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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. 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.

  3. 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

  4. 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.

  5. Human evolutionary history and contemporary evolutionary theory provide insight when assessing cultural group selection.

    PubMed

    Fuentes, Agustin; Kissel, Marc

    2016-01-01

    Richerson et al. provide a much needed roadmap for assessing cultural group selection (CGS) theory and for applying it to understanding variation between contemporary human groups. However, the current proposal lacks connection to relevant evidence from the human evolutionary record and requires a better integration with contemporary evolutionary theory. The article also misapplies the F st statistic. PMID:27562510

  6. 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.

  7. Strategy selection in evolutionary game dynamics on group interaction networks.

    PubMed

    Tan, Shaolin; Feng, Shasha; Wang, Pei; Chen, Yao

    2014-11-01

    Evolutionary game theory provides an appropriate tool for investigating the competition and diffusion of behavioral traits in biological or social populations. A core challenge in evolutionary game theory is the strategy selection problem: Given two strategies, which one is favored by the population? Recent studies suggest that the answer depends not only on the payoff functions of strategies but also on the interaction structure of the population. Group interactions are one of the fundamental interactive modes within populations. This work aims to investigate the strategy selection problem in evolutionary game dynamics on group interaction networks. In detail, the strategy selection conditions are obtained for some typical networks with group interactions. Furthermore, the obtained conditions are applied to investigate selection between cooperation and defection in populations. The conditions for evolution of cooperation are derived for both the public goods game and volunteer's dilemma game. Numerical experiments validate the above analytical results.

  8. An Evolutionary Perspective of Friendship Selection

    ERIC Educational Resources Information Center

    Coutinho, Savia A.

    2007-01-01

    The research reported in this article investigates whether promiscuity plays a role in same-sex and opposite-sex friend selection. Since same-sex friends share strong similarity and spend time with their friends' mates or potential mates, it becomes important to select same-sex friends who will not be sexual rivals. One way to determine rivalry in…

  9. 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.

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

    PubMed Central

    Morris, Douglas W.

    2011-01-01

    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. PMID:21613295

  11. 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.

  12. Model selection methodology in supervised learning with evolutionary computation.

    PubMed

    Rowland, J J

    2003-11-01

    The expressive power, powerful search capability, and the explicit nature of the resulting models make evolutionary methods very attractive for supervised learning applications in bioinformatics. However, their characteristics also make them highly susceptible to overtraining or to discovering chance relationships in the data. Identification of appropriate criteria for terminating evolution and for selecting an appropriately validated model is vital. Some approaches that are commonly applied to other modelling methods are not necessarily applicable in a straightforward manner to evolutionary methods. An approach to model selection is presented that is not unduly computationally intensive. To illustrate the issues and the technique two bioinformatic datasets are used, one relating to metabolite determination and the other to disease prediction from gene expression data.

  13. 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.

  14. 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. PMID:27531600

  15. 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. PMID:26248868

  16. 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.

  17. Population, evolutionary and genomic consequences of interference selection.

    PubMed Central

    Comeron, Josep M; Kreitman, Martin

    2002-01-01

    Weakly selected mutations are most likely to be physically clustered across genomes and, when sufficiently linked, they alter each others' fixation probability, a process we call interference selection (IS). Here we study population genetics and evolutionary consequences of IS on the selected mutations themselves and on adjacent selectively neutral variation. We show that IS reduces levels of polymorphism and increases low-frequency variants and linkage disequilibrium, in both selected and adjacent neutral mutations. IS can account for several well-documented patterns of variation and composition in genomic regions with low rates of crossing over in Drosophila. IS cannot be described simply as a reduction in the efficacy of selection and effective population size in standard models of selection and drift. Rather, IS can be better understood with models that incorporate a constant "traffic" of competing alleles. Our simulations also allow us to make genome-wide predictions that are specific to IS. We show that IS will be more severe at sites in the center of a region containing weakly selected mutations than at sites located close to the edge of the region. Drosophila melanogaster genomic data strongly support this prediction, with genes without introns showing significantly reduced codon bias in the center of coding regions. As expected, if introns relieve IS, genes with centrally located introns do not show reduced codon bias in the center of the coding region. We also show that reasonably small differences in the length of intermediate "neutral" sequences embedded in a region under selection increase the effectiveness of selection on the adjacent selected sequences. Hence, the presence and length of sequences such as introns or intergenic regions can be a trait subject to selection in recombining genomes. In support of this prediction, intron presence is positively correlated with a gene's codon bias in D. melanogaster. Finally, the study of temporal dynamics of

  18. Adaptive Topographies and Equilibrium Selection in an Evolutionary Game

    PubMed Central

    Osinga, Hinke M.; Marshall, James A. R.

    2015-01-01

    It has long been known in the field of population genetics that adaptive topographies, in which population equilibria maximise mean population fitness for a trait regardless of its genetic bases, do not exist. Whether one chooses to model selection acting on a single locus or multiple loci does matter. In evolutionary game theory, analysis of a simple and general game involving distinct roles for the two players has shown that whether strategies are modelled using a single ‘locus’ or one ‘locus’ for each role, the stable population equilibria are unchanged and correspond to the fitness-maximising evolutionary stable strategies of the game. This is curious given the aforementioned population genetical results on the importance of the genetic bases of traits. Here we present a dynamical systems analysis of the game with roles detailing how, while the stable equilibria in this game are unchanged by the number of ‘loci’ modelled, equilibrium selection may differ under the two modelling approaches. PMID:25706762

  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

    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.

  2. Evolutionary consequences of mutation and selection within an individual.

    PubMed

    Otto, S P; Orive, M E

    1995-11-01

    Whether in sexual or asexual organisms, selection among cell lineages during development is an effective way of eliminating deleterious mutations. Using a mathematical analysis, we find that relatively small differences in cell replication rates during development can translate into large differences in the proportion of mutant cells within the adult, especially when development involves a large number of cell divisions. Consequently, intraorganismal selection can substantially reduce the deleterious mutation rate observed among offspring as well as the mutation load within a population, because cells rather than individuals provide the selective "deaths" necessary to stem the tide of deleterious mutations. The reduction in mutation rate among offspring is more pronounced in organisms with plastic development than in those with structured development. It is also more pronounced in asexual organisms that produce multicellular rather than unicellular offspring. By effecting the mutation rate, intraorganismal selection may have broad evolutionary implications; as an example, we consider its influence on the evolution of ploidy levels, finding that cell-lineage selection is more effective in haploids and tends to favor their evolution. PMID:8582622

  3. DETECTING EVOLUTIONARY TRANSFER OF GENES USING PhIGs(1).

    PubMed

    Boore, Jeffrey L

    2008-02-01

    Organisms have acquired plastids by convoluted paths that have provided multiple opportunities for gene transfer into a host nucleus from intracellular organisms, including the cyanobacterial ancestor of plastids, the proteobacterial ancestor of mitochondria, and both green and red algae whose engulfment has led to secondary acquisition of plastids. These gene movements are most accurately demonstrated by building phylogenetic trees that identify the evolutionary origin of each gene, and one effective tool for this is "PhIGs" (Phylogenetically Inferred Groups; http://PhIGs.org), a set of databases and computer tools with a Web interface for whole-genome evolutionary analysis. PhIGs takes as input gene sets of completely sequenced genomes, builds clusters of genes using a novel, graph-based approach, and reconstructs the evolutionary relationships among all gene families. The user can view and download the sequence alignments, compare intron-exon structures, and follow links to functional genomic databases. Currently, PhIGs contains 652,756 genes from 45 genomes grouped into 61,059 gene families. Graphical displays show the relative positions of these genes among genomes. PhIGs has been used to detect the evolutionary transfer of hundreds of genes from cyanobacteria and red algae into oömycete nuclear genomes, revealing that even though they have no plastids, their ancestors did, having secondarily acquired them from an intracellular red alga. A great number of genomes are soon to become available that are relevant to our broader understanding of the movement of genes among intracellular compartments after engulfing other organisms, and PhIGs will be an effective tool to interpret these gene movements.

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

    PubMed

    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. 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

  6. Evolutionary determinants of divergent calcium selectivity of TRPM channels.

    PubMed

    Mederos y Schnitzler, Michael; Wäring, Janine; Gudermann, Thomas; Chubanov, Vladimir

    2008-05-01

    The mammalian TRPM gene family can be subdivided into distinct categories of cation channels that are either highly permeable for Ca(2+) (TRPM3/6/7), nonselective (TRPM2/8), or even Ca(2+) impermeable (TRPM4/5). TRPM6/7 are fused to alpha-kinase domains, whereas TRPM2 is linked to an ADP-ribose phosphohydrolase (Nudix domain). At a molecular level, the evolutionary steps that gave rise to the structural and functional TRPM channel diversity remain elusive. Here, we provide phylogenetic evidence that Nudix-linked channels represent an ancestral type of TRPMs that is present in various phyla, ranging from protists to humans. Surprisingly, the pore-forming segments of invertebrate TRPM2-like proteins display high sequence similarity to those of Ca(2+)-selective TRPMs, while human TRPM2 is characterized by a loss of several conserved residues. Using the patch-clamp technique, Ca(2+) imaging, and site-directed mutagenesis, we demonstrate that restoration of only two "ancient" pore residues in human TRPM2 (Q981E/P983Y) significantly increased (approximately 4-fold) its permeability for Ca(2+). Conversely, introduction of a "modern" sequence motif into mouse TRPM7 (E1047Q/Y1049P) resulted in the loss of Ca(2+) permeation and a linear TRPM2-like current-voltage relationship. Overall, our findings provide an integrative view on the evolution of the domain architecture and the structural basis of the distinct ion permeation profiles of TRPM channels.

  7. 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

  8. 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

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

    PubMed

    Morgan, D L; Morgan, R K; Toth, J 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.

  10. 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…

  11. Testing hypotheses in evolutionary ecology with imperfect detection: capture-recapture structural equation modeling.

    PubMed

    Cubaynes, Sarah; Doutrelant, Claire; Grégoire, Arnaud; Perret, Philippe; Faivre, Bruno; Gimenez, Olivier

    2012-02-01

    Studying evolutionary mechanisms in natural populations often requires testing multifactorial scenarios of causality involving direct and indirect relationships among individual and environmental variables. It is also essential to account for the imperfect detection of individuals to provide unbiased demographic parameter estimates. To cope with these issues, we developed a new approach combining structural equation models with capture-recapture models (CR-SEM) that allows the investigation of competing hypotheses about individual and environmental variability observed in demographic parameters. We employ Markov chain Monte Carlo sampling in a Bayesian framework to (1) estimate model parameters, (2) implement a model selection procedure to evaluate competing hypotheses about causal mechanisms, and (3) assess the fit of models to data using posterior predictive checks. We illustrate the value of our approach using two case studies on wild bird populations. We first show that CR-SEM can be useful to quantify the action of selection on a set of phenotypic traits with an analysis of selection gradients on morphological traits in Common Blackbirds (Turdus merula). In a second case study on Blue Tits (Cyanistes caeruleus), we illustrate the use of CR-SEM to study evolutionary trade-offs in the wild, while accounting for varying environmental conditions. PMID:22624306

  12. 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

  13. 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

  14. 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.

  15. Trait associations across evolutionary time within a drosophila phylogeny: correlated selection or genetic constraint?

    PubMed

    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.

  16. 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

  17. Kinetic evolutionary behavior of catalysis-select migration

    NASA Astrophysics Data System (ADS)

    Wu, Yuan-Gang; Lin, Zhen-Quan; Ke, Jian-Hong

    2012-06-01

    We propose a catalysis-select migration driven evolution model of two-species (A- and B-species) aggregates, where one unit of species A migrates to species B under the catalysts of species C, while under the catalysts of species D the reaction will become one unit of species B migrating to species A. Meanwhile the catalyst aggregates of species C perform self-coagulation, as do the species D aggregates. We study this catalysis-select migration driven kinetic aggregation phenomena using the generalized Smoluchowski rate equation approach with C species catalysis-select migration rate kernel K(k;i,j) = Kkij and D species catalysis-select migration rate kernel J(k;i,j)= Jkij. The kinetic evolution behaviour is found to be dominated by the competition between the catalysis-select immigration and emigration, in which the competition is between JD0 and KC0 (D0 and C0 are the initial numbers of the monomers of species D and C, respectively). When JD0 -KC0 > 0, the aggregate size distribution of species A satisfies the conventional scaling form and that of species B satisfies a modified scaling form. And in the case of JD0-KC0 < 0, species A and B exchange their aggregate size distributions as in the above JD0-KC0 > 0 case.

  18. Is selection relevant in the evolutionary emergence of drug resistance?

    PubMed

    Day, Troy; Huijben, Silvie; Read, Andrew F

    2015-03-01

    The emergence of drug-resistant pathogens is often considered a canonical case of evolution by natural selection. Here we argue that the strength of selection can be a poor predictor of the rate of resistance emergence. It is possible for a resistant strain to be under negative selection and still emerge in an infection or spread in a population. Measuring the right parameters is a necessary first step toward the development of evidence-based resistance-management strategies. We argue that it is the absolute fitness of the resistant strains that matters most and that a primary determinant of the absolute fitness of a resistant strain is the ecological context in which it finds itself.

  19. 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

  20. Random drift versus selection in academic vocabulary: an evolutionary analysis of published keywords.

    PubMed

    Bentley, R Alexander

    2008-08-27

    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.

  1. 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.

  2. Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure

    PubMed Central

    Webber, Mark A.; Whitehead, Rebekah N.; Mount, Manuella; Loman, Nick J.; Pallen, Mark J.; Piddock, Laura J. V.

    2015-01-01

    Objectives Biocides are widely used to prevent infection. We aimed to determine whether exposure of Salmonella to various biocides could act as a driver of antibiotic resistance. Methods Salmonella enterica serovar Typhimurium was exposed to four biocides with differing modes of action. Antibiotic-resistant mutants were selected during exposure to all biocides and characterized phenotypically and genotypically to identify mechanisms of resistance. Results All biocides tested selected MDR mutants with decreased antibiotic susceptibility; these occurred randomly throughout the experiments. Mutations that resulted in de-repression of the multidrug efflux pump AcrAB-TolC were seen in MDR mutants. A novel mutation in rpoA was also selected and contributed to the MDR phenotype. Other mutants were highly resistant to both quinolone antibiotics and the biocide triclosan. Conclusions This study shows that exposure of bacteria to biocides can select for antibiotic-resistant mutants and this is mediated by clinically relevant mechanisms of resistance prevalent in human pathogens. PMID:25953808

  3. 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.

  4. 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.

  5. Older partner selection promotes the prevalence of cooperation in evolutionary games.

    PubMed

    Yang, Guoli; Huang, Jincai; Zhang, Weiming

    2014-10-21

    Evolutionary games typically come with the interplays between evolution of individual strategy and adaptation to network structure. How these dynamics in the co-evolution promote (or obstruct) the cooperation is regarded as an important topic in social, economic, and biological fields. Combining spatial selection with partner choice, the focus of this paper is to identify which neighbour should be selected as a role to imitate during the process of co-evolution. Age, an internal attribute and kind of local piece of information regarding the survivability of the agent, is a significant consideration for the selection strategy. The analysis and simulations presented, demonstrate that older partner selection for strategy imitation could foster the evolution of cooperation. The younger partner selection, however, may decrease the level of cooperation. Our model highlights the importance of agent׳s age on the promotion of cooperation in evolutionary games, both efficiently and effectively. PMID:24956329

  6. Photobiont selectivity leads to ecological tolerance and evolutionary divergence in a polymorphic complex of lichenized fungi

    PubMed Central

    Muggia, Lucia; Pérez-Ortega, Sergio; Kopun, Theodora; Zellnig, Günther; Grube, Martin

    2014-01-01

    Background and Aims The integrity and evolution of lichen symbioses depend on a fine-tuned combination of algal and fungal genotypes. Geographically widespread species complexes of lichenized fungi can occur in habitats with slightly varying ecological conditions, and it remains unclear how this variation correlates with symbiont selectivity patterns in lichens. In an attempt to address this question, >300 samples were taken of the globally distributed and ecologically variable lichen-forming species complex Tephromela atra, together with closely allied species, in order to study genetic diversity and the selectivity patterns of their photobionts. Methods Lichen thalli of T. atra and of closely related species T. grumosa, T. nashii and T. atrocaesia were collected from six continents, across 24 countries and 62 localities representing a wide range of habitats. Analyses of genetic diversity and phylogenetic relationships were carried out both for photobionts amplified directly from the lichen thalli and from those isolated in axenic cultures. Morphological and anatomical traits were studied with light and transmission electron microscopy in the isolated algal strains. Key Results Tephromela fungal species were found to associate with 12 lineages of Trebouxia. Five new clades demonstrate the still-unrecognized genetic diversity of lichen algae. Culturable, undescribed lineages were also characterized by phenotypic traits. Strong selectivity of the mycobionts for the photobionts was observed in six monophyletic Tephromela clades. Seven Trebouxia lineages were detected in the poorly resolved lineage T. atra sensu lato, where co-occurrence of multiple photobiont lineages in single thalli was repeatedly observed. Conclusions Low selectivity apparently allows widespread lichen-forming fungi to establish successful symbioses with locally adapted photobionts in a broader range of habitats. This flexibility might correlate with both lower phylogenetic resolution and

  7. 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.

  8. 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

  9. Symmetry breaking and coarsening in spatially distributed evolutionary processes including sexual reproduction and disruptive selection

    NASA Astrophysics Data System (ADS)

    Sayama, Hiroki; Kaufman, Les; Bar-Yam, Yaneer

    2000-11-01

    Sexual reproduction presents significant challenges to formal treatment of evolutionary processes. A starting point for systematic treatments of ecological and evolutionary phenomena has been provided by the gene-centered view of evolution which assigns effective fitness to each allele instead of each organism. The gene-centered view can be formalized as a dynamic mean-field approximation applied to genes in reproduction and selection dynamics. We show that the gene-centered view breaks down for symmetry breaking and pattern formation within a population and show that spatial distributions of organisms with local mating neighborhoods in the presence of disruptive selection give rise to such symmetry breaking and pattern formation in the genetic composition of local populations. Global dynamics follows conventional coarsening of systems with nonconserved order parameters. The results have significant implications for the ecology of genetic diversity and species formation.

  10. Sex-ratio control erodes sexual selection, revealing evolutionary feedback from adaptive plasticity.

    PubMed

    Fawcett, Tim W; Kuijper, Bram; Weissing, Franz J; Pen, Ido

    2011-09-20

    Female choice is a powerful selective force, driving the elaboration of conspicuous male ornaments. This process of sexual selection has profound implications for many life-history decisions, including sex allocation. For example, females with attractive partners should produce more sons, because these sons will inherit their father's attractiveness and enjoy high mating success, thereby yielding greater fitness returns than daughters. However, previous research has overlooked the fact that there is a reciprocal feedback from life-history strategies to sexual selection. Here, using a simple mathematical model, we show that if mothers adaptively control offspring sex in relation to their partner's attractiveness, sexual selection is weakened and male ornamentation declines. This weakening occurs because the ability to determine offspring sex reduces the fitness difference between females with attractive and unattractive partners. We use individual-based, evolutionary simulations to show that this result holds under more biologically realistic conditions. Sexual selection and sex allocation thus interact in a dynamic fashion: The evolution of conspicuous male ornaments favors sex-ratio adjustment, but this conditional strategy then undermines the very same process that generated it, eroding sexual selection. We predict that, all else being equal, the most elaborate sexual displays should be seen in species with little or no control over offspring sex. The feedback process we have described points to a more general evolutionary principle, in which a conditional strategy weakens directional selection on another trait by reducing fitness differences.

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

    PubMed

    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

    2015-07-01

    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

  13. Evolutionary Effects on Brightest Cluster Galaxy (BCG) Detections in the CFHTLS-Deep Fields

    NASA Astrophysics Data System (ADS)

    Alis, S.

    2009-09-01

    Brightest cluster galaxies (BCGs) are the most massive and most luminous galaxies in the universe. These galaxies dominate galaxy clusters and lie at the top of the potential well of clusters. Investigating these galaxies can improve our understandings on galaxy cluster evolution. In this work, evolutionary effects on BCG detections are emphasized. For detecting BCGs, CFHTLS (Canada-France-Hawaii Telescope Legacy Survey) galaxy clusters, detected by Olsen et al. (2007) were used. To make a proper BCG detection, modeled galaxy colors should be evolved according to redshift. In this work, it is shown how unevolved galaxy colors can effect BCG detection.

  14. Evolutionary history of pearl millet (Pennisetum glaucum [L.] R. Br.) and selection on flowering genes since its domestication.

    PubMed

    Clotault, Jérémy; Thuillet, Anne-Céline; Buiron, Marylène; De Mita, Stéphane; Couderc, Marie; Haussmann, Bettina I G; Mariac, Cédric; Vigouroux, Yves

    2012-04-01

    The plant domestication process is associated with considerable modifications of plant phenotype. The identification of the genetic basis of this adaptation is of great interest for evolutionary biology. One of the methods used to identify such genes is the detection of signatures of selection. However, domestication is generally associated with major demographic effects. It is therefore crucial to disentangle the effects of demography and selection on diversity. In this study, we investigated selection in a flowering time pathway during domestication of pearl millet. We first used a random set of 20 genes to model pearl millet domestication using approximate Bayesian computation. This analysis showed that a model with exponential growth and wild-cultivated gene flow was well supported by our data set. Under this model, the domestication date of pearl millet is estimated at around 4,800 years ago. We assessed selection in 15 pearl millet DNA sequences homologous to flowering time genes and showed that these genes underwent selection more frequently than expected. We highlighted significant signatures of selection in six pearl millet flowering time genes associated with domestication or improvement of pearl millet. Moreover, higher deviations from neutrality were found for circadian clock-associated genes. Our study provides new insights into the domestication process of pearl millet and shows that a category of genes of the flowering pathway were preferentially selected during pearl millet domestication.

  15. 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

  16. 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

  17. 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.

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

    PubMed Central

    Queller, David C.

    2014-01-01

    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. PMID:24686940

  19. 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...

  20. 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

  1. 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

  2. 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

  3. Detection of selection utilizing molecular phylogenetics: a possible approach.

    PubMed

    Yang, Ming; Wyckoff, Gerald J

    2011-05-01

    The neutral theory of molecular evolution (Kimura 1985) is the basis for most current statistical tests for detecting selection, mainly using polymorphism data within species, divergence data between species, and/or genomic structures like linkage disequilibrium (Wang et al. 2006). In most cases informative tests can only be constructed with ample variations within these parameters and many common tests are difficult to formulate when identity-by-descent is not clear, for example in gene families or repetitive elements. With the current progress being made toward whole-genome sequencing and re-sequencing efforts, as well as protein sequencing via tandem mass spectrometry where genomic sequencing is lacking, we felt it was necessary to re-visit possible methods for rapid screening and detection of evolutionary outliers. These outliers might be of interest for other research, such as candidate gene association studies or genome annotations, drug- and disease-target searches, and functional studies. We focused on methods that would work on both protein and nucleotide data, could be used on large gene or protein domain families, and could be generated quickly in order for "first pass" annotation of large scale data. For these reasons, we chose properties of trees generated routinely in molecular phylogenetic studies; genetic distance, tree shape and balance, and internal node statistics (Heard 1992). Our current research looking at protein domain family data and phylogenetic trees from PFAM (Finn et al. 2008) suggests this approach towards detecting evolutionary outliers is feasible, but additional work will be necessary to determine the parameters that suggest either positive or negative selection is occurring in specific gene families. This is particularly true when other factors such as rapid duplication and deletion of genes containing these domains is taking place, and we suggest phylogenetic statistics may be useful in combination with existing methodologies for

  4. Detection of unusual trajectories using multi-objective evolutionary algorithms and rough sets

    NASA Astrophysics Data System (ADS)

    Smolinski, Tomasz G.; Newell, Trevor; McDaniel, Samantha; Pokrajac, David

    2013-09-01

    Detection of unusual trajectories of moving objects (e.g., people, automobiles, etc.) is an important problem in many civilian and military surveillance applications. In this work, we propose a multi-objective evolutionary algorithms and rough sets-based approach that breaks down 2-dimensional trajectories into a set of additive components, which then can be used to build a classifier capable of recognizing typical, but yet unseen trajectories, and identifying those that seem suspicious.

  5. 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

  6. 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

  7. 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

  8. If there is an evolutionary selection pressure for the high frequency of MBL2 polymorphisms, what is it?

    PubMed

    Eisen, D P; Osthoff, M

    2014-05-01

    Either immune selection or stochastic processes may have influenced the frequency of highly polymorphic genes such as mannose-binding lectin 2 (MBL2). This pattern recognition receptor of the innate immune system recognizes and binds to pathogenic microorganisms and apoptotic cells leading to lectin pathway complement killing or clearance. In almost all of a large number of studies in different ethnic groups worldwide there is 20-25% carriage of low MBL2 haplotypes, with 8-10% of each population having no MBL detectable in the blood. The source of this high variability of MBL2 remains cryptic. It arises from six main snps in the prompter and exon regions of the gene that assort into seven common haplotypes under linkage disequilibrium. While global studies of MBL2 show that it is not under immune selection pressure, these results are not the same when the same population genetic tools are used on large national studies. Other analyses point to the silenced MBL1 pseudogene and development of promoter polymorphisms in humans as evidence of selection pressure favouring low-producing haplotypes. While these analyses cannot be reconciled readily, there are two processes by which MBL heterozygosity could have been advantageous in an evolutionary sense; protection against adverse effects of various infectious diseases and lethal manifestations of atherosclerosis - a disease that now seems to have a more ancient history than assumed previously. Ultimately, consideration of the context for possible future therapeutic manipulation of MBL means that this can proceed independently of resolution of the evolutionary forces that have shaped MBL2 polymorphism.

  9. If there is an evolutionary selection pressure for the high frequency of MBL2 polymorphisms, what is it?

    PubMed Central

    Eisen, D P; Osthoff, M

    2014-01-01

    Either immune selection or stochastic processes may have influenced the frequency of highly polymorphic genes such as mannose-binding lectin 2 (MBL2). This pattern recognition receptor of the innate immune system recognizes and binds to pathogenic microorganisms and apoptotic cells leading to lectin pathway complement killing or clearance. In almost all of a large number of studies in different ethnic groups worldwide there is 20–25% carriage of low MBL2 haplotypes, with 8–10% of each population having no MBL detectable in the blood. The source of this high variability of MBL2 remains cryptic. It arises from six main snps in the prompter and exon regions of the gene that assort into seven common haplotypes under linkage disequilibrium. While global studies of MBL2 show that it is not under immune selection pressure, these results are not the same when the same population genetic tools are used on large national studies. Other analyses point to the silenced MBL1 pseudogene and development of promoter polymorphisms in humans as evidence of selection pressure favouring low-producing haplotypes. While these analyses cannot be reconciled readily, there are two processes by which MBL heterozygosity could have been advantageous in an evolutionary sense; protection against adverse effects of various infectious diseases and lethal manifestations of atherosclerosis – a disease that now seems to have a more ancient history than assumed previously. Ultimately, consideration of the context for possible future therapeutic manipulation of MBL means that this can proceed independently of resolution of the evolutionary forces that have shaped MBL2 polymorphism. PMID:24255984

  10. Altered tumor formation and evolutionary selection of genetic variants in the human MDM4 oncogene.

    PubMed

    Atwal, Gurinder Singh; Kirchhoff, Tomas; Bond, Elisabeth E; Montagna, Marco; Monagna, Marco; Menin, Chiara; Bertorelle, Roberta; Scaini, Maria Chiara; Bartel, Frank; Böhnke, Anja; Pempe, Christina; Gradhand, Elise; Hauptmann, Steffen; Offit, Kenneth; Levine, Arnold J; Bond, Gareth L

    2009-06-23

    A large body of evidence strongly suggests that the p53 tumor suppressor pathway is central in reducing cancer frequency in vertebrates. The protein product of the haploinsufficient mouse double minute 2 (MDM2) oncogene binds to and inhibits the p53 protein. Recent studies of human genetic variants in p53 and MDM2 have shown that single nucleotide polymorphisms (SNPs) can affect p53 signaling, confer cancer risk, and suggest that the pathway is under evolutionary selective pressure (1-4). In this report, we analyze the haplotype structure of MDM4, a structural homolog of MDM2, in several different human populations. Unusual patterns of linkage disequilibrium (LD) in the haplotype distribution of MDM4 indicate the presence of candidate SNPs that may also modify the efficacy of the p53 pathway. Association studies in 5 different patient populations reveal that these SNPs in MDM4 confer an increased risk for, or early onset of, human breast and ovarian cancers in Ashkenazi Jewish and European cohorts, respectively. This report not only implicates MDM4 as a key regulator of tumorigenesis in the human breast and ovary, but also exploits for the first time evolutionary driven linkage disequilibrium as a means to select SNPs of p53 pathway genes that might be clinically relevant.

  11. 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.

  12. 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.

  13. 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)

  14. 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

  15. Detection vs. selection: integration of genetic, epigenetic and environmental cues in fluctuating environments.

    PubMed

    McNamara, John M; Dall, Sasha R X; Hammerstein, Peter; Leimar, Olof

    2016-10-01

    There are many inputs during development that influence an organism's fit to current or upcoming environments. These include genetic effects, transgenerational epigenetic influences, environmental cues and developmental noise, which are rarely investigated in the same formal framework. We study an analytically tractable evolutionary model, in which cues are integrated to determine mature phenotypes in fluctuating environments. Environmental cues received during development and by the mother as an adult act as detection-based (individually observed) cues. The mother's phenotype and a quantitative genetic effect act as selection-based cues (they correlate with environmental states after selection). We specify when such cues are complementary and tend to be used together, and when using the most informative cue will predominate. Thus, we extend recent analyses of the evolutionary implications of subsets of these effects by providing a general diagnosis of the conditions under which detection and selection-based influences on development are likely to evolve and coexist.

  16. Detection vs. selection: integration of genetic, epigenetic and environmental cues in fluctuating environments.

    PubMed

    McNamara, John M; Dall, Sasha R X; Hammerstein, Peter; Leimar, Olof

    2016-10-01

    There are many inputs during development that influence an organism's fit to current or upcoming environments. These include genetic effects, transgenerational epigenetic influences, environmental cues and developmental noise, which are rarely investigated in the same formal framework. We study an analytically tractable evolutionary model, in which cues are integrated to determine mature phenotypes in fluctuating environments. Environmental cues received during development and by the mother as an adult act as detection-based (individually observed) cues. The mother's phenotype and a quantitative genetic effect act as selection-based cues (they correlate with environmental states after selection). We specify when such cues are complementary and tend to be used together, and when using the most informative cue will predominate. Thus, we extend recent analyses of the evolutionary implications of subsets of these effects by providing a general diagnosis of the conditions under which detection and selection-based influences on development are likely to evolve and coexist. PMID:27600658

  17. Detecting genetic drift versus selection in human evolution

    PubMed Central

    Ackermann, Rebecca Rogers; Cheverud, James M.

