for the study of evolutionary change in developmental mechanisms by artificial selection

    PubMed Central

    Tsai, Hsin-Yuan; Chang, Mariann; Liu, Shih-Chieh; Abe, Gembu; Ota, Kinya G

    2013-01-01

    Background: Highly divergent morphology among the different goldfish strains (Carassius auratus) may make it a suitable model for investigating how artificial selection has altered developmental mechanisms. Here we describe the embryological development of the common goldfish (the single fin Wakin), which retains the ancestral morphology of this species. Results: We divided goldfish embryonic development into seven periods consisting of 34 stages, using previously reported developmental indices of zebrafish and goldfish. Although several differences were identified in terms of their yolk size, epiboly process, pigmentation patterns, and development rate, our results indicate that the embryonic features of these two teleost species are highly similar in their overall morphology from the zygote to hatching stage. Conclusions: These results provide an opportunity for further study of the evolutionary relationship between domestication and development, through applying well-established zebrafish molecular biological resources to goldfish embryos. Developmental Dynamics 242:1262–1283, 2013. © 2013 Wiley Periodicals, Inc. Key findings This study provides the first reliable descriptions of normal embryonic stages of wild-type goldfish. The embryonic features of goldfish and zebrafish are almost directly comparable. Goldfish embryos provide a novel model for the investigation of the evolutionary relationship between domestication and development. PMID:23913853

  13. Semiconducting Metal Oxide Based Sensors for Selective Gas Pollutant Detection

    PubMed Central

    Kanan, Sofian M.; El-Kadri, Oussama M.; Abu-Yousef, Imad A.; Kanan, Marsha C.

    2009-01-01

    A review of some papers published in the last fifty years that focus on the semiconducting metal oxide (SMO) based sensors for the selective and sensitive detection of various environmental pollutants is presented. PMID:22408500

  14. Divergent natural selection promotes immigrant inviability at early and late stages of evolutionary divergence.

    PubMed

    Ingley, Spencer J; Johnson, Jerald B

    2016-03-01

    Natural selection's role in speciation has been of fundamental importance since Darwin first outlined his theory. Recently, work has focused on understanding how selection drives trait divergence, and subsequently reproductive isolation. "Immigrant inviability," a barrier that arises from selection against immigrants in their nonnative environment, appears to be of particular importance. Although immigrant inviability is likely ubiquitous, we know relatively little about how selection acts on traits to drive immigrant inviability, and how important immigrant inviability is at early-versus-late stages of divergence. We present a study evaluating the role of predation in the evolution of immigrant inviability in recently diverged population pairs and a well-established species pair of Brachyrhaphis fishes. We evaluate performance in a high-predation environment by assessing survival in the presence of a predator, and swimming endurance in a low-predation environment. We find strong signatures of local adaptation and immigrant inviability of roughly the same magnitude both early and late in divergence. We find remarkably conserved selection for burst-speed swimming (important in predator evasion), and selection for increased size in low-predation environments. Our results highlight the consistency with which selection acts during speciation, and suggest that similar factors might promote initial population differentiation and maintain differentiation at late stages of divergence.

  15. Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection

    PubMed Central

    Lenz, Tobias L.; Spirin, Victor; Jordan, Daniel M.; Sunyaev, Shamil R.

    2016-01-01

    Deleterious mutations are expected to evolve under negative selection and are usually purged from the population. However, deleterious alleles segregate in the human population and some disease-associated variants are maintained at considerable frequencies. Here, we test the hypothesis that balancing selection may counteract purifying selection in neighboring regions and thus maintain deleterious variants at higher frequency than expected from their detrimental fitness effect. We first show in realistic simulations that balancing selection reduces the density of polymorphic sites surrounding a locus under balancing selection, but at the same time markedly increases the population frequency of the remaining variants, including even substantially deleterious alleles. To test the predictions of our simulations empirically, we then use whole-exome sequencing data from 6,500 human individuals and focus on the most established example for balancing selection in the human genome, the major histocompatibility complex (MHC). Our analysis shows an elevated frequency of putatively deleterious coding variants in nonhuman leukocyte antigen (non-HLA) genes localized in the MHC region. The mean frequency of these variants declined with physical distance from the classical HLA genes, indicating dependency on genetic linkage. These results reveal an indirect cost of the genetic diversity maintained by balancing selection, which has hitherto been perceived as mostly advantageous, and have implications both for the evolution of recombination and also for the epidemiology of various MHC-associated diseases. PMID:27436009

  16. Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow

    PubMed Central

    Rivas, M. J.; Domínguez-García, S.; Carvajal-Rodríguez, A.

    2015-01-01

    The study of local adaptation is a main focus of evolutionary biology since it may contribute to explain the current species diversity. The genomic scan procedures permit for the first time to study the connection between specific DNA patterns and processes as natural selection, genetic drift, recombination, mutation and gene flow. Accordingly, the information on genomes from non-model organisms increases and the interest on detecting the signal of natural selection in the DNA sequences of different populations also raises. The main goal of the present work is to explore a sequence-based method for detecting natural selection in divergent populations connected by migration. In doing so, we rely on a recently published statistic based upon th e definition of haplotype allelic classes (HAC). The original measure was modified to be more sensitive to intermediate frequencies in non-model species. A linkage-disequilibrium-based method was also assayed and individual-based simulations were performed to test the methods. The results suggest that the HAC-based methods and, specifically, the new proposed method are quite powerful for detecting the footprint of moderate divergent selection. They are also robust to reasonable model misspecification. One obvious advantage of the new algorithm is that it does not require knowledge of the allelic state. PMID:26069460

  17. ATLASGAL-selected massive clumps in the inner Galaxy. III. Dust continuum characterization of an evolutionary sample

    NASA Astrophysics Data System (ADS)

    König, C.; Urquhart, J. S.; Csengeri, T.; Leurini, S.; Wyrowski, F.; Giannetti, A.; Wienen, M.; Pillai, T.; Kauffmann, J.; Menten, K. M.; Schuller, F.

    2017-03-01

    Context. Massive-star formation and the processes involved are still poorly understood. The ATLASGAL survey provides an ideal basis for detailed studies of large numbers of massive-star forming clumps covering the whole range of evolutionary stages. The ATLASGAL Top100 is a sample of clumps selected by their infrared and radio properties to be representative for the whole range of evolutionary stages. Aims: The ATLASGAL Top100 sources are the focus of a number of detailed follow-up studies that will be presented in a series of papers. In the present work we use the dust continuum emission to constrain the physical properties of this sample and identify trends as a function of source evolution. Methods: We determine flux densities from mid-infrared to submillimeter wavelength (8-870 μm) images and use these values to fit their spectral energy distributions and determine their dust temperature and flux. Combining these with recent distances from the literature including maser parallax measurements we determine clump masses, luminosities and column densities. Results: We define four distinct source classes from the available continuum data and arrange these into an evolutionary sequence. This begins with sources found to be dark at 70 μm, followed by 24 μm weak sources with an embedded 70 μm source, continues through mid-infrared bright sources and ends with infrared bright sources associated with radio emission (i.e., H ii regions). We find trends for increasing temperature, luminosity, and column density with the proposed evolution sequence, confirming that this sample is representative of different evolutionary stages of massive star formation. Our sources span temperatures from approximately 11 to 41 K, with bolometric luminosities in the range 57 L⊙-3.8 × 106L⊙. The highest masses reach 4.3 × 104M⊙ and peak column densities up to 1.1 × 1024 cm-1, and therefore have the potential to form the most massive O-type stars. We show that at least 93 sources

  18. More rapid climate change promotes evolutionary rescue through selection for increased dispersal distance.

    PubMed

    Boeye, Jeroen; Travis, Justin M J; Stoks, Robby; Bonte, Dries

    2013-02-01

    Species can either adapt to new conditions induced by climate change or shift their range in an attempt to track optimal environmental conditions. During current range shifts, species are simultaneously confronted with a second major anthropogenic disturbance, landscape fragmentation. Using individual-based models with a shifting climate window, we examine the effect of different rates of climate change on the evolution of dispersal distances through changes in the genetically determined dispersal kernel. Our results demonstrate that the rate of climate change is positively correlated to the evolved dispersal distances although too fast climate change causes the population to crash. When faced with realistic rates of climate change, greater dispersal distances evolve than those required for the population to keep track of the climate, thereby maximizing population size. Importantly, the greater dispersal distances that evolve when climate change is more rapid, induce evolutionary rescue by facilitating the population in crossing large gaps in the landscape. This could ensure population persistence in case of range shifting in fragmented landscapes. Furthermore, we highlight problems in using invasion speed as a proxy for potential range shifting abilities under climate change.

  19. Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences

    PubMed Central

    Nguyen Ba, Alex N.; Strome, Bob; Hua, Jun Jie; Desmond, Jonathan; Gagnon-Arsenault, Isabelle; Weiss, Eric L.; Landry, Christian R.; Moses, Alan M.

    2014-01-01

    Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization. Consistent with functional divergence after gene duplication, recent studies have shown accelerated evolution in retained paralogs. However, little is known in general about the impact of this accelerated evolution on the molecular functions of retained paralogs. For example, do new functions typically involve changes in enzymatic activities, or changes in protein regulation? Here we study the evolution of posttranslational regulation by examining the evolution of important regulatory sequences (short linear motifs) in retained duplicates created by the whole-genome duplication in budding yeast. To do so, we identified short linear motifs whose evolutionary constraint has relaxed after gene duplication with a likelihood-ratio test that can account for heterogeneity in the evolutionary process by using a non-central chi-squared null distribution. We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes. We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation. Finally, we experimentally confirm our prediction that for the Ace2/Swi5 paralogs, Cbk1 regulated localization was lost along the lineage leading to SWI5 after gene duplication. Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication. PMID:25474245

  20. Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences.

    PubMed

    Nguyen Ba, Alex N; Strome, Bob; Hua, Jun Jie; Desmond, Jonathan; Gagnon-Arsenault, Isabelle; Weiss, Eric L; Landry, Christian R; Moses, Alan M

    2014-12-01

    Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization. Consistent with functional divergence after gene duplication, recent studies have shown accelerated evolution in retained paralogs. However, little is known in general about the impact of this accelerated evolution on the molecular functions of retained paralogs. For example, do new functions typically involve changes in enzymatic activities, or changes in protein regulation? Here we study the evolution of posttranslational regulation by examining the evolution of important regulatory sequences (short linear motifs) in retained duplicates created by the whole-genome duplication in budding yeast. To do so, we identified short linear motifs whose evolutionary constraint has relaxed after gene duplication with a likelihood-ratio test that can account for heterogeneity in the evolutionary process by using a non-central chi-squared null distribution. We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes. We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation. Finally, we experimentally confirm our prediction that for the Ace2/Swi5 paralogs, Cbk1 regulated localization was lost along the lineage leading to SWI5 after gene duplication. Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication.

  1. Physiological Exploration of the Long Term Evolutionary Selection against Expression of N-Glycolylneuraminic Acid in the Brain*♦

    PubMed Central

    Naito-Matsui, Yuko; Davies, Leela R. L.; Takematsu, Hiromu; Chou, Hsun-Hua; Tangvoranuntakul, Pam; Carlin, Aaron F.; Verhagen, Andrea; Heyser, Charles J.; Yoo, Seung-Wan; Choudhury, Biswa; Paton, James C.; Paton, Adrienne W.; Varki, Nissi M.; Schnaar, Ronald L.; Varki, Ajit

    2017-01-01

    All vertebrate cell surfaces display a dense glycan layer often terminated with sialic acids, which have multiple functions due to their location and diverse modifications. The major sialic acids in most mammalian tissues are N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc), the latter being derived from Neu5Ac via addition of one oxygen atom at the sugar nucleotide level by CMP-Neu5Ac hydroxylase (Cmah). Contrasting with other organs that express various ratios of Neu5Ac and Neu5Gc depending on the variable expression of Cmah, Neu5Gc expression in the brain is extremely low in all vertebrates studied to date, suggesting that neural expression is detrimental to animals. However, physiological exploration of the reasons for this long term evolutionary selection has been lacking. To explore the consequences of forced expression of Neu5Gc in the brain, we have established brain-specific Cmah transgenic mice. Such Neu5Gc overexpression in the brain resulted in abnormal locomotor activity, impaired object recognition memory, and abnormal axon myelination. Brain-specific Cmah transgenic mice were also lethally sensitive to a Neu5Gc-preferring bacterial toxin, even though Neu5Gc was overexpressed only in the brain and other organs maintained endogenous Neu5Gc expression, as in wild-type mice. Therefore, the unusually strict evolutionary suppression of Neu5Gc expression in the vertebrate brain may be explained by evasion of negative effects on neural functions and by selection against pathogens. PMID:28049733

  2. Physiological Exploration of the Long Term Evolutionary Selection against Expression of N-Glycolylneuraminic Acid in the Brain.

    PubMed

    Naito-Matsui, Yuko; Davies, Leela R L; Takematsu, Hiromu; Chou, Hsun-Hua; Tangvoranuntakul, Pam; Carlin, Aaron F; Verhagen, Andrea; Heyser, Charles J; Yoo, Seung-Wan; Choudhury, Biswa; Paton, James C; Paton, Adrienne W; Varki, Nissi M; Schnaar, Ronald L; Varki, Ajit

    2017-02-17

    All vertebrate cell surfaces display a dense glycan layer often terminated with sialic acids, which have multiple functions due to their location and diverse modifications. The major sialic acids in most mammalian tissues are N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc), the latter being derived from Neu5Ac via addition of one oxygen atom at the sugar nucleotide level by CMP-Neu5Ac hydroxylase (Cmah). Contrasting with other organs that express various ratios of Neu5Ac and Neu5Gc depending on the variable expression of Cmah, Neu5Gc expression in the brain is extremely low in all vertebrates studied to date, suggesting that neural expression is detrimental to animals. However, physiological exploration of the reasons for this long term evolutionary selection has been lacking. To explore the consequences of forced expression of Neu5Gc in the brain, we have established brain-specific Cmah transgenic mice. Such Neu5Gc overexpression in the brain resulted in abnormal locomotor activity, impaired object recognition memory, and abnormal axon myelination. Brain-specific Cmah transgenic mice were also lethally sensitive to a Neu5Gc-preferring bacterial toxin, even though Neu5Gc was overexpressed only in the brain and other organs maintained endogenous Neu5Gc expression, as in wild-type mice. Therefore, the unusually strict evolutionary suppression of Neu5Gc expression in the vertebrate brain may be explained by evasion of negative effects on neural functions and by selection against pathogens.

  3. Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population

    PubMed Central

    Wandeler, Peter; Camenisch, Glauco

    2017-01-01

    In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called “stasis paradox” highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is

  4. 46 CFR 108.404 - Selection of fire detection system.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ....404 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) A-MOBILE OFFSHORE DRILLING UNITS DESIGN AND EQUIPMENT Fire Extinguishing Systems § 108.404 Selection of fire detection system. (a) If a... space. (b) The fire detection system must be designed to minimize false alarms....

  5. Geographical gradients in selection can reveal genetic constraints for evolutionary responses to ocean acidification.

    PubMed

    Gaitán-Espitia, Juan Diego; Marshall, Dustin; Dupont, Sam; Bacigalupe, Leonardo D; Bodrossy, Levente; Hobday, Alistair J

    2017-02-01

    Geographical gradients in selection can shape different genetic architectures in natural populations, reflecting potential genetic constraints for adaptive evolution under climate change. Investigation of natural pH/pCO2 variation in upwelling regions reveals different spatio-temporal patterns of natural selection, generating genetic and phenotypic clines in populations, and potentially leading to local adaptation, relevant to understanding effects of ocean acidification (OA). Strong directional selection, associated with intense and continuous upwellings, may have depleted genetic variation in populations within these upwelling regions, favouring increased tolerances to low pH but with an associated cost in other traits. In contrast, diversifying or weak directional selection in populations with seasonal upwellings or outside major upwelling regions may have resulted in higher genetic variances and the lack of genetic correlations among traits. Testing this hypothesis in geographical regions with similar environmental conditions to those predicted under climate change will build insights into how selection may act in the future and how populations may respond to stressors such as OA.

  6. Exact solutions for the selection-mutation equilibrium in the Crow-Kimura evolutionary model.

    PubMed

    Semenov, Yuri S; Novozhilov, Artem S

    2015-08-01

    We reformulate the eigenvalue problem for the selection-mutation equilibrium distribution in the case of a haploid asexually reproduced population in the form of an equation for an unknown probability generating function of this distribution. The special form of this equation in the infinite sequence limit allows us to obtain analytically the steady state distributions for a number of particular cases of the fitness landscape. The general approach is illustrated by examples; theoretical findings are compared with numerical calculations.

  7. Evolutionary Endocrinology of Juvenile Hormone Esterase in Gryllus Assimilis: Direct and Correlated Responses to Selection

    PubMed Central

    Zera, A. J.; Zhang, C.

    1995-01-01

    Hemolymph juvenile hormone esterase (JHE) activity on the third day of the last stadium in the cricket, Gryllus assimilis, exhibited a significant response to selection in each of six replicate lines. Mean realized heritability was 0.26 +/- 0.04. The response was due to changes in whole-organism enzyme activity as well as to changes in the proportion of enzyme allocated to the hemolymph compartment. In vivo juvenile hormone metabolism differed between some lines selected for high vs. low enzyme activity. Only minimal differences were observed between lines with respect to hemolymph protein concentration or whole-cricket activity of juvenile hormone epoxide hydrolase, the other major JH-degrading enzyme. Dramatic correlated responses to selection, equal in magnitude to the direct response, were observed for JHE activity on each of three other days of the last juvenile stadium. In contrast, no correlated responses in JHE activity were observed in adults. This indicates that JHE activities throughout the last stadium will evolve as a highly correlated unit independent of adult activities and the evolution of endocrine mechanisms regulating juvenile development can be decoupled from those controlling adult reproduction. This study represents the first quantitative-genetic analysis of naturally occurring endocrine variation in an insect species. PMID:8582618

  8. Bands selection and classification of hyperspectral images based on hybrid kernels SVM by evolutionary algorithm

    NASA Astrophysics Data System (ADS)

    Hu, Yan-Yan; Li, Dong-Sheng

    2016-01-01

    The hyperspectral images(HSI) consist of many closely spaced bands carrying the most object information. While due to its high dimensionality and high volume nature, it is hard to get satisfactory classification performance. In order to reduce HSI data dimensionality preparation for high classification accuracy, it is proposed to combine a band selection method of artificial immune systems (AIS) with a hybrid kernels support vector machine (SVM-HK) algorithm. In fact, after comparing different kernels for hyperspectral analysis, the approach mixed radial basis function kernel (RBF-K) with sigmoid kernel (Sig-K) and applied the optimized hybrid kernels in SVM classifiers. Then the SVM-HK algorithm used to induce the bands selection of an improved version of AIS. The AIS was composed of clonal selection and elite antibody mutation, including evaluation process with optional index factor (OIF). Experimental classification performance was on a San Diego Naval Base acquired by AVIRIS, the HRS dataset shows that the method is able to efficiently achieve bands redundancy removal while outperforming the traditional SVM classifier.

  9. Multi-objective entropy evolutionary algorithm for marine oil spill detection using cosmo-skymed satellite data

    NASA Astrophysics Data System (ADS)

    Marghany, M.

    2015-06-01

    Oil spill pollution has a substantial role in damaging the marine ecosystem. Oil spill that floats on top of water, as well as decreasing the fauna populations, affects the food chain in the ecosystem. In fact, oil spill is reducing the sunlight penetrates the water, limiting the photosynthesis of marine plants and phytoplankton. Moreover, marine mammals for instance, disclosed to oil spills their insulating capacities are reduced, and so making them more vulnerable to temperature variations and much less buoyant in the seawater. This study has demonstrated a design tool for oil spill detection in SAR satellite data using optimization of Entropy based Multi-Objective Evolutionary Algorithm (E-MMGA) which based on Pareto optimal solutions. The study also shows that optimization entropy based Multi-Objective Evolutionary Algorithm provides an accurate pattern of oil slick in SAR data. This shown by 85 % for oil spill, 10 % look-alike and 5 % for sea roughness using the receiver-operational characteristics (ROC) curve. The E-MMGA also shows excellent performance in SAR data. In conclusion, E-MMGA can be used as optimization for entropy to perform an automatic detection of oil spill in SAR satellite data.

  10. Evaluating the performance of selection scans to detect selective sweeps in domestic dogs

    PubMed Central

    Schlamp, Florencia; van der Made, Julian; Stambler, Rebecca; Chesebrough, Lewis; Boyko, Adam R.; Messer, Philipp W.

    2015-01-01

    Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analyzed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used, and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks. PMID:26589239

  11. Evaluating the performance of selection scans to detect selective sweeps in domestic dogs.

    PubMed

    Schlamp, Florencia; van der Made, Julian; Stambler, Rebecca; Chesebrough, Lewis; Boyko, Adam R; Messer, Philipp W

    2016-01-01

    Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analysed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks.

  12. Evolutionary Pressure of a Receptor Competitor Selects Different Subgroup A Avian Leukosis Virus Escape Variants with Altered Receptor Interactions

    PubMed Central

    Melder, Deborah C.; Pankratz, V. Shane; Federspiel, Mark J.

    2003-01-01

    A complex interaction between the retroviral envelope glycoproteins and a specific cell surface protein initiates viral entry into cells. The avian leukosis-sarcoma virus (ALV) group of retroviruses provides a useful experimental system for studying the retroviral entry process and the evolution of receptor usage. In this study, we demonstrate that evolutionary pressure on subgroup A ALV [ALV(A)] entry exerted by the presence of a competitive inhibitor, a soluble form of the ALV(A) Tva receptor linked to a mouse immunoglobulin G tag (quail sTva-mIgG), can select different populations of escape variants. This escape population contained three abundant ALV(A) variant viruses, all with mutations in the surface glycoprotein hypervariable regions: a previously identified variant containing the Y142N mutation in the hr1 region; a new variant with two mutations, W141G in hr1 and K261E in vr3; and another new variant with two mutations, W145R in hr1 and K261E. The W141G K261E and W145R K261E viruses escape primarily by lowering their binding affinities for the quail Tva receptor competitive inhibitor while retaining wild-type levels of binding affinity for the chicken Tva receptor. A secondary phenotype of the new variants was an alteration in receptor interference patterns from that of wild-type ALV(A), indicating that the mutant glycoproteins are possibly interacting with other cellular proteins. One result of these altered interactions was that the variants caused a transient period of cytotoxicity. We could also directly demonstrate that the W141G K261E variant glycoproteins bound significant levels of a soluble form of the TvbS3 ALV receptor in a binding assay. Alterations in the normally extreme specificity of the ALV(A) glycoproteins for Tva may represent an evolutionary first step toward expanding viral receptor usage in response to inefficient viral entry. PMID:12970435

  13. A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure

    NASA Astrophysics Data System (ADS)

    Tsai, Ming-Chi; Blelloch, Guy; Ravi, R.; Schwartz, Russell

    The random accumulation of variations in the human genome over time implicitly encodes a history of how human populations have arisen, dispersed, and intermixed since we emerged as a species. Reconstructing that history is a challenging computational and statistical problem but has important applications both to basic research and to the discovery of genotype-phenotype correlations. In this study, we present a novel approach to inferring human evolutionary history from genetic variation data. Our approach uses the idea of consensus trees, a technique generally used to reconcile species trees from divergent gene trees, adapting it to the problem of finding the robust relationships within a set of intraspecies phylogenies derived from local regions of the genome. We assess the quality of the method on two large-scale genetic variation data sets: the HapMap Phase II and the Human Genome Diversity Project. Qualitative comparison to a consensus model of the evolution of modern human population groups shows that our inferences closely match our best current understanding of human evolutionary history. A further comparison with results of a leading method for the simpler problem of population substructure assignment verifies that our method provides comparable accuracy in identifying meaningful population subgroups in addition to inferring the relationships among them.

  14. Sex differences in immune responses: Hormonal effects, antagonistic selection, and evolutionary consequences.

    PubMed

    Roved, Jacob; Westerdahl, Helena; Hasselquist, Dennis

    2017-02-01

    Males and females differ in both parasite load and the strength of immune responses and these effects have been verified in humans and other vertebrates. Sex hormones act as important modulators of immune responses; the male sex hormone testosterone is generally immunosuppressive while the female sex hormone estrogen tends to be immunoenhancing. Different sets of T-helper cells (Th) have important roles in adaptive immunity, e.g. Th1 cells trigger type 1 responses which are primarily cell-mediated, and Th2 cells trigger type 2 responses which are primarily humoral responses. In our review of the literature, we find that estrogen and progesterone enhance type 2 and suppress type 1 responses in females, whereas testosterone suppresses type 2 responses and shows an inconsistent pattern for type 1 responses in males. When we combine these patterns of generally immunosuppressive and immunoenhancing effects of the sex hormones, our results imply that the sex differences in immune responses should be particularly strong in immune functions associated with type 2 responses, and less pronounced with type 1 responses. In general the hormone-mediated sex differences in immune responses may lead to genetic sexual conflicts on immunity. Thus, we propose the novel hypothesis that sexually antagonistic selection may act on immune genes shared by the sexes, and that the strength of this sexually antagonistic selection should be stronger for type 2- as compared with type 1-associated immune genes. Finally, we put the consequences of sex hormone-induced effects on immune responses into behavioral and ecological contexts, considering social mating system, sexual selection, geographical distribution of hosts, and parasite abundance.

  15. Combining Crowding Estimation in Objective and Decision Space With Multiple Selection and Search Strategies for Multi-Objective Evolutionary Optimization.

    PubMed

    Xia, Hu; Zhuang, Jian; Yu, Dehong

    2014-03-01

    Many multi-objective evolutionary algorithms (MOEAs) have been successful in approximating the Pareto Front. However, well-distributed solutions in the objective and decision spaces are still required in many real-life applications. In this paper, a novel MOEA is proposed to this problem. Distinct from other MOEAs, the proposed algorithm suggests a framework, which includes two crowding estimation methods, multiple selection methods for mating and search strategies for variation, to improve the MOEA' s searching ability, and the diversity of its solutions. The algorithm emphasizes the importance of using the decision space and the objective space diversities. The objective space crowding and decision space crowding distances are designed using different ideas. To produce new individuals, three different types of mating selections and their respective search strategies are constructed for the main population and the two sparse populations, with the help of the two crowding measurements. Finally, based on the experimental tests on 17 unconstrained multi-objective optimization problems, the proposed algorithm is demonstrated to have better results compared to several state-of-the-art MOEAs. A detailed analysis on the effectiveness and robustness of the framework is also presented.

  16. Extraordinarily high evolutionary rate of pseudogenes: evidence for the presence of selective pressure against changes between synonymous codons.

    PubMed Central

    Miyata, T; Hayashida, H

    1981-01-01

    Comparisons of nucleotide sequences of several pseudogenes described to date, including alpha- and beta-globin and immunoglobulin kappa-type variable domain pseudogenes, with those of functional counterparts revealed that pseudogenes accumulate mutations at an extremely high rate uniformly over their entirety. It is remarkable that the evolutionary rate exceeds the rate of changes between synonymous codons, the highest known rate, in functional genes. Because no pseudogenes appear to function, this result strongly supports the neutral theory. In addition this result apparently indicates the presence of selective pressure against changes between synonymous codons in functional genes. Close examinations of codon utilization patterns in pseudogenes and functional genes revealed a significant correlation between the rate of changes at synonymous codon sites and the strength of bias in code word usage. This implies that even synonymous codon changes are not completely free from selective pressure but are constrained in part, although presumably weakly, depending on the degree of bias in code word usage. We also reexamined alignment between mouse beta h3 (pseudogene) and beta maj sequences and found a unique structure of the beta h3 that is homologous in sequence to the beta maj gene overall but contains a long deletion (about 150 base pairs) in the middle of the gene. PMID:6795634

  17. Evolutionary diversification of multigene families: allelic selection of toxins in predatory cone snails.

    PubMed

    Duda, T F; Palumbi, S R

    2000-09-01

    In order to investigate the evolution of conotoxin multigene families among two closely related vermivorous CONUS: species, we sequenced 104 four-loop conotoxin mRNAs from two individuals of CONUS: ebraeus and compared these with sequences already obtained from CONUS: abbreviatus. In contrast to the diversity of conotoxin sequences obtained from C. abbreviatus, only two common sequence variants were recovered from C. ebraeus. Segregation patterns of the variants in these two individuals and restriction digests of four-loop conotoxin amplification products from nine additional individuals suggest that the common variants are alleles from a single locus. These two putative alleles differ at nine positions that occur nonrandomly in the toxin-coding region of the sequences. Moreover, all substitutions are at nonsynonymous sites and are responsible for seven amino acid differences among the predicted amino acid sequences of the alleles. These results imply that conotoxin diversity is driven by strong diversifying selection and some form of frequency-dependent or overdominant selection at conotoxin loci, and they suggest that diverse conotoxin multigene families can originate from duplications at polymorphic loci. Furthermore, none of the sequences recovered from C. ebraeus appeared to be orthologs of loci from C. abbreviatus, and attempts to amplify orthologous sequences with locus-specific primers were unsuccessful among these species. These patterns suggest that venoms of closely related CONUS: species may differ due to the differential expression of conotoxin loci.

  18. Colour variation in cichlid fish: Developmental mechanisms, selective pressures and evolutionary consequences☆

    PubMed Central

    Maan, Martine E.; Sefc, Kristina M.

    2013-01-01

    Cichlid fishes constitute one of the most species-rich families of vertebrates. In addition to complex social behaviour and morphological versatility, they are characterised by extensive diversity in colouration, both within and between species. Here, we review the cellular and molecular mechanisms underlying colour variation in this group and the selective pressures responsible for the observed variation. We specifically address the evidence for the hypothesis that divergence in colouration is associated with the evolution of reproductive isolation between lineages. While we conclude that cichlid colours are excellent models for understanding the role of animal communication in species divergence, we also identify taxonomic and methodological biases in the current research effort. We suggest that the integration of genomic approaches with ecological and behavioural studies, across the entire cichlid family and beyond it, will contribute to the utility of the cichlid model system for understanding the evolution of biological diversity. PMID:23665150

  19. Nanomaterials for the Selective Detection of Hydrogen Sulfide in Air

    PubMed Central

    Llobet, Eduard; Brunet, Jérôme; Pauly, Alain; Ndiaye, Amadou; Varenne, Christelle

    2017-01-01

    This paper presents a focused review on the nanomaterials and associated transduction schemes that have been developed for the selective detection of hydrogen sulfide. It presents a quite comprehensive overview of the latest developments, briefly discusses the hydrogen sulfide detection mechanisms, identifying the reasons for the selectivity (or lack of) observed experimentally. It critically reviews performance, shortcomings, and identifies missing or overlooked important aspects. It identifies the most mature/promising materials and approaches for achieving inexpensive hydrogen sulfide sensors that could be employed in widespread, miniaturized, and inexpensive detectors and, suggests what research should be undertaken for ensuring that requirements are met. PMID:28218674

  20. Reflections on Behavior Analysis and Evolutionary Biology: A Selective Review of Evolution Since Darwin—The First 150 Years. Edited by M. A. Bell, D. J. Futuyama, W. F. Eanes, & J. S. Levinton

    PubMed Central

    Donahoe, John W

    2012-01-01

    This review focuses on parallels between the selectionist sciences of evolutionary biology and behavior analysis. In selectionism, complex phenomena are interpreted as the cumulative products of relatively simple processes acting over time—natural selection in evolutionary biology and reinforcement in behavior analysis. Because evolutionary biology is the more mature science, an examination of the factors that led to the triumph of natural selection provides clues whereby reinforcement may achieve a similar fate in the science of behavior.

  1. ATLASGAL-selected massive clumps in the inner Galaxy. II. Characterisation of different evolutionary stages and their SiO emission

    NASA Astrophysics Data System (ADS)

    Csengeri, T.; Leurini, S.; Wyrowski, F.; Urquhart, J. S.; Menten, K. M.; Walmsley, M.; Bontemps, S.; Wienen, M.; Beuther, H.; Motte, F.; Nguyen-Luong, Q.; Schilke, P.; Schuller, F.; Zavagno, A.; Sanna, C.

    2016-02-01

    Context. The processes leading to the birth of high-mass stars are poorly understood. The key first step to reveal their formation processes is characterising the clumps and cores from which they form. Aims: We define a representative sample of massive clumps in different evolutionary stages selected from the APEX Telescope Large Area Survey of the Galaxy (ATLASGAL), from which we aim to establish a census of molecular tracers of their evolution. As a first step, we study the shock tracer, SiO, mainly associated with shocks from jets probing accretion processes. In low-mass young stellar objects (YSOs), outflow and jet activity decreases with time during the star formation processes. Recently, a similar scenario was suggested for massive clumps based on SiO observations. Here we analyse observations of the SiO (2-1) and (5-4) lines in a statistically significant sample to constrain the change of SiO abundance and the excitation conditions as a function of evolutionary stage of massive star-forming clumps. Methods: We performed an unbiased spectral line survey covering the 3-mm atmospheric window between 84-117 GHz with the IRAM 30 m telescope of a sample of 430 sources of the ATLASGAL survey, covering various evolutionary stages of massive clumps. A smaller sample of 128 clumps has been observed in the SiO (5-4) transition with the APEX telescope to complement the (2-1) line and probe the excitation conditions of the emitting gas. We derived detection rates to assess the star formation activity of the sample, and we estimated the column density and abundance using both an LTE approximation and non-LTE calculations for a smaller subsample, where both transitions have been observed. Results: We characterise the physical properties of the selected sources, which greatly supersedes the largest samples studied so far, and show that they are representative of different evolutionary stages. We report a high detection rate of >75% of the SiO (2-1) line and a >90% detection

  2. Greenhouse Effect Detection Experiment (GEDEX). Selected data sets

    NASA Technical Reports Server (NTRS)

    Olsen, Lola M.; Warnock, Archibald, III

    1992-01-01

    This CD-ROM contains selected data sets compiled by the participants of the Greenhouse Effect Detection Experiment (GEDEX) workshop on atmospheric temperature. The data sets include surface, upper air, and/or satellite-derived measurements of temperature, solar irradiance, clouds, greenhouse gases, fluxes, albedo, aerosols, ozone, and water vapor, along with Southern Oscillation Indices and Quasi-Biennial Oscillation statistics.

  3. Detecting Bias in Selection for Higher Education: Three Different Methods

    ERIC Educational Resources Information Center

    Kennet-Cohen, Tamar; Turvall, Elliot; Oren, Carmel

    2014-01-01

    This study examined selection bias in Israeli university admissions with respect to test language and gender, using three approaches for the detection of such bias: Cleary's model of differential prediction, boundary conditions for differential prediction and difference between "d's" (the Constant Ratio Model). The university admissions…

  4. QCM-based aptamer selection and detection of Salmonella typhimurium.

    PubMed

    Wang, Lijun; Wang, Ronghui; Chen, Fang; Jiang, Tieshan; Wang, Hong; Slavik, Michael; Wei, Hua; Li, Yanbin

    2017-04-15

    In this study, quartz crystal microbalance (QCM) was used to select aptamers against Salmonella typhimurium. To increase the success rate of Systematic Evolution of Ligands Exponential Enrichment (SELEX), the affinity of DNA pool in each round was simultaneously tracked using QCM in order to avoid the loss of high-quality aptamers. When the frequency change reached a maximum value after several rounds of selection and counter-selection, the candidate pool was cloned and sequenced. Out of three aptamer candidates, aptamer B5 showed high specificity and binding affinity with dissociation constant (Kd value) of 58.5nM, and was chosen for further studies. Subsequently, a QCM-based aptasensor was developed to detect S. typhimurium. This aptasensor was able to detect 10(3)CFU/mL of S. typhimurium with less than 1h. This study demonstrated QCM-based selection could be more effective selection of aptamers and QCM-based aptasensor could be more sensitive in detecting S. typhimurium.

  5. Open and closed evolutionary paths for drastic morphological changes, involving serial gene duplication, sub-functionalization, and selection

    PubMed Central

    Abe, Gembu; Lee, Shu-Hua; Li, Ing-Jia; Chang, Chun-Ju; Tamura, Koji; Ota, Kinya G.

    2016-01-01

    Twin-tail goldfish strains are examples of drastic morphological alterations that emerged through domestication. Although this mutation is known to be caused by deficiency of one of two duplicated chordin genes, it is unknown why equivalent mutations have not been observed in other domesticated fish species. Here, we compared the chordin gene morphant phenotypes of single-tail goldfish and common carp (close relatives, both of which underwent chordin gene duplication and domestication). Morpholino-induced knockdown depleted chordin gene expression in both species; however, while knockdown reproduced twin-tail morphology in single-tail goldfish, it had no effect on common carp morphology. This difference can be explained by the observation that expression patterns of the duplicated chordin genes overlap completely in common carp, but are sub-functionalized in goldfish. Our finding implies that goldfish drastic morphological changes might be enhanced by the subsequent occurrence of three different types of evolutionary event (duplication, sub-functionalization, and selection) in a certain order. PMID:27220684

  6. Pattern Recognition for Selective Odor Detection with Gas Sensor Arrays

    PubMed Central

    Kim, Eungyeong; Lee, Seok; Kim, Jae Hun; Kim, Chulki; Byun, Young Tae; Kim, Hyung Seok; Lee, Taikjin

    2012-01-01

    This paper presents a new pattern recognition approach for enhancing the selectivity of gas sensor arrays for clustering intelligent odor detection. The aim of this approach was to accurately classify an odor using pattern recognition in order to enhance the selectivity of gas sensor arrays. This was achieved using an odor monitoring system with a newly developed neural-genetic classification algorithm (NGCA). The system shows the enhancement in the sensitivity of the detected gas. Experiments showed that the proposed NGCA delivered better performance than the previous genetic algorithm (GA) and artificial neural networks (ANN) methods. We also used PCA for data visualization. Our proposed system can enhance the reproducibility, reliability, and selectivity of odor sensor output, so it is expected to be applicable to diverse environmental problems including air pollution, and monitor the air quality of clean-air required buildings such as a kindergartens and hospitals. PMID:23443378

  7. Selective detection of bacterial layers with terahertz plasmonic antennas

    PubMed Central

    Berrier, Audrey; Schaafsma, Martijn C.; Nonglaton, Guillaume; Bergquist, Jonas; Rivas, Jaime Gómez

    2012-01-01

    Current detection and identification of micro-organisms is based on either rather unspecific rapid microscopy or on more accurate but complex and time-consuming procedures. In a medical context, the determination of the bacteria Gram type is of significant interest. The diagnostic of microbial infection often requires the identification of the microbiological agent responsible for the infection, or at least the identification of its family (Gram type), in a matter of minutes. In this work, we propose to use terahertz frequency range antennas for the enhanced selective detection of bacteria types. Several microorganisms are investigated by terahertz time-domain spectroscopy: a fast, contactless and damage-free investigation method to gain information on the presence and the nature of the microorganisms. We demonstrate that plasmonic antennas enhance the detection sensitivity for bacterial layers and allow the selective recognition of the Gram type of the bacteria. PMID:23162730

  8. Double-layer evolutionary algorithm for distributed optimization of particle detection on the Grid

    NASA Astrophysics Data System (ADS)

    Padée, Adam; Kurek, Krzysztof; Zaremba, Krzysztof

    2013-08-01

    Reconstruction of particle tracks from information collected by position-sensitive detectors is an important procedure in HEP experiments. It is usually controlled by a set of numerical parameters which have to be manually optimized. This paper proposes an automatic approach to this task by utilizing evolutionary algorithm (EA) operating on both real-valued and binary representations. Because of computational complexity of the task a special distributed architecture of the algorithm is proposed, designed to be run in grid environment. It is two-level hierarchical hybrid utilizing asynchronous master-slave EA on the level of clusters and island model EA on the level of the grid. The technical aspects of usage of production grid infrastructure are covered, including communication protocols on both levels. The paper deals also with the problem of heterogeneity of the resources, presenting efficiency tests on a benchmark function. These tests confirm that even relatively small islands (clusters) can be beneficial to the optimization process when connected to the larger ones. Finally a real-life usage example is presented, which is an optimization of track reconstruction in Large Angle Spectrometer of NA-58 COMPASS experiment held at CERN, using a sample of Monte Carlo simulated data. The overall reconstruction efficiency gain, achieved by the proposed method, is more than 4%, compared to the manually optimized parameters.

  9. A Multi Agent System for Flow-Based Intrusion Detection Using Reputation and Evolutionary Computation

    DTIC Science & Technology

    2011-03-01

    for a new, self-organized, multi agent, flow-based intrusion detection system; and 2 ) a network simulation envi- ronment suitable for evaluating an...six years of service in the Air Force, and I am indebted to him for his efforts. I also thank Dr. Gilbert Peterson and Dr. Barry Mullins for valuable...1 1.1 The Generic Intrusion Detection Problem . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.2 Scope of Investigative Domain

  10. Considerations in detecting CDC select agents under field conditions

    NASA Astrophysics Data System (ADS)

    Spinelli, Charles; Soelberg, Scott; Swanson, Nathaneal; Furlong, Clement; Baker, Paul

    2008-04-01

    Surface Plasmon Resonance (SPR) has become a widely accepted technique for real-time detection of interactions between receptor molecules and ligands. Antibody may serve as receptor and can be attached to the gold surface of the SPR device, while candidate analyte fluids contact the detecting antibody. Minute, but detectable, changes in refractive indices (RI) indicate that analyte has bound to the antibody. A decade ago, an inexpensive, robust, miniature and fully integrated SPR chip, called SPREETA, was developed. University of Washington (UW) researchers subsequently developed a portable, temperature-regulated instrument, called SPIRIT, to simultaneously use eight of these three-channel SPREETA chips. A SPIRIT prototype instrument was tested in the field, coupled to a remote reporting system on a surrogate unmanned aerial vehicle (UAV). Two target protein analytes were released sequentially as aerosols with low analyte concentration during each of three flights and were successfully detected and verified. Laboratory experimentation with a more advanced SPIRIT instrument demonstrated detection of very low levels of several select biological agents that might be employed by bioterrorists. Agent detection under field-like conditions is more challenging, especially as analyte concentrations are reduced and complex matricies are introduced. Two different sample preconditioning protocols have been developed for select agents in complex matrices. Use of these preconditioning techniques has allowed laboratory detection in spiked heavy mud of Francisella tularensis at 10 3 CFU/ml, Bacillus anthracis spores at 10 3 CFU/ml, Staphylococcal enterotoxin B (SEB) at 1 ng/ml, and Vaccinia virus (a smallpox simulant) at 10 5 PFU/ml. Ongoing experiments are aimed at simultaneous detection of multiple agents in spiked heavy mud, using a multiplex preconditioning protocol.

  11. EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

    PubMed Central

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

    2015-01-01

    Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution 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 others to speed the development of evolutionary molecular medicine. PMID:22544168

  12. Fluorescein Tri-Aldehyde Promotes the Selective Detection of Homocysteine.

    PubMed

    Barve, Aabha; Lowry, Mark; Escobedo, Jorge O; Thainashmuthu, Josephrajan; Strongin, Robert M

    2016-03-01

    Elevated homocysteine levels are a well-known independent risk factor for cardiovascular disease. To date, relatively few selective fluorescent probes for homocysteine detection have been reported. The lack of sensing reagents and remaining challenges largely derive from issues of sensitivity and/or selectivity. For example, homocysteine is a structural homologue of the more abundant (ca, 20-25 fold) aminothiol cysteine, differing only by an additional methylene group side chain. Fluorescein tri-aldehyde, described herein, has been designed and synthesized as a sensitive and selective fluorophore for the detection of homocysteine in human plasma samples. It responds to analytes selectively via a photoinduced electron transfer (PET) inhibition process that is modulated by predictable analyte-dye product hybridization and ionization states. Mulliken population analysis of fluorescein tri-aldehyde and its reaction products reveals that the characteristic formation of multiple cationic of homocysteine-derived heterocycles leads to enhanced relative negative charge build up on the proximal phenolate oxygen of the fluorophore as a contributing factor to selective emission enhancement.

  13. A dynamic evolutionary clustering perspective: Community detection in signed networks by reconstructing neighbor sets

    NASA Astrophysics Data System (ADS)

    Chen, Jianrui; Wang, Hua; Wang, Lina; Liu, Weiwei

    2016-04-01

    Community detection in social networks has been intensively studied in recent years. In this paper, a novel similarity measurement is defined according to social balance theory for signed networks. Inter-community positive links are found and deleted due to their low similarity. The positive neighbor sets are reconstructed by this method. Then, differential equations are proposed to imitate the constantly changing states of nodes. Each node will update its state based on the difference between its state and average state of its positive neighbors. Nodes in the same community will evolve together with time and nodes in the different communities will evolve far away. Communities are detected ultimately when states of nodes are stable. Experiments on real world and synthetic networks are implemented to verify detection performance. The thorough comparisons demonstrate the presented method is more efficient than two acknowledged better algorithms.

  14. Detecting and Measuring Selection from Gene Frequency Data

    PubMed Central

    Vitalis, Renaud; Gautier, Mathieu; Dawson, Kevin J.; Beaumont, Mark A.

    2014-01-01

    The recent advent of high-throughput sequencing and genotyping technologies makes it possible to produce, easily and cost effectively, large amounts of detailed data on the genotype composition of populations. Detecting locus-specific effects may help identify those genes that have been, or are currently, targeted by natural selection. How best to identify these selected regions, loci, or single nucleotides remains a challenging issue. Here, we introduce a new model-based method, called SelEstim, to distinguish putative selected polymorphisms from the background of neutral (or nearly neutral) ones and to estimate the intensity of selection at the former. The underlying population genetic model is a diffusion approximation for the distribution of allele frequency in a population subdivided into a number of demes that exchange migrants. We use a Markov chain Monte Carlo algorithm for sampling from the joint posterior distribution of the model parameters, in a hierarchical Bayesian framework. We present evidence from stochastic simulations, which demonstrates the good power of SelEstim to identify loci targeted by selection and to estimate the strength of selection acting on these loci, within each deme. We also reanalyze a subset of SNP data from the Stanford HGDP–CEPH Human Genome Diversity Cell Line Panel to illustrate the performance of SelEstim on real data. In agreement with previous studies, our analyses point to a very strong signal of positive selection upstream of the LCT gene, which encodes for the enzyme lactase–phlorizin hydrolase and is associated with adult-type hypolactasia. The geographical distribution of the strength of positive selection across the Old World matches the interpolated map of lactase persistence phenotype frequencies, with the strongest selection coefficients in Europe and in the Indus Valley. PMID:24361938

  15. Selective detection of gold using genetically engineered bacterial reporters.

    PubMed

    Cerminati, Sebastián; Soncini, Fernando C; Checa, Susana K

    2011-11-01

    Salmonella typhimurium harbours a Au-resistance system whose expression is controlled by GolS, a transcriptional regulator of the MerR family that selectively detects Au with high sensitivity. We developed both Salmonella and genetically engineered Escherichia coli strains as Au-selective whole-cell biosensors by coupling the strictly regulated GolS-dependent golB promoter to the gfp reporter gene. The bio-reporters were evaluated under different laboratory conditions and calibrated for their use as selective Au detectors. Due to the intrinsic characteristics of the regulatory protein, the transgenic E. coli sensor exhibits low background, high signal-to-noise ratio, and improved sensitivity for detection of Au ions in a wide range of concentrations (up to 470 nM) with a calculated detection limit of ∼33 nM (6 µg L(-1) or parts per billion) Au(I). The fluorescent Au-sensing bacteria exhibit also minimal interference by chemically related metals such as Cu or Ag that are commonly found in Au deposits. These highly specific and sensitive Au detectors might allow the development of rapid and robust screening tools to improve discovery and extraction procedures.

  16. Fast Selective Detection of Pyocyanin Using Cyclic Voltammetry

    PubMed Central

    Alatraktchi, Fatima AlZahra’a; Breum Andersen, Sandra; Krogh Johansen, Helle; Molin, Søren; Svendsen, Winnie E.

    2016-01-01

    Pyocyanin is a virulence factor uniquely produced by the pathogen Pseudomonas aeruginosa. The fast and selective detection of pyocyanin in clinical samples can reveal important information about the presence of this microorganism in patients. Electrochemical sensing of the redox-active pyocyanin is a route to directly quantify pyocyanin in real time and in situ in hospitals and clinics. The selective quantification of pyocyanin is, however, limited by other redox-active compounds existing in human fluids and by other metabolites produced by pathogenic bacteria. Here we present a direct selective method to detect pyocyanin in a complex electroactive environment using commercially available electrodes. It is shown that cyclic voltammetry measurements between −1.0 V to 1.0 V reveal a potential detection window of pyocyanin of 0.58–0.82 V that is unaffected by other redox-active interferents. The linear quantification of pyocyanin has an R2 value of 0.991 across the clinically relevant concentration range of 2–100 µM. The proposed method was tested on human saliva showing a standard deviation of 2.5% ± 1% (n = 5) from the known added pyocyanin concentration to the samples. This inexpensive procedure is suggested for clinical use in monitoring the presence and state of P. aeruginosa infection in patients. PMID:27007376

  17. Fast Selective Detection of Pyocyanin Using Cyclic Voltammetry.

    PubMed

    Alatraktchi, Fatima AlZahra'a; Andersen, Sandra Breum; Johansen, Helle Krogh; Molin, Søren; Svendsen, Winnie E

    2016-03-19

    Pyocyanin is a virulence factor uniquely produced by the pathogen Pseudomonas aeruginosa. The fast and selective detection of pyocyanin in clinical samples can reveal important information about the presence of this microorganism in patients. Electrochemical sensing of the redox-active pyocyanin is a route to directly quantify pyocyanin in real time and in situ in hospitals and clinics. The selective quantification of pyocyanin is, however, limited by other redox-active compounds existing in human fluids and by other metabolites produced by pathogenic bacteria. Here we present a direct selective method to detect pyocyanin in a complex electroactive environment using commercially available electrodes. It is shown that cyclic voltammetry measurements between -1.0 V to 1.0 V reveal a potential detection window of pyocyanin of 0.58-0.82 V that is unaffected by other redox-active interferents. The linear quantification of pyocyanin has an R² value of 0.991 across the clinically relevant concentration range of 2-100 µM. The proposed method was tested on human saliva showing a standard deviation of 2.5% ± 1% (n = 5) from the known added pyocyanin concentration to the samples. This inexpensive procedure is suggested for clinical use in monitoring the presence and state of P. aeruginosa infection in patients.

  18. Robust online tracking via adaptive samples selection with saliency detection

    NASA Astrophysics Data System (ADS)

    Yan, Jia; Chen, Xi; Zhu, QiuPing

    2013-12-01

    Online tracking has shown to be successful in tracking of previously unknown objects. However, there are two important factors which lead to drift problem of online tracking, the one is how to select the exact labeled samples even when the target locations are inaccurate, and the other is how to handle the confusors which have similar features with the target. In this article, we propose a robust online tracking algorithm with adaptive samples selection based on saliency detection to overcome the drift problem. To deal with the problem of degrading the classifiers using mis-aligned samples, we introduce the saliency detection method to our tracking problem. Saliency maps and the strong classifiers are combined to extract the most correct positive samples. Our approach employs a simple yet saliency detection algorithm based on image spectral residual analysis. Furthermore, instead of using the random patches as the negative samples, we propose a reasonable selection criterion, in which both the saliency confidence and similarity are considered with the benefits that confusors in the surrounding background are incorporated into the classifiers update process before the drift occurs. The tracking task is formulated as a binary classification via online boosting framework. Experiment results in several challenging video sequences demonstrate the accuracy and stability of our tracker.

