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Sample records for chemically diverse analytes

  1. Separation and Quantification of Chemically Diverse Analytes in Neutron Irradiated Fissile Materials

    SciTech Connect

    Douglas, Matthew; Friese, Judah I.; Greenwood, Lawrence R.; Farmer, Orville T.; Thomas, Linda MP; Maiti, Tapas C.; Finn, Erin C.; Garofoli, Stephanie J.; Gassman, Paul L.; Huff, Morgan M.; Schulte, Shannon M.; Smith, Steven C.; Thomas, Kathie K.; Bachelor, Paula P.

    2009-10-01

    Quantitative measurement of fission and activation products resulting from neutron irradiation of fissile materials is of interest for applications in environmental monitoring, nuclear waste management, and national security. To overcome mass and spectral interferences, and the relative small quantities of some target analytes, an extensive series of chemical separations is necessary. Based on established separations processes involving co-precipitation, solvent extraction, and ion-exchange and extraction chromatography, we have been evaluating and optimizing a proposed sequence of separation steps to allow for the timely quantification of analytes of interest. For simplicity, much of the chemical separation development work has been performed using stable elements as surrogates for the radioactive material. We have recently evaluated the optimized procedures using an irradiated sample to examine the adequacy of separations for measurement of desired analytes by gamma spectrometry. Here we present the results of this evaluation and describe the radiochemical separations utilized.

  2. Sensor for detecting and differentiating chemical analytes

    DOEpatents

    Yi, Dechang; Senesac, Lawrence R.; Thundat, Thomas G.

    2011-07-05

    A sensor for detecting and differentiating chemical analytes includes a microscale body having a first end and a second end and a surface between the ends for adsorbing a chemical analyte. The surface includes at least one conductive heating track for heating the chemical analyte and also a conductive response track, which is electrically isolated from the heating track, for producing a thermal response signal from the chemical analyte. The heating track is electrically connected with a voltage source and the response track is electrically connected with a signal recorder. The microscale body is restrained at the first end and the second end and is substantially isolated from its surroundings therebetween, thus having a bridge configuration.

  3. Analytic considerations for measuring environmental chemicals in breast milk.

    PubMed Central

    Needham, Larry L; Wang, Richard Y

    2002-01-01

    The presence of environmental chemicals in human breast milk is of general concern because of the potential health consequence of these chemicals to the breast-fed infant and the mother. In addition to the mother's exposure, several features determine the presence of environmental chemicals in breast milk and their ability to be determined analytically. These include maternal factors and properties of the environmental chemical--both physical and chemical--such as its lipid solubility, degree of ionization, and molecular weight. Environmental chemicals with high lipid solubility are likely to be found in breast milk; they include polyhalogenated compounds such as polychlorinated biphenyls, polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans, organochlorine insecticides, and polybrominated diphenylethers. These fat-soluble chemicals are incorporated into the milk as it is synthesized, and they must be measured in accordance with the fat content of the milk to allow for meaningful comparisons within an individual and among populations. Although the analytic approach selected to measure the environmental chemical is predominantly determined by the characteristics of the chemical, the concentration of the chemical in the milk sample and the existence of structurally similar chemicals (e.g., congeners) must be considered as well. In general, the analytic approach for measuring environmental chemicals in breast milk is similar to the approach for measuring the same chemicals in other matrices, except special considerations must be given for the relatively high fat content of milk. The continued efforts of environmental scientists to measure environmental chemicals in breast milk is important for defining the true contribution of these chemicals to public health, especially to the health of the newborn. Work is needed for identifying and quantifying additional environmental chemicals in breast milk from the general population and for developing analytic

  4. Analytical methods applied to diverse types of Brazilian propolis

    PubMed Central

    2011-01-01

    Propolis is a bee product, composed mainly of plant resins and beeswax, therefore its chemical composition varies due to the geographic and plant origins of these resins, as well as the species of bee. Brazil is an important supplier of propolis on the world market and, although green colored propolis from the southeast is the most known and studied, several other types of propolis from Apis mellifera and native stingless bees (also called cerumen) can be found. Propolis is usually consumed as an extract, so the type of solvent and extractive procedures employed further affect its composition. Methods used for the extraction; analysis the percentage of resins, wax and insoluble material in crude propolis; determination of phenolic, flavonoid, amino acid and heavy metal contents are reviewed herein. Different chromatographic methods applied to the separation, identification and quantification of Brazilian propolis components and their relative strengths are discussed; as well as direct insertion mass spectrometry fingerprinting. Propolis has been used as a popular remedy for several centuries for a wide array of ailments. Its antimicrobial properties, present in propolis from different origins, have been extensively studied. But, more recently, anti-parasitic, anti-viral/immune stimulating, healing, anti-tumor, anti-inflammatory, antioxidant and analgesic activities of diverse types of Brazilian propolis have been evaluated. The most common methods employed and overviews of their relative results are presented. PMID:21631940

  5. Analytic models of the chemical evolution of galaxies

    NASA Technical Reports Server (NTRS)

    Clayton, Donald D.

    1986-01-01

    Techniques are described for constructing analytic models of the chemical evolution of galaxies subject to infall of metal-poor material onto a maturing disk. A class of linear models is discussed which takes the star-formation rate within a defined region to be proportional to the mass of interstellar gas within that region, and the instantaneous recycling approximation is adopted. The solutions are obtained by approximately matching the infall rate to parametrized familiies of functions for which the equations are exactly soluble. The masses, the primary and secondary metallicities, and the gas concentrations of radioactive chronometers can all then be analytically expressed. Surveys of galactic abundances in location and in time can be compared to the parameter spaces of the analytic representations.

  6. A decision analytic approach to exposure-based chemical prioritization.

    PubMed

    Mitchell, Jade; Pabon, Nicolas; Collier, Zachary A; Egeghy, Peter P; Cohen-Hubal, Elaine; Linkov, Igor; Vallero, Daniel A

    2013-01-01

    The manufacture of novel synthetic chemicals has increased in volume and variety, but often the environmental and health risks are not fully understood in terms of toxicity and, in particular, exposure. While efforts to assess risks have generally been effective when sufficient data are available, the hazard and exposure data necessary to assess risks adequately are unavailable for the vast majority of chemicals in commerce. The US Environmental Protection Agency has initiated the ExpoCast Program to develop tools for rapid chemical evaluation based on potential for exposure. In this context, a model is presented in which chemicals are evaluated based on inherent chemical properties and behaviorally-based usage characteristics over the chemical's life cycle. These criteria are assessed and integrated within a decision analytic framework, facilitating rapid assessment and prioritization for future targeted testing and systems modeling. A case study outlines the prioritization process using 51 chemicals. The results show a preliminary relative ranking of chemicals based on exposure potential. The strength of this approach is the ability to integrate relevant statistical and mechanistic data with expert judgment, allowing for an initial tier assessment that can further inform targeted testing and risk management strategies. PMID:23940664

  7. A Thermo-Chemical Reactor for analytical atomic spectrometry

    NASA Astrophysics Data System (ADS)

    Gilmutdinov, A. Kh.; Nagulin, K. Yu.