    2004-01-01

    Recent paleoanthropological discoveries reveal a diverse, potentially speciose human fossil record. Such extensive morphological diversity results from the action of divergent evolutionary forces on an evolving lineage. Here, we apply quantitative evolutionary theory to test whether random evolutionary processes alone can explain the morphological diversity seen among fossil australopith and early Homo crania from the Plio–Pleistocene. We show that although selection may have played an important role in diversifying hominin facial morphology in the late Pliocene, this is not the case during the early evolution of the genus Homo, where genetic drift was probably the primary force responsible for facial diversification. PMID:15604148

  18. Similarly Strong Purifying Selection Acts on Human Disease Genes of All Evolutionary Ages

    PubMed Central

    Cai, James J.; Borenstein, Elhanan; Chen, Rong

    2009-01-01

    A number of studies have showed that recently created genes differ from the genes created in deep evolutionary past in many aspects. Here, we determined the age of emergence and propensity for gene loss (PGL) of all human protein–coding genes and compared disease genes with non-disease genes in terms of their evolutionary rate, strength of purifying selection, mRNA expression, and genetic redundancy. The older and the less prone to loss, non-disease genes have been evolving 1.5- to 3-fold slower between humans and chimps than young non-disease genes, whereas Mendelian disease genes have been evolving very slowly regardless of their ages and PGL. Complex disease genes showed an intermediate pattern. Disease genes also have higher mRNA expression heterogeneity across multiple tissues than non-disease genes regardless of age and PGL. Young and middle-aged disease genes have fewer similar paralogs as non-disease genes of the same age. We reasoned that genes were more likely to be involved in human disease if they were under a strong functional constraint, expressed heterogeneously across tissues, and lacked genetic redundancy. Young human genes that have been evolving under strong constraint between humans and chimps might also be enriched for genes that encode important primate or even human-specific functions. PMID:20333184

  19. Evolutionary ecology of plant-microbe interactions: soil microbial structure alters selection on plant traits.

    PubMed

    Lau, Jennifer A; Lennon, Jay T

    2011-10-01

    • Below-ground microbial communities influence plant diversity, plant productivity, and plant community composition. Given these strong ecological effects, are interactions with below-ground microbes also important for understanding natural selection on plant traits? • Here, we manipulated below-ground microbial communities and the soil moisture environment on replicated populations of Brassica rapa to examine how microbial community structure influences selection on plant traits and mediates plant responses to abiotic environmental stress. • In soils with experimentally simplified microbial communities, plants were smaller, had reduced chlorophyll content, produced fewer flowers, and were less fecund when compared with plant populations grown in association with more complex soil microbial communities. Selection on plant growth and phenological traits also was stronger when plants were grown in simplified, less diverse soil microbial communities, and these effects typically were consistent across soil moisture treatments. • Our results suggest that microbial community structure affects patterns of natural selection on plant traits. Thus, the below-ground microbial community can influence evolutionary processes, just as recent studies have demonstrated that microbial diversity can influence plant community and ecosystem processes.

  20. Evolutionary ecology of plant-microbe interactions: soil microbial structure alters selection on plant traits.

    PubMed

    Lau, Jennifer A; Lennon, Jay T

    2011-10-01

    • Below-ground microbial communities influence plant diversity, plant productivity, and plant community composition. Given these strong ecological effects, are interactions with below-ground microbes also important for understanding natural selection on plant traits? • Here, we manipulated below-ground microbial communities and the soil moisture environment on replicated populations of Brassica rapa to examine how microbial community structure influences selection on plant traits and mediates plant responses to abiotic environmental stress. • In soils with experimentally simplified microbial communities, plants were smaller, had reduced chlorophyll content, produced fewer flowers, and were less fecund when compared with plant populations grown in association with more complex soil microbial communities. Selection on plant growth and phenological traits also was stronger when plants were grown in simplified, less diverse soil microbial communities, and these effects typically were consistent across soil moisture treatments. • Our results suggest that microbial community structure affects patterns of natural selection on plant traits. Thus, the below-ground microbial community can influence evolutionary processes, just as recent studies have demonstrated that microbial diversity can influence plant community and ecosystem processes. PMID:21658184

  1. Detection of Fundus Lesions Using Classifier Selection

    NASA Astrophysics Data System (ADS)

    Nagayoshi, Hiroto; Hiramatsu, Yoshitaka; Sako, Hiroshi; Himaga, Mitsutoshi; Kato, Satoshi

    A system for detecting fundus lesions caused by diabetic retinopathy from fundus images is being developed. The system can screen the images in advance in order to reduce the inspection workload on doctors. One of the difficulties that must be addressed in completing this system is how to remove false positives (which tend to arise near blood vessels) without decreasing the detection rate of lesions in other areas. To overcome this difficulty, we developed classifier selection according to the position of a candidate lesion, and we introduced new features that can distinguish true lesions from false positives. A system incorporating classifier selection and these new features was tested in experiments using 55 fundus images with some lesions and 223 images without lesions. The results of the experiments confirm the effectiveness of the proposed system, namely, degrees of sensitivity and specificity of 98% and 81%, respectively.

  2. Hybridization of Evolutionary Mechanisms for Feature Subset Selection in Unsupervised Learning

    NASA Astrophysics Data System (ADS)

    Torres, Dolores; Ponce-de-León, Eunice; Torres, Aurora; Ochoa, Alberto; Díaz, Elva

    Feature subset selection for unsupervised learning, is a very important topic in artificial intelligence because it is the base for saving computational resources. In this implementation we use a typical testor’s methodology in order to incorporate an importance index for each variable. This paper presents the general framework and the way two hybridized meta-heuristics work in this NP-complete problem. The evolutionary mechanisms are based on the Univariate Marginal Distribution Algorithm (UMDA) and the Genetic Algorithm (GA). GA and UMDA - Estimation of Distribution Algorithm (EDA) use a very useful rapid operator implemented for finding typical testors on a very large dataset and also, both algorithms, have a local search mechanism for improving time and fitness. Experiments show that EDA is faster than GA because it has a better exploitation performance; nevertheless, GA’ solutions are more consistent.

  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. 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. PMID:25914359

  5. New insights into short-chain prenyltransferases: structural features, evolutionary history and potential for selective inhibition.

    PubMed

    Vandermoten, Sophie; Haubruge, Eric; Cusson, Michel

    2009-12-01

    Isoprenoids form an extensive group of natural products involved in a number of important biological processes. Their biosynthesis proceeds through sequential 1'-4 condensations of isopentenyl diphosphate (C5) with an allylic acceptor, the first of which is dimethylallyl diphosphate (C5). The reactions leading to the production of geranyl diphosphate (C10), farnesyl diphosphate (C15) and geranylgeranyl diphosphate (C20), which are the precursors of mono-, sesqui- and diterpenes, respectively, are catalyzed by a group of highly conserved enzymes known as short-chain isoprenyl diphosphate synthases, or prenyltransferases. In recent years, the sequences of many new prenyltransferases have become available, including those of several plant and animal geranyl diphosphate synthases, revealing novel mechanisms of product chain-length selectivity and an intricate evolutionary path from a putative common ancestor. Finally, there is considerable interest in designing inhibitors specific to short-chain prenyltransferases, for the purpose of developing new drugs or pesticides that target the isoprenoid biosynthetic pathway.

  6. 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

  7. 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

  8. Computational Study of Evolutionary Selection Pressure on Rainbow Trout Estrogen Receptors

    PubMed Central

    Shyu, Conrad; Brown, Celeste J.; Ytreberg, F. Marty

    2010-01-01

    Molecular dynamics simulations were used to determine the binding affinities between the hormone 17-estradiol (E2) and different estrogen receptor (ER) isoforms in the rainbow trout, Oncorhynchus mykiss. Previous phylogenetic analysis indicates that a whole genome duplication prior to the divergence of ray-finned fish led to two distinct ER isoforms, ER and ER, and the recent whole genome duplication in the ancestral salmonid created two ER isoforms, ER and ER. The objective of our computational studies is to provide insight into the underlying evolutionary pressures on these isoforms. For the ER subtype our results show that E2 binds preferentially to ER over ER. Tests of lineage specific N/S ratios indicate that the ligand binding domain of the ER gene is evolving under relaxed selection relative to all other ER genes. Comparison with the highly conserved DNA binding domain suggests that ER may be undergoing neofunctionalization possibly by binding to another ligand. By contrast, both ER and ER bind similarly to E2 and the best fitting model of selection indicates that the ligand binding domain of all ER genes are evolving under the same level of purifying selection, comparable to ER. PMID:20231885

  9. Mutagenicity of tocopheryl quinones: evolutionary advantage of selective accumulation of dietary alpha-tocopherol.

    PubMed

    Cornwell, David G; Williams, Marshall V; Wani, Altaf A; Wani, Gulzar; Shen, Elaine; Jones, Kenneth H

    2002-01-01

    We have shown that phenolic antioxidant tocopherols are oxidized to nonarylating alpha-tocopheryl quinone (alpha-TQ) and arylating gamma- and delta-TQ electrophiles. The arylating quinones stimulate apoptosis and are highly cytotoxic in mammalian cells. Some xenobiotic phenolic antioxidants are mutagens, and it has been suggested that their arylating quinone metabolites are the active agents in mutagenesis related to carcinogenesis. We found that neither alpha- nor gamma-TQ was directly genotoxic in supercoiled-to-nicked circular DNA conversions, but these agents interacted with the cytomegalovirus reporter-driven plasmid and enhanced luciferase transfection, with gamma-TQ > alpha-TQ. The Ames test, using gamma-TQ and a number of Salmonella strains, showed no evidence of bacterial mutagenesis. gamma-TQ was highly cytotoxic and alpha-TQ slightly cytotoxic in eukaryocyte AS52 cells. A guanosine phosphoribosyltransferase gene assay showed that gamma-TQ was highly mutagenic and alpha-TQ slightly mutagenic in AS52 cells. A review of the literature identified associations where a decrease in dietary gamma-tocopherol (gamma-T) diminishes and an increase in dietary gamma-T and its quinone enhances carcinogenicity. Humans and other omnivores selectively accumulate alpha-tocopherol, even though gamma-T is their principal dietary tocopherol. We suggest that this selectivity confers an evolutionary advantage by limiting tissue gamma-T, a putative precursor of the mutagen gamma-TQ.

  10. 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.

  11. 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.

  12. 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. PMID:16761810

  13. 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

    2016-01-01

    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.

  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

    2016-01-01

    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

  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. Chaos enhanced differential evolution in the task of evolutionary control of selected set of discrete chaotic systems.

    PubMed

    Senkerik, Roman; Zelinka, Ivan; 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.

  17. 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

  18. 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

  19. Landscape-scale eco-evolutionary dynamics: selection by seed predators and fire determine a major reproductive strategy.

    PubMed

    Talluto, Matt V; Benkman, Craig W

    2013-06-01

    Recent work in model systems has demonstrated significant effects of rapid evolutionary change on ecological processes (eco-evolutionary dynamics). Fewer studies have addressed whether eco-evolutionary dynamics structure natural ecosystems. We investigated variation in the frequency of serotiny in lodgepole pine (Pinus contorta), a widespread species in which postfire seedling density and ecosystem structure are largely determined by serotiny. Serotiny, the retention of mature seeds in cones in a canopy seed bank, is thought to be an adaptation for stand-replacing fire, but less attention has been paid to the potential selective effects of seed predation on serotiny. We hypothesized that spatial variation in percentage serotiny in lodgepole pine forests results from an eco-evolutionary dynamic where the local level of serotiny depends on the relative strengths of conflicting directional selection from fire (favoring serotiny) and seed predation (favoring cones that open at maturity). We measured percentage serotiny, the abundance of American red squirrels (Tamiasciurus hudsonicus; the primary pre-dispersal seed predator of lodgepole pine), and several measures of forest structure in Yellowstone National Park, USA. Fire frequency strongly predicted the frequency of serotiny, a pattern that is well-supported in the literature. At sites with high fire frequency (return intervals of -135-185 years) where fire favors increased serotiny, squirrel abundance was negatively associated with serotiny, suggesting that selection from predation can overwhelm selection from fire when squirrels are abundant. At sites with low fire frequency (return intervals of -280-310 years), serotiny was nearly universally uncommon (< 10%). Finally, forest structure strongly predicted squirrel density independently of serotiny, and serotiny provided no additional explanatory power, suggesting that the correlation is caused by selection against serotiny exerted by squirrels, rather than

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

    PubMed Central

    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. PMID:26213999

  1. 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

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

    PubMed Central

    Vy, Ha My T.; Kim, Yuseob

    2015-01-01

    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. PMID:25911658

  3. 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.

  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. Evolutionary Patterns of the Mitochondrial Genome in Metazoa: Exploring the Role of Mutation and Selection in Mitochondrial Protein–Coding Genes

    PubMed Central

    Castellana, S.; Vicario, S.; Saccone, C.

    2011-01-01

    The mitochondrial genome is a fundamental component of the eukaryotic domain of life, encoding for several important subunits of the respiratory chain, the main energy production system in cells. The processes by means of which mitochondrial DNA (mtDNA) replicates, expresses itself and evolves have been explored over the years, although various aspects are still debated. In this review, we present several key points in modern research on the role of evolutionary forces in affecting mitochondrial genomes in Metazoa. In particular, we assemble the main data on their evolution, describing the contributions of mutational pressure, purifying, and adaptive selection, and how they are related. We also provide data on the evolutionary fate of the mitochondrial synonymous variation, related to the nonsynonymous variation, in comparison with the pattern detected in the nucleus. Elevated mutational pressure characterizes the evolution of the mitochondrial synonymous variation, whereas purging selection, physiologically due to phenomena such as cell atresia and intracellular mtDNA selection, guarantees coding sequence functionality. This enables mitochondrial adaptive mutations to emerge and fix in the population, promoting mitonuclear coevolution. PMID:21551352

  6. Detecting remote evolutionary relationships among proteins by large-scale semantic embedding.

    PubMed

    Melvin, Iain; Weston, Jason; Noble, William Stafford; Leslie, Christina

    2011-01-01

    Virtually every molecular biologist has searched a protein or DNA sequence database to find sequences that are evolutionarily related to a given query. Pairwise sequence comparison methods--i.e., measures of similarity between query and target sequences--provide the engine for sequence database search and have been the subject of 30 years of computational research. For the difficult problem of detecting remote evolutionary relationships between protein sequences, the most successful pairwise comparison methods involve building local models (e.g., profile hidden Markov models) of protein sequences. However, recent work in massive data domains like web search and natural language processing demonstrate the advantage of exploiting the global structure of the data space. Motivated by this work, we present a large-scale algorithm called ProtEmbed, which learns an embedding of protein sequences into a low-dimensional "semantic space." Evolutionarily related proteins are embedded in close proximity, and additional pieces of evidence, such as 3D structural similarity or class labels, can be incorporated into the learning process. We find that ProtEmbed achieves superior accuracy to widely used pairwise sequence methods like PSI-BLAST and HHSearch for remote homology detection; it also outperforms our previous RankProp algorithm, which incorporates global structure in the form of a protein similarity network. Finally, the ProtEmbed embedding space can be visualized, both at the global level and local to a given query, yielding intuition about the structure of protein sequence space.

  7. Evolutionary pattern in the OXT-OXTR system in primates: Coevolution and positive selection footprints

    PubMed Central

    Vargas-Pinilla, Pedro; Paré, Pamela; Tovo-Rodrigues, Luciana; Vieira, Carlos Meton de Alencar Gadelha; Xavier, Agatha; Comas, David; Pissinatti, Alcides; Sinigaglia, Marialva; Rigo, Maurício Menegatti; Vieira, Gustavo Fioravanti; Lucion, Aldo B.; Salzano, Francisco Mauro; Bortolini, Maria Cátira

    2015-01-01

    Oxytocin is a nonapeptide involved in a wide range of physiologic and behavioral functions. Until recently, it was believed that an unmodified oxytocin sequence was present in all placental mammals. This study analyzed oxytocin (OXT) in 29 primate species and the oxytocin receptor (OXTR) in 21 of these species. We report here three novel OXT forms in the New World monkeys, as well as a more extensive distribution of a previously described variant (Leu8Pro). In structural terms, these OXTs share the same three low-energy conformations in solution during molecular dynamic simulations, with subtle differences in their side chains. A consistent signal of positive selection was detected in the Cebidae family, and OXT position 8 showed a statistically significant (P = 0.013) correlation with litter size. Several OXTR changes were identified, some of them promoting gain or loss of putative phosphorylation sites, with possible consequences for receptor internalization and desensitization. OXTR amino acid sites are under positive selection, and intramolecular and intermolecular coevolutionary processes with OXT were also detected. We suggest that some New World monkey OXT-OXTR forms can be correlated to male parental care through the increase of cross-reactivity with its correlated vasopressin system. PMID:25535371

  8. Evolutionary pattern in the OXT-OXTR system in primates: coevolution and positive selection footprints.

    PubMed

    Vargas-Pinilla, Pedro; Paixão-Côrtes, Vanessa Rodrigues; Paré, Pamela; Tovo-Rodrigues, Luciana; Vieira, Carlos Meton de Alencar Gadelha; Xavier, Agatha; Comas, David; Pissinatti, Alcides; Sinigaglia, Marialva; Rigo, Maurício Menegatti; Vieira, Gustavo Fioravanti; Lucion, Aldo B; Salzano, Francisco Mauro; Bortolini, Maria Cátira

    2015-01-01

    Oxytocin is a nonapeptide involved in a wide range of physiologic and behavioral functions. Until recently, it was believed that an unmodified oxytocin sequence was present in all placental mammals. This study analyzed oxytocin (OXT) in 29 primate species and the oxytocin receptor (OXTR) in 21 of these species. We report here three novel OXT forms in the New World monkeys, as well as a more extensive distribution of a previously described variant (Leu8Pro). In structural terms, these OXTs share the same three low-energy conformations in solution during molecular dynamic simulations, with subtle differences in their side chains. A consistent signal of positive selection was detected in the Cebidae family, and OXT position 8 showed a statistically significant (P = 0.013) correlation with litter size. Several OXTR changes were identified, some of them promoting gain or loss of putative phosphorylation sites, with possible consequences for receptor internalization and desensitization. OXTR amino acid sites are under positive selection, and intramolecular and intermolecular coevolutionary processes with OXT were also detected. We suggest that some New World monkey OXT-OXTR forms can be correlated to male parental care through the increase of cross-reactivity with its correlated vasopressin system. PMID:25535371

  9. 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.

  10. 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

  11. Decomposition-based multiobjective evolutionary algorithm for community detection in dynamic social networks.

    PubMed

    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.

  12. 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.

  13. 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

  14. 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...

  15. 46 CFR 108.404 - Selection of fire detection system.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 4 2011-10-01 2011-10-01 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...

  16. 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...

  17. 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...

  18. Detecting and profiling tissue-selective genes.

    PubMed

    Liang, Shuang; Li, Yizheng; Be, Xiaobing; Howes, Steve; Liu, Wei

    2006-07-12

    The widespread use of DNA microarray technologies has generated large amounts of data from various tissue and/or cell types. These data set the stage to answer the question of tissue specificity of human transcriptome in a comprehensive manner. Our focus is to uncover the tissue-gene relationship by identifying genes that are preferentially expressed in a small number of tissue types. The tissue selectivity would shed light on the potential physiological functions of these genes and provides an indispensable reference to compare against disease pathophysiology and to identify or validate tissue-specific drug targets. Here we describe a systematic computational and statistical approach to profile gene expression data to identify tissue-selective genes with the use of a more extensive data set and a well-established multiple-comparison procedure with error rate control. Expression data of 35,152 probe sets in 97 normal human tissue types were analyzed, and 3,919 genes were identified to be selective to one or a few tissue types. We presented results of these tissue-selective genes and compared them to those identified by other studies.

  19. Evolution of Site-Selection Stabilizes Population Dynamics, Promotes Even Distribution of Individuals, and Occasionally Causes Evolutionary Suicide.

    PubMed

    Parvinen, Kalle; Brännström, Åke

    2016-08-01

    Species that compete for access to or use of sites, such as parasitic mites attaching to honey bees or apple maggots laying eggs in fruits, can potentially increase their fitness by carefully selecting sites at which they face little or no competition. Here, we systematically investigate the evolution of site-selection strategies among animals competing for discrete sites. By developing and analyzing a mechanistic and population-dynamical model of site selection in which searching individuals encounter sites sequentially and can choose to accept or continue to search based on how many conspecifics are already there, we give a complete characterization of the different site-selection strategies that can evolve. We find that evolution of site-selection stabilizes population dynamics, promotes even distribution of individuals among sites, and occasionally causes evolutionary suicide. We also discuss the broader implications of our findings and propose how they can be reconciled with an earlier study (Nonaka et al. in J Theor Biol 317:96-104, 2013) that reported selection toward ever higher levels of aggregation among sites as a consequence of site-selection. PMID:27647007

  20. Evolution of Site-Selection Stabilizes Population Dynamics, Promotes Even Distribution of Individuals, and Occasionally Causes Evolutionary Suicide.

    PubMed

    Parvinen, Kalle; Brännström, Åke

    2016-08-01

    Species that compete for access to or use of sites, such as parasitic mites attaching to honey bees or apple maggots laying eggs in fruits, can potentially increase their fitness by carefully selecting sites at which they face little or no competition. Here, we systematically investigate the evolution of site-selection strategies among animals competing for discrete sites. By developing and analyzing a mechanistic and population-dynamical model of site selection in which searching individuals encounter sites sequentially and can choose to accept or continue to search based on how many conspecifics are already there, we give a complete characterization of the different site-selection strategies that can evolve. We find that evolution of site-selection stabilizes population dynamics, promotes even distribution of individuals among sites, and occasionally causes evolutionary suicide. We also discuss the broader implications of our findings and propose how they can be reconciled with an earlier study (Nonaka et al. in J Theor Biol 317:96-104, 2013) that reported selection toward ever higher levels of aggregation among sites as a consequence of site-selection.

  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. 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

  4. 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 PMID:27078076

  5. Detecting evolutionary strata on the human x chromosome in the absence of gametologous y-linked sequences.

    PubMed

    Pandey, Ravi Shanker; Wilson Sayres, Melissa A; Azad, Rajeev K

    2013-01-01

    Mammalian sex chromosomes arose from a pair of homologous autosomes that differentiated into the X and Y chromosomes following a series of recombination suppression events between the X and Y. The stepwise recombination suppressions from the distal long arm to the distal short arm of the chromosomes are reflected as regions with distinct X-Y divergence, referred to as evolutionary strata on the X. All current methods for stratum detection depend on X-Y comparisons but are severely limited by the paucity of X-Y gametologs. We have developed an integrative method that combines a top-down, recursive segmentation algorithm with a bottom-up, agglomerative clustering algorithm to decipher compositionally distinct regions on the X, which reflect regions of unique X-Y divergence. In application to human X chromosome, our method correctly classified a concatenated set of 35 previously assayed X-linked gene sequences by evolutionary strata. We then extended our analysis, applying this method to the entire sequence of the human X chromosome, in an effort to define stratum boundaries. The boundaries of more recently formed strata on X-added region, namely the fourth and fifth strata, have been defined by previous studies and are recapitulated with our method. The older strata, from the first up to the third stratum, have remained poorly resolved due to paucity of X-Y gametologs. By analyzing the entire X sequence, our method identified seven evolutionary strata in these ancient regions, where only three could previously be assayed, thus demonstrating the robustness of our method in detecting the evolutionary strata.

  6. 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. PMID:26930198

  7. 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

  8. 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

  9. 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

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

    PubMed

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

    2015-06-01

    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.

  11. 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

  12. 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

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

    PubMed

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

    2016-10-01

    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

  14. Analysis of channel confined selective area growth in evolutionary growth of GaN on SiO2

    NASA Astrophysics Data System (ADS)

    Leung, Benjamin; Tsai, Miao-Chan; Song, Jie; Zhang, Yu; Xiong, Kanglin; Yuan, Ge; Coltrin, Michael E.; Han, Jung

    2015-09-01

    Here, we analyze the chemical vapor deposition of semiconductor crystals by selective area growth in a non-planar geometry. Specifically, the growth process in laterally and vertically confined masks forming single-crystal GaN on SiO2 by metal-organic chemical vapor deposition is considered in detail. A textured AlN seed is used to initiate growth of oriented GaN selectively through the mask, allowing the reduction of degrees of freedom by the evolutionary grain selection process. As shown by measurements of growth rates within the mask, the sub micron length scale of the channel opening is comparable to the mean free path of precursors in the gas phase, resulting in transport characteristics that can be described by an intermediate flow regime between continuum and free-molecular. Mass transport is modeled through kinetic theory to explain the growth rate enhancements of more than a factor of two by changes in reactor pressure. The growth conditions that enable the modification of nucleation density within the channel are then discussed, and are measured by electron-back scatter diffraction of the nucleated grains on the AlN seed. Finally, the selectivity behavior using the low fill factor masks needed in these configurations has been optimized by control of precursor flow rates and the H2 enhanced etching of the polycrystalline GaN nuclei.

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

    PubMed Central

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

    2013-01-01

    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. PMID:23467649

  16. 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.

  17. Ion-Selective Detection with Glass Nanopipette for Living Cells

    NASA Astrophysics Data System (ADS)

    Takami, T.; Son, J. W.; Kang, E. J.; Deng, X. L.; Kawai, T.; Lee, S.-W.; Park, B. H.

    2013-05-01

    We developed a method to probe local ion concentration with glass nanopipette in which poly(vinyl chloride) membrane containing ionophore for separate ion detection is prepared. Here we demonstrate how ion-selective detections are available for living cells such as HeLa cell, rat vascular myocyte, and neuron cell.

  18. Natural selection and the evolutionary ecology of the arbuscular mycorrhizal fungi (Phylum Glomeromycota).

    PubMed

    Helgason, Thorunn; Fitter, Alastair H

    2009-01-01

    Darwin's model of evolution by natural selection was based on his observations of change in discrete organisms in which individuals are easy to define. Many of the most abundant functional groups in ecosystems, such as fungi and bacteria, do not fit this paradigm. In this review, we seek to understand how the elegant logic of Darwinian natural selection can be applied to distributed clonal organisms. The arbuscular mycorrhizal (AM) fungi are one such group. Globally, they are ubiquitous in terrestrial ecosystems, are locally distributed among many host plant species, and are significant drivers of nutrient cycling in ecosystems. The AM fungi are intractable to study, as the few taxa that can be cultured cannot be grown in the absence of plant roots. Research has focused on the plant-fungus interface, and thus on the symbiotic phenotype. A model is discussed for the interchange of materials at the interface that throws the emphasis of research onto the behaviour of the individual organisms and removes the need to test for phenomena such as selectivity, co-evolution, and cheating. The AM fungi are distributed organisms with an extensive external mycelium that is likely to be under strong environmental selection. AM fungi show sufficient phenotypic variation and fitness differentials for selection to occur, and developments in genetic analyses suggest that a better understanding of heritability in these organisms is not far away. It is argued that direct selection on fungal traits related to their survival and performance in the soil independent of the host is likely to be the major driver of differentiation in the AM fungi, and the evidence for direct fungal responses to soil conditions such as pH, hypoxia, and temperature is reviewed.

  19. The use of selection experiments for detecting quantitative trait loci.

    PubMed

    Ollivier, L; Messer, L A; Rothschild, M F; Legault, C

    1997-06-01

    Gene frequency changes following selection may reveal the existence of gene effects on the trait selected. Loci for the selected quantitative trait (SQTL) may thus be detected. Additionally, one can estimate the average effect (alpha) of a marker allele associated with an SQTL from the allele frequency change (delta q) due to selection of given intensity (i). In a sample of unrelated individuals, it is optimal to select the upper and lower 27% for generating delta q in order to estimate alpha. For a given number of individuals genotyped, this estimator is 0.25i2 times more efficient than the classical estimator of alpha, based on the regression of the trait on the genotype at the marker locus. The method is extended to selection criteria using information from relatives, showing that combined selection considerably increases the efficiency of estimation for traits of low heritability. The method has been applied to the detection of SQTL in a selection experiment in which the trait selected was pig litter size averaged over the first four parities, with i = 3. Results for four genes are provided, one of which yielded a highly significant effect. The conditions required for valid application of the method are discussed, including selection experiments over several generations. Additional advantages of the method can be anticipated from determining gene frequencies on pooled samples of blood or DNA.

  20. 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.

  1. The artful mind: sexual selection and an evolutionary neurobiological approach to aesthetic appreciation.

    PubMed

    De Ridder, Dirk; Vanneste, Sven

    2013-01-01

    Based on functional imaging of beauty appreciation in art and of beautiful faces, a heuristic model is presented that proposes that beauty appreciation in art is based on a sexual selection mechanism that led to the preference of beautiful faces. Beauty is linked to sexual selection as a sign of fitness. Beautiful traits, like the peacock's tail, are costly and thereby signal superior genetic quality. Mechanistically, beauty is a construct of the brain that links positive feedback of the reward system with hedonic experience, namely pleasure, which itself might be encoded in the orbito-frontal cortex. The context determines whether a stimulus should lead to further approach or withdrawal in order to maintain a hedonic homeostasis. The fact that aesthetic appreciation of art uses the same circuitry as the aesthetic appreciation of faces suggests that there is no special art circuitry in the brain, but that available networks are used for aesthetic appreciation of art.

  2. 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.

  3. 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. PMID:26589239

  4. Evolutionary endocrinology of juvenile hormone esterase in Gryllus assimilis: direct and correlated responses to selection.

    PubMed

    Zera, A J; Zhang, C

    1995-11-01

    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.

  5. 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.

  6. 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.