  19. A Novel Automatic Detection System for ECG Arrhythmias Using Maximum Margin Clustering with Immune Evolutionary Algorithm

    PubMed Central

    Zhu, Bohui; Ding, Yongsheng; Hao, Kuangrong

    2013-01-01

    This paper presents a novel maximum margin clustering method with immune evolution (IEMMC) for automatic diagnosis of electrocardiogram (ECG) arrhythmias. This diagnostic system consists of signal processing, feature extraction, and the IEMMC algorithm for clustering of ECG arrhythmias. First, raw ECG signal is processed by an adaptive ECG filter based on wavelet transforms, and waveform of the ECG signal is detected; then, features are extracted from ECG signal to cluster different types of arrhythmias by the IEMMC algorithm. Three types of performance evaluation indicators are used to assess the effect of the IEMMC method for ECG arrhythmias, such as sensitivity, specificity, and accuracy. Compared with K-means and iterSVR algorithms, the IEMMC algorithm reflects better performance not only in clustering result but also in terms of global search ability and convergence ability, which proves its effectiveness for the detection of ECG arrhythmias. PMID:23690875

  20. Interest area selection for navigation based on structured edge detection

    NASA Astrophysics Data System (ADS)

    Sun, Xiao; Shang, Ke; Li, ShaoJun; Dou, Hao; Tian, JinWen; Ming, Delie

    2015-12-01

    The scene matching based navigation is an important precision navigation technology for unmanned aerial vehicles (UAV). Selection of interest area where reference image is made has an important influence on the precision of matching result besides the performance of match algorithm. In this paper, a method to select interest area based on structured edge detection is proposed. We use a data driven approach that classifies each pixel with a typical structured edge label. We propose a method that combines these labels into a feature measuring suitable to match of a region. Then a SVM classifier is trained to classify the features and get the final result of the selection of interest area. The experimental result shows that the proposed method is valid and effective.

  1. Variable selection based cotton bollworm odor spectroscopic detection

    NASA Astrophysics Data System (ADS)

    Lü, Chengxu; Gai, Shasha; Luo, Min; Zhao, Bo

    2016-10-01

    Aiming at rapid automatic pest detection based efficient and targeting pesticide application and shooting the trouble of reflectance spectral signal covered and attenuated by the solid plant, the possibility of near infrared spectroscopy (NIRS) detection on cotton bollworm odor is studied. Three cotton bollworm odor samples and 3 blank air gas samples were prepared. Different concentrations of cotton bollworm odor were prepared by mixing the above gas samples, resulting a calibration group of 62 samples and a validation group of 31 samples. Spectral collection system includes light source, optical fiber, sample chamber, spectrometer. Spectra were pretreated by baseline correction, modeled with partial least squares (PLS), and optimized by genetic algorithm (GA) and competitive adaptive reweighted sampling (CARS). Minor counts differences are found among spectra of different cotton bollworm odor concentrations. PLS model of all the variables was built presenting RMSEV of 14 and RV2 of 0.89, its theory basis is insect volatilizes specific odor, including pheromone and allelochemics, which are used for intra-specific and inter-specific communication and could be detected by NIR spectroscopy. 28 sensitive variables are selected by GA, presenting the model performance of RMSEV of 14 and RV2 of 0.90. Comparably, 8 sensitive variables are selected by CARS, presenting the model performance of RMSEV of 13 and RV2 of 0.92. CARS model employs only 1.5% variables presenting smaller error than that of all variable. Odor gas based NIR technique shows the potential for cotton bollworm detection.

  2. Comparative Genomics Uncovers Unique Gene Turnover and Evolutionary Rates in a Gene Family Involved in the Detection of Insect Cuticular Pheromones

    PubMed Central

    Torres-Oliva, Montserrat; Almeida, Francisca C.; Sánchez-Gracia, Alejandro; Rozas, Julio

    2016-01-01

    Chemoreception is an essential process for the survival and reproduction of animals. Many of the proteins responsible for recognizing and transmitting chemical stimuli in insects are encoded by genes that are members of moderately sized multigene families. The members of the CheB family are specialized in gustatory-mediated detection of long-chain hydrocarbon pheromones in Drosophila melanogaster and play a central role in triggering and modulating mating behavior in this species. Here, we present a comprehensive comparative genomic analysis of the CheB family across 12 species of the Drosophila genus. We have identified a total of 102 new CheB genes in the genomes of these species, including a functionally divergent member previously uncharacterized in D. melanogaster. We found that, despite its relatively small repertory size, the CheB family has undergone multiple gain and loss events and various episodes of diversifying selection during the divergence of the surveyed species. Present estimates of gene turnover and coding sequence substitution rates show that this family is evolving faster than any known Drosophila chemosensory family. To date, only other insect gustatory-related genes among these families had shown evolutionary dynamics close to those observed in CheBs. Our findings reveal the high adaptive potential of molecular components of the gustatory system in insects and anticipate a key role of genes involved in this sensory modality in species adaptation and diversification.

  3. Frequency selective detection of nuclear quadrupole resonance (NQR) spin echoes

    NASA Astrophysics Data System (ADS)

    Somasundaram, Samuel D.; Jakobsson, Andreas; Smith, John A. S.; Althoefer, Kaspar A.

    2006-05-01

    Nuclear Quadrupole Resonance (NQR) is a radio frequency (RF) technique that can be used to detect the presence of quadrupolar nuclei, such as the 14N nucleus prevalent in many explosives and narcotics. The technique has been hampered by low signal-to-noise ratios and is further aggravated by the presence of RF interference (RFI). To ensure accurate detection, proposed detectors should exploit the rich form of the NQR signal. Furthermore, the detectors should also be robust to any remaining residual interference, left after suitable RFI mitigation has been employed. In this paper, we propose a new NQR data model, particularly for the realistic case where multiple pulse sequences are used to generate trains of spin echoes. Furthermore, we refine two recently proposed approximative maximum likelihood (AML) detectors, enabling the algorithm to optimally exploit the data model of the entire echo train and also incorporate knowledge of the temperature dependent spin-echo decay time. The AML-based detectors ensure accurate detection and robustness against residual RFI, even when the temperature of the sample is not precisely known, by exploiting the dependencies of the NQR resonant lines on temperature. Further robustness against residual interference is gained as the proposed detector is frequency selective; exploiting only those regions of the spectrum where the NQR signal is expected. Extensive numerical evaluations based on both simulated and measured NQR data indicate that the proposed Frequency selective Echo Train AML (FETAML) detector offers a significant improvement as compared to other existing detectors.

  4. The evolutionary history of Drosophila buzzatii. XXXIII. Are Opuntia hosts a selective factor for the inversion polymorphism?

    PubMed

    Fanara, J J; Hasson, E; Rodríguez, C; Santos, M; Fontdevila, A

    1996-11-01

    Previous work has shown fitness differences among chromosomal arrangements by means of selection component analysis in two Drosophila buzzatii natural populations, one of which is native to Argentina and the other a colonized population from Carboneras, Spain. Founder effects or niche shifts were proposed to explain the differences observed in the pattern of pleiotropic effects of inversions on fitness components. In this paper, we address the possible role of niche shifts by determining whether differential attraction to, oviposition on, or utilization of the rotting cladodes of two different Opuntia species (O. quimilo and O. ficus-indica) occurred among individuals carrying different second chromosome karyotypes in a natural Argentinian population. Through the analysis of more than 2500 individuals comprising five different life cycle stages associated with the necroses of these two cactus species, we found that the distributions of inversion frequencies in samples of adult flies, third instar larvae and emerging adults collected on both Opuntia species were not significantly different. Likewise, no evidence of differential oviposition was observed. These findings suggest that niche shifts cannot, solely, account for the changes observed in the Carboneras population. In addition, the selection component analysis did not reveal any significant relationship between chromosomal arrangements and the fitness components tested. These results suggest either that fitness differences might be too small to be detected or that the assumptions of the model concerning the mode of selection may not be tenable in the studied population.

  5. Multitemporal spectroscopy for crop stress detection using band selection methods

    NASA Astrophysics Data System (ADS)

    Mewes, Thorsten; Franke, Jonas; Menz, Gunter

    2008-08-01

    A fast and precise sensor-based identification of pathogen infestations in wheat stands is essential for the implementation of site-specific fungicide applications. Several works have shown possibilities and limitations for the detection of plant stress using spectral sensor data. Hyperspectral data provide the opportunity to collect spectral reflectance in contiguous bands over a broad range of the electromagnetic spectrum. Individual phenomena like the light absorption of leaf pigments can be examined in detail. The precise knowledge of stress-dependent shifting in certain spectral wavelengths provides great advantages in detecting fungal infections. This study focuses on band selection techniques for hyperspectral data to identify relevant and redundant information in spectra regarding a detection of plant stress caused by pathogens. In a laboratory experiment, five 1 sqm boxes with wheat were multitemporarily measured by a ASD Fieldspec® 3 FR spectroradiometer. Two stands were inoculated with Blumeria graminis - the pathogen causing powdery mildew - and one stand was used to simulate the effect of water deficiency. Two stands were kept healthy as control stands. Daily measurements of the spectral reflectance were taken over a 14-day period. Three ASD Pro Lamps were used to illuminate the plots with constant light. By applying band selection techniques, the three types of different wheat vitality could be accurately differentiated at certain stages. Hyperspectral data can provide precise information about pathogen infestations. The reduction of the spectral dimension of sensor data by means of band selection procedures is an appropriate method to speed up the data supply for precision agriculture.

  6. Bayesian analysis. II. Signal detection and model selection

    NASA Astrophysics Data System (ADS)

    Bretthorst, G. Larry

    In the preceding. paper, Bayesian analysis was applied to the parameter estimation problem, given quadrature NMR data. Here Bayesian analysis is extended to the problem of selecting the model which is most probable in view of the data and all the prior information. In addition to the analytic calculation, two examples are given. The first example demonstrates how to use Bayesian probability theory to detect small signals in noise. The second example uses Bayesian probability theory to compute the probability of the number of decaying exponentials in simulated T1 data. The Bayesian answer to this question is essentially a microcosm of the scientific method and a quantitative statement of Ockham's razor: theorize about possible models, compare these to experiment, and select the simplest model that "best" fits the data.

  7. Element Selective X-ray Detected Magnetic Resonance

    SciTech Connect

    Goulon, J.; Rogalev, A.; Wilhelm, F.; Jaouen, N.; Goulon-Ginet, C.; Goujon, G.; Youssef, J. Ben; Indenbom, M. V.

    2007-01-19

    Element selective X-ray Detected Magnetic Resonance (XDMR) was measured on exciting the Fe K-edge in a high quality YIG thin film. Resonant pumping at high microwave power was achieved in the nonlinear foldover regime and X-ray Magnetic Circular Dichroism (XMCD) was used to probe the time-invariant change of the magnetization {delta}Mz due to the precession of orbital magnetization densities of states (DOS) at the Fe sites. This challenging experiment required us to design a specific instrumentation which is briefly described.

  8. Method for detection of selected chemicals in an open environment

    NASA Technical Reports Server (NTRS)

    Duong, Tuan (Inventor); Ryan, Margaret (Inventor)

    2009-01-01

    The present invention relates to a space-invariant independent component analysis and electronic nose for detection of selective chemicals in an unknown environment, and more specifically, an approach to analysis of sensor responses to mixtures of unknown chemicals by an electronic nose in an open and changing environment. It is intended to fill the gap between an alarm, which has little or no ability to distinguish among chemical compounds causing a response, and an analytical instrument, which can distinguish all compounds present but with no real-time or continuous event monitoring ability.

  9. Detecting non-coding selective pressure in coding regions

    PubMed Central

    Chen, Hui; Blanchette, Mathieu

    2007-01-01

    Background Comparative genomics approaches, where orthologous DNA regions are compared and inter-species conserved regions are identified, have proven extremely powerful for identifying non-coding regulatory regions located in intergenic or intronic regions. However, non-coding functional elements can also be located within coding region, as is common for exonic splicing enhancers, some transcription factor binding sites, and RNA secondary structure elements affecting mRNA stability, localization, or translation. Since these functional elements are located in regions that are themselves highly conserved because they are coding for a protein, they generally escaped detection by comparative genomics approaches. Results We introduce a comparative genomics approach for detecting non-coding functional elements located within coding regions. Codon evolution is modeled as a mixture of codon substitution models, where each component of the mixture describes the evolution of codons under a specific type of coding selective pressure. We show how to compute the posterior distribution of the entropy and parsimony scores under this null model of codon evolution. The method is applied to a set of growth hormone 1 orthologous mRNA sequences and a known exonic splicing elements is detected. The analysis of a set of CORTBP2 orthologous genes reveals a region of several hundred base pairs under strong non-coding selective pressure whose function remains unknown. Conclusion Non-coding functional elements, in particular those involved in post-transcriptional regulation, are likely to be much more prevalent than is currently known. With the numerous genome sequencing projects underway, comparative genomics approaches like that proposed here are likely to become increasingly powerful at detecting such elements. PMID:17288582

  10. A review on Monte Carlo simulation methods as they apply to mutation and selection as formulated in Wright-Fisher models of evolutionary genetics.

    PubMed

    Mode, Charles J; Gallop, Robert J

    2008-02-01

    A case has made for the use of Monte Carlo simulation methods when the incorporation of mutation and natural selection into Wright-Fisher gametic sampling models renders then intractable from the standpoint of classical mathematical analysis. The paper has been organized around five themes. Among these themes was that of scientific openness and a clear documentation of the mathematics underlying the software so that the results of any Monte Carlo simulation experiment may be duplicated by any interested investigator in a programming language of his choice. A second theme was the disclosure of the random number generator used in the experiments to provide critical insights as to whether the generated uniform random variables met the criterion of independence satisfactorily. A third theme was that of a review of recent literature in genetics on attempts to find signatures of evolutionary processes such as natural selection, among the millions of segments of DNA in the human genome, that may help guide the search for new drugs to treat diseases. A fourth theme involved formalization of Wright-Fisher processes in a simple form that expedited the writing of software to run Monte Carlo simulation experiments. Also included in this theme was the reporting of several illustrative Monte Carlo simulation experiments for the cases of two and three alleles at some autosomal locus, in which attempts were to made to apply the theory of Wright-Fisher models to gain some understanding as to how evolutionary signatures may have developed in the human genome and those of other diploid species. A fifth theme was centered on recommendations that more demographic factors, such as non-constant population size, be included in future attempts to develop computer models dealing with signatures of evolutionary process in genomes of various species. A brief review of literature on the incorporation of demographic factors into genetic evolutionary models was also included to expedite and

  11. Evolutionary novelties.

    PubMed

    Wagner, Günter P; Lynch, Vincent J

    2010-01-26

    How novel traits arise in organisms has long been a major problem in biology. Indeed, the sharpest critiques of Darwin's theory of evolution by natural selection often centered on explaining how novel body parts arose. In his response to The Origin of Species, St. George J. Mivart challenged Darwin to explain the origin of evolutionary novelties such as the mammary gland, asking if it was "conceivable that the young of any animal was ever saved from destruction by accidentally sucking a drop of scarcely nutritious fluid from an accidentally hypertrophied cutaneous gland of its mother?" It is only now that modern molecular and genomic tools are being brought to bear on this question that we are finally in a position to answer Mivart's challenge and explain one of the most fundamental questions of biology: how does novelty arise in evolution?

  12. Bayesian Variable Selection for Detecting Adaptive Genomic Differences Among Populations

    PubMed Central

    Riebler, Andrea; Held, Leonhard; Stephan, Wolfgang

    2008-01-01

    We extend an Fst-based Bayesian hierarchical model, implemented via Markov chain Monte Carlo, for the detection of loci that might be subject to positive selection. This model divides the Fst-influencing factors into locus-specific effects, population-specific effects, and effects that are specific for the locus in combination with the population. We introduce a Bayesian auxiliary variable for each locus effect to automatically select nonneutral locus effects. As a by-product, the efficiency of the original approach is improved by using a reparameterization of the model. The statistical power of the extended algorithm is assessed with simulated data sets from a Wright–Fisher model with migration. We find that the inclusion of model selection suggests a clear improvement in discrimination as measured by the area under the receiver operating characteristic (ROC) curve. Additionally, we illustrate and discuss the quality of the newly developed method on the basis of an allozyme data set of the fruit fly Drosophila melanogaster and a sequence data set of the wild tomato Solanum chilense. For data sets with small sample sizes, high mutation rates, and/or long sequences, however, methods based on nucleotide statistics should be preferred. PMID:18245358

  13. Selective detection and quantification of carbon nanotubes in soil.

    PubMed

    Jeong, Junhoe; Lee, Yong-ju; Hwang, Yu sik; Hong, In Seok

    2015-09-01

    Carbon nanotubes (CNTs) have been widely applied in many industrial fields. As world production of CNTs increases, the risk of environmental exposure to CNTs also increases. Therefore, to evaluate the impact on the environment, many cell and animal studies have reported on the toxicity of CNTs. It is important to determine the degree of contamination of CNTs in soil and to find the pollution pathways for assessment of the environmental toxicity of CNTs. However, selective detection methods for CNTs in soil or water have rarely been reported. In the present study, a novel technique was developed to quantify the amount of CNTs in soil mixtures using fluorescent SYBR Green I dye after isolation of the CNTs with specific DNA oligomers. As a result, a limit of detection of CNTs in soil was obtained in the range of 250 ppb. This limit can easily be extended to the level of 10 ppb using magnetic well plates with a greater capacity. This method also worked well in the presence of graphene oxide and could be applied to the detection of CNTs in a variety of surroundings (e.g., fish and other tissues).

  14. Selective Detection of Neurotransmitters by Fluorescence and Chemiluminescence Imaging

    SciTech Connect

    Ziqiang Wang; Edward S. Yeung

    2001-08-06

    In recent years, luminescence imaging has been widely employed in neurochemical analysis. It has a number of advantages for the study of neuronal and other biological cells: (1) a particular molecular species or cellular constituent can be selectively visualized in the presence of a large excess of other species in a heterogeneous environment; (2) low concentration detection limits can be achieved because of the inherent sensitivity associated with fluorescence and chemiluminescence; (3) low excitation intensities can be used so that long-term observation can be realized while the viability of the specimen is preserved; and (4) excellent spatial resolution can be obtained with the light microscope so subcellular compartments can be identified. With good sensitivity, temporal and spatial resolution, the flux of ions and molecules and the distribution and dynamics of intracellular species can be measured in real time with specific luminescence probes, substrates, or with native fluorescence. A noninvasive detection scheme based on glutamate dehydrogenase (GDH) enzymatic assay combined with microscopy was developed to measure the glutamate release in cultured cells from the central nervous system (CNS). The enzyme reaction is very specific and sensitive. The detection limit with CCD imaging is down to {micro}M levels of glutamate with reasonable response time. They also found that chemiluminescence associated with the ATP-dependent reaction between luciferase and luciferin can be used to image ATP at levels down to 10 nM in the millisecond time scale. Similar imaging experiments should be feasible in a broad spectrum of biological systems.

  15. Evolutionary process of Bos taurus cattle in favourable versus unfavourable environments and its implications for genetic selection

    PubMed Central

    O'Neill, Christopher J; Swain, David L; Kadarmideen, Haja N

    2010-01-01

    The evolutionary processes that have enabled Bos taurus cattle to establish around the globe are at the core to the future success of livestock production. Our study focuses on the history of cattle domestication including the last 60 years of B. taurus breeding programmes in both favourable and unfavourable environments and its consequences on evolution and fitness of cattle. We discuss the emergence of ‘production diseases’ in temperate production systems and consider the evolutionary genetics of tropical adaptation in cattle and conclude that the Senepol, N'Dama, Adaptaur and Criollo breeds, among others with similar evolutionary trajectories, would possess genes capable of improving the productivity of cattle in challenging environments. Using our own experimental evidence from northern Australia, we review the evolution of the Adaptaur cattle breed which has become resistant to cattle tick. We emphasize that the knowledge of interactions between genotype, environment and management in the livestock systems will be required to generate genotypes for efficient livestock production that are both economically and environmentally sustainable. Livestock producers in the 21st century will have less reliance on infrastructure and veterinary products to alleviate environmental stress and more on the animal's ability to achieve fitness in a given production environment. PMID:25567936

  16. Impact of informative band selection on target detection performance

    NASA Astrophysics Data System (ADS)

    Gholizadeh, Hamed; Valadan Zoej, Mohammad Javad; Mojaradi, Barat

    2011-11-01

    In this paper, the effect of dimensionality reduction of hyperspectral data on 10 subpixel target detectors is investigated. The genetic algorithm (GA) and wavelet feature extraction methods are used for dimensionality reduction as they maintain physically meaningful bands and physical structure of the spectra, respectively. In the former case, the wrapper method is used to improve subpixel target detectors' results in terms of the area under the curve (AUC) of the receiver operating characteristic (ROC) curve. Meanwhile, in the latter case, the AUC is used as a criterion to choose the optimum level of wavelet decomposition. Experimental results obtained from a real-world hyperspectral data and a challenging synthetic dataset approved that band selection with the wrapper method is more efficient than using target detection methods without dimensionality reduction, especially in the presence of difficult targets at subpixel level.

  17. Statistical feature selection for enhanced detection of brain tumor

    NASA Astrophysics Data System (ADS)

    Chaddad, Ahmad; Colen, Rivka R.

    2014-09-01

    Feature-based methods are widely used in the brain tumor recognition system. Robust of early cancer detection is one of the most powerful image processing tools. Specifically, statistical features, such as geometric mean, harmonic mean, mean excluding outliers, median, percentiles, skewness and kurtosis, have been extracted from brain tumor glioma to aid in discriminating two levels namely, Level I and Level II using fluid attenuated inversion recovery (FLAIR) sequence in the diagnosis of brain tumor. Statistical feature describes the major characteristics of each level from glioma which is an important step to evaluate heterogeneity of cancer area pixels. In this paper, we address the task of feature selection to identify the relevant subset of features in the statistical domain, while discarding those that are either redundant or confusing, thereby improving the performance of feature-based scheme to distinguish between Level I and Level II. We apply a Decision Structure algorithm to find the optimal combination of nonhomogeneity based statistical features for the problem at hand. We employ a Naïve Bayes classifier to evaluate the performance of the optimal statistical feature based scheme in terms of its glioma Level I and Level II discrimination capability and use real-data collected from 17 patients have a glioblastoma multiforme (GBM). Dataset provided from 3 Tesla MR imaging system by MD Anderson Cancer Center. For the specific data analyzed, it is shown that the identified dominant features yield higher classification accuracy, with lower number of false alarms and missed detections, compared to the full statistical based feature set. This work has been proposed and analyzed specific GBM types which Level I and Level II and the dominant features were considered as feature aid to prognostic indicators. These features were selected automatically to be better able to determine prognosis from classical imaging studies.

  18. Selective detection of Escherichia coli DNA using fluorescent carbon spindles.

    PubMed

    Roy, Anurag; Chatterjee, Sabyasachi; Pramanik, Srikrishna; Devi, Parukuttyamma Sujatha; Suresh Kumar, Gopinatha

    2016-04-28

    We investigate the interaction of hydrophilic blue emitting carbon spindles with various deoxyribonucleic acids (DNA) having different base pair compositions, such as Herring testes (HT), calf thymus (CT), Escherichia coli (EC) and Micrococcus lysodeikticus (ML) DNA, to understand the mode of interaction. Interestingly, the fluorescent carbon spindles selectively interacted with E. coli DNA resulting in enhanced fluorescence of the former. Interaction of the same carbon with other DNAs exhibited insignificant changes in fluorescence. In addition, in the presence of EC DNA, the D band in the Raman spectrum attributed to the defect state completely disappeared, resulting in enhanced crystallinity. Microscopy images confirmed the wrapping of DNA on the carbon spindles leading to the assembly of spindles in the form of flowers. Dissociation of double-stranded DNA occurred upon interaction with carbon spindles, resulting in selective E. coli DNA interaction. The carbon spindles also exhibited a similar fluorescence enhancement upon treating with E. coli bacteria. These results confirm the possibility of E. coli detection in water and other liquid foods using such fluorescent carbon.

  19. Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae.

    PubMed

    Zhao, Lei; Zhang, Ning; Ma, Peng-Fei; Liu, Qi; Li, De-Zhu; Guo, Zhen-Hua

    2013-01-01

    BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family.

  20. Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae

    PubMed Central

    Zhao, Lei; Zhang, Ning; Ma, Peng-Fei; Liu, Qi; Li, De-Zhu; Guo, Zhen-Hua

    2013-01-01

    BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family. PMID:23734211

  1. Evolutionary Fingerprinting of Genes

    PubMed Central

    Kosakovsky Pond, Sergei L.; Scheffler, Konrad; Gravenor, Michael B.; Poon, Art F.Y.; Frost, Simon D.W.

    2010-01-01

    Over time, natural selection molds every gene into a unique mosaic of sites evolving rapidly or resisting change—an “evolutionary fingerprint” of the gene. Aspects of this evolutionary fingerprint, such as the site-specific ratio of nonsynonymous to synonymous substitution rates (dN/dS), are commonly used to identify genetic features of potential biological interest; however, no framework exists for comparing evolutionary fingerprints between genes. We hypothesize that protein-coding genes with similar protein structure and/or function tend to have similar evolutionary fingerprints and that comparing evolutionary fingerprints can be useful for discovering similarities between genes in a way that is analogous to, but independent of, discovery of similarity via sequence-based comparison tools such as Blast. To test this hypothesis, we develop a novel model of coding sequence evolution that uses a general bivariate discrete parameterization of the evolutionary rates. We show that this approach provides a better fit to the data using a smaller number of parameters than existing models. Next, we use the model to represent evolutionary fingerprints as probability distributions and present a methodology for comparing these distributions in a way that is robust against variations in data set size and divergence. Finally, using sequences of three rapidly evolving RNA viruses (HIV-1, hepatitis C virus, and influenza A virus), we demonstrate that genes within the same functional group tend to have similar evolutionary fingerprints. Our framework provides a sound statistical foundation for efficient inference and comparison of evolutionary rate patterns in arbitrary collections of gene alignments, clustering homologous and nonhomologous genes, and investigation of biological and functional correlates of evolutionary rates. PMID:19864470

  2. Genomic resources and their influence on the detection of the signal of positive selection in genome scans.

    PubMed

    Manel, S; Perrier, C; Pratlong, M; Abi-Rached, L; Paganini, J; Pontarotti, P; Aurelle, D

    2016-01-01

    Genome scans represent powerful approaches to investigate the action of natural selection on the genetic variation of natural populations and to better understand local adaptation. This is very useful, for example, in the field of conservation biology and evolutionary biology. Thanks to Next Generation Sequencing, genomic resources are growing exponentially, improving genome scan analyses in non-model species. Thousands of SNPs called using Reduced Representation Sequencing are increasingly used in genome scans. Besides, genome sequences are also becoming increasingly available, allowing better processing of short-read data, offering physical localization of variants, and improving haplotype reconstruction and data imputation. Ultimately, genome sequences are also becoming the raw material for selection inferences. Here, we discuss how the increasing availability of such genomic resources, notably genome sequences, influences the detection of signals of selection. Mainly, increasing data density and having the information of physical linkage data expand genome scans by (i) improving the overall quality of the data, (ii) helping the reconstruction of demographic history for the population studied to decrease false-positive rates and (iii) improving the statistical power of methods to detect the signal of selection. Of particular importance, the availability of a high-quality reference genome can improve the detection of the signal of selection by (i) allowing matching the potential candidate loci to linked coding regions under selection, (ii) rapidly moving the investigation to the gene and function and (iii) ensuring that the highly variable regions of the genomes that include functional genes are also investigated. For all those reasons, using reference genomes in genome scan analyses is highly recommended.

  3. Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs)

    PubMed Central

    2015-01-01

    Background Over the past 50,000 years, shifts in human-environmental or human-human interactions shaped genetic differences within and among human populations, including variants under positive selection. Shaped by environmental factors, such variants influence the genetics of modern health, disease, and treatment outcome. Because evolutionary processes tend to act on gene regulation, we test whether regulatory variants are under positive selection. We introduce a new approach to enhance detection of genetic markers undergoing positive selection, using conditional entropy to capture recent local selection signals. Results We use conditional logistic regression to compare our Adjusted Haplotype Conditional Entropy (H|H) measure of positive selection to existing positive selection measures. H|H and existing measures were applied to published regulatory variants acting in cis (cis-eQTLs), with conditional logistic regression testing whether regulatory variants undergo stronger positive selection than the surrounding gene. These cis-eQTLs were drawn from six independent studies of genotype and RNA expression. The conditional logistic regression shows that, overall, H|H is substantially more powerful than existing positive-selection methods in identifying cis-eQTLs against other Single Nucleotide Polymorphisms (SNPs) in the same genes. When broken down by Gene Ontology, H|H predictions are particularly strong in some biological process categories, where regulatory variants are under strong positive selection compared to the bulk of the gene, distinct from those GO categories under overall positive selection. . However, cis-eQTLs in a second group of genes lack positive selection signatures detectable by H|H, consistent with ancient short haplotypes compared to the surrounding gene (for example, in innate immunity GO:0042742); under such other modes of selection, H|H would not be expected to be a strong predictor.. These conditional logistic regression models are

  4. Selective ciprofloxacin antibiotic detection by fluorescent siderophore pyoverdin.

    PubMed

    Pawar, Madhuri K; Tayade, Kundan C; Sahoo, Suban K; Mahulikar, Pramod P; Kuwar, Anil S; Chaudhari, Bhushan L

    2016-07-15

    Fluorescent siderophore pyoverdin (PVD) was produced from a soil isolate Pseudomonas monteilii strain MKP 213. The PVD was purified near to homogeneity and applied for the fluorescent chemosensing of various antibiotics in aqueous solution (pH=7.0). Upon addition of ciprofloxacin, PVD showed new UV-vis absorption bands at 252 and 321nm due to an internal charge transfer mechanism. Also, the addition of ciprofloxacin induced a highly selective fluorescence enhancement of PVD with a 13nm blue shift from 458 to 445nm. The combination of a long peptide chain along with the chromophore unit of PVD generates a converging cleft for ciprofloxacin recognition with LOD and LOQ of 7.13μM and 21.6μM, respectively without interference from other studied antibiotics. The association constant (Ka) of PVD with ciprofloxacin was calculated to be as low as 1.40×10(5)M(-1) using Benesi-Hildebrand plot depicting its significance in detection. The pharmaceutical tablet analysis measures the sensing with negligible matrix effect and quantitative recovery.

  5. Detection of selective antibacterial peptides by the Polarity Profile method.

    PubMed

    Polanco, Carlos; Buhse, Thomas; Samaniego, José Lino; Castañón-González, Jorge Alberto

    2013-01-01

    Antimicrobial peptides occupy a prominent place in the production of pharmaceuticals, because of their effective contribution to the protection of the immune system against almost all types of pathogens. These peptides are thoroughly studied by computational methods designed to shed light on their main functions. In this paper, we propose a computational approach, named the Polarity Profile method that represents an improvement to the former Polarity Index method. The Polarity Profile method is very effective in detecting the subgroup of antibacterial peptides called selective cationic amphipathic antibacterial peptides (SCAAP) that show high toxicity towards bacterial membranes and exhibit almost zero toxicity towards mammalian cells. Our study was restricted to the peptides listed in the antimicrobial peptides database (APD2) of December 19, 2012. Performance of the Polarity Profile method is demonstrated through a comparison to the former Polarity Index method by using the same sets of peptides. The efficiency of the Polarity Profile method exceeds 85% taking into account the false positive and/or false negative peptides.

  6. Spectroscopic detection of metals ions using a novel selective sensor

    NASA Astrophysics Data System (ADS)

    Peralta-Domínguez, D.; Ramos-Ortiz, G.; Maldonado, J. L.; Rodriguez, M.; Meneses-Nava, M. A.; Barbosa-Garcia, O.; Santillan, R.; Farfan, N.

    2011-09-01

    Colorimetric chemosensors are simple, economical and practical optical approach for detecting toxic metal ions (Hg2+, Pb2+, Ni2+, etc.) in the environment. In this work, we present a simple but highly specific organic compound 4-chloro-2-((E)-((E)-3-(4-(dimethylamino)phenyl)allylidene)amino)phenol (L1) that acts as a colorimetric sensor for divalent metal ions in H2O. The mechanism of the interaction between L1 and various metal-ions has been established by UV-vis absorption and emission spectroscopic experiments that indicate favorable coordination of metal ions with L1 in different solvents. Experimental results indicate that the shape of the electronic transition band of L1 (receptor compound) changed after the interaction with divalent metal-ions, such as Hg2+, Pb2+, Mn2+, Co2+, Cu2+, and Ni2+ in aqueous solution. We found that L1 have a considerable selectivity for Ni2+ ions, even in presence of other metals ions when mixtures of DMSO/H2O as are used as solvents. L1, which has been targeted for sensing transition metal ions, exhibits binding-induced color changes from yellow to pink observed even by the naked eye in presence of Ni2+ ions.

  7. The evolutionary analysis on complement genes reveals that fishes C3 and C9 experience different evolutionary patterns.

    PubMed

    Wang, Shanchen; Wang, Rixin; Xu, Tianjun

    2013-12-01

    Complement is a humoral factor of innate immunity and plays an essential role in altering the host of the presence of potential pathogens and clearing of invading microorganisms. The third complement component (C3) not only is regarded as the crossing of the three pathways of complement activation, but also serves one of the bridges linking innate and acquired immunity. The nine complement component (C9) can combine with C5b, C6, C7 and C8 to form MAC which bounds to the surface of microorganisms to kill them. The evidence of evolution on C3 genes which have multiple functions and plays central role in innate immunity was documented in our previous study. Now we were interested in the evolution of C9 genes which were the terminal complement components. For these reasons, we want to explore the evolutionary patterns of C9 and whether C3 and C9 experience different evolutionary patterns. In our study, we used the sliding window method to separately calculate the values of ω among fishes and mammals of C3 and C9 codons. In order to detect the positive selection sites, we used the maximum likelihood (ML) method to study the evolutionary pattern on C3 and C9 genes. Positive selection sites were detected in mammalian C9 genes and no positive selection sites were detected in fishes C9 genes. However, no positive selection sites were detected in mammalian C3 genes and positive selection sites were detected in fishes C3 genes. The result indicated that C3 and C9 had different evolutionary patterns on mammals and fishes. In conclusion, different living environments lead to different evolutionary patterns on C3 and C9 in mammals and fishes. Besides, different complement components may have different evolutionary patterns on mammals and fishes.

  8. Evolutionary consequences of fishing and their implications for salmon

    PubMed Central

    Hard, Jeffrey J; Gross, Mart R; Heino, Mikko; Hilborn, Ray; Kope, Robert G; Law, Richard; Reynolds, John D

    2008-01-01

    We review the evidence for fisheries-induced evolution in anadromous salmonids. Salmon are exposed to a variety of fishing gears and intensities as immature or maturing individuals. We evaluate the evidence that fishing is causing evolutionary changes to traits including body size, migration timing and age of maturation, and we discuss the implications for fisheries and conservation. Few studies have fully evaluated the ingredients of fisheries-induced evolution: selection intensity, genetic variability, correlation among traits under selection, and response to selection. Most studies are limited in their ability to separate genetic responses from phenotypic plasticity, and environmental change complicates interpretation. However, strong evidence for selection intensity and for genetic variability in salmon fitness traits indicates that fishing can cause detectable evolution within ten or fewer generations. Evolutionary issues are therefore meaningful considerations in salmon fishery management. Evolutionary biologists have rarely been involved in the development of salmon fishing policy, yet evolutionary biology is relevant to the long-term success of fisheries. Future management might consider fishing policy to (i) allow experimental testing of evolutionary responses to exploitation and (ii) improve the long-term sustainability of the fishery by mitigating unfavorable evolutionary responses to fishing. We provide suggestions for how this might be done. PMID:25567639

  9. Feature Extraction and Selection From the Perspective of Explosive Detection

    SciTech Connect

    Sengupta, S K

    2009-09-01

    -dimensional attenuation images with a voxel resolution of the order of one quarter of a milimeter. In the task of feature extraction and subsequent selection of an appropriate subset thereof, several important factors need to be considered. Foremost among them are: (1) Definition of the sampling unit from which the features will be extracted for the purpose of detection/ identification of the explosives. (2) The choice of features ( given the sampling unit) to be extracted that can be used to signal the existence / identity of the explosive. (3) Robustness of the computed features under different inspection conditions. To attain robustness, invariance under the transformations of translation, scaling, rotation and change of orientation is highly desirable. (4) The computational costs in the process of feature extraction, selection and their use in explosive detection/ identification In the search for extractable features, we have done a thorough literature survey with the above factors in mind and come out with a list of features that could possibly help us in meeting our objective. We are assuming that features will be based on sampling units that are single CT slices of the target. This may however change when appropriate modifications should be made to the feature extraction process. We indicate below some of the major types of features in 2- or 3-dimensional images that have been used in the literature on application of pattern recognition (PR) techniques in image understanding and are possibly pertinent to our study. In the following paragraph, we briefly indicate the motivation that guided us in the choice of these features, and identify the nature of the constraints. The principal feature types derivable from an image will be discussed in section 2. Once the features are extracted, one must select a subset of this feature set that will retain the most useful information and remove any redundant and irrelevant information that may have a detrimental effect on the

  10. Evolutionary Consequences of Male Driven Sexual Selection and Sex-Biased Fitness Modifications in Drosophila melanogaster and Members of the simulans Clade

    PubMed Central

    Jagadeeshan, Santosh; Haerty, Wilfried; Moglinicka, Monika; Ahuja, Abha; De Vito, Scot; Singh, Rama S.

    2015-01-01

    Males have evolved a variety of behavioral, morphological, and physiological traits to manipulate their mates in order to maximize their chances of success. These traits are bound to influence how females respond to male behaviors and influence the nature of sexual selection/conflict. A common consequence of aggressive male mating strategies in Drosophila melanogaster is the reduction of female lifespan. Our study shows that this is common across members of the simulans clade. Reduced life expectancy of females implies that female contribution to a population is less than that of males per generation. Fitness differences between the sexes in every generation will invariably affect overall population fitness. How natural selection responds to the female deaths and thereby the unequal fitness of the sexes has rarely been addressed. We shed light on this issue and provide evidence, which suggests that additional gains of fitness by males due to their longevity and continued mating may provide one explanation as to why the loss of female fitness may be “invisible” (effectively neutral) to natural selection. Male driven sexual selection and additional, transgenerational gains of male fitness can be an important force of evolutionary change and need to be tested with other organisms. PMID:26421208

  11. Contrasting evolutionary histories of MHC class I and class II loci in grouse--effects of selection and gene conversion.

    PubMed

    Minias, P; Bateson, Z W; Whittingham, L A; Johnson, J A; Oyler-McCance, S; Dunn, P O

    2016-05-01

    Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens.

  12. Contrasting evolutionary histories of MHC class I and class II loci in grouse—Effects of selection and gene conversion

    USGS Publications Warehouse

    Minias, Piotr; Bateson, Zachary W; Whittingham, Linda A; Johnson, Jeff A.; Oyler-McCance, Sara J.; Dunn, Peter O

    2016-01-01

    Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens.

  13. Evolutionary response to selection on clutch size in a long-term study of the mute swan.

    PubMed

    Charmantier, Anne; Perrins, Christopher; McCleery, Robin H; Sheldon, Ben C

    2006-03-01

    Life-history traits in wild populations are often regarded as being subject to directional selection, and the existence of substantial variation and microevolutionary stasis of these characters is therefore a problem in need of explanation. Avian clutch size is an archetypal life-history trait in this context, and many studies have sought to test explanations for stasis in clutch size. Surprisingly, there are many fewer studies that used long-term data to ask how selection acts on clutch size, particularly in a multivariate framework. In this article, we report selection, inheritance, and evolution of clutch size over 25 years in a colony of mute swans using a multivariate quantitative genetic framework to control for correlations with breeding time. We show that clutch size is influenced by both additive genetic and permanent environmental effects and that selection acts on clutch size in combination with breeding time. Natural selection on clutch size is strongly directional, favoring larger clutches, and we observe an increase in clutch size of 0.35 standard deviations, consistent with the expected response based on selection and inheritance of clutch size. We hypothesize that these changes result from recent relaxation of food constraints and predation risks experienced by this colony.

  14. SNP Detection from De Novo Transcriptome Sequencing in the Bivalve Macoma balthica: Marker Development for Evolutionary Studies

    PubMed Central

    Becquet, Vanessa; Belkhir, Khalid; Bierne, Nicolas; Garcia, Pascale

    2012-01-01

    Hybrid zones are noteworthy systems for the study of environmental adaptation to fast-changing environments, as they constitute reservoirs of polymorphism and are key to the maintenance of biodiversity. They can move in relation to climate fluctuations, as temperature can affect both selection and migration, or remain trapped by environmental and physical barriers. There is therefore a very strong incentive to study the dynamics of hybrid zones subjected to climate variations. The infaunal bivalve Macoma balthica emerges as a noteworthy model species, as divergent lineages hybridize, and its native NE Atlantic range is currently contracting to the North. To investigate the dynamics and functioning of hybrid zones in M. balthica, we developed new molecular markers by sequencing the collective transcriptome of 30 individuals. Ten individuals were pooled for each of the three populations sampled at the margins of two hybrid zones. A single 454 run generated 277 Mb from which 17K SNPs were detected. SNP density averaged 1 polymorphic site every 14 to 19 bases, for mitochondrial and nuclear loci, respectively. An scan detected high genetic divergence among several hundred SNPs, some of them involved in energetic metabolism, cellular respiration and physiological stress. The high population differentiation, recorded for nuclear-encoded ATP synthase and NADH dehydrogenase as well as most mitochondrial loci, suggests cytonuclear genetic incompatibilities. Results from this study will help pave the way to a high-resolution study of hybrid zone dynamics in M. balthica, and the relative importance of endogenous and exogenous barriers to gene flow in this system. PMID:23300636

  15. Evolutionary thinking

    PubMed Central

    Hunt, Tam

    2014-01-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps’ book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging “integral” or “evolutionary” cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps. PMID:26478766

  16. Plastic scintillators modifications for a selective radiation detection

    SciTech Connect

    Hamel, Matthieu; Bertrand, Guillaume H.V.; Carrel, Frederick; Coulon, Romain; Dumazert, Jonathan; Montbarbon, Eva; Sguerra, Fabien

    2015-07-01

    Recent developments of plastic scintillators are reviewed, from January 2000 to June 2015. All examples are distributed into the main application, i.e. how the plastic scintillator was modified to enhance the detection towards a given radiation particle. The main characteristics of these newly created scintillators and their detection properties are given. (authors)

  17. Contaminant detection on poultry carcasses using hyperspectral data: Part I. Algorithms for selection of individual wavebands

    NASA Astrophysics Data System (ADS)

    Nakariyakul, Songyot; Casasent, David P.

    2007-09-01

    Contaminant detection on chicken carcasses is an important product inspection application. The four contaminant types of interest contain three types of feces from different gastrointestinal regions (duodenum, ceca, and colon) and ingesta (undigested food) from the gizzard. Use of automated or semi-automated inspection systems for detecting fecal contaminant regions is of great interest. Hyperspectral data provided by ARS (Athens, GA) were used to examine detection of contaminants on carcasses. We address quasi-optimal algorithms for selecting a set of spectral bands (wavelengths) in hyperspectral data for on-line contaminant detection (feature selection). We introduce our new improved forward floating selection (IFFS) algorithm and compare its performance to that of other state-of-the-art feature selection algorithms. Our initial results indicate that our method gives an excellent detection rate and performs better than other feature selection algorithms. We also show that combination feature selection algorithms perform worse.

  18. Evolutionary screening and adsorption behavior of engineered M13 bacteriophage and derived dodecapeptide for selective decoration of gold interfaces.

    PubMed

    Causa, F; Della Moglie, R; Iaccino, E; Mimmi, S; Marasco, D; Scognamiglio, P L; Battista, E; Palmieri, C; Cosenza, C; Sanguigno, L; Quinto, I; Scala, G; Netti, P A

    2013-01-01

    There is a growing interest in identifying biomacromolecules such as proteins and peptides to functionalize metallic surfaces through noncovalent binding. One method for functionalizing materials without fundamentally changing their inherent structure is using biorecognition moieties. Here, we proved a general route to select a biomolecule adhesive motif for surface functionalization by comprehensively screening phage displayed peptides. In particular, we selected a genetically engineered M13 bacteriophage and a linear dodecapeptide derived from its pIII domain for recognizing gold surfaces in a specific and selective manner. In the phage context, we demonstrated the adhesive motif was capable to adsorb on gold in a preferential way with a morphological and viscoelastic signature of the adsorbed layer as evidenced by QCM-D and AFM investigations. Out of the phage context, the linear dodecapeptide is reproducibly found to adhere to the gold surface, and by quantitative SPR measurements, high affinity constants (K(eq)~10(6)M(-1), binding energy ~-8 kcal/mol) were determined. We proved that the interactions occurring at gold interface were mainly hydrophobic as a consequence of high frequency of hydrophobic residues in the peptide sequence. Moreover, by CD, molecular dynamics and steered molecular dynamics, we demonstrated that the molecular flexibility only played a minor role in the peptide adsorption. Such noncovalent but specific modification of inorganic surfaces through high affinity biomolecule adsorption represents a general strategy to modulate the functionality of multipurpose metallic surfaces.

  19. Strong selection against hybrids at a hybrid zone in the Ensatina ring species complex and its evolutionary implications.

    PubMed

    Alexandrino, João; Baird, Stuart J E; Lawson, Lucinda; Macey, J Robert; Moritz, Craig; Wake, David B

    2005-06-01

    The analysis of interactions between lineages at varying levels of genetic divergence can provide insights into the process of speciation through the accumulation of incompatible mutations. Ring species, and especially the Ensatina eschscholtzii system exemplify this approach. The plethodontid salamanders E. eschscholtzii xanthoptica and E. eschscholtzii platensis hybridize in the central Sierran foothills of California. We compared the genetic structure across two transects (southern and northern Calaveras Co.), one of which was resampled over 20 years, and examined diagnostic molecular markers (eight allozyme loci and mitochondrial DNA) and a diagnostic quantitative trait (color pattern). Key results across all studies were: (1) cline centers for all markers were coincident and the zones were narrow, with width estimates of 730 m to 2000 m; (2) cline centers at the northern Calaveras transect were coincident between 1981 and 2001, demonstrating repeatability over five generations; (3) there were very few if any putative F1s, but a relatively high number of backcrossed individuals in the central portion of transects; and (4) we found substantial linkage disequilibrium in all three studies and strong heterozygote deficit both in northern Calaveras, in 2001, and southern Calaveras. Both linkage disequilibrium and heterozygote deficit showed maximum values near the center of the zones. Using estimates of cline width and dispersal, we infer strong selection against hybrids. This is sufficient to promote accumulation of differences at loci that are neutral or under divergent selection, but would still allow for introgression of adaptive alleles. The evidence for strong but incomplete isolation across this centrally located contact is consistent with theory suggesting a gradual increase in postzygotic incompatibility between allopatric populations subject to divergent selection and reinforces the value of Ensatina as a system for the study of divergence and speciation

  20. Medical genetic polymorphisms as markers of evolutionary forces within the human genome: hypotheses focusing on natural selection in the Basque population.

    PubMed

    Bauduer, Frédéric; Degioanni, Anna; Dutour, Olivier

    2009-02-01

    Natural selection, drift, and gene flow are the three major evolutionary forces at the origin of genetic diversity among human populations. To further explore these mechanisms, we present an innovative approach using various medical genetic markers and focusing on the Basque population. From this study we can confirm the important role of drift in this endogamous human group and can report some disorders related to founder effects. Most important, the peculiar distribution of various polymorphisms, such as blood group O, factor V Leiden, DF508, C282Y, and CCR5 D32 mutations, which are implicated in resistance to infection, hemostasis, or iron conservation, could be interpreted as an adaptive profile. Multidisciplinary data have shown that the Neolithic period arrived significantly later in this southwestern corner of Europe. We hypothesize that the long-lasting Paleolithic mode of life, especially regarding nutrition and microbial exposure, was at the origin of this selective pressure within this population of ancient local ancestry. This approach could open new avenues in the field of population genetics.

  1. Critical reflections on evolutionary psychology and sexual selection theory as explanatory account of emergence of sex differences in psychopathology: comment on Martel (2013).

    PubMed

    Hankin, Benjamin L

    2013-11-01

    Martel (2013) proposed a metatheory, based on sexual selection theory and broad evolutionary psychological (EP) principles, to account for well-known sex differences in the emergence of common behavioral and certain internalizing disorders across childhood and adolescence, respectively. In this comment, I first enumerate several strengths and then offer 2 primary critiques about Martel's proposal. Martel provides an exceptional, integrative review that organizes several disparate literatures that hold promise to enhance understanding of such sex differences. At the same time, I raise critical questions regarding EP generally, and sexual selection theory specifically, as the metatheoretical framework chosen to bind together these different influences and mechanisms as drivers of the sex difference in different psychopathologies. Indeed, it is not clear that EP is necessary--nor does it provide unique explanatory power-to explicate the emergence of sex differences in internalizing and externalizing disorders among youth. Moreover, Martel's EP-based proposal pertains to adolescent-onset depression and social phobia but does not provide an explanation for known sex differences in other common childhood-onset and early adult-onset anxiety disorders.

  2. The chemically homogeneous evolutionary channel for binary black hole mergers: rates and properties of gravitational-wave events detectable by advanced LIGO

    NASA Astrophysics Data System (ADS)

    de Mink, S. E.; Mandel, I.

    2016-08-01

    We explore the predictions for detectable gravitational-wave signals from merging binary black holes formed through chemically homogeneous evolution in massive short-period stellar binaries. We find that ˜500 events per year could be detected with advanced ground-based detectors operating at full sensitivity. We analyse the distribution of detectable events, and conclude that there is a very strong preference for detecting events with nearly equal components (mass ratio >0.66 at 90 per cent confidence in our default model) and high masses (total source-frame mass between 57 and 103 M⊙ at 90 per cent confidence). We consider multiple alternative variations to analyse the sensitivity to uncertainties in the evolutionary physics and cosmological parameters, and conclude that while the rates are sensitive to assumed variations, the mass distributions are robust predictions. Finally, we consider the recently reported results of the analysis of the first 16 double-coincident days of the O1 LIGO (Laser Interferometer Gravitational-wave Observatory) observing run, and find that this formation channel is fully consistent with the inferred parameters of the GW150914 binary black hole detection and the inferred merger rate.