    2009-01-01

    A novel atomization/vaporization system for analytical atomic spectrometry is developed. It consists of two electrically and thermally separated parts that can be heated separately. Unlike conventional electrothermal atomizers in which atomization occurs immediately above the vaporization site and at the same instant of time, the proposed system allows analyte atomization via an intermediate stage of fractional condensation as a two stage process: Vaporization → Condensation → Atomization. The condensation step is selective since vaporized matrix constituents are mainly non-condensable gases and leave the system by diffusion while analyte species are trapped on the cold surface of a condenser. This kind of sample distillation keeps all the advantages of traditional electrothermal atomization and allows significant reduction of matrix interferences. Integration into one design a vaporizer, condenser and atomizer gives much more flexibility for in situ sample treatment and thus the system is called a Thermo-Chemical Reactor (TCR). Details of the design, temperature measurements, vaporization-condensation-atomization mechanisms of various elements in variety of matrices are investigated in the TCR with spectral, temporal and spatial resolution. The ability of the TCR to significantly reduce interferences and to conduct sample pyrolysis at much higher temperatures as compared to conventional electrothermal atomizers is demonstrated. The analytical potential of the system is shown when atomic absorption determination of Cd and Pb in citrus leaves and milk powder without the use of any chemical modification.

  8. Unifying Approach to Analytical Chemistry and Chemical Analysis: Problem-Oriented Role of Chemical Analysis.

    ERIC Educational Resources Information Center

    Pardue, Harry L.; Woo, Jannie

    1984-01-01

    Proposes an approach to teaching analytical chemistry and chemical analysis in which a problem to be resolved is the focus of a course. Indicates that this problem-oriented approach is intended to complement detailed discussions of fundamental and applied aspects of chemical determinations and not replace such discussions. (JN)

  9. Chemically Modifying Viruses for Diverse Applications.

    PubMed

    Mohan, Kritika; Weiss, Gregory A

    2016-05-20

    Long fascinating to biologists, viruses offer nanometer-scale benchtops for building molecular-scale devices and materials. Viruses tolerate a wide range of chemical modifications including reaction conditions, pH values, and temperatures. Recent examples of nongenetic manipulation of viral surfaces have extended viruses into applications ranging from biomedical imaging, drug delivery, tissue regeneration, and biosensors to materials for catalysis and energy generation. Chemical reactions on the phage surface include both covalent and noncovalent modifications, including some applied in conjunction with genetic modifications. Here, we survey viruses chemically augmented with capabilities limited only by imagination. PMID:26930417

  10. A Decision Analytic Approach to Exposure-Based Chemical Prioritization

    PubMed Central

    Mitchell, Jade; Pabon, Nicolas; Collier, Zachary A.; Egeghy, Peter P.; Cohen-Hubal, Elaine; Linkov, Igor; Vallero, Daniel A.

    2013-01-01

    The manufacture of novel synthetic chemicals has increased in volume and variety, but often the environmental and health risks are not fully understood in terms of toxicity and, in particular, exposure. While efforts to assess risks have generally been effective when sufficient data are available, the hazard and exposure data necessary to assess risks adequately are unavailable for the vast majority of chemicals in commerce. The US Environmental Protection Agency has initiated the ExpoCast Program to develop tools for rapid chemical evaluation based on potential for exposure. In this context, a model is presented in which chemicals are evaluated based on inherent chemical properties and behaviorally-based usage characteristics over the chemical’s life cycle. These criteria are assessed and integrated within a decision analytic framework, facilitating rapid assessment and prioritization for future targeted testing and systems modeling. A case study outlines the prioritization process using 51 chemicals. The results show a preliminary relative ranking of chemicals based on exposure potential. The strength of this approach is the ability to integrate relevant statistical and mechanistic data with expert judgment, allowing for an initial tier assessment that can further inform targeted testing and risk management strategies. PMID:23940664

  11. Analytical Chemical Sensing in the Submillimeter/terahertz Spectral Range

    NASA Astrophysics Data System (ADS)

    Moran, Benjamin L.; Fosnight, Alyssa M.; Medvedev, Ivan R.; Neese, Christopher F.

    2012-06-01

    Highly sensitive and selective Terahertz sensor utilized to quantitatively analyze a complex mixture of Volatile Organic Compounds is reported. To best demonstrate analytical capabilities of THz chemical sensors we chose to perform analytical quantitative analysis of a certified gas mixture using a novel prototype chemical sensor that couples a commercial preconcentration system (Entech 7100A) to a high resolution THz spectrometer. We selected Method TO-14A certified mixture of 39 volatile organic compounds (VOCs) diluted to 1 part per million (ppm) in nitrogen. 26 of the 39 chemicals were identified by us as suitable for THz spectroscopic detection. Entech 7100A system is designed and marketed as an inlet system for Gas Chromatography-Mass Spectrometry (GC-MS) instruments with a specific focus on TO-14 and TO-15 EPA sampling methods. Its preconcentration efficiency is high for the 39 chemicals in the mixture used for this study and our preliminary results confirm this. Here we present the results of this study which serves as basis for our ongoing research in environmental sensing and analysis of exhaled human breath.

  12. New chemical evolution analytical solutions including environment effects

    NASA Astrophysics Data System (ADS)

    Spitoni, E.

    2015-07-01

    In the last years, more and more interest has been devoted to analytical solutions, including inflow and outflow, to study the metallicity enrichment in galaxies. In this framework, we assume a star formation rate which follows a linear Schmidt law, and we present new analytical solutions for the evolution of the metallicity (Z) in galaxies. In particular, we take into account environmental effects including primordial and enriched gas infall, outflow, different star formation efficiencies and galactic fountains. The enriched infall is included to take into account galaxy-galaxy interactions. Our main results can be summarized as: (i) when a linear Schmidt law of star formation is assumed, the resulting time evolution of the metallicity Z is the same either for a closed-box model or for an outflow model. (ii) The mass-metallicity relation for galaxies which suffer a chemically enriched infall, originating from another evolved galaxy with no pre-enriched gas, is shifted down in parallel at lower Z values, if compared to the closed box model. (iii) When a galaxy suffers at the same time a primordial infall and a chemically enriched one, the primordial infall always dominates the chemical evolution. (iv) We present new solutions for the metallicity evolution in a galaxy which suffers galactic fountains and an enriched infall from another galaxy at the same time. The analytical solutions presented here can be very important to study the metallicity (oxygen), which is measured in high-redshift objects. These solutions can be very useful: (a) in the context of cosmological semi-analytical models for galaxy formation and evolution, and (b) for the study of compact groups of galaxies.

  13. Analytical Derivation of Moment Equations in Stochastic Chemical Kinetics

    PubMed Central

    Sotiropoulos, Vassilios; Kaznessis, Yiannis N.