  7. Shifts in the evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication.

    PubMed

    Zhao, Meixia; Du, Jianchang; Lin, Feng; Tong, Chaobo; Yu, Jingyin; Huang, Shunmou; Wang, Xiaowu; Liu, Shengyi; Ma, Jianxin

    2013-10-01

    Recent sequencing of the Brassica rapa and Brassica oleracea genomes revealed extremely contrasting genomic features such as the abundance and distribution of transposable elements between the two genomes. However, whether and how these structural differentiations may have influenced the evolutionary rates of the two genomes since their split from a common ancestor are unknown. Here, we investigated and compared the rates of nucleotide substitution between two long terminal repeats (LTRs) of individual orthologous LTR-retrotransposons, the rates of synonymous and non-synonymous substitution among triplicated genes retained in both genomes from a shared whole genome triplication event, and the rates of genetic recombination estimated/deduced by the comparison of physical and genetic distances along chromosomes and ratios of solo LTRs to intact elements. Overall, LTR sequences and genic sequences showed more rapid nucleotide substitution in B. rapa than in B. oleracea. Synonymous substitution of triplicated genes retained from a shared whole genome triplication was detected at higher rates in B. rapa than in B. oleracea. Interestingly, non-synonymous substitution was observed at lower rates in the former than in the latter, indicating shifted densities of purifying selection between the two genomes. In addition to evolutionary asymmetry, orthologous genes differentially regulated and/or disrupted by transposable elements between the two genomes were also characterized. Our analyses suggest that local genomic and epigenomic features, such as recombination rates and chromatin dynamics reshaped by independent proliferation of transposable elements and elimination between the two genomes, are perhaps partially the causes and partially the outcomes of the observed inter-specific asymmetric evolution.

  8. A model of selective masking in chromatic detection.

    PubMed

    Shepard, Timothy G; Swanson, Emily A; McCarthy, Comfrey L; Eskew, Rhea T

    2016-07-01

    Narrowly tuned, selective noise masking of chromatic detection has been taken as evidence for the existence of a large number of color mechanisms (i.e., higher order color mechanisms). Here we replicate earlier observations of selective masking of tests in the (L,M) plane of cone space when the noise is placed near the corners of the detection contour. We used unipolar Gaussian blob tests with three different noise color directions, and we show that there are substantial asymmetries in the detection contours-asymmetries that would have been missed with bipolar tests such as Gabor patches. We develop a new chromatic detection model, which is based on probability summation of linear cone combinations, and incorporates a linear contrast energy versus noise power relationship that predicts how the sensitivity of these mechanisms changes with noise contrast and chromaticity. With only six unipolar color mechanisms (the same number as the cardinal model), the new model accounts for the threshold contours across the different noise conditions, including the asymmetries and the selective effects of the noises. The key for producing selective noise masking in the (L,M) plane is having more than two mechanisms with opposed L- and M-cone inputs, in which case selective masking can be produced without large numbers of color mechanisms. PMID:27442723

  9. MOEPGA: A novel method to detect protein complexes in yeast protein-protein interaction networks based on MultiObjective Evolutionary Programming Genetic Algorithm.

    PubMed

    Cao, Buwen; Luo, Jiawei; Liang, Cheng; Wang, Shulin; Song, Dan

    2015-10-01

    The identification of protein complexes in protein-protein interaction (PPI) networks has greatly advanced our understanding of biological organisms. Existing computational methods to detect protein complexes are usually based on specific network topological properties of PPI networks. However, due to the inherent complexity of the network structures, the identification of protein complexes may not be fully addressed by using single network topological property. In this study, we propose a novel MultiObjective Evolutionary Programming Genetic Algorithm (MOEPGA) which integrates multiple network topological features to detect biologically meaningful protein complexes. Our approach first systematically analyzes the multiobjective problem in terms of identifying protein complexes from PPI networks, and then constructs the objective function of the iterative algorithm based on three common topological properties of protein complexes from the benchmark dataset, finally we describe our algorithm, which mainly consists of three steps, population initialization, subgraph mutation and subgraph selection operation. To show the utility of our method, we compared MOEPGA with several state-of-the-art algorithms on two yeast PPI datasets. The experiment results demonstrate that the proposed method can not only find more protein complexes but also achieve higher accuracy in terms of fscore. Moreover, our approach can cover a certain number of proteins in the input PPI network in terms of the normalized clustering score. Taken together, our method can serve as a powerful framework to detect protein complexes in yeast PPI networks, thereby facilitating the identification of the underlying biological functions.

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. The evolutionary origin of the vertebrate basal ganglia and its role in action selection

    PubMed Central

    Grillner, Sten; Robertson, Brita; Stephenson-Jones, Marcus

    2013-01-01

    The group of nuclei within the basal ganglia of the forebrain is central to the control of movement. We present data showing that the structure and function of the basal ganglia have been conserved throughout vertebrate evolution over some 560 million years. The interaction between the different nuclei within the basal ganglia is conserved as well as the cellular and synaptic properties and transmitters. We consider the role of the conserved basal ganglia circuitry for basic patterns of motor behaviour controlled via brainstem circuits. The output of the basal ganglia consists of tonically active GABAergic neurones, which target brainstem motor centres responsible for different patterns of behaviour, such as eye and locomotor movements, posture, and feeding. A prerequisite for activating or releasing a motor programme is that this GABAergic inhibition is temporarily reduced. This can be achieved through activation of GABAergic projection neurons from striatum, the input level of the basal ganglia, given an appropriate synaptic drive from cortex, thalamus and the dopamine system. The tonic inhibition of the motor centres at rest most likely serves to prevent the different motor programmes from becoming active when not intended. Striatal projection neurones are subdivided into one group with dopamine 1 receptors that provides increased excitability of the direct pathway that can initiate movements, while inhibitory dopamine 2 receptors are expressed on neurones that instead inhibit movements and are part of the ‘indirect loop’ in mammals as well as lamprey. We review the evidence showing that all basic features of the basal ganglia have been conserved throughout vertebrate phylogeny, and discuss these findings in relation to the role of the basal ganglia in selection of behaviour. PMID:23318875

  15. Pattern recognition for selective odor detection with gas sensor arrays.

    PubMed

    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

  16. 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

  17. Novelty detection in a changing environment: A negative selection approach

    NASA Astrophysics Data System (ADS)

    Surace, Cecilia; Worden, Keith

    2010-05-01

    In the recent past, there have been a number of engineering studies motivated by analogies with the human immune system. The immune system has provided a rich source of inspiration for pattern recognition, machine learning and data mining analyses. One of the properties of the immune system which proves particularly useful for novelty detection is that of self/non-self discrimination and this forms the basis of the negative selection algorithm which has previously been applied by other researchers to the problem of time-series novelty detection. The object of the current paper is to apply the negative selection algorithm to more general feature sets and also to consider the case of novelty detection where the normal condition set is significantly non-Gaussian or varies with operational or environmental conditions.

  18. Selective detection of bacterial layers with terahertz plasmonic antennas.

    PubMed

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

    2012-11-01

    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.

  19. Selective detection of bacterial layers with terahertz plasmonic antennas.

    PubMed

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

    2012-11-01

    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

  20. Combining evolutionary algorithms with oblique decision trees to detect bent double galaxies

    SciTech Connect

    Cantu-Paz, E; Kamath, C

    2000-06-22

    Decision trees have long been popular in classification as they use simple and easy-to-understand tests at each node. Most variants of decision trees test a single attribute at a node, leading to axis-parallel trees, where the test results in a hyperplane which is parallel to one of the dimensions in the attribute space. These trees can be rather large and inaccurate in cases where the concept to be learnt is best approximated by oblique hyperplanes. In such cases, it may be more appropriate to use an oblique decision tree, where the decision at each node is a linear combination of the attributes. Oblique decision trees have not gained wide popularity in part due to the complexity of constructing good oblique splits and the tendency of existing splitting algorithms to get stuck in local minima. Several alternatives have been proposed to handle these problems including randomization in conjunction with deterministic hill climbing and the use of simulated annealing. In this paper, they use evolutionary algorithms (EAs) to determine the split. EAs are well suited for this problem because of their global search properties, their tolerance to noisy fitness evaluations, and their scalability to large dimensional search spaces. They demonstrate the technique on a practical problem from astronomy, namely, the classification of galaxies with a bent-double morphology, and describe their experiences with several split evaluation criteria.

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

    PubMed

    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

  2. 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

  3. Detection of cancerous masses in mammograms by template matching: optimization of template brightness distribution by means of evolutionary algorithm.

    PubMed

    Bator, Marcin; Nieniewski, Mariusz

    2012-02-01

    Optimization of brightness distribution in the template used for detection of cancerous masses in mammograms by means of correlation coefficient is presented. This optimization is performed by the evolutionary algorithm using an auxiliary mass classifier. Brightness along the radius of the circularly symmetric template is coded indirectly by its second derivative. The fitness function is defined as the area under curve (AUC) of the receiver operating characteristic (ROC) for the mass classifier. The ROC and AUC are obtained for a teaching set of regions of interest (ROIs), for which it is known whether a ROI is true-positive (TP) or false-positive (F). The teaching set is obtained by running the mass detector using a template with a predetermined brightness. Subsequently, the evolutionary algorithm optimizes the template by classifying masses in the teaching set. The optimal template (OT) can be used for detection of masses in mammograms with unknown ROIs. The approach was tested on the training and testing sets of the Digital Database for Screening Mammography (DDSM). The free-response receiver operating characteristic (FROC) obtained with the new mass detector seems superior to the FROC for the hemispherical template (HT). Exemplary results are the following: in the case of the training set in the DDSM, the true-positive fraction (TPF) = 0.82 for the OT and 0.79 for the HT; in the case of the testing set, TPF = 0.79 for the OT and 0.72 for the HT. These values were obtained for disease cases, and the false-positive per image (FPI) = 2.

  4. 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.

  5. Evolutionary theory and teleology.

    PubMed

    O'Grady, R T

    1984-04-21

    The order within and among living systems can be explained rationally by postulating a process of descent with modification, effected by factors which are extrinsic or intrinsic to the organisms. Because at the time Darwin proposed his theory of evolution there was no concept of intrinsic factors which could evolve, he postulated a process of extrinsic effects--natural selection. Biological order was thus seen as an imposed, rather than an emergent, property. Evolutionary change was seen as being determined by the functional efficiency (adaptedness) of the organism in its environment, rather than by spontaneous changes in intrinsically generated organizing factors. The initial incompleteness of Darwin's explanatory model, and the axiomatization of its postulates in neo-Darwinism, has resulted in a theory of functionalism, rather than structuralism. As such, it introduces an unnecessary teleology which confounds evolutionary studies and reduces the usefulness of the theory. This problem cannot be detected from within the neo-Darwinian paradigm because the different levels of end-directed activity--teleomatic, teleonomic, and teleological--are not recognized. They are, in fact, considered to influence one another. The theory of nonequilibrium evolution avoids these problems by returning to the basic principles of biological order and developing a structuralist explanation of intrinsically generated change. Extrinsic factors may affect the resultant evolutionary pattern, but they are neither necessary nor sufficient for evolution to occur.

  6. Detecting negative selection on recurrent mutations using gene genealogy

    PubMed Central

    2013-01-01

    Background Whether or not a mutant allele in a population is under selection is an important issue in population genetics, and various neutrality tests have been invented so far to detect selection. However, detection of negative selection has been notoriously difficult, partly because negatively selected alleles are usually rare in the population and have little impact on either population dynamics or the shape of the gene genealogy. Recently, through studies of genetic disorders and genome-wide analyses, many structural variations were shown to occur recurrently in the population. Such “recurrent mutations” might be revealed as deleterious by exploiting the signal of negative selection in the gene genealogy enhanced by their recurrence. Results Motivated by the above idea, we devised two new test statistics. One is the total number of mutants at a recurrently mutating locus among sampled sequences, which is tested conditionally on the number of forward mutations mapped on the sequence genealogy. The other is the size of the most common class of identical-by-descent mutants in the sample, again tested conditionally on the number of forward mutations mapped on the sequence genealogy. To examine the performance of these two tests, we simulated recurrently mutated loci each flanked by sites with neutral single nucleotide polymorphisms (SNPs), with no recombination. Using neutral recurrent mutations as null models, we attempted to detect deleterious recurrent mutations. Our analyses demonstrated high powers of our new tests under constant population size, as well as their moderate power to detect selection in expanding populations. We also devised a new maximum parsimony algorithm that, given the states of the sampled sequences at a recurrently mutating locus and an incompletely resolved genealogy, enumerates mutation histories with a minimum number of mutations while partially resolving genealogical relationships when necessary. Conclusions With their

  7. 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.

  8. Selective detection of singlet gerade metastable states of N2

    NASA Astrophysics Data System (ADS)

    Kedzierski, W.; McConkey, J. W.

    2016-07-01

    Metastable N2 molecules produced by electron impact on N2 are detected using a unique solid nitrogen matrix detector. The time-of-flight system is shown to be selectively sensitive to a1Πg and 1Σg+ or 1Γg metastable species. The latter species had been identified theoretically previously but was detected experimentally for the first time in the present investigation. Their identification and excitation as a function of electron energy from threshold to 300 eV are presented. Comparison is made with the data obtained by other techniques.

  9. Design strategies of fluorescent probes for selective detection among biothiols.

    PubMed

    Niu, Li-Ya; Chen, Yu-Zhe; Zheng, Hai-Rong; Wu, Li-Zhu; Tung, Chen-Ho; Yang, Qing-Zheng

    2015-10-01

    Simple thiol derivatives, such as cysteine (Cys), homocysteine (Hcy), and glutathione (GSH), play key roles in biological processes, and the fluorescent probes to detect such thiols in vivo selectively with high sensitivity and fast response times are critical for understanding their numerous functions. However, the similar structures and reactivities of these thiols pose considerable challenges to the development of such probes. This review focuses on various strategies for the design of fluorescent probes for the selective detection of biothiols. We classify the fluorescent probes for discrimination among biothiols according to reaction types between the probes and thiols such as cyclization with aldehydes, conjugate addition-cyclization with acrylates, native chemical ligation, and aromatic substitution-rearrangement.

  10. 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

  11. Detecting and measuring selection from gene frequency data.

    PubMed

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

    2014-03-01

    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

  12. Inferring population structure and relationship using minimal independent evolutionary markers in Y-chromosome: a hybrid approach of recursive feature selection for hierarchical clustering

    PubMed Central

    Srivastava, Amit Kumar; Chopra, Rupali; Ali, Shafat; Aggarwal, Shweta; Vig, Lovekesh; Koul Bamezai, Rameshwar Nath

    2014-01-01

    Inundation of evolutionary markers expedited in Human Genome Project and 1000 Genome Consortium has necessitated pruning of redundant and dependent variables. Various computational tools based on machine-learning and data-mining methods like feature selection/extraction have been proposed to escape the curse of dimensionality in large datasets. Incidentally, evolutionary studies, primarily based on sequentially evolved variations have remained un-facilitated by such advances till date. Here, we present a novel approach of recursive feature selection for hierarchical clustering of Y-chromosomal SNPs/haplogroups to select a minimal set of independent markers, sufficient to infer population structure as precisely as deduced by a larger number of evolutionary markers. To validate the applicability of our approach, we optimally designed MALDI-TOF mass spectrometry-based multiplex to accommodate independent Y-chromosomal markers in a single multiplex and genotyped two geographically distinct Indian populations. An analysis of 105 world-wide populations reflected that 15 independent variations/markers were optimal in defining population structure parameters, such as FST, molecular variance and correlation-based relationship. A subsequent addition of randomly selected markers had a negligible effect (close to zero, i.e. 1 × 10−3) on these parameters. The study proves efficient in tracing complex population structures and deriving relationships among world-wide populations in a cost-effective and expedient manner. PMID:25030906

  13. Detection of novel members, structure–function analysis and evolutionary classification of the 2H phosphoesterase superfamily

    PubMed Central

    Mazumder, Raja; Iyer, Lakshminarayan M.; Vasudevan, Sona; Aravind, L.

    2002-01-01

    2′,3′ Cyclic nucleotide phosphodiesterases are enzymes that catalyze at least two distinct steps in the splicing of tRNA introns in eukaryotes. Recently, the biochemistry and structure of these enzymes, from yeast and the plant Arabidopsis thaliana, have been extensively studied. They were found to share a common active site, characterized by two conserved histidines, with the bacterial tRNA-ligating enzyme LigT and the vertebrate myelin-associated 2′,3′ phosphodiesterases. Using sensitive sequence profile analysis methods, we show that these enzymes define a large superfamily of predicted phosphoesterases with two conserved histidines (hence 2H phosphoesterase superfamily). We identify several new families of 2H phosphoesterases and present a complete evolutionary classification of this superfamily. We also carry out a structure– function analysis of these proteins and present evidence for diverse interactions for different families, within this superfamily, with RNA substrates and protein partners. In particular, we show that eukaryotes contain two ancient families of these proteins that might be involved in RNA processing, transcriptional co-activation and post-transcriptional gene silencing. Another eukaryotic family restricted to vertebrates and insects is combined with UBA and SH3 domains suggesting a role in signal transduction. We detect these phosphoesterase modules in polyproteins of certain retroviruses, rotaviruses and coronaviruses, where they could function in capping and processing of viral RNAs. Furthermore, we present evidence for multiple families of 2H phosphoesterases in bacteria, which might be involved in the processing of small molecules with the 2′,3′ cyclic phosphoester linkages. The evolutionary analysis suggests that the 2H domain emerged through a duplication of a simple structural unit containing a single catalytic histidine prior to the last common ancestor of all life forms. Initially, this domain appears to have been

  14. Fusobacterium necrophorum- detection and identification on a selective agar.

    PubMed

    Bank, Steffen; Nielsen, Hanne Merete; Mathiasen, Boris Hoyer; Leth, Dorte Christiansen; Kristensen, Lena Hagelskjaer; Prag, Jørgen

    2010-12-01

    Within the last decade, Fusobacterium necrophorum subsp. funduliforme has been considered a clinically important pathogen causing pharyngitis especially in adolescents and young adults. F. necrophorum pharyngitis can progress into Lemierre's syndrome, which is a severe and life-threatening infection. However, throat swabs are not cultured anaerobically in the routine and even if cultured anaerobically, it can be difficult to identify F. necrophorum from the normal flora of the throat. F. necrophorum is therefore often overlooked as the cause of pharyngitis. In our laboratory, a F. necrophorum selective agar has been developed containing vancomycin and nalidixin, which inhibit the growth of most Gram-positive and many Gram-negative bacteria, respectively. β-haemolysis of horse blood can be detected, which further facilitates the detection and identification of F. necrophorum. The F. necrophorum selective agar was evaluated against a quantitative real-time polymerase chain reaction assay and shown to have a significantly higher sensitivity for detecting F. necrophorum than the anaerobic agar commonly used in Denmark. Furthermore, the F. necrophorum selective agar does not require experienced laboratory technicians, require fewer subcultures, is probably less expensive and is faster to perform than other culture methods.

  15. Selection of advanced technologies for detection of trucks

    NASA Astrophysics Data System (ADS)

    Middleton, Dan

    1998-01-01

    The North American Free Trade Agreement is anticipated an already increasing trend in highway freight movement across the international border between Texas and Mexico. The Texas Department of Transportation is concerned about safeguarding its motoring public and protection of its highway infrastructure. By sponsoring this research, it hopes to improve traffic signal operations, especially at isolated intersections. Recent advances in sensing technologies and signalization enable safer and more efficient intersection control. This research evaluated advanced detection technologies that can be used to increase green time to trucks and reduce their stops and delays. Equipment selection criteria required devices that were reasonably accurate in classification of vehicles under all weather and lighting conditions and determination of vehicle speeds. The research team selected active IR and passive acoustic technologies. Components of the detection system include: an Industrial PC, proprietary boards inside the computer, IR and acoustic detectors, a pole for mounting the selected systems, and a classifier system using pavement sensors for verification purposes. The purpose of the node computer was to interpret signals from detectors, store data, and communicate with the controller cabinet upon detection of a truck.

  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. Binding-regulated click ligation for selective detection of proteins.

    PubMed

    Cao, Ya; Han, Peng; Wang, Zhuxin; Chen, Weiwei; Shu, Yongqian; Xiang, Yang

    2016-04-15

    Herein, a binding-regulated click ligation (BRCL) strategy for endowing selective detection of proteins is developed with the incorporation of small-molecule ligand and clickable DNA probes. The fundamental principle underlying the strategy is the regulating capability of specific protein-ligand binding against the ligation between clickable DNA probes, which could efficiently combine the detection of particular protein with enormous DNA-based sensing technologies. In this work, the feasibly of the BRCL strategy is first verified through agarose gel electrophoresis and electrochemical impedance spectroscopy measurements, and then confirmed by transferring it to a nanomaterial-assisted fluorescence assay. Significantly, the BRCL strategy-based assay is able to respond to target protein with desirable selectivity, attributing to the specific recognition between small-molecule ligand and its target. Further experiments validate the general applicability of the sensing method by tailoring the ligand toward different proteins (i.e., avidin and folate receptor), and demonstrate its usability in complex biological samples. To our knowledge, this work pioneers the practice of click chemistry in probing specific small-molecule ligand-protein binding, and therefore may pave a new way for selective detection of proteins.

  18. [Evolutionary medicine: an emergent basic science].

    PubMed

    Spotorno, Angel E

    2005-02-01

    Evolutionary Medicine is an emergent basic science that offers new and varied perspectives to the comprehension of human health. The application of classic evolutionary theories (descent with modification, and natural selection) to the human organism, to its pathogens, and their mutual co-evolution, provides new explanations about why we get sick, how we can prevent this, and how we can heal. Medicine has focused mainly on the proximate or immediate causes of diseases and the treatment of symptoms, and very little on its evolutionary or mediate causes. For instance, the present human genome and phenotypes are essentially paleolithic ones: they are not adapted to modern life style, thus favoring the so-called diseases of civilization (ie: ateroesclerosis, senescence, myopia, phobias, panic attacks, stress, reproductive cancers). With the evolutionary approach, post-modern medicine is detecting better the vulnerabilities, restrictions, biases, adaptations and maladaptations of human body, its actual diseases, and its preventions.

  19. 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.

  20. ULTRASENSITIVE HIGH-TEMPERATURE SELECTIVE GAS DETECTION USING PIEZOELECTRIC MICROCANTILEVERS

    SciTech Connect

    Wan Y. Shih; Tejas Patil; Qiang Zhao; Yi-Shi Chiu; Wei-Heng Shih

    2004-03-05

    We have obtained very promising results in the Phase I study. Specifically, for temperature effects, we have established that piezoelectric cantilever sensors could retain their resonance peak strength at high temperatures, i.e., the Q values of the resonance peaks remained above 10 even when the temperature was very close to the Curie temperature. This confirms that a piezoelectric cantilever sensor can be used as a sensor up to its Curie temperature. Furthermore, we have shown that the mass detection sensitivity remained unchanged at different temperatures. For selective gas detection, we have demonstrated selective NH{sub 3} detection using piezoelectric cantilever sensors coated with mesoporous SiO{sub 2}. For high-temperature sensor materials development, we have achieved highly oriented Sr-doped lead titanate thin films that possessed superior dielectric and ferroelectric properties. Such highly oriented films can be microfabricated into high-performance piezoelectric microcantilever sensors that can be used up to 490 C. We have accomplished the goal of Phase I study in exploring the various aspects of a high-temperature gas sensor. We propose to continue the study in Phase II to develop a sensor that is suitable for high-temperature applications using piezoelectrics with a high Curie temperature and by controlling the effects of temperature. The lead titanate based thin film developed in Phase I is good for applications up to 490 C. In phase II, we will develop lithium niobate thin film based cantilevers for applications up to 1000 C.

  1. 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.

  2. Evolutionary Differences in Glycosaminoglycan Fine Structure Detected by Quantitative Glycan Reductive Isotope Labeling*S⃞

    PubMed Central

    Lawrence, Roger; Olson, Sara K.; Steele, Robert E.; Wang, Lianchun; Warrior, Rahul; Cummings, Richard D.; Esko, Jeffrey D.

    2008-01-01

    To facilitate qualitative and quantitative analysis of glycosaminoglycans, we tagged the reducing end of lyase-generated disaccharides with aniline-containing stable isotopes (12C6 and 13C6). Because different isotope tags have no effect on chromatographic retention times but can be discriminated by a mass detector, differentially isotope-tagged samples can be compared simultaneously by liquid chromatography/mass spectrometry and quantified by admixture with known amounts of standards. The technique is adaptable to all types of glycosaminoglycans, and its sensitivity is only limited by the type of mass spectrometer available. We validated the method using commercial heparin and keratan sulfate as well as heparan sulfate isolated from mutant and wild-type Chinese hamster ovary cells, and select tissues from mutant and wild-type mice. This new method provides more robust, reliable, and sensitive means of quantitative evaluation of glycosaminoglycan disaccharide compositions than existing techniques allowing us to compare the chondroitin and heparan sulfate compositions of Hydra vulgaris, Drosophila melanogaster, Caenorhabditis elegans, and mammalian cells. Our results demonstrate significant differences in glycosaminoglycan structure among these organisms that might represent evolutionarily distinct functional motifs. PMID:18818196

  3. 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.

  4. Feature selection on movement imagery discrimination and attention detection

    PubMed Central

    Dias, N. S.; Kamrunnahar, M.; Mendes, P. M.; Schiff, S. J.; Correia, J. H.

    2010-01-01

    Noninvasive brain–computer interfaces (BCI) translate subject's electroencephalogram (EEG) features into device commands. Large feature sets should be down-selected for efficient feature translation. This work proposes two different feature down-selection algorithms for BCI: (a) a sequential forward selection; and (b) an across-group variance. Power rar ratios (PRs) were extracted from the EEG data for movement imagery discrimination. Event-related potentials (ERPs) were employed in the discrimination of cue-evoked responses. While center-out arrows, commonly used in calibration sessions, cued the subjects in the first experiment (for both PR and ERP analyses), less stimulating arrows that were centered in the visual field were employed in the second experiment (for ERP analysis). The proposed algorithms outperformed other three popular feature selection algorithms in movement imagery discrimination. In the first experiment, both algorithms achieved classification errors as low as 12.5% reducing the feature set dimensionality by more than 90%. The classification accuracy of ERPs dropped in the second experiment since centered cues reduced the amplitude of cue-evoked ERPs. The two proposed algorithms effectively reduced feature dimensionality while increasing movement imagery discrimination and detected cue-evoked ERPs that reflect subject attention. PMID:20112135

  5. Nanofluidic redox cycling amplification for the selective detection of catechol.

    PubMed

    Wolfrum, Bernhard; Zevenbergen, Marcel; Lemay, Serge

    2008-02-15

    We have developed a chip-based nanofluidic device to amplify the electrochemical signal of catechols by orders of magnitude. The amplification is based on rapid redox cycling between plane parallel electrodes inside a nanochannel. We show that it is possible to monitor the signal of only a few hundred molecules residing in the active area of the nanofluidic sensor. Furthermore, due to the nanochannel design, the sensor is immune to interference by molecules undergoing irreversible redox reactions. We demonstrate the selectivity of the device by detecting catechol in the presence of ascorbic acid, whose oxidized form is only stable for a short time. The interference of ascorbic acid is usually a challenge in the detection of catecholamines in biological samples.

  6. 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.

  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. Functional Feature Selection by Weighted Projections in Pathological Voice Detection

    NASA Astrophysics Data System (ADS)

    Sánchez Giraldo, Luis; Martínez Tabares, Fernando; Castellanos Domínguez, Germán

    In this paper, we introduce an adaptation of a multivariate feature selection method to deal with functional features. In our case, observations are described by a set of functions defined over a common domain (e.g. a time interval). The feature selection method consists on combining variable weighting with a feature extraction projection. Although the employed method was primarily intended for observations described by vectors in ℝ n , we propose a simple extension that allows us to select a set of functional features, which is well suited for classification. This study is complemented by the incorporation of Functional Principal Component Analysis (FPCA) that project functions into a finite dimensional space were we can perform classification easily. Another remarkable property of FPCA is that it can provide insight about the nature of the functional features. The proposed algorithms are tested on a pathological voice detection task. Two databases are considered: Massachusetts Eye and Ear Infirmary Voice Laboratory voice disorders database and Universidad Politécnica de Madrid voice database. As a result, we obtain a canonical function whose time average is enough to reach similar performances to the ones reported in the literature.

  9. 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

  10. Selective TERS detection and imaging through controlled plasmonics.

    PubMed

    Wang, Hao; Carrier, Stacey L; Park, Sheldon; Schultz, Zachary D

    2015-01-01

    Enhanced Raman spectroscopy offers capabilities to detect molecules in the complex molecular environments and image chemical heterogeneity in a wide range of samples. It has been shown that plasmonic interactions between a TERS tip and a metal surface produce significant enhancements. In this report we show how SERS spectra from purified molecules can be used to selectively image proteins on surfaces and in cell membranes. The SERS response from the purified protein can be used to create a multivariate regression model that can be applied to nanoparticles that bind to protein receptors. Filtering the observed TERS spectra with the regression model can then selectively image the protein receptor. Experiments with mutant proteins suggest that key amino acids provide significant contributions to the observed TERS signal, which enables the differentiation of protein receptors. These results demonstrate the selectivity that can be obtained in TERS images through a controlled plasmonic interaction. This approach has further implications for identifying membrane receptors that bind specific molecules relevant to drug targeting and chemical signaling.

  11. 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.

  12. 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).

  13. Detecting recent selective sweeps while controlling for mutation rate and background selection.

    PubMed

    Huber, Christian D; DeGiorgio, Michael; Hellmann, Ines; Nielsen, Rasmus

    2016-01-01

    A composite likelihood ratio test implemented in the program sweepfinder is a commonly used method for scanning a genome for recent selective sweeps. sweepfinder uses information on the spatial pattern (along the chromosome) of the site frequency spectrum around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power to detect and localize selective sweeps can be greatly improved if invariable sites are also included in the analysis. In the spirit of a Hudson-Kreitman-Aguadé test, we suggest adding fixed differences relative to an out-group to account for variation in mutation rate, thereby facilitating more robust and powerful analyses. We also develop a method for including background selection, modelled as a local reduction in the effective population size. Using simulations, we show that these advances lead to a gain in power while maintaining robustness to mutation rate variation. Furthermore, the new method also provides more precise localization of the causative mutation than methods using the spatial pattern of segregating sites alone. PMID:26290347

  14. 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

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

    PubMed

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

    2010-09-01

    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. 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.