  3. BMD Loci Contribute to Ethnic and Developmental Differences in Skeletal Fragility across Populations: Assessment of Evolutionary Selection Pressures

    PubMed Central

    Medina-Gómez, Carolina; Chesi, Alessandra; Heppe, Denise H.M.; Zemel, Babette S.; Yin, Jia-Lian; Kalkwarf, Heidi J.; Hofman, Albert; Lappe, Joan M.; Kelly, Andrea; Kayser, Manfred; Oberfield, Sharon E.; Gilsanz, Vicente; Uitterlinden, André G.; Shepherd, John A.; Jaddoe, Vincent W.V.; Grant, Struan F.A.; Lao, Oscar; Rivadeneira, Fernando

    2015-01-01

    Bone mineral density (BMD) is a highly heritable trait used both for the diagnosis of osteoporosis in adults and to assess bone health in children. Ethnic differences in BMD have been documented, with markedly higher levels in individuals of African descent, which partially explain disparity in osteoporosis risk across populations. To date, 63 independent genetic variants have been associated with BMD in adults of Northern-European ancestry. Here, we demonstrate that at least 61 of these variants are predictive of BMD early in life by studying their compound effect within two multiethnic pediatric cohorts. Furthermore, we show that within these cohorts and across populations worldwide the frequency of those alleles associated with increased BMD is systematically elevated in individuals of Sub-Saharan African ancestry. The amount of differentiation in the BMD genetic scores among Sub-Saharan and non-Sub-Saharan populations together with neutrality tests, suggest that these allelic differences are compatible with the hypothesis of selective pressures acting on the genetic determinants of BMD. These findings constitute an explorative contribution to the role of selection on ethnic BMD differences and likely a new example of polygenic adaptation acting on a human trait. PMID:26226985

  4. Changes in selection and evolutionary responses in migratory brown trout following the construction of a fish ladder

    PubMed Central

    Haugen, Thrond Oddvar; Aass, Per; Stenseth, Nils Christian; Vøllestad, Leif Asbjørn

    2008-01-01

    Brown trout (Salmo trutta) are extensively harvested and its habitat highly influenced by human encroachments. Using a 40-year time series of mark–recapture data we estimate vital rates for a piscivorous trout population. This population spawns upstream of a waterfall, which historically acted as a migration barrier for smaller trout. In 1966, the waterfall was dammed and a fish ladder constructed. All fish ascending the fish ladder were individually tagged and measured for a variety of traits. The fish ladder overall favoured access to upstream spawning areas for middle-sized trout, resulting in stabilizing selection acting on size at spawning. Over time, natural and fishing mortality have varied, with fishing mortality generally decreasing and natural mortality increasing. The average and, particularly, variance in size-at-first-spawning, and growth rates during the first years of lake residence have all decreased over the 1966–2003 period. These changes are all consistent with a shift from directional to stabilizing selection on age and size at spawning. Estimated rates of phenotypic change are relatively high, in particular for size at first spawning, adding further support for the growing notion that human interference may lead to rapid life-history trait evolution. PMID:25567634

  5. Changes in selection and evolutionary responses in migratory brown trout following the construction of a fish ladder.

    PubMed

    Haugen, Thrond Oddvar; Aass, Per; Stenseth, Nils Christian; Vøllestad, Leif Asbjørn

    2008-05-01

    Brown trout (Salmo trutta) are extensively harvested and its habitat highly influenced by human encroachments. Using a 40-year time series of mark-recapture data we estimate vital rates for a piscivorous trout population. This population spawns upstream of a waterfall, which historically acted as a migration barrier for smaller trout. In 1966, the waterfall was dammed and a fish ladder constructed. All fish ascending the fish ladder were individually tagged and measured for a variety of traits. The fish ladder overall favoured access to upstream spawning areas for middle-sized trout, resulting in stabilizing selection acting on size at spawning. Over time, natural and fishing mortality have varied, with fishing mortality generally decreasing and natural mortality increasing. The average and, particularly, variance in size-at-first-spawning, and growth rates during the first years of lake residence have all decreased over the 1966-2003 period. These changes are all consistent with a shift from directional to stabilizing selection on age and size at spawning. Estimated rates of phenotypic change are relatively high, in particular for size at first spawning, adding further support for the growing notion that human interference may lead to rapid life-history trait evolution.

  6. Evolutionary branching under slow directional evolution.

    PubMed

    Ito, Hiroshi C; Dieckmann, Ulf

    2014-11-07

    Evolutionary branching is the process by which ecological interactions induce evolutionary diversification. In asexual populations with sufficiently rare mutations, evolutionary branching occurs through trait-substitution sequences caused by the sequential invasion of successful mutants. A necessary and sufficient condition for evolutionary branching of univariate traits is the existence of a convergence stable trait value at which selection is locally disruptive. Real populations, however, undergo simultaneous evolution in multiple traits. Here we extend conditions for evolutionary branching to bivariate trait spaces in which the response to disruptive selection on one trait can be suppressed by directional selection on another trait. To obtain analytical results, we study trait-substitution sequences formed by invasions that possess maximum likelihood. By deriving a sufficient condition for evolutionary branching of bivariate traits along such maximum-likelihood-invasion paths (MLIPs), we demonstrate the existence of a threshold ratio specifying how much disruptive selection in one trait direction is needed to overcome the obstruction of evolutionary branching caused by directional selection in the other trait direction. Generalizing this finding, we show that evolutionary branching of bivariate traits can occur along evolutionary-branching lines on which residual directional selection is sufficiently weak. We then present numerical analyses showing that our generalized condition for evolutionary branching is a good indicator of branching likelihood even when trait-substitution sequences do not follow MLIPs and when mutations are not rare. Finally, we extend the derived conditions for evolutionary branching to multivariate trait spaces.

  7. Emergence of drug tolerance in cancer cell populations: an evolutionary outcome of selection, nongenetic instability, and stress-induced adaptation.

    PubMed

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

    2015-03-15

    In recent experiments on isogenetic cancer cell lines, it was observed that exposure to high doses of anticancer drugs can induce the emergence of a subpopulation of weakly proliferative and drug-tolerant cells, which display markers associated with stem cell-like cancer cells. After a period of time, some of the surviving cells were observed to change their phenotype to resume normal proliferation and eventually repopulate the sample. Furthermore, the drug-tolerant cells could be drug resensitized following drug washout. Here, we propose a theoretical mechanism for the transient emergence of such drug tolerance. In this framework, we formulate an individual-based model and an integro-differential equation model of reversible phenotypic evolution in a cell population exposed to cytotoxic drugs. The outcomes of both models suggest that nongenetic instability, stress-induced adaptation, selection, and the interplay between these mechanisms can push an actively proliferating cell population to transition into a weakly proliferative and drug-tolerant state. Hence, the cell population experiences much less stress in the presence of the drugs and, in the long run, reacquires a proliferative phenotype, due to phenotypic fluctuations and selection pressure. These mechanisms can also reverse epigenetic drug tolerance following drug washout. Our study highlights how the transient appearance of the weakly proliferative and drug-tolerant cells is related to the use of high-dose therapy. Furthermore, we show how stem-like characteristics can act to stabilize the transient, weakly proliferative, and drug-tolerant subpopulation for a longer time window. Finally, using our models as in silico laboratories, we propose new testable hypotheses that could help uncover general principles underlying the emergence of cancer drug tolerance.

  8. Selected References on Asbestos: Its Nature, Hazards, Detection, and Control.

    ERIC Educational Resources Information Center

    National Education Association, Washington, DC.

    This document provides teachers with sources of information about the nature, hazards, detection, and control of asbestos. Because many school buildings include asbestos-containing materials, teachers and other school personnel must be aware of the potential dangers to students and to themselves and take steps to have asbestos hazards contained or…

  9. A common evolutionary origin for the ON- and OFF-edge motion detection pathways of the Drosophila visual system

    PubMed Central

    Shinomiya, Kazunori; Takemura, Shin-ya; Rivlin, Patricia K.; Plaza, Stephen M.; Scheffer, Louis K.; Meinertzhagen, Ian A.

    2015-01-01

    Synaptic circuits for identified behaviors in the Drosophila brain have typically been considered from either a developmental or functional perspective without reference to how the circuits might have been inherited from ancestral forms. For example, two candidate pathways for ON- and OFF-edge motion detection in the visual system act via circuits that use respectively either T4 or T5, two cell types of the fourth neuropil, or lobula plate (LOP), that exhibit narrow-field direction-selective responses and provide input to wide-field tangential neurons. T4 or T5 both have four subtypes that terminate one each in the four strata of the LOP. Representatives are reported in a wide range of Diptera, and both cell types exhibit various similarities in: (1) the morphology of their dendritic arbors; (2) their four morphological and functional subtypes; (3) their cholinergic profile in Drosophila; (4) their input from the pathways of L3 cells in the first neuropil, or lamina (LA), and by one of a pair of LA cells, L1 (to the T4 pathway) and L2 (to the T5 pathway); and (5) their innervation by a single, wide-field contralateral tangential neuron from the central brain. Progenitors of both also express the gene atonal early in their proliferation from the inner anlage of the developing optic lobe, being alone among many other cell type progeny to do so. Yet T4 receives input in the second neuropil, or medulla (ME), and T5 in the third neuropil or lobula (LO). Here we suggest that these two cell types were originally one, that their ancestral cell population duplicated and split to innervate separate ME and LO neuropils, and that a fiber crossing—the internal chiasma—arose between the two neuropils. The split most plausibly occurred, we suggest, with the formation of the LO as a new neuropil that formed when it separated from its ancestral neuropil to leave the ME, suggesting additionally that ME input neurons to T4 and T5 may also have had a common origin. PMID:26217193

  10. DRIFTSEL: an R package for detecting signals of natural selection in quantitative traits.

    PubMed

    Karhunen, M; Merilä, J; Leinonen, T; Cano, J M; Ovaskainen, O

    2013-07-01

    Approaches and tools to differentiate between natural selection and genetic drift as causes of population differentiation are of frequent demand in evolutionary biology. Based on the approach of Ovaskainen et al. (2011), we have developed an R package (DRIFTSEL) that can be used to differentiate between stabilizing selection, diversifying selection and random genetic drift as causes of population differentiation in quantitative traits when neutral marker and quantitative genetic data are available. Apart from illustrating the use of this method and the interpretation of results using simulated data, we apply the package on data from three-spined sticklebacks (Gasterosteus aculeatus) to highlight its virtues. DRIFTSEL can also be used to perform usual quantitative genetic analyses in common-garden study designs.

  11. Radiography by selective detection of scatter field velocity components

    NASA Technical Reports Server (NTRS)

    Jacobs, Alan M. (Inventor); Dugan, Edward T. (Inventor); Shedlock, Daniel (Inventor)

    2007-01-01

    A reconfigurable collimated radiation detector, system and related method includes at least one collimated radiation detector. The detector has an adjustable collimator assembly including at least one feature, such as a fin, optically coupled thereto. Adjustments to the adjustable collimator selects particular directions of travel of scattered radiation emitted from an irradiated object which reach the detector. The collimated detector is preferably a collimated detector array, where the collimators are independently adjustable. The independent motion capability provides the capability to focus the image by selection of the desired scatter field components. When an array of reconfigurable collimated detectors is provided, separate image data can be obtained from each of the detectors and the respective images cross-correlated and combined to form an enhanced image.

  12. Applying Evolutionary Anthropology

    PubMed Central

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. PMID:25684561

  13. Paleoanthropology and evolutionary theory.

    PubMed

    Tattersall, Ian

    2012-01-01

    Paleoanthropologists of the first half of the twentieth century were little concerned either with evolutionary theory or with the technicalities and broader implications of zoological nomenclature. In consequence, the paleoanthropological literature of the period consisted largely of a series of descriptions accompanied by authoritative pronouncements, together with a huge excess of hominid genera and species. Given the intellectual flimsiness of the resulting paleoanthropological framework, it is hardly surprising that in 1950 the ornithologist Ernst Mayr met little resistance when he urged the new postwar generation of paleoanthropologists to accept not only the elegant reductionism of the Evolutionary Synthesis but a vast oversimplification of hominid phylogenetic history and nomenclature. Indeed, the impact of Mayr's onslaught was so great that even when developments in evolutionary biology during the last quarter of the century brought other paleontologists to the realization that much more has been involved in evolutionary histories than the simple action of natural selection within gradually transforming lineages, paleoanthropologists proved highly reluctant to follow. Even today, paleoanthropologists are struggling to reconcile an intuitive realization that the burgeoning hominid fossil record harbors a substantial diversity of species (bringing hominid evolutionary patterns into line with that of other successful mammalian families), with the desire to cram a huge variety of morphologies into an unrealistically minimalist systematic framework. As long as this theoretical ambivalence persists, our perception of events in hominid phylogeny will continue to be distorted.

  14. Applying evolutionary anthropology.

    PubMed

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution.

  15. Synthetic receptors for selectively detecting erythrocyte ABO subgroups.

    PubMed

    Seifner, Alexandra; Lieberzeit, Peter; Jungbauer, Christof; Dickert, Franz L

    2009-10-05

    Surface imprinting techniques with erythrocytes as templates yield polymer coatings with selective recognition sites towards red blood cells. The resulting cavities in the respective surface exhibit selectivity between blood subgroups as shown by Quartz Crystal Microbalance (QCM) measurements. Mass sensitive effects in the kilohertz range could be observed for concentrations down to 0.5 x 10(8) cells/mL. Frequency response as well as recovery of the sensor took place within a few minutes, indicating that no covalent binding is involved. Linear concentration dependence over a defined region provides ideal conditions for cross selectivity measurements. A1 imprinted sensor coatings resulted in an effect of 40 kHz when exposed to the template blood group, while A2 erythrocytes yielded just 11% of that value on the same layer. Furthermore, A2 imprinted coatings incorporated only one third the amount of A1 erythrocytes as compared to A2 ones. Therefore, imprinted materials depict the entire cell surface and utilize it for recognition, whereas natural antibodies bind on the defined antigen position and thus usually cannot distinguish between cells carrying different amounts of them.

  16. Selective detection of linear features in geological remote sensing data

    NASA Astrophysics Data System (ADS)

    Parikh, Jo Ann; DaPonte, John S.; DiNicola, Emily G.; Pedersen, Robert A.

    1992-09-01

    One of the major problems in the development of computer-assisted systems for geologic mapping is how to individualize the system to meet user needs. Ideally, the system should be responsive to specifications of desired types of output structures. Also, the system should be able to incorporate the user's knowledge of regional characteristics into the feature extraction/selection and classification components. Automatic techniques for classification of remote sensing data typically require relatively large, labeled training sets which are well- organized with respect to the desired mapping between input and output patterns. The present paper focuses on the feature extraction/selection component of the system. Kohonen self- organizing feature maps in conjunction with image processing procedures for linear feature extraction are used for explorative data analysis, feature selection, and construction of exemplar patterns. The results of training Kohonen feature maps with different pattern sets and different feature combinations provide insight into the nature of pattern relationships which enables the user to develop sets of positive and negative training patterns for the classification component.

  17. Persistence of evolutionary memory: primordial six-transmembrane helical domain mu opiate receptors selectively linked to endogenous morphine signaling.

    PubMed

    Kream, Richard M; Sheehan, Melinda; Cadet, Patrick; Mantione, Kirk J; Zhu, Wei; Casares, Federico; Stefano, George B

    2007-12-01

    Biochemical, molecular and pharmacological evidence for two unique six-transmembrane helical (TMH) domain opiate receptors expressed from the micro opioid receptor (MOR) gene have been shown. Designated micro3 and micro4 receptors, both protein species are Class A rhodopsin-like members of the superfamily of G-protein coupled receptors but are selectively tailored to mediate the cellular regulatory effects of endogenous morphine and related morphinan alkaloids via stimulation of nitric oxide (NO) production and release. Both micro3 and micro4 receptors lack an amino acid sequence of approximately 90 amino acids that constitute the extracellular N-terminal and TMH1 domains and part of the first intracellular loop of the micro1 receptor, but retain the empirically defined ligand binding pocket distributed across conserved TMH2, TMH3, and TMH7 domains of the micro1 sequence. Additionally, the receptor proteins are terminated by unique intracellular C-terminal amino acid sequences that serve as putative coupling or docking domains required for constitutive NO synthase activation. Because the recognition profile of micro3 and micro4 receptors is restricted to rigid benzylisoquinoline alkaloids typified by morphine and its extended family of chemical congeners, it is hypothesized that conformational stabilization provided by interaction of extended extracellular N-terminal protein domains and the extracellular loops is required for binding of endogenous opioid peptides as well as synthetic flexible opiate alkaloids.

  18. Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

    PubMed Central

    Fedrigo, Olivier; Babbitt, Courtney C.; Wortham, Matthew; Tewari, Alok K.; London, Darin; Song, Lingyun; Lee, Bum-Kyu; Iyer, Vishwanath R.; Parker, Stephen C. J.; Margulies, Elliott H.; Wray, Gregory A.; Furey, Terrence S.; Crawford, Gregory E.

    2012-01-01

    Understanding the molecular basis for phenotypic differences between humans and other primates remains an outstanding challenge. Mutations in non-coding regulatory DNA that alter gene expression have been hypothesized as a key driver of these phenotypic differences. This has been supported by differential gene expression analyses in general, but not by the identification of specific regulatory elements responsible for changes in transcription and phenotype. To identify the genetic source of regulatory differences, we mapped DNaseI hypersensitive (DHS) sites, which mark all types of active gene regulatory elements, genome-wide in the same cell type isolated from human, chimpanzee, and macaque. Most DHS sites were conserved among all three species, as expected based on their central role in regulating transcription. However, we found evidence that several hundred DHS sites were gained or lost on the lineages leading to modern human and chimpanzee. Species-specific DHS site gains are enriched near differentially expressed genes, are positively correlated with increased transcription, show evidence of branch-specific positive selection, and overlap with active chromatin marks. Species-specific sequence differences in transcription factor motifs found within these DHS sites are linked with species-specific changes in chromatin accessibility. Together, these indicate that the regulatory elements identified here are genetic contributors to transcriptional and phenotypic differences among primate species. PMID:22761590

  19. Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon).

    PubMed

    Bernal, Moisés A; Gaither, Michelle R; Simison, W Brian; Rocha, Luiz A

    2017-01-01

    Closely related marine species with large overlapping ranges provide opportunities to study mechanisms of speciation, particularly when there is evidence of gene flow between such lineages. Here, we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via restriction site-associated DNA sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI and low divergence for CytB and CR between the sister-species. On the other hand, complete lineage sorting was observed at the nuclear loci and most of the SNPs. Under neutral expectations, the smaller effective population size of mtDNA should lead to fixation of mutations faster than nDNA. Thus, these results suggest that hybridization in the recent past (0.174-0.263 Ma) led to introgression of the mtDNA, with little effect on the nuclear genome. Analyses of the SNP data revealed 28 loci potentially under divergent selection between the two species. The combination of mtDNA introgression and limited nuclear DNA introgression provides a mechanism for the evolution of independent lineages despite recurrent hybridization events. This study adds to the growing body of research that exemplifies how genetic divergence can be maintained in the presence of gene flow between closely related species.

  20. Reagent Selection Methodology for a Novel Explosives Detection Platform

    ScienceCinema

    None

    2016-07-12

    This video describes research being conducted by Dr. Marvin Warner, a research scientist at Pacific Northwest National Laboratory, in the individual pieces of antibodies used to set up a chemical reaction that will give off light just by mixing reagents together with a sample that contains an explosive molecule. This technology would help detect if explosives are present with just the use of a handheld system or container.

  1. Biomimetic Nanosensor Arrays for Selective Small Molecule Detection

    DTIC Science & Technology

    2012-02-21

    bacteria is genetically engineered to display a peptide sequence on the coat protein or flagella of the cell membrane protein, respectively. A large... bacteria (E. coli). Finally, individual clones are sequenced to extract the amino acid sequence of the polypeptides binding to the target substrate...Tao, J. D. Clayton, A. Sengupta, D. L. Kaplan, R. R. Naik, N. Verma, F. G. Omenetto, M. C. McAlpine. “Graphene-Based Wireless Bacteria Detection on

  2. Feature Selection and Pedestrian Detection Based on Sparse Representation

    PubMed Central

    Yao, Shihong; Wang, Tao; Shen, Weiming; Pan, Shaoming; Chong, Yanwen; Ding, Fei

    2015-01-01

    Pedestrian detection have been currently devoted to the extraction of effective pedestrian features, which has become one of the obstacles in pedestrian detection application according to the variety of pedestrian features and their large dimension. Based on the theoretical analysis of six frequently-used features, SIFT, SURF, Haar, HOG, LBP and LSS, and their comparison with experimental results, this paper screens out the sparse feature subsets via sparse representation to investigate whether the sparse subsets have the same description abilities and the most stable features. When any two of the six features are fused, the fusion feature is sparsely represented to obtain its important components. Sparse subsets of the fusion features can be rapidly generated by avoiding calculation of the corresponding index of dimension numbers of these feature descriptors; thus, the calculation speed of the feature dimension reduction is improved and the pedestrian detection time is reduced. Experimental results show that sparse feature subsets are capable of keeping the important components of these six feature descriptors. The sparse features of HOG and LSS possess the same description ability and consume less time compared with their full features. The ratios of the sparse feature subsets of HOG and LSS to their full sets are the highest among the six, and thus these two features can be used to best describe the characteristics of the pedestrian and the sparse feature subsets of the combination of HOG-LSS show better distinguishing ability and parsimony. PMID:26295480

  3. The Integration of Color-Selective Mechanisms in Symmetry Detection

    PubMed Central

    Wu, Chia-Ching; Chen, Chien-Chung

    2017-01-01

    We studied how the visual system detects multicolor symmetric patterns by manipulating the number of colors in an image in both isoluminance and luminance conditions. With a two-interval forced choice noise masking paradigm, we presented a noise mask in both intervals of each trial. A vertically symmetric target was randomly presented in one interval while a noise control was presented in the other. The task of the observers was to determine which interval contained the target. The target detection threshold was measured at various noise mask densities, which was found to decrease 1.4- to 2.5-fold as the number of colors in the image went up at median to high noise densities across different conditions. In addition, this color facilitation effect was greater in luminance conditions than in isoluminance conditions. Our data cannot be explained by the probability summation theory or simple signal-to-noise ratio. We therefore propose a computational model that incorporates a linear chromatic symmetry register, a nonlinear transducer response, noise manipulation and a multiple channel decision making process. This model suggests that the increment of the number of colors reduces the interference to the symmetry channels produced by noise, and in turn facilitates symmetry detection. PMID:28230091

  4. First detections of FS Canis Majoris stars in clusters. Evolutionary state as constrained by coeval massive stars

    NASA Astrophysics Data System (ADS)

    de la Fuente, D.; Najarro, F.; Trombley, C.; Davies, B.; Figer, D. F.

    2015-03-01

    Context. FS CMa stars are low-luminosity objects showing the B[e] phenomenon whose evolutionary state remains a puzzle. These stars are surrounded by compact disks of warm dust of unknown origin. Hitherto, membership of FS CMa stars to coeval populations has never been confirmed. Aims: The discovery of low-luminosity line emitters in the young massive clusters Mercer 20 and Mercer 70 prompts us to investigate the nature of such objects. We intend to confirm membership to coeval populations in order to characterize these emission-line stars through the cluster properties. Methods: Based on ISAAC/VLT medium-resolution spectroscopy and NICMOS/HST photometry of massive cluster members, new characterizations of Mercer 20 and Mercer 70 are performed. Coevality of each cluster and membership of the newly-discovered B[e] objects are investigated using our observations as well as literature data of the surroundings. Infrared excess and narrow-band photometric properties of the B[e] stars are also studied. Results: We confirm and classify 22 new cluster members, including Wolf-Rayet stars and blue hypergiants. Spectral types (O9-B1.5 V) and radial velocities of B[e] objects are compatible with the remaining cluster members, while emission features of Mg ii, Fe ii], and [Fe ii] are identified in their spectra. The ages of these stars are 4.5 and 6 Myr, and they show mild infrared excesses. Conclusions: We confirm the presence of FS CMa stars in the coeval populations of Mercer 20 and Mercer 70. We discuss the nature and evolutionary state of FS CMa stars, discarding a post-AGB nature and introducing a new hypothesis about mergers. A new search method for FS CMa candidates in young massive clusters based on narrow-band Paschen-α photometry is proposed and tested in photometric data of other clusters, yielding three new candidates. Based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere, Chile, under program IDs 083.D

  5. Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly

    PubMed Central

    Wragg, David; Marti-Marimon, Maria; Basso, Benjamin; Bidanel, Jean-Pierre; Labarthe, Emmanuelle; Bouchez, Olivier; Le Conte, Yves; Vignal, Alain

    2016-01-01

    Four main evolutionary lineages of A. mellifera have been described including eastern Europe (C) and western and northern Europe (M). Many apiculturists prefer bees from the C lineage due to their docility and high productivity. In France, the routine importation of bees from the C lineage has resulted in the widespread admixture of bees from the M lineage. The haplodiploid nature of the honeybee Apis mellifera, and its small genome size, permits affordable and extensive genomics studies. As a pilot study of a larger project to characterise French honeybee populations, we sequenced 60 drones sampled from two commercial populations managed for the production of honey and royal jelly. Results indicate a C lineage origin, whilst mitochondrial analysis suggests two drones originated from the O lineage. Analysis of heterozygous SNPs identified potential copy number variants near to genes encoding odorant binding proteins and several cytochrome P450 genes. Signatures of selection were detected using the hapFLK haplotype-based method, revealing several regions under putative selection for royal jelly production. The framework developed during this study will be applied to a broader sampling regime, allowing the genetic diversity of French honeybees to be characterised in detail. PMID:27255426

  6. Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly.

    PubMed

    Wragg, David; Marti-Marimon, Maria; Basso, Benjamin; Bidanel, Jean-Pierre; Labarthe, Emmanuelle; Bouchez, Olivier; Le Conte, Yves; Vignal, Alain

    2016-06-03

    Four main evolutionary lineages of A. mellifera have been described including eastern Europe (C) and western and northern Europe (M). Many apiculturists prefer bees from the C lineage due to their docility and high productivity. In France, the routine importation of bees from the C lineage has resulted in the widespread admixture of bees from the M lineage. The haplodiploid nature of the honeybee Apis mellifera, and its small genome size, permits affordable and extensive genomics studies. As a pilot study of a larger project to characterise French honeybee populations, we sequenced 60 drones sampled from two commercial populations managed for the production of honey and royal jelly. Results indicate a C lineage origin, whilst mitochondrial analysis suggests two drones originated from the O lineage. Analysis of heterozygous SNPs identified potential copy number variants near to genes encoding odorant binding proteins and several cytochrome P450 genes. Signatures of selection were detected using the hapFLK haplotype-based method, revealing several regions under putative selection for royal jelly production. The framework developed during this study will be applied to a broader sampling regime, allowing the genetic diversity of French honeybees to be characterised in detail.

  7. Illumination, wavelength selection, and detection in fluorescence microscopy.

    PubMed

    Spring, K R

    1991-07-01

    The presently available devices for the illumination, changing of wavelengths, and detection of the resultant fluorescence of biological samples viewed in the light microscope have been described and compared. The optimal choice for illumination is a xenon arc lamp with a filter wheel wavelength selector. The optimal choice for an imaging detector is an intensified CCD (charge-coupled-device) camera. These combinations produce the most rapid, stable, and reproducible results when fluorescence measurements are made on living epithelial cells or isolated renal tubules. Techniques for the simultaneous acquisition of fluorescence and differential interference contrast (DIC) images have also been described and compared.

  8. An FPGA Implementation to Detect Selective Cationic Antibacterial Peptides

    PubMed Central

    Polanco González, Carlos; Nuño Maganda, Marco Aurelio; Arias-Estrada, Miguel; del Rio, Gabriel

    2011-01-01

    Exhaustive prediction of physicochemical properties of peptide sequences is used in different areas of biological research. One example is the identification of selective cationic antibacterial peptides (SCAPs), which may be used in the treatment of different diseases. Due to the discrete nature of peptide sequences, the physicochemical properties calculation is considered a high-performance computing problem. A competitive solution for this class of problems is to embed algorithms into dedicated hardware. In the present work we present the adaptation, design and implementation of an algorithm for SCAPs prediction into a Field Programmable Gate Array (FPGA) platform. Four physicochemical properties codes useful in the identification of peptide sequences with potential selective antibacterial activity were implemented into an FPGA board. The speed-up gained in a single-copy implementation was up to 108 times compared with a single Intel processor cycle for cycle. The inherent scalability of our design allows for replication of this code into multiple FPGA cards and consequently improvements in speed are possible. Our results show the first embedded SCAPs prediction solution described and constitutes the grounds to efficiently perform the exhaustive analysis of the sequence-physicochemical properties relationship of peptides. PMID:21738652

  9. An FPGA implementation to detect selective cationic antibacterial peptides.

    PubMed

    Polanco González, Carlos; Nuño Maganda, Marco Aurelio; Arias-Estrada, Miguel; del Rio, Gabriel

    2011-01-01

    Exhaustive prediction of physicochemical properties of peptide sequences is used in different areas of biological research. One example is the identification of selective cationic antibacterial peptides (SCAPs), which may be used in the treatment of different diseases. Due to the discrete nature of peptide sequences, the physicochemical properties calculation is considered a high-performance computing problem. A competitive solution for this class of problems is to embed algorithms into dedicated hardware. In the present work we present the adaptation, design and implementation of an algorithm for SCAPs prediction into a Field Programmable Gate Array (FPGA) platform. Four physicochemical properties codes useful in the identification of peptide sequences with potential selective antibacterial activity were implemented into an FPGA board. The speed-up gained in a single-copy implementation was up to 108 times compared with a single Intel processor cycle for cycle. The inherent scalability of our design allows for replication of this code into multiple FPGA cards and consequently improvements in speed are possible. Our results show the first embedded SCAPs prediction solution described and constitutes the grounds to efficiently perform the exhaustive analysis of the sequence-physicochemical properties relationship of peptides.

  10. Evolutionary developmental psychology.

    PubMed

    King, Ashley C; Bjorklund, David F

    2010-02-01

    The field of evolutionary developmental psychology can potentially broaden the horizons of mainstream evolutionary psychology by combining the principles of Darwinian evolution by natural selection with the study of human development, focusing on the epigenetic effects that occur between humans and their environment in a way that attempts to explain how evolved psychological mechanisms become expressed in the phenotypes of adults. An evolutionary developmental perspective includes an appreciation of comparative research and we, among others, argue that contrasting the cognition of humans with that of nonhuman primates can provide a framework with which to understand how human cognitive abilities and intelligence evolved. Furthermore, we argue that several aspects of childhood (e.g., play and immature cognition) serve both as deferred adaptations as well as imparting immediate benefits. Intense selection pressure was surely exerted on childhood over human evolutionary history and, as a result, neglecting to consider the early developmental period of children when studying their later adulthood produces an incomplete picture of the evolved adaptations expressed through human behavior and cognition.

  11. Geographic Variation in the Acoustic Traits of Greater Horseshoe Bats: Testing the Importance of Drift and Ecological Selection in Evolutionary Processes

    PubMed Central

    Sun, Keping; Luo, Li; Kimball, Rebecca T.; Wei, Xuewen; Jin, Longru; Jiang, Tinglei; Li, Guohong; Feng, Jiang

    2013-01-01

    Patterns of intraspecific geographic variation of signaling systems provide insight into the microevolutionary processes driving phenotypic divergence. The acoustic calls of bats are sensitive to diverse evolutionary forces, but processes that shape call variation are largely unexplored. In China, Rhinolophus ferrumequinum displays a diverse call frequency and inhabits a heterogeneous landscape, presenting an excellent opportunity for this kind of research. We quantified geographic variation in resting frequency (RF) of echolocation calls, estimated genetic structure and phylogeny of R. ferrumequinum populations, and combined this with climatic factors to test three hypotheses to explain acoustic variation: genetic drift, cultural drift, and local adaptation. Our results demonstrated significant regional divergence in frequency and phylogeny among the bat populations in China's northeast (NE), central-east (CE) and southwest (SW) regions. The CE region had higher frequencies than the NE and SW regions. Drivers of RF divergence were estimated in the entire range and just the CE/NE region (since these two regions form a clade). In both cases, RF divergence was not correlated with mtDNA or nDNA genetic distance, but was significantly correlated with geographic distance and mean annual temperature, indicating cultural drift and ecological selection pressures are likely important in shaping RF divergence among different regions in China. PMID:23950926

  12. Geographic variation in the acoustic traits of greater horseshoe bats: testing the importance of drift and ecological selection in evolutionary processes.

    PubMed

    Sun, Keping; Luo, Li; Kimball, Rebecca T; Wei, Xuewen; Jin, Longru; Jiang, Tinglei; Li, Guohong; Feng, Jiang

    2013-01-01

    Patterns of intraspecific geographic variation of signaling systems provide insight into the microevolutionary processes driving phenotypic divergence. The acoustic calls of bats are sensitive to diverse evolutionary forces, but processes that shape call variation are largely unexplored. In China, Rhinolophus ferrumequinum displays a diverse call frequency and inhabits a heterogeneous landscape, presenting an excellent opportunity for this kind of research. We quantified geographic variation in resting frequency (RF) of echolocation calls, estimated genetic structure and phylogeny of R. ferrumequinum populations, and combined this with climatic factors to test three hypotheses to explain acoustic variation: genetic drift, cultural drift, and local adaptation. Our results demonstrated significant regional divergence in frequency and phylogeny among the bat populations in China's northeast (NE), central-east (CE) and southwest (SW) regions. The CE region had higher frequencies than the NE and SW regions. Drivers of RF divergence were estimated in the entire range and just the CE/NE region (since these two regions form a clade). In both cases, RF divergence was not correlated with mtDNA or nDNA genetic distance, but was significantly correlated with geographic distance and mean annual temperature, indicating cultural drift and ecological selection pressures are likely important in shaping RF divergence among different regions in China.

  13. Proteomics in evolutionary ecology.

    PubMed

    Baer, B; Millar, A H

    2016-03-01

    Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein

  14. Taste detection and discrimination performance of rats following selective desalivation.

    PubMed

    Brosvic, G M; Hoey, N E

    1990-11-01

    Taste sensitivity and responsivity, two-tastant and taste-mixture discrimination performance, and taste preferences were examined prior to and after the selective desalivation of 48 male Long-Evans rats. Altered preference behavior was observed in rats after removal of the major salivary glands, as well as after removal of only the submandibular-sublingual complexes. In 9 of 12 desalivated rats, decreased sensitivity and increased responsivity to near-threshold sodium chloride solutions were observed, although these changes were less than one-half an order of magnitude. No between-group differences in performance on two-tastant and taste-mixture discrimination tasks were observed. These results suggest that decrements in absolute sensitivity do not result in concomitant deficits in the discrimination of taste qualities.

  15. Selective chemical detection by energy modulation of sensors

    DOEpatents

    Stetter, J.R.; Otagawa, T.

    1985-05-20

    A portable instrument for use in the field in detecting, identifying, and quantifying a component of a sampled fluid includes a sensor which chemically reacts with the component of interest or a derivative thereof, an electrical heating filament for heating the sample before it is applied to the sensor, and modulating means for continuously varying the temperature of the filament (and hence the reaction rate) between two values sufficient to produce the chemical reaction. In response to this thermal modulation, the sensor produces a modulated output signal, the modulation of which is a function of the activation energy of the chemical reaction, which activation energy is specific to the particular component of interest and its concentration. Microprocessor means compares the modulated output signal with standard responses for a plurality of components to identify and quantify the particular component of interest. 4 figs.

  16. Evolutionary adaptations to dietary changes.

    PubMed

    Luca, F; Perry, G H; Di Rienzo, A

    2010-08-21

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area.

  17. Evolutionary Adaptations to Dietary Changes

    PubMed Central

    Luca, F.; Perry, G.H.; Di Rienzo, A.

    2014-01-01

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area. PMID:20420525

  18. Evolutionary Computing

    SciTech Connect

    Patton, Robert M; Cui, Xiaohui; Jiao, Yu; Potok, Thomas E

    2008-01-01

    The rate at which information overwhelms humans is significantly more than the rate at which humans have learned to process, analyze, and leverage this information. To overcome this challenge, new methods of computing must be formulated, and scientist and engineers have looked to nature for inspiration in developing these new methods. Consequently, evolutionary computing has emerged as new paradigm for computing, and has rapidly demonstrated its ability to solve real-world problems where traditional techniques have failed. This field of work has now become quite broad and encompasses areas ranging from artificial life to neural networks. This chapter focuses specifically on two sub-areas of nature-inspired computing: Evolutionary Algorithms and Swarm Intelligence.

  19. Toward an evolutionary definition of cheating.

    PubMed

    Ghoul, Melanie; Griffin, Ashleigh S; West, Stuart A

    2014-02-01

    The term "cheating" is used in the evolutionary and ecological literature to describe a wide range of exploitative or deceitful traits. Although many find this a useful short hand, others have suggested that it implies cognitive intent in a misleading way, and is used inconsistently. We provide a formal justification of the use of the term "cheat" from the perspective of an individual as a maximizing agent. We provide a definition for cheating that can be applied widely, and show that cheats can be broadly classified on the basis of four distinctions: (i) whether cooperation is an option; (ii) whether deception is involved; (iii) whether members of the same or different species are cheated; and (iv) whether the cheat is facultative or obligate. Our formal definition and classification provide a framework that allow us to resolve and clarify a number of issues, regarding the detection and evolutionary consequences of cheating, as well as illuminating common principles and similarities in the underlying selection pressures.

  20. Selective chemical detection by energy modulation of sensors

    DOEpatents

    Stetter, J.R.; Otagawa, T.

    1991-09-10

    A portable instrument for use in the field in detecting, identifying, and quantifying a component of a sampled fluid includes a sensor which chemically reacts with the component of interest or a derivative thereof, an electrical heating filament for heating the sample before it is applied to the sensor, and modulator for continuously varying the temperature of the filament (and hence the reaction rate) between two values sufficient to produce the chemical reaction. In response to this thermal modulation, the sensor produces a modulated output signal, the modulation of which is a function of the activation energy of the chemical reaction, which activation energy is specific to the particular component of interest and its concentration. Microprocessor which compares the modulated output signal with standard responses for a plurality of components to identify and quantify the particular component of interest. In particular, the concentration of the component of interest is proportional to the amplitude of the modulated output signal, while the identifying activation output energy of the chemical interaction indicative of that component is proportional to a normalized parameter equal to the peak-to-peak amplitude divided by the height of the upper peaks above a base line signal level. 5 figures.

  1. Selective chemical detection by energy modulation of sensors

    DOEpatents

    Stetter, Joseph R.; Otagawa, Takaaki

    1991-01-01

    A portable instrument for use in the field in detecting, identifying, and quantifying a component of a sampled fluid includes a sensor which chemically reacts with the component of interest or a derivative thereof, an electrical heating filament for heating the sample before it is applied to the sensor, and modulator for continuously varying the temperature of the filament (and hence the reaction rate) between two values sufficient to produce the chemical reaction. In response to this thermal modulation, the sensor produces a modulated output signal, the modulation of which is a function of the activation energy of the chemical reaction, which activation energy is specific to the particular component of interest and its concentration. Microprocessor which compares the modulated output signal with standard responses for a plurality of components to identify and quantify the particular component of interest. In particular, the concentration of the component of interest is proportional to the amplitude of the modulated output signal, while the identifying activation output energy of the chemical interaction indicative of that component is proportional to a normalized parameter equal to the peak-to-peak amplitude divided by the height of the upper peaks above a base line signal level.

  2. Robust Ground Target Detection by SAR and IR Sensor Fusion Using Adaboost-Based Feature Selection

    PubMed Central

    Kim, Sungho; Song, Woo-Jin; Kim, So-Hyun

    2016-01-01

    Long-range ground targets are difficult to detect in a noisy cluttered environment using either synthetic aperture radar (SAR) images or infrared (IR) images. SAR-based detectors can provide a high detection rate with a high false alarm rate to background scatter noise. IR-based approaches can detect hot targets but are affected strongly by the weather conditions. This paper proposes a novel target detection method by decision-level SAR and IR fusion using an Adaboost-based machine learning scheme to achieve a high detection rate and low false alarm rate. The proposed method consists of individual detection, registration, and fusion architecture. This paper presents a single framework of a SAR and IR target detection method using modified Boolean map visual theory (modBMVT) and feature-selection based fusion. Previous methods applied different algorithms to detect SAR and IR targets because of the different physical image characteristics. One method that is optimized for IR target detection produces unsuccessful results in SAR target detection. This study examined the image characteristics and proposed a unified SAR and IR target detection method by inserting a median local average filter (MLAF, pre-filter) and an asymmetric morphological closing filter (AMCF, post-filter) into the BMVT. The original BMVT was optimized to detect small infrared targets. The proposed modBMVT can remove the thermal and scatter noise by the MLAF and detect extended targets by attaching the AMCF after the BMVT. Heterogeneous SAR and IR images were registered automatically using the proposed RANdom SAmple Region Consensus (RANSARC)-based homography optimization after a brute-force correspondence search using the detected target centers and regions. The final targets were detected by feature-selection based sensor fusion using Adaboost. The proposed method showed good SAR and IR target detection performance through feature selection-based decision fusion on a synthetic database generated

  3. Robust Ground Target Detection by SAR and IR Sensor Fusion Using Adaboost-Based Feature Selection.

    PubMed

    Kim, Sungho; Song, Woo-Jin; Kim, So-Hyun

    2016-07-19

    Long-range ground targets are difficult to detect in a noisy cluttered environment using either synthetic aperture radar (SAR) images or infrared (IR) images. SAR-based detectors can provide a high detection rate with a high false alarm rate to background scatter noise. IR-based approaches can detect hot targets but are affected strongly by the weather conditions. This paper proposes a novel target detection method by decision-level SAR and IR fusion using an Adaboost-based machine learning scheme to achieve a high detection rate and low false alarm rate. The proposed method consists of individual detection, registration, and fusion architecture. This paper presents a single framework of a SAR and IR target detection method using modified Boolean map visual theory (modBMVT) and feature-selection based fusion. Previous methods applied different algorithms to detect SAR and IR targets because of the different physical image characteristics. One method that is optimized for IR target detection produces unsuccessful results in SAR target detection. This study examined the image characteristics and proposed a unified SAR and IR target detection method by inserting a median local average filter (MLAF, pre-filter) and an asymmetric morphological closing filter (AMCF, post-filter) into the BMVT. The original BMVT was optimized to detect small infrared targets. The proposed modBMVT can remove the thermal and scatter noise by the MLAF and detect extended targets by attaching the AMCF after the BMVT. Heterogeneous SAR and IR images were registered automatically using the proposed RANdom SAmple Region Consensus (RANSARC)-based homography optimization after a brute-force correspondence search using the detected target centers and regions. The final targets were detected by feature-selection based sensor fusion using Adaboost. The proposed method showed good SAR and IR target detection performance through feature selection-based decision fusion on a synthetic database generated

  4. Tuning the chemical selectivity of SWNT-FETs for detection of heavy-metal ions.

    PubMed

    Forzani, Erica S; Li, Xiulan; Zhang, Peiming; Tao, Nongjian; Zhang, Ruth; Amlani, Islamshah; Tsui, Raymond; Nagahara, Larry A

    2006-11-01

    A method to functionalize single-walled carbon nanotubes (SWNTs) in a field-effect transistor (FET) device for the selective detection of heavy-metal ions is presented. In this method, peptide-modified polymers were electrochemically deposited onto SWNTs and the selective detection of metal ions was demonstrated by choosing appropriate peptide sequences. The signal transduction mechanism of the peptide-modified SWNT-FETs has also been studied.

  5. Detection of Bacillus cereus on selected retail chicken products.

    PubMed

    Smith, D P; Berrang, M E; Feldner, P W; Phillips, R W; Meinersmann, R J

    2004-08-01

    Samples from five chicken meat products, obtained at retail stores, were evaluated for the presence of Bacillus cereus. The products tested were as follows: breaded, fully cooked, frozen nuggets (NUGGETS); breaded, fully cooked, frozen tenders (TENDERS); fully cooked, frozen, white-meat fajita-style strips (STRIPS); raw, refrigerated, boneless, skinless, marinated breast fillets (FILLETS); and raw, refrigerated, cut-up, tray-pack bone-in parts (PARTS), either split breasts or thighs. Four packages of each item were obtained on three different days (n = 60). Frozen and refrigerated products were held overnight in their respective environments as appropriate; then packages were opened aseptically, and a total of 25 g of tissue was excised from multiple pieces within a package. The 25-g samples were enriched in 225 ml of Trypticase soy-polymixin broth for 18 to 24 h at 30 degrees C and then plated on mannitol-egg yolk-polymixin agar and incubated for 18 to 24 h at 30 degrees C. Colonies characteristic of B. cereus were chosen and replated for isolation on mannitol-egg yolk-polymixin agar. Suspect colonies were confirmed as Bacillus spp. by Gram stain, hemolysis on blood agar, and a biochemical test strip. Isolates were further confirmed as B. cereus using Bacteriological Analytical Manual procedures, including tests for motility, rhizoid growth, hemolysis, and protein toxin crystal production. B. cereus was detected in 27 of 60 total samples. By product, the prevalence levels were as follows: NUGGETS, 11 of 12 positive; TENDERS, 8 of 12 positive; STRIPS, 6 of 12 positive; FILLETS, 0 of 12 positive; and PARTS, 2 of 12 positive. Isolates were tested by PCR for presence of the toxin-encoding genes bceT, nheABC, hblACD, and cytK. Results indicate that B. cereus organisms were present on four of the five retail poultry products tested in this study, with the highest rates reported for the three fully cooked items, especially the two breaded products. All strains isolated

  6. Electrolyte-gated organic field-effect transistor for selective reversible ion detection.

    PubMed

    Schmoltner, Kerstin; Kofler, Johannes; Klug, Andreas; List-Kratochvil, Emil J W

    2013-12-17

    An ion-sensitive electrolyte-gated organic field-effect transistor for selective and reversible detection of sodium (Na(+) ) down to 10(-6) M is presented. The inherent low voltage - high current operation of these transistors in combination with a state-of-the-art ion-selective membrane proves to be a novel, versatile modular sensor platform.

  7. Sequence-selective DNA detection using multiple laminar streams: a novel microfluidic analysis method.

    PubMed

    Yamashita, Kenichi; Yamaguchi, Yoshiko; Miyazaki, Masaya; Nakamura, Hiroyuki; Shimizu, Hazime; Maeda, Hideaki

    2004-02-01

    On-site detection methods for DNA have been demanded in the pathophysiology field. Such analysis requires a simple and accurate method, rather than high-throughput. This report describes a novel microfluidic analysis method and its application for simple sequence-selective DNA detection. The method uses a microchannel device with a serpentine structure. Sequence-specific binding of probe DNA can be detected at one side of the microchannel. This method is capable of sequence-specific detection of DNA with high accuracy. Single base mutations can also be analyzed. Combination of laminar stream and laminar secondary flow in the microchannel enable specific detection of probe-bound DNA.

  8. Integrating landscape genomics and spatially explicit approaches to detect loci under selection in clinal populations.

    PubMed

    Jones, Matthew R; Forester, Brenna R; Teufel, Ashley I; Adams, Rachael V; Anstett, Daniel N; Goodrich, Betsy A; Landguth, Erin L; Joost, Stéphane; Manel, Stéphanie

    2013-12-01

    Uncovering the genetic basis of adaptation hinges on the ability to detect loci under selection. However, population genomics outlier approaches to detect selected loci may be inappropriate for clinal populations or those with unclear population structure because they require that individuals be clustered into populations. An alternate approach, landscape genomics, uses individual-based approaches to detect loci under selection and reveal potential environmental drivers of selection. We tested four landscape genomics methods on a simulated clinal population to determine their effectiveness at identifying a locus under varying selection strengths along an environmental gradient. We found all methods produced very low type I error rates across all selection strengths, but elevated type II error rates under "weak" selection. We then applied these methods to an AFLP genome scan of an alpine plant, Campanula barbata, and identified five highly supported candidate loci associated with precipitation variables. These loci also showed spatial autocorrelation and cline patterns indicative of selection along a precipitation gradient. Our results suggest that landscape genomics in combination with other spatial analyses provides a powerful approach for identifying loci potentially under selection and explaining spatially complex interactions between species and their environment.

  9. Mode-selective excitation and detection of ultrasonic guided waves for delamination detection in laminated aluminum plates.

    PubMed

    Shelke, Amit; Kundu, Tribikram; Amjad, Umar; Hahn, Katrin; Grill, Wolfgang

    2011-03-01

    Selective modes of guided Lamb waves are generated in a laminated aluminum plate for damage detection using a broadband piezoelectric transducer structured with a rigid electrode. Appropriate excitation frequencies and modes for inspection are selected from theoretical and experimental dispersion curves. Dispersion curves are obtained experimentally by short time Fourier transform of the transient signals. Sensitivity of antisymmetric and symmetric modes for delamination detection are investigated. The antisymmetric mode is found to be more reliable for delamination detection. Unlike other studies, in which the attenuation of the propagating waves is related to the extent of the internal damage, in this investigation, the changes in the time-of-flight (TOF) of guided Lamb waves are related to the damage progression. The mode conversion phenomenon of Lamb waves during progressive delamination is investigated. Close matching between the theoretical and experimentally derived dispersion curves and TOF assures the reliability of the results presented here.

  10. Sequential Model Selection based Segmentation to Detect DNA Copy Number Variation

    PubMed Central

    Hu, Jianhua; Zhang, Liwen; Wang, Huixia Judy

    2016-01-01

    Summary Array-based CGH experiments are designed to detect genomic aberrations or regions of DNA copy-number variation that are associated with an outcome, typically a state of disease. Most of the existing statistical methods target on detecting DNA copy number variations in a single sample or array. We focus on the detection of group effect variation, through simultaneous study of multiple samples from multiple groups. Rather than using direct segmentation or smoothing techniques, as commonly seen in existing detection methods, we develop a sequential model selection procedure that is guided by a modified Bayesian information criterion. This approach improves detection accuracy by accumulatively utilizing information across contiguous clones, and has computational advantage over the existing popular detection methods. Our empirical investigation suggests that the performance of the proposed method is superior to that of the existing detection methods, in particular, in detecting small segments or separating neighboring segments with differential degrees of copy-number variation. PMID:26954760

  11. Culturomics as a data playground for tests of selection: Mathematical approaches to detecting selection in word use.

    PubMed

    Sindi, Suzanne S; Dale, Rick

    2016-09-21

    In biological evolution traits may rise and fall in frequency due to genetic drift, where variant frequencies change by chance, or by selection where advantageous variants will rise in frequency. The neutral model of evolution, first developed by Kimura in the 1960s, has become the standard against which selection is detected. While the balance between these two important forces - drift and selection - has been well established in biology there are other domains where the contribution of these processes is still coming together. Although the idea of natural selection has been applied to the cultural domain since the time of Darwin, it has proven more challenging to positively identify cultural traits under selection both because of a lack of established tests for selection and a lack of large cultural data sets. However, in recent years with the accumulation of large cultural data sets many cultural features from pre-history pottery to modern baby names have been shown to evolve according to the neutral theory. But there is accumulating empirical evidence from cultural processes suggesting that the neutral theory alone cannot account for all features of the data. As such, there has been a renewed interest in determining whether there is selection amidst drift. Here we analyze a subset English word frequencies, and determine whether frequency change reveals processes of selection. Inspired by the Moran and Wright-Fisher models in population genetics, we developed a neutral model of word frequency variation to assess when linguistic data appears to depart from neutral evolution. As such, our model represents a possible "test for selection" in the linguistic domain. We explore how the distribution of word use has changed for sets of words in English for more than 100 years (1901-2008) as expressed in vocabulary usage in published books, made available by Google Ngram. When comparing empirical word frequency changes to our neutral model we find pervasive and systematic

  12. Site-selective imination of an anthracenone sensor: selective fluorescence detection of barium(II).

    PubMed

    Basa, Prem N; Bhowmick, Arundhati; Schulz, Mariah M; Sykes, Andrew G

    2011-10-07

    Site-selective imination of anthraquinone-based macrocyclic crown ethers using titanium tetrachloride as the catalyst yields imines where only the external carbonyl group of the anthraquinone forms Schiff-bases. The following aromatic amines yield monomeric compounds (aniline, 4-nitroaniline, 4-pyrrolaniline, and 1,3-phenylenediamine). Reaction of 2 equiv of the macrocyclic anthraquinone host with 1,2- and 1,4-phenylenediamine yields dimeric imine compounds. The 1,2-diimino host acts as a luminescence sensor, exhibiting enhanced selectivity for Ba(II) ion. Spectroscopic data indicate that two barium ions coordinate to the sensor. Due to E/Z isomerization of the imine, the monomeric complexes are nonluminescent. Restricted rotation about the 1,2 oriented C═N groups or other noncovalent/coordinate-covalent interactions acting between neighboring crown ether rings may inhibit E/Z isomerization in this example, which is different from current examples that employ coordination of a metal cation with a chelating imine nitrogen atom to suppress E/Z isomerization and activate luminescence. The 1,4-diimino adduct, where the crown rings remain widely separated, remains nonluminescent.