    2011-01-01

    The master probability equation captures the dynamic behavior of a variety of stochastic phenomena that can be modeled as Markov processes. Analytical solutions to the master equation are hard to come by though because they require the enumeration of all possible states and the determination of the transition probabilities between any two states. These two tasks quickly become intractable for all but the simplest of systems. Instead of determining how the probability distribution changes in time, we can express the master probability distribution as a function of its moments, and, we can then write transient equations for the probability distribution moments. In 1949, Moyal defined the derivative, or jump, moments of the master probability distribution. These are measures of the rate of change in the probability distribution moment values, i.e. what the impact is of any given transition between states on the moment values. In this paper we present a general scheme for deriving analytical moment equations for any N-dimensional Markov process as a function of the jump moments. Importantly, we propose a scheme to derive analytical expressions for the jump moments for any N-dimensional Markov process. To better illustrate the concepts, we focus on stochastic chemical kinetics models for which we derive analytical relations for jump moments of arbitrary order. Chemical kinetics models are widely used to capture the dynamic behavior of biological systems. The elements in the jump moment expressions are a function of the stoichiometric matrix and the reaction propensities, i.e the probabilistic reaction rates. We use two toy examples, a linear and a non-linear set of reactions, to demonstrate the applicability and limitations of the scheme. Finally, we provide an estimate on the minimum number of moments necessary to obtain statistical significant data that would uniquely determine the dynamics of the underlying stochastic chemical kinetic system. The first two moments

  14. JOVIAN STRATOSPHERE AS A CHEMICAL TRANSPORT SYSTEM: BENCHMARK ANALYTICAL SOLUTIONS

    SciTech Connect

    Zhang Xi; Shia Runlie; Yung, Yuk L.

    2013-04-20

    We systematically investigated the solvable analytical benchmark cases in both one- and two-dimensional (1D and 2D) chemical-advective-diffusive systems. We use the stratosphere of Jupiter as an example but the results can be applied to other planetary atmospheres and exoplanetary atmospheres. In the 1D system, we show that CH{sub 4} and C{sub 2}H{sub 6} are mainly in diffusive equilibrium, and the C{sub 2}H{sub 2} profile can be approximated by modified Bessel functions. In the 2D system in the meridional plane, analytical solutions for two typical circulation patterns are derived. Simple tracer transport modeling demonstrates that the distribution of a short-lived species (such as C{sub 2}H{sub 2}) is dominated by the local chemical sources and sinks, while that of a long-lived species (such as C{sub 2}H{sub 6}) is significantly influenced by the circulation pattern. We find that an equator-to-pole circulation could qualitatively explain the Cassini observations, but a pure diffusive transport process could not. For slowly rotating planets like the close-in extrasolar planets, the interaction between the advection by the zonal wind and chemistry might cause a phase lag between the final tracer distribution and the original source distribution. The numerical simulation results from the 2D Caltech/JPL chemistry-transport model agree well with the analytical solutions for various cases.

  15. Leaf chemical and spectral diversity in Australian tropical forests.

    PubMed

    Asner, Gregory P; Martin, Roberta E; Ford, Andrew J; Metcalfe, Daniel J; Liddell, Michael J

    2009-01-01

    Leaf chemical and spectral properties of 162 canopy species were measured at 11 tropical forest sites along a 6024 mm precipitation/yr and 8.7 degrees C climate gradient in Queensland, Australia. We found that variations in foliar nitrogen, phosphorus, chlorophyll a and b, and carotenoid concentrations, as well as specific leaf area (SLA), were expressed more strongly among species within a site than along the entire climate gradient. Integrated chemical signatures consisting of all leaf properties did not aggregate well at the genus or family levels. Leaf chemical diversity was maximal in the lowland tropical forest sites with the highest temperatures and moderate precipitation levels. Cooler and wetter montane tropical forests contained species with measurably lower variation in their chemical signatures. Foliar optical properties measured from 400 to 2500 nm were also highly diverse at the species level, and were well correlated with an ensemble of leaf chemical properties and SLA (r2 = 0.54-0.83). A probabilistic diversity model amplified the leaf chemical differences among species, revealing that lowland tropical forests maintain a chemical diversity per unit richness far greater than that of higher elevation forests in Australia. Modeled patterns in spectral diversity and species richness paralleled those of chemical diversity, demonstrating a linkage between the taxonomic and remotely sensed properties of tropical forest canopies. We conclude that species are the taxonomic unit causing chemical variance in Australian tropical forest canopies, and thus ecological and remote sensing studies should consider the role that species play in defining the functional properties of these forests. PMID:19323186

  16. Chemical diversity in basil (Ocimum sp.) germplasm.

    PubMed

    da Costa, Andréa Santos; Arrigoni-Blank, Maria de Fátima; de Carvalho Filho, José Luiz Sandes; de Santana, Aléa Dayane Dantas; Santos, Darlisson de Alexandria; Alves, Péricles Barreto; Blank, Arie Fitzgerald

    2015-01-01

    The present study aimed to chemically characterize 31 accessions and seven cultivars of basil. The percentage composition of the essential oils of the accessions and cultivars was based on the 14 most abundant constituents: 1,8-cineole, linalool, methyl chavicol, neral, nerol, geraniol, geranial, methyl cinnamate, β-bourbonene, methyl eugenol, α-trans-bergamotene, germacrene-D, epi-α-cadinol, and δ-cadinene. The genetic materials were classified into eight clusters according to the chemical composition of the essential oils: Cluster 1--mostly linalool and 1,8-cineole; Cluster 2--mostly linalool, geraniol, and α-trans-bergamotene; Cluster 3--mostly linalool, methyl chavicol, methyl cinnamate, and β-bourbonene; Cluster 4--mostly linalool, methyl chavicol, epi-α-cadinol, and α-trans-bergamotene; Cluster 5--mainly linalool, methyl eugenol, α-trans-bergamotene, and epi-α-cadinol; Cluster 6--mainly linalool, geraniol, and epi-α-cadinol; Cluster 7--mostly linalool and methyl chavicol; Cluster 8--mainly geranial and neral. PMID:25629084

  17. Chemical Diversity, Origin, and Analysis of Phycotoxins.

    PubMed

    Rasmussen, Silas Anselm; Andersen, Aaron John Christian; Andersen, Nikolaj Gedsted; Nielsen, Kristian Fog; Hansen, Per Juel; Larsen, Thomas Ostenfeld

    2016-03-25

    Microalgae, particularly those from the lineage Dinoflagellata, are very well-known for their ability to produce phycotoxins that may accumulate in the marine food chain and eventually cause poisoning in humans. This includes toxins accumulating in shellfish, such as saxitoxin, okadaic acid, yessotoxins, azaspiracids, brevetoxins, and pinnatoxins. Other toxins, such as ciguatoxins and maitotoxins, accumulate in fish, where, as is the case for the latter compounds, they can be metabolized to even more toxic metabolites. On the other hand, much less is known about the chemical nature of compounds that are toxic to fish, the so-called ichthyotoxins. Despite numerous reports of algal blooms causing massive fish kills worldwide, only a few types of compounds, such as the karlotoxins, have been proven to be true ichthyotoxins. This review will highlight marine microalgae as the source of some of the most complex natural compounds known to mankind, with chemical structures that show no resemblance to what has been characterized from plants, fungi, or bacteria. In addition, it will summarize algal species known to be related to fish-killing blooms, but from which ichthyotoxins are yet to be characterized. PMID:26901085

  18. Chemical Diversity in Basil (Ocimum sp.) Germplasm

    PubMed Central

    da Costa, Andréa Santos; Arrigoni-Blank, Maria de Fátima; de Carvalho Filho, José Luiz Sandes; de Santana, Aléa Dayane Dantas; Santos, Darlisson de Alexandria; Alves, Péricles Barreto; Blank, Arie Fitzgerald