  17. Active link selection for efficient semi-supervised community detection.

    PubMed

    Yang, Liang; Jin, Di; Wang, Xiao; Cao, Xiaochun

    2015-01-01

    Several semi-supervised community detection algorithms have been proposed recently to improve the performance of traditional topology-based methods. However, most of them focus on how to integrate supervised information with topology information; few of them pay attention to which information is critical for performance improvement. This leads to large amounts of demand for supervised information, which is expensive or difficult to obtain in most fields. For this problem we propose an active link selection framework, that is we actively select the most uncertain and informative links for human labeling for the efficient utilization of the supervised information. We also disconnect the most likely inter-community edges to further improve the efficiency. Our main idea is that, by connecting uncertain nodes to their community hubs and disconnecting the inter-community edges, one can sharpen the block structure of adjacency matrix more efficiently than randomly labeling links as the existing methods did. Experiments on both synthetic and real networks demonstrate that our new approach significantly outperforms the existing methods in terms of the efficiency of using supervised information. It needs ~13% of the supervised information to achieve a performance similar to that of the original semi-supervised approaches. PMID:25761385

  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. PMID:27081680

  19. Evolutionary biology of language.

    PubMed Central

    Nowak, M A

    2000-01-01

    Language is the most important evolutionary invention of the last few million years. It was an adaptation that helped our species to exchange information, make plans, express new ideas and totally change the appearance of the planet. How human language evolved from animal communication is one of the most challenging questions for evolutionary biology The aim of this paper is to outline the major principles that guided language evolution in terms of mathematical models of evolutionary dynamics and game theory. I will discuss how natural selection can lead to the emergence of arbitrary signs, the formation of words and syntactic communication. PMID:11127907

  20. Photo-SRM: laser-induced dissociation improves detection selectivity of Selected Reaction Monitoring mode.

    PubMed

    Enjalbert, Quentin; Simon, Romain; Salvador, Arnaud; Antoine, Rodolphe; Redon, Sébastien; Ayhan, Mehmet Menaf; Darbour, Florence; Chambert, Stéphane; Bretonnière, Yann; Dugourd, Philippe; Lemoine, Jérôme

    2011-11-30

    Selected Reaction Monitoring (SRM) carried out on triple-quadrupole mass spectrometers coupled to liquid chromatography has been a reference method to develop quantitative analysis of small molecules in biological or environmental matrices for years and is currently emerging as a promising tool in clinical proteomic. However, sensitive assays in complex matrices are often hampered by the presence of co-eluted compounds that share redundant transitions with the target species. On-the-fly better selection of the precursor ion by high-field asymmetric waveform ion mobility spectrometry (FAIMS) or increased quadrupole resolution is one way to escape from interferences. In the present work we document the potential interest of substituting classical gas-collision activation mode by laser-induced dissociation in the visible wavelength range to improve the specificity of the fragmentation step. Optimization of the laser beam pathway across the different quadrupoles to ensure high photo-dissociation yield in Q2 without detectable fragmentation in Q1 was assessed with sucrose tagged with a push-pull chromophore. Next, the proof of concept that photo-SRM ensures more specific detection than does conventional collision-induced dissociation (CID)-based SRM was carried out with oxytocin peptide. Oxytocin was derivatized by the thiol-reactive QSY® 7 C(5)-maleimide quencher on cysteine residues to shift its absorption property into the visible range. Photo-SRM chromatograms of tagged oxytocin spiked in whole human plasma digest showed better detection specificity and sensitivity than CID, that resulted in extended calibration curve linearity. We anticipate that photo-SRM might significantly improve the limit of quantification of classical SRM-based assays targeting cysteine-containing peptides. PMID:22002689

  1. [Detection and analysis of Tetrahymena pyriformis 26S ribosomal DNA domain sequences, differing in degree of evolutionary conservation].

    PubMed

    Mukha, D V; Sidorenko, A P

    1995-01-01

    Domains of different evolutionary conservatism were defined in the 26S rDNA sequence of T. pyriformis. The fragment of studied DNA (1212 bp) showing high evolutionary conservatism was cloned. It was shown this fragment of DNA may be used to a probe for blot-hybridization analysis of the structure of rDNA from various taxa, protists to mammals. Superconservative and hypervariable domains were defined. The first are good for the primers for PCR analysis of rDNA from various taxa, the second--for species specific primers.

  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. 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.

  4. Fluorescent Peptide Beacons for the Selective Ratiometric Detection of Heparin.

    PubMed

    Maity, Debabrata; Schmuck, Carsten

    2016-09-01

    Heparin is extensively used as an anticoagulant drug during surgery. Two fluorophore-functionalized cationic oligopeptides HS 1 and HS 2 were developed to monitor heparin ratiometrically in aqueous media. Upon binding to heparin, HS 1 and HS 2 undergo a conformational change from an open form to a folded form, which leads to a distinct change in the fluorescence properties. HS 1 switches from pyrene monomer emission to an excimer emission. For HS 2, a fluorescence resonance energy transfer (FRET) process is enabled between a naphthalene donor and a dansyl acceptor. This method is highly selective for heparin relative to other similar biological analytes such as hyaluronic acid or chondroitin sulfate. HS 1 and HS 2 could also detect heparin ratiometrically in diluted bovine serum. The strong ratiometric emission color change can also be observed by the naked eye. Addition of the polycationic protein protamine releases both HS 1 and HS 2 from their heparin complex, which simultaneously restores pyrene monomer emission for the first case and decreases the FRET process for the latter case, respectively. Dynamic light scattering (DLS) and AFM studies confirm aggregate formation of heparin with HS 1 and HS 2. PMID:27534383

  5. Fluorescent Peptide Beacons for the Selective Ratiometric Detection of Heparin.

    PubMed

    Maity, Debabrata; Schmuck, Carsten

    2016-09-01

    Heparin is extensively used as an anticoagulant drug during surgery. Two fluorophore-functionalized cationic oligopeptides HS 1 and HS 2 were developed to monitor heparin ratiometrically in aqueous media. Upon binding to heparin, HS 1 and HS 2 undergo a conformational change from an open form to a folded form, which leads to a distinct change in the fluorescence properties. HS 1 switches from pyrene monomer emission to an excimer emission. For HS 2, a fluorescence resonance energy transfer (FRET) process is enabled between a naphthalene donor and a dansyl acceptor. This method is highly selective for heparin relative to other similar biological analytes such as hyaluronic acid or chondroitin sulfate. HS 1 and HS 2 could also detect heparin ratiometrically in diluted bovine serum. The strong ratiometric emission color change can also be observed by the naked eye. Addition of the polycationic protein protamine releases both HS 1 and HS 2 from their heparin complex, which simultaneously restores pyrene monomer emission for the first case and decreases the FRET process for the latter case, respectively. Dynamic light scattering (DLS) and AFM studies confirm aggregate formation of heparin with HS 1 and HS 2.

  6. 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. PMID:26971273

  7. 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

  8. 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.

  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 Theory of Mate Selection and Partners of Trans People: A Qualitative Study Using Interpretative Phenomenological Analysis

    ERIC Educational Resources Information Center

    Forde, Amanda

    2011-01-01

    Despite much research into mate selection, non-heterosexual populations are often only included for comparison purposes, while trans people and their partners are overlooked. This study attempts to address this using qualitative methodology to explore the mate selection of the partners of trans people. Six participants were recruited from online…

  11. 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

  12. SNP detection from de novo transcriptome sequencing in the bivalve Macoma balthica: marker development for evolutionary studies.

    PubMed

    Pante, Eric; Rohfritsch, Audrey; 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 [Formula: see text] 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

  13. 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.

  14. Detecting signatures of selection from DNA sequences using Datamonkey.

    PubMed

    Poon, Art F Y; Frost, Simon D W; Pond, Sergei L Kosakovsky

    2009-01-01

    Natural selection is a fundamental process affecting all evolving populations. In the simplest case, positive selection increases the frequency of alleles that confer a fitness advantage relative to the rest of the population, or increases its genetic diversity, and negative selection removes those alleles that are deleterious. Codon-based models of molecular evolution are able to infer signatures of selection from alignments of homologous sequences by estimating the relative rates of synonymous (dS) and non-synonymous substitutions (dN). Datamonkey (http://www.datamonkey.org) provides a user-friendly web interface to a wide collection of state-of-the-art statistical techniques for estimating dS and dN and identifying codons and lineages under selection, even in the presence of recombinant sequences.

  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. 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.

  17. Child Development and Evolutionary Psychology.

    ERIC Educational Resources Information Center

    Bjorklund, David F.; Pellegrini, Anthony D.

    2000-01-01

    Argues that an evolutionary account provides insight into developmental function and individual differences. Outlines some assumptions of evolutionary psychology related to development. Introduces the developmental systems approach, differential influence of natural selection at different points in ontogeny, and development of evolved…

  18. Origins of evolutionary transitions.

    PubMed

    Clarke, Ellen

    2014-04-01

    An 'evolutionary transition in individuality' or 'major transition' is a transformation in the hierarchical level at which natural selection operates on a population. In this article I give an abstract (i.e. level-neutral and substrate-neutral) articulation of the transition process in order to precisely understand how such processes can happen, especially how they can get started. PMID:24736161

  19. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology.

    PubMed

    Delport, Wayne; Poon, Art F Y; Frost, Simon D W; Kosakovsky Pond, Sergei L

    2010-10-01

    Datamonkey is a popular web-based suite of phylogenetic analysis tools for use in evolutionary biology. Since the original release in 2005, we have expanded the analysis options to include recently developed algorithmic methods for recombination detection, evolutionary fingerprinting of genes, codon model selection, co-evolution between sites, identification of sites, which rapidly escape host-immune pressure and HIV-1 subtype assignment. The traditional selection tools have also been augmented to include recent developments in the field. Here, we summarize the analyses options currently available on Datamonkey, and provide guidelines for their use in evolutionary biology. Availability and documentation: http://www.datamonkey.org.

  20. Role of selective sorption in chemiresistor sensors for organophosphorus detection

    SciTech Connect

    Grate, J.W.; Klusty, M.; Barger, W.R.; Snow, A.W. )

    1990-09-15

    Nickel, palladium, platinum, and copper tetrakis(cumylphenoxy)phthalocyanines were combined with an elastomeric, oligomeric fluoropolyol material in mixed Langmuir-Blodgett films on chemiresistor sensors for organophosphorus vapors. The phthalocyanine carried the electronic current, while the fluoropolyol improved the sorption characteristics of the film. This strategy produced sensors with improved response and recovery times and high sensitivity. Factors influencing the selectivity of the sensor responses were analyzed in terms of two steps: sorption and transduction. Sorption was shown to be the primary determinant of selectivity among the organic vapors tested.

  1. 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.

  2. 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.

  3. Optical turn-on sensor based on graphene oxide for selective detection of D-glucosamine.

    PubMed

    Cheng, Rumei; Liu, Yong; Ou, Shengju; Pan, Yaqiong; Zhang, Shu; Chen, Hao; Dai, Liming; Qu, Jia

    2012-07-01

    By incorporating the well-known fluorophore 8-aminoquinoline into graphene oxide, we have successfully prepared a turn-on fluorescent sensor capable of specific detection of D-glucosamine with a high selectivity and sensitivity. This methodology provides a new concept for the design and development of highly selective and sensitive turn-on optical sensors for selective detection of aminosaccharides and many other biomolecules. PMID:22655914

  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. 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

  6. 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…

  7. Evolutionary awareness.

    PubMed

    Gorelik, Gregory; Shackelford, Todd K

    2014-08-27

    In this article, we advance the concept of "evolutionary awareness," a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities-which we refer to as "intergenerational extended phenotypes"-by helping us to construct a better future for ourselves, for other sentient beings, and for our environment.

  8. 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

  9. How competition affects evolutionary rescue

    PubMed Central

    Osmond, Matthew Miles; de Mazancourt, Claire

    2013-01-01

    Populations facing novel environments can persist by adapting. In nature, the ability to adapt and persist will depend on interactions between coexisting individuals. Here we use an adaptive dynamic model to assess how the potential for evolutionary rescue is affected by intra- and interspecific competition. Intraspecific competition (negative density-dependence) lowers abundance, which decreases the supply rate of beneficial mutations, hindering evolutionary rescue. On the other hand, interspecific competition can aid evolutionary rescue when it speeds adaptation by increasing the strength of selection. Our results clarify this point and give an additional requirement: competition must increase selection pressure enough to overcome the negative effect of reduced abundance. We therefore expect evolutionary rescue to be most likely in communities which facilitate rapid niche displacement. Our model, which aligns to previous quantitative and population genetic models in the absence of competition, provides a first analysis of when competitors should help or hinder evolutionary rescue. PMID:23209167

  10. 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.

  11. Arrays of dual nanomechanical resonators for selective biological detection.

    PubMed

    Ramos, Daniel; Arroyo-Hernández, María; Gil-Santos, Eduardo; Tong, Hien Duy; Van Rijn, Cees; Calleja, Montserrat; Tamayo, Javier

    2009-03-15

    Arrays of small nanomechanical resonators with dual geometry have been fabricated for sensitive biological detection. The arrays consist of silicon nitride resonating 100 nm thick cantilevers with sensing gold areas alternately placed on the free and fixed cantilever ends. The Au areas act as sensing regions as can be functionalized by means of thiol chemistry. The nanomechanical arrays provide a double flavor of the adsorbed molecules: the added mass reported by the cantilevers with the Au area at the tip and the nanoscale elasticity reported by the cantilevers with the Au area at the clamp. The devices were applied for DNA detection based on Watson-Crick pairing rules. The proposed design for nanomechanical resonators provides higher specificity for DNA sensing in comparison with conventional single cantilevers. The nanoscale elasticity induced by the DNA hybridization arises from the intermolecular interactions between the adsorbates bound to the cantilever and the surface stress.

  12. 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.

  13. Reagent Selection Methodology for a Novel Explosives Detection Platform

    SciTech Connect

    2010-06-01

    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.

  14. A selective-differential medium for detection of Streptococcus agalactiae.

    PubMed

    Guthrie, R K; Brunson, K W; Stiles, J C

    1968-01-01

    A practical culture medium which allows direct plating of milk samples for detection and differentiation of Streptococcus agalactiae within 48 hours is described. Most other micro-organisms likely to be present in these samples are inhibited. Although some strains of Staphylococcus species and ofStreptococcus faecalis are able to grow, they may be differentiated on the basis of reaction in the medium surrounding the colonies.

  15. Feature Selection and Pedestrian Detection Based on Sparse Representation.

    PubMed

    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

  16. 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

  17. The Evolving Theory of Evolutionary Radiations.

    PubMed

    Simões, M; Breitkreuz, L; Alvarado, M; Baca, S; Cooper, J C; Heins, L; Herzog, K; Lieberman, B S

    2016-01-01

    Evolutionary radiations have intrigued biologists for more than 100 years, and our understanding of the patterns and processes associated with these radiations continues to grow and evolve. Recently it has been recognized that there are many different types of evolutionary radiation beyond the well-studied adaptive radiations. We focus here on multifarious types of evolutionary radiations, paying special attention to the abiotic factors that might trigger diversification in clades. We integrate concepts such as exaptation, species selection, coevolution, and the turnover-pulse hypothesis (TPH) into the theoretical framework of evolutionary radiations. We also discuss other phenomena that are related to, but distinct from, evolutionary radiations that have relevance for evolutionary biology.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. Fluorescent Cancer-Selective Alkylphosphocholine Analogs For Intraoperative Glioma Detection

    PubMed Central

    Swanson, Kyle I.; Clark, Paul A.; Zhang, Ray R.; Kandela, Irawati K.; Farhoud, Mohammed; Weichert, Jamey P.; Kuo, John S.

    2015-01-01

    Background 5-ALA induced tumor fluorescence aids brain tumor resections but is not approved for routine use in the United States. We developed and describe testing of two novel fluorescent, cancer-selective alkylphosphocholine analogs, CLR1501 (green) and CLR1502 (near-infrared), in a proof-of-principle study for fluorescence-guided glioma surgery. Objective To demonstrate CLR1501 and CLR1502 are cancer cell-selective fluorescence agents in glioblastoma models and compare tumor (T) to normal brain (N) fluorescence ratios with 5-ALA. Methods CLR1501, CLR1502, 5-ALA were administered to mice with MRI-verified orthotopic U251 GBM and GSC-derived xenografts. Harvested brains were imaged using confocal microscopy (CLR1501), IVIS Spectrum imaging system (CLR1501, CLR1502, and 5-ALA), or Fluobeam near-infrared fluorescence imaging system (CLR1502). Imaging and quantitative analysis of T:N fluorescence ratios were performed. Results Excitation/emission peaks are 500/517nm for CLR1501, and 760/778nm for CLR1502. The observed T:N ratio of CLR1502 (9.28±1.08) was significantly higher (p<0.01) than CLR1501 (3.51±0.44 on confocal imaging; 7.23±1.63 on IVIS imaging) and 5-ALA (4.81±0.92). Near-infrared Fluobeam CLR1502 imaging in a mouse xenograft model demonstrated high contrast tumor visualization compatible with surgical applications. Conclusion CLR1501 (green) and CLR1502 (near infrared) are novel tumor-selective fluorescent agents for discriminating tumor from normal brain. CLR1501 exhibits a tumor to brain fluorescence ratio similar to 5-ALA, whereas CLR1502 has a superior tumor to brain fluorescence ratio. This study demonstrates the potential use of CLR1501 and CLR1502 in fluorescence-guided tumor surgery. PMID:25549194

  3. Evolutionary medicine.

    PubMed

    Swynghedauw, B

    2004-04-01

    Nothing in biology makes sense except in the light of evolution. Evolutionary, or darwinian, medicine takes the view that contemporary diseases result from incompatibility between the conditions under which the evolutionary pressure had modified our genetic endowment and the lifestyle and dietary habits in which we are currently living, including the enhanced lifespan, the changes in dietary habits and the lack of physical activity. An evolutionary trait express a genetic polymorphism which finally improve fitness, it needs million years to become functional. A limited genetic diversity is a necessary prerequisite for evolutionary medicine. Nevertheless, search for a genetic endowment would become nearly impossible if the human races were genetically different. From a genetic point of view, homo sapiens, is homogeneous, and the so-called human races have only a socio-economic definition. Historically, Heart Failure, HF, had an infectious origin and resulted from mechanical overload which triggered mechanoconversion by using phylogenically ancient pleiotropic pathways. Adaptation was mainly caused by negative inotropism. Recently, HF was caused by a complex remodelling caused by the trophic effects of mechanics, ischemia, senescence, diabetes and, neurohormones. The generally admitted hypothesis is that cancers were largely caused by a combination of modern reproductive and dietary lifestyles mismatched with genotypic traits, plus the longer time available for a confrontation. Such a concept is illustrated for skin and breast cancers, and also for the link between cancer risk and dietary habits.

  4. Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach.

    PubMed

    Stern, Adi; Doron-Faigenboim, Adi; Erez, Elana; Martz, Eric; Bacharach, Eran; Pupko, Tal

    2007-07-01

    Biologically significant sites in a protein may be identified by contrasting the rates of synonymous (K(s)) and non-synonymous (K(a)) substitutions. This enables the inference of site-specific positive Darwinian selection and purifying selection. We present here Selecton version 2.2 (http://selecton.bioinfo.tau.ac.il), a web server which automatically calculates the ratio between K(a) and K(s) (omega) at each site of the protein. This ratio is graphically displayed on each site using a color-coding scheme, indicating either positive selection, purifying selection or lack of selection. Selecton implements an assembly of different evolutionary models, which allow for statistical testing of the hypothesis that a protein has undergone positive selection. Specifically, the recently developed mechanistic-empirical model is introduced, which takes into account the physicochemical properties of amino acids. Advanced options were introduced to allow maximal fine tuning of the server to the user's specific needs, including calculation of statistical support of the omega values, an advanced graphic display of the protein's 3-dimensional structure, use of different genetic codes and inputting of a pre-built phylogenetic tree. Selecton version 2.2 is an effective, user-friendly and freely available web server which implements up-to-date methods for computing site-specific selection forces, and the visualization of these forces on the protein's sequence and structure.

  5. 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

  6. 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

  7. 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.

  8. 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

    2016-01-01

    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

  9. 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.

  10. TIR fluorescence reader for selective detection of cell membranes

    NASA Astrophysics Data System (ADS)

    Bruns, Thomas; Strauss, Wolfgang S. L.; Sailer, Reinhard; Wagner, Michael; Schneckenburger, Herbert

    2005-08-01

    A novel setup for fluorescence measurements of surfaces of biological samples, in particular cell membranes, is described. The method is based on multiple total internal reflections (TIR) of a laser beam at the surface of a multi-well plate, such that 96 individual samples are excited simultaneously. Main prerequisites are an appropriate thickness and high transmission of the glass bottom, a non-cytotoxic adhesive, and appropriate glass rods for TIR illumination. Fluorescence from the cell surface is detected simultaneously using an integrating CCD camera and appropriate optical filters. For validation of the system, cells incubated with the fluorescence marker NBD as well as transfected cells expressing a fluorescent membrane protein are used. In addition, intracellular translocation of a fluorescent protein kinase c fusion protein upon stimulation is examined. The method appears well suitable for high throughput screening (HTS), since neither washing of the samples nor any readjustment of the equipment after changing of individual plates are necessary.

  11. Urban Detection, Delimitation and Morphology: Comparative Analysis of Selective "MEGACITIES"

    NASA Astrophysics Data System (ADS)

    Alhaddad, B.; Arellano, B. E.; Roca, J.

    2012-08-01

    Over the last 50 years, the world has faced an impressive growth of urban population. The walled city, close to the outside, an "island"for economic activities and population density within the rural land, has led to the spread of urban life and urban networks in almost all the territory. There was, as said Margalef (1999), "a topological inversion of the landscape". The "urban" has gone from being an island in the ocean of rural land vastness, to represent the totally of the space in which are inserted natural and rural "systems". New phenomena such as the fall of the fordist model of production, the spread of urbanization known as urban sprawl, and the change of scale of the metropolis, covering increasingly large regions, called "megalopolis" (Gottmann, 1961), have characterized the century. However there are no rigorous databases capable of measuring and evaluating the phenomenon of megacities and in general the process of urbanization in the contemporary world. The aim of this paper is to detect, identify and analyze the morphology of the megacities through remote sensing instruments as well as various indicators of landscape. To understand the structure of these heterogeneous landscapes called megacities, land consumption and spatial complexity needs to be quantified accurately. Remote sensing might be helpful in evaluating how the different land covers shape urban megaregions. The morphological landscape analysis allows establishing the analogies and the differences between patterns of cities and studying the symmetry, growth direction, linearity, complexity and compactness of the urban form. The main objective of this paper is to develop a new methodology to detect urbanized land of some megacities around the world (Tokyo, Mexico, Chicago, New York, London, Moscow, Sao Paulo and Shanghai) using Landsat 7 images.

  12. 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.

  13. 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

  14. 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

  15. 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

  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. PMID:20420525

  17. Detection of bacterioplankton in immersed cadavers using selective agar plates.

    PubMed

    Kakizaki, Eiji; Kozawa, Shuji; Tashiro, Noriko; Sakai, Masahiro; Yukawa, Nobuhiro

    2009-04-01

    We measured bacterioplankton in blood from cadavers retrieved from the sea (n=12), near estuaries (n=4), rivers (fresh water, n=8) and from bathtubs (n=4) as well as from non-drowned victims (n=10) discovered near aquatic environments. Blood from 11 victims drowned in seawater developed bioluminescent and/or blue colonies (oxidase test positive) on selective media containing 2-4% NaCl. Homology analyses of the 16S rRNA gene showed that all of them were marine bacteria (genera: Photobacterium, Vibrio, Shewanella, Psychrobacter). Blood from all victims drowned in rivers generated blue colonies on plates containing 3%, but not 4% NaCl. Homology analyses showed that the blue colonies were generated from bacteria that inhabit fresh water (Aeromonas). None of the blood samples from victims that drowned in bathtubs generated bioluminescent and blue colonies. However, all cadavers contained bacteria that produced unstained colonies (Staphylococcus, Bacillus, Enterobacter, Escherichia, etc.). Among non-drowned victims, blood from two gave rise to blue colonies on plates containing < or =3% NaCl (Pseudomonas). Of the cadavers found near estuaries, bioluminescent and blue colonies developed from two of them on media containing 2-4% NaCl (Photobacterium, Vibrio, Listonella), but not from two others on plates containing 4% NaCl (at < or =3%; blue colonies, Aeromonas; unstained colonies, Citrobacter, Vagococcus, Proteus, Enterobacter). These results suggested that the presence of numerous bacterioplankton in immersed cadavers could support a conclusion of death by drowning.

  18. 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.

  19. 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.

  20. 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

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

    PubMed

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

    2016-01-01

    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

  2. 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

  3. 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. PMID:17192975

  4. 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.

  5. Evolutionary biology of cancer.

    PubMed

    Crespi, Bernard; Summers, Kyle

    2005-10-01

    Cancer is driven by the somatic evolution of cell lineages that have escaped controls on replication and by the population-level evolution of genes that influence cancer risk. We describe here how recent evolutionary ecological studies have elucidated the roles of predation by the immune system and competition among normal and cancerous cells in the somatic evolution of cancer. Recent analyses of the evolution of cancer at the population level show how rapid changes in human environments have augmented cancer risk, how strong selection has frequently led to increased cancer risk as a byproduct, and how anticancer selection has led to tumor-suppression systems, tissue designs that slow somatic evolution, constraints on morphological evolution and even senescence itself. We discuss how applications of the tools of ecology and evolutionary biology are poised to revolutionize our understanding and treatment of this disease.

  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. BODIPY based colorimetric fluorescent probe for selective thiophenol detection: theoretical and experimental studies.

    PubMed

    Kand, Dnyaneshwar; Mishra, Pratyush Kumar; Saha, Tanmoy; Lahiri, Mayurika; Talukdar, Pinaki

    2012-09-01

    A BODIPY-based selective thiophenol probe capable of discriminating aliphatic thiols is reported. The fluorescence off-on effect upon reaction with thiol is elucidated with theoretical calculations. The sensing of thiophenol is associated with a color change from red to yellow and 63-fold enhancement in green fluorescence. Application of the probe for selective thiophenol detection is demonstrated by live cell imaging.

  8. Selective detection and characterization of nanoparticles from motor vehicles.

    PubMed

    Johnston, Murray V; Klems, Joseph P; Zordan, Christopher A; Pennington, M Ross; Smith, James N

    2013-02-01

    distance or transit time from emission to sampling increased, the size distribution shifted to a larger particle size, which confirmed the source assignments. To determine the distribution of emissions from individual vehicles, we correlated camera images with the spike contribution to particle number concentration at each time point. A small percentage of motor vehicles were found to emit a disproportionally large concentration of nanoparticles, and these high emitters included both spark-ignition (SI) and heavy-duty diesel (HDD) vehicles. In addition to characterizing the contribution of the spikes (local sources) to the ambient number concentration, we developed a method to determine the net contribution of motor vehicles (all sources) to the total mass concentration of ambient nanoparticles. To do this, we correlated the concentration of spikes with measurements of fast changes in the chemical composition of nanoparticles measured with the nano aerosol mass spectrometer (NAMS; built by the Johnston group). The NAMS irradiates individual, size-selected nanoparticles with a high-energy laser pulse to generate a mass spectrum consisting of multiply charged atomic ions. The elemental composition of each particle was determined from the ion signal intensities of each element. However, overlapping mass-to-charge ratios (m/z) at 4 m/z (O(+4) and C(+3)) and at 8 m/z (O(+2) and S(+4)) needed to be separated into their component ions to obtain a representative composition. To do this, we developed a method to deconvolute these ion signals using sucrose and ammonium sulfate [(NH4)2SO4] as calibration standards. With this approach, the differences between the expected and measured elemental mole fractions of carbon (C), oxygen (O), nitrogen (N), and sulfur (S) for a variety of test particles were generally much less than 10%. Ambient nanoparticles were found to consist mostly of C, O, N, and S. Many particles also contained silicon (Si). The elemental compositions were apportioned

  9. Evolutionary Conservation of Orthoretroviral Long Terminal Repeats (LTRs) and ab initio Detection of Single LTRs in Genomic Data

    PubMed Central

    Benachenhou, Farid; Jern, Patric; Oja, Merja; Sperber, Göran; Blikstad, Vidar; Somervuo, Panu; Kaski, Samuel; Blomberg, Jonas

    2009-01-01

    Background Retroviral LTRs, paired or single, influence the transcription of both retroviral and non-retroviral genomic sequences. Vertebrate genomes contain many thousand endogenous retroviruses (ERVs) and their LTRs. Single LTRs are difficult to detect from genomic sequences without recourse to repetitiveness or presence in a proviral structure. Understanding of LTR structure increases understanding of LTR function, and of functional genomics. Here we develop models of orthoretroviral LTRs useful for detection in genomes and for structural analysis. Principal Findings Although mutated, ERV LTRs are more numerous and diverse than exogenous retroviral (XRV) LTRs. Hidden Markov models (HMMs), and alignments based on them, were created for HML- (human MMTV-like), general-beta-, gamma- and lentiretroviruslike LTRs, plus a general-vertebrate LTR model. Training sets were XRV LTRs and RepBase LTR consensuses. The HML HMM was most sensitive and detected 87% of the HML LTRs in human chromosome 19 at 96% specificity. By combining all HMMs with a low cutoff, for screening, 71% of all LTRs found by RepeatMasker in chromosome 19 were found. HMM consensus sequences had a conserved modular LTR structure. Target site duplications (TG-CA), TATA (occasionally absent), an AATAAA box and a T-rich region were prominent features. Most of the conservation was located in, or adjacent to, R and U5, with evidence for stem loops. Several of the long HML LTRs contained long ORFs inserted after the second A rich module. HMM consensus alignment allowed comparison of functional features like transcriptional start sites (sense and antisense) between XRVs and ERVs. Conclusion The modular conserved and redundant orthoretroviral LTR structure with three A-rich regions is reminiscent of structurally relaxed Giardia promoters. The five HMMs provided a novel broad range, repeat-independent, ab initio LTR detection, with prospects for greater generalisation, and insight into LTR structure, which may

  10. Optimal Intermittence in Search Strategies under Speed-Selective Target Detection

    NASA Astrophysics Data System (ADS)

    Campos, Daniel; Méndez, Vicenç; Bartumeus, Frederic

    2012-01-01

    Random search theory has been previously explored for both continuous and intermittent scanning modes with full target detection capacity. Here we present a new class of random search problems in which a single searcher performs flights of random velocities, the detection probability when it passes over a target location being conditioned to the searcher speed. As a result, target detection involves an N-passage process for which the mean search time is here analytically obtained through a renewal approximation. We apply the idea of speed-selective detection to random animal foraging since a fast movement is known to significantly degrade perception abilities in many animals. We show that speed-selective detection naturally introduces an optimal level of behavioral intermittence in order to solve the compromise between fast relocations and target detection capability.