  13. Structural Variant Detection by Large-scale Sequencing Reveals New Evolutionary Evidence on Breed Divergence between Chinese and European Pigs

    PubMed Central

    Zhao, Pengju; Li, Junhui; Kang, Huimin; Wang, Haifei; Fan, Ziyao; Yin, Zongjun; Wang, Jiafu; Zhang, Qin; Wang, Zhiquan; Liu, Jian-Feng

    2016-01-01

    In this study, we performed a genome-wide SV detection among the genomes of thirteen pigs from diverse Chinese and European originated breeds by next genetation sequencing, and constrcuted a single-nucleotide resolution map involving 56,930 putative SVs. We firstly identified a SV hotspot spanning 35 Mb region on the X chromosome specifically in the genomes of Chinese originated individuals. Further scrutinizing this region by large-scale sequencing data of extra 111 individuals, we obtained the confirmatory evidence on our initial finding. Moreover, thirty five SV-related genes within the hotspot region, being of importance for reproduction ability, rendered significant different evolution rates between Chinese and European originated breeds. The SV hotspot identified herein offers a novel evidence for assessing phylogenetic relationships, as well as likely explains the genetic difference of corresponding phenotypes and features, among Chinese and European pig breeds. Furthermore, we employed various SVs to infer genetic structure of individuls surveyed. We found SVs can clearly detect the difference of genetic background among individuals. This clues us that genome-wide SVs can capture majority of geneic variation and be applied into cladistic analyses. Characterizing whole genome SVs demonstrated that SVs are significantly enriched/depleted with various genomic features. PMID:26729041

  14. Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants

    PubMed Central

    Zaitlen, Noah A.; Ye, Chun Jimmie; Witte, John S.

    2016-01-01

    The role of rare alleles in complex phenotypes has been hotly debated, but most rare variant association tests (RVATs) do not account for the evolutionary forces that affect genetic architecture. Here, we use simulation and numerical algorithms to show that explosive population growth, as experienced by human populations, can dramatically increase the impact of very rare alleles on trait variance. We then assess the ability of RVATs to detect causal loci using simulations and human RNA-seq data. Surprisingly, we find that statistical performance is worst for phenotypes in which genetic variance is due mainly to rare alleles, and explosive population growth decreases power. Although many studies have attempted to identify causal rare variants, few have reported novel associations. This has sometimes been interpreted to mean that rare variants make negligible contributions to complex trait heritability. Our work shows that RVATs are not robust to realistic human evolutionary forces, so general conclusions about the impact of rare variants on complex traits may be premature. PMID:27197206

  15. Detecting and characterizing genomic signatures of positive selection in global populations.

    PubMed

    Liu, Xuanyao; Ong, Rick Twee-Hee; Pillai, Esakimuthu Nisha; Elzein, Abier M; Small, Kerrin S; Clark, Taane G; Kwiatkowski, Dominic P; Teo, Yik-Ying

    2013-06-06

    Natural selection is a significant force that shapes the architecture of the human genome and introduces diversity across global populations. The question of whether advantageous mutations have arisen in the human genome as a result of single or multiple mutation events remains unanswered except for the fact that there exist a handful of genes such as those that confer lactase persistence, affect skin pigmentation, or cause sickle cell anemia. We have developed a long-range-haplotype method for identifying genomic signatures of positive selection to complement existing methods, such as the integrated haplotype score (iHS) or cross-population extended haplotype homozygosity (XP-EHH), for locating signals across the entire allele frequency spectrum. Our method also locates the founder haplotypes that carry the advantageous variants and infers their corresponding population frequencies. This presents an opportunity to systematically interrogate the whole human genome whether a selection signal shared across different populations is the consequence of a single mutation process followed subsequently by gene flow between populations or of convergent evolution due to the occurrence of multiple independent mutation events either at the same variant or within the same gene. The application of our method to data from 14 populations across the world revealed that positive-selection events tend to cluster in populations of the same ancestry. Comparing the founder haplotypes for events that are present across different populations revealed that convergent evolution is a rare occurrence and that the majority of shared signals stem from the same evolutionary event.

  16. Detecting directional selection in the presence of recent admixture in African-Americans.

    PubMed

    Lohmueller, Kirk E; Bustamante, Carlos D; Clark, Andrew G

    2011-03-01

    We investigate the performance of tests of neutrality in admixed populations using plausible demographic models for African-American history as well as resequencing data from African and African-American populations. The analysis of both simulated and human resequencing data suggests that recent admixture does not result in an excess of false-positive results for neutrality tests based on the frequency spectrum after accounting for the population growth in the parental African population. Furthermore, when simulating positive selection, Tajima's D, Fu and Li's D, and haplotype homozygosity have lower power to detect population-specific selection using individuals sampled from the admixed population than from the nonadmixed population. Fay and Wu's H test, however, has more power to detect selection using individuals from the admixed population than from the nonadmixed population, especially when the selective sweep ended long ago. Our results have implications for interpreting recent genome-wide scans for positive selection in human populations.

  17. Novel pyrazoline-based selective fluorescent probe for the detection of hydrazine.

    PubMed

    Zheng, Xiao-Xin; Wang, Sheng-Qing; Wang, Hao-Yan; Zhang, Rong-Rong; Liu, Jin-Ting; Zhao, Bao-Xiang

    2015-03-05

    A novel pyrazoline-based fluorescent probe, 2-[4-(3,5-diphenyl-4,5-dihydro-pyrazol-1-yl)-benzylidene]-malononitrile, with a simple structure and low detection limit (6.16×10(-6)M) for the detection of hydrazine is designed and synthesized. The probe responds selectively to hydrazine over other molecules with marked fluorescence enhancement. The probe can detect hydrazine effectively at pH 5.0-9.0 with a special emission wavelength at 520nm. Moreover, the probe can be used to detect hydrazine from variety of natural source water.

  18. Highly selective and sensitive fluorescent paper sensor for nitroaromatic explosive detection.

    PubMed

    Ma, Yingxin; Li, Hao; Peng, Shan; Wang, Leyu

    2012-10-02

    Rapid, sensitive, and selective detection of explosives such as 2,4,6-trinitrotoluene (TNT) and 2,4,6-trinitrophenol (TNP), especially using a facile paper sensor, is in high demand for homeland security and public safety. Although many strategies have been successfully developed for the detection of TNT, it is not easy to differentiate the influence from TNP. Also, few methods were demonstrated for the selective detection of TNP. In this work, via a facile and versatile method, 8-hydroxyquinoline aluminum (Alq(3))-based bluish green fluorescent composite nanospheres were successfully synthesized through self-assembly under vigorous stirring and ultrasonic treatment. These polymer-coated nanocomposites are not only water-stable but also highly luminescent. Based on the dramatic and selective fluorescence quenching of the nanocomposites via adding TNP into the aqueous solution, a sensitive and robust platform was developed for visual detection of TNP in the mixture of nitroaromatics including TNT, 2,4-dinitrotoluene (DNT), and nitrobenzene (NB). Meanwhile, the fluorescence intensity is proportional to the concentration of TNP in the range of 0.05-7.0 μg/mL with the 3σ limit of detection of 32.3 ng/mL. By handwriting or finger printing with TNP solution as ink on the filter paper soaked with the fluorescent nanocomposites, the bluish green fluorescence was instantly and dramatically quenched and the dark patterns were left on the paper. Therefore, a convenient and rapid paper sensor for TNP-selective detection was fabricated.

  19. Evolutionary foundations for cancer biology

    PubMed Central

    Aktipis, C Athena; Nesse, Randolph M

    2013-01-01

    New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles—cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations—provide a foundation for understanding, preventing, and treating cancer. PMID:23396885

  20. Evolutionary foundations for cancer biology.

    PubMed

    Aktipis, C Athena; Nesse, Randolph M

    2013-01-01

    New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles-cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations-provide a foundation for understanding, preventing, and treating cancer.

  1. Genome-Wide Analysis of Evolutionary Markers of Human Influenza A(H1N1)pdm09 and A(H3N2) Viruses May Guide Selection of Vaccine Strain Candidates.

    PubMed

    Belanov, Sergei S; Bychkov, Dmitrii; Benner, Christian; Ripatti, Samuli; Ojala, Teija; Kankainen, Matti; Kai Lee, Hong; Wei-Tze Tang, Julian; Kainov, Denis E

    2015-11-27

    Here we analyzed whole-genome sequences of 3,969 influenza A(H1N1)pdm09 and 4,774 A(H3N2) strains that circulated during 2009-2015 in the world. The analysis revealed changes at 481 and 533 amino acid sites in proteins of influenza A(H1N1)pdm09 and A(H3N2) strains, respectively. Many of these changes were introduced as a result of random drift. However, there were 61 and 68 changes that were present in relatively large number of A(H1N1)pdm09 and A(H3N2) strains, respectively, that circulated during relatively long time. We named these amino acid substitutions evolutionary markers, as they seemed to contain valuable information regarding the viral evolution. Interestingly, influenza A(H1N1)pdm09 and A(H3N2) viruses acquired non-overlapping sets of evolutionary markers. We next analyzed these characteristic markers in vaccine strains recommended by the World Health Organization for the past five years. Our analysis revealed that vaccine strains carried only few evolutionary markers at antigenic sites of viral hemagglutinin (HA) and neuraminidase (NA). The absence of these markers at antigenic sites could affect the recognition of HA and NA by human antibodies generated in response to vaccinations. This could, in part, explain moderate efficacy of influenza vaccines during 2009-2014. Finally, we identified influenza A(H1N1)pdm09 and A(H3N2) strains, which contain all the evolutionary markers of influenza A strains circulated in 2015, and which could be used as vaccine candidates for the 2015/2016 season. Thus, genome-wide analysis of evolutionary markers of influenza A(H1N1)pdm09 and A(H3N2) viruses may guide selection of vaccine strain candidates.

  2. Genome-Wide Analysis of Evolutionary Markers of Human Influenza A(H1N1)pdm09 and A(H3N2) Viruses May Guide Selection of Vaccine Strain Candidates

    PubMed Central

    Belanov, Sergei S.; Bychkov, Dmitrii; Benner, Christian; Ripatti, Samuli; Ojala, Teija; Kankainen, Matti; Kai Lee, Hong; Wei-Tze Tang, Julian; Kainov, Denis E.

    2015-01-01

    Here we analyzed whole-genome sequences of 3,969 influenza A(H1N1)pdm09 and 4,774 A(H3N2) strains that circulated during 2009–2015 in the world. The analysis revealed changes at 481 and 533 amino acid sites in proteins of influenza A(H1N1)pdm09 and A(H3N2) strains, respectively. Many of these changes were introduced as a result of random drift. However, there were 61 and 68 changes that were present in relatively large number of A(H1N1)pdm09 and A(H3N2) strains, respectively, that circulated during relatively long time. We named these amino acid substitutions evolutionary markers, as they seemed to contain valuable information regarding the viral evolution. Interestingly, influenza A(H1N1)pdm09 and A(H3N2) viruses acquired non-overlapping sets of evolutionary markers. We next analyzed these characteristic markers in vaccine strains recommended by the World Health Organization for the past five years. Our analysis revealed that vaccine strains carried only few evolutionary markers at antigenic sites of viral hemagglutinin (HA) and neuraminidase (NA). The absence of these markers at antigenic sites could affect the recognition of HA and NA by human antibodies generated in response to vaccinations. This could, in part, explain moderate efficacy of influenza vaccines during 2009–2014. Finally, we identified influenza A(H1N1)pdm09 and A(H3N2) strains, which contain all the evolutionary markers of influenza A strains circulated in 2015, and which could be used as vaccine candidates for the 2015/2016 season. Thus, genome-wide analysis of evolutionary markers of influenza A(H1N1)pdm09 and A(H3N2) viruses may guide selection of vaccine strain candidates. PMID:26615216

  3. Selective detection of 1000 B. anthracis spores within 15 minutes using a peptide functionalized SERS assay.

    PubMed

    Farquharson, Stuart; Shende, Chetan; Smith, Wayne; Huang, Hermes; Inscore, Frank; Sengupta, Atanu; Sperry, Jay; Sickler, Todd; Prugh, Amber; Guicheteau, Jason

    2014-12-21

    A surface-enhanced Raman spectroscopy (SERS) assay has been designed to detect Bacillus anthracis spores. The assay consists of silver nanoparticles embedded in a porous glass structure that have been functionalized with ATYPLPIR, a peptide developed to discriminately bind B. anthracis versus other species of Bacillus. Once bound, acetic acid was used to release the biomarker dipicolinic acid from the spores, which was detected by SERS through the addition of silver colloids. This SERS assay was used to selectively bind B. anthracis with a 100-fold selectivity versus B. cereus, and to detect B. anthracis Ames at concentrations of 1000 spores per mL within 15 minutes. The SERS assay measurements provide a basis for the development of systems that can detect spores collected from the air or from water supplies.

  4. A Novel Fluorescent Probe for the Highly Selective and Sensitive Detection of Palladium in Aqueous Medium.

    PubMed

    Ma, Zhiwei; Wang, Xiao; Sun, Yanling; Liu, Juntao; Tong, Yan; Liu, Zhijing

    2016-11-01

    Based on the Pd(0)-catalyzed Tsuji-Trost allylic oxidative insertion reaction, we developed a fluorescent probe PdL1 for sensing Pd(0). As expected, probe PdL1 exhibited high selectivity and excellent sensitivity in both absorbance and fluorescence detection of Pd(0) in CH3CH2OH/PBS (10 mM, pH = 7.4, 6:4, v/v) solution. The detection limit was calculated to be as low as 15 nM, which can meet the selective requirements for practical application.

  5. Effective Sensor Selection and Data Anomaly Detection for Condition Monitoring of Aircraft Engines.

    PubMed

    Liu, Liansheng; Liu, Datong; Zhang, Yujie; Peng, Yu

    2016-04-29

    In a complex system, condition monitoring (CM) can collect the system working status. The condition is mainly sensed by the pre-deployed sensors in/on the system. Most existing works study how to utilize the condition information to predict the upcoming anomalies, faults, or failures. There is also some research which focuses on the faults or anomalies of the sensing element (i.e., sensor) to enhance the system reliability. However, existing approaches ignore the correlation between sensor selecting strategy and data anomaly detection, which can also improve the system reliability. To address this issue, we study a new scheme which includes sensor selection strategy and data anomaly detection by utilizing information theory and Gaussian Process Regression (GPR). The sensors that are more appropriate for the system CM are first selected. Then, mutual information is utilized to weight the correlation among different sensors. The anomaly detection is carried out by using the correlation of sensor data. The sensor data sets that are utilized to carry out the evaluation are provided by National Aeronautics and Space Administration (NASA) Ames Research Center and have been used as Prognostics and Health Management (PHM) challenge data in 2008. By comparing the two different sensor selection strategies, the effectiveness of selection method on data anomaly detection is proved.

  6. Effective Sensor Selection and Data Anomaly Detection for Condition Monitoring of Aircraft Engines

    PubMed Central

    Liu, Liansheng; Liu, Datong; Zhang, Yujie; Peng, Yu

    2016-01-01

    In a complex system, condition monitoring (CM) can collect the system working status. The condition is mainly sensed by the pre-deployed sensors in/on the system. Most existing works study how to utilize the condition information to predict the upcoming anomalies, faults, or failures. There is also some research which focuses on the faults or anomalies of the sensing element (i.e., sensor) to enhance the system reliability. However, existing approaches ignore the correlation between sensor selecting strategy and data anomaly detection, which can also improve the system reliability. To address this issue, we study a new scheme which includes sensor selection strategy and data anomaly detection by utilizing information theory and Gaussian Process Regression (GPR). The sensors that are more appropriate for the system CM are first selected. Then, mutual information is utilized to weight the correlation among different sensors. The anomaly detection is carried out by using the correlation of sensor data. The sensor data sets that are utilized to carry out the evaluation are provided by National Aeronautics and Space Administration (NASA) Ames Research Center and have been used as Prognostics and Health Management (PHM) challenge data in 2008. By comparing the two different sensor selection strategies, the effectiveness of selection method on data anomaly detection is proved. PMID:27136561

  7. Scedo-Select III: a new semi-selective culture medium for detection of the Scedosporium apiospermum species complex.

    PubMed

    Pham, Trâm; Giraud, Sandrine; Schuliar, Gaëlle; Rougeron, Amandine; Bouchara, Jean-Philippe

    2015-06-01

    The Scedosporium apiospermum complex is responsible for a large variety of infections in human. Members of this complex have become emerging fungal pathogens with an increasing occurrence in patients with underlying conditions such as immunosuppression or cystic fibrosis. A better knowledge of these fungi and of the sources of contamination of the patients is required and more accurate detection methods from the environment are needed. In this context, a highly selective culture medium was developed in the present study. Thus, various aliphatic, cyclic, or aromatic compounds were tested as the sole carbon source, in combination with some inorganic nitrogen sources and fungicides. The best results were obtained with 4-hydroxy-benzoate combined with ammonium sulfate and the fungicides dichloran and benomyl. This new culture medium called Scedo-Select III was shown to support growth of all species of the S. apiospermum complex. Subsequently, this new culture medium was evaluated successfully on water and soil samples, exhibiting higher sensitivity and selectivity than the previously described SceSel+ culture medium. Therefore, this easy-to-prepare and synthetic semi-selective culture medium may be useful to clarify the ecology of these fungi and to identify their reservoirs in patients' environment.

  8. Detection of Bacillus Spores by Apatmer Selectivity Using Atomic Force Microscopy

    DTIC Science & Technology

    2005-06-01

    Caugant, Henning A. Johansen, Agnes Fouet, Michèle Mock, Ida Hegna, and Anne-Britt Kolsto. “ Bacillus anthracis, Bacillus cereus , and Bacillus ...DETECTION OF BACILLUS SPORES BY APATMER SELECTIVITY USING ATOMIC FORCE MICROSCOPY THESIS Nina M. Houtkooper, Captain, USAF...or position of the United States Air Force, Department of Defense, or the United States Government. AFIT/GAP/ENP/05-03 DETECTION OF BACILLUS

  9. Network intrusion detection by the coevolutionary immune algorithm of artificial immune systems with clonal selection

    NASA Astrophysics Data System (ADS)

    Salamatova, T.; Zhukov, V.

    2017-02-01

    The paper presents the application of the artificial immune systems apparatus as a heuristic method of network intrusion detection for algorithmic provision of intrusion detection systems. The coevolutionary immune algorithm of artificial immune systems with clonal selection was elaborated. In testing different datasets the empirical results of evaluation of the algorithm effectiveness were achieved. To identify the degree of efficiency the algorithm was compared with analogs. The fundamental rules based of solutions generated by this algorithm are described in the article.

  10. Surface-Enhanced Raman Spectroscopy-Based Approach for Ultrasensitive and Selective Detection of Hydrazine.

    PubMed

    Gu, Xin; Camden, Jon P

    2015-07-07

    A probe mediated SERS-based strategy is developed to selectively detect hydrazine with superb sensitivity. Ortho-phthaldialdehyde, a simple probe, reacts specifically with hydrazine to form phthalazine, a molecule that possesses a larger Raman cross section and better affinity toward the SERS substrate. We observed a limit of detection of 8.5 × 10(-11) M. Our method shows both qualitative and quantitative measurement of hydrazine with high sensitivity, low cost, and fast analysis time.

  11. Evolutionary Dynamics of Abundant Stop Codon Readthrough

    PubMed Central

    Jungreis, Irwin; Kellis, Manolis

    2016-01-01

    Translational stop codon readthrough emerged as a major regulatory mechanism affecting hundreds of genes in animal genomes, based on recent comparative genomics and ribosomal profiling evidence, but its evolutionary properties remain unknown. Here, we leverage comparative genomic evidence across 21 Anopheles mosquitoes to systematically annotate readthrough genes in the malaria vector Anopheles gambiae, and to provide the first study of abundant readthrough evolution, by comparison with 20 Drosophila species. Using improved comparative genomics methods for detecting readthrough, we identify evolutionary signatures of conserved, functional readthrough of 353 stop codons in the malaria vector, Anopheles gambiae, and of 51 additional Drosophila melanogaster stop codons, including several cases of double and triple readthrough and of readthrough of two adjacent stop codons. We find that most differences between the readthrough repertoires of the two species arose from readthrough gain or loss in existing genes, rather than birth of new genes or gene death; that readthrough-associated RNA structures are sometimes gained or lost while readthrough persists; that readthrough is more likely to be lost at TAA and TAG stop codons; and that readthrough is under continued purifying evolutionary selection in mosquito, based on population genetic evidence. We also determine readthrough-associated gene properties that predate readthrough, and identify differences in the characteristic properties of readthrough genes between clades. We estimate more than 600 functional readthrough stop codons in mosquito and 900 in fruit fly, provide evidence of readthrough control of peroxisomal targeting, and refine the phylogenetic extent of abundant readthrough as following divergence from centipede. PMID:27604222

  12. Impact of Amplified Fragment Length Polymorphism Size Homoplasy on the Estimation of Population Genetic Diversity and the Detection of Selective Loci

    PubMed Central

    Caballero, Armando; Quesada, Humberto; Rolán-Alvarez, Emilio

    2008-01-01

    AFLP markers are becoming one of the most popular tools for genetic analysis in the fields of evolutionary genetics and ecology and conservation of genetic resources. The technique combines a high-information content and fidelity with the possibility of carrying out genomewide scans. However, a potential problem with this technique is the lack of homology of bands with the same electrophoretic mobility, what is known as fragment-size homoplasy. We carried out a theoretical analysis aimed at quantifying the impact of AFLP homoplasy on the estimation of within- and between-neutral population genetic diversity in a model of a structured finite population with migration among subpopulations. We also investigated the performance of a currently used method (DFDIST software) to detect selective loci from the comparison between genetic differentiation and heterozygosis of dominant molecular markers, as well as the impact of AFLP homoplasy on its effectiveness. The results indicate that the biases produced by homoplasy are: (1) an overestimation of the frequency of the allele determining the presence of the band, (2) an underestimation of the degree of differentiation between subpopulations, and (3) an overestimation or underestimation of the heterozygosis, depending on the allele frequency of the markers. The impact of homoplasy is quickly diminished by reducing the number of fragments analyzed per primer combination. However, substantial biases on the expected heterozygosity (up to 15–25%) may occur with ∼50–100 fragments per primer combination. The performance of the DFDIST software to detect selective loci from dominant markers is highly dependent on the number of selective loci in the genome and their average effects, the estimate of genetic differentiation chosen to be used in the analysis, and the critical bound probability used to detect outliers. Overall, the results indicate that the software should be used with caution. AFLP homoplasy can produce a

  13. Evolutionary mysteries in meiosis.

    PubMed

    Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E; Wijnker, Erik; Haag, Christoph R

    2016-10-19

    Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often 'weird' features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.

  14. Genomic scans detect signatures of selection along a salinity gradient in populations of the intertidal seaweed Fucus serratus on a 12 km scale.

    PubMed

    Coyer, J A; Hoarau, G; Pearson, G; Mota, C; Jüterbock, A; Alpermann, T; John, U; Olsen, J L

    2011-03-01

    Detecting natural selection in wild populations is a central challenge in evolutionary biology and genomic scans are an important means of detecting allele frequencies that deviate from neutral expectations among marker loci. We used nine anonymous and 15 EST-linked microsatellites, 362 AFLP loci, and several neutrality tests, to identify outlier loci when comparing four populations of the seaweed Fucus serratus spaced along a 12km intertidal shore with a steep salinity gradient. Under criteria of at least two significant tests in at least two population pairs, three EST-derived and three anonymous loci revealed putative signatures of selection. Anonymous locus FsB113 was a consistent outlier when comparing least saline to fully marine sites. Locus F37 was an outlier when comparing the least saline to more saline areas, and was annotated as a polyol transporter/putative mannitol transporter - an important sugar-alcohol associated with osmoregulation by brown algae. The remaining loci could not be annotated using six different data bases. Exclusion of microsatellite outlier loci did not change either the degree or direction of differentiation among populations. In one outlier test, the number of AFLP outlier loci increased as the salinity differences between population pairs increased (up to 14); only four outliers were detected with the second test and only one was consistent with both tests. Consistency may be improved with a much more rigorous approach to replication and/or may be dependent upon the class of marker used.

  15. Specific determination of benzene in urine using dynamic headspace and mass-selective detection.

    PubMed

    Ljungkvist, G; Lärstad, M; Mathiasson, L

    1999-01-08

    A method for the determination of benzene in urine was developed, based on dynamic headspace and preconcentration of the analyte on a solid sorbent. The subsequent analysis by thermal desorption of the sorbent, capillary gas chromatography and mass-selective detection ascertained a low limit of detection (6.5 ng/l) and a highly specific determination. The limit of detection is an order of magnitude lower than that reported earlier and allows reliable quantitation of occupational exposure and of most environmental exposures. Samples could be stored frozen for at least a month without significant loss.

  16. Unsupervised Spectral-Spatial Feature Selection-Based Camouflaged Object Detection Using VNIR Hyperspectral Camera

    PubMed Central

    2015-01-01

    The detection of camouflaged objects is important for industrial inspection, medical diagnoses, and military applications. Conventional supervised learning methods for hyperspectral images can be a feasible solution. Such approaches, however, require a priori information of a camouflaged object and background. This letter proposes a fully autonomous feature selection and camouflaged object detection method based on the online analysis of spectral and spatial features. The statistical distance metric can generate candidate feature bands and further analysis of the entropy-based spatial grouping property can trim the useless feature bands. Camouflaged objects can be detected better with less computational complexity by optical spectral-spatial feature analysis. PMID:25879073

  17. Selective detection of target proteins by peptide-enabled graphene biosensor.

    PubMed

    Khatayevich, Dmitriy; Page, Tamon; Gresswell, Carolyn; Hayamizu, Yuhei; Grady, William; Sarikaya, Mehmet

    2014-04-24

    Direct molecular detection of biomarkers is a promising approach for diagnosis and monitoring of numerous diseases, as well as a cornerstone of modern molecular medicine and drug discovery. Currently, clinical applications of biomarkers are limited by the sensitivity, complexity and low selectivity of available indirect detection methods. Electronic 1D and 2D nano-materials such as carbon nanotubes and graphene, respectively, offer unique advantages as sensing substrates for simple, fast and ultrasensitive detection of biomolecular binding. Versatile methods, however, have yet to be developed for simultaneous functionalization and passivation of the sensor surface to allow for enhanced detection and selectivity of the device. Herein, we demonstrate selective detection of a model protein against a background of serum protein using a graphene sensor functionalized via self-assembling multifunctional short peptides. The two peptides are engineered to bind to graphene and undergo co-assembly in the form of an ordered monomolecular film on the substrate. While the probe peptide displays the bioactive molecule, the passivating peptide prevents non-specific protein adsorption onto the device surface, ensuring target selectivity. In particular, we demonstrate a graphene field effect transistor (gFET) biosensor which can detect streptavidin against a background of serum bovine albumin at less than 50 ng/ml. Our nano-sensor design, allows us to restore the graphene surface and utilize each sensor in multiple experiments. The peptide-enabled gFET device has great potential to address a variety of bio-sensing problems, such as studying ligand-receptor interactions, or detection of biomarkers in a clinical setting.

  18. Thermodynamics and evolutionary genetics

    NASA Astrophysics Data System (ADS)

    Müller, Ingo

    2010-03-01

    Thermodynamics and evolutionary genetics have something in common. Thus, the randomness of mutation of cells may be likened to the random thermal fluctuations in a gas. And the probabilistic nature of entropy in statistical thermodynamics can be carried over to a population of haploid and diploid cells without any conceptual change. The energetic potential wells in which the atoms of a liquid are caught correspond to selective advantages for some phenotype over others. Thus, the eventual stable state in a population comes about as a compromise in the universal competition between entropy and energy.

  19. Approaches to Improving the Lower Detection Limit of Polymeric Membrane Ion-Selective Electrodes

    PubMed Central

    Szigeti, Zsófia; Vigassy, Tamás; Bakker, Eric; Pretsch, Ernö

    2010-01-01

    More than ten different approaches for improving the lower detection limit of polymeric membrane ion-selective electrodes have been suggested during the recent years. In this contribution, their principles are briefly summarized with a focus to their general practical applicability. The methods that are the most rugged and the easiest to implement in a routine laboratory will be highlighted. PMID:20336172

  20. Hyperspectral imaging-based classification and wavebands selection for internal defect detection of pickling cucumbers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hyperspectral imaging is useful for detecting internal defect of pickling cucumbers. The technique, however, is not yet suitable for high-speed online implementation due to the challenges for analyzing large-scale hyperspectral images. This research was aimed to select the optimal wavebands from the...

  1. Hyperspectral Waveband Selection for Internal Defect Detection of Pickling Cucumbers and Whole Pickles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hyperspectral imaging under transmittance mode has shown potential for detecting internal defect, however, the technique still cannot meet the on-line speed requirement because it needs to acquire and analyze a large amount of image data. This study was carried out to select important wavebands that...

  2. Graphene-carbon nanotube composite aerogel for selective detection of uric acid

    NASA Astrophysics Data System (ADS)

    Zhang, Feifei; Tang, Jie; Wang, Zonghua; Qin, Lu-Chang

    2013-12-01

    Graphene and single-walled carbon nanotube (SWNT) composite aerogel has been prepared by hydrothermal synthesis. The restacking of graphene is effectively reduced by SWNTs inserted in between graphene layers in order to make available more active sites and reactive surface area. Electrochemical experiments show that the graphene-SWNT composite electrode has superior catalytic performance in selective detection of uric acid (UA).

  3. [Quantitative analysis method of natural gas combustion process combining wavelength selection and outlier spectra detection].

    PubMed

    Cao, Hui; Hu, Luo-Na; Zhou, Yan

    2012-10-01

    The present paper uses a combination method of wavelength selection and outlier spectra detection for quantitative analysis of nature gas combustion process based on its near infrared spectra. According to the statistical distribution of partial least squares (PLS) model coefficients and prediction errors, the method realized wavelength selection and outlier spectra detection, respectively. In contrast with PLS, PLS after leave-one-out for outlier detection (LOO-PLS), uninformative variable elimination by PLS (UVE-PLS) and UVE-PLS after leave-one-out for outlier detection (LOO-UVE-PLS), the root-mean-squared error of prediction (RMSEP) based on the method for CH4 prediction model is reduced by 14.33%, 14.33%, 10.96% and 12.21%; the RMSEP value for CO prediction model is reduced by 67.26%, 72.58%, 11.32% and 4.52%; the RMSEP value for CO2 prediction model is reduced by 5.95%, 19.7%, 36.71% and 4.04% respectively. Experimental results demonstrate that the method can significantly decrease the number of selected wavelengths, reduce model complexity and effectively detect outlier spectra. The established prediction model of analytes is more accurate as well as robust.

  4. The influence of phylogenetic uncertainty on the detection of positive Darwinian selection.

    PubMed

    Pie, Marcio R

    2006-12-01

    The power of maximum likelihood tests of positive selection on protein-coding genes depends heavily on detecting and accounting for potential biases in the studied data set. Although the influence of transition:transversion and codon biases have been investigated in detail, little is known about how inaccuracy in the phylogeny used during the calculations affects the performance of these tests. In this study, 3 empirical data sets are analyzed using sets of simulated topologies corresponding to low, intermediate, and high levels of phylogenetic uncertainty. The detection of positive selection was largely unaffected by errors in the underlying phylogeny. However, the number of sites identified as being under positive selection tended to be overestimated.

  5. Redox cycling with facing interdigitated array electrodes as a method for selective detection of redox species.

    PubMed

    Dam, V A T; Olthuis, W; van den Berg, A

    2007-04-01

    A pair of interdigitated ultramicroelectrodes (UMEs) is used to electrochemically detect a weak reductor (dopamine) in the presence of a stronger one (K(4)[Fe(CN)(6)]). In the mixture of both reductors, one of the two interdigitated electrodes (the generator electrode) is used to oxidize both species at 700 mV vs. Ag/AgCl, followed by subsequent (selective) reduction of the oxidized dopamine at 400 mV. A regenerated dopamine molecule can thus be oxidized several times (redox cycling) and enable selective detection even in the presence of the stronger reductor. In order to obtain high redox cycling efficiency, we designed and realized platinum electrodes with widths of 2 and 4 microm and spacing of 2 microm, which gave redox cycling efficiencies of 9 and 4 respectively. Using this electrode design, a dopamine/K(4)[Fe(CN)(6)] selectivity of 2 could be obtained.

  6. Reversible Fluorescent Probe for Selective Detection and Cell Imaging of Oxidative Stress Indicator Bisulfite.

    PubMed

    Zhang, Yajiao; Guan, Lingmei; Yu, Huan; Yan, Yehan; Du, Libo; Liu, Yang; Sun, Mingtai; Huang, Dejian; Wang, Suhua

    2016-04-19

    In this paper, we report a benzothiazole-functionalized cyanine fluorescence probe and demonstrate that it is selectively reactive to bisulfite, an intermediate indicator for oxidative stress. The selective reaction can be monitored by distinct ratiometric fluorescence variation favorable for cell imaging and visualization. The original probe can be regenerated in high yield through the elimination of bisulfite from the product by peroxides such as hydrogen peroxide, accompanied by fluorescence turning on at 590 nm, showing a potential application for the detection of peroxides. We successfully applied this probe for fluorescence imaging of bisulfite in cancer cells (MCF-7) treated with bisulfite and hydrogen peroxide as well as a selective detection limit of 0.34 μM bisulfite in aqueous solution.

  7. Nanomolar colorimetric quantitative detection of Fe3 + and PPi with high selectivity

    NASA Astrophysics Data System (ADS)

    Li, Zhanxian; Li, Haixia; Shi, Caixia; Yu, Mingming; Wei, Liuhe; Ni, Zhonghai

    2016-04-01

    A novel rhodamine and 8-hydroxyquinoline-based derivative was synthesized, which is shown to act as a colorimetric chemosensor for Fe3 + in aqueous solution with high selectivity over various environmentally and biologically relevant metal ions and anions with a distinct color change from colorless to pink in very fast response time (< 1 min). Fe3 + can be detected quantitatively in the concentration range from 6.7 to 16 μM and the detection limit (LOD) on UV-vis response of the sensor can be as low as 15 nM. The 'in situ' prepared Fe3 + complex (1 ṡ Fe) showed high selectivity toward PPi against many common anions, and sensitivity (the LOD can be as low as 71 nM). In addition, both the chemosensor and the 'in situ' prepared Fe3 + complex are reusable for the detection of Fe3 + and PPi respectively.

  8. Neuronal boost to evolutionary dynamics.

    PubMed

    de Vladar, Harold P; Szathmáry, Eörs

    2015-12-06

    Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild.

  9. Neuronal boost to evolutionary dynamics

    PubMed Central

    de Vladar, Harold P.; Szathmáry, Eörs

    2015-01-01

    Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild. PMID:26640653

  10. Evolutionary engineering for industrial microbiology.

    PubMed

    Vanee, Niti; Fisher, Adam B; Fong, Stephen S

    2012-01-01

    Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering.

  11. Robustness of chemometrics-based feature selection methods in early cancer detection and biomarker discovery.

    PubMed

    Lee, Hae Woo; Lawton, Carl; Na, Young Jeong; Yoon, Seongkyu

    2013-03-13

    In omics studies aimed at the early detection and diagnosis of cancer, bioinformatics tools play a significant role when analyzing high dimensional, complex datasets, as well as when identifying a small set of biomarkers. However, in many cases, there are ambiguities in the robustness and the consistency of the discovered biomarker sets, since the feature selection methods often lead to irreproducible results. To address this, both the stability and the classification power of several chemometrics-based feature selection algorithms were evaluated using the Monte Carlo sampling technique, aiming at finding the most suitable feature selection methods for early cancer detection and biomarker discovery. To this end, two data sets were analyzed, which comprised of MALDI-TOF-MS and LC/TOF-MS spectra measured on serum samples in order to diagnose ovarian cancer. Using these datasets, the stability and the classification power of multiple feature subsets found by different feature selection methods were quantified by varying either the number of selected features, or the number of samples in the training set, with special emphasis placed on the property of stability. The results show that high consistency does not necessarily guarantee high predictive power. In addition, differences in the stability, as well as agreement in feature lists between several feature selection methods, depend on several factors, such as the number of available samples, feature sizes, quality of the information in the dataset, etc. Among the tested methods, only the variable importance in projection (VIP)-based method shows complementary properties, providing both highly consistent and accurate subsets of features. In addition, successive projection analysis (SPA) was excellent with regards to maintaining high stability over a wide range of experimental conditions. The stability of several feature selection methods is highly variable, stressing the importance of making the proper choice among

  12. Determination of target detection limits in hyperspectral data using band selection and dimensionality reduction

    NASA Astrophysics Data System (ADS)

    Gross, W.; Boehler, J.; Twizer, K.; Kedem, B.; Lenz, A.; Kneubuehler, M.; Wellig, P.; Oechslin, R.; Schilling, H.; Rotman, S.; Middelmann, W.

    2016-10-01

    Hyperspectral remote sensing data can be used for civil and military applications to robustly detect and classify target objects. High spectral resolution of hyperspectral data can compensate for the comparatively low spatial resolution, which allows for detection and classification of small targets, even below image resolution. Hyperspectral data sets are prone to considerable spectral redundancy, affecting and limiting data processing and algorithm performance. As a consequence, data reduction strategies become increasingly important, especially in view of near-real-time data analysis. The goal of this paper is to analyze different strategies for hyperspectral band selection algorithms and their effect on subpixel classification for different target and background materials. Airborne hyperspectral data is used in combination with linear target simulation procedures to create a representative amount of target-to-background ratios for evaluation of detection limits. Data from two different airborne hyperspectral sensors, AISA Eagle and Hawk, are used to evaluate transferability of band selection when using different sensors. The same target objects were recorded to compare the calculated detection limits. To determine subpixel classification results, pure pixels from the target materials are extracted and used to simulate mixed pixels with selected background materials. Target signatures are linearly combined with different background materials in varying ratios. The commonly used classification algorithms Adaptive Coherence Estimator (ACE) is used to compare the detection limit for the original data with several band selection and data reduction strategies. The evaluation of the classification results is done by assuming a fixed false alarm ratio and calculating the mean target-to-background ratio of correctly detected pixels. The results allow drawing conclusions about specific band combinations for certain target and background combinations. Additionally

  13. Detection of Selection Signatures on the X Chromosome in Three Sheep Breeds.

    PubMed

    Zhu, Caiye; Fan, Hongying; Yuan, Zehu; Hu, Shijin; Zhang, Li; Wei, Caihong; Zhang, Qin; Zhao, Fuping; Du, Lixin

    2015-08-28

    Artificial selection has played a critical role in animal breeding. Detection of artificial selection footprints in genomic regions can provide insights for understanding the function of specific phenotypic traits and better guide animal breeding. To more fully understand the relationship between genomic composition and phenotypic diversity arising from breed development, a genome-wide scan was conducted using an OvineSNP50 BeadChip and integrated haplotype score and fixation index analyses to detect selection signatures on the X chromosome in three sheep breeds. We identified 49, 34, and 55 candidate selection regions with lengths of 27.49, 16.47, and 25.42 Mb in German Mutton, Dorper, and Sunit sheep, respectively. Bioinformatics analysis showed that some of the genes in these regions with selection signatures, such as BMP15, were relevant to reproduction. We also identified some selection regions harboring genes that had human orthologs, including BKT, CENPI, GUCY2F, MSN, PCDH11X, PLP1, VSIG4, PAK3, WAS, PCDH19, PDHA1, and SRPX2. The VSIG4 and PCDH11X genes are associated with the immune system and disease, PDHA1 is associated with biosynthetic related pathways, and PCDH19 is expressed in the nervous system and skin. These genes may be useful as candidate genes for molecular breeding.

  14. Development of a selective agar plate for the detection of Campylobacter spp. in fresh produce.

    PubMed

    Yoo, Jin-Hee; Choi, Na-Young; Bae, Young-Min; Lee, Jung-Su; Lee, Sun-Young

    2014-10-17

    This study was conducted to develop a selective medium for the detection of Campylobacter spp. in fresh produce. Campylobacter spp. (n=4), non-Campylobacter (showing positive results on Campylobacter selective agar) strains (n=49) isolated from fresh produce, indicator bacteria (n=13), and spoilage bacteria isolated from fresh produce (n=15) were plated on four Campylobacter selective media. Bolton agar and modified charcoal cefoperazone deoxycholate agar (mCCDA) exhibited higher sensitivity for Campylobacter spp. than did Preston agar and Hunt agar, although certain non-Campylobacter strains isolated from fresh produce by using a selective agar isolation method, were still able to grow on Bolton agar and mCCDA. To inhibit the growth of non-Campylobacter strains, Bolton agar and mCCDA were supplemented with 5 antibiotics (rifampicin, polymyxin B, sodium metabisulfite, sodium pyruvate, ferrous sulfate) and the growth of Campylobacter spp. (n=7) and non-Campylobacter strains (n=44) was evaluated. Although Bolton agar supplemented with rifampicin (BR agar) exhibited a higher selectivity for Campylobacter spp. than did mCCDA supplemented with antibiotics, certain non-Campylobacter strains were still able to grow on BR agar (18.8%). When BR agar with various concentrations of sulfamethoxazole-trimethoprim were tested with Campylobacter spp. (n=8) and non-Campylobacter (n=7), sulfamethoxazole-trimethoprim was inhibitory against 3 of 7 non-Campylobacter strains. Finally, we validated the use of BR agar containing 50mg/L sulfamethoxazole (BRS agar) or 0.5mg/L ciprofloxacin (BRCS agar) and other selective agars for the detection of Campylobacter spp. in chicken and fresh produce. All chicken samples were positive for Campylobacter spp. when tested on mCCDA, BR agar, and BRS agar. In fresh produce samples, BRS agar exhibited the highest selectivity for Campylobacter spp., demonstrating its suitability for the detection of Campylobacter spp. in fresh produce.

  15. Evolutionary Divergence of Arabidopsis thaliana Classical Peroxidases.

    PubMed

    Kupriyanova, E V; Mamoshina, P O; Ezhova, T A

    2015-10-01

    Polymorphisms of 62 peroxidase genes derived from Arabidopsis thaliana were investigated to evaluate evolutionary dynamics and divergence of peroxidase proteins. By comparing divergence of duplicated genes AtPrx53-AtPrx54 and AtPrx36-AtPrx72 and their products, nucleotide and amino acid substitutions were identified that were apparently targets of positive selection. These substitutions were detected among paralogs of 461 ecotypes from Arabidopsis thaliana. Some of these substitutions are conservative and matched paralogous peroxidases in other Brassicaceae species. These results suggest that after duplication, peroxidase genes evolved under the pressure of positive selection, and amino acid substitutions identified during our study provided divergence of properties and physiological functions in peroxidases. Our predictions regarding functional significance for amino acid residues identified in variable sites of peroxidases may allow further experimental assessment of evolution of peroxidases after gene duplication.

  16. Reactive chromophores for sensitive and selective detection of chemical warfare agents and toxic industrial chemicals

    NASA Astrophysics Data System (ADS)

    Frye-Mason, Greg; Leuschen, Martin; Wald, Lara; Paul, Kateri; Hancock, Lawrence F.

    2005-05-01

    A reactive chromophore developed at MIT exhibits sensitive and selective detection of surrogates for G-class nerve agents. This reporter acts by reacting with the agent to form an intermediate that goes through an internal cyclization reaction. The reaction locks the molecule into a form that provides a strong fluorescent signal. Using a fluorescent sensor platform, Nomadics has demonstrated rapid and sensitive detection of reactive simulants such as diethyl chloro-phosphate (simulant for sarin, soman, and related agents) and diethyl cyanophosphate (simulant for tabun). Since the unreacted chromophore does not fluoresce at the excitation wavelength used for the cyclized reporter, the onset of fluo-rescence can be easily detected. This fluorescence-based detection method provides very high sensitivity and could enable rapid detection at permissible exposure levels. Tests with potential interferents show that the reporter is very selective, with responses from only a few highly toxic, electrophilic chemicals such as phosgene, thionyl chloride, and strong acids such as HF, HCl, and nitric acid. Dimethyl methyl phosphonate (DMMP), a common and inactive simu-lant for other CW detectors, is not reactive enough to generate a signal. The unique selectivity to chemical reactivity means that a highly toxic and hazardous chemical is present when the reporter responds and illustrates that this sensor can provide very low false alarm rates. Current efforts focus on demonstrating the sensitivity and range of agents and toxic industrial chemicals detected with this reporter as well as developing additional fluorescent reporters for a range of chemical reactivity classes. The goal is to produce a hand-held sensor that can sensitively detect a broad range of chemical warfare agent and toxic industrial chemical threats.

  17. Selection of Ceratitis capitata (Diptera: Tephritidae) Specific Recombinant Monoclonal Phage Display Antibodies for Prey Detection Analysis

    PubMed Central

    Monzó, César; Urbaneja, Alberto; Ximénez-Embún, Miguel; García-Fernández, Julia; García, José Luis; Castañera, Pedro

    2012-01-01

    Several recombinant antibodies against the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), one of the most important pests in agriculture worldwide, were selected for the first time from a commercial phage display library of human scFv antibodies. The specificity and sensitivity of the selected recombinant antibodies were compared with that of a rabbit polyclonal serum raised in parallel using a wide range of arthropod species as controls. The selected recombinant monoclonal antibodies had a similar or greater specificity when compared with classical monoclonal antibodies. The selected recombinant antibodies were successfully used to detect the target antigen in the gut of predators and the scFv antibodies were sequenced and compared. These results demonstrate the potential for recombinant scFv antibodies to be used as an alternative to the classical monoclonal antibodies or even molecular probes in the post-mortem analysis studies of generalist predators. PMID:23272105

  18. Damage Detection by the Mode-Selectable Magnetostrictive Transducer for Cylindrical Ferromagnetic Waveguides

    NASA Astrophysics Data System (ADS)

    Kim, Youngkyu; Kim, Ikkyu; Kim, Yoon Young

    2004-02-01

    In recent years, ultrasonic inspection techniques adopting magnetostrictive effects have received much attention, because they are non-destructive and require no direct physical contact with target systems. By selecting the desired wave mode and thus rejecting the unwanted modes amongst propagating waves in cylindrical ferromagnetic waveguides, we can effectively detect various types of flaws. However, a bending wave mode selecting technique, in particular, has not been fully developed yet. The purpose of this work is to present a technique to select either bending or longitudinal waves alone from compound waves propagating in ferromagnetic cylindrical waveguide. To achieve this goal, a new bias magnet configuration suitable for bending mode selection is suggested. The experimental results verify the effectiveness of the proposed method.

  19. Selection of Ceratitis capitata (Diptera: Tephritidae) specific recombinant monoclonal phage display antibodies for prey detection analysis.

    PubMed

    Monzó, César; Urbaneja, Alberto; Ximénez-Embún, Miguel; García-Fernández, Julia; García, José Luis; Castañera, Pedro

    2012-01-01

    Several recombinant antibodies against the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), one of the most important pests in agriculture worldwide, were selected for the first time from a commercial phage display library of human scFv antibodies. The specificity and sensitivity of the selected recombinant antibodies were compared with that of a rabbit polyclonal serum raised in parallel using a wide range of arthropod species as controls. The selected recombinant monoclonal antibodies had a similar or greater specificity when compared with classical monoclonal antibodies. The selected recombinant antibodies were successfully used to detect the target antigen in the gut of predators and the scFv antibodies were sequenced and compared. These results demonstrate the potential for recombinant scFv antibodies to be used as an alternative to the classical monoclonal antibodies or even molecular probes in the post-mortem analysis studies of generalist predators.

  20. Evolutionary genetics of maternal effects

    PubMed Central

    Wolf, Jason B.; Wade, Michael J.

    2016-01-01

    Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single‐locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype‐phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype‐phenotype relationship frequency dependent, resulting in the appearance of negative frequency‐dependent selection, while additive MGEs contribute a component of parent‐of‐origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be “available” to the evolving population. PMID:26969266

  1. Using Scent Detection Dogs in Conservation Settings: A Review of Scientific Literature Regarding Their Selection

    PubMed Central

    Beebe, Sarah C.; Howell, Tiffani J.; Bennett, Pauleen C.

    2016-01-01

    Dogs are widely used for scent detection work, assisting in searches for, among other things, missing persons, explosives, and even cancers. They are also increasingly used in conservation settings, being deployed for a range of diverse purposes. Although scent detecting dogs have been used in conservation roles for over 100 years, it is only recently that the scientific literature has begun to document their effectiveness and, importantly, how suitable dogs should initially be selected by organizations wanting to develop a detection program. In this paper, we review this literature, with the aim of extracting information that might be of value to conservation groups considering whether to invest in the use of dogs. We conclude that selection of appropriate dogs is no easy task. While olfactory ability is critical, so also are a range of other characteristics. These include biological, psychological, and social traits. At present, no validated selection tools have been published. Existing organizations have adapted selection instruments from other contexts for their use, but very little published information is available regarding the effectiveness of these instruments in a conservation setting. In the absence of clear guidelines, we urge those wanting to invest in one or more dogs for conservation purposes to proceed with extreme caution and, preferably, under the watchful eyes of an experienced professional. PMID:27840815

  2. Leveraging zinc interstitials and oxygen vacancies for sensitive biomolecule detection through selective surface functionalization

    NASA Astrophysics Data System (ADS)

    Radha Shanmugam, Nandhinee; Muthukumar, Sriram; Chaudhry, Shajee; Prasad, Shalini

    2015-03-01

    In this study, functionally engineered EIS technique was implemented to investigate the influence of surface functionalization on sensitivity of biomolecule detection using nanostructured ZnO platform. Organic molecules with thiol and carboxylic functional groups were chosen to control biomolecule immobilization on zinc and oxygen-terminated 2D planar and 1D nanostructured ZnO surfaces. The amount of functionalization and its influence on charge perturbations at the ZnO-electrolyte interface were studied using fluorescence and EIS measurements. We observed the dependence of charge transfer on both the polarity of platform and concentration of cross-linker molecules. Such selectively modified surfaces were used for detection of cortisol, a major stress indicator. Results demonstrated preferential binding of thiol groups to Zn terminations and thus leveraging ZnO interstitials increases the sensitivity of detection over larger dynamic range with detection limit at 10fg/mL.

  3. A Functional polymorphism under positive evolutionary selection in ADRB2 is associated with human intelligence with opposite effects in the young and the elderly.