    2015-01-01

    The present study aimed to chemically characterize 31 accessions and seven cultivars of basil. The percentage composition of the essential oils of the accessions and cultivars was based on the 14 most abundant constituents: 1,8-cineole, linalool, methyl chavicol, neral, nerol, geraniol, geranial, methyl cinnamate, β-bourbonene, methyl eugenol, α-trans-bergamotene, germacrene-D, epi-α-cadinol, and δ-cadinene. The genetic materials were classified into eight clusters according to the chemical composition of the essential oils: Cluster 1—mostly linalool and 1,8-cineole; Cluster 2—mostly linalool, geraniol, and α-trans-bergamotene; Cluster 3—mostly linalool, methyl chavicol, methyl cinnamate, and β-bourbonene; Cluster 4—mostly linalool, methyl chavicol, epi-α-cadinol, and α-trans-bergamotene; Cluster 5—mainly linalool, methyl eugenol, α-trans-bergamotene, and epi-α-cadinol; Cluster 6—mainly linalool, geraniol, and epi-α-cadinol; Cluster 7—mostly linalool and methyl chavicol; Cluster 8—mainly geranial and neral. PMID:25629084

  19. Chemical diversity in the comet population

    NASA Astrophysics Data System (ADS)

    Biver, Nicolas

    2015-08-01

    For the last 3 decades, infrared and microwave techniques have enabled the detection of up to 25 different parent molecules in the coma of comets. Several molecules have been detected in over 40 different comets. A large diversity of composition is seen in the sample, comprising comets of various dynamical origin. Abundances relative to water for the molecules can vary by a factor 3 to more than 10. The taxonomic study of a sample of comets in which the abundance of several molecules (e.g., HCN, CH3OH, CO, CH4, C2H6, H2S, H2CO, CH3CN, cs,...) has been measured does not show any clear grouping. Except for fragments of a common parent comet, every comet observed shows a different composition. The absence of any clear correlation between the volatile content of the comets and their dynamical origin (Kuiper Belt versus Oort Cloud) suggest that there is no clear dychotomy between two origins for the comets. Their diveristy in composition may also suggest that radial and temporal mixing in the early protoplanetary nebula may have played an important role.

  20. Secondary metallicity in analytic models of chemical evolution of galaxies

    NASA Technical Reports Server (NTRS)

    Clayton, D. D.; Pantelaki, I.

    1986-01-01

    Analytic models of the chemical evolution of galactic regions that grow in mass owing to the continuous infall of matter are characterized, emphasizing the solutions for secondary nuclei (defined as those nuclei whose stellar yields are proportional to the abundance of a primary seed nucleus) in the families of models described by Clayton (1984 and 1985). Wide variations in time dependence of both primary and secondary nuclei as well as in the ratio of secondary to primary are displayed by these model families, confirming again the usefulness of these families as interpretive guides if galaxies do in fact evolve with substantial infall. Additionally, analytic solutions are presented for two other possible interesting systems: the evolution of abundances if the primary metallicity in the infall is increasing in time, and the evolution of abundances if the primary yield changes linearly with time owing to continuous changes in the stellar mass function, the opacity, or other astrophysical agents. Finally, test evaluations of the instantaneous recycling approximation on which these analytic models rely are presented.

  1. Amazonian functional diversity from forest canopy chemical assembly.

    PubMed

    Asner, Gregory P; Martin, Roberta E; Tupayachi, Raul; Anderson, Christopher B; Sinca, Felipe; Carranza-Jiménez, Loreli; Martinez, Paola

    2014-04-15

    Patterns of tropical forest functional diversity express processes of ecological assembly at multiple geographic scales and aid in predicting ecological responses to environmental change. Tree canopy chemistry underpins forest functional diversity, but the interactive role of phylogeny and environment in determining the chemical traits of tropical trees is poorly known. Collecting and analyzing foliage in 2,420 canopy tree species across 19 forests in the western Amazon, we discovered (i) systematic, community-scale shifts in average canopy chemical traits along gradients of elevation and soil fertility; (ii) strong phylogenetic partitioning of structural and defense chemicals within communities independent of variation in environmental conditions; and (iii) strong environmental control on foliar phosphorus and calcium, the two rock-derived elements limiting CO2 uptake in tropical forests. These findings indicate that the chemical diversity of western Amazonian forests occurs in a regionally nested mosaic driven by long-term chemical trait adjustment of communities to large-scale environmental filters, particularly soils and climate, and is supported by phylogenetic divergence of traits essential to foliar survival under varying environmental conditions. Geographically nested patterns of forest canopy chemical traits will play a role in determining the response and functional rearrangement of western Amazonian ecosystems to changing land use and climate. PMID:24591585

  2. Amazonian functional diversity from forest canopy chemical assembly

    PubMed Central

    Asner, Gregory P.; Martin, Roberta E.; Tupayachi, Raul; Anderson, Christopher B.; Sinca, Felipe; Carranza-Jiménez, Loreli; Martinez, Paola

    2014-01-01

    Patterns of tropical forest functional diversity express processes of ecological assembly at multiple geographic scales and aid in predicting ecological responses to environmental change. Tree canopy chemistry underpins forest functional diversity, but the interactive role of phylogeny and environment in determining the chemical traits of tropical trees is poorly known. Collecting and analyzing foliage in 2,420 canopy tree species across 19 forests in the western Amazon, we discovered (i) systematic, community-scale shifts in average canopy chemical traits along gradients of elevation and soil fertility; (ii) strong phylogenetic partitioning of structural and defense chemicals within communities independent of variation in environmental conditions; and (iii) strong environmental control on foliar phosphorus and calcium, the two rock-derived elements limiting CO2 uptake in tropical forests. These findings indicate that the chemical diversity of western Amazonian forests occurs in a regionally nested mosaic driven by long-term chemical trait adjustment of communities to large-scale environmental filters, particularly soils and climate, and is supported by phylogenetic divergence of traits essential to foliar survival under varying environmental conditions. Geographically nested patterns of forest canopy chemical traits will play a role in determining the response and functional rearrangement of western Amazonian ecosystems to changing land use and climate. PMID:24591585

  3. Galactic chemical evolution and nucleocosmochronology - Analytic quadratic models

    NASA Technical Reports Server (NTRS)

    Clayton, D. D.

    1985-01-01

    Quadratic models of the chemical evolution of the Galaxy for a star formation rate proportional to the square of the gas mass are studied. The search for analytic solutions to the gas mass and star mass for time-dependent rates of gaseous infall onto the disk is examined. The quadratic models are compared to models having linear star formation rates. The mass, metallicity, number of stars, and U-235/U-238 isotopic ratio for the models which are subjected to the same infall rate, the same initial disk mass, and the same final gas fraction are compared. The results of the comparison indicate that: (1) the average dwarf age is greater in the quadratic model, (2) the metallicity grows initially faster in the quadratic model, (3) the quadratic model has a smaller percentage of low-Z dwarfs, and (4) the U-235/U-238 isotopic ratio indicates a younger quadratic model.

  4. Analytical techniques for the detection and identification of chemical warfare materials from environmental samples

    SciTech Connect

    Beaudry, W.T.; Weimaster, J.F.

    1995-06-01

    The detection and identification of chemical warfare (CW) material in diverse and complex matrices has become increasingly important to support the environmental clean-up of military and industrial sites that were historically used in the research, production, use, storage and/or demilitarization of chemical weapons. Reliable and defensible identification of hazardous materials (HM) is necessary to comply with the increasingly stringent regulations imposed by local, state, and federal agencies which govern handling, treatment, storage, and disposal of HM. In addition, before sites can be reutilized, existing HM must be properly identified so that the proper methods of removal, treatment and disposal can be determined. An overview of sample preparation and analytical techniques for the detection and identification of CW materials is presented in this paper.