  11. Selective detection and characterization of nanoparticles from motor vehicles.

    PubMed

    Johnston, Murray V; Klems, Joseph P; Zordan, Christopher A; Pennington, M Ross; Smith, James N

    2013-02-01

    distance or transit time from emission to sampling increased, the size distribution shifted to a larger particle size, which confirmed the source assignments. To determine the distribution of emissions from individual vehicles, we correlated camera images with the spike contribution to particle number concentration at each time point. A small percentage of motor vehicles were found to emit a disproportionally large concentration of nanoparticles, and these high emitters included both spark-ignition (SI) and heavy-duty diesel (HDD) vehicles. In addition to characterizing the contribution of the spikes (local sources) to the ambient number concentration, we developed a method to determine the net contribution of motor vehicles (all sources) to the total mass concentration of ambient nanoparticles. To do this, we correlated the concentration of spikes with measurements of fast changes in the chemical composition of nanoparticles measured with the nano aerosol mass spectrometer (NAMS; built by the Johnston group). The NAMS irradiates individual, size-selected nanoparticles with a high-energy laser pulse to generate a mass spectrum consisting of multiply charged atomic ions. The elemental composition of each particle was determined from the ion signal intensities of each element. However, overlapping mass-to-charge ratios (m/z) at 4 m/z (O(+4) and C(+3)) and at 8 m/z (O(+2) and S(+4)) needed to be separated into their component ions to obtain a representative composition. To do this, we developed a method to deconvolute these ion signals using sucrose and ammonium sulfate [(NH4)2SO4] as calibration standards. With this approach, the differences between the expected and measured elemental mole fractions of carbon (C), oxygen (O), nitrogen (N), and sulfur (S) for a variety of test particles were generally much less than 10%. Ambient nanoparticles were found to consist mostly of C, O, N, and S. Many particles also contained silicon (Si). The elemental compositions were apportioned

  12. 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.

  13. Selective detection of 5-formyl-2'-deoxycytidine in DNA using a fluorogenic hydroxylamine reagent.

    PubMed

    Guo, Pu; Yan, Shengyong; Hu, Jianlin; Xing, Xiwen; Wang, Changcheng; Xu, Xiaowei; Qiu, Xiaoyu; Ma, Wen; Lu, Chunjiang; Weng, Xiaocheng; Zhou, Xiang

    2013-07-01

    Fluorogenic hydroxylamine reagents were used for detecting 5-fC through a labeling pathway. Chemical synthesis, HPLC, denaturing PAGE, and DNA MS were applied to testify that the probe reacted with 5-fC with oligodeoxynucleotide selectivity to achieve 5-fC detection conveniently and quantificationally with the method of fluorescence. The feasibility of fluorescently detecting 5-fC in a genome was also investigated.

  14. A naphthalimide based PET probe with Fe3+ selective detection ability: theoretical and experimental study.

    PubMed

    Chereddy, Narendra Reddy; Niladri Raju, M V; Nagaraju, Peethani; Krishnaswamy, Venkat Raghavan; Korrapati, Purna Sai; Bangal, Prakriti Ranjan; Rao, Vaidya Jayathirtha

    2014-12-21

    A naphthalimide based fluorescent probe '1' that operates based on photoinduced electron transfer phenomenon is synthesized and its chemosensory application is explored. Among various metal ions, 1 selectively detects Fe(3+) with a detection limit of 3.0 × 10(-8) M. 1 is stable at physiological pH, nontoxic under experimental conditions and suitable for the detection of Fe(3+) ions present in aqueous samples and live cells. PMID:25340936

  15. 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

  16. 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

  17. 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

  18. A New Multiplex-PCR for Urinary Tract Pathogen Detection Using Primer Design Based on an Evolutionary Computation Method.

    PubMed

    García, Liliana Torcoroma; Cristancho, Laura Maritza; Vera, Erika Patricia; Begambre, Oscar

    2015-10-01

    This work describes a new strategy for optimal design of Multiplex-PCR primer sequences. The process is based on the Particle Swarm Optimization-Simplex algorithm (Mult-PSOS). Diverging from previous solutions centered on heuristic tools, the Mult-PSOS is selfconfigured because it does not require the definition of the algorithm's initial search parameters. The successful performance of this method was validated in vitro using Multiplex- PCR assays. For this validation, seven gene sequences of the most prevalent bacteria implicated in urinary tract infections were taken as DNA targets. The in vitro tests confirmed the good performance of the Mult-PSOS, with respect to infectious disease diagnosis, in the rapid and efficient selection of the optimal oligonucleotide sequences for Multiplex-PCRs. The predicted sequences allowed the adequate amplification of all amplicons in a single step (with the correct amount of DNA template and primers), reducing significantly the need for trial and error experiments. In addition, owing to its independence from the initial selection of the heuristic constants, the Mult-PSOS can be employed by non-expert users in computational techniques or in primer design problems.

  19. 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

  20. 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

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

    PubMed

    Uricchio, Lawrence H; Zaitlen, Noah A; Ye, Chun Jimmie; Witte, John S; Hernandez, Ryan D

    2016-07-01

    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.

  2. 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

    2013-06-01

    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. PMID:23731540

  3. 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

    2013-06-01

    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.

  4. Detecting and Characterizing Genomic Signatures of Positive Selection in Global Populations

    PubMed Central

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

    2013-01-01

    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. PMID:23731540

  5. Evaluation of two outlier-detection-based methods for detecting tissue-selective genes from microarray data.

    PubMed

    Kadota, Koji; Konishi, Tomokazu; Shimizu, Kentaro

    2007-01-01

    Large-scale expression profiling using DNA microarrays enables identification of tissue-selective genes for which expression is considerably higher and/or lower in some tissues than in others. Among numerous possible methods, only two outlier-detection-based methods (an AIC-based method and Sprent's non-parametric method) can treat equally various types of selective patterns, but they produce substantially different results. We investigated the performance of these two methods for different parameter settings and for a reduced number of samples. We focused on their ability to detect selective expression patterns robustly. We applied them to public microarray data collected from 36 normal human tissue samples and analyzed the effects of both changing the parameter settings and reducing the number of samples. The AIC-based method was more robust in both cases. The findings confirm that the use of the AIC-based method in the recently proposed ROKU method for detecting tissue-selective expression patterns is correct and that Sprent's method is not suitable for ROKU. PMID:19936074

  6. Bacterial pathogens of otitis media and sinusitis: detection in the nasopharynx with selective agar media.

    PubMed

    Dudley, S; Ashe, K; Winther, B; Hendley, J O

    2001-11-01

    Carriage rates for the bacterial pathogens associated with otitis media (Streptococcus pneumoniae [SP], Hemophilus influenzae [HI], and Moraxella catarrhalis [MC]) are of interest. Culture on three selective agars was compared with culture on two standard agars to determine the more accurate method for detection of these species in the nasopharynx of healthy children. Weekly samples were obtained in winter from 18 healthy children (ages 1 through 9 years) as part of a longitudinal study. A 0.1-mL sample of 116 nasopharyngeal aspirate/washes was inoculated onto each of five agars. Two were standard (sheep blood and chocolate), and three were selective (blood with gentamicin for SP; chocolate with vancomycin, bacitracin, and clindamycin for HI; blood with amphotericin B, vancomycin, trimethoprim, and acetazolamide for MC). One technician read the standard plates and another the selective; both were blinded to the results of the other. SP was found in 44% of samples with selective agar versus 25% with standard agar; HI was found in 31% with selective versus 9% with standard; MC was found in 56% with selective versus 37% with standard. Overall, 80% of samples had one or more pathogens detected with selective agars as compared with 58% with standard agars (P =.0004). Selective agars were more accurate than standard agars for detecting otitis pathogens in the nasopharynx, where they are a common part of normal flora in healthy children.

  7. Evolutionary genetics as a tool to target genes involved in phenotypes of medical relevance

    PubMed Central

    Heyer, Evelyne; Quintana-Murci, Lluis

    2009-01-01

    There is an increasing interest in detecting genes, or genomic regions, that have been targeted by natural selection. Indeed, the evolutionary approach for inferring the action of natural selection in the human genome represents a powerful tool for predicting regions of the genome potentially associated with disease and of interest in epidemiological genetic studies. Here, we review several examples going from candidate gene studies associated with specific phenotypes, including nutrition, infectious disease and climate adaptation, to whole genome scans for natural selection. All these studies illustrate the power of the evolutionary approach in identifying regions of the genome having played a major role in human survival and adaptation. PMID:25567848

  8. Gene discovery, evolutionary affinity and molecular detection of Oxyspirura petrowi, an eye worm parasite of game birds

    PubMed Central

    2013-01-01

    Background Oxyspirura petrowi appears to be emerging as a nematode parasite that could negatively impact Northern Bobwhite quail individuals and populations within Texas and other regions of the United States. Despite this eye worm's potential importance in the conservation of wild quail, little is known about the general biology and genome composition of O. petrowi. To fill the knowledge gap, we performed a small scale random genome sequence survey, sequenced its 18S rRNA and the intergenic region between the 18S and 28S rRNA genes, studied its phylogenetic affinity, and developed a PCR protocol for the detection of this eye worm. Results We have generated ~240 kb of genome sequence data derived from 348 clones by a random genome survey of an O. petrowi genomic library. The eye worm genome is AT-rich (i.e., 62.2% AT-content), and contains a high number of microsatellite sequences. The discovered genes encode a wide-range of proteins including hypothetical proteins, enzymes, nematode-specific proteins. Phylogenetic analysis based on 18S rRNA sequences indicate that the Spiruroidea is paraphyletic, in which Oxyspirura and its closely related species are sisters to the filarial nematodes. We have also developed a PCR protocol based on the ITS2 sequence that allows sensitive and specific detection of eye worm DNA in feces. Using this newly developed protocol, we have determined that ~28% to 33% of the fecal samples collected from Northern Bobwhites and Scaled Quail in Texas in the spring of 2013 are O. petrowi positive. Conclusions The O. petrowi genome is rich in microsatellite sequences that may be used in future genotyping and molecular fingerprinting analysis. This eye worm is evolutionarily close to the filarial nematodes, implying that therapeutic strategies for filariasis such as Loa loa would be referential in developing treatments for the Thelazoidea parasites. Our qPCR-based survey has confirmed that O. petrowi infection is of potential concern to quail

  9. Millimeter Detection of Spitzer-selected High Redshift Hyperluminus Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Lonsdale, Carol J.; Omont, A.; del Carmen Polletta, M.; Zylka, R.; Shupe, D.; Smith, H. E., Jr.; Berta, S.; Bavouzet, N.; Lagache, G.; Farrah, D.; Bertoldi, F.; Cox, P.; de Breuck, C.; Dole, H.; Lutz, D.; Tacconi, L.; Perez-Fournon, I.; Aussel, H.; McCracken, H.; Clements, D.; Rowan-Robinson, M.; Franceschini, A.; Frayer, D.; Surace, J.; Siana, B.

    2006-12-01

    We have used the Mambo instrument on the IRAM 30m telescope to observe at 1.2mm 63 Spitzer-selected z>1 hyperluminous infrared galaxy candidates (HLIRGs) with starburst-dominated mid-infrared (MIR) spectral energy distributions from the SWIRE Legacy survey. The primary selection criteria are a peak in the IRAC 5.8μm band due to the rest frame near-infrared spectrum of evolved stars, a bright detection at 24μm, and very faint optical counterparts. The detection rate with Mambo is very high at 45%, and both the detection rate and the average 1.2mm/24μm flux ratio are much higher than found for previous Spitzer MIR-selected samples, due to the fact that earlier samples favored systems with AGN-dominated MIR emission. Our sample, on the other hand, shows systematically lower 1.2mm/24μm ratios than a sample of Spitzer-detected submillimeter-selected galaxies (SMGs) in a similar redshift range. Thus Spitzer MIR selection complements submillimeter selection of high redshift starburst-dominated HLIRGs, finding a population with substantially different SED shapes. The large MIR/submillimeter flux ratios probably indicate exceptionally luminous 7.7μm PAH emission, based on Spitzer IRS spectra for a subset of these objects (Weedman et al. 2007).

  10. Mitochondrial DNA Detects a Complex Evolutionary History with Pleistocene Epoch Divergence for the Neotropical Malaria Vector Anopheles nuneztovari Sensu Lato

    PubMed Central

    Scarpassa, Vera Margarete; Conn, Jan E.

    2011-01-01

    Cryptic species and lineages characterize Anopheles nuneztovari s.l. Gabaldón, an important malaria vector in South America. We investigated the phylogeographic structure across the range of this species with cytochrome oxidase subunit I (COI) mitochondrial DNA sequences to estimate the number of clades and levels of divergence. Bayesian and maximum-likelihood phylogenetic analyses detected four groups distributed in two major monophyletic clades (I and II). Samples from the Amazon Basin were clustered in clade I, as were subclades II-A and II-B, whereas those from Bolivia/Colombia/Venezuela were restricted to one basal subclade (II-C). These data, together with a statistical parsimony network, confirm results of previous studies that An. nuneztovari is a species complex consisting of at least two cryptic taxa, one occurring in Colombia and Venezuela and the another occurring in the Amazon Basin. These data also suggest that additional incipient species may exist in the Amazon Basin. Divergence time and expansion tests suggested that these groups separated and expanded in the Pleistocene Epoch. In addition, the COI sequences clearly separated An. nuneztovari s.l. from the closely related species An. dunhami Causey, and three new records are reported for An. dunhami in Amazonian Brazil. These findings are relevant for vector control programs in areas where both species occur. Our analyses support dynamic geologic and landscape changes in northern South America, and infer particularly active divergence during the Pleistocene Epoch for New World anophelines. PMID:22049039

  11. Evolutionary optimum for male sexual traits characterized using the multivariate Robertson-Price Identity.

    PubMed

    Delcourt, Matthieu; Blows, Mark W; Aguirre, J David; Rundle, Howard D

    2012-06-26

    Phenotypes tend to remain relatively constant in natural populations, suggesting a limit to trait evolution. Although stationary phenotypes suggest stabilizing selection, directional selection is more commonly reported. However, selection on phenotypes will have no evolutionary consequence if the traits do not genetically covary with fitness, a covariance known as the Robertson-Price Identity. The nature of this genetic covariance determines if phenotypes will evolve directionally or whether they reside at an evolutionary optimum. Here, we show how a set of traits can be shown to be under net stabilizing selection through an application of the multivariate Robertson-Price Identity. We characterize how a suite of male sexual displays genetically covaries with fitness in a population of Drosophila serrata. Despite strong directional sexual selection on these phenotypes directly and significant genetic variance in them, little genetic covariance was detected with overall fitness. Instead, genetic analysis of trait deviations showed substantial stabilizing selection on the genetic variance of these traits with respect to overall fitness, indicating that they reside at an evolutionary optimum. In the presence of widespread pleiotropy, stabilizing selection on focal traits will arise through the net effects of selection on other, often unmeasured, traits and will tend to be stronger on trait combinations than single traits. Such selection may be difficult to detect in phenotypic analyses if the environmental covariance between the traits and fitness obscures the underlying genetic associations. The genetic analysis of trait deviations provides a way of detecting the missing stabilizing selection inferred by recent metaanalyses.

  12. The application of atomic emission spectroscopy to chromatographic analyses for element-selective detection

    SciTech Connect

    Seeley, J.A.

    1992-01-01

    The goal of this work was to investigate the properties of existing atomic emission systems which are useful for element-selective detection of chromatographic effluent. A microwave induced plasma (MIP) system has been optimized for the selective detection of boron in the effluent of a gas chromatograph. A method was developed for the analysis of total boron present in several lubrication oil additives and in several formulated lubrication oils. Values obtained by this method compare favorably with those obtained by other atomic emission spectroscopic (AES) methods. A direct current plasma (DCP) system has been optimized for the selective detection of boron in flowing organic liquid streams. A method was developed for the analysis of total boron present in several lubrication oil additives by flow injection analysis (FIA). A method was also developed for the qualitative separation [open quotes]speciation[close quotes] of these additives by size exclusion chromatography-DCP. Values obtained through this method compare favorably with values obtained through other AES methods. The MIP system was optimized for the selective detection of titanium in the effluent of the gas chromatograph. This system was used to analyze a group of reaction mixtures containing novel titanium chelates and organo-metallic compounds, as well as several organo-titanium-boron compounds. The MIP system was optimized for the selective detection of several of the group VA and group VIA elements in the effluent of the gas chromatograph. This system was used to characterize a series of coal standards (the Argonne Premium Coal Standards) by pyrolysis-GC-AES. Volatile compounds containing nitrogen, oxygen and sulfur were detected. The Py-GC-AES method was used to characterize several other coal, sedimentary and kerogen samples. Volatile phosphorous, arsenic, and selenium compounds were detected, as were compounds of nitrogen, oxygen and sulfur.

  13. Selective fluorescence and fluorescence-free detection of single biomolecules on nanobiochips.

    PubMed

    Lee, Seungah; Kang, Seong Ho

    2014-10-01

    This topical review provides an overview of selective fluorescence and fluorescence-free detection on nanobiochips fabricated by nanopatterning techniques such as nanolithography and the use of artificial nanostructures (arrays of pillars, holes, and wires). The unique properties of nanostructured surfaces have led to applications in biomedical nanoarrays used for either diagnostic or functional assays on chips. Some targets can be optically detected using not only colorimetry, chemiluminescence or the most developed fluorescence mode, but also more recent non-conventional optical methods. Two main approaches have been used: fluorescence (e.g., epifluorescence and total internal reflection) and fluorescence-free (e.g., surface plasmon resonance, optical resonance, dark-field scattering, atom force microscopy, electrochemical method, etc.) detection. The aim of the present paper is to review the most recent progress in nanobiochips in the development of new selective fluorescence and fluorescence-free detection at the single-molecule level.

  14. Trypsin-stabilized fluorescent gold nanocluster for sensitive and selective Hg2+ detection.

    PubMed

    Kawasaki, Hideya; Yoshimura, Kouta; Hamaguchi, Kenji; Arakawa, Ryuichi

    2011-01-01

    We report on trypsin-stabilized fluorescent gold nanoclusters (Au NCs) for the sensitive and selective detection of Hg(2+) ions. The Au NCs have an average size of 1 nm and show a red emission at 645 nm. The photostable properties of the trypsin-stabilized Au NCs were examined, and their photochemical stability was found to be similar to that of CdSe quantum dots. The fluorescence was particularly quenched by Hg(2+), and therefore the Au NCs can be used as fluorescent sensors for sensitive and selective Hg(2+) detection to a detection limit of 50 ± 10 nM and the quantitative detection of Hg(2+) in wide and low concentration range of 50-600 nM.

  15. 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

  16. Active surfaces engineered by immobilizing protein-polymer nanoreactors for selectively detecting sugar alcohols.

    PubMed

    Zhang, Xiaoyan; Lomora, Mihai; Einfalt, Tomaz; Meier, Wolfgang; Klein, Noreen; Schneider, Dirk; Palivan, Cornelia G

    2016-05-01

    We introduce active surfaces generated by immobilizing protein-polymer nanoreactors on a solid support for sensitive sugar alcohols detection. First, such selective nanoreactors were engineered in solution by simultaneous encapsulation of specific enzymes in copolymer polymersomes, and insertion of membrane proteins for selective conduct of sugar alcohols. Despite the artificial surroundings, and the thickness of the copolymer membrane, functionality of reconstituted Escherichia coli glycerol facilitator (GlpF) was preserved, and allowed selective diffusion of sugar alcohols to the inner cavity of the polymersome, where encapsulated ribitol dehydrogenase (RDH) enzymes served as biosensing entities. Ribitol, selected as a model sugar alcohol, was detected quantitatively by the RDH-nanoreactors with GlpF-mediated permeability in a concentration range of 1.5-9 mM. To obtain "active surfaces" for detecting sugar alcohols, the nanoreactors optimized in solution were then immobilized on a solid support: aldehyde groups exposed at the compartment external surface reacted via an aldehyde-amino reaction with glass surfaces chemically modified with amino groups. The nanoreactors preserved their architecture and activity after immobilization on the glass surface, and represent active biosensing surfaces for selective detection of sugar alcohols, with high sensitivity.

  17. 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.

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

    PubMed

    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

  19. BODIPY based colorimetric fluorescent probe for selective thiophenol detection: theoretical and experimental studies.

    PubMed

    Kand, Dnyaneshwar; Mishra, Pratyush Kumar; Saha, Tanmoy; Lahiri, Mayurika; Talukdar, Pinaki

    2012-09-01

    A BODIPY-based selective thiophenol probe capable of discriminating aliphatic thiols is reported. The fluorescence off-on effect upon reaction with thiol is elucidated with theoretical calculations. The sensing of thiophenol is associated with a color change from red to yellow and 63-fold enhancement in green fluorescence. Application of the probe for selective thiophenol detection is demonstrated by live cell imaging. PMID:22751002

  20. Multi-Layer Approach for the Detection of Selective Forwarding Attacks.

    PubMed

    Alajmi, Naser; Elleithy, Khaled

    2015-01-01

    Security breaches are a major threat in wireless sensor networks (WSNs). WSNs are increasingly used due to their broad range of important applications in both military and civilian domains. WSNs are prone to several types of security attacks. Sensor nodes have limited capacities and are often deployed in dangerous locations; therefore, they are vulnerable to different types of attacks, including wormhole, sinkhole, and selective forwarding attacks. Security attacks are classified as data traffic and routing attacks. These security attacks could affect the most significant applications of WSNs, namely, military surveillance, traffic monitoring, and healthcare. Therefore, there are different approaches to detecting security attacks on the network layer in WSNs. Reliability, energy efficiency, and scalability are strong constraints on sensor nodes that affect the security of WSNs. Because sensor nodes have limited capabilities in most of these areas, selective forwarding attacks cannot be easily detected in networks. In this paper, we propose an approach to selective forwarding detection (SFD). The approach has three layers: MAC pool IDs, rule-based processing, and anomaly detection. It maintains the safety of data transmission between a source node and base station while detecting selective forwarding attacks. Furthermore, the approach is reliable, energy efficient, and scalable. PMID:26610499

  1. Multi-Layer Approach for the Detection of Selective Forwarding Attacks.

    PubMed

    Alajmi, Naser; Elleithy, Khaled

    2015-11-19

    Security breaches are a major threat in wireless sensor networks (WSNs). WSNs are increasingly used due to their broad range of important applications in both military and civilian domains. WSNs are prone to several types of security attacks. Sensor nodes have limited capacities and are often deployed in dangerous locations; therefore, they are vulnerable to different types of attacks, including wormhole, sinkhole, and selective forwarding attacks. Security attacks are classified as data traffic and routing attacks. These security attacks could affect the most significant applications of WSNs, namely, military surveillance, traffic monitoring, and healthcare. Therefore, there are different approaches to detecting security attacks on the network layer in WSNs. Reliability, energy efficiency, and scalability are strong constraints on sensor nodes that affect the security of WSNs. Because sensor nodes have limited capabilities in most of these areas, selective forwarding attacks cannot be easily detected in networks. In this paper, we propose an approach to selective forwarding detection (SFD). The approach has three layers: MAC pool IDs, rule-based processing, and anomaly detection. It maintains the safety of data transmission between a source node and base station while detecting selective forwarding attacks. Furthermore, the approach is reliable, energy efficient, and scalable.

  2. Multi-Layer Approach for the Detection of Selective Forwarding Attacks

    PubMed Central

    Alajmi, Naser; Elleithy, Khaled

    2015-01-01

    Security breaches are a major threat in wireless sensor networks (WSNs). WSNs are increasingly used due to their broad range of important applications in both military and civilian domains. WSNs are prone to several types of security attacks. Sensor nodes have limited capacities and are often deployed in dangerous locations; therefore, they are vulnerable to different types of attacks, including wormhole, sinkhole, and selective forwarding attacks. Security attacks are classified as data traffic and routing attacks. These security attacks could affect the most significant applications of WSNs, namely, military surveillance, traffic monitoring, and healthcare. Therefore, there are different approaches to detecting security attacks on the network layer in WSNs. Reliability, energy efficiency, and scalability are strong constraints on sensor nodes that affect the security of WSNs. Because sensor nodes have limited capabilities in most of these areas, selective forwarding attacks cannot be easily detected in networks. In this paper, we propose an approach to selective forwarding detection (SFD). The approach has three layers: MAC pool IDs, rule-based processing, and anomaly detection. It maintains the safety of data transmission between a source node and base station while detecting selective forwarding attacks. Furthermore, the approach is reliable, energy efficient, and scalable. PMID:26610499

  3. Optimal neural network architecture selection: effects on computer-aided detection of mammographic microcalcifications

    NASA Astrophysics Data System (ADS)

    Gurcan, Metin N.; Chan, Heang-Ping; Sahiner, Berkman; Hadjiiski, Lubomir M.; Petrick, Nicholas; Helvie, Mark A.

    2002-05-01

    We evaluated the effectiveness of an optimal convolution neural network (CNN) architecture selected by simulated annealing for improving the performance of a computer-aided diagnosis (CAD) system designed for the detection of microcalcification clusters on digitized mammograms. The performances of the CAD programs with manually and optimally selected CNNs were compared using an independent test set. This set included 472 mammograms and contained 253 biopsy-proven malignant clusters. Free-response receiver operating characteristic (FROC) analysis was used for evaluation of the detection accuracy. At a false positive (FP) rate of 0.7 per image, the film-based sensitivity was 84.6% with the optimized CNN, in comparison with 77.2% with the manually selected CNN. If clusters having images in both craniocaudal and mediolateral oblique views were analyzed together and a cluster was considered to be detected when it was detected in one or both views, at 0.7 FPs/image, the sensitivity was 93.3% with the optimized CNN and 87.0% with the manually selected CNN. This study indicates that classification of true positive and FP signals is an important step of the CAD program and that the detection accuracy of the program can be considerably improved by optimizing this step with an automated optimization algorithm.

  4. Evolutionary inevitability of sexual antagonism.

    PubMed

    Connallon, Tim; Clark, Andrew G

    2014-02-01

    Sexual antagonism, whereby mutations are favourable in one sex and disfavourable in the other, is common in natural populations, yet the root causes of sexual antagonism are rarely considered in evolutionary theories of adaptation. Here, we explore the evolutionary consequences of sex-differential selection and genotype-by-sex interactions for adaptation in species with separate sexes. We show that sexual antagonism emerges naturally from sex differences in the direction of selection on phenotypes expressed by both sexes or from sex-by-genotype interactions affecting the expression of such phenotypes. Moreover, modest sex differences in selection or genotype-by-sex effects profoundly influence the long-term evolutionary trajectories of populations with separate sexes, as these conditions trigger the evolution of strong sexual antagonism as a by-product of adaptively driven evolutionary change. The theory demonstrates that sexual antagonism is an inescapable by-product of adaptation in species with separate sexes, whether or not selection favours evolutionary divergence between males and females.

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. Inference of Evolutionary Forces Acting on Human Biological Pathways

    PubMed Central

    Daub, Josephine T.; Dupanloup, Isabelle; Robinson-Rechavi, Marc; Excoffier, Laurent

    2015-01-01

    Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past selection on the genetic diversity of human biological pathways. We first show that genes included in gene sets are generally under stronger selective constraints than other genes and that their evolutionary response is correlated. We then introduce a new procedure to detect selection at the pathway level based on a decomposition of the classical McDonald–Kreitman test extended to multiple genes. This new test, called 2DNS, detects outlier gene sets and takes into account past demographic effects and evolutionary constraints specific to gene sets. Selective forces acting on gene sets can be easily identified by a mere visual inspection of the position of the gene sets relative to their two-dimensional null distribution. We thus find several outlier gene sets that show signals of positive, balancing, or purifying selection but also others showing an ancient relaxation of selective constraints. The principle of the 2DNS test can also be applied to other genomic contrasts. For instance, the comparison of patterns of polymorphisms private to African and non-African populations reveals that most pathways show a higher proportion of nonsynonymous mutations in non-Africans than in Africans, potentially due to different demographic histories and selective pressures. PMID:25971280

  10. Highly Efficient State-Selective Submicrosecond Photoionization Detection of Single Atoms

    SciTech Connect

    Henkel, F.; Krug, M.; Hofmann, J.; Rosenfeld, W.; Weber, M.; Weinfurter, H.

    2010-12-17

    We experimentally demonstrate a detection scheme suitable for state analysis of single optically trapped atoms in less than 1 {mu}s with an overall detection efficiency {eta} exceeding 98%. The method is based on hyperfine-state-selective photoionization and subsequent registration of the correlated photoion-electron pairs by coincidence counting via two opposing channel electron multipliers. The scheme enables the calibration of absolute detection efficiencies and might be a key ingredient for future quantum information applications or precision spectroscopy of ultracold atoms.

  11. Performance of SaSelect, a Chromogenic Medium for Detection of Staphylococci in Clinical Specimens

    PubMed Central

    Kerttula, Anne-Marie; Kaukoranta, Suvi-Sirkku

    2014-01-01

    In a preliminary study, known staphylococcus (n = 86) and other microbial (n = 12) isolates were plated on three chromogenic media, SaSelect (Bio-Rad, Hercules, CA, USA), CHROMagar Staph. aureus (CHROMagar Microbiology, Paris, France), and S. aureus ID (bioMérieux, Marcy l'Etoile, France). The sensitivities of all the media to detect Staphylococcus aureus after 24 h of incubation were high (100.0%). However, their specificities varied at 93.3% (95% confidence interval [CI], 86.0% to 100.0%) (CHROMagar Staph. aureus), 97.8% (95% CI, 93.5% to 100.0%) (S. aureus ID), and 100.0% (SaSelect). SaSelect also showed the highest sensitivity for recovery and differentiation of other staphylococci. As the best performing chromogenic medium, SaSelect was then prospectively compared to conventional culture and identification tests for the detection of staphylococci from 2,780 clinical specimens. A total of 1,589 staphylococcal isolates were recovered. Of these, 912 were S. aureus and 677 were other staphylococci. The sensitivity and specificity of SaSelect to detect S. aureus in clinical specimens after 24 h of incubation were 99.6% and 99.9% (95% CI, 99.2% to 100.0% and 99.8% to 100.0%), respectively, whereas the sensitivity and specificity using conventional plates combined with laboratory identification methods were 96.8% and 99.5% (95% CI, 95.7 to 97.9% and 99.2% to 99.8%). For the recovery and preliminary identification of other staphylococci, the sensitivity and specificity of SaSelect were 94.4% and 99.9%. SaSelect is a well-performing chromogenic medium that significantly improved the detection of staphylococci, especially S. aureus, compared to conventional culture (P < 0.0001). PMID:24430448

  12. Study of vegetation index selection and changing detection thresholds in land cover change detection assessment using change vector analysis

    NASA Astrophysics Data System (ADS)

    Nguyen, Duy; Tran, Giang

    2012-07-01

    In recent years, Vietnamese rapidly developing economy has led to speedy changes in land cover. The study of changing detection of land cover plays an important role in making the strategy of the managers. There are two main approaches in changing detection research by using remote sensing and GIS: post- classification change detection analysis approach and pre-classification changing spectral determination approach. Each has their own different advantages and disadvantages. The second one is further divided into: Image Differencing, Multi-date Principal Component Analysis (MPCA); Change Vector Analysis (CVA). In this study, researchers introduce CVA method. This method is based on two important index to show the primary feature of land cover, such as: vegetation index (NDVI-) and barren land index (-BI). Ability to apply methods of CVA has been mentioned in the studies [1, 2, 3, and 4]. However, in these studies did not mention the NDVI index selection and changing detection threshold in changing detection assessment? This paper proposes application to solve these two problems.