    PubMed

    Bochdanovits, Zoltán; Gosso, Florencia M; van den Berg, Linda; Rizzu, Patrizia; Polderman, Tinca J C; Pardo, Luba M; Houlihan, Lorna M; Luciano, Michelle; Starr, John M; Harris, Sarah E; Deary, Ian J; de Geus, Eco J C; Boomsma, Dorret I; Heutink, Peter; Posthuma, Danielle

    2009-01-01

    Comparative genomics offers a novel approach to unravel the genetic basis of complex traits. We performed a two stage analysis where genes ascertained for enhanced protein evolution in primates are subsequently searched for the presence of non-synonymous coding SNPs in the current human population at amino acid sites that differ between humans and chimpanzee. Positively selected genes among primates are generally presumed to determine phenotypic differences between humans and chimpanzee, such as the enhanced cognitive ability of our species. Amino acid substitutions segregating in humans at positively selected amino acid sites are expected to affect phenotypic differences among humans. Therefore we conducted an association study in two family based cohorts and one population based cohort between cognitive ability and the most likely candidate gene among the five that harbored more than one such polymorphism. The derived, human-specific allele of the beta-2 adrenergic receptor Arg16Gly polymorphism was found to be the increaser allele for performance IQ in the young, family based cohort but the decreaser allele for two different measures of cognition in the large Scottish cohort of unrelated individuals. The polymorphism is known to affect signaling activity and modulation of beta-2 adrenergic signaling has been shown to adjust memory consolidation, a trait related to cognition. The opposite effect of the polymorphism on cognition in the two age classes observed in the different cohorts resembles the effect of ADRB2 on hypertension, which also has been reported to be age dependent. This result illustrates the relevance of comparative genomics to detect genes that are involved in human behavior.

  4. Bipyridine hydrogel for selective and visible detection and absorption of Cd2+

    NASA Astrophysics Data System (ADS)

    Miao, Qingqing; Wu, Ziye; Hai, Zijuan; Tao, Changlu; Yuan, Qingpan; Gong, Yadi; Guan, Yafeng; Jiang, Jun; Liang, Gaolin

    2015-01-01

    Herein, we report for the first time the use of bipyridine-based hydrogel for selective and visible detection and absorption of Cd2+. At low concentrations, hydrogelator 1 was applied for selective detection of Cd2+in vitro and in living cells with high sensitivity. In the absence of metal ions, 1 is nonfluorescent at 470 nm. Upon addition of metal ions, 1 selectively coordinates to Cd2+, causing an 86-fold increase of fluorescence intensity at 470 nm via the chelation enhanced fluorescence (CHEF) effect, as revealed by first-principles simulations. At 1.5 wt% and pH 5.5, 1 self-assembles into nanofibers to form hydrogel Gel I. Since Cd2+ could actively participate in the hydrogelation and promote the self-assembly, we also successfully applied Gel I for visible detection and absorption of Cd2+. With these excellent properties, Gel I is expected to be explored as one type of versatile biomaterial for not only environmental monitoring but also for pollution treatment in the near future.Herein, we report for the first time the use of bipyridine-based hydrogel for selective and visible detection and absorption of Cd2+. At low concentrations, hydrogelator 1 was applied for selective detection of Cd2+in vitro and in living cells with high sensitivity. In the absence of metal ions, 1 is nonfluorescent at 470 nm. Upon addition of metal ions, 1 selectively coordinates to Cd2+, causing an 86-fold increase of fluorescence intensity at 470 nm via the chelation enhanced fluorescence (CHEF) effect, as revealed by first-principles simulations. At 1.5 wt% and pH 5.5, 1 self-assembles into nanofibers to form hydrogel Gel I. Since Cd2+ could actively participate in the hydrogelation and promote the self-assembly, we also successfully applied Gel I for visible detection and absorption of Cd2+. With these excellent properties, Gel I is expected to be explored as one type of versatile biomaterial for not only environmental monitoring but also for pollution treatment in the near future

  5. Genome-wide detection of natural selection in African Americans pre- and post-admixture.

    PubMed

    Jin, Wenfei; Xu, Shuhua; Wang, Haifeng; Yu, Yongguo; Shen, Yiping; Wu, Bailin; Jin, Li

    2012-03-01

    It is particularly meaningful to investigate natural selection in African Americans (AfA) due to the high mortality their African ancestry has experienced in history. In this study, we examined 491,526 autosomal single nucleotide polymorphisms (SNPs) genotyped in 5210 individuals and conducted a genome-wide search for selection signals in 1890 AfA. Several genomic regions showing an excess of African or European ancestry, which were considered the footprints of selection since population admixture, were detected based on a commonly used approach. However, we also developed a new strategy to detect natural selection both pre- and post-admixture by reconstructing an ancestral African population (AAF) from inferred African components of ancestry in AfA and comparing it with indigenous African populations (IAF). Interestingly, many selection-candidate genes identified by the new approach were associated with AfA-specific high-risk diseases such as prostate cancer and hypertension, suggesting an important role these disease-related genes might have played in adapting to a new environment. CD36 and HBB, whose mutations confer a degree of protection against malaria, were also located in the highly differentiated regions between AAF and IAF. Further analysis showed that the frequencies of alleles protecting against malaria in AAF were lower than those in IAF, which is consistent with the relaxed selection pressure of malaria in the New World. There is no overlap between the top candidate genes detected by the two approaches, indicating the different environmental pressures AfA experienced pre- and post-population admixture. We suggest that the new approach is reasonably powerful and can also be applied to other admixed populations such as Latinos and Uyghurs.

  6. Selective transgene expression for detection and elimination of contaminating carcinoma cells in hematopoietic stem cell sources.

    PubMed Central

    Chen, L; Pulsipher, M; Chen, D; Sieff, C; Elias, A; Fine, H A; Kufe, D W

    1996-01-01

    Tumor contamination of bone marrow (BM) and peripheral blood (PB) may affect the outcome of patients receiving high dose chemotherapy with autologous transplantation of hematopoietic stem cell products. In this report, we demonstrate that replication defective adenoviral vectors containing the cytomegalovirus (CMV) or DF3/MUC1 carcinoma-selective promoter can be used to selectively transduce contaminating carcinoma cells. Adenoviral-mediated reporter gene expression in breast cancer cells was five orders of magnitude higher than that found in BM, PB, and CD34+ cells. Our results demonstrate that CD34+ cells have low to undetectable levels of integrins responsible for adenoviral internalization. We show that adenoviral-mediated transduction of a reporter gene can detect one breast cancer cell in 5 x 10(5) BM or PB cells with a vector containing the DF3/MUC1 promoter. We also show that transduction of the HSV-tk gene for selective killing by ganciclovir can be exploited for purging cancer cells from hematopoietic stem cell populations. The selective expression of TK followed by ganciclovir treatment resulted in the elimination of 6-logs of contaminating cancer cells. By contrast, there was little effect on CFU-GM and BFU-E formulation or on long term culture initiating cells. These results indicate that adenoviral vectors with a tumor-selective promoter provide a highly efficient and effective approach for the detection and purging of carcinoma cells in hematopoietic stem cell preparations. PMID:8958216

  7. A Smart Near-Infrared Fluorescence Probe for Selective Detection of Tau Fibrils in Alzheimer's Disease.

    PubMed

    Seo, Yujin; Park, Kwang-Su; Ha, Taewoong; Kim, Mi Kyoung; Hwang, Yu Jin; Lee, Junghee; Ryu, Hoon; Choo, Hyunah; Chong, Youhoon

    2016-11-16

    Development of a novel, tau-selective smart near-infrared fluorescence (NIRF) probe was attempted by combining the previously identified core scaffold 3,5-dimethoxy-N,N-dimethylaniline-4-yl moiety, with the characteristic donor-π-acceptor architecture of the smart NIRF Aβ probes DANIR-2c and MCAAD-3. A series of compounds (2 and 3) were prepared, which were identified as "turn-on" NIRF probes for the visual detection of tau aggregates and Aβ fibrils (λem = 650 nm, Stokes shifts = 70-110 nm). In particular, combination of the 3,5-dimethoxy-N,N-dimethylanilin-4-yl moiety and the donor part of MCAAD-3 endowed the resulting probes, 3g and 3h, with significant selectivity toward tau aggregates (selectivity for tau over Aβ = 5.7 and 3.8); they showed much higher fluorescence intensities upon binding to tau aggregates (FItau = 49 and 108) than when bound to Aβ fibrils (FIAβ = 9 and 28). Quantitative analysis of binding affinities and fluorescence properties of 3g and 3h revealed that microenvironment-sensitive molecular rotor-like behavior, rather than binding affinity to the target, is responsible for their selective turn-on fluorescence detection of tau fibrils. Selective fluorescent labeling of tau fibrils by 3g and 3h was further demonstrated by immunofluorescence staining of human Alzheimer's disease brain sections, which showed colocalization of the probes (3g and 3h) and phosphorylated tau antibody.

  8. Detecting the footprints of divergent selection in oaks with linked markers

    PubMed Central

    Goicoechea, P G; Petit, R J; Kremer, A

    2012-01-01

    Genome scans are increasingly used to study ecological speciation, providing a useful genome-wide perspective on divergent selection in the presence of gene flow. Here, we compare current approaches to detect footprints of divergent selection in closely related species. We analyzed 192 individuals from two interfertile European temperate oak species using 30 nuclear microsatellites from eight linkage groups. These markers present little intraspecific differentiation and can be used in combination to assign individual genotypes to species. We first show that different outlier detection tests give somewhat different results, possibly due to model constraints. Second, using linkage information for these markers, we further characterize the signature of divergent selection in the presence of gene flow. In particular, we show that recombination estimates for regions with outlier markers are lower than those for a control region, in line with a prediction from ecological speciation theory. Most importantly, we show that analyses at the haplotype level can distinguish between truly divergent (bi-directional) selection and positive selection in one of the two species, offering a new and improved method for characterizing the speciation process. PMID:22990311

  9. Highly selective detection of oil spill polycyclic aromatic hydrocarbons using molecularly imprinted polymers for marine ecosystems.

    PubMed

    Krupadam, Reddithota J; Nesterov, Evgueni E; Spivak, David A

    2014-06-15

    Im*plications due to oil spills on marine ecosystems have created a great interest toward developing more efficient and selective materials for oil spill toxins detection and remediation. This research paper highlights the application of highly efficient molecularly imprinted polymer (MIP) adsorbents based on a newly developed functional crosslinker (N,O-bismethacryloyl ethanolamine, NOBE) for detection of highly toxic polycyclic aromatic hydrocarbons (PAHs) in seawater. The binding capacity of MIP for oil spill toxin pyrene is 35 mg/g as compared to the value of 3.65 mg/g obtained using a non-imprinted polymer (NIP). The selectivity of all three high molecular weight PAHs (pyrene, chrysene and benzo[a]pyrene) on the NOBE-MIP shows an excellent selective binding with only 5.5% and 7% cross-reactivity for chrysene and benzo[a]pyrene, respectively. Not only is this particularly significant because the rebinding solvent is water, which is known to promote non-selective hydrophobic interactions; the binding remains comparable under salt-water conditions. These selective and high capacity adsorbents will find wide application in industrial and marine water monitoring/remediation.

  10. Contrast based band selection for optimized weathered oil detection in hyperspectral images

    NASA Astrophysics Data System (ADS)

    Levaux, Florian; Bostater, Charles R., Jr.; Neyt, Xavier

    2012-09-01

    Hyperspectral imagery offers unique benefits for detection of land and water features due to the information contained in reflectance signatures such as the bi-directional reflectance distribution function or BRDF. The reflectance signature directly shows the relative absorption and backscattering features of targets. These features can be very useful in shoreline monitoring or surveillance applications, for example to detect weathered oil. In real-time detection applications, processing of hyperspectral data can be an important tool and Optimal band selection is thus important in real time applications in order to select the essential bands using the absorption and backscatter information. In the present paper, band selection is based upon the optimization of target detection using contrast algorithms. The common definition of the contrast (using only one band out of all possible combinations available within a hyperspectral image) is generalized in order to consider all the possible combinations of wavelength dependent contrasts using hyperspectral images. The inflection (defined here as an approximation of the second derivative) is also used in order to enhance the variations in the reflectance spectra as well as in the contrast spectrua in order to assist in optimal band selection. The results of the selection in term of target detection (false alarms and missed detection) are also compared with a previous method to perform feature detection, namely the matched filter. In this paper, imagery is acquired using a pushbroom hyperspectral sensor mounted at the bow of a small vessel. The sensor is mechanically rotated using an optical rotation stage. This opto-mechanical scanning system produces hyperspectral images with pixel sizes on the order of mm to cm scales, depending upon the distance between the sensor and the shoreline being monitored. The motion of the platform during the acquisition induces distortions in the collected HSI imagery. It is therefore

  11. Validation of the ANSR® Listeria Method for Detection of Listeria spp. in Selected Foods.

    PubMed

    Caballero, Oscar; Alles, Susan; Wendorf, Michael; Gray, R Lucas; Walton, Kayla; Pinkava, Lisa; Mozola, Mark; Rice, Jennifer

    2015-01-01

    ANSR® Listeria was previously certified as Performance Tested Method(SM) 101202 for detection of Listeria spp. on selected environmental surfaces. This study proposes a matrix extension to the method for detection of Listeria spp. in selected food matrixes. The method is an isothermal nucleic acid amplification assay based on the nicking enzyme amplification reaction technology. Following single-step sample enrichment for 16-24 h, the assay is completed in less than 50 min, requiring only simple instrumentation. Inclusivity testing was performed using a panel of 51 strains of Listeria spp., representing the species L. grayi, L. innocua, L. ivanovii, L. monocytogenes, L. seeligeri, and L. welshimeri. All strains tested were detected by the ANSR assay. Exclusivity testing of 30 strains representing non-Listeria Gram-positive bacteria yielded no evidence of cross-reactivity. Performance of the ANSR method for detection of Listeria spp. was compared to that of reference culture procedures for pasteurized liquid egg, pasteurized 2% milk, Mexican-style cheese, ice cream, smoked salmon, lettuce, cantaloupe, and guacamole. Data obtained in these unpaired studies and analyzed using a probability of detection model demonstrated that there were no statistically significant differences in results between the ANSR and reference culture methods, except for milk at 16 h and cantaloupe. In milk and smoked salmon, ANSR sensitivity was low at 16 h and therefore the recommended incubation time is 24 h. In cantaloupe, ANSR was found to be more sensitive than the reference culture method at both 16 and 24 h in independent laboratory testing. The ANSR Listeria method can be used as an accurate, rapid, and simple alternative to standard culture methods for detection of Listeria spp. in selected food types.

  12. FTIR gas analysis with improved sensitivity and selectivity for CWA and TIC detection

    NASA Astrophysics Data System (ADS)

    Phillips, Charles M.; Tan, Huwei

    2010-04-01

    This presentation describes the use of an FTIR (Fourier Transform Infrared)-based spectrometer designed to continuously monitor ambient air for the presence of chemical warfare agents (CWAs) and toxic industrial chemicals (TICs). The necessity of a reliable system capable of quickly and accurately detecting very low levels of CWAs and TICs while simultaneously retaining a negligible false alarm rate will be explored. Technological advancements in FTIR sensing have reduced noise while increasing selectivity and speed of detection. These novel analyzer design characteristics are discussed in detail and descriptions are provided which show how optical throughput, gas cell form factor, and detector response are optimized. The hardware and algorithms described here will explain why this FTIR system is very effective for the simultaneous detection and speciation of a wide variety of toxic compounds at ppb concentrations. Analytical test data will be reviewed demonstrating the system's sensitivity to and selectivity for specific CWAs and TICs; this will include recent data acquired as part of the DHS ARFCAM (Autonomous Rapid Facility Chemical Agent Monitor) project. These results include analyses of the data from live agent testing for the determination of CWA detection limits, immunity to interferences, detection times, residual noise analysis and false alarm rates. Sensing systems such as this are critical for effective chemical hazard identification which is directly relevant to the CBRNE community.

  13. Selective Virus Detection in Complex Sample Matrices with Photonic Crystal Optical Cavities

    PubMed Central

    Pal, Sudeshna; Yadav, Amrita R.; Lifson, Mark A.; Baker, James E.; Fauchet, Philippe M.; Miller, Benjamin L.

    2013-01-01

    Rapid, sensitive, and selective detection of viruses is critical for applications in medical diagnostics, biosecurity, and environmental safety. In this article, we report the application of a point-defect-coupled W1 photonic crystal (PhC) waveguide biosensor to label-free optical detection of viruses. Fabricated on a silicon-on-insulator (SOI) substrate using electron-beam (e-beam) lithography and reactive-ion-etching, the PhC sensing platform allows optical detection based on resonant mode shifts in response to ambient refractive index changes produced by infiltration of target biomaterial within the holes of the PhC structure. Finite difference time domain (FDTD) calculations were performed to assist with design of the sensor, and to serve as a theoretical benchmark against which experimental results could be compared. Using Human Papillomavirus virus-like particles (VLPs) spiked in 10% fetal bovine serum as a model system, we observed a limit of detection of 1.4 nM in simple (buffer only) or complex (10% serum) sample matrices. The use of anti-VLP antibodies specific for intact VLPs with the PhC sensors provided highly selective VLP detection. PMID:23434758

  14. Ultra-sensitive and selective Hg{sup 2+} detection based on fluorescent carbon dots

    SciTech Connect

    Liu, Ruihua; Li, Haitao; Kong, Weiqian; Liu, Juan; Liu, Yang; Tong, Cuiyan; Zhang, Xing; Kang, Zhenhui

    2013-07-15

    Graphical abstract: Fluorescent carbon dots were efficiently synthesized by one-step sodium hydroxide-assisted reflux method from PEG and demonstrated to show high selectivity toward Hg2+ ions detection. - Highlights: • FCDs were synthesized by one-step sodium hydroxide-assisted reflux method from PEG. • The FCDs emit blue photoluminescence and have upconversion fluorescent property. • The FCDs show ultra-sensitive detective ability for Hg{sup 2+} ions. - Abstract: Fluorescent carbon dots (FCDs) were efficiently synthesized by one-step sodium hydroxide-assisted reflux method from poly(ethylene glycol) (PEG). The obtained FCDs exhibit excellent water-solubility and high stability. Under the UV irradiation, the FCDs could emit bright blue photoluminescence, and also they were found to show excellent up-conversion fluorescence. It was further demonstrated that such FCDs can serve as effective fluorescent sensing platform for Hg{sup 2+} ions detection with ultra-sensitivity and selectivity. The sensing system achieved a limit of detection as low as 1 fM, which is much lower than all the previous reported sensing systems for Hg{sup 2+} ions detection. This FCDs sensing system has been successfully applied for the analysis of Hg{sup 2+} ions in water samples from river, lake, and tap water, showing good practical feasibility.

  15. Feature Selection and Classifier Parameters Estimation for EEG Signals Peak Detection Using Particle Swarm Optimization

    PubMed Central

    Adam, Asrul; Mohd Tumari, Mohd Zaidi; Mohamad, Mohd Saberi

    2014-01-01

    Electroencephalogram (EEG) signal peak detection is widely used in clinical applications. The peak point can be detected using several approaches, including time, frequency, time-frequency, and nonlinear domains depending on various peak features from several models. However, there is no study that provides the importance of every peak feature in contributing to a good and generalized model. In this study, feature selection and classifier parameters estimation based on particle swarm optimization (PSO) are proposed as a framework for peak detection on EEG signals in time domain analysis. Two versions of PSO are used in the study: (1) standard PSO and (2) random asynchronous particle swarm optimization (RA-PSO). The proposed framework tries to find the best combination of all the available features that offers good peak detection and a high classification rate from the results in the conducted experiments. The evaluation results indicate that the accuracy of the peak detection can be improved up to 99.90% and 98.59% for training and testing, respectively, as compared to the framework without feature selection adaptation. Additionally, the proposed framework based on RA-PSO offers a better and reliable classification rate as compared to standard PSO as it produces low variance model. PMID:25243236

  16. Selective virus detection in complex sample matrices with photonic crystal optical cavities.

    PubMed

    Pal, Sudeshna; Yadav, Amrita R; Lifson, Mark A; Baker, James E; Fauchet, Philippe M; Miller, Benjamin L

    2013-06-15

    Rapid, sensitive, and selective detection of viruses is critical for applications in medical diagnostics, biosecurity, and environmental safety. In this article, we report the application of a point-defect-coupled W1 photonic crystal (PhC) waveguide biosensor to label-free optical detection of viruses. Fabricated on a silicon-on-insulator (SOI) substrate using electron-beam (e-beam) lithography and reactive-ion-etching, the PhC sensing platform allows optical detection based on resonant mode shifts in response to ambient refractive index changes produced by infiltration of target biomaterial within the holes of the PhC structure. Finite difference time domain (FDTD) calculations were performed to assist with design of the sensor, and to serve as a theoretical benchmark against which experimental results could be compared. Using Human Papillomavirus virus-like particles (VLPs) spiked in 10% fetal bovine serum as a model system, we observed a limit of detection of 1.5 nM in simple (buffer only) or complex (10% serum) sample matrices. The use of anti-VLP antibodies specific for intact VLPs with the PhC sensors provided highly selective VLP detection.

  17. Highly sensitive and selective detection of cancer cell with a label-free electrochemical cytosensor.

    PubMed

    Liu, Jiyang; Qin, Yinan; Li, Dan; Wang, Tianshu; Liu, Yaqing; Wang, Jin; Wang, Erkang

    2013-03-15

    Electrochemical methods have attracted considerable attention for developing cytosensing system since they can decrease the cost and time requirement for cell detection with simple instrumentation. Herein, a label-free electrochemical cytosensor with surface-confined ferrocene as signal indicator was developed for highly sensitive and selective detection of cancer cell. With layer-by-layer (LBL) self-assembly technique, positively charged poly(ethylene imine) functionalized with ferrocene (Fc-PEI) and negatively charged single-wall carbon nanotubes (SWNTs) were alternately assembled on 3-mercaptopropionic acid (MPA) modified gold substrate. Folic acid (FA) was covalently bonded onto SWNTs surface to specifically recognize cancer cells according to the high affinity of FA for folate receptor (FR) on cellular surface. The developed cytosensor presented high sensitivity and selectivity for the detection of human cervical carcinoma (HeLa) cell. By using fast-response differential pulse voltammetry (DPV) method, a wide detection range from 10 to 10(6) cells/mL with a detection limit as low as 10 cells/mL was reached even in the presence of a large amount of non-cancerous cells.

  18. Human pheromone detection by the vomeronasal organ: unnecessary for mate selection?

    PubMed

    Mast, Thomas G; Samuelsen, Chad L

    2009-07-01

    Recently, Foltan and Sedy proposed a hypothesis stating that the adult human VNO is integral to the prevention of inappropriate mate selection. In this commentary, we address the authors' assumption that humans have a functional VNO, that pheromones are detected exclusively by the VNO, and that human pheromones are responsible for negative stimuli during mate selection. After examining the published literature on human vomeronasal function, we argue that their hypothesis is critically flawed. We offer a brief review of the adult human VNO in support of our argument.

  19. Sequence selective naked-eye detection of DNA harnessing extension of oligonucleotide-modified nucleotides.

    PubMed

    Verga, Daniela; Welter, Moritz; Marx, Andreas

    2016-02-01

    DNA polymerases can efficiently and sequence selectively incorporate oligonucleotide (ODN)-modified nucleotides and the incorporated oligonucleotide strand can be employed as primer in rolling circle amplification (RCA). The effective amplification of the DNA primer by Φ29 DNA polymerase allows the sequence-selective hybridisation of the amplified strand with a G-quadruplex DNA sequence that has horse radish peroxidase-like activity. Based on these findings we develop a system that allows DNA detection with single-base resolution by naked eye.

  20. Selective detection of bacteria in urine with a long-range surface plasmon waveguide biosensor

    PubMed Central

    Béland, Paul; Krupin, Oleksiy; Berini, Pierre

    2015-01-01

    Experimentation demonstrates long-range surface plasmon polariton waveguides as a useful biosensor to selectively detect gram negative or gram positive bacteria in human urine having a low concentration of constituents. The biosensor can detect bacteria at concentrations of 105 CFU/ml, the internationally recommended threshold for diagnostic of urinary tract infection. Using a negative control urine solution of bacterial concentration 1000☓ higher than the targeted bacteria, we obtain a ratio of 5.4 for the positive to negative signals. PMID:26309755

  1. Screening and selection of synthetic peptides for a novel and optimized endotoxin detection method.

    PubMed

    Mujika, M; Zuzuarregui, A; Sánchez-Gómez, S; Martínez de Tejada, G; Arana, S; Pérez-Lorenzo, E

    2014-09-30

    The current validated endotoxin detection methods, in spite of being highly sensitive, present several drawbacks in terms of reproducibility, handling and cost. Therefore novel approaches are being carried out in the scientific community to overcome these difficulties. Remarkable efforts are focused on the development of endotoxin-specific biosensors. The key feature of these solutions relies on the proper definition of the capture protocol, especially of the bio-receptor or ligand. The aim of the presented work is the screening and selection of a synthetic peptide specifically designed for LPS detection, as well as the optimization of a procedure for its immobilization onto gold substrates for further application to biosensors.

  2. Selective detection of mitochondrial malfunction in situ by energy transfer spectroscopy

    NASA Astrophysics Data System (ADS)

    Schneckenburger, Herbert; Gschwend, Michael H.; Sailer, Reinhard; Strauss, Wolfgang S. L.; Schoch, Lars; Schuh, Alexander; Stock, Karl; Steiner, Rudolf W.; Zipfl, Peter

    1999-01-01

    To establish optical in situ detection of mitochondrial malfunction, non-radiative energy transfer from the coenzyme NADH to the mitochondrial marker rhodamine 123 (R123) was examined. Dual excitation of R123 via energy transfer from excited NADH molecules as well as by direct absorption of light results in two fluorescence signals whose ratio is a measure of mitochondrial NADH. These signals are detected simultaneously using a time-gated (nanosecond) technique for energy transfer measurements and a frequency selective technique for direct excitation and fluorescence monitoring of R123. Optical and electronic components of the experimental setup are described and compared with a previously established microscopic system.

  3. Liquid crystal-based sensors for selective and quantitative detection of nitrogen dioxide

    PubMed Central

    Sen, Avijit; Kupcho, Kurt A.; Grinwald, Bart A.; VanTreeck, Heidi J.; Acharya, Bharat R.

    2013-01-01

    A highly sensitive nitrogen dioxide (NO2) sensor based on orientational transition of a thin film of liquid crystal (LC) supported on a gold surface is reported. Transport of NO2 molecules through the LC film to the LC-gold interface induces an orientation transition in the LC film. The dynamic behavior of the sensor response exhibits a concentration-dependent response rate that is employed to generate an algorithm for quantitative determination of unknown concentrations. Sensitive, selective and reversible detection with minimal effects of environmental fluctuations suggest that these sensors can be used for quantitative NO2 detection for a number of applications. PMID:23526230

  4. Anxiety: an evolutionary approach.

    PubMed

    Bateson, Melissa; Brilot, Ben; Nettle, Daniel

    2011-12-01

    Anxiety disorders are among the most common mental illnesses, with huge attendant suffering. Current treatments are not universally effective, suggesting that a deeper understanding of the causes of anxiety is needed. To understand anxiety disorders better, it is first necessary to understand the normal anxiety response. This entails considering its evolutionary function as well as the mechanisms underlying it. We argue that the function of the human anxiety response, and homologues in other species, is to prepare the individual to detect and deal with threats. We use a signal detection framework to show that the threshold for expressing the anxiety response ought to vary with the probability of threats occurring, and the individual's vulnerability to them if they do occur. These predictions are consistent with major patterns in the epidemiology of anxiety. Implications for research and treatment are discussed.

  5. Evolutionary dynamics of enzymes.

    PubMed

    Demetrius, L

    1995-08-01

    This paper codifies and rationalizes the large diversity in reaction rates and substrate specificity of enzymes in terms of a model which postulates that the kinetic properties of present-day enzymes are the consequence of the evolutionary force of mutation and selection acting on a class of primordial enzymes with poor catalytic activity and broad substrate specificity. Enzymes are classified in terms of their thermodynamic parameters, activation enthalpy delta H* and activation entropy delta S*, in their kinetically significant transition states as follows: type 1, delta H* > 0, delta S* < 0; type 2, delta H* < or = 0, delta S* < or = 0; type 3, delta H* > 0, delta S* > 0. We study the evolutionary dynamics of these three classes of enzymes subject to mutation, which acts at the level of the gene which codes for the enzyme and selection, which acts on the organism that contains the enzyme. Our model predicts the following evolutionary trends in the reaction rate and binding specificity for the three classes of molecules. In type 1 enzymes, evolution results in random, non-directional changes in the reaction rate and binding specificity. In type 2 and 3 enzymes, evolution results in a unidirectional increase in both the reaction rate and binding specificity. We exploit these results in order to codify the diversity in functional properties of present-day enzymes. Type 1 molecules will be described by intermediate reaction rates and broad substrate specificity. Type 2 enzymes will be characterized by diffusion-controlled rates and absolute substrate specificity. The type 3 catalysts can be further subdivided in terms of their activation enthalpy into two classes: type 3a (delta H* small) and type 3b (delta H* large). We show that type 3a will be represented by the same functional properties that identify type 2, namely, diffusion-controlled rates and absolute substrate specificity, whereas type 3b will be characterized by non-diffusion-controlled rates and absolute

  6. Selectable Ultrasensitive Detection of Hg2+ with Rhodamine 6G-Modified Nanoporous Gold Optical Sensor

    NASA Astrophysics Data System (ADS)

    Wang, Zheng; Yang, Min; Chen, Chao; Zhang, Ling; Zeng, Heping

    2016-07-01

    An extremely sensitive fluorescence sensor has been developed for selectively detection of mercury ions based on metallophilic Hg2+-Au+ interactions, which results in an effective release of pre-adsorbed rhodamine 6G (R6G) molecules from the nanoporous gold substrate, associated with a significant decrease of fluorescence intensity. The optical sensor has a detection sensitivity down to 0.6 pM for Hg2+ and CH3Hg+ ions, in particular a superior selectivity in a complex aqueous system containing 13 different types of metal ions, meanwhile maintaining a long-term stability after 10 cycles. Such a fluorescence sensor combining multiple advantages therefore present promising potentials in various applications.

  7. Magnetically recoverable fluorescence chemosensor for the adsorption and selective detection of Hg2+ in water.

    PubMed

    Lv, Qiang; Li, Gang; Cheng, Zhuhong; Lu, Hong; Gao, Xiaoxia

    2014-01-01

    In order to conveniently and effectively detect the heavy metal ion Hg(2+) existing in water, a magnetic fluorescence chemosensor has been strategically prepared by immobilizing a Rhodamine B derivative RhB-tris(2-aminoethyl)amine on Fe3O4@SiO2-Au@PSiO2 composites via gold particles. The adsorption and detection for Hg(2+) ions were investigated with fluorophotometry. This chemosensor shows high sensitivity and high selectivity for Hg(2+) over other metal cations owing to the ring opening of the rhodamine fluorophore selectively induced by Hg(2+). In addition, the presence of Fe3O4 in the sensor also facilitates the magnetic separation of the Fe3O4@SiO2-Au-Hg(2+)@PSiO2 from the solution.

  8. Glycan-functionalized graphene-FETs toward selective detection of human-infectious avian influenza virus

    NASA Astrophysics Data System (ADS)

    Ono, Takao; Oe, Takeshi; Kanai, Yasushi; Ikuta, Takashi; Ohno, Yasuhide; Maehashi, Kenzo; Inoue, Koichi; Watanabe, Yohei; Nakakita, Shin-ichi; Suzuki, Yasuo; Kawahara, Toshio; Matsumoto, Kazuhiko

    2017-03-01

    There are global concerns about threat of pandemic caused by the human-infectious avian influenza virus. To prevent the oncoming pandemic, it is crucial to analyze the viral affinity to human-type or avian-type sialoglycans with high sensitivity at high speed. Graphene-FET (G-FET) realizes such high-sensitive electrical detection of the targets, owing to graphene’s high carrier mobility. In the present study, G-FET was functionalized using sialoglycans and employed for the selective detection of lectins from Sambucus sieboldiana and Maackia amurensis as alternatives of the human and avian influenza viruses. Glycan-functionalized G-FET selectively monitored the sialoglycan-specific binding reactions at subnanomolar sensitivity.

  9. Selectable Ultrasensitive Detection of Hg2+ with Rhodamine 6G-Modified Nanoporous Gold Optical Sensor

    PubMed Central

    Wang, Zheng; Yang, Min; Chen, Chao; Zhang, Ling; Zeng, Heping

    2016-01-01

    An extremely sensitive fluorescence sensor has been developed for selectively detection of mercury ions based on metallophilic Hg2+-Au+ interactions, which results in an effective release of pre-adsorbed rhodamine 6G (R6G) molecules from the nanoporous gold substrate, associated with a significant decrease of fluorescence intensity. The optical sensor has a detection sensitivity down to 0.6 pM for Hg2+ and CH3Hg+ ions, in particular a superior selectivity in a complex aqueous system containing 13 different types of metal ions, meanwhile maintaining a long-term stability after 10 cycles. Such a fluorescence sensor combining multiple advantages therefore present promising potentials in various applications. PMID:27403721

  10. Transcriptomics of two evolutionary novelties: how to make a sperm-transfer organ out of an anal fin and a sexually selected “sword” out of a caudal fin

    PubMed Central

    Kang, Ji Hyoun; Manousaki, Tereza; Franchini, Paolo; Kneitz, Susanne; Schartl, Manfred; Meyer, Axel

    2015-01-01

    Swords are exaggerated male ornaments of swordtail fishes that have been of great interest to evolutionary biologists ever since Darwin described them in the Descent of Man (1871). They are a novel sexually selected trait derived from modified ventral caudal fin rays and are only found in the genus Xiphophorus. Another phylogenetically more widespread and older male trait is the gonopodium, an intromittent organ found in all poeciliid fishes, that is derived from a modified anal fin. Despite many evolutionary and behavioral studies on both traits, little is known so far about the molecular mechanisms underlying their development. By investigating transcriptomic changes (utilizing a RNA-Seq approach) in response to testosterone treatment in the swordtail fish, Xiphophorus hellerii, we aimed to better understand the architecture of the gene regulatory networks underpinning the development of these two evolutionary novelties. Large numbers of genes with tissue-specific expression patterns were identified. Among the “sword genes” those involved in embryonic organ development, sexual character development and coloration were highly expressed, while in the gonopodium rather more morphogenesis-related genes were found. Interestingly, many genes and genetic pathways are shared between both developing novel traits derived from median fins: the sword and the gonopodium. Our analyses show that a larger set of gene networks was co-opted during the development and evolution of the “older” gonopodium than in the “younger,” and morphologically less complex trait, the sword. We provide a catalog of candidate genes for future efforts to dissect the development of those sexually selected exaggerated male traits in swordtails. PMID:25750712

  11. Selective Real-time Detection of Gaseous Nerve Agent Simulants Using Multiwavelength Photoacoustics

    DTIC Science & Technology

    2012-08-15

    Selective real-time detection of gaseous nerve agent simulants using multiwavelength photoacoustics Kristan P. Gurton,* Melvin Felton, and Richard...concentrations. The technique is based on a modified version of conventional laser photoacoustic (PA) spectroscopy, in which optical absorption is typically...spec- troscopic approach [1–4]. One of the more direct methods to implement in prac- tice (without sacrificing sensitivity) is laser photoacoustic

  12. An adapted modulation transfer function for x-ray backscatter radiography by selective detection

    NASA Astrophysics Data System (ADS)

    Sabri, Nissia; Dugan, Edward T.; Jacobs, Alan M.; Shedlock, Daniel

    2007-09-01

    The Modulation Transfer Function (MTF) is a quantitative function based on frequency resolution that characterizes imaging system performance. In this study, a new MTF methodology is investigated for application to Radiography by Selective Detection (RSD), an enhanced single-side x-ray Compton backscatter imaging (CBI) technique which detects selected scatter components. The RSD imaging modality is a unique type of real-time radiography that uses a set of fin and sleeve collimators to preferentially select different components of the x-ray backscattered field. Radiography by selective detection has performed successfully in different non-destructive evaluation (NDE) applications. A customized RSD imaging system was built at the University of Florida for inspection of the space shuttle external tank spray-on foam insulation (SOFI). The x-ray backscatter RSD imaging system has been successfully used for crack and corrosion detection in a variety of materials. The conventional transmission x-ray image quality characterization tools do not apply for RSD because of the different physical process involved. Thus, the main objective of this project is to provide an adapted tool for dynamic evaluation of RSD system image quality. For this purpose, an analytical model of the RSD imaging system response is developed and supported. Two approaches are taken for the MTF calculations: one using the Fourier Transform of a line spread function and the other one using a sine function pattern. Calibration and test targets are then designed according to this proposed model. A customized Matlab code using image contrast and digital curve recognition is developed to support the experimental data and provide the Modulation Transfer Functions for RSD.

  13. A simple ratiometric and colorimetric chemosensor for the selective detection of fluoride in DMSO buffered solution

    NASA Astrophysics Data System (ADS)

    Niu, Hu; Shu, Qinghai; Jin, Shaohua; Li, Bingjun; Zhu, Jiaping; Li, Lijie; Chen, Shusen

    2016-01-01

    A derivative of squaramide (cyclobuta[b]quinoxaline-1, 2(3H, 8H)-dione) has been synthesized for the ratiometric and colorimetric sensing of F- in aqueous solution in competitive fashion. With F-, probe 1 showed a highly selective naked-eye detectable color change along with a characteristic UV-Vis absorbance over other tested ions, which probably originates from the deprotonation occurred between 1 and F-, as proved by the 1H NMR titration experiments and DFT calculations.

  14. Selective detection of live pathogens via surface-confined electric field perturbation on interdigitated silicon transducers.

    PubMed

    de la Rica, Roberto; Baldi, Antonio; Fernández-Sánchez, César; Matsui, Hiroshi

    2009-05-15

    Detection of physical changes of cells is emerging as a new diagnostic approach to determine their phenotypical features. One of such changes is related to their viability; live (viable) cells are more voluminous than the dead ones, and monitoring this parameter in tissue cells becomes essential in fields such as drug discovery and hazard evaluation. In the area of pathogen detection, an analytical system capable of specifically detecting viable cells with the simple sample preparation and detection process would be highly desirable since live microorganisms can rapidly increase their numbers even at extremely low concentration and become a severe health risk. However, current sensing strategies cannot clearly determine the viability of cells, and hence they are susceptible to false-positive signals from harmless dead pathogens. Here we developed a robust electronic immunoassay that uses a pair of polycrystalline silicon interdigitated electrodes for the rapid detection of pathogens with high specificity for live cells. After bacterial cells were specifically anchored to the surface of the antibody-modified electrode, the characteristic geometry of the transducer enables the selective detection of viable cells with a limit of detection of 3 x 10(2) cfu/mL and an incubation time of only 1 h. The CMOS compatible fabrication process of the chip along with the label-free, reagent-less electronic detection and the easy electrode regeneration to recycle for another impedance measurement make this approach an excellent candidate for oncoming economical in-field viable-cell detection systems, fully integrable with sophisticated signal processing circuits.

  15. Supersensitive and selective detection of picric acid explosive by fluorescent Ag nanoclusters.

    PubMed

    Zhang, Jian Rong; Yue, Yuan Yuan; Luo, Hong Qun; Li, Nian Bing

    2016-02-07

    Picric acid (PA) explosive is a hazard to public safety and health, so the sensitive and selective detection of PA is very important. In the present work, polyethyleneimine stabilized Ag nanoclusters were successfully used for the sensitive and selective quantification of PA on the basis of fluorescence quenching. The quenching efficiency of Ag nanoclusters is proportional to the concentration of PA and the logarithm of PA concentration over two different concentration ranges (1.0 nM-1 μM for the former and 0.25-20 μM for the latter), thus the proposed quantitative strategy for PA provides a wide linear range of 1.0 nM-20 μM. The detection limit based on 3σ/K is 0.1 nM. The quenching mechanism of Ag nanoclusters by PA is discussed in detail. The results indicate that the selective detection of PA over other nitroaromatics including 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), p-nitrotoluene (p-NT), m-dinitrobenzene (m-DNB), and nitrobenzene (NB), is due to the electron transfer and energy transfer between PA and polyethyleneimine-capped Ag nanoclusters. In addition, the experimental data obtained for the analysis of artificial samples show that the proposed PA sensor is potentially applicable in the determination of trace PA explosive in real samples.

  16. Selective and reversible ammonia gas detection with nanoporous film functionalized silicon photonic micro-ring resonator.

    PubMed

    Yebo, Nebiyu A; Sree, Sreeprasanth Pulinthanathu; Levrau, Elisabeth; Detavernier, Christophe; Hens, Zeger; Martens, Johan A; Baets, Roel

    2012-05-21

    Portable, low cost and real-time gas sensors have a considerable potential in various biomedical and industrial applications. For such applications, nano-photonic gas sensors based on standard silicon fabrication technology offer attractive opportunities. Deposition of high surface area nano-porous coatings on silicon photonic sensors is a means to achieve selective, highly sensitive and multiplexed gas detection on an optical chip. Here we demonstrate selective and reversible ammonia gas detection with functionalized silicon-on-insulator optical micro-ring resonators. The micro-ring resonators are coated with acidic nano-porous aluminosilicate films for specific ammonia sensing, which results in a reversible response to NH(3)with selectivity relative to CO(2). The ammonia detection limit is estimated at about 5 ppm. The detectors reach a steady response to NH(3) within 30 and return to their base level within 60 to 90 seconds. The work opens perspectives on development of nano-photonic sensors for real-time, non-invasive, low cost and light weight biomedical and industrial sensing applications.

  17. Highly sensitive and selective sugar detection by terahertz nano-antennas.

    PubMed

    Lee, Dong-Kyu; Kang, Ji-Hun; Lee, Jun-Seok; Kim, Hyo-Seok; Kim, Chulki; Kim, Jae Hun; Lee, Taikjin; Son, Joo-Hiuk; Park, Q-Han; Seo, Minah

    2015-10-23

    Molecular recognition and discrimination of carbohydrates are important because carbohydrates perform essential roles in most living organisms for energy metabolism and cell-to-cell communication. Nevertheless, it is difficult to identify or distinguish various carbohydrate molecules owing to the lack of a significant distinction in the physical or chemical characteristics. Although there has been considerable effort to develop a sensing platform for individual carbohydrates selectively using chemical receptors or an ensemble array, their detection and discrimination limits have been as high in the millimolar concentration range. Here we show a highly sensitive and selective detection method for the discrimination of carbohydrate molecules using nano-slot-antenna array-based sensing chips which operate in the terahertz (THz) frequency range (0.5-2.5 THz). This THz metamaterial sensing tool recognizes various types of carbohydrate molecules over a wide range of molecular concentrations. Strongly localized and enhanced terahertz transmission by nano-antennas can effectively increase the molecular absorption cross sections, thereby enabling the detection of these molecules even at low concentrations. We verified the performance of nano-antenna sensing chip by both THz spectra and images of transmittance. Screening and identification of various carbohydrates can be applied to test even real market beverages with a high sensitivity and selectivity.

  18. Highly sensitive and selective sugar detection by terahertz nano-antennas

    PubMed Central

    Lee, Dong-Kyu; Kang, Ji-Hun; Lee, Jun-Seok; Kim, Hyo-Seok; Kim, Chulki; Hun Kim, Jae; Lee, Taikjin; Son, Joo-Hiuk; Park, Q-Han; Seo, Minah

    2015-01-01

    Molecular recognition and discrimination of carbohydrates are important because carbohydrates perform essential roles in most living organisms for energy metabolism and cell-to-cell communication. Nevertheless, it is difficult to identify or distinguish various carbohydrate molecules owing to the lack of a significant distinction in the physical or chemical characteristics. Although there has been considerable effort to develop a sensing platform for individual carbohydrates selectively using chemical receptors or an ensemble array, their detection and discrimination limits have been as high in the millimolar concentration range. Here we show a highly sensitive and selective detection method for the discrimination of carbohydrate molecules using nano-slot-antenna array-based sensing chips which operate in the terahertz (THz) frequency range (0.5–2.5 THz). This THz metamaterial sensing tool recognizes various types of carbohydrate molecules over a wide range of molecular concentrations. Strongly localized and enhanced terahertz transmission by nano-antennas can effectively increase the molecular absorption cross sections, thereby enabling the detection of these molecules even at low concentrations. We verified the performance of nano-antenna sensing chip by both THz spectra and images of transmittance. Screening and identification of various carbohydrates can be applied to test even real market beverages with a high sensitivity and selectivity. PMID:26494203

  19. Highly sensitive and selective sugar detection by terahertz nano-antennas

    NASA Astrophysics Data System (ADS)

    Lee, Dong-Kyu; Kang, Ji-Hun; Lee, Jun-Seok; Kim, Hyo-Seok; Kim, Chulki; Hun Kim, Jae; Lee, Taikjin; Son, Joo-Hiuk; Park, Q.-Han; Seo, Minah

    2015-10-01

    Molecular recognition and discrimination of carbohydrates are important because carbohydrates perform essential roles in most living organisms for energy metabolism and cell-to-cell communication. Nevertheless, it is difficult to identify or distinguish various carbohydrate molecules owing to the lack of a significant distinction in the physical or chemical characteristics. Although there has been considerable effort to develop a sensing platform for individual carbohydrates selectively using chemical receptors or an ensemble array, their detection and discrimination limits have been as high in the millimolar concentration range. Here we show a highly sensitive and selective detection method for the discrimination of carbohydrate molecules using nano-slot-antenna array-based sensing chips which operate in the terahertz (THz) frequency range (0.5-2.5 THz). This THz metamaterial sensing tool recognizes various types of carbohydrate molecules over a wide range of molecular concentrations. Strongly localized and enhanced terahertz transmission by nano-antennas can effectively increase the molecular absorption cross sections, thereby enabling the detection of these molecules even at low concentrations. We verified the performance of nano-antenna sensing chip by both THz spectra and images of transmittance. Screening and identification of various carbohydrates can be applied to test even real market beverages with a high sensitivity and selectivity.

  20. Selective and sensitive detection of chromium(VI) in waters using electrospray ionization mass spectrometry.

    PubMed

    Weldy, Effie; Wolff, Chloe; Miao, Zhixin; Chen, Hao

    2013-09-01

    From 2000 through 2011, there were 14 criminal cases of violations of the Clean Water Act involving the discharge of chromium, a toxic heavy metal, into drinking and surface water sources. As chromium(VI), a potential carcinogen present in the environment, represents a significant safety concern, it is currently the subject of an EPA health risk assessment. Therefore, sensitive and selective detection of this species is highly desired. This study reports the analysis of chromium(VI) in water samples by electrospray ionization mass spectrometry (ESI-MS) following its reduction and complexation with ammonium pyrrolidinedithiocarbamate (APDC). The reduction and subsequent complexation produce a characteristic [Cr(III)O]-PDC complex which can be detected as a protonated ion of m/z 507 in the positive ion mode. The detection is selective to chromium(VI) under acidic pH, even in the presence of chromium(III) and other metal ions, providing high specificity. Different water samples were examined, including deionized, tap, and river waters, and sensitive detection was achieved. In the case of deionized water, quantification over the concentration range of 3.7 to 148ppb gave an excellent correlation coefficient of 0.9904 using the enhanced MS mode scan. Using the single-reaction monitoring (SRM) mode (monitoring the characteristic fragmentation of m/z 507 to m/z 360), the limit of detection (LOD) was found to be 0.25ppb. The LOD of chromium(VI) for both tap and river water samples was determined to be 2.0ppb. A preconcentration strategy using simple vacuum evaporation of the aqueous sample was shown to further improve the ESI signal by 15 fold. This method, with high sensitivity and selectivity, should provide a timely solution for the real-world analysis of toxic chromium(VI).

  1. Selective detection of heavy metal ions by self assembled chemical field effect transistors

    NASA Astrophysics Data System (ADS)

    Ruan, Hang; Kang, Yuhong; Gladwin, Elizabeth; Claus, Richard O.

    2015-04-01

    Multiple layer-by-layer sensor material modifications were designed and implemented to achieve selectivity of semiconductor based chemical field effect transistors (ChemFETs) to particular heavy metal ions. The ChemFET sensors were fabricated and modified in three ways, with the intent to initially target first mercury and lead ions and then chromium ions, respectively. Sensor characterization was performed with the gate regions of the sensor elements exposed to different concentrations of target heavy metal ion solutions. A minimum detection level in the range of 0.1 ppm and a 10%-90% response time of less than 10 s were demonstrated. By combining layer-by-layer gold nanoparticles and lead ionophores, a sensor is produced that is sensitive and selective not only to chromium but also to Cr3+ and Cr6+. This result supports the claim that high selectivity can be achieved by designing self-assembled bonding for lead, arsenic, chromium, cesium, mercury, and cadmium.

  2. State-selective detection of velocity-filtered ND{sub 3} molecules

    SciTech Connect

    Bertsche, Benjamin; Osterwalder, Andreas

    2010-09-15

    Translationally cold and slow ND{sub 3} is prepared by filtering the slow molecules from a thermal gas-phase sample using a curved electrostatic hexapole guide. This filter, like the curved quadrupole guide introduced by Rangwala et al. [Phys. Rev. A 67, 043406 (2003)] selects molecules by their forward velocity and effective electric dipole moment. Here we describe two main modifications with respect to previous work: (1) A segmented hexapole guide is used that produces a harmonic potential for the linearly Stark-shifted levels of ND{sub 3}. A curved guide is combined with a straight hexapole guide, and independent high-voltage supplies are employed to allow for bandpass velocity filtering. (2) State-selective laser ionization is used to obtain time- and state-selective detection of the guided molecules. This enables the experimental determination of the rotational state population of the guided molecules.

  3. A powerful score test to detect positive selection in genome-wide scans

    PubMed Central

    Zhong, Ming; Lange, Kenneth; Papp, Jeanette C; Fan, Ruzong

    2010-01-01

    One of the surest signatures of recent positive selection is a local elevation of advantageous allele frequency and linkage disequilibrium (LD). We proposed to detect such hitchhiking effects by using extended stretches of homozygosity as a surrogate indicator of recent positive selection. An extended haplotype-based homozygosity score test (EHHST) was developed to detect excess homozygosity. The EHHST conditioned on existing LD and it tested the haplotype version of the Hardy–Weinberg equilibrium. Compared with existing popular tests, which usually lack clear distribution, the EHHST is asymptotically normal, which makes analysis and applications easier. In particular, the EHHST facilitates the computation of an asymptotic P-value instead of an empirical P-value, using simulations. We evaluated by simulation that the EHHST led to appropriate false-positive rates, and it had higher or similar power as the existing popular methods. The method was applied to HapMap Phase II data. We were able to replicate previous findings of strong positive selection in 17 autosome genomic regions out of 20 reported candidates. On the basis of high EHHST values and population differentiations, we identified 15 new candidate regions that could undergo recent selection. PMID:20461112

  4. A surface acoustic wave sensor functionalized with a polypyrrole molecularly imprinted polymer for selective dopamine detection.

    PubMed

    Maouche, Naima; Ktari, Nadia; Bakas, Idriss; Fourati, Najla; Zerrouki, Chouki; Seydou, Mahamadou; Maurel, François; Chehimi, Mohammed Mehdi

    2015-11-01

    A surface acoustic wave sensor operating at 104 MHz and functionalized with a polypyrrole molecularly imprinted polymer has been designed for selective detection of dopamine (DA). Optimization of pyrrole/DA ratio, polymerization and immersion times permitted to obtain a highly selective sensor, which has a sensitivity of 0.55°/mM (≈ 550 Hz/mM) and a detection limit of ≈ 10 nM. Morphology and related roughness parameters of molecularly imprinted polymer surfaces, before and after extraction of DA, as well as that of the non imprinted polymer were characterized by atomic force microscopy. The developed chemosensor selectively recognized dopamine over the structurally similar compound 4-hydroxyphenethylamine (referred as tyramine), or ascorbic acid,which co-exists with DA in body fluids at a much higher concentration. Selectivity tests were also carried out with dihydroxybenzene, for which an unexpected phase variation of order of 75% of the DA one was observed. Quantum chemical calculations, based on the density functional theory, were carried out to determine the nature of interactions between each analyte and the PPy matrix and the DA imprinted PPy polypyrrole sensing layer in order to account for the important phase variation observed during dihydroxybenzene injection.