  5. Pretreatment and integrated analysis of spectral data reveal seaweed similarities based on chemical diversity.

    PubMed

    Wei, Feifei; Ito, Kengo; Sakata, Kenji; Date, Yasuhiro; Kikuchi, Jun

    2015-03-01

    Extracting useful information from high dimensionality and large data sets is a major challenge for data-driven approaches. The present study was aimed at developing novel integrated analytical strategies for comprehensively characterizing seaweed similarities based on chemical diversity. The chemical compositions of 107 seaweed and 2 seagrass samples were analyzed using multiple techniques, including Fourier transform infrared (FT-IR) and solid- and solution-state nuclear magnetic resonance (NMR) spectroscopy, thermogravimetry-differential thermal analysis (TG-DTA), inductively coupled plasma-optical emission spectrometry (ICP-OES), CHNS/O total elemental analysis, and isotope ratio mass spectrometry (IR-MS). The spectral data were preprocessed using non-negative matrix factorization (NMF) and NMF combined with multivariate curve resolution-alternating least-squares (MCR-ALS) methods in order to separate individual component information from the overlapping and/or broad spectral peaks. Integrated analysis of the preprocessed chemical data demonstrated distinct discrimination of differential seaweed species. Further network analysis revealed a close correlation between the heavy metal elements and characteristic components of brown algae, such as cellulose, alginic acid, and sulfated mucopolysaccharides, providing a componential basis for its metal-sorbing potential. These results suggest that this integrated analytical strategy is useful for extracting and identifying the chemical characteristics of diverse seaweeds based on large chemical data sets, particularly complicated overlapping spectral data. PMID:25647718

  6. Novel Algorithms for the Identification of Biologically Informative Chemical Diversity Metrics

    PubMed Central

    Theertham, Bhargav; Wang, Jenna. L.; Fang, Jianwen; Lushington, Gerald H.

    2009-01-01

    Despite great advances in the efficiency of analytical and synthetic chemistry, time and available starting material still limit the number of unique compounds that can be practically synthesized and evaluated as prospective therapeutics. Chemical diversity analysis (the capacity to identify finite diverse subsets that reliably represent greater manifolds of drug-like chemicals) thus remains an important resource in drug discovery. Despite an unproven track record, chemical diversity has also been used to posit, from preliminary screen hits, new compounds with similar or better activity. Identifying diversity metrics that demonstrably encode bioactivity trends is thus of substantial potential value for intelligent assembly of targeted screens. This paper reports novel algorithms designed to simultaneously reflect chemical similarity or diversity trends and apparent bioactivity in compound collections. An extensive set of descriptors are evaluated within large NCI screening data sets according to bioactivity differentiation capacities, quantified as the ability to co-localize known active species into bioactive-rich K-means clusters. One method tested for descriptor selection orders features according to relative variance across a set of training compounds, and samples increasingly finer subset meshes for descriptors whose exclusion from the model induces drastic drops in relative bioactive colocalization. This yields metrics with reasonable bioactive enrichment (greater than 50% of all bioactive compounds collected into clusters or cells with significantly enriched active/inactive rates) for each of the four data sets examined herein. A second method replaces variance by an active/inactive divergence score, achieving comparable enrichment via a much more efficient search process. Combinations of the above metrics are tested in 2D rectilinear diversity models, achieving similarly successful colocalization statistics, with metrics derived from the active

  7. Lignocellulose-based analytical devices: bamboo as an analytical platform for chemical detection

    PubMed Central

    Kuan, Chen-Meng; York, Roger L.; Cheng, Chao-Min

    2015-01-01

    This article describes the development of lignocellulose-based analytical devices (LADs) for rapid bioanalysis in low-resource settings. LADs are constructed using either a single lignocellulose or a hybrid design consisting of multiple types of lignocellulose. LADs are simple, low-cost, easy to use, provide rapid response, and do not require external instrumentation during operation. Here, we demonstrate the implementation of LADs for food and water safety (i.e., nitrite assay in hot-pot soup, bacterial detection in water, and resazurin assay in milk) and urinalysis (i.e., nitrite, urobilinogen, and pH assays in human urine). Notably, we created a unique approach using simple chemicals to achieve sensitivity similar to that of commercially available immunochromatographic strips that is low-cost, and provides on-site, rapid detection, for instance, of Eschericia coli (E. coli) in water. PMID:26686576

  8. Automating the analytical laboratory via the Chemical Analysis Automation paradigm

    SciTech Connect

    Hollen, R.; Rzeszutko, C.

    1997-10-01

    To address the need for standardization within the analytical chemistry laboratories of the nation, the Chemical Analysis Automation (CAA) program within the US Department of Energy, Office of Science and Technology`s Robotic Technology Development Program is developing laboratory sample analysis systems that will automate the environmental chemical laboratories. The current laboratory automation paradigm consists of islands-of-automation that do not integrate into a system architecture. Thus, today the chemist must perform most aspects of environmental analysis manually using instrumentation that generally cannot communicate with other devices in the laboratory. CAA is working towards a standardized and modular approach to laboratory automation based upon the Standard Analysis Method (SAM) architecture. Each SAM system automates a complete chemical method. The building block of a SAM is known as the Standard Laboratory Module (SLM). The SLM, either hardware or software, automates a subprotocol of an analysis method and can operate as a standalone or as a unit within a SAM. The CAA concept allows the chemist to easily assemble an automated analysis system, from sample extraction through data interpretation, using standardized SLMs without the worry of hardware or software incompatibility or the necessity of generating complicated control programs. A Task Sequence Controller (TSC) software program schedules and monitors the individual tasks to be performed by each SLM configured within a SAM. The chemist interfaces with the operation of the TSC through the Human Computer Interface (HCI), a logical, icon-driven graphical user interface. The CAA paradigm has successfully been applied in automating EPA SW-846 Methods 3541/3620/8081 for the analysis of PCBs in a soil matrix utilizing commercially available equipment in tandem with SLMs constructed by CAA.

  9. Physical and Chemical Analytical Analysis: A key component of Bioforensics

    SciTech Connect

    Velsko, S P

    2005-02-15

    The anthrax letters event of 2001 has raised our awareness of the potential importance of non-biological measurements on samples of biological agents used in a terrorism incident. Such measurements include a variety of mass spectral, spectroscopic, and other instrumental techniques that are part of the current armamentarium of the modern materials analysis or analytical chemistry laboratory. They can provide morphological, trace element, isotopic, and other molecular ''fingerprints'' of the agent that may be key pieces of evidence, supplementing that obtained from genetic analysis or other biological properties. The generation and interpretation of such data represents a new domain of forensic science, closely aligned with other areas of ''microbial forensics''. This paper describes some major elements of the R&D agenda that will define this sub-field in the immediate future and provide the foundations for a coherent national capability. Data from chemical and physical analysis of BW materials can be useful to an investigation of a bio-terror event in two ways. First, it can be used to compare evidence samples collected at different locations where such incidents have occurred (e.g. between the powders in the New York and Washington letters in the Amerithrax investigation) or between the attack samples and those seized during the investigation of sites where it is suspected the material was manufactured (if such samples exist). Matching of sample properties can help establish the relatedness of disparate incidents, and mis-matches might exclude certain scenarios, or signify a more complex etiology of the events under investigation. Chemical and morphological analysis for sample matching has a long history in forensics, and is likely to be acceptable in principle in court, assuming that match criteria are well defined and derived from known limits of precision of the measurement techniques in question. Thus, apart from certain operational issues (such as how to