  13. Evolutionary Dynamics of Biological Games

    NASA Astrophysics Data System (ADS)

    Nowak, Martin A.; Sigmund, Karl

    2004-02-01

    Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.

  14. A Locked Nucleic Acid Probe Based on Selective Salt-Induced Effect Detects Single Nucleotide Polymorphisms

    PubMed Central

    Zhang, Jing; Wu, Huizhe; Chen, Qiuchen; Zhao, Pengfei; Zhao, Haishan; Yao, Weifan; Wei, Minjie

    2015-01-01

    Detection of single based genetic mutation by using oligonucleotide probes is one of the common methods of detecting single nucleotide polymorphisms at known loci. In this paper, we demonstrated a hybridization system which included a buffer solution that produced selective salt-induced effect and a locked nucleic acid modified 12 nt oligonucleotide probe. The hybridization system is suitable for hybridization under room temperature. By using magnetic nanoparticles as carriers for PCR products, the SNPs (MDR1 C3435T/A) from 45 volunteers were analyzed, and the results were consistent with the results from pyrophosphoric acid sequencing. The method presented in this paper differs from the traditional method of using molecular beacons to detect SNPs in that it is suitable for research institutions lacking real-time quantitative PCR detecting systems, to detect PCR products at room temperature. PMID:26347880

  15. 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'.

  16. 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'. PMID:27619705

  17. 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...

  18. A highly sensitive and selective immunoassay for the detection of tetrabromobisphenol A in soil and sediment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tetrabromobisphenol A (TBBPA) is the most widely used brominated flame retardant. A sensitive and selective enzyme-linked immunosorbent assay (ELISA) for the detection of TBBPA was developed. Six haptens (T1-T6) mimicking different structural elements of TBBPA were synthesized and coupled to keyhole...

  19. 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...

  20. Environmental changes bridge evolutionary valleys

    PubMed Central

    Steinberg, Barrett; Ostermeier, Marc

    2016-01-01

    In the basic fitness landscape metaphor for molecular evolution, evolutionary pathways are presumed to follow uphill steps of increasing fitness. How evolution can cross fitness valleys is an open question. One possibility is that environmental changes alter the fitness landscape such that low-fitness sequences reside on a hill in alternate environments. We experimentally test this hypothesis on the antibiotic resistance gene TEM-15 β-lactamase by comparing four evolutionary strategies shaped by environmental changes. The strategy that included initial steps of selecting for low antibiotic resistance (negative selection) produced superior alleles compared with the other three strategies. We comprehensively examined possible evolutionary pathways leading to one such high-fitness allele and found that an initially deleterious mutation is key to the allele’s evolutionary history. This mutation is an initial gateway to an otherwise relatively inaccessible area of sequence space and participates in higher-order, positive epistasis with a number of neutral to slightly beneficial mutations. The ability of negative selection and environmental changes to provide access to novel fitness peaks has important implications for natural evolutionary mechanisms and applied directed evolution. PMID:26844293

  1. 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. PMID:27030140

  2. 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.

  3. A sensitive and selective fluorescence sensor for the detection of arsenic(III) in organic media.

    PubMed

    Ezeh, Vivian C; Harrop, Todd C

    2012-02-01

    Arsenic contamination is a leading environmental problem. As such, levels of this toxic metalloid must be constantly monitored by reliable and low-cost methodologies. Because the currently accepted upper limit for arsenic in water is 10 ppb, very sensitive and selective detection strategies must be developed. Herein we describe the synthesis and characterization of a fluorescent chemical probe, namely, ArsenoFluor1, which is the first example of a chemosensor for As(3+) detection in organic solvents at 298 K. AF1 exhibits a 25-fold fluorescence increase in the presence of As(3+) at λ(em) = 496 nm in THF, which is selective for As(3+) over other biologically relevant ions (such as Na(+), Mg(2+), Fe(2+), and Zn(2+)) and displays a sub-ppb detection limit.

  4. [Evolutionary medicine: the future looking at the past].

    PubMed

    Carvalho, Serafim; Rosado, Margarida

    2008-01-01

    Evolutionary medicine is an emergent basic science that offers new and varied perspectives to the comprehension of the human health and disease, considering them as a result of a gap between our modern lives and the environment where human beings evolve. This work's goals are to understand the importance of the evolutionary theories on concepts of health and disease, providing a new insight on medicine investigation. This bibliography review is based on Medline and PsycINFO articles research between 1996 and 2007 about review and experimental studies published in English, using the key words evolutionary and medicine, psychiatry, psychology, behaviour, health, disease, gene. There were selected forty-five articles based on and with special interest on the authors' practice. There were also consulted some allusive books. The present human genome and phenotypes are essentially Palaeolithic ones: they are not adapted to the modern life style, thus favouring the so called diseases of civilization. Fitting evolutionary strategies, apparently protective ones, when excessive, are the core syndromes of many emotional disruptive behaviours and diseases. Having the stone age's genes, we are obliged to live in the space age. With the evolutionary approach, postmodern medicine is detecting better the vulnerabilities, restrictions, biases, adaptations and maladaptations of human body, its actual diseases and its preventions and treatment.

  5. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26343642

  7. Challenges of Detecting Directional Selection After a Bottleneck: Lessons From Sorghum bicolor

    PubMed Central

    Hamblin, Martha T.; Casa, Alexandra M.; Sun, Hong; Murray, Seth C.; Paterson, Andrew H.; Aquadro, Charles F.; Kresovich, Stephen

    2006-01-01

    Multilocus surveys of sequence variation can be used to identify targets of directional selection, which are expected to have reduced levels of variation. Following a population bottleneck, the signal of directional selection may be hard to detect because many loci may have low variation by chance and the frequency spectrum of variation may be perturbed in ways that resemble the effects of selection. Cultivated Sorghum bicolor contains a subset of the genetic diversity found in its wild ancestor(s) due to the combined effects of a domestication bottleneck and human selection on traits associated with agriculture. As a framework for distinguishing between the effects of demography and selection, we sequenced 204 loci in a diverse panel of 17 cultivated S. bicolor accessions. Genomewide patterns of diversity depart strongly from equilibrium expectations with regard to the variance of the number of segregating sites, the site frequency spectrum, and haplotype configuration. Furthermore, gene genealogies of most loci with an excess of low frequency variants and/or an excess of segregating sites do not show the characteristic signatures of directional and diversifying selection, respectively. A simple bottleneck model provides an improved but inadequate fit to the data, suggesting the action of other population-level factors, such as population structure and migration. Despite a known history of recent selection, we find little evidence for directional selection, likely due to low statistical power and lack of an appropriate null model. PMID:16547110

  8. Feature Transformation Detection Method with Best Spectral Band Selection Process for Hyper-spectral Imaging

    NASA Astrophysics Data System (ADS)

    Chen, Hai-Wen; McGurr, Mike; Brickhouse, Mark

    2015-11-01

    We present a newly developed feature transformation (FT) detection method for hyper-spectral imagery (HSI) sensors. In essence, the FT method, by transforming the original features (spectral bands) to a different feature domain, may considerably increase the statistical separation between the target and background probability density functions, and thus may significantly improve the target detection and identification performance, as evidenced by the test results in this paper. We show that by differentiating the original spectral, one can completely separate targets from the background using a single spectral band, leading to perfect detection results. In addition, we have proposed an automated best spectral band selection process with a double-threshold scheme that can rank the available spectral bands from the best to the worst for target detection. Finally, we have also proposed an automated cross-spectrum fusion process to further improve the detection performance in lower spectral range (<1000 nm) by selecting the best spectral band pair with multivariate analysis. Promising detection performance has been achieved using a small background material signature library for concept-proving, and has then been further evaluated and verified using a real background HSI scene collected by a HYDICE sensor.

  9. 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.

  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. 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

  12. Neuronal boost to evolutionary dynamics.

    PubMed

    de Vladar, Harold P; Szathmáry, Eörs

    2015-12-01

    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.

  13. Single-carbon discrimination by selected peptides for individual detection of volatile organic compounds

    PubMed Central

    Ju, Soomi; Lee, Ki-Young; Min, Sun-Joon; Yoo, Yong Kyoung; Hwang, Kyo Seon; Kim, Sang Kyung; Yi, Hyunjung

    2015-01-01

    Although volatile organic compounds (VOCs) are becoming increasingly recognized as harmful agents and potential biomarkers, selective detection of the organic targets remains a tremendous challenge. Among the materials being investigated for target recognition, peptides are attractive candidates because of their chemical robustness, divergence, and their homology to natural olfactory receptors. Using a combinatorial peptide library and either a graphitic surface or phenyl-terminated self-assembled monolayer as relevant target surfaces, we successfully selected three interesting peptides that differentiate a single carbon deviation among benzene and its analogues. The heterogeneity of the designed target surfaces provided peptides with varying affinity toward targeted molecules and generated a set of selective peptides that complemented each other. Microcantilever sensors conjugated with each peptide quantitated benzene, toluene and xylene to sub-ppm levels in real time. The selection of specific receptors for a group of volatile molecules will provide a strong foundation for general approach to individually monitoring VOCs. PMID:25779765

  14. Single-carbon discrimination by selected peptides for individual detection of volatile organic compounds

    NASA Astrophysics Data System (ADS)

    Ju, Soomi; Lee, Ki-Young; Min, Sun-Joon; Yoo, Yong Kyoung; Hwang, Kyo Seon; Kim, Sang Kyung; Yi, Hyunjung

    2015-03-01

    Although volatile organic compounds (VOCs) are becoming increasingly recognized as harmful agents and potential biomarkers, selective detection of the organic targets remains a tremendous challenge. Among the materials being investigated for target recognition, peptides are attractive candidates because of their chemical robustness, divergence, and their homology to natural olfactory receptors. Using a combinatorial peptide library and either a graphitic surface or phenyl-terminated self-assembled monolayer as relevant target surfaces, we successfully selected three interesting peptides that differentiate a single carbon deviation among benzene and its analogues. The heterogeneity of the designed target surfaces provided peptides with varying affinity toward targeted molecules and generated a set of selective peptides that complemented each other. Microcantilever sensors conjugated with each peptide quantitated benzene, toluene and xylene to sub-ppm levels in real time. The selection of specific receptors for a group of volatile molecules will provide a strong foundation for general approach to individually monitoring VOCs.

  15. 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

  16. 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.

  17. Sequential feature selection for detecting buried objects using forward looking ground penetrating radar

    NASA Astrophysics Data System (ADS)

    Shaw, Darren; Stone, Kevin; Ho, K. C.; Keller, James M.; Luke, Robert H.; Burns, Brian P.

    2016-05-01

    Forward looking ground penetrating radar (FLGPR) has the benefit of detecting objects at a significant standoff distance. The FLGPR signal is radiated over a large surface area and the radar signal return is often weak. Improving detection, especially for buried in road targets, while maintaining an acceptable false alarm rate remains to be a challenging task. Various kinds of features have been developed over the years to increase the FLGPR detection performance. This paper focuses on investigating the use of as many features as possible for detecting buried targets and uses the sequential feature selection technique to automatically choose the features that contribute most for improving performance. Experimental results using data collected at a government test site are presented.

  18. 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.

  19. A ROC-based feature selection method for computer-aided detection and diagnosis

    NASA Astrophysics Data System (ADS)

    Wang, Songyuan; Zhang, Guopeng; Liao, Qimei; Zhang, Junying; Jiao, Chun; Lu, Hongbing

    2014-03-01

    Image-based computer-aided detection and diagnosis (CAD) has been a very active research topic aiming to assist physicians to detect lesions and distinguish them from benign to malignant. However, the datasets fed into a classifier usually suffer from small number of samples, as well as significantly less samples available in one class (have a disease) than the other, resulting in the classifier's suboptimal performance. How to identifying the most characterizing features of the observed data for lesion detection is critical to improve the sensitivity and minimize false positives of a CAD system. In this study, we propose a novel feature selection method mR-FAST that combines the minimal-redundancymaximal relevance (mRMR) framework with a selection metric FAST (feature assessment by sliding thresholds) based on the area under a ROC curve (AUC) generated on optimal simple linear discriminants. With three feature datasets extracted from CAD systems for colon polyps and bladder cancer, we show that the space of candidate features selected by mR-FAST is more characterizing for lesion detection with higher AUC, enabling to find a compact subset of superior features at low cost.

  20. On selecting reference image models for anomaly detection in industrial systems

    NASA Astrophysics Data System (ADS)

    Xiao, Xinhua; Quan, Jin; Ferro, Andrew; Han, Chia Y.; Zhou, Xuefu; Wee, William G.

    2013-09-01

    Automatic X-ray inspection of industrial parts usually uses reference-based methods, in which a set of model images or statistics extracted from the model image set are selected as the benchmark. Based on these methods, many systems are developed and are used extensively for anomaly detection. However, the performance of these systems relies heavily on the model image set. Thus, the selection of the model images is very important. This paper presents an approach for automatically selecting a set of model images to be used in a reference-based assisted defect recognition (ADR) system for anomaly detection of turbine blades of jet engines. The proposed approach to generating a model image set is based on feature extraction. Features are extracted from callout images of ADR, including potential defect indication type, size and location. Experimental results show that the proposed approach is fast and a low false alarm rate with acceptable detection rate is ensured. Moreover, the approach is applicable to different blade types and varied views of the blade. Further validation shows that the approach can be applied to the update of the model image set, when more images are generated from new blades and the model becomes inaccurate for anomaly detection in the new images.

  1. Selective and sensitive colorimetric detection of stringent alarmone ppGpp with Fenton-like reagent.

    PubMed

    Zheng, Lin Ling; Huang, Cheng Zhi

    2014-12-01

    Stringent alarmone, namely, guanosine 3'-diphosphate-5'-diphosphate (ppGpp), is a global regulator that plays a critical role in the survival, growth, metabolism, and many other vital processes of microorganisms. Because of its structural similarity to normal nucleotides, it is also a challenge for the selective and sensitive detection of ppGpp nowadays. Herein, we developed a colorimetric method for the selective detection of ppGpp by inhibiting the redox reaction between Fenton-like reagent (composed of Fe(3+) and H2O2) with 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS). Owing to the strong coordination affinity between ppGpp and Fe(3+), the chromogenic reaction between ABTS and Fenton-like reagent, occurred in aqueous medium at 37 °C and resulted in a bluish-green solution, which was inhibited with the addition of ppGpp. This phenomenon forms the basis for the colorimetric detection of ppGpp, with a detection limit of 0.19 μM and good selectivity for ppGpp over other nucleotides and anions. Furthermore, the results could be visualized by the naked eye, and the sensitivity of the naked-eye observation could even be further improved with the aid of the introduction of a background color.

  2. Enhancing the mathematical properties of new haplotype homozygosity statistics for the detection of selective sweeps.

    PubMed

    Garud, Nandita R; Rosenberg, Noah A

    2015-06-01

    Soft selective sweeps represent an important form of adaptation in which multiple haplotypes bearing adaptive alleles rise to high frequency. Most statistical methods for detecting selective sweeps from genetic polymorphism data, however, have focused on identifying hard selective sweeps in which a favored allele appears on a single haplotypic background; these methods might be underpowered to detect soft sweeps. Among exceptions is the set of haplotype homozygosity statistics introduced for the detection of soft sweeps by Garud et al. (2015). These statistics, examining frequencies of multiple haplotypes in relation to each other, include H12, a statistic designed to identify both hard and soft selective sweeps, and H2/H1, a statistic that conditional on high H12 values seeks to distinguish between hard and soft sweeps. A challenge in the use of H2/H1 is that its range depends on the associated value of H12, so that equal H2/H1 values might provide different levels of support for a soft sweep model at different values of H12. Here, we enhance the H12 and H2/H1 haplotype homozygosity statistics for selective sweep detection by deriving the upper bound on H2/H1 as a function of H12, thereby generating a statistic that normalizes H2/H1 to lie between 0 and 1. Through a reanalysis of resequencing data from inbred lines of Drosophila, we show that the enhanced statistic both strengthens interpretations obtained with the unnormalized statistic and leads to empirical insights that are less readily apparent without the normalization. PMID:25891325

  3. Enhancing the mathematical properties of new haplotype homozygosity statistics for the detection of selective sweeps

    PubMed Central

    Garud, Nandita R.; Rosenberg, Noah A.

    2015-01-01

    Soft selective sweeps represent an important form of adaptation in which multiple haplotypes bearing adaptive alleles rise to high frequency. Most statistical methods for detecting selective sweeps from genetic polymorphism data, however, have focused on identifying hard selective sweeps in which a favored allele appears on a single haplotypic background; these methods might be underpowered to detect soft sweeps. Among exceptions is the set of haplotype homozygosity statistics introduced for the detection of soft sweeps by Garud et al. (2015). These statistics, examining frequencies of multiple haplotypes in relation to each other, include H12, a statistic designed to identify both hard and soft selective sweeps, and H2/H1, a statistic that conditional on high H12 values seeks to distinguish between hard and soft sweeps. A challenge in the use of H2/H1 is that its range depends on the associated value of H12, so that equal H2/H1 values might provide different levels of support for a soft sweep model at different values of H12. Here, we enhance the H12 and H2/H1 haplotype homozygosity statistics for selective sweep detection by deriving the upper bound on H2/H1 as a function of H12, thereby generating a statistic that normalizes H2/H1 to lie between 0 and 1. Through a reanalysis of resequencing data from inbred lines of Drosophila, we show that the enhanced statistic both strengthens interpretations obtained with the unnormalized statistic and leads to empirical insights that are less readily apparent without the normalization. PMID:25891325

  4. Detection of methicillin-resistant Staphylococcus aureus in clinical specimens from cystic fibrosis patients by use of chromogenic selective agar.

    PubMed

    Perez, Leandro Reus Rodrigues; Antunes, Ana Lúcia Souza; Bonfanti, Jéssica Weiss; Pinto, Jaqueline Becker; Roesch, Eliane Wurdig; Rodrigues, Diógenes; Dias, Cícero Armídio Gomes

    2012-07-01

    We evaluated the use of a chromogenic selective medium (MRSA ID) as a useful tool for the detection of methicillin-resistant Staphylococcus aureus (MRSA) in cystic fibrosis (CF) patient samples. Fifty-four MRSA isolates were detected by MRSA ID, while only 24/54 (44%) (odds ratio [OR], 2.79; 95% confidence interval [CI], 1.63 to 4.76) were detected by conventional methods. A chromogenic selective medium for MRSA detection may improve its surveillance in CF patients.

  5. 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

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

    PubMed Central

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

    2012-01-01

    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. PMID:22128132

  7. 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.

  8. 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

  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. Detection of Allelic Frequency Differences between the Sexes in Humans: A Signature of Sexually Antagonistic Selection

    PubMed Central

    Lucotte, Elise A.; Laurent, Romain; Heyer, Evelyne; Ségurel, Laure; Toupance, Bruno

    2016-01-01

    Sexually antagonistic (SA) selection, a form of selection that can occur when both sexes have different fitness optima for a trait, is a major force shaping the evolution of organisms. A seminal model developed by Rice (Rice WR. 1984. Sex chromosomes and the evolution of sexual dimorphism. Evolution 38:735–742.) predicts that the X chromosome should be a hotspot for the accumulation of loci under SA selection as compared with the autosomes. Here, we propose a methodological framework designed to detect a specific signature of SA selection on viability, differences in allelic frequencies between the sexes. Applying this method on genome-wide single nucleotide polymorphism (SNP) data in human populations where no sex-specific population stratification could be detected, we show that there are overall significantly more SNPs exhibiting differences in allelic frequencies between the sexes on the X chromosome as compared with autosomes, supporting the predictions of Rice’s model. This pattern is consistent across populations and is robust to correction for potential biases such as differences in linkage disequilibrium, sample size, and genotyping errors between chromosomes. Although SA selection is not the only factor resulting in allelic frequency differences between the sexes, we further show that at least part of the identified X-linked loci is caused by such a sex-specific processes. PMID:27189992

  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. A ratiometric fluorescence nanosensor for highly selective and sensitive detection of selenite.

    PubMed

    Chen, Linfeng; Tian, Xike; Zhao, Yuan; Li, Yong; Yang, Chao; Zhou, Zhaoxin; Liu, Xiangwen

    2016-08-01

    The instant and on-site detection of selenium still remains a challenge for environmental monitoring and medical prevention. We herein developed a ratiometric fluorescent nanosensor for accurate and on-site sensing of SeO3(2-) by linking the recognition molecule 3,3'-diaminobenzidine (DAB) onto the surface of carboxyl group modified CdTe@SiO2. The fluorescence of DAB on the surface of silica nanospheres could be selectively and efficiently enhanced by SeO3(2-) through a surface chelating reaction between DAB and SeO3(2-). Thus, in the presence of SeO3(2-), the nanosensor would show two characteristic fluorescence emissions of Se-DAB and CdTe QDs under a single excitation wavelength. The selectivity and the optimal conditions for the detection of SeO3(2-) were carefully investigated. The ratio of F530/F635 linearly increased with increasing SeO3(2-) concentration in the range of 0 to 2.5 μM and the detection limit reaches as low as 6.68 nM (0.53 ppb). This developed nanosensor has the capability of on-site detection in an aqueous system without any separation step. The Se concentrations in selenium-rich food were detected and the results were consistent with the values determined by ICP-AES. PMID:27241591

  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. 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

  16. Evolutionary genetics of maternal effects.

    PubMed

    Wolf, Jason B; Wade, Michael J

    2016-04-01

    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

  17. 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.

  18. 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. PMID:26774580

  19. Fluorescent probes for the selective detection of chemical species inside mitochondria.

    PubMed

    Xu, Zheng; Xu, Lin

    2016-01-21

    During the last few years, the preparation of novel fluorescent probes for the selective detection of chemical species inside mitochondria has attracted considerable attention because of their wide applications in chemistry, biology, and medical science. This feature article focuses on the recent advances in the design principles and recognition mechanisms of these kinds of fluorescent probes. In addition, their applications for the detection of reactive oxygen species (ROS), nitric oxide, reactive sulfur species (RSS), thioredoxin (Trx), metal ions, anions, etc. in the mitochondrion is discussed as well.

  20. Chloride accelerated Fenton chemistry for the ultrasensitive and selective colorimetric detection of copper.

    PubMed

    Shan, Zhi; Lu, Mingsheng; Wang, Li; MacDonald, Bruce; MacInnis, Judy; Mkandawire, Martin; Zhang, Xu; Oakes, Ken D

    2016-02-01

    A highly selective, ultrasensitive (visual and instrumental detection limits of 40 nM and 0.1 nM, respectively), environmentally-friendly, simple and rapid colorimetric sensor was developed for the detection of copper(II) in water. This sensor is based on a novel signal-amplification mechanism involving reactive halide species (RHSs) including chlorides or bromides, which accelerate copper Fenton reactions oxidizing the chromogenic substrate to develop colour. The results of this study expand our understanding of copper-based Fenton chemistry. PMID:26685747

  1. 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

  2. Liquid crystal-based sensors for selective and quantitative detection of nitrogen dioxide.

    PubMed

    Sen, Avijit; Kupcho, Kurt A; Grinwald, Bart A; Vantreeck, Heidi J; Acharya, Bharat R

    2013-03-01

    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

  3. A highly selective fluorescent probe for direct detection and isolation of mouse embryonic stem cells.

    PubMed

    Chandran, Yogeswari; Kang, Nam-Young; Park, Sung-Jin; Alamudi, Samira Husen; Kim, Jun-Young; Sahu, Srikanta; Su, Dongdong; Lee, Jungyeol; Vendrell, Marc; Chang, Young-Tae

    2015-11-01

    Stem cell research has gathered immense attention in the past decade due to the remarkable ability of stem cells for self-renewal and tissue-specific differentiation. Despite having numerous advancements in stem cell isolation and manipulation techniques, there is a need for highly reliable probes for the specific detection of live stem cells. Herein we developed a new fluorescence probe (CDy9) with high selectivity for mouse embryonic stem cells. CDy9 allows the detection and isolation of intact stem cells with marginal impact on their function and capabilities. PMID:26115574

  4. 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

  5. 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. PMID:25034430

  6. Detecting Adaptive Trait Introgression Between Iris fulva and I. brevicaulis in Highly Selective Field Conditions

    PubMed Central

    Martin, Noland H.; Bouck, Amy C.; Arnold, Michael L.

    2006-01-01

    The idea that natural hybridization has served as an important force in evolutionary and adaptive diversification has gained considerable momentum in recent years. By combining genome analyses with a highly selective field experiment, we provide evidence for adaptive trait introgression between two naturally hybridizing Louisiana Iris species, flood-tolerant Iris fulva and dry-adapted I. brevicaulis. We planted reciprocal backcross (BC1) hybrids along with pure-species plants into natural settings that, due to a flooding event, favored I. fulva. As expected, I. fulva plants survived at much higher rates than I. brevicaulis plants. Backcross hybrids toward I. fulva (BCIF) also survived at significantly higher rates than the reciprocal backcross toward I. brevicaulis (BCIB). Survivorship of BCIB hybrids was strongly influenced by the presence of a number of introgressed I. fulva alleles located throughout the genome, while survivorship in the reciprocal BCIF hybrids was heavily influenced by two epistatically acting QTL of opposite effects. These results demonstrate the potential for adaptive trait introgression between these two species and may help to explain patterns of genetic variation observed in naturally occurring hybrid zones. PMID:16415358

  7. 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

  8. 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.

  9. 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.

  10. Selectable Ultrasensitive Detection of Hg(2+) with Rhodamine 6G-Modified Nanoporous Gold Optical Sensor.

    PubMed

    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 Hg(2+)-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 Hg(2+) 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

  11. Rhodium Nanoparticle-mesoporous Silicon Nanowire Nanohybrids for Hydrogen Peroxide Detection with High Selectivity

    PubMed Central

    Song, Zhiqian; Chang, Hucheng; Zhu, Weiqin; Xu, Chenlong; Feng, Xinjian

    2015-01-01

    Developing nanostructured electrocatalysts, with low overpotential, high selectivity and activity has fundamental and technical importance in many fields. We report here rhodium nanoparticle and mesoporous silicon nanowire (RhNP@mSiNW) hybrids for hydrogen peroxide (H2O2) detection with high electrocatalytic activity and selectivity. By employing electrodes that loaded with RhNP@mSiNW nanohybrids, interference caused from both many electroactive substances and dissolved oxygen were eliminated by electrochemical assaying at an optimal potential of +75 mV. Furthermore, the electrodes exhibited a high detection sensitivity of 0.53 μA/mM and fast response (< 5 s). This high-performance nanohybrid electrocatalyst has great potential for future practical application in various oxidase-base biosensors. PMID:25588953

  12. 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. PMID:24270323

  13. The Evolving Theory of Evolutionary Radiations.

    PubMed

    Simões, M; Breitkreuz, L; Alvarado, M; Baca, S; Cooper, J C; Heins, L; Herzog, K; Lieberman, B S

    2016-01-01

    Evolutionary radiations have intrigued biologists for more than 100 years, and our understanding of the patterns and processes associated with these radiations continues to grow and evolve. Recently it has been recognized that there are many different types of evolutionary radiation beyond the well-studied adaptive radiations. We focus here on multifarious types of evolutionary radiations, paying special attention to the abiotic factors that might trigger diversification in clades. We integrate concepts such as exaptation, species selection, coevolution, and the turnover-pulse hypothesis (TPH) into the theoretical framework of evolutionary radiations. We also discuss other phenomena that are related to, but distinct from, evolutionary radiations that have relevance for evolutionary biology. PMID:26632984

  14. 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.

  15. Interdigitated gate electrode field effect transistor for the selective detection of nitrogen dioxide and diisopropyl methylphosphonate

    SciTech Connect

    Kolesar, E.S. Jr.; Wiseman, J.M. )

    1989-11-01

    An interdigitated gate electrode field effect transistor (IGE-FET) coupled to an electron beam evaporated copper phthalocyanine thin film was used to selectively detect part-per-billion concentration levels of nitrogen dioxide (NO{sub 2}) and diisopropyl methylphosphonate (DIMP). The sensor is excited with a voltage pulse, and the time- and frequency-domain responses are measured. The envelopes of the magnitude of the normalized difference frequency spectrums reveal features that unambiguously distinguish NO{sub 2} and DIMP exposures.

  16. A novel donor-acceptor receptor for selective detection of Pb2+ and Fe3+ ions.

    PubMed

    Nandre, Kamlakar P; Puyad, Avinash L; Bhosale, Sheshanath V; Bhosale, Sidhanath V

    2014-12-01

    An efficient and highly selective colorimetric and fluorescent receptor DTPDA has been synthesized for sensitive detection of Pb(2+) and Fe(3+) cations. The sensor DTPDA produces a facile, cost-effective and naked eye sensing platform to determine trace amounts of Pb(2+) and Fe(3+) metal ions by complexation with pendent S-termini of thiophenes, which commonly coordinates to central N-termini of pyridine. PMID:25159385

  17. Detection limits of thin layer coulometry with ionophore based ion-selective membranes.

    PubMed

    Shvarev, Alexey; Neel, Bastien; Bakker, Eric

    2012-09-18

    We report here on a significant improvement in lowering the low detection limit of thin layer coulometric sensors based on liquid ion-selective membranes, using a potassium-selective system as a model example. Various possible processes that may result in an elevated residual current reading after electrolysis were eliminated. Self-dissolution of AgCl on the Ag/AgCl inner element may result in a residual ion flux that could adversely affect the lower detection limit. It was here replaced with an Ag/AgI inner pseudoreference electrode where the self-dissolution equilibrium is largely suppressed. Possible residual currents originating from a direct contact between inner element and ion-selective membranes were eliminated by introducing an inert PVDF separator of 50 μm diameter that was coiled around the inner element by a custom-made instrument. Finally, the influence of electrolyte fluxes from the outer solution across the membrane into the sample was evaluated by altering its lipophilic nature and reducing its concentration. It was found that this last effect is most likely responsible for the observed residual current for the potassium-selective membranes studied here. For the optimized conditions, the calibration curves demonstrated a near zero intercept, thereby paving the way to the coulometric calibration-free sensing of ionic species. A linear calibration curve for the coulometric cell with valinomycin potassium-selective membrane was obtained in the range of 100 nM to 10 μM potassium in the presence of a 10 μM sodium background. In the presence of a higher (100 μM) concentration of sodium, a reliable detection of 1-100 μM of potassium was achieved.