  5. Potentiometric enzyme immunoassay using miniaturized anion-selective electrodes for detection

    PubMed Central

    Szűcs, Júlia; Pretsch, Ernö; Gyurcsányi, Róbert E.

    2010-01-01

    An enzyme-linked immunosorbent assay (ELISA) for prostate specific antigen (PSA) detection in human serum was developed based on the potentiometric detection of 6,8-difluoro-4-methylumbelliferone (DiFMU). The assays were carried out in anti-human PSA capture-antibody modified microtiter plates (150 µl volume). After incubation in the PSA containing serum samples, β-galactosidase-labeled PSA tracer antibody was added. The β-galactosidase label catalyzed the hydrolysis of 6,8-difluoro-4-methylumbelliferyl-β-D-galactopyranoside (DiFMUG) and the resulting DiFMU− anion was detected by potentiometric microelectrodes with anion-exchanger membrane. The selectivity of the anion-exchanger electrode is governed by the lipophilicity of the anions in the sample. Since DiFMU− is much more lipophilic (log P = 1.83) than any of the inorganic anions normally present in the working buffers and occurs in its anionic form at the physiological pH (pKa = 4.19), it was chosen as the species to be detected. The potentiometric ELISA-based method detects PSA in serum with a linear concentration range of 0.1–50 ng/mL. These results confirm the applicability of potentiometric detection in diagnostic PSA assays. Owing to simple methodology and low cost, potentiometric immunoassays seem to offer a feasible alternative to the development of in vitro diagnostic platforms. PMID:20448926

  6. Multispectral band selection and spatial characterization: Application to mitosis detection in breast cancer histopathology.

    PubMed

    Irshad, H; Gouaillard, A; Roux, L; Racoceanu, D

    2014-07-01

    Breast cancer is the second most frequent cancer. The reference process for breast cancer prognosis is Nottingham grading system. According to this system, mitosis detection is one of the three important criteria required for grading process and quantifying the locality and prognosis of a tumor. Multispectral imaging, as relatively new to the field of histopathology, has the advantage, over traditional RGB imaging, to capture spectrally resolved information at specific frequencies, across the electromagnetic spectrum. This study aims at evaluating the accuracy of mitosis detection on histopathological multispectral images. The proposed framework includes: selection of spectral bands and focal planes, detection of candidate mitotic regions and computation of morphological and multispectral statistical features. A state-of-the-art of the methods for mitosis classification is also provided. This framework has been evaluated on MITOS multispectral dataset and achieved higher detection rate (67.35%) and F-Measure (63.74%) than the best MITOS contest results (Roux et al., 2013). Our results indicate that the selected multispectral bands have more discriminant information than a single spectral band or all spectral bands for mitotic figures, validating the interest of using multispectral images to improve the quality of the diagnostic in histopathology.

  7. Platinum(II)-Oligonucleotide Coordination Based Aptasensor for Simple and Selective Detection of Platinum Compounds.

    PubMed

    Cai, Sheng; Tian, Xueke; Sun, Lianli; Hu, Haihong; Zheng, Shirui; Jiang, Huidi; Yu, Lushan; Zeng, Su

    2015-10-20

    Wide use of platinum-based chemotherapeutic regimens for the treatment for carcinoma calls for a simple and selective detection of platinum compound in biological samples. On the basis of the platinum(II)-base pair coordination, a novel type of aptameric platform for platinum detection has been introduced. This chemiluminescence (CL) aptasensor consists of a designed streptavidin (SA) aptamer sequence in which several base pairs were replaced by G-G mismatches. Only in the presence of platinum, coordination occurs between the platinum and G-G base pairs as opposed to the hydrogen-bonded G-C base pairs, which leads to SA aptamer sequence activation, resulting in their binding to SA coated magnetic beads. These Pt-DNA coordination events were monitored by a simple and direct luminol-peroxide CL reaction through horseradish peroxidase (HRP) catalysis with a strong chemiluminescence emission. The validated ranges of quantification were 0.12-240 μM with a limit of detection of 60 nM and selectivity over other metal ions. This assay was also successfully used in urine sample determination. It will be a promising candidate for the detection of platinum in biomedical and environmental samples.

  8. Power analysis of QTL detection in half-sib families using selective DNA pooling.

    PubMed

    Baro JA; Carleos, C; Corral, N; López, T; Cañón, J

    2001-01-01

    Individual loci of economic importance (QTL) can be detected by comparing the inheritance of a trait and the inheritance of loci with alleles readily identifiable by laboratory methods (genetic markers). Data on allele segregation at the individual level are costly and alternatives have been proposed that make use of allele frequencies among progeny, rather than individual genotypes. Among the factors that may affect the power of the set up, the most important are those intrinsic to the QTL: the additive effect of the QTL, and its dominance, and distance between markers and QTL. Other factors are relative to the choice of animals and markers, such as the frequency of the QTL and marker alleles among dams and sires. Data collection may affect the detection power through the size of half-sib families, selection rate within families, and the technical error incurred when estimating genetic frequencies. We present results for a sensitivity analysis for QTL detection using pools of DNA from selected half-sibs. Simulations showed that conclusive detection may be achieved with families of at least 500 half-sibs if sires are chosen on the criteria that most of their marker alleles are either both missing, or one is fixed, among dams.

  9. Detection of Impaired Cerebral Autoregulation Using Selected Correlation Analysis: A Validation Study

    PubMed Central

    Brawanski, Alexander

    2017-01-01

    Multimodal brain monitoring has been utilized to optimize treatment of patients with critical neurological diseases. However, the amount of data requires an integrative tool set to unmask pathological events in a timely fashion. Recently we have introduced a mathematical model allowing the simulation of pathophysiological conditions such as reduced intracranial compliance and impaired autoregulation. Utilizing a mathematical tool set called selected correlation analysis (sca), correlation patterns, which indicate impaired autoregulation, can be detected in patient data sets (scp). In this study we compared the results of the sca with the pressure reactivity index (PRx), an established marker for impaired autoregulation. Mean PRx values were significantly higher in time segments identified as scp compared to segments showing no selected correlations (nsc). The sca based approach predicted cerebral autoregulation failure with a sensitivity of 78.8% and a specificity of 62.6%. Autoregulation failure, as detected by the results of both analysis methods, was significantly correlated with poor outcome. Sca of brain monitoring data detects impaired autoregulation with high sensitivity and sufficient specificity. Since the sca approach allows the simultaneous detection of both major pathological conditions, disturbed autoregulation and reduced compliance, it may become a useful analysis tool for brain multimodal monitoring data. PMID:28255331

  10. Amplified electrochemical detection of nucleic acid hybridization via selective preconcentration of unmodified gold nanoparticles.

    PubMed

    Li, Yuan; Tian, Rui; Zheng, Xingwang; Huang, Rongfu

    2016-08-31

    The common drawback of optical methods for rapid detection of nucleic acid by exploiting the differential affinity of single-/double-stranded nucleic acids for unmodified gold nanoparticles (AuNPs) is its relatively low sensitivity. In this article, on the basis of selective preconcentration of AuNPs unprotected by single-stranded DNA (ssDNA) binding, a novel electrochemical strategy for nucleic acid sequence identification assay has been developed. Through detecting the redox signal mediated by AuNPs on 1, 6-hexanedithiol blocked gold electrode, the proposed method is able to ensure substantial signal amplification and a low background current. This strategy is demonstrated for quantitative analysis of the target microRNA (let-7a) in human breast adenocarcinoma cells, and a detection limit of 16 fM is readily achieved with desirable specificity and sensitivity. These results indicate that the selective preconcentration of AuNPs for electrochemical signal readout can offer a promising platform for the detection of specific nucleic acid sequence.

  11. A highly facile and selective Chemo-Paper-Sensor (CPS) for detection of strontium.

    PubMed

    Kang, Sung-Min; Jang, Sung-Chan; Huh, Yun Suk; Lee, Chang-Soo; Roh, Changhyun

    2016-06-01

    Chemosensors have attracted increasing attention for their usefulness on-site detection and monitoring. In this study, we elucidated a novel, facile, and highly selective Chemo-Paper-Sensor (CPS) for detection and monitoring of strontium (Sr(2+)) ions, which means a potent colorimetric sensor based on a Chrysoidine G (CG)-coated paper strip. The CPS for highly selective colorimetric detection of strontium ion was handily analyzed to determine the red-green-blue (RGB) value using portable devices such as desktop digital scanner and mobile phone camera, quantitatively. Interestingly, an orange to dark orange color transition was observed when the aqueous and solid paper colorimetric sensor was introduced to Sr(2+) ion, respectively. It was demonstrated that the value of the signal has a linear relationship with concentrations of the strontium in the 500 ppm to 100 ppb range with a detection limit of 200 ppb. We believe that a newly developed Chemo-Paper-Sensor will be useful in a wide range of sensing applications.

  12. Investigation of microcantilever array with ordered nanoporous coatings for selective chemical detection.

    SciTech Connect

    Allendorf, Mark D.; Thornberg, Steven Michael; Lee, J. -H.; Robinson, Alex Lockwood; Hesketh, Peter J.; Greathouse, Jeffery A.; Houk, Ronald J. T.

    2010-03-01

    In this paper we demonstrate the potential for novel nanoporous framework materials (NFM) such as metal-organic frameworks (MOFs) to provide selectivity and sensitivity to a broad range of analytes including explosives, nerve agents, and volatile organic compounds (VOCs). NFM are highly ordered, crystalline materials with considerable synthetic flexibility resulting from the presence of both organic and inorganic components within their structure. Detection of chemical weapons of mass destruction (CWMD), explosives, toxic industrial chemicals (TICs), and volatile organic compounds (VOCs) using micro-electro-mechanical-systems (MEMS) devices, such as microcantilevers and surface acoustic wave sensors, requires the use of recognition layers to impart selectivity. Traditional organic polymers are dense, impeding analyte uptake and slowing sensor response. The nanoporosity and ultrahigh surface areas of NFM enhance transport into and out of the NFM layer, improving response times, and their ordered structure enables structural tuning to impart selectivity. Here we describe experiments and modeling aimed at creating NFM layers tailored to the detection of water vapor, explosives, CWMD, and VOCs, and their integration with the surfaces of MEMS devices. Force field models show that a high degree of chemical selectivity is feasible. For example, using a suite of MOFs it should be possible to select for explosives vs. CWMD, VM vs. GA (nerve agents), and anthracene vs. naphthalene (VOCs). We will also demonstrate the integration of various NFM with the surfaces of MEMS devices and describe new synthetic methods developed to improve the quality of VFM coatings. Finally, MOF-coated MEMS devices show how temperature changes can be tuned to improve response times, selectivity, and sensitivity.

  13. Investigation of microcantilever array with ordered nanoporous coatings for selective chemical detection

    NASA Astrophysics Data System (ADS)

    Lee, J.-H.; Houk, R. T. J.; Robinson, A.; Greathouse, J. A.; Thornberg, S. M.; Allendorf, M. D.; Hesketh, P. J.

    2010-04-01

    In this paper we demonstrate the potential for novel nanoporous framework materials (NFM) such as metal-organic frameworks (MOFs) to provide selectivity and sensitivity to a broad range of analytes including explosives, nerve agents, and volatile organic compounds (VOCs). NFM are highly ordered, crystalline materials with considerable synthetic flexibility resulting from the presence of both organic and inorganic components within their structure. Detection of chemical weapons of mass destruction (CWMD), explosives, toxic industrial chemicals (TICs), and volatile organic compounds (VOCs) using micro-electro-mechanical-systems (MEMS) devices, such as microcantilevers and surface acoustic wave sensors, requires the use of recognition layers to impart selectivity. Traditional organic polymers are dense, impeding analyte uptake and slowing sensor response. The nanoporosity and ultrahigh surface areas of NFM enhance transport into and out of the NFM layer, improving response times, and their ordered structure enables structural tuning to impart selectivity. Here we describe experiments and modeling aimed at creating NFM layers tailored to the detection of water vapor, explosives, CWMD, and VOCs, and their integration with the surfaces of MEMS devices. Force field models show that a high degree of chemical selectivity is feasible. For example, using a suite of MOFs it should be possible to select for explosives vs. CWMD, VM vs. GA (nerve agents), and anthracene vs. naphthalene (VOCs). We will also demonstrate the integration of various NFM with the surfaces of MEMS devices and describe new synthetic methods developed to improve the quality of VFM coatings. Finally, MOF-coated MEMS devices show how temperature changes can be tuned to improve response times, selectivity, and sensitivity.

  14. Detecting recent positive selection with high accuracy and reliability by conditional coalescent tree.

    PubMed

    Wang, Minxian; Huang, Xin; Li, Ran; Xu, Hongyang; Jin, Li; He, Yungang

    2014-11-01

    Studies of natural selection, followed by functional validation, are shedding light on understanding of genetic mechanisms underlying human evolution and adaptation. Classic methods for detecting selection, such as the integrated haplotype score (iHS) and Fay and Wu's H statistic, are useful for candidate gene searching underlying positive selection. These methods, however, have limited capability to localize causal variants in selection target regions. In this study, we developed a novel method based on conditional coalescent tree to detect recent positive selection by counting unbalanced mutations on coalescent gene genealogies. Extensive simulation studies revealed that our method is more robust than many other approaches against biases due to various demographic effects, including population bottleneck, expansion, or stratification, while not sacrificing its power. Furthermore, our method demonstrated its superiority in localizing causal variants from massive linked genetic variants. The rate of successful localization was about 20-40% higher than that of other state-of-the-art methods on simulated data sets. On empirical data, validated functional causal variants of four well-known positive selected genes were all successfully localized by our method, such as ADH1B, MCM6, APOL1, and HBB. Finally, the computational efficiency of this new method was much higher than that of iHS implementations, that is, 24-66 times faster than the REHH package, and more than 10,000 times faster than the original iHS implementation. These magnitudes make our method suitable for applying on large sequencing data sets. Software can be downloaded from https://github.com/wavefancy/scct.

  15. Sensitive and selective detection of copper ions with highly stable polyethyleneimine-protected silver nanoclusters.

    PubMed

    Yuan, Zhiqin; Cai, Na; Du, Yi; He, Yan; Yeung, Edward S

    2014-01-07

    Copper is a highly toxic environmental pollutant with bioaccumulative properties. Therefore, sensitive Cu(2+) detection is very important to prevent over-ingestion, and visual detection using unaugmented vision is preferred for practical applications. In this study, hyperbranched polyethyleneimine-protected silver nanoclusters (hPEI-AgNCs) were successfully synthesized using a facile, one-pot reaction under mild conditions. The hPEI-AgNCs were very stable against extreme pH, ionic strength, temperature, and photoillumination and could act as sensitive and selective Cu(2+) sensing nanoprobes in aqueous solutions with a 10 nM limit of detection. In addition, hPEI-AgNCs-doped agarose hydrogels were developed as an instrument-free and regenerable platform for visual Cu(2+) and water quality monitoring.

  16. Fast and Selective Plasmonic Serotonin Detection with Aptamer-Gold Nanoparticle Conjugates.

    PubMed

    Chávez, Jorge L; Hagen, Joshua A; Kelley-Loughnane, Nancy

    2017-03-25

    Neurotransmitters detection is critical to understanding communication between the brain and peripheral tissue. Serotonin is a key neurotransmitter linked to a number of conditions, but a full understanding of its role in disease is still lacking. The development of fast and selective serotonin detection platforms will provide researchers with tools to monitor serotonin in individuals before and after treatment for the condition of interest. Aptamer-gold nanoparticles conjugates that responded colorimetrically to serotonin with minimal response to its metabolite and other neurotransmitters were designed by simply adsorbing the DNA on the surface of AuNPs. A plasmonic assay for serotonin detection was designed with a response to biologically relevant serotonin levels. Importantly, the assay performance was not compromised when tested in filtered spiked fetal bovine serum as a mimic of biofluids. This work shows that these simple and stable Apt-AuNP conjugates are promising tools to develop fast assays for point-of-care and personalized diagnostics applications.

  17. Novel pyridyl based azo-derivative for the selective and colorimetric detection of nickel(II)

    NASA Astrophysics Data System (ADS)

    Biswas, Sujan; Acharyya, Samik; Sarkar, Deblina; Gharami, Saswati; Mondal, Tapan Kumar

    2016-04-01

    A highly sensitive and selective pyridyl based colorimetric chemosensor (H2L) for the efficient detection of Ni2 + has been reported. The synthesized chemosensor H2L is highly efficient in detecting Ni2 + even in the presence of other metal ions that commonly co-exist with Ni2 +. H2L also shows distinct color change from green to deep red visible under naked eye due to specific binding with Ni2 +. This color change is due to formation of a new band at 510 nm upon gradual addition of Ni2 +. The association constant has been found to be 1.27 × 105 M- 1 with limit of detection (LOD) of 8.3 × 10- 7 M. Electronic structure of the H2L-Ni2 + complex and sensing mechanism have been interpreted theoretically by DFT and TDDFT calculations.

  18. Advanced selective non-invasive ketone body detection sensors based on new ionophores

    NASA Astrophysics Data System (ADS)

    Sathyapalan, A.; Sarswat, P. K.; Zhu, Y.; Free, M. L.

    2014-12-01

    New molecules and methods were examined that can be used to detect trace level ketone bodies. Diseases such as type 1 diabetes, childhood hypo-glycaemia-growth hormone deficiency, toxic inhalation, and body metabolism changes are linked with ketone bodies concentration. Here we introduce, selective ketone body detection sensors based on small, environmentally friendly organic molecules with Lewis acid additives. Density functional theory (DFT) simulation of the sensor molecules (Bromo-acetonaphthone tungstate (BANT) and acetonaphthophenyl ether propiono hydroxyl tungstate (APPHT)), indicated a fully relaxed geometry without symmetry attributes and specific coordination which enhances ketone bodies sensitivity. A portable sensing unit was made in which detection media containing ketone bodies at low concentration and new molecules show color change in visible light as well as unique irradiance during UV illumination. RGB analysis, electrochemical tests, SEM characterization, FTIR, absorbance and emission spectroscopy were also performed in order to validate the ketone sensitivity of these new molecules.

  19. Sensitive and Selective Detection of HIV-1 RRE RNA Using Vertical Silicon Nanowire Electrode Array

    NASA Astrophysics Data System (ADS)

    Lee, Jaehyung; Hong, Min-Ho; Han, Sanghun; Na, Jukwan; Kim, Ilsoo; Kwon, Yong-Joon; Lim, Yong-beom; Choi, Heon-Jin

    2016-07-01

    In this study, HIV-1 Rev response element (RRE) RNA was detected via an Au-coated vertical silicon nanowire electrode array (VSNEA). The VSNEA was fabricated by combining bottom-up and top-down approaches and then immobilized by artificial peptides for the recognition of HIV-1 RRE. Differential pulse voltammetry (DPV) analysis was used to measure the electrochemical response of the peptide-immobilized VSNEA to the concentration and types of HIV-1 RRE RNA. DPV peaks showed linearity to the concentration of RNA with a detection limit down to 1.513 fM. It also showed the clear different peaks to the mutated HIV-1 RRE RNA. The high sensitivity and selectivity of VSNEA for the detection of HIV-1 RRE RNA may be attributed to the high surface-to-volume ratio and total overlap diffusion mode of ions of the one-dimensional nanowire electrodes.

  20. Human adoption in evolutionary perspective.

    PubMed

    Silk, J B

    1990-03-01

    Exploitation is a fundamental element of the parental strategies of many species of birds. Cuckoos, for example, lay their eggs in the nest of other birds, who often unwittingly rear the alien nestlings as their own. Nest parasitism is an efficient reproductive strategy for cuckoos, who do not have to worry about building a nest, incubating their eggs, or feeding their nestlings. But not all hosts respond passively to such intrusions. In response to parasitic cowbirds, for example, robins have evolved the ability to detect and selectively eject alien young from their nests. Human parenting strategies differ sharply from the strategies of cuckoos and robins. Unlike cuckoos, we are reluctant to allow our children to be raised by others. Unlike robins, we knowingly rear strange young. What makes human behavior toward children so different from that of cuckoos and robins? Humans seem to share a number of predispositions that facilitate successful adoptive relationships, and the desire to raise children seems to be pervasive among modern humans. Despite these commonalities, patterns of adoption transactions vary greatly among contemporary human societies. This paper considers the origins and causes of cross-cultural variation in human adoptive behavior from an evolutionary perspective.

  1. Recombination in viruses: mechanisms, methods of study, and evolutionary consequences.

    PubMed

    Pérez-Losada, Marcos; Arenas, Miguel; Galán, Juan Carlos; Palero, Ferran; González-Candelas, Fernando

    2015-03-01

    Recombination is a pervasive process generating diversity in most viruses. It joins variants that arise independently within the same molecule, creating new opportunities for viruses to overcome selective pressures and to adapt to new environments and hosts. Consequently, the analysis of viral recombination attracts the interest of clinicians, epidemiologists, molecular biologists and evolutionary biologists. In this review we present an overview of three major areas related to viral recombination: (i) the molecular mechanisms that underlie recombination in model viruses, including DNA-viruses (Herpesvirus) and RNA-viruses (Human Influenza Virus and Human Immunodeficiency Virus), (ii) the analytical procedures to detect recombination in viral sequences and to determine the recombination breakpoints, along with the conceptual and methodological tools currently used and a brief overview of the impact of new sequencing technologies on the detection of recombination, and (iii) the major areas in the evolutionary analysis of viral populations on which recombination has an impact. These include the evaluation of selective pressures acting on viral populations, the application of evolutionary reconstructions in the characterization of centralized genes for vaccine design, and the evaluation of linkage disequilibrium and population structure.

  2. Evolutionary potential of Chamaecrista fasciculata in relation to climate change. I. Clinal patterns of selection along an environmental gradient in the great plains.

    PubMed

    Etterson, Julie R

    2004-07-01

    Climate change will alter natural selection on native plant populations. Little information is available to predict how selection will change in the future and how populations will respond. Insight can be obtained by comparing selection regimes in current environments to selection regimes in environments similar to those predicted for the future. To mimic predicted temporal change in climate, three natural populations of the annual legume Chamaecrista fasciculata were sampled from a climate gradient in the Great Plains and progeny of formal crosses were reciprocally planted back into common gardens across this climate gradient. In each garden, native populations produced significantly more seed than the other populations, providing strong evidence of local adaptation. Phenotypic selection analysis conducted by site showed that plants with slower reproductive development, more leaves, and thicker leaves were favored in the most southern garden. Evidence of clinal variation in selection regimes was also found; selection coefficients were ordered according to the latitude of the common gardens. The adaptive value of native traits was indicated by selection toward the mean of local populations. Repeated clinal patterns in linear and nonlinear selection coefficients among populations and within and between sites were found. To the extent that temporal change in climate into the future will parallel the differences in selection across this spatial gradient, this study suggests that selection regimes will be displaced northward and different trait values will be favored in natural populations.

  3. Reusable optical bioassay platform with permeability-controlled hydrogel pads for selective saccharide detection.

    PubMed

    Cheung, Kwan Yee; Mak, Wing Cheung; Trau, Dieter

    2008-01-28

    A reusable optical bioassay platform using permeability-controlled hydrogel pads for selective saccharide detection has been developed. An optical glucose detection assay based on fluorescence resonance energy transfer (FRET) between dye-labeled dextran and Concanavalin A (ConA) was incorporated into hydrogel pads by entrapment. The hydrogel pads are constructed from hemispherical hydrogel attached onto hydrophobic surfaces of a microtiter plate. The resulted hemispherical hydrogel pads entrapping the sensing biological materials were further surface coated with polyelectrolyte multilayers through a Layer-by-Layer (LbL) self-assembly process to create a permeability-controlled membrane with nanometer thickness. The selective permeable LbL film deposited on the hydrogel surface allows small molecular weight analytes to diffuse into the hydrogel pads while the large molecular weight sensing biological molecules are immobilized. An encapsulation efficiency of 75% for the ConA/Dextran complex within the coated hydrogel pads was achieved and no significant leakage of the complex was observed. Glucose calibration curve with linear range from 0 to 10mM glucose was obtained. Selective permeability of the hydrogel pads has been demonstrated by measurement of saccharides with various molecular weights. The LbL hydrogel pads could selectively detect monosaccharides (glucose, MW=180) and disaccharides (sucrose, MW=342) while polysaccharides (dextran, MW approximately 70kDa) cannot diffuse through the LbL layer and are excluded. LbL hydrogel pads allow regeneration of the FRET system with good signal reproducibility of more than 90% to construct a reusable and reagentless optical bioassay platform.

  4. Genome-wide detection and characterization of positive selection in human populations

    PubMed Central

    Sabeti, Pardis C.; Varilly, Patrick; Fry, Ben; Lohmueller, Jason; Hostetter, Elizabeth; Cotsapas, Chris; Xie, Xiaohui; Byrne, Elizabeth H.; McCarroll, Steven A.; Gaudet, Rachelle; Schaffner, Stephen F.; Lander, Eric S.

    2009-01-01

    With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2)1. We used ‘long-range haplotype’ methods, which were developed to identify alleles segregating in a population that have undergone recent selection2, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population: LARGE and DMD, both related to infection by the Lassa virus3, in West Africa; SLC24A5 and SLC45A2, both involved in skin pigmentation4,5, in Europe; and EDAR and EDA2R, both involved in development of hair follicles6, in Asia. PMID:17943131

  5. Genome-wide detection and characterization of positive selection in human populations.

    PubMed

    Sabeti, Pardis C; Varilly, Patrick; Fry, Ben; Lohmueller, Jason; Hostetter, Elizabeth; Cotsapas, Chris; Xie, Xiaohui; Byrne, Elizabeth H; McCarroll, Steven A; Gaudet, Rachelle; Schaffner, Stephen F; Lander, Eric S; Frazer, Kelly A; Ballinger, Dennis G; Cox, David R; Hinds, David A; Stuve, Laura L; Gibbs, Richard A; Belmont, John W; Boudreau, Andrew; Hardenbol, Paul; Leal, Suzanne M; Pasternak, Shiran; Wheeler, David A; Willis, Thomas D; Yu, Fuli; Yang, Huanming; Zeng, Changqing; Gao, Yang; Hu, Haoran; Hu, Weitao; Li, Chaohua; Lin, Wei; Liu, Siqi; Pan, Hao; Tang, Xiaoli; Wang, Jian; Wang, Wei; Yu, Jun; Zhang, Bo; Zhang, Qingrun; Zhao, Hongbin; Zhao, Hui; Zhou, Jun; Gabriel, Stacey B; Barry, Rachel; Blumenstiel, Brendan; Camargo, Amy; Defelice, Matthew; Faggart, Maura; Goyette, Mary; Gupta, Supriya; Moore, Jamie; Nguyen, Huy; Onofrio, Robert C; Parkin, Melissa; Roy, Jessica; Stahl, Erich; Winchester, Ellen; Ziaugra, Liuda; Altshuler, David; Shen, Yan; Yao, Zhijian; Huang, Wei; Chu, Xun; He, Yungang; Jin, Li; Liu, Yangfan; Shen, Yayun; Sun, Weiwei; Wang, Haifeng; Wang, Yi; Wang, Ying; Xiong, Xiaoyan; Xu, Liang; Waye, Mary M Y; Tsui, Stephen K W; Xue, Hong; Wong, J Tze-Fei; Galver, Luana M; Fan, Jian-Bing; Gunderson, Kevin; Murray, Sarah S; Oliphant, Arnold R; Chee, Mark S; Montpetit, Alexandre; Chagnon, Fanny; Ferretti, Vincent; Leboeuf, Martin; Olivier, Jean-François; Phillips, Michael S; Roumy, Stéphanie; Sallée, Clémentine; Verner, Andrei; Hudson, Thomas J; Kwok, Pui-Yan; Cai, Dongmei; Koboldt, Daniel C; Miller, Raymond D; Pawlikowska, Ludmila; Taillon-Miller, Patricia; Xiao, Ming; Tsui, Lap-Chee; Mak, William; Song, You Qiang; Tam, Paul K H; Nakamura, Yusuke; Kawaguchi, Takahisa; Kitamoto, Takuya; Morizono, Takashi; Nagashima, Atsushi; Ohnishi, Yozo; Sekine, Akihiro; Tanaka, Toshihiro; Tsunoda, Tatsuhiko; Deloukas, Panos; Bird, Christine P; Delgado, Marcos; Dermitzakis, Emmanouil T; Gwilliam, Rhian; Hunt, Sarah; Morrison, Jonathan; Powell, Don; Stranger, Barbara E; Whittaker, Pamela; Bentley, David R; Daly, Mark J; de Bakker, Paul I W; Barrett, Jeff; Chretien, Yves R; Maller, Julian; McCarroll, Steve; Patterson, Nick; Pe'er, Itsik; Price, Alkes; Purcell, Shaun; Richter, Daniel J; Sabeti, Pardis; Saxena, Richa; Schaffner, Stephen F; Sham, Pak C; Varilly, Patrick; Altshuler, David; Stein, Lincoln D; Krishnan, Lalitha; Smith, Albert Vernon; Tello-Ruiz, Marcela K; Thorisson, Gudmundur A; Chakravarti, Aravinda; Chen, Peter E; Cutler, David J; Kashuk, Carl S; Lin, Shin; Abecasis, Gonçalo R; Guan, Weihua; Li, Yun; Munro, Heather M; Qin, Zhaohui Steve; Thomas, Daryl J; McVean, Gilean; Auton, Adam; Bottolo, Leonardo; Cardin, Niall; Eyheramendy, Susana; Freeman, Colin; Marchini, Jonathan; Myers, Simon; Spencer, Chris; Stephens, Matthew; Donnelly, Peter; Cardon, Lon R; Clarke, Geraldine; Evans, David M; Morris, Andrew P; Weir, Bruce S; Tsunoda, Tatsuhiko; Johnson, Todd A; Mullikin, James C; Sherry, Stephen T; Feolo, Michael; Skol, Andrew; Zhang, Houcan; Zeng, Changqing; Zhao, Hui; Matsuda, Ichiro; Fukushima, Yoshimitsu; Macer, Darryl R; Suda, Eiko; Rotimi, Charles N; Adebamowo, Clement A; Ajayi, Ike; Aniagwu, Toyin; Marshall, Patricia A; Nkwodimmah, Chibuzor; Royal, Charmaine D M; Leppert, Mark F; Dixon, Missy; Peiffer, Andy; Qiu, Renzong; Kent, Alastair; Kato, Kazuto; Niikawa, Norio; Adewole, Isaac F; Knoppers, Bartha M; Foster, Morris W; Clayton, Ellen Wright; Watkin, Jessica; Gibbs, Richard A; Belmont, John W; Muzny, Donna; Nazareth, Lynne; Sodergren, Erica; Weinstock, George M; Wheeler, David A; Yakub, Imtaz; Gabriel, Stacey B; Onofrio, Robert C; Richter, Daniel J; Ziaugra, Liuda; Birren, Bruce W; Daly, Mark J; Altshuler, David; Wilson, Richard K; Fulton, Lucinda L; Rogers, Jane; Burton, John; Carter, Nigel P; Clee, Christopher M; Griffiths, Mark; Jones, Matthew C; McLay, Kirsten; Plumb, Robert W; Ross, Mark T; Sims, Sarah K; Willey, David L; Chen, Zhu; Han, Hua; Kang, Le; Godbout, Martin; Wallenburg, John C; L'Archevêque, Paul; Bellemare, Guy; Saeki, Koji; Wang, Hongguang; An, Daochang; Fu, Hongbo; Li, Qing; Wang, Zhen; Wang, Renwu; Holden, Arthur L; Brooks, Lisa D; McEwen, Jean E; Guyer, Mark S; Wang, Vivian Ota; Peterson, Jane L; Shi, Michael; Spiegel, Jack; Sung, Lawrence M; Zacharia, Lynn F; Collins, Francis S; Kennedy, Karen; Jamieson, Ruth; Stewart, John

    2007-10-18

    With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.

  6. Genome-wide scans to detect positive selection in Large White and Tongcheng pigs.

    PubMed

    Li, Xiuling; Yang, Songbai; Tang, Zhonglin; Li, Kui; Rothschild, Max F; Liu, Bang; Fan, Bin

    2014-06-01

    Due to the direction, intensity, duration and consistency of genetic selection, especially recent artificial selection, the production performance of domestic pigs has been greatly changed. Therefore, we reasoned that there must be footprints or selection signatures that had been left during domestication. In this study, with porcine 60K BeadChip genotyping data from both commercial Large White and local Chinese Tongcheng pigs, we calculated the extended haplotype homozygosity values of the two breeds using the long-range haplotype method to detect selection signatures. We found 34 candidate regions, including 61 known genes, from Large White pigs and 25 regions comprising 57 known genes from Tongcheng pigs. Many selection signatures were found on SSC1, SSC4, SSC7 and SSC14 regions in both populations. According to quantitative trait loci and network pathway analyses, most of the regions and genes were linked to growth, reproduction and immune responses. In addition, the average genetic differentiation coefficient FST was 0.254, which means that there had already been a significant differentiation between the breeds. The findings from this study can contribute to further research on molecular mechanisms of pig evolution and domestication and also provide valuable references for improvement of their breeding and cultivation.

  7. Evolutionary Design in Biology

    NASA Astrophysics Data System (ADS)

    Wiese, Kay C.

    Much progress has been achieved in recent years in molecular biology and genetics. The sheer volume of data in the form of biological sequences has been enormous and efficient methods for dealing with these huge amounts of data are needed. In addition, the data alone does not provide information on the workings of biological systems; hence much research effort has focused on designing mathematical and computational models to address problems from molecular biology. Often, the terms bioinformatics and computational biology are used to refer to the research fields concerning themselves with designing solutions to molecular problems in biology. However, there is a slight distinction between bioinformatics and computational biology: the former is concerned with managing the enormous amounts of biological data and extracting information from it, while the latter is more concerned with the design and development of new algorithms to address problems such as protein or RNA folding. However, the boundary is blurry, and there is no consistent usage of the terms. We will use the term bioinformatics to encompass both fields. To cover all areas of research in bioinformatics is beyond the scope of this section and we refer the interested reader to [2] for a general introduction. A large part of what bioinformatics is concerned about is evolution and function of biological systems on a molecular level. Evolutionary computation and evolutionary design are concerned with developing computational systems that "mimic" certain aspects of natural evolution (mutation, crossover, selection, fitness). Much of the inner workings of natural evolutionary systems have been copied, sometimes in modified format into evolutionary computation systems. Artificial neural networks mimic the functioning of simple brain cell clusters. Fuzzy systems are concerned with the "fuzzyness" in decision making, similar to a human expert. These three computational paradigms fall into the category of

  8. DETECTING SELECTION IN NATURAL POPULATIONS: MAKING SENSE OF GENOME SCANS AND TOWARDS ALTERNATIVE SOLUTIONS

    PubMed Central

    Haasl, Ryan J.; Payseur, Bret A.

    2016-01-01

    Genomewide scans for natural selection (GWSS) have become increasingly common over the last 15 years due to increased availability of genome-scale genetic data. Here, we report a representative survey of GWSS from 1999 to present and find that (i) between 1999 and 2009, 35 of 49 (71%) GWSS focused on human, while from 2010 to present, only 38 of 83 (46%) of GWSS focused on human, indicating increased focus on nonmodel organisms; (ii) the large majority of GWSS incorporate interpopulation or interspecific comparisons using, for example FST, cross-population extended haplotype homozygosity or the ratio of nonsynonymous to synonymous substitutions; (iii) most GWSS focus on detection of directional selection rather than other modes such as balancing selection; and (iv) in human GWSS, there is a clear shift after 2004 from microsatellite markers to dense SNP data. A survey of GWSS meant to identify loci positively selected in response to severe hypoxic conditions support an approach to GWSS in which a list of a priori candidate genes based on potential selective pressures are used to filter the list of significant hits a posteriori. We also discuss four frequently ignored determinants of genomic heterogeneity that complicate GWSS: mutation, recombination, selection and the genetic architecture of adaptive traits. We recommend that GWSS methodology should better incorporate aspects of genomewide heterogeneity using empirical estimates of relevant parameters and/or realistic, whole-chromosome simulations to improve interpretation of GWSS results. Finally, we argue that knowledge of potential selective agents improves interpretation of GWSS results and that new methods focused on correlations between environmental variables and genetic variation can help automate this approach. PMID:26224644

  9. Reactive chromophores for sensitive and selective detection of chemical warfare agents

    NASA Astrophysics Data System (ADS)

    Frye-Mason, Greg; Leuschen, Martin; la Grone, Marcus; Wald, Lara; Aker, Craig; Dock, Matt; Hancock, Lawrence F.; Fagan, Steve; Paul, Kateri

    2004-08-01

    A new sensor for highly toxic species including chemical warfare (CW) agents has been developed. This sensor is based on a unique CW indicating chromophore (CWIC) developed by Professor Tim Swager at MIT. The CWIC was designed to be sensitive to the reactivity that makes these chemicals so toxic. Since it requires the reactivity of the agent to be detected, the CWIC technology has shown remarkable selectivity for nerve agent surrogates and some other highly toxic species, thereby demonstrating the potential to provide low false alarm rate detection. Since the chromophore has mini-mal fluorescence prior to reaction with an electrophilic and toxic chemical, the sensor acts in a dark field fluorescence mode. This provides the sensor with exceptional sensitivity and a potential to detect priority analytes well below levels detected by current hand held sensors. Finally, it is based on a simple optical detection scheme that enables small and rugged sensors to be developed and produced at a low enough cost so they can be widely utilized.

  10. Highly sensitive and selective colorimetric detection of cartap residue in agricultural products.

    PubMed

    Liu, Wei; Zhang, Daohong; Tang, Yafan; Wang, Yashan; Yan, Fei; Li, Zhonghong; Wang, Jianlong; Zhou, H Susan

    2012-11-15

    The residue of pesticide has posed a serious threat to human health. Fast, broad-spectrum detection methods are necessary for on-site screening of various types of pesticides. With citrate-coated Au nanoparticles (Au NPs) as colorimetric probes, a visual and spectrophotometric method for rapid assay of cartap, which is one of the most important pesticides in agriculture, is reported for the first time. Based on the color change of Au colloid solution from wine-red to blue resulting from the aggregation of Au NPs, cartap could be detected in the concentration range of 0.05-0.6 mg/kg with a low detection limit of 0.04 mg/kg, which is much lower than the strictest cartap safety requirement of 0.1 mg/kg. Due to the limited research on the rapid detection of cartap based on Au NPs, the performance of the present method was evaluated through aggregation kinetics, interference influence, and sample pretreatment. To further demonstrate the selectivity and applicability of the method, cartap detection is realized in cabbage and tea with excellent analyte concentration recovery. These results demonstrate that the present method provides an easy and effective way to analyze pesticide residue in common products, which is of benefit for the rapid risk evaluation and on-site screening of pesticide residue.

  11. Selecting an acceptable and safe antibody detection test can present a dilemma.

    PubMed

    Combs, M R; Bredehoeft, S J

    2001-01-01

    The Transfusion Service at Duke University Hospital has changed antibody detection methods from the use of albumin in indirect antiglobulin tests to low-ionic-strength solution (LISS), and from LISS to polyethylene glycol (PEG) in an effort to enhance the rapid detection of clinically significant antibodies. In 1996, staffing issues required the consideration of automation. Although previous studies indicated that the gel test was not as sensitive as PEG for detection of clinically significant antibodies, we chose to implement the gel test to be used with the Tecan MegaFlex-ID. We performed a retrospective analysis of identified antibodies and transfusion reactions to compare the outcomes of one year's experience with gel and PEG. We found comparable detection of potentially clinically significant antibodies by both methods and significantly fewer unwanted or clinically insignificant antibodies detected with the use of gel. Fewer delayed serologic transfusion reactions and no transfusion-associated hemolytic events occurred in the year that gel was used. Although we initially found the selection of the gel test to be a dilemma, our ultimate decision appears to have successfully protected patient safety and balanced sensitivity with specificity.

  12. Ecological aspects of the evolutionary processes.

    PubMed

    Bock, Walter J

    2003-03-01

    Darwin in his On the Origin of species made it clear that evolutionary change depends on the combined action of two different causes, the first being the origin of genetically based phenotypic variation in the individual organisms comprising the population and the second being the action of selective agents of the external environment placing demands on the individual organisms. For over a century following Darwin, most evolutionists focused on the origin of inherited variation and its transmission; many workers continue to regard genetics to be the core of evolutionary theory. Far less attention has been given to the exact nature of the selective agents with most evolutionists still treating this cause imprecisely to the detriment of our understanding of both nomological and historical evolutionary theory. Darwin was vague in the meaning of his new concept of "Natural Selection," using it interchangeably as one of the causes for evolutionary change and as the final outcome (= evolutionary change). In 1930, natural selection was defined clearly as "non-random, differential reproduction of genes" by R. Fisher and J.B.S. Haldane which is a statement of the outcome of evolutionary process and which omits mention of the causes bringing about this change. Evolutionists quickly accepted this outcome definition of natural selection, and have used interchangeably selection both as a cause and as the result of evolutionary change, causing great confusion. Herein, the details will be discussed of how the external environment (i.e., the environment-phenotype interaction) serves as selective agents and exerts demands on the phenotypic organisms. Included are the concepts of fitness and of the components of fitness (= adaptations) which are respectively (a) survival, (b) direct reproductive and (c) indirect reproductive features. Finally, it will be argued that historical-narrative analyses of organisms, including classification and phylogenetic history, are possible only with

  13. Algorithmic Mechanism Design of Evolutionary Computation

    PubMed Central

    Pei, Yan

    2015-01-01

    We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm. PMID:26257777

  14. A research of selected textural features for detection of asbestos-cement roofing sheets using orthoimages

    NASA Astrophysics Data System (ADS)

    Książek, Judyta

    2015-10-01

    At present, there has been a great interest in the development of texture based image classification methods in many different areas. This study presents the results of research carried out to assess the usefulness of selected textural features for detection of asbestos-cement roofs in orthophotomap classification. Two different orthophotomaps of southern Poland (with ground resolution: 5 cm and 25 cm) were used. On both orthoimages representative samples for two classes: asbestos-cement roofing sheets and other roofing materials were selected. Estimation of texture analysis usefulness was conducted using machine learning methods based on decision trees (C5.0 algorithm). For this purpose, various sets of texture parameters were calculated in MaZda software. During the calculation of decision trees different numbers of texture parameters groups were considered. In order to obtain the best settings for decision trees models cross-validation was performed. Decision trees models with the lowest mean classification error were selected. The accuracy of the classification was held based on validation data sets, which were not used for the classification learning. For 5 cm ground resolution samples, the lowest mean classification error was 15.6%. The lowest mean classification error in the case of 25 cm ground resolution was 20.0%. The obtained results confirm potential usefulness of the texture parameter image processing for detection of asbestos-cement roofing sheets. In order to improve the accuracy another extended study should be considered in which additional textural features as well as spectral characteristics should be analyzed.

  15. Source and path corrections, feature selection, and outlier detection applied to regional event discrimination in China

    SciTech Connect

    Hartse, H.E.; Taylor, S.R.; Phillips, W.S.; Velasco, A.A.

    1999-03-01

    The authors are investigating techniques to improve regional discrimination performance in uncalibrated regions. These include combined source and path corrections, spatial path corrections, path-specific waveguide corrections to construct frequency-dependent amplitude corrections that remove attenuation, corner frequency scaling, and source region/path effects (such as blockages). The spatial method and the waveguide method address corrections for specific source regions and along specific paths. After applying the above corrections to phase amplitudes, the authors form amplitude ratios and use a combination of feature selection and outlier detection to choose the best-performing combination of discriminants. Feature selection remains an important issue. Most stations have an inadequate population of nuclear explosions on which to base discriminant selection. Additionally, mining explosions are probably not good surrogates for nuclear explosions. The authors are exploring the feasibility of sampling the source and path corrected amplitudes for each phase as a function of frequency in an outlier detection framework. In this case, the source identification capability will be based on the inability of the earthquake source model to fit data from explosion sources.

  16. Tellurium-nanowire-coated glassy carbon electrodes for selective and sensitive detection of dopamine.

    PubMed

    Tsai, Hsiang-Yu; Lin, Zong-Hong; Chang, Huan-Tsung

    2012-05-15

    Tellurium-nanowire-coated glassy carbon electrodes (TNGCEs) have been fabricated and employed for selective and sensitive detection of dopamine (DA). TNGCEs were prepared by direct deposition of tellurium nanowires, 600 ± 150 nm in length and 16 ± 3 nm in diameter, onto glassy carbon electrodes, which were further coated with Nafion to improve their selectivity and stability. Compared to the GCE, the TNGCE is more electroactive (by approximately 1.9-fold) for DA, and its selectivity toward DA over ascorbic acid (AA) and uric acid (UA) is also greater. By applying differential pulse voltammetry, at a signal-to-noise ratio of 3, the TNGCE provides a limit of detection of 1 nM for DA in the presence of 0.5mM AA and UA. Linearity (R(2)=0.9955) of the oxidation current at 0.19 V against the concentration of DA is found over the range 5 nM-1 μM. TNGCEs have been applied to determine the concentration of dopamine to be 0.59 ± 0.07 μM in PC12 cells.

  17. Fluorescent sensors for selective detection of thiols: expanding the intramolecular displacement based mechanism to new chromophores.

    PubMed

    Niu, Li-Ya; Zheng, Hai-Rong; Chen, Yu-Zhe; Wu, Li-Zhu; Tung, Chen-Ho; Yang, Qing-Zheng

    2014-03-21

    Biological thiols, including cysteine (Cys), homocystein (Hcy) and glutathione (GSH), play crucial roles in maintaining the appropriate redox status of biological systems. An abnormal level of biothiols is associated with different diseases, therefore, the discrimination between them is of great importance. Herein, we present two fluorescent sensors for selective detection of biothiols based on our recently reported intramolecular displacement mechanism. We expanded this mechanism to commercially available chromophores, 4-chloro-7-nitro-2,1,3-benzoxadiazole (NBD-Cl) and heptamethine cyanine dye IR-780. The sensors operate by undergoing displacement of chloride by thiolate. The amino groups of Cys/Hcy further replace the thiolate to form amino-substituted products, which exhibit dramatically different photophysical properties compared to sulfur-substituted products from the reaction with GSH. NBD-Cl is highly selective towards Cys/Hcy and exhibits significant fluorescence enhancement. IR-780 showed a variation in its fluorescence ratio towards Cys over other thiols. Both of the sensors can be used for live-cell imaging of Cys. The wide applicability of the mechanism may provide a powerful tool for developing novel fluorescent sensors for selective detection of biothiols.

  18. Triazole-based highly selective supramolecular sensor for the detection of diclofenac in real samples.

    PubMed

    Ahmed, Farid; Shah, Kiramat; Awan, Iqra Zubair; Shah, Muhammad Raza

    2016-07-01

    A triazole-based supramolecular chemosensor 6 for the selective spectrophotometric detection of diclofenac in human plasma and tap water was developed. The 6 was synthesized through click approach and characterized via UV-vis spectroscopy, FT-IR, Mass and NMR spectroscopy. The supramolecular interaction of compound 6 with commonly used drugs has been investigated with the help of UV-vis spectral titrations, FT-IR and (1)H, (13)C NMR spectroscopy. The UV-visible spectral changes upon addition of various commonly used drugs showed that compound 6 is highly selective for diclofenac over other drugs. The supramolecule 6 exhibited a selective enhancement in the absorbance intensity after mixing with diclofenac in human plasma and water samples in the presence of other drugs at pH 6-7, with a linear range of 0.938 (R(2)=0.938) and a limit of detection 10µM. The relative standard deviation (RSD) for 100µM diclofenac was found to be 0.462. The Job's plot analysis revealed that diclofenac bind to compound 6 in 1:1 stoichiometry.

  19. Label free selective detection of estriol using graphene oxide-based fluorescence sensor

    NASA Astrophysics Data System (ADS)

    Kushwaha, H. S.; Sao, Reshma; Vaish, Rahul

    2014-07-01

    Water-soluble and fluorescent Graphene oxide (GO) is biocompatible, easy, and economical to synthesize. Interestingly, GO is also capable of quenching fluorescence. On the basis of its fluorescence and quenching abilities, GO has been reported to serve as an energy acceptor in a fluorescence resonance energy transfer (FRET) sensor. GO-based FRET biosensors have been widely reported for sensing of proteins, nucleic acid, ATP (Adenosine triphosphate), etc. GO complexes with fluorescent dyes and enzymes have been used to sense metal ions. Graphene derivatives have been used for sensing endocrine-disrupting chemicals like bisphenols and chlorophenols with high sensitivity and good reproducibility. On this basis, a novel GO based fluorescent sensor has been successfully designed to detect estriol with remarkable selectivity and sensitivity. Estriol is one of the three estrogens in women and is considered to be medically important. Estriol content of maternal urine or plasma acts as an important screening marker for estimating foetal growth and development. In addition, estriol is also used as diagnostic marker for diseases like breast cancer, osteoporosis, neurodegenerative and cardiovascular diseases, insulin resistance, lupus erythematosus, endometriosis, etc. In this present study, we report for the first time a rapid, sensitive with detection limit of 1.3 nM, selective and highly biocompatible method for label free detection of estriol under physiological conditions using fluorescence assay.

  20. Selectivity verification of cardiac troponin monoclonal antibodies for cardiac troponin detection by using conventional ELISA

    NASA Astrophysics Data System (ADS)

    Fathil, M. F. M.; Arshad, M. K. Md; Gopinath, Subash C. B.; Adzhri, R.; Ruslinda, A. R.; Hashim, U.

    2017-03-01

    This paper presents preparation and characterization of conventional enzyme-linked immunosorbent assay (ELISA) for cardiac troponin detection to determine the selectivity of the cardiac troponin monoclonal antibodies. Monoclonal antibodies, used to capture and bind the targets in this experiment, are cTnI monoclonal antibody (MAb-cTnI) and cTnT monoclonal antibody (MAb-cTnT), while both cardiac troponin I (cTnI) and T (cTnT) are used as targets. ELISA is performed inside two microtiter plates for MAb-cTnI and MAb-cTnT. For each plate, monoclonal antibodies are tested by various concentrations of cTnI and cTnT ranging from 0-6400 µg/l. The binding selectivity and level of detection between monoclonal antibodies and antigen are determined through visual observation based on the color change inside each well on the plate. ELISA reader is further used to quantitatively measured the optical density of the color changes, thus produced more accurate reading. The results from this experiment are utilized to justify the use of these monoclonal antibodies as bio-receptors for cardiac troponin detection by using field-effect transistor (FET)-based biosensors coupled with substrate-gate in the future.