  10. Opportunities for synthetic biology in antibiotics: expanding glycopeptide chemical diversity.

    PubMed

    Thaker, Maulik N; Wright, Gerard D

    2015-03-20

    Synthetic biology offers a new path for the exploitation and improvement of natural products to address the growing crisis in antibiotic resistance. All antibiotics in clinical use are facing eventual obsolesce as a result of the evolution and dissemination of resistance mechanisms, yet there are few new drug leads forthcoming from the pharmaceutical sector. Natural products of microbial origin have proven over the past 70 years to be the wellspring of antimicrobial drugs. Harnessing synthetic biology thinking and strategies can provide new molecules and expand chemical diversity of known antibiotic scaffolds to provide much needed new drug leads. The glycopeptide antibiotics offer paradigmatic scaffolds suitable for such an approach. We review these strategies here using the glycopeptides as an example and demonstrate how synthetic biology can expand antibiotic chemical diversity to help address the growing resistance crisis. PMID:23654249

  11. ANALYTICAL METHODS FOR A NATIONAL STUDY OF CHEMICAL RESIDUES IN FISH - II. PESTICIDES AND POLYCHLORINATED BIPHENYLS

    EPA Science Inventory

    Analytical methods and a quality assurance plan have been developed to determine the concentration of a select group of bioaccumulatable chemicals in fish tissue. he analytes include PCBs and 21 pesticides and industrial chemicals. he methodology has been used to conduct a survey...

  12. How does plant chemical diversity contribute to biodiversity at higher trophic levels?

    PubMed

    Schuman, Meredith C; van Dam, Nicole M; Beran, Franziska; Harpole, W Stanley

    2016-04-01

    Plants, perhaps Earth's most accomplished chemists, produce thousands of specialized metabolites having no direct role in cell division or growth. These phytochemicals vary by taxon, with many taxa producing characteristic substance classes; and within taxa, with individual variation in structural variety and production patterns. Observations of corresponding variation in herbivore metabolism, behavior, and diet breadth motivated the development of chemical ecology research. We discuss the importance of plant biodiversity in general and phytochemical diversity in particular for biodiversity and ecological interactions at higher trophic levels. We then provide an overview of the descriptive, molecular and analytical tools which allow modern biologists to investigate phytochemical diversity and its effects on higher trophic levels, from physiological mechanisms to ecological communities. PMID:27436646

  13. Diversity in Chemical Constituents of Ligularia longihastata Collected in China.

    PubMed

    Okamoto, Yasuko; Taniguchi, Mizuho; Terada, Kaori; Nakashima, Katsuyuki; Gong, Xun; Hanai, Ryo; Tori, Motoo; Kuroda, Chiaki

    2016-02-01

    Root constituents of Ligularia longihastata were examined for the first time. Fourteen eremophilane sesquiterpenes, including two new eremophilanes identified as 3α-isobutyroyloxy-7βH-eremophila-9,11-dien-8-one and 3β-angeloyloxy-1β,10β-epoxyfuranoeremophilan-9-one, and three eudesmanes were isolated. From samples collected in Baiyu County, Sichuan Province, furanoeremophilane derivatives were isolated, while various eremophilan-8-ones were isolated from samples collected in Kangding County, Sichuan. The results suggest chemical diversity in the species. PMID:27032187

  14. Covering Chemical Diversity of Genetically-Modified Tomatoes Using Metabolomics for Objective Substantial Equivalence Assessment

    PubMed Central

    Hirai, Tadayoshi; Oikawa, Akira; Matsuda, Fumio; Fukushima, Atsushi; Arita, Masanori; Watanabe, Shin; Yano, Megumu; Hiwasa-Tanase, Kyoko; Ezura, Hiroshi; Saito, Kazuki

    2011-01-01

    As metabolomics can provide a biochemical snapshot of an organism's phenotype it is a promising approach for charting the unintended effects of genetic modification. A critical obstacle for this application is the inherently limited metabolomic coverage of any single analytical platform. We propose using multiple analytical platforms for the direct acquisition of an interpretable data set of estimable chemical diversity. As an example, we report an application of our multi-platform approach that assesses the substantial equivalence of tomatoes over-expressing the taste-modifying protein miraculin. In combination, the chosen platforms detected compounds that represent 86% of the estimated chemical diversity of the metabolites listed in the LycoCyc database. Following a proof-of-safety approach, we show that % had an acceptable range of variation while simultaneously indicating a reproducible transformation-related metabolic signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms. PMID:21359231

  15. Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment.

    PubMed

    Kusano, Miyako; Redestig, Henning; Hirai, Tadayoshi; Oikawa, Akira; Matsuda, Fumio; Fukushima, Atsushi; Arita, Masanori; Watanabe, Shin; Yano, Megumu; Hiwasa-Tanase, Kyoko; Ezura, Hiroshi; Saito, Kazuki

    2011-01-01

    As metabolomics can provide a biochemical snapshot of an organism's phenotype it is a promising approach for charting the unintended effects of genetic modification. A critical obstacle for this application is the inherently limited metabolomic coverage of any single analytical platform. We propose using multiple analytical platforms for the direct acquisition of an interpretable data set of estimable chemical diversity. As an example, we report an application of our multi-platform approach that assesses the substantial equivalence of tomatoes over-expressing the taste-modifying protein miraculin. In combination, the chosen platforms detected compounds that represent 86% of the estimated chemical diversity of the metabolites listed in the LycoCyc database. Following a proof-of-safety approach, we show that % had an acceptable range of variation while simultaneously indicating a reproducible transformation-related metabolic signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms. PMID:21359231

  16. Propolis volatile compounds: chemical diversity and biological activity: a review

    PubMed Central

    2014-01-01

    Propolis is a sticky material collected by bees from plants, and used in the hive as building material and defensive substance. It has been popular as a remedy in Europe since ancient times. Nowadays, propolis use in over-the-counter preparations, “bio”-cosmetics and functional foods, etc., increases. Volatile compounds are found in low concentrations in propolis, but their aroma and significant biological activity make them important for propolis characterisation. Propolis is a plant-derived product: its chemical composition depends on the local flora at the site of collection, thus it offers a significant chemical diversity. The role of propolis volatiles in identification of its plant origin is discussed. The available data about chemical composition of propolis volatiles from different geographic regions are reviewed, demonstrating significant chemical variability. The contribution of volatiles and their constituents to the biological activities of propolis is considered. Future perspectives in research on propolis volatiles are outlined, especially in studying activities other than antimicrobial. PMID:24812573

  17. CTEPP NC DATA ANALYTICAL RESULTS ORGANIZED BY CHEMICAL AND MEDIA

    EPA Science Inventory

    This data set contains the field sample data by chemical and matrix. The data are organized at the sample, chemical level.

    The Children’s Total Exposure to Persistent Pesticides and Other Persistent Pollutant (CTEPP) study was one of the largest aggregate exposure studies of y...

  18. Analytical methods for environmental sampling of chemical warfare agents and their degradation products

    SciTech Connect

    Watson, A.P.; Kistner, S.