  18. Detection limits of thin layer coulometry with ionophore based ion-selective membranes.

    PubMed

    Shvarev, Alexey; Neel, Bastien; Bakker, Eric

    2012-09-18

    We report here on a significant improvement in lowering the low detection limit of thin layer coulometric sensors based on liquid ion-selective membranes, using a potassium-selective system as a model example. Various possible processes that may result in an elevated residual current reading after electrolysis were eliminated. Self-dissolution of AgCl on the Ag/AgCl inner element may result in a residual ion flux that could adversely affect the lower detection limit. It was here replaced with an Ag/AgI inner pseudoreference electrode where the self-dissolution equilibrium is largely suppressed. Possible residual currents originating from a direct contact between inner element and ion-selective membranes were eliminated by introducing an inert PVDF separator of 50 μm diameter that was coiled around the inner element by a custom-made instrument. Finally, the influence of electrolyte fluxes from the outer solution across the membrane into the sample was evaluated by altering its lipophilic nature and reducing its concentration. It was found that this last effect is most likely responsible for the observed residual current for the potassium-selective membranes studied here. For the optimized conditions, the calibration curves demonstrated a near zero intercept, thereby paving the way to the coulometric calibration-free sensing of ionic species. A linear calibration curve for the coulometric cell with valinomycin potassium-selective membrane was obtained in the range of 100 nM to 10 μM potassium in the presence of a 10 μM sodium background. In the presence of a higher (100 μM) concentration of sodium, a reliable detection of 1-100 μM of potassium was achieved. PMID:22917023

  19. 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). PMID:23937937

  20. A nonionic surfactant-decorated liquid crystal sensor for sensitive and selective detection of proteins.

    PubMed

    Wang, Yi; Hu, Qiongzheng; Tian, Tongtong; Gao, Yan'an; Yu, Li

    2016-09-21

    Proteins are responsible for most biochemical events in human body. It is essential to develop sensitive and selective methods for the detection of proteins. In this study, liquid crystal (LC)-based sensor for highly selective and sensitive detection of lysozyme, concanavalin A (Con A), and bovine serum albumin (BSA) was constructed by utilizing the LC interface decorated with a nonionic surfactant, dodecyl β-d-glucopyranoside. A change of the LC optical images from bright to dark appearance was observed after transferring dodecyl β-d-glucopyranoside onto the aqueous/LC interface due to the formation of stable self-assembled surfactant monolayer, regardless of pH and ion concentrations studied in a wide range. The optical images turned back from dark to bright appearance after addition of lysozyme, Con A and BSA, respectively. Noteworthy is that these proteins can be further distinguished by adding enzyme inhibitors and controlling incubation temperature of the protein solutions based on three different interaction mechanisms between proteins and dodecyl β-d-glucopyranoside, viz. enzymatic hydrolysis, specific saccharide binding, and physical absorption. The LC-based sensor decorated with dodecyl β-d-glucopyranoside shows high sensitivity for protein detection. The limit of detection (LOD) for lysozyme, Con A and BSA reaches around 0.1 μg/mL, 0.01 μg/mL and 0.001 μg/mL, respectively. These results might provide new insights into increasing selectivity and sensitivity of LC-based sensors for the detection of proteins.

  1. 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).

  2. A nonionic surfactant-decorated liquid crystal sensor for sensitive and selective detection of proteins.

    PubMed

    Wang, Yi; Hu, Qiongzheng; Tian, Tongtong; Gao, Yan'an; Yu, Li

    2016-09-21

    Proteins are responsible for most biochemical events in human body. It is essential to develop sensitive and selective methods for the detection of proteins. In this study, liquid crystal (LC)-based sensor for highly selective and sensitive detection of lysozyme, concanavalin A (Con A), and bovine serum albumin (BSA) was constructed by utilizing the LC interface decorated with a nonionic surfactant, dodecyl β-d-glucopyranoside. A change of the LC optical images from bright to dark appearance was observed after transferring dodecyl β-d-glucopyranoside onto the aqueous/LC interface due to the formation of stable self-assembled surfactant monolayer, regardless of pH and ion concentrations studied in a wide range. The optical images turned back from dark to bright appearance after addition of lysozyme, Con A and BSA, respectively. Noteworthy is that these proteins can be further distinguished by adding enzyme inhibitors and controlling incubation temperature of the protein solutions based on three different interaction mechanisms between proteins and dodecyl β-d-glucopyranoside, viz. enzymatic hydrolysis, specific saccharide binding, and physical absorption. The LC-based sensor decorated with dodecyl β-d-glucopyranoside shows high sensitivity for protein detection. The limit of detection (LOD) for lysozyme, Con A and BSA reaches around 0.1 μg/mL, 0.01 μg/mL and 0.001 μg/mL, respectively. These results might provide new insights into increasing selectivity and sensitivity of LC-based sensors for the detection of proteins. PMID:27590553

  3. 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

  4. 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.

  5. 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.

  6. 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

    2015-01-01

    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

  7. 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.

  8. Sensitive and selective electrochemical detection of artemisinin based on its reaction with p-aminophenylboronic acid.

    PubMed

    Wang, Chao; Zholudov, Yuriy T; Nsabimana, Anaclet; Xu, Guobao; Li, Jianping

    2016-09-21

    The electrochemical detection of artemisinin generally requires high oxidation potential or the use of complex electrode modification. We find that artemisinin can react with p-aminophenylboronic acid to produce easily electrochemically detectable aminophenol for the first time. By making use of the new reaction, we report an alternative method to detect artemisinin through the determination of p-aminophenol. The calibration curve for the determination of artemisinin is linear in the range of 2 μmol L(-1) to 200 μmol L(-1) with the detection limit of 0.8 μmol L(-1), which is more sensitive than other reported electrochemical methods. The relative standard deviation is 4.83% for the determination of 10 μM artemisinin. Because the oxidation potential of p-aminophenol is around 0 V, the present method is high selective. When 40 μM, 90 μM and 140 μM of artemisinin were spiked to compound naphthoquine phosphate tablet samples, the recoveries are 107.6%, 105.4% and 101.7%, respectively. This detection strategy is attractive for the detection of artemisinin and its derivatives. The finding that artemisinin can react with aromatic boronic acid has the potential to be exploited for the development of other sensors, such as fluorescence artemisinin sensors. PMID:27590543

  9. Autonomously Sensing Hydrogels for the Rapid and Selective Detection of Pathogenic Bacteria.

    PubMed

    Ebrahimi, Mir-Morteza Sadat; Laabei, Maisem; Jenkins, A Tobias A; Schönherr, Holger

    2015-12-01

    The development of a versatile approach for the rapid and sensitive detection of relevant pathogenic bacteria and autonomous signaling of the detection events in reporter hydrogel film coatings is reported. Exploiting chitosan hydrogel films equipped with chromogenic or fluorogenic reporter moieties, the presence of the Gram-negative bacterium Pseudomonas aeruginosa and the Gram-positive bacterium Staphylococcus aureus is sensed within 1 h by detecting the characteristic enzymes α-glucosidase and elastase with limits of detection (LOD) <45 × 10(-9) M and <20 × 10(-9) M, respectively, for this observation time. The values for the LOD are two to three orders of magnitude smaller than the concentrations of the enzymes detected in the corresponding bacterial supernatants. The results show that the covalently conjugated reporter moieties are exclusively and efficiently reacted by the associated enzyme, allowing in principle for discrimination among different types of bacteria. Since high enzyme concentrations are a result of proliferating bacteria, e.g., in wounds or food, and since the selectivity of the reporting function is easily adapted to bacteria of choice, these reporter hydrogels comprise an interesting platform for the rapid detection of bacteria.

  10. Determination of acenocoumarol in human plasma by capillary gas chromatography with mass-selective detection.

    PubMed

    Pommier, F; Ackermann, R; Sioufi, A; Godbillon, J

    1994-03-18

    A method for the determination of acenocoumarol in human plasma by capillary gas chromatography-mass-selective detection is described. After addition of a structurally related analogue as the internal standard, the compounds are extracted from plasma at acidic pH into toluene, back-extracted with a basic solution and re-extracted from hydrochloric acid solution with toluene, which is then evaporated to dryness. The compounds are converted into their methyl derivatives, which are determined by gas chromatography using a mass-selective detector at m/z 324 for acenocoumarol and m/z 338 for the internal standard. The reproducibility and accuracy of the method were found to be suitable over the acenocoumarol concentrations range 2.2-74 nmol/l. The method could be considered as selective for acenocoumarol in the presence of its major metabolites in plasma.

  11. 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.

  12. A highly selective and picomolar level photoelectrochemical sensor for PCB 101 detection in environmental water samples.

    PubMed

    Shi, Huijie; Zhao, Jinzhi; Wang, Yingling; Zhao, Guohua

    2016-07-15

    A highly selective and sensitive photoelectrochemical (PEC) sensor was fabricated for fast and convenient detection of PCB 101 in environmental water samples with a low detection limit of 1.0×10(-14)molL(-1) based on single crystalline TiO2 nanorods (NRs). By integration with molecular imprinting (MI) technique, the PEC sensor's selectivity towards PCB 101 was significantly improved, so that the interference caused by 100-fold excess of PCB 126 and PCB 77 which had similar structure with PCB 101 was below 37%, not to mention other coexisted pollutants. This high selectivity could be attributed to the high-quality expression of the molecular imprinting sites on the rigid and smooth surface of single crystalline TiO2 NRs on which PCB 101 could be selectively and preferentially adsorbed. The oriented and multiple halogen bonds formed between PCB 101 and the molecular imprinting sites played a critical role in improving the recognition ability of the PEC sensor. Meanwhile, the one dimensional nanorods structure of TiO2 was beneficial for the efficient separation of photogenerated electrons and holes, leading to enhanced photocurrent response and further improving the sensitivity of the PEC sensor. PMID:27016911

  13. Small sample training and test selection method for optimized anomaly detection algorithms in hyperspectral imagery

    NASA Astrophysics Data System (ADS)

    Mindrup, Frank M.; Friend, Mark A.; Bauer, Kenneth W.

    2012-01-01

    There are numerous anomaly detection algorithms proposed for hyperspectral imagery. Robust parameter design (RPD) techniques provide an avenue to select robust settings capable of operating consistently across a large variety of image scenes. Many researchers in this area are faced with a paucity of data. Unfortunately, there are no data splitting methods for model validation of datasets with small sample sizes. Typically, training and test sets of hyperspectral images are chosen randomly. Previous research has developed a framework for optimizing anomaly detection in HSI by considering specific image characteristics as noise variables within the context of RPD; these characteristics include the Fisher's score, ratio of target pixels and number of clusters. We have developed method for selecting hyperspectral image training and test subsets that yields consistent RPD results based on these noise features. These subsets are not necessarily orthogonal, but still provide improvements over random training and test subset assignments by maximizing the volume and average distance between image noise characteristics. The small sample training and test selection method is contrasted with randomly selected training sets as well as training sets chosen from the CADEX and DUPLEX algorithms for the well known Reed-Xiaoli anomaly detector.

  14. 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. PMID:26095144

  15. 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.

  16. 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.

  17. Human telomeric G-quadruplex formation and highly selective fluorescence detection of toxic strontium ions.

    PubMed

    Qu, Konggang; Zhao, Chuanqi; Ren, Jinsong; Qu, Xiaogang

    2012-03-01

    Strontium ions play important roles in biological systems. The inhalation of strontium can cause severe respiratory difficulties, anaphylactic reaction and extreme tachycardia. Strontium can replace calcium in organisms, inhibit normal calcium absorption and induce strontium "rickets" in childhood. Thus, the development of sensitive and selective methods for the determination of trace amounts of Sr(2+) in aqueous media is of considerable importance for environmental and human health protection. A number of methodologies, such as X-ray energy dispersive spectrometry, inductively coupled argon plasma atomic emission spectroscopy (ICP-AES), atomic absorption spectrometry (AAS) and instrumental thermal neutron activation analysis, have been reported. However, these methods are somewhat complex, costly, time consuming and, especially, need special instruments. Thus, the design of convenient and inexpensive approaches for the sensitive and selective detection of Sr(2+) with rapid, easy manipulation is in ever-increasing demand. To the best of our knowledge, using DNA conformational change to detect Sr(2+) has not yet been reported. Herein we utilized thiazole orange (TO) as a signal reporter to devise a simple Sr(2+) detection assay based on Sr(2+) induced human telomeric DNA conformational change in the presence of SWNTs. The limit of detection is 10 nM Sr(2+) (0.87 μg L(-1)), far below 4 mg L(-1), the U.S. Federal threshold in drinking water defined by the U.S. EPA.

  18. 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. PMID:26953730

  19. 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

  20. 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.

  1. 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.

  2. Sensitive and Selective Detection of HIV-1 RRE RNA Using Vertical Silicon Nanowire Electrode Array.

    PubMed

    Lee, Jaehyung; Hong, Min-Ho; Han, Sanghun; Na, Jukwan; Kim, Ilsoo; Kwon, Yong-Joon; Lim, Yong-Beom; Choi, Heon-Jin

    2016-12-01

    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.

  3. Selectivity and sensitivity of some thin-layer chromatographic detection systems.

    PubMed

    Fodor-Csorba, K; Dutka, F

    1986-09-19

    The selectivity and sensitivity of some thin-layer chromatographic detection systems widely used internationally and developed in our laboratory were studied. Halogenated organophosphorus pesticides were found to interfere with the detection of organochlorine pesticides when using silver nitrate-2-phenoxyethanol. The stability of colours formed by the 4-(4'-nitrobenzyl)pyridine-tetraethylenepentamine system was enhanced by spraying with acetic acid and allowed densitometric evaluation. The most sensitive detection method for thiocarbamates is the reaction with 2,6-dichlorobenzoquinone-N-chloroimine or its dibromo analogue (50 ng). Application of this method for sulphur-containing organophosphorus insecticides results in the same or better sensitivity. Quantitation of these compounds was carried out by densitometry.

  4. 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.

  5. 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.

  6. 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.

  7. Antibody modified gold nanoparticles for fast and selective, colorimetric T7 bacteriophage detection.

    PubMed

    Lesniewski, Adam; Los, Marcin; Jonsson-Niedziółka, Martin; Krajewska, Anna; Szot, Katarzyna; Los, Joanna M; Niedziolka-Jonsson, Joanna

    2014-04-16

    Herein, we report a colorimetric immunosensor for T7 bacteriophage based on gold nanoparticles modified with covalently bonded anti-T7 antibodies. The new immunosensor allows for a fast, simple, and selective detection of T7 virus. T7 virions form immunological complexes with the antibody modified gold nanoparticles which causes them to aggregate. The aggregation can be observed with the naked eye as a color change from red to purple, as well as with a UV-vis spectrophotometer. The aggregate formation was confirmed with SEM imaging. Sensor selectivity against the M13 bacteriophage was demonstrated. The limit of detection (LOD) is 1.08 × 10(10) PFU/mL (18 pM) T7. The new method was compared with a traditional plaque test. In contrast to biological tests the colorimetric method allows for detection of all T7 phages, not only those biologically active. This includes phage ghosts and fragments of virions. T7 virus has been chosen as a model organism for adenoviruses. The described method has several advantages over the traditional ones. It is much faster than a standard plaque test. It is more robust since no bacteria-virus interactions are utilized in the detection process. Since antibodies are available for a large variety of pathogenic viruses, the described concept is very flexible and can be adapted to detect many different viruses, not only bacteriophages. Contrary to the classical immunoassays, it is a one-step detection method, and no additional amplification, e.g., enzymatic, is needed to read the result.

  8. Ischemia episode detection in ECG using kernel density estimation, support vector machine and feature selection

    PubMed Central

    2012-01-01

    Background Myocardial ischemia can be developed into more serious diseases. Early Detection of the ischemic syndrome in electrocardiogram (ECG) more accurately and automatically can prevent it from developing into a catastrophic disease. To this end, we propose a new method, which employs wavelets and simple feature selection. Methods For training and testing, the European ST-T database is used, which is comprised of 367 ischemic ST episodes in 90 records. We first remove baseline wandering, and detect time positions of QRS complexes by a method based on the discrete wavelet transform. Next, for each heart beat, we extract three features which can be used for differentiating ST episodes from normal: 1) the area between QRS offset and T-peak points, 2) the normalized and signed sum from QRS offset to effective zero voltage point, and 3) the slope from QRS onset to offset point. We average the feature values for successive five beats to reduce effects of outliers. Finally we apply classifiers to those features. Results We evaluated the algorithm by kernel density estimation (KDE) and support vector machine (SVM) methods. Sensitivity and specificity for KDE were 0.939 and 0.912, respectively. The KDE classifier detects 349 ischemic ST episodes out of total 367 ST episodes. Sensitivity and specificity of SVM were 0.941 and 0.923, respectively. The SVM classifier detects 355 ischemic ST episodes. Conclusions We proposed a new method for detecting ischemia in ECG. It contains signal processing techniques of removing baseline wandering and detecting time positions of QRS complexes by discrete wavelet transform, and feature extraction from morphology of ECG waveforms explicitly. It was shown that the number of selected features were sufficient to discriminate ischemic ST episodes from the normal ones. We also showed how the proposed KDE classifier can automatically select kernel bandwidths, meaning that the algorithm does not require any numerical values of the parameters

  9. Theoretical developments in evolutionary computation

    NASA Astrophysics Data System (ADS)

    Fogel, David B.

    1999-11-01

    Recent developments in the theory of evolutionary computation offer evidence and proof that overturns several conventionally held beliefs. In particular, the no free lunch theorem and other related theorems show that there can be no best evolutionary algorithm, and that no particular variation operator or selection mechanism provides a general advantage over another choice. Furthermore, the fundamental nature of the notion of schema processing is called into question by recent theory that shows that the schema theorem does not hold when schema fitness is stochastic. Moreover, the analysis that underlies schema theory, namely the k- armed bandit analysis, does not generate a sampling plan that yields an optimal allocation of trials, as has been suggested in the literature for almost 25 years. The importance of these new findings is discussed in the context of future progress in the field of evolutionary computation.

  10. 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

  11. 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. PMID:17943131

  12. 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. PMID:25541518

  13. 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

  14. Selective Electrochemical Detection of Ciprofloxacin with a Porous Nafion/Multiwalled Carbon Nanotube Composite Film Electrode.

    PubMed

    Gayen, Pralay; Chaplin, Brian P

    2016-01-27

    This study focuses on the development of electrochemical sensors for the detection of Ciprofloxacin (CFX) in natural waters and wastewater effluents. The sensors are prepared by depositing a layer of multiwalled carbon nanotubes (MWCNTs) dispersed in a porous Nafion film on to a boron-doped diamond (BDD) electrode substrate. The porous-Nafion-MWCNT/BDD electrode enhanced detection of CFX due to selective adsorption, which was accomplished by a combination of electrostatic attraction at -SO3(-) sites in the porous Nafion film and the formation of charge assisted hydrogen bonding between CFX and -COOH MWCNT surface functional groups. By contrast, the bare BDD electrode did not show any activity for CFX oxidation. The sensors were selective for CFX detection in the presence of other antibiotics (i.e., amoxicillin) and other nontarget water constituents (i.e., Cl(-), Ca(2+), humic acid, sodium dodecylbenzenesulfonate, salicylic acid, 4-aminobenzoic acid, and 4-hydroxybenzoic acid). A limit of detection of 5 nM (S/N = 5.04 ± 0.26) in a 0.1 M KH2PO4 supporting electrolyte (pH = 4.5) was obtained using differential pulse voltammetry. The linear dynamic ranges with respect to CFX concentration were 0.005-0.05 μM and 0.05-10 μM, and the sensitivities were 41 ± 5.2 μA μM(-1) and 2.1 ± 0.22 μA μM(-1), respectively. Sensor fouling was observed at high concentrations of some organic compounds such as 1 mM 4-aminobenzoic acid and 4-hydroxybenzoic acid. However, a short cathodic treatment fully restores sensor response. The results indicate that these sensors have application in detecting CFX in natural waters and wastewater effluents. PMID:26711553

  15. Selective Electrochemical Detection of Ciprofloxacin with a Porous Nafion/Multiwalled Carbon Nanotube Composite Film Electrode.

    PubMed

    Gayen, Pralay; Chaplin, Brian P

    2016-01-27

    This study focuses on the development of electrochemical sensors for the detection of Ciprofloxacin (CFX) in natural waters and wastewater effluents. The sensors are prepared by depositing a layer of multiwalled carbon nanotubes (MWCNTs) dispersed in a porous Nafion film on to a boron-doped diamond (BDD) electrode substrate. The porous-Nafion-MWCNT/BDD electrode enhanced detection of CFX due to selective adsorption, which was accomplished by a combination of electrostatic attraction at -SO3(-) sites in the porous Nafion film and the formation of charge assisted hydrogen bonding between CFX and -COOH MWCNT surface functional groups. By contrast, the bare BDD electrode did not show any activity for CFX oxidation. The sensors were selective for CFX detection in the presence of other antibiotics (i.e., amoxicillin) and other nontarget water constituents (i.e., Cl(-), Ca(2+), humic acid, sodium dodecylbenzenesulfonate, salicylic acid, 4-aminobenzoic acid, and 4-hydroxybenzoic acid). A limit of detection of 5 nM (S/N = 5.04 ± 0.26) in a 0.1 M KH2PO4 supporting electrolyte (pH = 4.5) was obtained using differential pulse voltammetry. The linear dynamic ranges with respect to CFX concentration were 0.005-0.05 μM and 0.05-10 μM, and the sensitivities were 41 ± 5.2 μA μM(-1) and 2.1 ± 0.22 μA μM(-1), respectively. Sensor fouling was observed at high concentrations of some organic compounds such as 1 mM 4-aminobenzoic acid and 4-hydroxybenzoic acid. However, a short cathodic treatment fully restores sensor response. The results indicate that these sensors have application in detecting CFX in natural waters and wastewater effluents.

  16. 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

  17. Novel screening assay for the selective detection of G-protein-coupled receptor heteromer signaling.

    PubMed

    van Rijn, Richard M; Harvey, Jessica H; Brissett, Daniela I; DeFriel, Julia N; Whistler, Jennifer L

    2013-01-01

    Drugs targeting G-protein-coupled receptors (GPCRs) make up more than 25% of all prescribed medicines. The ability of GPCRs to form heteromers with unique signaling properties suggests an entirely new and unexplored pool of drug targets. However, current in vitro assays are ill equipped to detect heteromer-selective compounds. We have successfully adapted an approach, using fusion proteins of GPCRs and chimeric G proteins, to create an in vitro screening assay (in human embryonic kidney cells) in which only activated heteromers are detectable. Here we show that this assay can demonstrate heteromer-selective G-protein bias as well as measure transinhibition. Using this assay, we reveal that the δ-opioid receptor agonist ADL5859, which is currently in clinical trials, has a 10-fold higher potency against δ-opioid receptor homomers than δ/μ-opioid receptor heteromers (pEC(50) = 6.7 ± 0.1 versus 5.8 ± 0.2). The assay enables the screening of large compound libraries to identify heteromer-selective compounds that could then be used in vivo to determine the functional role of heteromers and develop potential therapeutic agents.

  18. A highly selective electrochemical impedance spectroscopy-based aptasensor for sensitive detection of acetamiprid.

    PubMed

    Fan, Lifang; Zhao, Guohua; Shi, Huijie; Liu, Meichuan; Li, Zhengxin

    2013-05-15

    A simple aptasensor for sensitive and selective detection of acetamiprid has been developed based on electrochemical impedance spectroscopy (EIS). To improve sensitivity of the aptasensor, gold nanoparticles (AuNPs) were electrodeposited on the bare gold electrode surface by cycle voltammetry (CV), which was employed as a platform for aptamer immobilization. With the addition of acetamiprid, the formation of acetamiprid-aptamer complex on the AuNPs-deposited electrode surface resulted in an increase of electron transfer resistance (Ret). The change of Ret strongly depends on acetamiprid concentration, which is applied for acetamiprid quantification. A wide linear range was obtained from 5 to 600nM with a low detection limit of 1nM. The control experiments performed by employing the pesticides that may coexist or have similar structure with acetamiprid demonstrate that the aptasensor has only specific recognition to acetamiprid, resulting in high selectivity of the aptasensor. The dissociation constant, Kd of 23.41nM for acetamiprid-aptamer complex has been determined from the differential capacitance (Cd) by assuming a Langmuir isotherm, which indicates strong interaction between acetamiprid and aptamer, further proving high selectivity of the aptasensor. Besides, the applicability of the developed aptasensor has been successfully evaluated by determining acetamiprid in the real samples, wastewater and tomatoes. PMID:23274191

  19. A Highly Sensitive ESIPT-Based Ratiometric Fluorescence Sensor for Selective Detection of Al(3.).

    PubMed

    Sinha, Sanghamitra; Chowdhury, Bijit; Ghosh, Pradyut

    2016-09-19

    An excited-state intramolecular proton transfer (ESIPT)-based highly sensitive ratiometric fluorescence sensor, 1H was developed for selective detection of aluminum (Al(3+)) in acetonitrile as well as in 90% aqueous system. Single-crystal X-ray diffraction analysis reveals almost planar and conjugated structure of 1H. Photophysical properties of the sensor as well as its selectivity toward Al(3+) are explored using UV-visible, steady-state, and time-resolved fluorescence spectroscopic studies. The bright cyan (λem = 445 nm) fluorescence of 1H in acetonitrile turns into deep blue (λem = 412 nm) with ∼2.3-fold enhancement in emission intensity, in the presence of parts per billion level Al(3+) (detection limit = 0.5 nM). Interestingly, the probe 1H exhibits increased selectivity toward Al(3+) in H2O/acetonitrile (9:1 v/v) solvent system with a change in fluorescence color from pale green to deep blue associated with ca. sixfold enhancement in emission intensity. Density functional theoretical (DFT) calculations provide the ground- and excited-state energy optimized structures and properties of the proposed aluminum complex [Al(1) (OH)]2(2+), which is in harmony with the solution-state experimental findings and also supports the occurrence of ESIPT process in 1H. The ESIPT mechanism was also ascertained by comparing the basic photophysical properties of 1H with a similar O-methylated analogue, 1'Me. PMID:27571218

  20. Hydrazide d-luciferin for in vitro selective detection and intratumoral imaging of Cu(2.).

    PubMed

    Zheng, Zhen; Wang, Lin; Tang, Wei; Chen, Peiyao; Zhu, Hui; Yuan, Yue; Li, Gongyu; Zhang, Huafeng; Liang, Gaolin

    2016-09-15

    Copper is an essential micronutrient involved in fundamental life processes but using a bioluminescence (BL) probe to selectively sense Cu(2+)in vitro or image Cu(2+)in vivo is still unavailable. Herein, a latent BL probe hydrazide d-luciferin (1) was rationally designed and successfully applied it for selective detection of Cu(2+)in vitro and imaging Cu(2+) in living cells and in tumors. Upon the catalysis of Cu(2+), 1 was converted to d-luciferin and turned on the BL in the presence of firefly luciferase (fLuc). In vitro tests indicated that 1 could be applied for highly selective sensing Cu(2+) within the range of 0-80μM with a limit of detection (LOD) of 39.0nM. Cell and animal experiments indicated that 1 could be applied for specific BL imaging of Cu(2+) in living cells and tumors and the BL signal of 1 was more stable and longer than that of d-luciferin. We envision that this unique probe 1 might serve as an elucidative tool for further exploration of the biological roles of Cu(2+) in physiological and pathological processes in the near future. PMID:27131992

  1. 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. PMID:24466567

  2. 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.

  3. 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.

  4. 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

  5. Ultrasensitive and selective non-enzymatic glucose detection using copper nanowires.

    PubMed

    Zhang, Yuchan; Su, Liang; Manuzzi, Dan; de los Monteros, Honorio Valdés Espinosa; Jia, Wenzhao; Huo, Danqun; Hou, Changjun; Lei, Yu

    2012-01-15

    In the pursuit of more economical electrocatalysts for non-enzymatic glucose sensors, one-dimensional Cu nanowires (Cu NWs) with uniform size distribution and a large aspect ratio (>200) were synthesized by a facile, scalable, wet-chemistry approach. The morphology, crystallinity, and surface property of the as-prepared Cu NWs were examined by SEM, XRD, and XPS, respectively. The electrochemical property of Cu NWs for glucose electrooxidation was thoroughly investigated by cyclic voltammetry. In the amperometric detection of glucose, the Cu NWs modified glassy carbon electrode exhibited an extraordinary limit of detection as low as 35 nM and a wide dynamic range with excellent sensitivity of 420.3 μA cm(-2) mM(-1), which was more than 10,000 times higher than that of the control electrode without Cu NWs. The performance of the developed glucose sensor was also independent to oxygen concentration and free from chloride poisoning. Furthermore, the interference from uric acid, ascorbic acid, acetaminophen, fructose, and sucrose at the level of their physiological concentration were insignificant, indicating excellent selectivity. Finally, good accuracy and high precision for the quantification of glucose concentration in human serum samples implicate the applicability of Cu NWs in sensitive and selective non-enzymatic glucose detection. PMID:22154404

  6. 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. PMID:26515011

  7. 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.

  8. 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.

  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. 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.

  11. Synthesis of Au/graphene oxide composites for selective and sensitive electrochemical detection of ascorbic acid.

    PubMed

    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

  12. 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

    2014-01-01

    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 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. PMID:25005836

  13. Synthesis of Au/graphene oxide composites for selective and sensitive electrochemical detection of ascorbic acid.

    PubMed

    Song, Jian; Xu, Lin; Xing, Ruiqing; Li, Qingling; Zhou, Chunyang; Liu, Dali; Song, Hongwei

    2014-12-17

    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.

  14. 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.

  15. 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.

  16. Chitosan coated carbon fiber microelectrode for selective in vivo detection of neurotransmitters in live zebrafish embryos.