  1. Carbon nanotube field effect transistors for the fast and selective detection of human immunoglobulin G.

    PubMed

    Cid, Cristina C; Riu, Jordi; Maroto, Alicia; Rius, F Xavier

    2008-08-01

    We report a field effect transistor (FET) based on a network of single-walled carbon nanotubes (SWCNTs) which can selectively detect human immunoglobulin G (HIgG). HIgG antibodies, which are strongly adsorbed onto the walls of the SWCNTs, are the basic elements of the recognition layer. The non-specific binding of proteins and the effects of other interferences are avoided by covering the non-adsorbed areas of the SWCNTs with Tween 20. The selectivity of the sensor has been tested against bovine serum albumin (BSA), the most abundant protein in plasma. HIgG in aqueous solution with concentrations from 1.25 mg L(-1) (8 nM) can be readily detected with response times of about 10 min. The SWCNT networks that form the basis of the sensor are easily grown by chemical vapour deposition. Silver screen-printed electrodes make the sensor quick to build. The sensitivity obtained with this sensor is similar to other FET devices based on SWCNTs built using much more complicated lithography processes. Moreover, the sensor is a reagentless device that does not need labels to detect HIgG.

  2. Selecting a sensitive battery of bioassays to detect toxic effects of metals in effluents.

    PubMed

    de Paiva Magalhães, Danielly; da Costa Marques, Mônica Regina; Fernandes Baptista, Darcilio; Forsin Buss, Daniel

    2014-09-07

    The use of bioassay batteries is necessary to evaluate toxic effects at various biological levels. The selection of bioassays without prior testing and determination of the most sensitive/suitable groups for each impact may allow the discharge of effluents that pose a threat to the environment. The present study tested and selected a battery of sensitive ecotoxicological bioassays for detecting toxic effects of metals. The sensitivities of six organisms were evaluated (algae Pseudokirchneriella subcapitata and Chlorella vulgaris, Cladocera Daphnia similis and Ceriodaphnia dubia, and fish Poecilia reticulata and Danio rerio) after exposure to 10 individual metal species deemed toxic to the aquatic environment (Ag(+), Cd(2+), Cu(+), Cu(2+), Cr(3+), Cr(6+), Pb(2+), Ni(2+), Zn(2+), and Hg(2+)) and to real (steel-mill) and laboratory simulated effluents. In the bioassays, fish were the least sensitive; D. rerio showed no sensitivity to any of the effluents tested. P. subcapitata was a good bioindicator of Cr(3+) toxicity, and D. similis was the most sensitive organism to Hg(2+); but the toxic effect of effluents with higher levels of Hg(2+) was better detected by C. dubia. The most sensitive battery of bioassays to detect low concentrations of dissolved metals in effluents was the 72-h chronic test with C. vulgaris and the 48-h acute test with C. dubia.

  3. Selective detection of dopamine with an all PEDOT:PSS Organic Electrochemical Transistor.

    PubMed

    Gualandi, Isacco; Tonelli, Domenica; Mariani, Federica; Scavetta, Erika; Marzocchi, Marco; Fraboni, Beatrice

    2016-10-14

    An all PEDOT:PSS Organic Electrochemical Transistor (OECT) has been developed and used for the selective detection of dopamine (DA) in the presence of interfering compounds (ascorbic acid, AA and uric acid, UA). The selective response has been implemented using a potentiodynamic approach, by varying the operating gate voltage and the scan rate. The trans-conductance curves allow to obtain a linear calibration plot for AA, UA and DA and to separate the redox waves associated to each compound; for this purpose, the scan rate is an important parameter to achieve a good resolution. The sensitivities and limits of detection obtained with the OECT have been compared with those obtained by potential step amperometric techniques (cyclic voltammetry and differential pulse voltammetry), employing a PEDOT:PSS working electrode: our results prove that the all-PEDOT:PSS OECT sensitivities and limits of detection are comparable or even better than those obtained by DPV, a technique that employs a sophisticate potential wave and read-out system in order to maximize the performance of electrochemical sensors and that can hardly be considered a viable readout method in practical applications.

  4. Ultrasensitive quantum dot fluorescence quenching assay for selective detection of mercury ions in drinking water.

    PubMed

    Ke, Jun; Li, Xinyong; Zhao, Qidong; Hou, Yang; Chen, Junhong

    2014-07-09

    Mercury is one of the most acutely toxic substances at trace level to human health and living thing. Developing a rapid, cheap and water soluble metal sensor for detecting mercury ions at ppb level remains a challenge. Herein, a metal sensor consisting of MPA coated Mn doped ZnSe/ZnS colloidal nanoparticles was utilized to ultrasensitively and selectively detect Hg(2+) ions with a low detection limit (0.1 nM) over a dynamic range from 0 to 20 nM. According to strong interaction between thiol(s) and mercury ions, mercaptopropionic acid (MPA) was used as a highly unique acceptor for mercury ions in the as-obtained ultrasensitive sensor. In the presence of mercury ions, colloidal nanoparticles rapidly agglomerated due to changes of surface chemical properties, which results in severe quenching of fluorescent intensity. Meanwhile, we find that the original ligands are separated from the surface of colloidal nanoparticles involving strongly chelation between mercury ion and thiol(s) proved by controlled IR analysis. The result shows that the QD-based metal ions sensor possesses satisfactory precision, high sensitivity and selectivity, and could be applied for the quantification analysis of real samples.

  5. Selective detection of dopamine with an all PEDOT:PSS Organic Electrochemical Transistor

    NASA Astrophysics Data System (ADS)

    Gualandi, Isacco; Tonelli, Domenica; Mariani, Federica; Scavetta, Erika; Marzocchi, Marco; Fraboni, Beatrice

    2016-10-01

    An all PEDOT:PSS Organic Electrochemical Transistor (OECT) has been developed and used for the selective detection of dopamine (DA) in the presence of interfering compounds (ascorbic acid, AA and uric acid, UA). The selective response has been implemented using a potentiodynamic approach, by varying the operating gate voltage and the scan rate. The trans-conductance curves allow to obtain a linear calibration plot for AA, UA and DA and to separate the redox waves associated to each compound; for this purpose, the scan rate is an important parameter to achieve a good resolution. The sensitivities and limits of detection obtained with the OECT have been compared with those obtained by potential step amperometric techniques (cyclic voltammetry and differential pulse voltammetry), employing a PEDOT:PSS working electrode: our results prove that the all-PEDOT:PSS OECT sensitivities and limits of detection are comparable or even better than those obtained by DPV, a technique that employs a sophisticate potential wave and read-out system in order to maximize the performance of electrochemical sensors and that can hardly be considered a viable readout method in practical applications.

  6. Ultrasensitive Quantum Dot Fluorescence quenching Assay for Selective Detection of Mercury Ions in Drinking Water

    PubMed Central

    Ke, Jun; Li, Xinyong; Zhao, Qidong; Hou, Yang; Chen, Junhong

    2014-01-01

    Mercury is one of the most acutely toxic substances at trace level to human health and living thing. Developing a rapid, cheap and water soluble metal sensor for detecting mercury ions at ppb level remains a challenge. Herein, a metal sensor consisting of MPA coated Mn doped ZnSe/ZnS colloidal nanoparticles was utilized to ultrasensitively and selectively detect Hg2+ ions with a low detection limit (0.1 nM) over a dynamic range from 0 to 20 nM. According to strong interaction between thiol(s) and mercury ions, mercaptopropionic acid (MPA) was used as a highly unique acceptor for mercury ions in the as-obtained ultrasensitive sensor. In the presence of mercury ions, colloidal nanoparticles rapidly agglomerated due to changes of surface chemical properties, which results in severe quenching of fluorescent intensity. Meanwhile, we find that the original ligands are separated from the surface of colloidal nanoparticles involving strongly chelation between mercury ion and thiol(s) proved by controlled IR analysis. The result shows that the QD-based metal ions sensor possesses satisfactory precision, high sensitivity and selectivity, and could be applied for the quantification analysis of real samples. PMID:25005836

  7. Ultrasensitive Quantum Dot Fluorescence quenching Assay for Selective Detection of Mercury Ions in Drinking Water

    NASA Astrophysics Data System (ADS)

    Ke, Jun; Li, Xinyong; Zhao, Qidong; Hou, Yang; Chen, Junhong

    2014-07-01

    Mercury is one of the most acutely toxic substances at trace level to human health and living thing. Developing a rapid, cheap and water soluble metal sensor for detecting mercury ions at ppb level remains a challenge. Herein, a metal sensor consisting of MPA coated Mn doped ZnSe/ZnS colloidal nanoparticles was utilized to ultrasensitively and selectively detect Hg2+ ions with a low detection limit (0.1 nM) over a dynamic range from 0 to 20 nM. According to strong interaction between thiol(s) and mercury ions, mercaptopropionic acid (MPA) was used as a highly unique acceptor for mercury ions in the as-obtained ultrasensitive sensor. In the presence of mercury ions, colloidal nanoparticles rapidly agglomerated due to changes of surface chemical properties, which results in severe quenching of fluorescent intensity. Meanwhile, we find that the original ligands are separated from the surface of colloidal nanoparticles involving strongly chelation between mercury ion and thiol(s) proved by controlled IR analysis. The result shows that the QD-based metal ions sensor possesses satisfactory precision, high sensitivity and selectivity, and could be applied for the quantification analysis of real samples.

  8. Synthesis of Au/Graphene Oxide Composites for Selective and Sensitive Electrochemical Detection of Ascorbic Acid

    NASA Astrophysics Data System (ADS)

    Song, Jian; Xu, Lin; Xing, Ruiqing; Li, Qingling; Zhou, Chunyang; Liu, Dali; Song, Hongwei

    2014-12-01

    In this work, we present a novel ascorbic acid (AA) sensor applied to the detection of AA in human sera and pharmaceuticals. A series of Au nanoparticles (NPs) and graphene oxide sheets (Au NP/GO) composites were successfully synthesized by reduction of gold (III) using sodium citrate. Then the Au NP/GO composites were used to construct nonenzymatic electrodes in practical AA measurement. The electrode that has the best performance presents attractive analytical features, such as a low working potential of +0.15 V, a high sensitivity of 101.86 μA mM-1 cm-2 to AA, a low detection limit of 100 nM, good reproducibility and excellent selectivity. And more,it was also employed to accurately and practically detect AA in human serum and clinical vitamin C tablet with the existence of some food additive. The enhanced AA electrochemical properties of the Au NP/GO modified electrode in our work can be attributed to the improvement of electroactive surface area of Au NPs and the synergistic effect from the combination of Au NPs and GO sheets. This work shows that the Au NP/GO/GCEs hold the prospect for sensitive and selective determination of AA in practical clinical application.

  9. Synthesis of Au/Graphene Oxide Composites for Selective and Sensitive Electrochemical Detection of Ascorbic Acid

    PubMed Central

    Song, Jian; Xu, Lin; Xing, Ruiqing; Li, Qingling; Zhou, Chunyang; Liu, Dali; Song, Hongwei

    2014-01-01

    In this work, we present a novel ascorbic acid (AA) sensor applied to the detection of AA in human sera and pharmaceuticals. A series of Au nanoparticles (NPs) and graphene oxide sheets (Au NP/GO) composites were successfully synthesized by reduction of gold (III) using sodium citrate. Then the Au NP/GO composites were used to construct nonenzymatic electrodes in practical AA measurement. The electrode that has the best performance presents attractive analytical features, such as a low working potential of +0.15 V, a high sensitivity of 101.86 μA mM−1 cm−2 to AA, a low detection limit of 100 nM, good reproducibility and excellent selectivity. And more,it was also employed to accurately and practically detect AA in human serum and clinical vitamin C tablet with the existence of some food additive. The enhanced AA electrochemical properties of the Au NP/GO modified electrode in our work can be attributed to the improvement of electroactive surface area of Au NPs and the synergistic effect from the combination of Au NPs and GO sheets. This work shows that the Au NP/GO/GCEs hold the prospect for sensitive and selective determination of AA in practical clinical application. PMID:25515430

  10. Rapidly responsive and highly selective fluorescent probe for sulfite detection in real samples and living cells.

    PubMed

    Li, Hongda

    2015-10-15

    Sulfites (HSO3(-) or SO3(-)) have very significant toxicity in the environment and in the system. However, developing specific identification of sulfite probes is still very important. In this paper, a highly selective colorimetric and fluorescent probe (HHC) was synthesized to detect HSO3(-) in real samples and living cells. Sensing performance and preponderance are listed as follows. First, probe HHC showed remarkable selectivity for HSO3(-) over varieties of other species, including cysteine, glutathione, S(2-), CN(-), and reactive oxygen species, mainly because of the introduction of the electron-poor C=C double bond for HSO3(-). Second, probe HHC has great molar absorptivity, allowing it to act as a visual detection of probe for HSO3(-). Third, the fluorescence intensities of HHC linearly correlate with the concentration of HSO3(-), with a detection limit of 6.8 nm. Finally, our proposed probe can be applied to the visually determination of trace HSO3(-) in real samples and living HeLa cells with high precision. We hope that our proposed probe will greatly benefit biological sciences when biological researchers survey the role of HSO3(-) in biological systems.

  11. Selective detection of dopamine with an all PEDOT:PSS Organic Electrochemical Transistor

    PubMed Central

    Gualandi, Isacco; Tonelli, Domenica; Mariani, Federica; Scavetta, Erika; Marzocchi, Marco; Fraboni, Beatrice

    2016-01-01

    An all PEDOT:PSS Organic Electrochemical Transistor (OECT) has been developed and used for the selective detection of dopamine (DA) in the presence of interfering compounds (ascorbic acid, AA and uric acid, UA). The selective response has been implemented using a potentiodynamic approach, by varying the operating gate voltage and the scan rate. The trans-conductance curves allow to obtain a linear calibration plot for AA, UA and DA and to separate the redox waves associated to each compound; for this purpose, the scan rate is an important parameter to achieve a good resolution. The sensitivities and limits of detection obtained with the OECT have been compared with those obtained by potential step amperometric techniques (cyclic voltammetry and differential pulse voltammetry), employing a PEDOT:PSS working electrode: our results prove that the all-PEDOT:PSS OECT sensitivities and limits of detection are comparable or even better than those obtained by DPV, a technique that employs a sophisticate potential wave and read-out system in order to maximize the performance of electrochemical sensors and that can hardly be considered a viable readout method in practical applications. PMID:27739467

  12. Hybrid Tuning of an Evolutionary Algorithm for Sensor Allocation

    DTIC Science & Technology

    2011-06-01

    13. SUPPLEMENTARY NOTES 2011 IEEE Conference on Evolutionary Computation , 5-8 June, New Orleans, LA. 14. ABSTRACT The application of evolutionary ...i.e. metrics) through multi-objective optimization and its capability to address non-linear classes of optimization problem. Evolutionary computation ...Yilmaz, B. N. Mcquay, H. Yu, A. S. Wu, and J. C. Sciortino, “Evolving sensor suites for enemy radar detection,” in Genetic and Evolutionary Computation

  13. Monopolar Detection Thresholds Predict Spatial Selectivity of Neural Excitation in Cochlear Implants: Implications for Speech Recognition

    PubMed Central

    2016-01-01

    The objectives of the study were to (1) investigate the potential of using monopolar psychophysical detection thresholds for estimating spatial selectivity of neural excitation with cochlear implants and to (2) examine the effect of site removal on speech recognition based on the threshold measure. Detection thresholds were measured in Cochlear Nucleus® device users using monopolar stimulation for pulse trains that were of (a) low rate and long duration, (b) high rate and short duration, and (c) high rate and long duration. Spatial selectivity of neural excitation was estimated by a forward-masking paradigm, where the probe threshold elevation in the presence of a forward masker was measured as a function of masker-probe separation. The strength of the correlation between the monopolar thresholds and the slopes of the masking patterns systematically reduced as neural response of the threshold stimulus involved interpulse interactions (refractoriness and sub-threshold adaptation), and spike-rate adaptation. Detection threshold for the low-rate stimulus most strongly correlated with the spread of forward masking patterns and the correlation reduced for long and high rate pulse trains. The low-rate thresholds were then measured for all electrodes across the array for each subject. Subsequently, speech recognition was tested with experimental maps that deactivated five stimulation sites with the highest thresholds and five randomly chosen ones. Performance with deactivating the high-threshold sites was better than performance with the subjects’ clinical map used every day with all electrodes active, in both quiet and background noise. Performance with random deactivation was on average poorer than that with the clinical map but the difference was not significant. These results suggested that the monopolar low-rate thresholds are related to the spatial neural excitation patterns in cochlear implant users and can be used to select sites for more optimal speech

  14. A new and fast image feature selection method for developing an optimal mammographic mass detection scheme

    PubMed Central

    Tan, Maxine; Pu, Jiantao; Zheng, Bin

    2014-01-01

    Purpose: Selecting optimal features from a large image feature pool remains a major challenge in developing computer-aided detection (CAD) schemes of medical images. The objective of this study is to investigate a new approach to significantly improve efficacy of image feature selection and classifier optimization in developing a CAD scheme of mammographic masses. Methods: An image dataset including 1600 regions of interest (ROIs) in which 800 are positive (depicting malignant masses) and 800 are negative (depicting CAD-generated false positive regions) was used in this study. After segmentation of each suspicious lesion by a multilayer topographic region growth algorithm, 271 features were computed in different feature categories including shape, texture, contrast, isodensity, spiculation, local topological features, as well as the features related to the presence and location of fat and calcifications. Besides computing features from the original images, the authors also computed new texture features from the dilated lesion segments. In order to select optimal features from this initial feature pool and build a highly performing classifier, the authors examined and compared four feature selection methods to optimize an artificial neural network (ANN) based classifier, namely: (1) Phased Searching with NEAT in a Time-Scaled Framework, (2) A sequential floating forward selection (SFFS) method, (3) A genetic algorithm (GA), and (4) A sequential forward selection (SFS) method. Performances of the four approaches were assessed using a tenfold cross validation method. Results: Among these four methods, SFFS has highest efficacy, which takes 3%–5% of computational time as compared to GA approach, and yields the highest performance level with the area under a receiver operating characteristic curve (AUC) = 0.864 ± 0.034. The results also demonstrated that except using GA, including the new texture features computed from the dilated mass segments improved the AUC

  15. Highly selective detection of individual nuclear spins with rotary echo on an electron spin probe

    DOE PAGES

    Mkhitaryan, V. V.; Jelezko, F.; Dobrovitski, V. V.

    2015-10-26

    We consider an electronic spin, such as a nitrogen-vacancy center in diamond, weakly coupled to a large number of nuclear spins, and subjected to the Rabi driving with a periodically alternating phase. We show that by switching the driving phase synchronously with the precession of a given nuclear spin, the interaction to this spin is selectively enhanced, while the rest of the bath remains decoupled. The enhancement is of resonant character. The key feature of the suggested scheme is that the width of the resonance is adjustable, and can be greatly decreased by increasing the driving strength. Thus, the resonancemore » can be significantly narrowed, by a factor of 10–100 in comparison with the existing detection methods. Significant improvement in selectivity is explained analytically and confirmed by direct numerical many-spin simulations. As a result, the method can be applied to a wide range of solid-state systems.« less

  16. Benzophenone based fluorophore for selective detection of Sn2 + ion: Experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Jadhav, Amol G.; Shinde, Suvidha S.; Lanke, Sandip K.; Sekar, Nagaiyan

    2017-03-01

    Synthesis of novel benzophenone-based chemosensor is presented for the selective sensing of Sn2 + ion. Screening of competitive metal ions was performed by competitive experiments. The specific cation recognition ability of chemosensor towards Sn2 + was investigated by experimental (UV-visible, fluorescence spectroscopy, 1H NMR, 13C NMR, FTIR and HRMS) methods and further supported by Density Functional Theory study. The stoichiometric binding ratio and binding constant (Ka) for complex is found to be 1:1 and 1.50 × 104, respectively. The detection limit of Sn2 + towards chemosensor was found to be 0.3898 ppb. Specific selectivity and superiority of chemosensor over another recently reported chemosensor is presented.

  17. Highly selective detection of individual nuclear spins with rotary echo on an electron spin probe

    SciTech Connect

    Mkhitaryan, V. V.; Jelezko, F.; Dobrovitski, V. V.

    2015-10-26

    We consider an electronic spin, such as a nitrogen-vacancy center in diamond, weakly coupled to a large number of nuclear spins, and subjected to the Rabi driving with a periodically alternating phase. We show that by switching the driving phase synchronously with the precession of a given nuclear spin, the interaction to this spin is selectively enhanced, while the rest of the bath remains decoupled. The enhancement is of resonant character. The key feature of the suggested scheme is that the width of the resonance is adjustable, and can be greatly decreased by increasing the driving strength. Thus, the resonance can be significantly narrowed, by a factor of 10–100 in comparison with the existing detection methods. Significant improvement in selectivity is explained analytically and confirmed by direct numerical many-spin simulations. As a result, the method can be applied to a wide range of solid-state systems.

  18. Measurement point selection in damage detection using the mutual information concept

    NASA Astrophysics Data System (ADS)

    Trendafilova, I.; Heylen, W.; Van Brussel, H.

    2001-06-01

    The problem for measurement point selection in damage detection procedures is addressed. The concept of average mutual information is applied in order to find the optimal distance between measurement points. The idea is to select the measurement points in such a way that the taken measurements are independent, i.e. the measurements do not `learn' from each other. The average mutual information can be utilized as a kind of an autocorrelation function for the purpose. It gives the average amount of information that two points `learn' from each other. Thus the minimum of the average mutual information will provide the distance between measurement points with independent measurements. The idea to use the first minimum of the average mutual information is taken from nonlinear dynamics. The proposed approach is demonstrated on a test case. The results show that it is possible to decrease significantly the number of measurement points, without decreasing the precision of the solution.

  19. Self-assembled block copolymer photonic crystal for selective fructose detection.

    PubMed

    Ayyub, Omar B; Ibrahim, Michael B; Briber, Robert M; Kofinas, Peter

    2013-08-15

    The use of one-dimensional photonic crystals fabricated from a self-assembled lamellar block copolymer as a sensitive and selective fructose sensor is investigated. The polystyrene-b-poly(2-vinyl pyridine) (PS-b-P2VP) films are functionalized with 2-(bromomethyl)phenylboronic acid. The boronic acid moiety confined within the lamellar morphology can reversibly bind to sugars such as fructose, imparting the photonic properties of the PS-b-P2VP film. The films exhibit a detection limit of 500 μM in water and 1mM in phosphate buffered saline. Exposure to a 50 mM solution of fructose invokes a highly visible color change from blue to orange. The films are also able to selectively recognize and respond to fructose in competitive studies in the presence of glucose, mannose and sucrose.

  20. Joint Covariate Detection on Expression Profiles for Selecting Prognostic miRNAs in Glioblastoma

    PubMed Central

    Sun, Chengqi

    2017-01-01

    An important application of expression profiles is to stratify patients into high-risk and low-risk groups using limited but key covariates associated with survival outcomes. Prior to that, variables considered to be associated with survival outcomes are selected. A combination of single variables, each of which is significantly related to survival outcomes, is always regarded to be candidates for posterior patient stratification. Instead of individually significant variables, a combination that contains not only significant but also insignificant variables is supposed to be concentrated on. By means of bottom-up enumeration on each pair of variables, we propose a joint covariate detection strategy to select candidates that not only correspond to close association with survival outcomes but also help to make a clear stratification of patients. Experimental results on a publicly available dataset of glioblastoma multiforme indicate that the selected pair composed of an individually significant and an insignificant miRNA keeps a better performance than the combination of significant single variables. The selected miRNA pair is ultimately regarded to be associated with the prognosis of glioblastoma multiforme by further pathway analysis.

  1. A Wearable Channel Selection-Based Brain-Computer Interface for Motor Imagery Detection.

    PubMed

    Lo, Chi-Chun; Chien, Tsung-Yi; Chen, Yu-Chun; Tsai, Shang-Ho; Fang, Wai-Chi; Lin, Bor-Shyh

    2016-02-06

    Motor imagery-based brain-computer interface (BCI) is a communication interface between an external machine and the brain. Many kinds of spatial filters are used in BCIs to enhance the electroencephalography (EEG) features related to motor imagery. The approach of channel selection, developed to reserve meaningful EEG channels, is also an important technique for the development of BCIs. However, current BCI systems require a conventional EEG machine and EEG electrodes with conductive gel to acquire multi-channel EEG signals and then transmit these EEG signals to the back-end computer to perform the approach of channel selection. This reduces the convenience of use in daily life and increases the limitations of BCI applications. In order to improve the above issues, a novel wearable channel selection-based brain-computer interface is proposed. Here, retractable comb-shaped active dry electrodes are designed to measure the EEG signals on a hairy site, without conductive gel. By the design of analog CAR spatial filters and the firmware of EEG acquisition module, the function of spatial filters could be performed without any calculation, and channel selection could be performed in the front-end device to improve the practicability of detecting motor imagery in the wearable EEG device directly or in commercial mobile phones or tablets, which may have relatively low system specifications. Finally, the performance of the proposed BCI is investigated, and the experimental results show that the proposed system is a good wearable BCI system prototype.

  2. A highly selective fluorescent probe based on Michael addition for fast detection of hydrogen sulfide.

    PubMed

    Gao, Baozhen; Cui, Lixia; Pan, Yong; Xue, Minjie; Zhu, Boyu; Zhang, Guomei; Zhang, Caihong; Shuang, Shaomin; Dong, Chuan

    2017-02-15

    A new 4-hydroxy-1,8-naphthalimide-based compound (probe 1) has been designed and synthesized. The colorimetric and fluorescent properties of probe 1 towards hydrogen sulfide (H2S) were investigated in detail. The results show that the probe 1 could selectively and sensitively recognize H2S rather than other reactive sulfur species. The reaction mechanism of this probe is an intramolecular cyclization caused by the Michael addition of H2S to give 4-hydroxy-1,8-naphthalimide. The intramolecular charge transfer of 4-hydroxy-1,8-naphthalimide is significant. Probe 1 quickly responded to H2S and showed a 75-fold fluorescence enhancement in 5min. Moreover, probe 1 could detect H2S quantitatively with a detection limit as low as 0.23μM.

  3. A highly selective fluorescent probe based on Michael addition for fast detection of hydrogen sulfide

    NASA Astrophysics Data System (ADS)

    Gao, Baozhen; Cui, Lixia; Pan, Yong; Xue, Minjie; Zhu, Boyu; Zhang, Guomei; Zhang, Caihong; Shuang, Shaomin; Dong, Chuan

    2017-02-01

    A new 4-hydroxy-1,8-naphthalimide-based compound (probe 1) has been designed and synthesized. The colorimetric and fluorescent properties of probe 1 towards hydrogen sulfide (H2S) were investigated in detail. The results show that the probe 1 could selectively and sensitively recognize H2S rather than other reactive sulfur species. The reaction mechanism of this probe is an intramolecular cyclization caused by the Michael addition of H2S to give 4-hydroxy-1,8-naphthalimide. The intramolecular charge transfer of 4-hydroxy-1,8-naphthalimide is significant. Probe 1 quickly responded to H2S and showed a 75-fold fluorescence enhancement in 5 min. Moreover, probe 1 could detect H2S quantitatively with a detection limit as low as 0.23 μM.

  4. EXONEST: Bayesian Model Selection Applied to the Detection and Characterization of Exoplanets via Photometric Variations

    NASA Astrophysics Data System (ADS)

    Placek, Ben; Knuth, Kevin H.; Angerhausen, Daniel

    2014-11-01

    EXONEST is an algorithm dedicated to detecting and characterizing the photometric signatures of exoplanets, which include reflection and thermal emission, Doppler boosting, and ellipsoidal variations. Using Bayesian inference, we can test between competing models that describe the data as well as estimate model parameters. We demonstrate this approach by testing circular versus eccentric planetary orbital models, as well as testing for the presence or absence of four photometric effects. In addition to using Bayesian model selection, a unique aspect of EXONEST is the potential capability to distinguish between reflective and thermal contributions to the light curve. A case study is presented using Kepler data recorded from the transiting planet KOI-13b. By considering only the nontransiting portions of the light curve, we demonstrate that it is possible to estimate the photometrically relevant model parameters of KOI-13b. Furthermore, Bayesian model testing confirms that the orbit of KOI-13b has a detectable eccentricity.

  5. Brief Report: Negative Controls to Detect Selection Bias and Measurement Bias in Epidemiologic Studies

    PubMed Central

    Ercumen, Ayse; Benjamin-Chung, Jade; Colford, John M.

    2016-01-01

    Biomedical laboratory experiments routinely use negative controls to identify possible sources of bias, but epidemiologic studies have infrequently used this type of control in their design or measurement approach. Recently, epidemiologists proposed the routine use of negative controls in observational studies and defined the structure of negative controls to detect bias due to unmeasured confounding. We extend this previous study and define the structure of negative controls to detect selection bias and measurement bias in both observational studies and randomized trials. We illustrate the strengths and limitations of negative controls in this context using examples from the epidemiologic literature. Given their demonstrated utility and broad generalizability, the routine use of prespecified negative controls will strengthen the evidence from epidemiologic studies. PMID:27182642

  6. EXONEST: Bayesian model selection applied to the detection and characterization of exoplanets via photometric variations

    SciTech Connect

    Placek, Ben; Knuth, Kevin H.; Angerhausen, Daniel E-mail: kknuth@albany.edu

    2014-11-10

    EXONEST is an algorithm dedicated to detecting and characterizing the photometric signatures of exoplanets, which include reflection and thermal emission, Doppler boosting, and ellipsoidal variations. Using Bayesian inference, we can test between competing models that describe the data as well as estimate model parameters. We demonstrate this approach by testing circular versus eccentric planetary orbital models, as well as testing for the presence or absence of four photometric effects. In addition to using Bayesian model selection, a unique aspect of EXONEST is the potential capability to distinguish between reflective and thermal contributions to the light curve. A case study is presented using Kepler data recorded from the transiting planet KOI-13b. By considering only the nontransiting portions of the light curve, we demonstrate that it is possible to estimate the photometrically relevant model parameters of KOI-13b. Furthermore, Bayesian model testing confirms that the orbit of KOI-13b has a detectable eccentricity.

  7. Detection of selective cationic amphipatic antibacterial peptides by Hidden Markov models.

    PubMed

    Polanco, Carlos; Samaniego, Jose L

    2009-01-01

    Antibacterial peptides are researched mainly for the potential benefit they have in a variety of socially relevant diseases, used by the host to protect itself from different types of pathogenic bacteria. We used the mathematical-computational method known as Hidden Markov models (HMMs) in targeting a subset of antibacterial peptides named Selective Cationic Amphipatic Antibacterial Peptides (SCAAPs). The main difference in the implementation of HMMs was focused on the detection of SCAAP using principally five physical-chemical properties for each candidate SCAAPs, instead of using the statistical information about the amino acids which form a peptide. By this method a cluster of antibacterial peptides was detected and as a result the following were found: 9 SCAAPs, 6 synthetic antibacterial peptides that belong to a subregion of Cecropin A and Magainin 2, and 19 peptides from the Cecropin A family. A scoring function was developed using HMMs as its core, uniquely employing information accessible from the databases.

  8. Selective chlorine dioxide determination using gas-diffusion flow injection analysis with chemiluminescent detection

    SciTech Connect

    Hollowell, D.A.; Gord, J.R.; Gordon, G.; Pacey, G.E.

    1986-06-01

    An automated chemiluminescent technique has been developed utilizing the advantages of gas-diffusion flow injection analysis. A gas-diffusion membrane separates the donor (sampling) stream from the acceptor (detecting) stream and removes ionic interferences. A novel chemiluminescence flow-through detector cell is used to measure the concentration of chlorine dioxide as a function of the intensity of the chemiluminescence produced from its reaction with luminol. The chemiluminescent reagent merges with the analyte directly in front of the photomultiplier tube in order to maximize the sensitivity of the system. The detection limit for chlorine dioxide is approximately 5 ppb. The method is over 1500 times more selective for chlorine dioxide than for chlorine on a mole basis. This method eliminates interference from iron and manganese compounds, as well as other oxychlorinated compounds such as chlorite ion and chlorate ion.

  9. Highly selective and sensitive nucleic acid detection based on polysaccharide-functionalized silver nanoparticles

    NASA Astrophysics Data System (ADS)

    Yan, Jing-Kun; Ma, Hai-Le; Cai, Pan-Fu; Wu, Jian-Yong

    2015-01-01

    Polysaccharide-functionalized silver nanoparticles (Oc-AgNPs) with a mean diameter of 15 nm were utilized as a novel and effective fluorescence-sensing platform for nucleic acid detection. Tests on the oligonucleotide sequences associated with the human immunodeficiency virus as a model system showed that the Oc-AgNPs effectively absorbed and quenched dye-labeled single-stranded DNA through strong hydrogen bonding interactions and slight electrostatic attractive interactions. The proposed system efficiently differentiated between complementary and mismatched nucleic acid sequences with high selectivity and good reproducibility at room temperature.

  10. Highly selective and sensitive nucleic acid detection based on polysaccharide-functionalized silver nanoparticles.

    PubMed

    Yan, Jing-Kun; Ma, Hai-Le; Cai, Pan-Fu; Wu, Jian-Yong

    2015-01-05

    Polysaccharide-functionalized silver nanoparticles (Oc-AgNPs) with a mean diameter of 15 nm were utilized as a novel and effective fluorescence-sensing platform for nucleic acid detection. Tests on the oligonucleotide sequences associated with the human immunodeficiency virus as a model system showed that the Oc-AgNPs effectively absorbed and quenched dye-labeled single-stranded DNA through strong hydrogen bonding interactions and slight electrostatic attractive interactions. The proposed system efficiently differentiated between complementary and mismatched nucleic acid sequences with high selectivity and good reproducibility at room temperature.

  11. Non-gated laser-induced breakdown spectroscopy in bulk water by position-selective detection

    SciTech Connect

    Tian, Ye; Xue, Boyang; Song, Jiaojian; Lu, Yuan; Zheng, Ronger

    2015-09-14

    Temporal and spatial evolutions of the laser-induced plasma in bulk water are investigated using fast imaging and emission spectroscopic techniques. By tightly focusing a single-pulse nanosecond Nd: YAG laser beam into the bulk water, we generate a strongly expanded plasma with high reproducibility. Such a strong expanding plasma enables us to obtain well-resolved spectral lines by means of position-selective detection; hence, the time-gated detector becomes abdicable. The present results suggest not only a possible non-gated approach for underwater laser-induced breakdown spectroscopy but also give an insight into the plasma generation and expansion in bulk water.

  12. Selective detection of carbon-13-labeled compounds by gas chromatography/emission spectroscopy

    SciTech Connect

    Quimby, B.D.; Dryden, P.C.; Sullivan, J.J. )

    1990-11-15

    This paper describes a technique which also provides selective GC detection of compounds with excess {sup 13}C content. Molecular emission from CO bands in the vacuum ultraviolet region is monitored with an atomic emission detector (AED) (4,5). Samples can also be analyzed for C, H, O, N, S, P, Cl, F, etc. by changing the reagent and makeup gas flows. This combination of {sup 13}C specificity with atomic information is useful in the identification of unknown compounds, especially when combined with mass spectral data, as shown by Hooker and DeZwaan (6).

  13. Model-based fault detection and identification with online aerodynamic model structure selection

    NASA Astrophysics Data System (ADS)

    Lombaerts, T.

    2013-12-01

    This publication describes a recursive algorithm for the approximation of time-varying nonlinear aerodynamic models by means of a joint adaptive selection of the model structure and parameter estimation. This procedure is called adaptive recursive orthogonal least squares (AROLS) and is an extension and modification of the previously developed ROLS procedure. This algorithm is particularly useful for model-based fault detection and identification (FDI) of aerospace systems. After the failure, a completely new aerodynamic model can be elaborated recursively with respect to structure as well as parameter values. The performance of the identification algorithm is demonstrated on a simulation data set.

  14. Voltammetric detection of sequence-selective DNA hybridization related to Toxoplasma gondii in PCR amplicons.

    PubMed

    Gokce, Gultekin; Erdem, Arzum; Ceylan, Cagdas; Akgöz, Muslum

    2016-01-01

    This work describes the single-use electrochemical DNA biosensor technology developed for voltammetric detection of sequence selective DNA hybridization related to important human and veterinary pathogen; Toxoplasma gondii. In the principle of electrochemical label-free detection assay, the duplex of DNA hybrid formation was detected by measuring guanine oxidation signal occured in the presence of DNA hybridization. The biosensor design consisted of the immobilization of an inosine-modified (guanine-free) probe onto the surface of pencil graphite electrode (PGE), and the detection of the duplex formation in connection with the differential pulse voltammetry(DPV) by measuring the guanine signal. Toxoplasma gondii capture probe was firstly immobilized onto the surface of the activated PGE by wet adsorption. The extent of hybridization at PGE surface between the probe and the target was then determined by measuring the guanine signal observed at +1.0V. The electrochemical monitoring of optimum DNA hybridization has been performed in the target concentration of 40µg/mL in 50min of hybridization time. The specificity of the electrochemical biosensor was then tested using non-complementary, or mismatch short DNA sequences. Under the optimum conditions, the guanine oxidation signal indicating full hybridization was measured in various target concentration from 0.5 to 25µg/mL and a detection limit was found to be 1.78µg/mL. This single-use biosensor platform was successfully applied for the voltammetric detection of DNA hybridization related to Toxoplasma gondii in PCR amplicons.

  15. The Predictive Power of Evolutionary Biology and the Discovery of Eusociality in the Naked Mole-Rat.

    ERIC Educational Resources Information Center

    Braude, Stanton

    1997-01-01

    Discusses how biologists use evolutionary theory and provides examples of how evolutionary biologists test hypotheses on specific modes of selection and evolution. Presents an example of the successful predictive power of one evolutionary hypothesis. Contains 38 references. (DDR)

  16. Ultrasensitive and selective homogeneous sandwich immunoassay detection by Surface Enhanced Raman Scattering (SERS).

    PubMed

    Pekdemir, Mustafa Ersin; Ertürkan, Deniz; Külah, Haluk; Boyacı, Ismail H; Ozgen, Canan; Tamer, Uğur

    2012-10-21

    In this report, a simple and highly selective homogeneous sandwich immunoassay was developed for ultrasensitive detection of Staphylococcal Enterotoxin B (SEB) using Surface Enhanced Raman Scattering (SERS). The assay uses polyclonal-antibody functionalized magnetic gold nanorod particles as capture probes for SEB, which can be collected via a simple magnet. After separating SEB from the sample matrix, they are sandwiched by using binding-specific antibody-antigen pairs with the help of gold nanorod particles. Gold nanorod particles are bifunctional by design and contain self-assembled monolayers (SAMs) of a SERS tag molecule (5,5-dithiobis (2-nitrobenzoic acid), DTNB) and carboxylic functionalities of DTNB for coupling with a suitable antibody. The correlation between the SEB concentration and SERS signal was found to be linear within the range of 3 fM to 0.3 μM. The limit of detection for the assay was determined to be 768 aM (ca., 9250 SEB molecules per 20 μL sample volume). The gold heterogeneous assay system for SEB detection was also compared with the same SERS probes and gold-coated surfaces as capture substrates. The developed method was further evaluated for detecting SEB in artificially contaminated milk. Finally, the method was used for investigating the SEB specificity on bovine serum albumin (BSA) and avidin.

  17. Assembly of polythiophenes on responsive polymer microgels for the highly selective detection of ammonia gas

    SciTech Connect

    Chang, Aiping; Peng, Yahui; Li, Zezhou; Yu, Xiang; Hong, Kunlun; Zhou, Shuiqin; Wu, Weitai

    2016-04-05

    For this study, a class of smart composite materials based on the assembly of conjugated polymers on responsive polymer microgels has been prepared. We have chosen poly(3-((2-(2-methoxyethoxy)ethoxy)methyl)-thiophene) as the model conjugated polymer and an ammonia-responsive microgel of phenoxazinium-functionalized poly(N-isopropylacrylamide-co-propargyl acrylate) as the model template. Under this design, the composite materials can combine the electrical conductivity of the conjugated polymers and the ammonia recognisability of the ammonia-responsive polymer microgels; the cooperation of these properties allows the reversible control of electrical conductivity by ammonia gas. Those composite materials can not only adapt to ammonia gas, but also convert changes in the concentration of ammonia into conductance, allowing the electrical detection of ammonia gas with high selectivity. This makes the composite materials different from the conductive polymer platforms reported previously, which may also respond to non-ammonia gases and the response induced by non-ammonia gases is close to that induced by ammonia gas. Using these composite materials as sensing materials for the electrical detection of ammonia gas, the detection limit can reach as low as 1.1 ppb. Finally, these features enable their use for the electrical detection of ammonia in breath.

  18. Assembly of polythiophenes on responsive polymer microgels for the highly selective detection of ammonia gas

    DOE PAGES

    Chang, Aiping; Peng, Yahui; Li, Zezhou; ...

    2016-04-05

    For this study, a class of smart composite materials based on the assembly of conjugated polymers on responsive polymer microgels has been prepared. We have chosen poly(3-((2-(2-methoxyethoxy)ethoxy)methyl)-thiophene) as the model conjugated polymer and an ammonia-responsive microgel of phenoxazinium-functionalized poly(N-isopropylacrylamide-co-propargyl acrylate) as the model template. Under this design, the composite materials can combine the electrical conductivity of the conjugated polymers and the ammonia recognisability of the ammonia-responsive polymer microgels; the cooperation of these properties allows the reversible control of electrical conductivity by ammonia gas. Those composite materials can not only adapt to ammonia gas, but also convert changes in the concentrationmore » of ammonia into conductance, allowing the electrical detection of ammonia gas with high selectivity. This makes the composite materials different from the conductive polymer platforms reported previously, which may also respond to non-ammonia gases and the response induced by non-ammonia gases is close to that induced by ammonia gas. Using these composite materials as sensing materials for the electrical detection of ammonia gas, the detection limit can reach as low as 1.1 ppb. Finally, these features enable their use for the electrical detection of ammonia in breath.« less

  19. Shift endpoint trace selection algorithm and wavelet analysis to detect the endpoint using optical emission spectroscopy

    NASA Astrophysics Data System (ADS)

    Ben Zakour, Sihem; Taleb, Hassen

    2016-06-01

    Endpoint detection (EPD) is very important undertaking on the side of getting a good understanding and figuring out if a plasma etching process is done on the right way. It is truly a crucial part of supplying repeatable effects in every single wafer. When the film to be etched has been completely erased, the endpoint is reached. In order to ensure the desired device performance on the produced integrated circuit, many sensors are used to detect the endpoint, such as the optical, electrical, acoustical/vibrational, thermal, and frictional. But, except the optical sensor, the other ones show their weaknesses due to the environmental conditions which affect the exactness of reaching endpoint. Unfortunately, some exposed area to the film to be etched is very low (<0.5%), reflecting low signal and showing the incapacity of the traditional endpoint detection method to determine the wind-up of the etch process. This work has provided a means to improve the endpoint detection sensitivity by collecting a huge numbers of full spectral data containing 1201 spectra for each run, then a new unsophisticated algorithm is proposed to select the important endpoint traces named shift endpoint trace selection (SETS). Then, a sensitivity analysis of linear methods named principal component analysis (PCA) and factor analysis (FA), and the nonlinear method called wavelet analysis (WA) for both approximation and details will be studied to compare performances of the methods mentioned above. The signal to noise ratio (SNR) is not only computed based on the main etch (ME) period but also the over etch (OE) period. Moreover, a new unused statistic for EPD, coefficient of variation (CV), is proposed to reach the endpoint in plasma etches process.

  20. Increasing the selectivity and sensitivity of gas sensors for the detection of explosives

    NASA Astrophysics Data System (ADS)

    Mallin, Daniel

    Over the past decade, the use of improvised explosive devices (IEDs) has increased, domestically and internationally, highlighting a growing need for a method to quickly and reliably detect explosive devices in both military and civilian environments before the explosive can cause damage. Conventional techniques have been successful in explosive detection, however they typically suffer from enormous costs in capital equipment and maintenance, costs in energy consumption, sampling, operational related expenses, and lack of continuous and real-time monitoring. The goal was thus to produce an inexpensive, portable sensor that continuously monitors the environment, quickly detects the presence of explosive compounds and alerts the user. In 2012, here at URI, a sensor design was proposed for the detection of triacetone triperoxide (TATP). The design entailed a thermodynamic gas sensor that measures the heat of decomposition between trace TATP vapor and a metal oxide catalyst film. The sensor was able to detect TATP vapor at the part per million level (ppm) and showed great promise for eventual commercial use, however, the sensor lacked selectivity. Thus, the specific objective of this work was to take the original sensor design proposed in 2012 and to make several key improvements to advance the sensor towards commercialization. It was demonstrated that a sensor can be engineered to detect TATP and ignore the effects of interferent H2O2 molecules by doping SnO2 films with varying amounts of Pd. Compared with a pure SnO2 catalyst, a SnO2, film doped with 8 wt. % Pd had the highest selectivity between TATP and H2O2. Also, at 12 wt. % Pd, the response to TATP and H2O2 was enhanced, indicating that sensitivity, not only selectivity, can be increased by modifying the composition of the catalyst. An orthogonal detection system was demonstrated. The platform consists of two independent sensing mechanisms, one thermodynamic and one conductometric, which take measurements from

  1. Do lions Panthera leo actively select prey or do prey preferences simply reflect chance responses via evolutionary adaptations to optimal foraging?

    PubMed

    Hayward, Matt W; Hayward, Gina J; Tambling, Craig J; Kerley, Graham I H

    2011-01-01

    Research on coursing predators has revealed that actions throughout the predatory behavioral sequence (using encounter rate, hunting rate, and kill rate as proxy measures of decisions) drive observed prey preferences. We tested whether similar actions drive the observed prey preferences of a stalking predator, the African lion Panthera leo. We conducted two 96 hour, continuous follows of lions in Addo Elephant National Park seasonally from December 2003 until November 2005 (16 follows), and compared prey encounter rate with prey abundance, hunt rate with prey encounter rate, and kill rate with prey hunt rate for the major prey species in Addo using Jacobs' electivity index. We found that lions encountered preferred prey species far more frequently than expected based on their abundance, and they hunted these species more frequently than expected based on this higher encounter rate. Lions responded variably to non-preferred and avoided prey species throughout the predatory sequence, although they hunted avoided prey far less frequently than expected based on the number of encounters of them. We conclude that actions of lions throughout the predatory behavioural sequence, but particularly early on, drive the prey preferences that have been documented for this species. Once a hunt is initiated, evolutionary adaptations to the predator-prey interactions drive hunting success.

  2. Cellulose-lanthanum hydroxide nanocomposite as a selective marker for detection of toxic copper

    NASA Astrophysics Data System (ADS)

    Marwani, Hadi M.; Lodhi, Mazhar Ullah; Khan, Sher Bahadar; Asiri, Abdullah M.

    2014-09-01

    In this current report, a simple, reliable, and rapid method based on modifying the cellulose surface by doping it with different percentages of lanthanum hydroxide (i.e., 1% La(OH)3-cellulose (LC), 5% La(OH)3-cellulose (LC2), and 10% La(OH)3-cellulose (LC3)) was proposed as a selective marker for detection of copper (Cu(II)) in aqueous medium. Surface properties of the newly modified cellulose phases were confirmed by Fourier transform infrared spectroscopy, field emission scanning electron microscope, energy dispersive X-ray spectroscopy, X-ray diffraction, and X-ray photoelectron spectroscopic analysis. The effect of pH on the adsorption of modified cellulose phases for Cu(II) was evaluated, and LC3 was found to be the most selective for Cu(II) at pH 6.0. Other parameters, influencing the maximum uptake of Cu(II) on LC3, were also investigated for a deeper mechanistic understanding of the adsorption phenomena. Results showed that the adsorption capacity for Cu(II) was improved by 211% on the LC3 phase as compared to diethylaminoethyl cellulose phase after only 2 h contact time. Adsorption isotherm data established that the adsorption process nature was monolayer with a homogeneous adsorbent surface. Results displayed that the adsorption of Cu(II) onto the LC3 phase obeyed a pseudo-second-order kinetic model. Selectivity studies toward eight metal ions, i.e., Cd(II), Co(II), Cr(III), Cr(VI), Cu(II), Fe(III), Ni(II), and Zn(II), were further performed at the optimized pH value. Based on the selectivity study, it was found that Cu(II) is highly selective toward the LC3 phase. Moreover, the efficiency of the proposed method was supported by implementing it to real environmental water samples with adequate results.

  3. Early Detection of NSCLC with scFv Selected against IgM Autoantibody

    PubMed Central

    Pedchenko, Tetyana; Mernaugh, Ray; Parekh, Dipti; Li, Ming; Massion, Pierre P.

    2013-01-01

    Survival of patients with lung cancer could be significantly prolonged should the disease be diagnosed early. Growing evidence indicates that the immune response in the form of autoantibodies to developing cancer is present before clinical presentation. We used a phage-displayed antibody library to select for recombinant scFvs that specifically bind to lung cancer-associated IgM autoantibodies. We selected for scFv recombinant antibodies reactive with circulating IgM autoantibodies found in the serum of patients with early stage lung adenocarcinoma but not matched controls. Discriminatory performance of 6 selected scFvs was validated in an independent set of serum from stage 1 adenocarcinoma and matching control groups using two independent novel methods developed for this application. The panel of 6 selected scFvs predicted cancer based on seroreactivity value with sensitivity of 0.8 and specificity of 0.87. Receiver Operative Characteristic curve (ROC) for combined 6 scFv has an AUC of 0.88 (95%CI, 0.76–1.0) as determined by fluorometric microvolume assay technology (FMAT) The ROC curve generated using a homogeneous bridging Mesa Scale Discovery (MSD) assay had an AUC of 0.72 (95% CI, 0.59–0.85). The panel of all 6 antibodies demonstrated better discriminative power than any single scFv alone. The scFv panel also demonstrated the association between a high score - based on seroreactivity - with poor survival. Selected scFvs were able to recognize lung cancer associated IgM autoantibodies in patient serum as early as 21 months before the clinical presentation of disease. The panel of antibodies discovered represents a potential unique non-invasive molecular tool to detect an immune response specific to lung adenocarcinoma at an early stage of disease. PMID:23585862

  4. Cellulose-lanthanum hydroxide nanocomposite as a selective marker for detection of toxic copper

    PubMed Central

    2014-01-01

    In this current report, a simple, reliable, and rapid method based on modifying the cellulose surface by doping it with different percentages of lanthanum hydroxide (i.e., 1% La(OH)3-cellulose (LC), 5% La(OH)3-cellulose (LC2), and 10% La(OH)3-cellulose (LC3)) was proposed as a selective marker for detection of copper (Cu(II)) in aqueous medium. Surface properties of the newly modified cellulose phases were confirmed by Fourier transform infrared spectroscopy, field emission scanning electron microscope, energy dispersive X-ray spectroscopy, X-ray diffraction, and X-ray photoelectron spectroscopic analysis. The effect of pH on the adsorption of modified cellulose phases for Cu(II) was evaluated, and LC3 was found to be the most selective for Cu(II) at pH 6.0. Other parameters, influencing the maximum uptake of Cu(II) on LC3, were also investigated for a deeper mechanistic understanding of the adsorption phenomena. Results showed that the adsorption capacity for Cu(II) was improved by 211% on the LC3 phase as compared to diethylaminoethyl cellulose phase after only 2 h contact time. Adsorption isotherm data established that the adsorption process nature was monolayer with a homogeneous adsorbent surface. Results displayed that the adsorption of Cu(II) onto the LC3 phase obeyed a pseudo-second-order kinetic model. Selectivity studies toward eight metal ions, i.e., Cd(II), Co(II), Cr(III), Cr(VI), Cu(II), Fe(III), Ni(II), and Zn(II), were further performed at the optimized pH value. Based on the selectivity study, it was found that Cu(II) is highly selective toward the LC3 phase. Moreover, the efficiency of the proposed method was supported by implementing it to real environmental water samples with adequate results. PMID:25258599

  5. GlutenTox® Pro Test for the Detection of Gluten in Select Foods and Surfaces.

    PubMed

    Síglez, Miguel A; Nocea, Bárbara; del Mar Pérez, María; Ma García, Eva; León, Laura; Galera, Carlos

    2015-01-01

    The GlutenTox® Pro Test is an immunochromatographic test for the detection of gluten in foods and on surfaces with varying compositions and levels of processing, from raw foods/ingredients to final product testing. The Method Developer evaluation for the validation of the GlutenTox Pro Test Kit (Biomedal Diagnostics, Sevilla, Spain) for the detection of gluten in foods and on surfaces was conducted at Biomedal, S. L., Camas, Sevilla, Spain. The GlutenTox Pro test method was evaluated by testing the following: cross-reactivity, interference, specificity and sensitivity, robustness, stability, lot-to-lot variation, food matrix, and environmental surface. To evaluate the performance of the GlutenToxPro test for the detection of gluten, 10 matrixes were selected: rice flour, bread/biscuit, rolled oat, pâté, and yogurt (and a second bread matrix for incurred sampled testing) for the food matrix study and food-grade painted wood, plastic, rubber, sealed ceramic, and stainless steel for the environmental surface matrix study. For the food matrix study, 30 replicates were evaluated at six spiked levels of gluten (0, 3, 8, 15, 25, and 45 ppm) against four detection thresholds (5, 10, 20, and 40 ppm) for each food matrix. Additionally, 10 replicates were evaluated at a concentration of 10,000 ppm using all four detection thresholds only for rice flour matrix. Three replicates of each concentration level of gluten were analyzed using paired samples by the AOAC OMA 2012.01 reference method for each food matrix. For the environmental surface study, 30 replicates were evaluated at a low spike level of gluten (16 ng/16 cm2), five replicates at a high spike level of gluten (400 ng/16 cm2), and five replicates at an unspiked control level (0 ng/16 cm2) for each surface matrix. Upon completion of testing, the probability of detection values and confidence intervals were calculated and plotted versus the concentration level as determined by the reference method when applicable. An

  6. Molecular imprinting ratiometric fluorescence sensor for highly selective and sensitive detection of phycocyanin.

    PubMed

    Wang, Xiaoyan; Yu, Jialuo; Kang, Qi; Shen, Dazhong; Li, Jinhua; Chen, Lingxin

    2016-03-15

    A facile strategy was developed to prepare molecular imprinting ratiometric fluorescence sensor for highly selective and sensitive detection of phycocyanin (PC) based on fluorescence resonance energy transfer (FRET), via a sol-gel polymerization process using nitrobenzoxadiazole (NBD) as fluorescent signal source. The ratio of two fluorescence peak emission intensities of NBD and PC was utilized to determine the concentration of PC, which could effectively reduce the background interference and fluctuation of diverse conditions. As a result, this sensor obtained high sensitivity with a low detection limit of 0.14 nM within 6 min, and excellent recognition specificity for PC over its analogues with a high imprinting factor of 9.1. Furthermore, the sensor attained high recoveries in the range of 93.8-110.2% at three spiking levels of PC, with precisions below 4.7% in seawater and lake water samples. The developed sensor strategy demonstrated simplicity, reliability, rapidity, high selectivity and high sensitivity, proving to be a feasible way to develop high efficient fluorescence sensors and thus potentially applicable for ultratrace analysis of complicated matrices.