    1995-06-01

    This first technical conference promoted the standardization of analytical procotols to reliably detect chemical warfare agents and their degradation products in soil, water, and other complex environmental media. This supports the various chemical weapons disposal and emergency preparedness programs, Chemical Weapons Convention treaty compliance, installation restoration and base closure decisions. Five major topics were addressed: Implementation for treaty compliance, installation, restoration and stockpile disposal decisions, existing analytical methods, practical applications of existing analytical techniques, immunoassay technologies, environmental and biological fate of agents and their degradation products. Selected papers have been indexed separately for inclusion in the Energy Science and Technology Database.

  19. Analytical verification of waterborne chemical treatment regimens in hatchery raceways

    USGS Publications Warehouse

    Rach, J.J.; Ramsay, R.T.

    2000-01-01

    Chemical therapy for control and prevention of fish diseases is a necessary and common practice in aquaculture. Many factors affect the accuracy of a chemical treatment application, such as the functioning of the chemical delivery system, calculation of chemical quantities to be delivered, water temperature, geometry of the culture unit, inlet-outlet structure, the influence of aerators, wind movement, and measurement of water volumes and flow rates. Three separate trials were conducted at the Osceola Fish Hatchery, a facility of the Wisconsin Department of Natural Resources, evaluating the accuracy of flow-through hydrogen peroxide treatments applied to 1, 3, or 9 raceways that were connected in series. Raceways were treated with 50 or 75 ??L/L of hydrogen peroxide for 30 min. Chemical concentrations were determined titrimetrically. The target treatment regimen was not realized in any of the applications. Chemical concentrations dropped and exposure times increased with each additional raceway treated in series. Single introduction of a therapeutant to more than three raceways in series is not recommended. Factors that interfered with the accuracy of the treatments were culture unit configuration, aeration, and flow rates. Several treatment modifications were identified that would result in more accurate chemical treatments.

  20. Effect-Based Screening Methods for Water Quality Characterization Will Augment Conventional Analyte-by-Analyte Chemical Methods in Research As Well As Regulatory Monitoring

    EPA Science Inventory

    Conventional approaches to water quality characterization can provide data on individual chemical components of each water sample. This analyte-by-analyte approach currently serves many useful research and compliance monitoring needs. However these approaches, which require a ...

  1. Chemically diverse, episodic volcanism offshore southern and peninsular California

    SciTech Connect

    Davis, A.S.; Gunn, S.H. ); Bohrson, W.A. . Dept. Earth and Space Sciences)

    1993-04-01

    Volcanic rocks recovered from eight seamounts offshore southern and peninsular California are chemically diverse. Compositions of lavas from seven small to moderately sized seamounts between 30.5[degree] and 34.0 N latitudes include low-K[sub 2]O tholeiitic, transitional, and mildly to moderately alkalic basalt. Volcanic rocks from the upper part of the much larger and morphologically complex edifice of Rocas Alijos, offshore central Baja California at about 25.0 N latitude, are highly differentiated trachyandesite and trachyte. The low-K[sub 2]O basalts are MORB-like with low abundances of incompatible elements and lower [sup 87]Sr/[sup 86]Sr and higher [sup 143]Nd/[sup 144]Nd ratios than MORB from the East Pacific Rise. The alkalic compositions have higher abundances of incompatible elements and isotopic data indicate more variably enriched mantle sources than those of seamounts near the East Pacific Rise, but the compositions of all samples are within the mantle array defined by other ocean-island basalts. [sup 40]Ar/[sup 39]Ar laser fusion ages for the seamounts span a large range. MORB-like lava from one of the northern edifices is as old as the underlying oceanic crust ([approximately]23 Ma), indicating that it originated at a spreading center. Other seamount lava ages are much younger (16.6--9.1 Ma) than the underlying oceanic crust. The trachytes from Rocas Alijos are less than 300,000 years old, indicating that the last volcanism on this large edifice occurred recently. The region offshore southern and peninsular California is tectonically complex and has many volcanic edifices of varying sizes, shapes, and orientations. The data available for volcanic rocks from this region suggest that the seamounts formed from multiple episodes of chemically diverse volcanism occurring sporadically from early Miocene to Recent.

  2. Single-Molecule Electronics: Chemical and Analytical Perspectives.

    PubMed

    Nichols, Richard J; Higgins, Simon J

    2015-01-01

    It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance. PMID:26048551

  3. Single-Molecule Electronics: Chemical and Analytical Perspectives

    NASA Astrophysics Data System (ADS)

    Nichols, Richard J.; Higgins, Simon J.

    2015-07-01

    It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance.

  4. Apparatus for thermally evolving chemical analytes from a removable substrate

    DOEpatents

    Linker, Kevin L.; Hannum, David W.

    2003-06-03

    Method and apparatus suited to convenient field use for heating a porous metallic substrate swiped on the surface of an article possibly bearing residue of contraband or other target chemical substances. The preferred embodiment of the device includes means for holding the swiped substrate between electrodes bearing opposite electrical charges, thereby completing an electrical circuit in which current can flow through the porous metallic substrate. Resistance causes the substrate to heat, thus driving adherent target chemicals, if present, into a space from which they are carried via gas flow into a detector such as a portable IMS for analysis.

  5. A Decision Analytic Approach to Exposure-Based Chemical Prioritization

    EPA Science Inventory

    The manufacture of novel synthetic chemicals has increased in volume and variety, but often the environmental and health risks are not fully understood in terms of toxicity and, in particular, exposure. While efforts to assess risks have generally been effective when sufficient d...

  6. Interfacial characterization and analytical applications of chemically-modified surfaces

    SciTech Connect

    Wang, J.

    1998-02-23

    The goal of this work is to explore several new strategies and approaches to the surface modification and the microscopic characterization of interfaces in the areas mainly targeting sensor technologies that are of interest to environmental control or monitoring, and scanning probe microscopies techniques that can monitor interfacial chemical reactions in real time. Centered on the main theme, four specific topics are presented as four chapters in this dissertation following the general introduction. Chapter 1 describes the development of two immobilization schemes for covalently immobilizing fluoresceinamine at cellulose acetate and its application as a pH sensing film. Chapter 2 investigates the applicability of SFM to following the base-hydrolysis of a dithio-bis(succinimidylundecanoate) monolayer at gold in situ. Chapter 3 studies the mechanism for the accelerated rate of hydrolysis of the dithio-bis(succinimidylundecanoate) monolayer at Au(111) surface. Chapter 4 focuses on the development of an electrochemical approach to the elimination of chloride interference in Chemical Oxygen Demand (COD) analysis of waste water. The procedures, results and conclusions are described in each chapter. This report contains the introduction, references, and general conclusions. Chapters have been processed separately for inclusion on the data base. 95 refs.