    PubMed

    Ozel, Rıfat Emrah; Wallace, Kenneth N; Andreescu, Silvana

    2011-06-10

    We report the development of a chitosan modified carbon fiber microelectrode for in vivo detection of serotonin. We find that chitosan has the ability to reject physiological levels of ascorbic acid interferences and facilitate selective and sensitive detection of in vivo levels of serotonin, a common catecholamine neurotransmitter. Presence of chitosan on the microelectrode surface was investigated using scanning electron microscopy (SEM) and cyclic voltammetry (CV). The electrode was characterized using differential pulse voltammetry (DPV). A detection limit of 1.6 nM serotonin with a sensitivity of 5.12 nA/μM, a linear range from 2 to 100 nM and a reproducibility of 6.5% for n=6 electrodes were obtained. Chitosan modified microelectrodes selectively measure serotonin in presence of physiological levels of ascorbic acid. In vivo measurements were performed to measure concentration of serotonin in the live embryonic zebrafish intestine. The sensor quantifies in vivo intestinal levels of serotonin while successfully rejecting ascorbic acid interferences. We demonstrate that chitosan can be used as an effective coating to reject ascorbic acid interferences at carbon fiber microelectrodes, as an alternative to Nafion, and that chitosan modified microelectrodes are reliable tools for in vivo monitoring of changes in neurotransmitter levels. PMID:21601035

  17. Chitosan coated carbon fiber microelectrode for selective in vivo detection of neurotransmitters in live zebrafish embryos

    PubMed Central

    Özel, Rıfat Emrah; Wallace, Kenneth N.; Andreescu, Silvana

    2011-01-01

    We report the development of a chitosan modified carbon fiber microelectrode for in vivo detection of serotonin. We find that chitosan has the ability to reject physiological levels of ascorbic acid interferences and facilitate selective and sensitive detection of in vivo levels of serotonin, a common catecholamine neurotransmitter. Presence of chitosan on the microelectrode surface was investigated using scanning electron microscopy (SEM) and cyclic voltammetry (CV). The electrode was characterized using differential pulse voltammetry (DPV). A detection limit of 1.6 nM serotonin with a sensitivity of 5.12 nA/µM, a linear range from 2 to 100 nM and a reproducibility of 6.5 % for n=6 electrodes were obtained. Chitosan modified microelectrodes selectively measure serotonin in presence of physiological levels of ascorbic acid. In vivo measurements were performed to measure concentration of serotonin in the live embryonic zebrafish intestine. The sensor quantifies in vivo intestinal levels of serotonin while successfully rejecting ascorbic acid interferences. We demonstrate that chitosan can be used as an effective coating to reject ascorbic acid interferences at carbon fiber microelectrodes, as an alternative to Nafion, and that chitosan modified microelectrodes are reliable tools for in vivo monitoring of changes in neurotransmitter levels. PMID:21601035

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. Identifying signatures of sexual selection using genomewide selection components analysis

    PubMed Central

    Flanagan, Sarah P; Jones, Adam G

    2015-01-01

    Sexual selection must affect the genome for it to have an evolutionary impact, yet signatures of selection remain elusive. Here we use an individual-based model to investigate the utility of genome-wide selection components analysis, which compares allele frequencies of individuals at different life history stages within a single population to detect selection without requiring a priori knowledge of traits under selection. We modeled a diploid, sexually reproducing population and introduced strong mate choice on a quantitative trait to simulate sexual selection. Genome-wide allele frequencies in adults and offspring were compared using weighted FST values. The average number of outlier peaks (i.e., those with significantly large FST values) with a quantitative trait locus in close proximity (“real” peaks) represented correct diagnoses of loci under selection, whereas peaks above the FST significance threshold without a quantitative trait locus reflected spurious peaks. We found that, even with moderate sample sizes, signatures of strong sexual selection were detectable, but larger sample sizes improved detection rates. The model was better able to detect selection with more neutral markers, and when quantitative trait loci and neutral markers were distributed across multiple chromosomes. Although environmental variation decreased detection rates, the identification of real peaks nevertheless remained feasible. We also found that detection rates can be improved by sampling multiple populations experiencing similar selection regimes. In short, genome-wide selection components analysis is a challenging but feasible approach for the identification of regions of the genome under selection. PMID:26257884

  3. Rotating disk potentiometry for inner solution optimization of low-detection-limit ion-selective electrodes.

    PubMed

    Radu, Aleksandar; Telting-Diaz, Martin; Bakker, Eric

    2003-12-15

    The extent of optimization of the lower detection limit of ion-selective electrodes (ISEs) can be assessed with an elegant new method. At the detection limit (i.e., in the absence of primary ions in the sample), one can observe a reproducible change in the membrane potential upon alteration of the aqueous diffusion layer thickness. This stir effect is predicted to depend on the composition of the inner solution, which is known to influence the lower detection limit of the potentiometric sensor dramatically. For an optimized electrode, the stir effect is calculated to be exactly one-half the value of the case when substantial coextraction occurs at the inner membrane side. In contrast, there is no stir effect when substantial ion exchange occurs at the inner membrane side. Consequently, this experimental method can be used to determine how well the inner filling solution has been optimized. A rotating disk electrode was used in this study because it provides adequate control of the aqueous diffusion layer thickness. Various ion-selective membranes with a variety of inner solutions that gave different calculated concentrations of the complex at the inner membrane side were studied to evaluate this principle. They contained the well-examined silver ionophore O,O' '-bis[2-(methylthio)ethyl]-tert-butylcalix[4]arene, the potassium ionophore valinomycin, or the iodide carrier [9]mercuracarborand-3. Stir effects were determined in different background solutions and compared to theoretical expectations. Correlations were good, and the results encourage the use of such stir-effect measurements to optimize ISE compositions for real-world applications. The technique was also found to be useful in estimating the level of primary ion impurities in the sample. For an iodide-selective electrode measured in phosphoric acid, for example, apparent iodide impurity levels were calculated as 5 x 10(-10) M.

  4. 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.

  5. Highly selective detection of individual nuclear spins with rotary echo on an electron spin probe

    DOE PAGESBeta

    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

  6. Selection of aptamers against inactive Vibrio alginolyticus and application in a qualitative detection assay.

    PubMed

    Tang, Xuemin; Zheng, Jiang; Yan, Qinpi; Li, Zhongbao; Li, Yubao

    2013-06-01

    Aptamers against inactive Vibrio alginolyticus were selected from an 82-nt ssDNA random library by systematic evolution of ligands by exponential enrichment. After 15 rounds of selection, the final pool of aptamers was highly specific for inactivated V. alginolyticus and had a dissociation constant of 27.5 ± 9.2 nM. Using these aptamers and PCR, V. alginolyticus could be detected at 100 cells/ml. Sequencing of the final pool of aptamers revealed that some sequences, termed high-frequency aptamers, appeared more than once; these may be of practical application. All sequences obtained were divided into nine families according to their homology tree, some conserved sequences were also found in each of the six families. One sequence was found in significant proportions of the aptamers, suggesting that this conserved sequence might be important for forming the three-dimensional aptamer structure.

  7. 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

  8. Cyclic Peptide-Decorated Self-Assembled Nanohybrids for Selective Recognition and Detection of Multivalent RNAs.

    PubMed

    Choi, Jun Shik; Han, So-hee; Kim, Hyoseok; Lim, Yong-Beom

    2016-03-16

    Although there has been substantial advancement in the development of nanostructures, the development of self-assembled nanostructures that can selectively recognize multivalent targets has been very difficult. Here we show the proof of concept that topology-controlled peptide nanoassemblies can selectively recognize and detect a multivalent RNA target. We compared the differential behaviors of peptides in a linear or cyclic topology in terms of peptide-gold nanoparticle hybrid nanostructure formation, conformational stabilization, monovalent and multivalent RNA binding in vitro, and multivalent RNA recognition in live cells. When the topology-dependent selectivity amplification of the cyclic peptide hybrids is combined with the noninvasive nature of dark-field microscopy, the cellular localization of the viral Rev response element (RRE) RNA can be monitored in situ. Because intracellular interactions are often mediated by overlapping binding partners with weak affinity, the topology-controlled peptide assemblies can provide a versatile means to convert weak ligands into multivalent ligands with high affinity and selectivity.

  9. A Wearable Channel Selection-Based Brain-Computer Interface for Motor Imagery Detection

    PubMed Central

    Lo, Chi-Chun; Chien, Tsung-Yi; Chen, Yu-Chun; Tsai, Shang-Ho; Fang, Wai-Chi; Lin, Bor-Shyh

    2016-01-01

    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. PMID:26861347

  10. 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.

  11. 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.

  12. 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.

  13. Selective identification and quantification of saccharin by liquid chromatography and fluorescence detection.

    PubMed

    Bruno, Sergio N F; Cardoso, Carlos R; Maciel, Márcia Mosca A; Vokac, Lidmila; da Silva Junior, Ademário I

    2014-09-15

    High-pressure liquid chromatography with ultra-violet detection (HPLC-UV) is one of the most commonly used methods to identify and quantify saccharin in non-alcoholic beverages. However, due to the wide variety of interfering UV spectra in saccharin-containing beverage matrices, the same method cannot be used to measure this analyte accurately. We have developed a new, highly effective method to identify and quantify saccharin using HPLC with fluorescence detection (HPLC-FLD). The excitation wavelength (250 nm) and emission wavelength (440 nm) chosen increased selectivity for all matrices and ensured few changes were required in the mobile phase or other parameters. The presence of saccharin in non-diet beverages - a fraud commonly used to replace more expensive sucrose - was confirmed by comparing coincident peaks as well as the emission spectra of standards and samples.

  14. 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

  15. Identifying predictors of time-inhomogeneous viral evolutionary processes

    PubMed Central

    Bielejec, Filip; Baele, Guy; Rodrigo, Allen G.; Suchard, Marc A.; Lemey, Philippe

    2016-01-01

    Various factors determine the rate at which mutations are generated and fixed in viral genomes. Viral evolutionary rates may vary over the course of a single persistent infection and can reflect changes in replication rates and selective dynamics. Dedicated statistical inference approaches are required to understand how the complex interplay of these processes shapes the genetic diversity and divergence in viral populations. Although evolutionary models accommodating a high degree of complexity can now be formalized, adequately informing these models by potentially sparse data, and assessing the association of the resulting estimates with external predictors, remains a major challenge. In this article, we present a novel Bayesian evolutionary inference method, which integrates multiple potential predictors and tests their association with variation in the absolute rates of synonymous and non-synonymous substitutions along the evolutionary history. We consider clinical and virological measures as predictors, but also changes in population size trajectories that are simultaneously inferred using coalescent modelling. We demonstrate the potential of our method in an application to within-host HIV-1 sequence data sampled throughout the infection of multiple patients. While analyses of individual patient populations lack statistical power, we detect significant evidence for an abrupt drop in non-synonymous rates in late stage infection and a more gradual increase in synonymous rates over the course of infection in a joint analysis across all patients. The former is predicted by the immune relaxation hypothesis while the latter may be in line with increasing replicative fitness during the asymptomatic stage. PMID:27774306

  16. 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.

  17. 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.

  18. 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.

  19. Selective detection of ordered sodium signals by a jump-and-return pulse sequence

    NASA Astrophysics Data System (ADS)

    Lee, Jae-Seung; Regatte, Ravinder R.; Jerschow, Alexej

    2009-09-01

    A simple pulse sequence, derived from the shaped pulse optimally exciting the central transition of a spin 3/2, can be used to selectively detect ordered sodium with a given quadrupolar coupling. The pulse sequence consists of two pulses with opposite phases and separated by a delay, called a quadrupolar jump-and-return (QJR) sequence. This QJR sequence is tested with a phantom made of sodium ions in bacteriophage and in aqueous solution and its feasibility for contrast modification based on the quadrupolar coupling is demonstrated.

  20. Detection of Bacillus larvae spores in Argentinian honeys by using a semi-selective medium.

    PubMed

    Alippi, A M

    1995-09-01

    A semi-selective medium for the detection in Argentinian honeys of spores of Bacillus larvae, a pathogen of American foulbrood, was developed. The technique involves dilution of samples (1:2) in phosphate buffer, concentration of spores by centrifugation and heat treatment prior to inoculation. Two media (JNxPa and JNxPb) were prepared from J-agar, to which nalidixic acid and pipemidic acid were added. Both JNxP media were reliable for the isolation of B. larvae colonies and, at the same time, prevented the development of other Bacillus species which normally develop on the plates before B. larvae spores can germinate.

  1. Fast, sensitive point of care electrochemical molecular system for point mutation and select agent detection.

    PubMed

    MacLeod, J A; Nemeth, A C; Dicke, W C; Wang, D; Manalili Wheeler, S; Hannis, J C; Collier, G B; Drader, J J

    2016-07-01

    Point of care molecular diagnostics benefits from a portable battery-operated device capable of performing a fast turnaround using reliable inexpensive cartridges. We describe a prototype device for performing a molecular diagnostics test for clinical and biodefense samples in 16 minutes using a prototype capable of an 8 minute PCR reaction, followed by hybridization and detection on an electrochemical microarray based on the i-STAT® system. We used human buccal swabs for hemochromatosis testing including in-device DNA extraction. Additional clinical and biodefense samples included influenza A and bacterial select agents Bacillus anthracis, Yersinia pestis and Francisella tularensis. PMID:27280174

  2. Detecting selection in population trees: the Lewontin and Krakauer test extended.

    PubMed

    Bonhomme, Maxime; Chevalet, Claude; Servin, Bertrand; Boitard, Simon; Abdallah, Jihad; Blott, Sarah; Sancristobal, Magali

    2010-09-01

    Detecting genetic signatures of selection is of great interest for many research issues. Common approaches to separate selective from neutral processes focus on the variance of F(ST) across loci, as does the original Lewontin and Krakauer (LK) test. Modern developments aim to minimize the false positive rate and to increase the power, by accounting for complex demographic structures. Another stimulating goal is to develop straightforward parametric and computationally tractable tests to deal with massive SNP data sets. Here, we propose an extension of the original LK statistic (T(LK)), named T(F-LK), that uses a phylogenetic estimation of the population's kinship (F) matrix, thus accounting for historical branching and heterogeneity of genetic drift. Using forward simulations of single-nucleotide polymorphisms (SNPs) data under neutrality and selection, we confirm the relative robustness of the LK statistic (T(LK)) to complex demographic history but we show that T(F-LK) is more powerful in most cases. This new statistic outperforms also a multinomial-Dirichlet-based model [estimation with Markov chain Monte Carlo (MCMC)], when historical branching occurs. Overall, T(F-LK) detects 15-35% more selected SNPs than T(LK) for low type I errors (P < 0.001). Also, simulations show that T(LK) and T(F-LK) follow a chi-square distribution provided the ancestral allele frequencies are not too extreme, suggesting the possible use of the chi-square distribution for evaluating significance. The empirical distribution of T(F-LK) can be derived using simulations conditioned on the estimated F matrix. We apply this new test to pig breeds SNP data and pinpoint outliers using T(F-LK), otherwise undetected using the less powerful T(LK) statistic. This new test represents one solution for compromise between advanced SNP genetic data acquisition and outlier analyses.

  3. A novel OFET-based biosensor for the selective and sensitive detection of lactate levels.

    PubMed

    Minami, Tsuyoshi; Sato, Tsubasa; Minamiki, Tsukuru; Fukuda, Kenjiro; Kumaki, Daisuke; Tokito, Shizuo

    2015-12-15

    Biosensors based on organic field effect transistors (OFETs) are one of the more promising device applications in organic electronics. However, OFET-based biosensors are still in their early stages of development compared to other electrochemical biosensors. This study is the first to report on an extended-gate type organic field effect transistor (OFET) for lactate detection in aqueous media. Here, the extended-gate electrode of the OFET was modified with layers of a lactate oxidase and a horseradish peroxidase osmium-redox polymer on a flexible plastic film substrate for an enzymatic redox reaction of lactate. The device exhibited both high selectivity and sensitivity. The limit of detection (LOD) and the limit of quantification (LOQ) were estimated to be 66 nM and 220 nM, respectively, which are the sufficient detection limit for practical sensor applications. The obtained results confirm that extended-gate type OFET devices are applicable to enzyme-based biosensors for detecting lactate levels. PMID:26101795

  4. Assembly of polythiophenes on responsive polymer microgels for the highly selective detection of ammonia gas

    DOE PAGESBeta

    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 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

  5. A ratiometric chemodosimeter for highly selective naked-eye and fluorogenic detection of cyanide.

    PubMed

    Lin, Wei-Chi; Hu, Jiun-Wei; Chen, Kew-Yu

    2015-09-17

    A simple indole-based chemosensor (1) with a very low molecular weight of 207 g mol(-1) has been synthesized for the highly reactive and selective detection of CN(-) in aqueous media, even in the presence of other anions, such as F(-), Cl(-), Br(-), AcO(-), [Formula: see text] , SCN(-), [Formula: see text] , [Formula: see text] , [Formula: see text] , BzO(-), [Formula: see text] , and [Formula: see text] . The sensor achieves rapid detection of cyanide anion in 2 min, and the pseudo-first-order rate constant is estimated as 1.576 min(-1). The colorimetric and ratiometric fluorescent response of the sensor to CN(-) is attributable to the addition of CN(-) to the electron-deficient dicyanovinyl group of 1, which prevents intramolecular charge transfer. The sensing mechanism is supported by density functional theory and time-dependent density functional theory calculations. Moreover, sensor 1 exhibits both high accuracy in determining the concentration of CN(-) in real samples and 1-based test strips can conveniently detect CN(-) without any additional equipment. The detection limit of the sensor 1 (1.1 μM) for cyanide is lower than the maximum permissible level of CN(-) (1.9 μM) in drinking water.

  6. 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.

  7. 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

  8. Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle

    PubMed Central

    2011-01-01

    Background 'Selection signatures' delimit regions of the genome that are, or have been, functionally important and have therefore been under either natural or artificial selection. In this study, two different and complementary methods--integrated Haplotype Homozygosity Score (|iHS|) and population differentiation index (FST)--were applied to identify traces of decades of intensive artificial selection for traits of economic importance in modern cattle. Results We scanned the genome of a diverse set of dairy and beef breeds from Germany, Canada and Australia genotyped with a 50 K SNP panel. Across breeds, a total of 109 extreme |iHS| values exceeded the empirical threshold level of 5% with 19, 27, 9, 10 and 17 outliers in Holstein, Brown Swiss, Australian Angus, Hereford and Simmental, respectively. Annotating the regions harboring clustered |iHS| signals revealed a panel of interesting candidate genes like SPATA17, MGAT1, PGRMC2 and ACTC1, COL23A1, MATN2, respectively, in the context of reproduction and muscle formation. In a further step, a new Bayesian FST-based approach was applied with a set of geographically separated populations including Holstein, Brown Swiss, Simmental, North American Angus and Piedmontese for detecting differentiated loci. In total, 127 regions exceeding the 2.5 per cent threshold of the empirical posterior distribution were identified as extremely differentiated. In a substantial number (56 out of 127 cases) the extreme FST values were found to be positioned in poor gene content regions which deviated significantly (p < 0.05) from the expectation assuming a random distribution. However, significant FST values were found in regions of some relevant genes such as SMCP and FGF1. Conclusions Overall, 236 regions putatively subject to recent positive selection in the cattle genome were detected. Both |iHS| and FST suggested selection in the vicinity of the Sialic acid binding Ig-like lectin 5 gene on BTA18. This region was recently reported

  9. 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

  10. 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

  11. 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.

  12. Cellulose-lanthanum hydroxide nanocomposite as a selective marker for detection of toxic copper.

    PubMed

    Marwani, Hadi M; Lodhi, Mazhar Ullah; Khan, Sher Bahadar; Asiri, Abdullah M

    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

  13. 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

  14. 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)

  15. On the complexity of triggering evolutionary radiations.

    PubMed

    Bouchenak-Khelladi, Yanis; Onstein, Renske E; Xing, Yaowu; Schwery, Orlando; Linder, H Peter

    2015-07-01

    Recent developments in phylogenetic methods have made it possible to reconstruct evolutionary radiations from extant taxa, but identifying the triggers of radiations is still problematic. Here, we propose a conceptual framework to explore the role of variables that may impact radiations. We classify the variables into extrinsic conditions vs intrinsic traits, whether they provide background conditions, trigger the radiation, or modulate the radiation. We used three clades representing angiosperm phylogenetic and structural diversity (Ericaceae, Fagales and Poales) as test groups. We located radiation events, selected variables potentially associated with diversification, and inferred the temporal sequences of evolution. We found 13 shifts in diversification regimes in the three clades. We classified the associated variables, and determined whether they originated before the relevant radiation (backgrounds), originated simultaneously with the radiations (triggers), or evolved later (modulators). By applying this conceptual framework, we establish that radiations require both extrinsic conditions and intrinsic traits, but that the sequence of these is not important. We also show that diversification drivers can be detected by being more variable within a radiation than conserved traits that only allow occupation of a new habitat. This framework facilitates exploration of the causative factors of evolutionary radiations.

  16. 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.

  17. 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.

  18. An Amidochlorin-Based Colorimetric Fluorescent Probe for Selective Cu(2+) Detection.

    PubMed

    Li, Wenting; Zhu, Guohua; Li, Jinghua; Wang, Zhiqiang; Jin, Yingxue

    2016-01-01

    The design and synthesis of selective and sensitive chemosensors for the quantification of environmentally and biologically important ionic species has attracted widespread attention. Amidochlorin p6 (ACP); an effective colorimetric and fluorescent probe for copper ions (Cu(2+)) in aqueous solution derived from methyl pheophorbide-a (MPa) was designed and synthesized. A remarkable color change from pale yellow to blue was easily observed by the naked eye upon addition of Cu(2+); and a fluorescence quenching was also determined. The research of fluorescent quenching of ACP-Cu(2+) complexation showed the detection limit was 7.5 × 10(-8) mol/L; which suggested that ACP can act as a high sensitive probe for Cu(2+) and can be used to quantitatively detect low levels of Cu(2+) in aqueous solution. In aqueous solution the probe exhibits excellent selectivity and sensitivity toward Cu(2+) ions over other metal ions (M = Zn(2+); Ni(2+); Ba(2+); Ag⁺; Co(2+); Na⁺; K⁺; Mg(2+); Cd(2+); Pb(2+); Mn(2+); Fe(3+); and Ca(2+)). The obvious change from pale yellow to blue upon the addition of Cu(2+) could make it a suitable "naked eye" indicator for Cu(2+). PMID:26797591

  19. 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.

  20. Tension promoted circular probe for highly selective microRNA detection and imaging.

    PubMed

    Tang, Yaqin; Wang, Tingting; Chen, Ming; He, Xiao; Qu, Xiaohuan; Feng, Xuli

    2016-11-15

    The crucial role of miRNA in cell regulation and its connection with diverse human cancers as a tumor suppressor or an oncogenic fragment poses great demand for an accurate and rapid approach for highly efficient miRNA detection and imaging in live cells. However, the ability to selectively detect and image miRNA remains a significant challenge in biomedical fields. Herein, a sealed circular probe (CP) has been prepared with copper free click ligation. The big tension force of the ring structure greatly increases the sequence recognition specificity. Toehold initiated strand displacement of CP further amplify the selectivity for miRNA determination. Impressively, the different site of single base mismatch could even be discriminated. More importantly, CP was successfully applied for imaging endogenous miRNA expression in live cells. We believe that this new probe would find wide application in profiling of endogenous miRNA and be potential candidate method for helping us diagnosing miRNA related diseases. PMID:27162146

  1. 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

  2. DNA aptamer-based fiber optic biosensor for selective and label-free detection of dopamine

    NASA Astrophysics Data System (ADS)

    Zibaii, M. I.; Latifi, H.; Asadollahi, A.; Bayat, A. H.; Haghparast, A.

    2015-09-01

    Dopamine (DA) analysis is complicated by the interference from other electrochemically active endogenous compounds present in the brain, including DA precursors and metabolites and other neurotransmitters (NT). Here we report a simple, sensitive and selective optical fiber biosensor for the detection of DA in the presence of other NT. It is composed of a 57-mer dopamine-binding aptamer (DBA) as recognition element and nonadiabatic tapered optical fiber (NATOF) as probe. Upon the addition of DA, the conformation of DBA would change from a random coil structure to a rigid tertiary structure like a pocket. The conformational change of DBA lead to the refractive index (RI) change around the tapered fiber surface. Specific recognition of DA by the aptamer allowed a selective optical detection of DA within the physiologically relevant 500 nM to 10 μM range. Some common interferents such as epinephrine (EP) and ascorbic acid (AA) showed no or just a little interference in the determination of DA.

  3. 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. PMID:26485176

  4. Frequency-selective absorbance detection: Refractive index and turbidity compensation with dual-wavelength measurement.

    PubMed

    Eom, In-Yong; Dasgupta, Purnendu K

    2006-06-15

    A frequency-selective absorbance detection approach and its applications are described. First, a digital signal processor-lock-in amplifier (DSP-LIA)-based absorbance detector was evaluated. Compared to a simple operational amplifier (TL082CP)-based detector, the DSP-LIA-based detector showed lower noise levels, but the relative advantage was reduced under very low photocurrent levels (down to few nA). A 7cm pathlength flow cell with this commercial LIA-based detector exhibited excellent Beer's law linearity (r(2)=0.9999) and a noise level of 7 micro absorbance units (muAU). The limit of detection (LOD, S/N=3) for methyl orange (MO) was 7nM with this detector. Finally, as a more affordable alternative to an LIA, a balanced demodulator integrated circuit chip was used to fabricate a dual wavelength-frequency-selective LED-based absorbance detector. This device successfully compensated refractive index (RI) effect and turbidity effect in test flow systems. The LOD for MO with this system was 8nM.

  5. Selective detection of live bacteria combining propidium monoazide sample treatment with microarray technology.

    PubMed

    Nocker, Andreas; Mazza, Alberto; Masson, Luke; Camper, Anne K; Brousseau, Roland

    2009-03-01

    The use of DNA-based molecular detection tools for bacterial diagnostics is hampered by the inability to distinguish signals originating from live and dead cells. The detection of live cells is typically most relevant in molecular diagnostics. DNA-intercalating dyes like ethidium monoazide and propidium monoazide (PMA) offer a possibility to selectively remove cells with compromised cell membranes from the analysis. Once these dyes enter a cell, they bind to DNA and can be covalently crosslinked to it by light exposure. PCR amplification of such modified DNA is strongly inhibited. In this study we evaluated the suitability of propidium monoazide treatment to exclude isopropanol-killed cells from detection in defined mixtures using diagnostic microarray technology. The organisms comprised Pseudomonas aeruginosa, Listeria monocytogenes, Salmonella typhimurium, Serratia marcescens, and Escherichia coli O157:H7. PCR products obtained from amplification of chaperonin 60 genes (cpn60; coding for GroEL) were hybridized to a custom-designed microarray containing strain-specific cpn60-based 35-mer oligonucleotide probes. Results were compared with data from quantitative PCR, which confirmed that PMA could successfully inhibit amplification of DNA from killed cells in the mixtures. Although microarray data based on analysis of end-point PCR amplicons is not quantitative, results showed a significant signal reduction when targeting killed cells and consistently agreed with qPCR results. Treatment of samples with PMA in combination with diagnostic microarray detection can therefore be considered beneficial when analyzing mixtures of intact and membrane-compromised cells. Minimization of detection signals deriving from dead cells will render data more relevant in studies including pathogen risk assessment.

  6. 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.

  7. [THE APPLICATION OF SELECTIVE CHROMOGENIC AGAR FOR DETECTING ENTEROBACTERIA WITH PRODUCTION OF BETA-LACTAMASES].

    PubMed

    Korobova, A G; Frolova, L N; Kliasova, G A

    2015-11-01

    The detection of enterobacteria with production of beta-lactamases of extended spectrum in selective chromogenic agar was analyzed The results ofdetection of beta-lactamases of extended spectrum was compared with "double disc" technique. The smears from mucous membrane of guttur and rectum from patients were analyzed in parallel on solid growth agar (Endo or Mac Conkey) and on selective agar CHROMagartm ESBL (CHROMagar France). The production of beta-lactamases of extended spectrum was confirmed using "double discs" technique. To exclude hyper-production of ampC beta-lactamases E-test was applied containing cefotetan and cefotetan with cloxacillin. The sampling consisted of 1552 samples from patients. The study permitted to isolate 1243 strains of enterobacteria on agar Endo or Mac Conkey and 409 strains of enterobacteria on selective agar CHROMagartm ESBL (Escherichia coli n = 226, Klebsiella pneumoniae n = 105, enterobacter spp. n = 35, Citrobacter spp. n = 21, others n = 22). The application of "double discs" technique confirmed production of beta-lactamases of extended spectrum in 386 (94%) out of 409 strains isolated on agar CHROMagartm ESBL. In 23 (6%) of strains no confirmation was established and hyper-production of ampC of beta-lactamases was established 15 out of total. Additionally, 8 were sensitive to cephalosporin of third generation. All enterobacteria isolated on agar Endo or Mac Conkey also were tested by "double discs" technique. Overall, 394 strains of enterobacteria with production of beta-lactamases of extended spectrum were obtained. On all agars (agar Endo or Mac Conkey and CHROMagartm ESBL)--263 (67%) strains; only on CHROMagartm ESBL--123 (31%) and only on agar Endo or Mac Conkey--8 (2%) (p < 0.0001). The sensitivity of selective agar CHROMagartm ESBL made up to 98% and specificity--97%. The resolution about detection of enterobacteria producing beta-lactamases of extended spectrum were submitted to clinic in 18-24 hours after arrival

  8. [THE APPLICATION OF SELECTIVE CHROMOGENIC AGAR FOR DETECTING ENTEROBACTERIA WITH PRODUCTION OF BETA-LACTAMASES].

    PubMed

    Korobova, A G; Frolova, L N; Kliasova, G A

    2015-11-01

    The detection of enterobacteria with production of beta-lactamases of extended spectrum in selective chromogenic agar was analyzed The results ofdetection of beta-lactamases of extended spectrum was compared with "double disc" technique. The smears from mucous membrane of guttur and rectum from patients were analyzed in parallel on solid growth agar (Endo or Mac Conkey) and on selective agar CHROMagartm ESBL (CHROMagar France). The production of beta-lactamases of extended spectrum was confirmed using "double discs" technique. To exclude hyper-production of ampC beta-lactamases E-test was applied containing cefotetan and cefotetan with cloxacillin. The sampling consisted of 1552 samples from patients. The study permitted to isolate 1243 strains of enterobacteria on agar Endo or Mac Conkey and 409 strains of enterobacteria on selective agar CHROMagartm ESBL (Escherichia coli n = 226, Klebsiella pneumoniae n = 105, enterobacter spp. n = 35, Citrobacter spp. n = 21, others n = 22). The application of "double discs" technique confirmed production