  7. Molecularly Imprinted Composite Membranes for Selective Detection of 2-Deoxyadenosine in Urine Samples

    PubMed Central

    Scorrano, Sonia; Mergola, Lucia; Di Bello, Maria Pia; Lazzoi, Maria Rosaria; Vasapollo, Giuseppe; Del Sole, Roberta

    2015-01-01

    An important challenge for scientific research is the production of artificial systems able to mimic the recognition mechanisms occurring at the molecular level in living systems. A valid contribution in this direction resulted from the development of molecular imprinting. In this work, a novel molecularly imprinted polymer composite membrane (MIM) was synthesized and employed for the selective detection in urine samples of 2-deoxyadenosine (2-dA), an important tumoral marker. By thermal polymerization, the 2-dA-MIM was cross-linked on the surface of a polyvinylidene-difluoride (PVDF) membrane. By characterization techniques, the linking of the imprinted polymer on the surface of the membrane was found. Batch-wise guest binding experiments confirmed the absorption capacity of the synthesized membrane towards the template molecule. Subsequently, a time-course of 2-dA retention on membrane was performed and the best minimum time (30 min) to bind the molecule was established. HPLC analysis was also performed to carry out a rapid detection of target molecule in urine sample with a recovery capacity of 85%. The experiments indicated that the MIM was highly selective and can be used for revealing the presence of 2-dA in urine samples. PMID:26086824

  8. Selective binding and detection of magnetic labels using PHR sensor via photoresist micro-wells.

    PubMed

    Oh, Sunjong; Baek, Nam Seob; Jung, Sang-Don; Chung, Myung-Ae; Hung, Tran Quang; Anandakumar, S; Rani, V Sudha; Jeong, Jong-Ryul; Kim, CheolGi

    2011-05-01

    We have developed a novel platform for selective binding of magnetic labels on planar Hall resistance sensor (PHR) for biosensing applications. The photoresist (PR) micro wells were prepared on the PHR sensor junctions to trap the magnetic bead at specified locations on the sensor surface and thin layer of Au was sputtered in the PR wells immobilize bimolecular. The Au surface is functionalized with single-stranded oligonucleotide and further biotin was used to immobilize streptavidin coated magnetic labels (Dynabeads Myone 1.0 microm, Invitrogen Co.). After removal of the PR wells on the sensor surface the non specific binding magnetic labels were successfully removed and only the chemically bounded magnetic labels were remained on the Au surface for detection of biomolecules using PHR sensor. We controlled the number of magnetic labels on the PHR sensor surface by using different sizes of the PR well on the junctions. The specifically bounded magnetic labels were successfully detected by characterizing the individual PHR sensor junctions. This technique enables the complete control over the magnetic labels for selective binding of biomolecules on the sensor surface for increasing the sensitivity of the PHR sensor as well as removal of the non specific bindings on the sensor surface.

  9. A cysteine-selective fluorescent probe for the cellular detection of cysteine.

    PubMed

    Jung, Hyo Sung; Han, Ji Hye; Pradhan, Tuhin; Kim, Sooyeon; Lee, Seok Won; Sessler, Jonathan L; Kim, Tae Woo; Kang, Chulhun; Kim, Jong Seung

    2012-01-01

    A series of coumarin fluorophores (1-3), each bearing a double bond conjugated quinoline unit that can undergo a Michael-type reaction with thiol-containing compounds, is reported. These systems, designed to provide so-called turn-on changes in fluorescence response when exposed to thiols, act as fluorescent chemical sensors for cysteine (Cys), homocysteine (Hcy), and glutathione (GSH). In the case of 1, selectivity for Cys over Hcy and GSH is observed, both in terms of analyte-induced signal enhancement and response time. On the basis of fluorescence spectroscopic analyses, DFT calculations, and pH dependent studies this substrate selectivity is ascribed to steric interactions between the substituents on the quinolone units present in 1 and the targeted thiols, as well as to the comparatively lower pK(a) value of Cys relative to Hcy and GSH. In aqueous solution, probe 1 was found capable of detecting Cys with a detection limit of 10(-7) m. This system was successfully applied to the fluorescence imaging of intracellular Cys in HepG2 cells.

  10. Selective detection of dopamine combining multilayers of conducting polymers with gold nanoparticles.

    PubMed

    Fabregat, Georgina; Armelin, Elaine; Alemán, Carlos

    2014-05-01

    Electrodes based on the combination of three-layered films formed by two different conducting polymers and gold nanoparticles have been developed for the selective voltammetric determination of dopamine in mixtures with ascorbic acid and uric acid and human urine samples with real interferents. Voltammetric studies of solution mixtures indicate that electrodes formed by alternated layers of poly(3,4-ethylenedioxithiophene) (internal and external layer) and poly(N-methylpyrrole) (intermediate layer) show the best performance in terms of sensitivity and resolution. Furthermore, the sensitivity of such three-layered electrodes increases only slightly after coating its surface with gold nanoparticles (AuNPs), indicating that the catalytic effect typically played by AuNPs in the oxidation of dopamine is less effective in this case. Electrochemical pretreatments based on the application of consecutive oxidation-reduction cycles to electrodes before the detection process have been found to improve the selectivity without altering the sensitivity. On the other hand, the flux of dopamine to the three-layered surface increases linearly with the scan rate. The detection limit for these electrodes is around 10 μM DA in mixtures with uric acid, ascorbic acid, and cetaminophen, decreasing to 2-3 μM in the absence of such interferents. The utility of three-layered electrodes as sensors has also been demonstrated by determining DA in human samples with real interferents.

  11. A rational design for the selective detection of dopamine using conducting polymers.

    PubMed

    Fabregat, Georgina; Casanovas, Jordi; Redondo, Edurne; Armelin, Elaine; Alemán, Carlos

    2014-05-07

    Poly(N-methylpyrrole) (PNMPy), poly(N-cyanoethylpyrrole) (PNCPy) and poly(3,4-ethylenedioxythiophene) (PEDOT) films have been prepared using both single and two polymerization steps for the selective determination of low concentrations of dopamine, ascorbic acid and uric acid in tertiary mixtures. Analysis of the sensitivity and resolution parameters derived from the electrochemical response of such films indicates that PEDOT is the most appropriate for the unambiguous detection of the three species. Indeed, the performance of PEDOT is practically independent of the presence of both gold nanoparticles at the surface of the film and interphases inside the film, even though these two factors are known to improve the electroactivity of conducting polymers. Quantum mechanical calculations on model complexes have been used to examine the intermolecular interaction involved in complexes formed by PEDOT chains and oxidized dopamine, ascorbic acid and uric acid. Results show that such complexes are mainly stabilized by C-HO interactions rather than by conventional hydrogen bonds. In order to improve the sensitivity of PEDOT through the formation of specific hydrogen bonds, a derivative bearing a hydroxymethyl group attached to the dioxane ring of each repeat unit has been designed. Poly(hydroxymethyl-3,4-ethylenedioxythiophene) (PHMeDOT) has been prepared and characterized by FTIR, UV-vis spectroscopy, cyclic voltammetry, scanning electron microscopy and atomic force microscopy. Finally, the performance of PHMeDOT and PEDOT for the selective detection of the species mentioned above has been compared.

  12. A highly selective molecularly imprinted electrochemiluminescence sensor for ultra-trace beryllium detection.

    PubMed

    Li, Jianping; Ma, Fei; Wei, Xiaoping; Fu, Cong; Pan, Hongcheng

    2015-04-29

    A new molecularly imprinted electrochemiluminescence (ECL) sensor was proposed for highly sensitive and selective determination of ultratrace Be(2+) determination. The complex of Be(2+) with 4-(2-pyridylazo)-resorcinol (PAR) was chosen as the template molecule for the molecularly imprinted polymer (MIP). In this assay, the complex molecule could be eluted from the MIP, and the cavities formed could then selectively recognize the complex molecules. The cavities formed could also work as the tunnel for the transfer of probe molecules to produce sound responsive signal. The determination was based on the intensity of the signal, which was proportional to the concentrations of the complex molecule in the sample solution, and the Be(2+) concentration could then be determined indirectly. The results showed that in the range of 7×10(-11 )mol L(-1) to 8.0×10(-9) mol L(-1), the ECL intensity had a linear relationship with the Be(2+) concentrations, with the limit of detection of 2.35×10(-11) mol L(-1). This method was successfully used to detect Be(2+) in real water samples.

  13. Flow Chronopotentiometry with Ion-Selective Membranes for Cation, Anion, and Polyion Detection.

    PubMed

    Ghahraman Afshar, Majid; Crespo, Gastón A; Bakker, Eric

    2016-04-05

    We report here on the development of a chronopotentiometric readout for ion-selective electrodes that allows one to record transition times in continuous flow conditions without the necessity to stop the flow. A sample plug of 150 μL is injected into the carrier solution (0.5 mM NaCl) and subsequently transported to the detection cell (∼20 μL) at moderate flow rates (∼0.5 mL min(-1)), where a short current pulse (5s) is applied between the ionophore-based working electrode and a biocompatible and nonpolarizable Donnan exclusion anion-exchanger membrane reference/counter electrode. Flow conditions bear an influence on the thickness of the aqueous diffusion layer and result in a shift of the chronopotentiometric transition time with respect to stopped flow. Two models based on rotating disk electrodes and flow chronopotentiometry at metal-based electrodes were used to corroborate the data. The method was successfully applied to the determination of calcium, chloride, alkalinity, acidity, and protamine with a range of ion-selective membranes. Because of the limiting exposure time of ca. 20 s of the membranes with the sample, this approach is demonstrated to be useful for the detection of protamine in the therapeutic range of undiluted human blood.

  14. Combining heterogeneous features for face detection using multiscale feature selection with binary particle swarm optimization

    NASA Astrophysics Data System (ADS)

    Pan, Hong; Xia, Si-Yu; Jin, Li-Zuo; Xia, Liang-Zheng

    2011-12-01

    We propose a fast multiscale face detector that boosts a set of SVM-based hierarchy classifiers constructed with two heterogeneous features, i.e. Multi-block Local Binary Patterns (MB-LBP) and Speeded Up Robust Features (SURF), at different image resolutions. In this hierarchical architecture, simple and fast classifiers using efficient MB-LBP descriptors remove large parts of the background in low and intermediate scale layers, thus only a small percentage of background patches look similar to faces and require a more accurate but slower classifier that uses distinctive SURF descriptor to avoid false classifications in the finest scale. By propagating only those patterns that are not classified as background, we can quickly decrease the amount of data need to be processed. To lessen the training burden of the hierarchy classifier, in each scale layer, a feature selection scheme using Binary Particle Swarm Optimization (BPSO) searches the entire feature space and filters out the minimum number of discriminative features that give the highest classification rate on a validation set, then these selected distinctive features are fed into the SVM classifier. We compared detection performance of the proposed face detector with other state-of-the-art methods on the CMU+MIT face dataset. Our detector achieves the best overall detection performance. The training time of our algorithm is 60 times faster than the standard Adaboost algorithm. It takes about 70 ms for our face detector to process a 320×240 image, which is comparable to Viola and Jones' detector.

  15. Molecular engineering of a fluorescent bioprobe for sensitive and selective detection of amphibole asbestos.

    PubMed

    Ishida, Takenori; Alexandrov, Maxym; Nishimura, Tomoki; Hirota, Ryuichi; Ikeda, Takeshi; Kuroda, Akio

    2013-01-01

    Fluorescence microscopy-based affinity assay could enable highly sensitive and selective detection of airborne asbestos, an inorganic environmental pollutant that can cause mesothelioma and lung cancer. We have selected an Escherichia coli histone-like nucleoid structuring protein, H-NS, as a promising candidate for an amphibole asbestos bioprobe. H-NS has high affinity to amphibole asbestos, but also binds to an increasingly common asbestos substitute, wollastonite. To develop a highly specific Bioprobe for amphibole asbestos, we first identified a specific but low-affinity amosite-binding sequence by slicing H-NS into several fragments. Second, we constructed a streptavidin tetramer complex displaying four amosite-binding fragments, resulting in the 250-fold increase in the probe affinity as compared to the single fragment. The tetramer probe had sufficient affinity and specificity for detecting all the five types of asbestos in the amphibole group, and could be used to distinguish them from wollastonite. In order to clarify the binding mechanism and identify the amino acid residues contributing to the probe's affinity to amosite fibers, we constructed a number of shorter and substituted peptides. We found that the probable binding mechanism is electrostatic interaction, with positively charged side chains of lysine residues being primarily responsible for the probe's affinity to asbestos.

  16. Construction and selection of lifting-based multiwavelets for mechanical fault detection

    NASA Astrophysics Data System (ADS)

    Yuan, Jing; He, Zhengjia; Zi, Yanyang; Wei, Ying

    2013-11-01

    The essence of wavelet transforms is a similar measurement between the signal and the wavelet basis functions. Thus, the construction and selection of the proper wavelet basis functions similar to the fault feature and possessing good properties such as vanishing moments have vital importance to the effective fault diagnosis. In this paper, the construction of lifting-based adaptive multiwavelets with various vanishing moments and the selection rules for different mechanical fault detection are proposed. On the basis of the fixed cubic Hermite multiwavelets, lifting schemes are adopted to construct new changeable multiwavelets with diverse vanishing moments. Then, the defined local spectral entropy minimization rules are proposed to determine the optimum multiwavelets providing the proper vanishing moments, classified into the typical shaft faults, gear faults and rolling bearing faults. The proposed method is applied to incipient fault diagnosis of rolling bearing and gearbox fault diagnosis of rolling mill to verify its effectiveness and feasibility in comparison with different wavelet transforms and spectral kurtosis. The results show that the proposed method can act as a promising tool for mechanical fault detection.

  17. Aptamers Selected to Postoperative Lung Adenocarcinoma Detect Circulating Tumor Cells in Human Blood

    PubMed Central

    Zamay, Galina S; Kolovskaya, Olga S; Zamay, Tatiana N; Glazyrin, Yury E; Krat, Alexey V; Zubkova, Olga; Spivak, Ekaterina; Wehbe, Mohammed; Gargaun, Ana; Muharemagic, Darija; Komarova, Mariia; Grigorieva, Valentina; Savchenko, Andrey; Modestov, Andrey A; Berezovski, Maxim V; Zamay, Anna S

    2015-01-01

    Circulating tumor cells (CTCs) are rare cells and valuable clinical markers of prognosis of metastasis formation and prediction of patient survival. Most CTC analyses are based on the antibody-based detection of a few epithelial markers; therefore miss an important portion of mesenchymal cancer cells circulating in blood. In this work, we selected and identified DNA aptamers as specific affinity probes that bind to lung adenocarcinoma cells derived from postoperative tissues. The unique feature of our selection strategy is that aptamers are produced for lung cancer cell biomarkers in their native state and conformation without previous knowledge of the biomarkers. The aptamers did not bind to normal lung cells and lymphocytes, and had very low affinity to A549 lung adenocarcinoma culture. We applied these aptamers to detect CTCs, apoptotic bodies, and microemboli in clinical samples of peripheral blood of lung cancer and metastatic lung cancer patients. We identified aptamer-associated protein biomarkers for lung cancer such as vimentin, annexin A2, annexin A5, histone 2B, neutrophil defensin, and clusterin. Tumor-specific aptamers can be produced for individual patients and synthesized many times during anticancer therapy, thereby opening up the possibility of personalized diagnostics. PMID:26061649

  18. The effects of alignment error and alignment filtering on the sitewise detection of positive selection.

    PubMed

    Jordan, Gregory; Goldman, Nick

    2012-04-01

    When detecting positive selection in proteins, the prevalence of errors resulting from misalignment and the ability of alignment filters to mitigate such errors are not well understood, but filters are commonly applied to try to avoid false positive results. Focusing on the sitewise detection of positive selection across a wide range of divergence levels and indel rates, we performed simulation experiments to quantify the false positives and false negatives introduced by alignment error and the ability of alignment filters to improve performance. We found that some aligners led to many false positives, whereas others resulted in very few. False negatives were a problem for all aligners, increasing with sequence divergence. Of the aligners tested, PRANK's codon-based alignments consistently performed the best and ClustalW performed the worst. Of the filters tested, GUIDANCE performed the best and Gblocks performed the worst. Although some filters showed good ability to reduce the error rates from ClustalW and MAFFT alignments, none were found to substantially improve the performance of PRANK alignments under most conditions. Our results revealed distinct trends in error rates and power levels for aligners and filters within a biologically plausible parameter space. With the best aligner, a low false positive rate was maintained even with extremely divergent indel-prone sequences. Controls using the true alignment and an optimal filtering method suggested that performance improvements could be gained by improving aligners or filters to reduce the prevalence of false negatives, especially at higher divergence levels and indel rates.

  19. X-ray backscatter imaging for radiography by selective detection and snapshot: Evolution, development, and optimization

    NASA Astrophysics Data System (ADS)

    Shedlock, Daniel

    Compton backscatter imaging (CBI) is a single-sided imaging technique that uses the penetrating power of radiation and unique interaction properties of radiation with matter to image subsurface features. CBI has a variety of applications that include non-destructive interrogation, medical imaging, security and military applications. Radiography by selective detection (RSD), lateral migration radiography (LMR) and shadow aperture backscatter radiography (SABR) are different CBI techniques that are being optimized and developed. Radiography by selective detection (RSD) is a pencil beam Compton backscatter imaging technique that falls between highly collimated and uncollimated techniques. Radiography by selective detection uses a combination of single- and multiple-scatter photons from a projected area below a collimation plane to generate an image. As a result, the image has a combination of first- and multiple-scatter components. RSD techniques offer greater subsurface resolution than uncollimated techniques, at speeds at least an order of magnitude faster than highly collimated techniques. RSD scanning systems have evolved from a prototype into near market-ready scanning devices for use in a variety of single-sided imaging applications. The design has changed to incorporate state-of-the-art detectors and electronics optimized for backscatter imaging with an emphasis on versatility, efficiency and speed. The RSD system has become more stable, about 4 times faster, and 60% lighter while maintaining or improving image quality and contrast over the past 3 years. A new snapshot backscatter radiography (SBR) CBI technique, shadow aperture backscatter radiography (SABR), has been developed from concept and proof-of-principle to a functional laboratory prototype. SABR radiography uses digital detection media and shaded aperture configurations to generate near-surface Compton backscatter images without scanning, similar to how transmission radiographs are taken. Finally, a

  20. Evolutionary dynamics of prey-predator systems with Holling type II.

    PubMed

    Jian, Zu; Wang, Wendi; Bo, Zu

    2007-04-01

    This paper considers the coevolution of phenotypes in a community comprising the populations of predators and prey. The evolutionary dynamics is constructed from a stochastic process of mutation and selection. We investigate the ecological and evolutionary conditions that allow for continuously stable strategy and evolutionary branching. It is shown that branching in the prey can induce secondary branching in the predators. Furthermore, it is shown that the evolutionary dynamics admits a stable limit cycle. The evolutionary cycle is a likely outcome of the process, which requires higher evolutionary speed of prey than of predators. It is also found that different evolutionary rates and conversion efficiencies can influence the lengths of evolutionary cycles.

  1. Evolutionary principles and their practical application

    PubMed Central

    Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P

    2011-01-01

    Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology. PMID:25567966

  2. Evolutionary origins of invasive populations

    PubMed Central

    Lee, Carol Eunmi; Gelembiuk, Gregory William

    2008-01-01

    What factors shape the evolution of invasive populations? Recent theoretical and empirical studies suggest that an evolutionary history of disturbance might be an important factor. This perspective presents hypotheses regarding the impact of disturbance on the evolution of invasive populations, based on a synthesis of the existing literature. Disturbance might select for life-history traits that are favorable for colonizing novel habitats, such as rapid population growth and persistence. Theoretical results suggest that disturbance in the form of fluctuating environments might select for organismal flexibility, or alternatively, the evolution of evolvability. Rapidly fluctuating environments might favor organismal flexibility, such as broad tolerance or plasticity. Alternatively, longer fluctuations or environmental stress might lead to the evolution of evolvability by acting on features of the mutation matrix. Once genetic variance is generated via mutations, temporally fluctuating selection across generations might promote the accumulation and maintenance of genetic variation. Deeper insights into how disturbance in native habitats affects evolutionary and physiological responses of populations would give us greater capacity to predict the populations that are most likely to tolerate or adapt to novel environments during habitat invasions. Moreover, we would gain fundamental insights into the evolutionary origins of invasive populations. PMID:25567726

  3. A multiobjective evolutionary algorithm to find community structures based on affinity propagation

    NASA Astrophysics Data System (ADS)

    Shang, Ronghua; Luo, Shuang; Zhang, Weitong; Stolkin, Rustam; Jiao, Licheng

    2016-07-01

    Community detection plays an important role in reflecting and understanding the topological structure of complex networks, and can be used to help mine the potential information in networks. This paper presents a Multiobjective Evolutionary Algorithm based on Affinity Propagation (APMOEA) which improves the accuracy of community detection. Firstly, APMOEA takes the method of affinity propagation (AP) to initially divide the network. To accelerate its convergence, the multiobjective evolutionary algorithm selects nondominated solutions from the preliminary partitioning results as its initial population. Secondly, the multiobjective evolutionary algorithm finds solutions approximating the true Pareto optimal front through constantly selecting nondominated solutions from the population after crossover and mutation in iterations, which overcomes the tendency of data clustering methods to fall into local optima. Finally, APMOEA uses an elitist strategy, called "external archive", to prevent degeneration during the process of searching using the multiobjective evolutionary algorithm. According to this strategy, the preliminary partitioning results obtained by AP will be archived and participate in the final selection of Pareto-optimal solutions. Experiments on benchmark test data, including both computer-generated networks and eight real-world networks, show that the proposed algorithm achieves more accurate results and has faster convergence speed compared with seven other state-of-art algorithms.

  4. Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data.

    PubMed

    Duforet-Frebourg, Nicolas; Luu, Keurcien; Laval, Guillaume; Bazin, Eric; Blum, Michael G B

    2016-04-01

    To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis (PCA). We show that the common FST index of genetic differentiation between populations can be viewed as the proportion of variance explained by the principal components. Considering the correlations between genetic variants and each principal component provides a conceptual framework to detect genetic variants involved in local adaptation without any prior definition of populations. To validate the PCA-based approach, we consider the 1000 Genomes data (phase 1) considering 850 individuals coming from Africa, Asia, and Europe. The number of genetic variants is of the order of 36 millions obtained with a low-coverage sequencing depth (3×). The correlations between genetic variation and each principal component provide well-known targets for positive selection (EDAR, SLC24A5, SLC45A2, DARC), and also new candidate genes (APPBPP2, TP1A1, RTTN, KCNMA, MYO5C) and noncoding RNAs. In addition to identifying genes involved in biological adaptation, we identify two biological pathways involved in polygenic adaptation that are related to the innate immune system (beta defensins) and to lipid metabolism (fatty acid omega oxidation). An additional analysis of European data shows that a genome scan based on PCA retrieves classical examples of local adaptation even when there are no well-defined populations. PCA-based statistics, implemented in the PCAdapt R package and the PCAdapt fast open-source software, retrieve well-known signals of human adaptation, which is encouraging for future whole-genome sequencing project, especially when defining populations is difficult.

  5. The Evolutionary Tempo of Sex Chromosome Degradation in Carica papaya.

    PubMed

    Wu, Meng; Moore, Richard C

    2015-06-01

    Genes on non-recombining heterogametic sex chromosomes may degrade over time through the irreversible accumulation of deleterious mutations. In papaya, the non-recombining male-specific region of the Y (MSY) consists of two evolutionary strata corresponding to chromosomal inversions occurring approximately 7.0 and 1.9 MYA. The step-wise recombination suppression between the papaya X and Y allows for a temporal examination of the degeneration progress of the young Y chromosome. Comparative evolutionary analyses of 55 X/Y gene pairs showed that Y-linked genes have more unfavorable substitutions than X-linked genes. However, this asymmetric evolutionary pattern is confined to the oldest stratum, and is only observed when recently evolved pseudogenes are included in the analysis, indicating a slow degeneration tempo of the papaya Y chromosome. Population genetic analyses of coding sequence variation of six Y-linked focal loci in the oldest evolutionary stratum detected an excess of nonsynonymous polymorphism and reduced codon bias relative to autosomal loci. However, this pattern was also observed for corresponding X-linked loci. Both the MSY and its corresponding X-specific region are pericentromeric where recombination has been shown to be greatly reduced. Like the MSY region, overall selective efficacy on the X-specific region may be reduced due to the interference of selective forces between highly linked loci, or the Hill-Robertson effect, that is accentuated in regions of low or suppressed recombination. Thus, a pattern of gene decay on the X-specific region may be explained by relaxed purifying selection and widespread genetic hitchhiking due to its pericentromeric location.

  6. Selective detection of heavy metal ions by self assembled chemical field effect transistors

    SciTech Connect

    Ruan, Hang Kang, Yuhong; Gladwin, Elizabeth; Claus, Richard O.

    2015-04-20

    Multiple layer-by-layer sensor material modifications were designed and implemented to achieve selectivity of semiconductor based chemical field effect transistors (ChemFETs) to particular heavy metal ions. The ChemFET sensors were fabricated and modified in three ways, with the intent to initially target first mercury and lead ions and then chromium ions, respectively. Sensor characterization was performed with the gate regions of the sensor elements exposed to different concentrations of target heavy metal ion solutions. A minimum detection level in the range of 0.1 ppm and a 10%–90% response time of less than 10 s were demonstrated. By combining layer-by-layer gold nanoparticles and lead ionophores, a sensor is produced that is sensitive and selective not only to chromium but also to Cr{sup 3+} and Cr{sup 6+}. This result supports the claim that high selectivity can be achieved by designing self-assembled bonding for lead, arsenic, chromium, cesium, mercury, and cadmium.

  7. A Selectivity based approach to Continuous Pattern Detection in Streaming Graphs

    SciTech Connect

    Choudhury, Sutanay; Holder, Larry; Chin, George; Agarwal, Khushbu; Feo, John T.

    2015-05-27

    Cyber security is one of the most significant technical challenges in current times. Detecting adversarial activities, prevention of theft of intellectual properties and customer data is a high priority for corporations and government agencies around the world. Cyber defenders need to analyze massive-scale, high-resolution network flows to identify, categorize, and mitigate attacks involving networks spanning institutional and national boundaries. Many of the cyber attacks can be described as subgraph patterns, with prominent examples being insider infiltrations (path queries), denial of service (parallel paths) and malicious spreads (tree queries). This motivates us to explore subgraph matching on streaming graphs in a continuous setting. The novelty of our work lies in using the subgraph distributional statistics collected from the streaming graph to determine the query processing strategy. We introduce a ``Lazy Search" algorithm where the search strategy is decided on a vertex-to-vertex basis depending on the likelihood of a match in the vertex neighborhood. We also propose a metric named ``Relative Selectivity" that is used to select between different query processing strategies. Our experiments performed on real online news, network traffic stream and a synthetic social network benchmark demonstrate 10-100x speedups over non-incremental, selectivity agnostic approaches.

  8. Different Levels of DNA Methylation Detected in Human Sperms after Morphological Selection Using High Magnification Microscopy

    PubMed Central

    Cassuto, Nino Guy; Montjean, Debbie; Siffroi, Jean-Pierre; Bouret, Dominique; Marzouk, Flora; Copin, Henri; Benkhalifa, Moncef

    2016-01-01

    Objective. To analyze DNA methylation levels between two groups of spermatozoa taken from the same sample, following morphological selection by high magnification (HM) at 6100x microscopy. A prospective study was conducted and studied 876 spermatozoa from 10 randomly selected men. Sperm morphology was characterized at HM according to criteria previously established. High-scoring Score 6 and low-scoring Score 0 sperm were selected. Sperm DNA methylation level was assessed using an immunoassay method targeting 5-methylcytosine residues by fluorescence microscopy with imaging analysis system to detect DNA methylation in single spermatozoon. Results. In total, 448 S6 spermatozoa and 428 S0 spermatozoa were analyzed. A strong relationship was found between sperm DNA methylation levels and sperm morphology observed at HM. Sperm DNA methylation level in the S6 group was significantly lower compared with that in the S0 group (p < 10−6), OR = 2.4; and p < 0.001, as determined using the Wilcoxon test. Conclusion. Differences in DNA methylation levels are associated with sperm morphology variations as observed at HM, which allows spermatozoa with abnormal levels to be discarded and ultimately decrease birth defects, malformations, and epigenetic diseases that may be transmitted from sperm to offspring in ICSI. PMID:27148551

  9. Quantifying evolutionary dynamics from variant-frequency time series

    PubMed Central

    Khatri, Bhavin S.

    2016-01-01

    From Kimura’s neutral theory of protein evolution to Hubbell’s neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher’s angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series. PMID:27616332

  10. Quantifying evolutionary dynamics from variant-frequency time series

    NASA Astrophysics Data System (ADS)

    Khatri, Bhavin S.

    2016-09-01

    From Kimura’s neutral theory of protein evolution to Hubbell’s neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher’s angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series.

  11. Selective Automated Perimetry Under Photopic, Mesopic, and Scotopic Conditions: Detection Mechanisms and Testing Strategies

    PubMed Central

    Simunovic, Matthew P.; Moore, Anthony T.; MacLaren, Robert E.

    2016-01-01

    Purpose Automated scotopic, mesopic, and photopic perimetry are likely to be important paradigms in the assessment of emerging treatments of retinal diseases, yet our knowledge of the photoreceptor mechanisms detecting targets under these conditions remains largely dependent on simian data. We therefore aimed to establish the photoreceptor/postreceptoral mechanisms detecting perimetric targets in humans under photopic, mesopic, and scotopic conditions and to make recommendations for suitable clinical testing strategies for selective perimetry. Methods Perimetric sensitivities within 30° of fixation were determined for eight wavelengths (410, 440, 480, 520, 560, 600, 640, and 680 nm) under scotopic, mesopic (1.3 cd.m−2) and photopic (10 cd.m−2) conditions. Data were fitted with vector combinations of rod, S-cone, nonopponent M+L-cone mechanism, and opponent M- versus L-cone mechanism templates. Results Scotopicperimetric sensitivity was determined by rods peripherally and by a combination of rods and cones at, and immediately around, fixation. Mesopic perimetric sensitivity was mediated by M+L-cones and S-cones centrally and by M+L-cones and rods more peripherally. Photopic perimetric sensitivity was determined by an opponent M- versus L-cone, a nonopponent M+L-cone, and an S-cone mechanism centrally and by a combination of an S-cone and an M+L-cone mechanism peripherally. Conclusions Under scotopic conditions, a 480-nm stimulus provides adequate isolation (≥28 dB) of the rod mechanism. Several mechanisms contribute to mesopic sensitivity: this redundancy in detection may cause both insensitivity to broadband white targets and ambiguity in determining which mechanism is being probed with short-wavelength stimuli. M- and L-cone–derived mechanisms are well isolated at 10 cd.m−2: these may be selectively probed by a stimulus at 640 nm (≥ 20 dB isolation). Translation Relevance In human observers, multiple mechanisms contribute to the detection of Goldmann

  12. Evolutionary indirect effects of biological invasions.

    PubMed

    Lau, Jennifer A

    2012-09-01

    Just as ecological indirect effects can have a wide range of consequences for community structure and ecosystem function, theory suggests that evolutionary indirect effects can also influence community dynamics and the outcome of species interactions. There is little empirical evidence documenting such effects, however. Here, I use a multi-generation selection experiment in the field to investigate: (1) how the exotic plant Medicago polymorpha and the exotic insect herbivore Hypera brunneipennis affect the evolution of anti-herbivore resistance traits in the native plant Lotus wrangelianus and (2) how observed Lotus evolutionary responses to Hypera alter interactions between Lotus and other members of the herbivore community. In one of two study populations, I document rapid evolutionary changes in Lotus resistance to Hypera in response to insecticide treatments that experimentally reduced Hypera abundance, and in response to Medicago-removal treatments that also reduced Hypera abundance. These evolutionary changes in response to Hypera result in reduced attack by aphids. Thus, an evolutionary change caused by one herbivore species alters interactions with other herbivore taxa, an example of an eco-evolutionary feedback. Given that many traits mediate interactions with multiple species, the effects of evolutionary changes in response to one key biotic selective agent may often cascade through interaction webs to influence additional community members.

  13. Facile fabrication and selective detection for cysteine of xylan/Au nanoparticles composite.

    PubMed

    Luo, Yuqiong; Shen, Zuguang; Liu, Pai; Zhao, Lihong; Wang, Xiaoying

    2016-04-20

    This work reported a facile and green method to prepare highly stable and uniformly distributed Au nanoparticles (AuNPs), using biopolymer xylan as stabilizing and reducing agent. Full characterizations were performed and the results revealed that AuNPs were well dispersed with the diameters of 10-30nm. The optimal condition was as follows: the ratio of xylan to HAuCl4 was 150mg:15mg, reaction temperature was 80°C and reaction time was 40min. The xylan/AuNPs composite exhibited highly selective and sensitive sensing of cysteine in aqueous solution, it could distinguish cysteine among dozens kinds of amino acids, and the limit of detection (LOD) for cysteine was calculated as 0.57μM. Besides, the xylan/AuNPs composite was applied for Cys detection in human serum. This study provides a new way for high-value utilization of the rich biomass resource and a cheap, rapid and simple method for Cys detection in real biological samples.

  14. GPR detection of buried symmetrically shaped minelike objects using selective independent component analysis

    NASA Astrophysics Data System (ADS)

    Karlsen, Brian; Sorensen, Helge B. D.; Larsen, Jan; Jakobsen, Kaj B.

    2003-09-01

    This paper addresses the detection of mine-like objects in stepped-frequency ground penetrating radar (SF-GPR) data as a function of object size, object content, and burial depth. The detection approach is based on a Selective Independent Component Analysis (SICA). SICA provides an automatic ranking of components, which enables the suppression of clutter, hence extraction of components carrying mine information. The goal of the investigation is to evaluate various time and frequency domain ICA approaches based on SICA. The performance comparison is based on a series of mine-like objects ranging from small-scale anti-personal (AP) mines to large-scale anti-tank (AT) mines. Large-scale SF-GPR measurements on this series of mine-like objects buried in soil were performed. The SF-GPR data was acquired using a wideband monostatic bow-tie antenna operating in the frequency range 750 MHz - 3.0 GHz. The detection and clutter reduction approaches based on SICA are successfully evaluated on this SF-GPR dataset.

  15. DNA-linked Inhibitor Antibody Assay (DIANA) for sensitive and selective enzyme detection and inhibitor screening

    PubMed Central

    Navrátil, Václav; Schimer, Jiří; Tykvart, Jan; Knedlík, Tomáš; Vik, Viktor; Majer, Pavel; Konvalinka, Jan; Šácha, Pavel

    2017-01-01

    Human diseases are often diagnosed by determining levels of relevant enzymes and treated by enzyme inhibitors. We describe an assay suitable for both ultrasensitive enzyme quantification and quantitative inhibitor screening with unpurified enzymes. In the DNA-linked Inhibitor ANtibody Assay (DIANA), the target enzyme is captured by an immobilized antibody, probed with a small-molecule inhibitor attached to a reporter DNA and detected by quantitative PCR. We validate the approach using the putative cancer markers prostate-specific membrane antigen and carbonic anhydrase IX. We show that DIANA has a linear range of up to six logs and it selectively detects zeptomoles of targets in complex biological samples. DIANA's wide dynamic range permits determination of target enzyme inhibition constants using a single inhibitor concentration. DIANA also enables quantitative screening of small-molecule enzyme inhibitors using microliters of human blood serum containing picograms of target enzyme. DIANA's performance characteristics make it a superior tool for disease detection and drug discovery. PMID:27679479

  16. Loose powder detection and surface characterization in selective laser sintering via optical coherence tomography

    PubMed Central

    Guan, Guangying; Hirsch, Matthias; Syam, Wahyudin P.; Leach, Richard K.; Huang, Zhihong

    2016-01-01

    Defects produced during selective laser sintering (SLS) are difficult to non-destructively detect after build completion without the use of X-ray-based methods. Overcoming this issue by assessing integrity on a layer-by-layer basis has become an area of significant interest for users of SLS apparatus. Optical coherence tomography (OCT) is used in this study to detect surface texture and sub-surface powder, which is un-melted/insufficiently sintered, is known to be a common cause of poor part integrity and would prevent the use of SLS where applications dictate assurance of defect-free parts. To demonstrate the capability of the instrument and associated data-processing algorithms, samples were built with graduated porosities which were embedded in fully dense regions in order to simulate defective regions. Simulated in situ measurements were then correlated with the process parameters used to generate variable density regions. Using this method, it is possible to detect loose powder and differentiate between densities of ±5% at a sub-surface depth of approximately 300 μm. In order to demonstrate the value of OCT as a surface-profiling technique, surface texture datasets are compared with focus variation microscopy. Comparable results are achieved after a spatial bandwidth- matching procedure. PMID:27493569

  17. Fluorescent cadmium sulfide nanoparticles for selective and sensitive detection of toxic pesticides in aqueous medium

    NASA Astrophysics Data System (ADS)

    Walia, Shanka; Acharya, Amitabha

    2014-12-01

    The detection of pesticide residues in ground water, food, or soil samples is extremely important. The currently available laboratory techniques have several drawbacks and needs to be replaced. Fluorescent chemosensors for pesticide detection were reported in the literature, with few reports published on quantum dot-based pesticide sensors, but none of these were focused toward differentiating organophosphorus and organochlorine pesticides specifically. In this respect, glutathione-coated CdS nanoparticles were synthesized and characterized. The TEM studies of the nanoparticles suggested mostly monodispersed spherical particles, with size in the range of 11.5±1 nm. The prepared fluorescent nanoparticles were found to selectively recognize organochlorine pesticide dicofol among all the other pesticides studied, by increasing the fluorescence intensity of the nanoparticles 2.5 times. Similar studies carried out with organophosphorous pesticide dimethoate did not result any change in the fluorescence intensity of the nanoparticles. Further studies carried out with commercially available pesticide solutions, also confirmed similar results. The TEM, SEM, and DLS studies suggested aggregation of the nanoparticles in the presence of dicofol. Control experiments suggested possible role of both amine and carboxylic acid functional groups of glutathione in the recognition of dicofol. The limit of detection of dicofol was found to be 55±11 ppb.

  18. Loose powder detection and surface characterization in selective laser sintering via optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Guan, Guangying; Hirsch, Matthias; Syam, Wahyudin P.; Leach, Richard K.; Huang, Zhihong; Clare, Adam T.

    2016-07-01

    Defects produced during selective laser sintering (SLS) are difficult to non-destructively detect after build completion without the use of X-ray-based methods. Overcoming this issue by assessing integrity on a layer-by-layer basis has become an area of significant interest for users of SLS apparatus. Optical coherence tomography (OCT) is used in this study to detect surface texture and sub-surface powder, which is un-melted/insufficiently sintered, is known to be a common cause of poor part integrity and would prevent the use of SLS where applications dictate assurance of defect-free parts. To demonstrate the capability of the instrument and associated data-processing algorithms, samples were built with graduated porosities which were embedded in fully dense regions in order to simulate defective regions. Simulated in situ measurements were then correlated with the process parameters used to generate variable density regions. Using this method, it is possible to detect loose powder and differentiate between densities of ±5% at a sub-surface depth of approximately 300 μm. In order to demonstrate the value of OCT as a surface-profiling technique, surface texture datasets are compared with focus variation microscopy. Comparable results are achieved after a spatial bandwidth- matching procedure.

  19. High selectivity of colorimetric detection of p-nitrophenol based on Ag nanoclusters

    NASA Astrophysics Data System (ADS)

    Qu, Fei; Chen, Ping; Zhu, Shuyun; You, Jinmao

    2017-01-01

    Ag nanoclusters (Ag NCs) templated by hyperbranched polyethyleneimine (PEI) with different terminal groups and molecular weights had been developed as a special optical sensor for detecting p-nitrophenol (p-NP). When adding p-NP into Ag NCs, an obvious color change from pale yellow to deep yellow could be observed by naked eyes, accompanying with an apparent red-shift of absorption peak, and the reason was attributed to the formation of oxygen anion of p-NP based on the transfer of H+ from p-NP to amine groups of PEI. The molecular weights of template would greatly affect the sensitivity of p-NP. Ag NCs capped by PEI terminated ethylenediamine (EDA) possessed better sensitivity than other Ag NCs, showing good linear range from 5 to 140 μM with the limit of detection as low as 1.28 μM. Most importantly, this present system displayed high selectivity toward p-NP even in the presence of other nitrophenols and nitrotoluenes. This reliable method had been successfully applied for the detection of p-NP in real water and soil samples.

  20. A Micro-Platinum Wire Biosensor for Fast and Selective Detection of Alanine Aminotransferase

    PubMed Central

    Thuy, Tran Nguyen Thanh; Tseng, Tina T.-C.

    2016-01-01

    In this study, a miniaturized biosensor based on permselective polymer layers (overoxidized polypyrrole (Ppy) and Nafion®) modified and enzyme (glutamate oxidase (GlutOx)) immobilized micro-platinum wire electrode for the detection of alanine aminotransferase (ALT) was fabricated. The proposed ALT biosensor was measured electrochemically by constant potential amperometry at +0.7 V vs. Ag/AgCl. The ALT biosensor provides fast response time (~5 s) and superior selectivity towards ALT against both negatively and positively charged species (e.g., ascorbic acid (AA) and dopamine (DA), respectively). The detection range of the ALT biosensor is found to be 10–900 U/L which covers the range of normal ALT levels presented in the serum and the detection limit and sensitivity are found to be 8.48 U/L and 0.059 nA/(U/L·mm2) (N = 10), respectively. We also found that one-day storage of the ALT biosensor at −20 °C right after the sensor being fabricated can enhance the sensor sensitivity (1.74 times higher than that of the sensor stored at 4 °C). The ALT biosensor is stable after eight weeks of storage at −20 °C. The sensor was tested in spiked ALT samples (ALT activities: 20, 200, 400, and 900 U/L) and reasonable recoveries (70%~107%) were obtained. PMID:27240366

  1. High selectivity of colorimetric detection of p-nitrophenol based on Ag nanoclusters.

    PubMed

    Qu, Fei; Chen, Ping; Zhu, Shuyun; You, Jinmao

    2017-01-15

    Ag nanoclusters (Ag NCs) templated by hyperbranched polyethyleneimine (PEI) with different terminal groups and molecular weights had been developed as a special optical sensor for detecting p-nitrophenol (p-NP). When adding p-NP into Ag NCs, an obvious color change from pale yellow to deep yellow could be observed by naked eyes, accompanying with an apparent red-shift of absorption peak, and the reason was attributed to the formation of oxygen anion of p-NP based on the transfer of H(+) from p-NP to amine groups of PEI. The molecular weights of template would greatly affect the sensitivity of p-NP. Ag NCs capped by PEI terminated ethylenediamine (EDA) possessed better sensitivity than other Ag NCs, showing good linear range from 5 to 140μM with the limit of detection as low as 1.28μM. Most importantly, this present system displayed high selectivity toward p-NP even in the presence of other nitrophenols and nitrotoluenes. This reliable method had been successfully applied for the detection of p-NP in real water and soil samples.

  2. Direct, label-free, selective, and sensitive microbial detection using a bacteriorhodopsin-based photoelectric immunosensor.

    PubMed

    Chen, Hsiu-Mei; Jheng, Kai-Ru; Yu, An-Dih

    2017-05-15

    A photoelectric immunosensor using purple membranes (PM) as the transducer, which contains photoactive bacteriorhodopsin, is here first demonstrated for direct and label-free microbial detection. Biotinylated polyclonal antibodies against Escherichia coli were immobilized on a PM-coated electrode through further surface biotinylation and bridging avidin or NeutrAvidin. The photocurrent generated by the antibody-coated sensor was reduced after incubation with E. coli K-12 cultures, with the reduction level increased with the culture populations. The immunosensor prepared via NeutrAvidin exhibited much better selectivity than the one prepared via avidin, recognizing almost none of the tested Gram-positive bacteria. Cultures with populations ranging from 1 to 10(7)CFU/10mL were detected in a single step without any preprocessing. Both AFM and Raman analysis confirmed the layer-by-layer fabrication of the antibody-coated substrates as well as the binding of microorganisms. By investigating the effect of illumination orientation and simulating the photocurrent responses with an equivalent circuit model containing a chemical capacitance, we suggest that the photocurrent reduction was primarily caused by the light-shielding effect of the captured bacteria. Using the current fabrication technique, versatile bacteriorhodopsin-based photoelectric immunosensors can be readily prepared to detect a wide variety of biological cells.

  3. Crystal Diagnostics Xpress S Kit for the Rapid Detection of Salmonella spp. in Selected Food Matrixes.

    PubMed

    Bullard, Brian; Stumpf, Curtis H; Zhao, Weidong; Kuzenko, Stephanie; Niehaus, Gary

    2017-03-07

    The Crystal Diagnostics (CDx) Xpress S Kit is a rapid- screening assay for Salmonella spp. in whole raw tomatoes, whole chicken c`arcasses, raw ground beef, raw beef trim, and whole liquid pasteurized eggs with citric acid when present at levels of 1 CFU/portion size. The Xpress S system comprises an automatic CDx Xpress Reader and a single-use CDx BioCassette that incorporates antibody-coupled microspheres and liquid crystal for the selective identification of the intended microbe. In internal evaluations, the CDx Xpress S Kit detected all 142 Salmonella strains tested, including non-enterica subspecies, and excluded all non-Salmonella species assayed. Method-developer studies, as well as a third-party evaluation, demonstrated that 15 h single-stage enrichment permits rapid detection equivalent to the U.S. Department of Agriculture and U.S. Food and Drug Administration reference methods. The results demonstrate that the CDx Xpress S Kit is one of the fastest, most sensitive, and most accurate methods for detecting Salmonella in food matrixes.

  4. PHACK: An Efficient Scheme for Selective Forwarding Attack Detection in WSNs

    PubMed Central

    Liu, Anfeng; Dong, Mianxiong; Ota, Kaoru; Long, Jun

    2015-01-01

    In this paper, a Per-Hop Acknowledgement (PHACK)-based scheme is proposed for each packet transmission to detect selective forwarding attacks. In our scheme, the sink and each node along the forwarding path generate an acknowledgement (ACK) message for each received packet to confirm the normal packet transmission. The scheme, in which each ACK is returned to the source node along a different routing path, can significantly increase the resilience against attacks because it prevents an attacker from compromising nodes in the return routing path, which can otherwise interrupt the return of nodes’ ACK packets. For this case, the PHACK scheme also has better potential to detect abnormal packet loss and identify suspect nodes as well as better resilience against attacks. Another pivotal issue is the network lifetime of the PHACK scheme, as it generates more acknowledgements than previous ACK-based schemes. We demonstrate that the network lifetime of the PHACK scheme is not lower than that of other ACK-based schemes because the scheme just increases the energy consumption in non-hotspot areas and does not increase the energy consumption in hotspot areas. Moreover, the PHACK scheme greatly simplifies the protocol and is easy to implement. Both theoretical and simulation results are given to demonstrate the effectiveness of the proposed scheme in terms of high detection probability and the ability to identify suspect nodes. PMID:26690178

  5. Highly selective and sensitive detection of neurotransmitters using receptor-modified single-walled carbon nanotube sensors

    NASA Astrophysics Data System (ADS)

    Kim, Byeongju; Song, Hyun Seok; Jin, Hye Jun; Park, Eun Jin; Lee, Sang Hun; Lee, Byung Yang; Park, Tai Hyun; Hong, Seunghun

    2013-07-01

    We present receptor-modified carbon nanotube sensors for the highly selective and sensitive detection of acetylcholine (ACh), one kind of neurotransmitter. Here, we successfully expressed the M1 muscarinic acetylcholine receptor (M1 mAChR), a family of G protein-coupled receptors (GPCRs), in E. coli and coated single-walled carbon nanotube (swCNT)-field effect transistors (FETs) with lipid membrane including the receptor, enabling highly selective and sensitive ACh detection. Using this sensor, we could detect ACh at 100 pM concentration. Moreover, we showed that this sensor could selectively detect ACh among other neurotransmitters. This is the first demonstration of the real-time detection of ACh using specific binding between ACh and M1 mAChR, and it may lead to breakthroughs for various applications such as disease diagnosis and drug screening.