  7. Searching chemical diversity for molecular recognition by ESI-MS

    SciTech Connect

    Smith, R.D.; Bruce, J.E.; Cheng, Xueheng

    1995-12-31

    The traditional approach to drug lead development has generally involved the synthesis or high purity isolation of individual compounds followed by their screening and evaluation through a series of chemical and biological assays. A key step in the screening process may involve identification of candidate compounds that display high binding affinity in vitro to a targeted biopolymer, e.g., a specific protein or DNA segment. More recently, the in vitro selection of pharmacologically active molecules from mixtures of compounds has been shown effective, leading to the development of potential new drugs. Identifying the biologically most active compounds, often those displaying the highest affinity of noncovalent binding, from such {open_quotes}libraries{close_quotes} has become a major enterprise. In particular, the generation and searching of large {open_quotes}combinatorial{close_quotes} libraries has become popular for certain classes of compounds. In the {open_quotes}combinatorial{close_quotes} approach, many compounds are synthesized to deliberately produce a complex mixture, and then subsequently examined for their affinity to the targeted biopolymer, often by partitioning subsets of the library so as to facilitate the identification of the most active components. This is commonly performed by binding either the target or library molecules to a solid support, often in some fashion designed to facilitate identification of the active components. The combinatorial approach has proven attractive since it allows much larger numbers of compounds to be screened more rapidly than other serial approaches involving the individual synthesis and assay of each prospective affinant. The new approach the authors demonstrate, `bioaffinity characterization mass spectrometry` (BACMS) may potentially aid studies involving conventional libraries by providing much more rapid and direct analysis, as well as applicability to chemically more diverse libraries.

  8. A results-based process for evaluation of diverse visual analytics tools

    NASA Astrophysics Data System (ADS)

    Rubin, Gary; Berger, David H.

    2013-05-01

    With the pervasiveness of still and full-motion imagery in commercial and military applications, the need to ingest and analyze these media has grown rapidly in recent years. Additionally, video hosting and live camera websites provide a near real-time view of our changing world with unprecedented spatial coverage. To take advantage of these controlled and crowd-sourced opportunities, sophisticated visual analytics (VA) tools are required to accurately and efficiently convert raw imagery into usable information. Whether investing in VA products or evaluating algorithms for potential development, it is important for stakeholders to understand the capabilities and limitations of visual analytics tools. Visual analytics algorithms are being applied to problems related to Intelligence, Surveillance, and Reconnaissance (ISR), facility security, and public safety monitoring, to name a few. The diversity of requirements means that a onesize- fits-all approach to performance assessment will not work. We present a process for evaluating the efficacy of algorithms in real-world conditions, thereby allowing users and developers of video analytics software to understand software capabilities and identify potential shortcomings. The results-based approach described in this paper uses an analysis of end-user requirements and Concept of Operations (CONOPS) to define Measures of Effectiveness (MOEs), test data requirements, and evaluation strategies. We define metrics that individually do not fully characterize a system, but when used together, are a powerful way to reveal both strengths and weaknesses. We provide examples of data products, such as heatmaps, performance maps, detection timelines, and rank-based probability-of-detection curves.

  9. State-of-the-Art of (Bio)Chemical Sensor Developments in Analytical Spanish Groups

    PubMed Central

    Plata, María Reyes; Contento, Ana María; Ríos, Angel

    2010-01-01

    (Bio)chemical sensors are one of the most exciting fields in analytical chemistry today. The development of these analytical devices simplifies and miniaturizes the whole analytical process. Although the initial expectation of the massive incorporation of sensors in routine analytical work has been truncated to some extent, in many other cases analytical methods based on sensor technology have solved important analytical problems. Many research groups are working in this field world-wide, reporting interesting results so far. Modestly, Spanish researchers have contributed to these recent developments. In this review, we summarize the more representative achievements carried out for these groups. They cover a wide variety of sensors, including optical, electrochemical, piezoelectric or electro-mechanical devices, used for laboratory or field analyses. The capabilities to be used in different applied areas are also critically discussed. PMID:22319260

  10. The impact of plant chemical diversity on plant-herbivore interactions at the community level.

    PubMed

    Salazar, Diego; Jaramillo, Alejandra; Marquis, Robert J

    2016-08-01

    Understanding the role of diversity in ecosystem processes and species interactions is a central goal of ecology. For plant-herbivore interactions, it has been hypothesized that when plant species diversity is reduced, loss of plant biomass to herbivores increases. Although long-standing, this hypothesis has received mixed support. Increasing plant chemical diversity with increasing plant taxonomic diversity is likely to be important for plant-herbivore interactions at the community level, but the role of chemical diversity is unexplored. Here we assess the effect of volatile chemical diversity on patterns of herbivore damage in naturally occurring patches of Piper (Piperaceae) shrubs in a Costa Rican lowland wet forest. Volatile chemical diversity negatively affected total, specialist, and generalist herbivore damage. Furthermore, there were differences between the effects of high-volatility and low-volatility chemical diversity on herbivore damage. High-volatility diversity reduced specialist herbivory, while low-volatility diversity reduced generalist herbivory. Our data suggest that, although increased plant diversity is expected to reduce average herbivore damage, this pattern is likely mediated by the diversity of defensive compounds and general classes of anti-herbivore traits, as well as the degree of specialization of the herbivores attacking those plants. PMID:27129320

  11. Statistical Data Analyses of Trace Chemical, Biochemical, and Physical Analytical Signatures

    SciTech Connect

    Udey, Ruth Norma

    2013-01-01

    Analytical and bioanalytical chemistry measurement results are most meaningful when interpreted using rigorous statistical treatments of the data. The same data set may provide many dimensions of information depending on the questions asked through the applied statistical methods. Three principal projects illustrated the wealth of information gained through the application of statistical data analyses to diverse problems.

  12. Unique marine derived cyanobacterial biosynthetic genes for chemical diversity.

    PubMed

    Kleigrewe, Karin; Gerwick, Lena; Sherman, David H; Gerwick, William H

    2016-02-01

    Cyanobacteria are a prolific source of structurally unique and biologically active natural products that derive from intriguing biochemical pathways. Advancements in genome sequencing have accelerated the identification of unique modular biosynthetic gene clusters in cyanobacteria and reveal a wealth of unusual enzymatic reactions involved in their construction. This article examines several interesting mechanistic transformations involved in cyanobacterial secondary metabolite biosynthesis with a particular focus on marine derived modular polyketide synthases (PKS), nonribosomal peptide synthetases (NRPS) and combinations thereof to form hybrid natural products. Further, we focus on the cyanobacterial genus Moorea and the co-evolution of its enzyme cassettes that create metabolic diversity. Progress in the development of heterologous expression systems for cyanobacterial gene clusters along with chemoenzymatic synthesis makes it possible to create new analogs. Additionally, phylum-wide genome sequencing projects have enhanced the discovery rate of new natural products and their distinctive enzymatic reactions. Summarizing, cyanobacterial biosynthetic gene clusters encode for a large toolbox of novel enzymes that catalyze unique chemical reactions, some of which may be useful in synthetic biology. PMID:26758451

  13. The delayed contribution of low and intermediate mass stars to chemical galactic enrichment: An analytical approach

    NASA Astrophysics Data System (ADS)

    Franco, I.; Carigi, L.

    2008-10-01

    We find a new analytical solution for the chemical evolution equations, taking into account the delayed contribution of all low and intermediate mass stars (LIMS) as one representative star that enriches the interstellar medium. This solution is built only for star formation rate proportional to the gas mass in a closed box model. We obtain increasing C/O and N/O ratios with increasing O/H, behavior impossible to match with the Instantaneous Recycling Approximation (IRA). Our results, obtained by two analytical equations, are very similar to those found by numerical models that consider the lifetimes of each star. This delayed model reproduces successfully the evolution of the C/O-O/H and Y - O relations in the solar vicinity. This analytical approximation is a useful tool to study the chemical evolution of elements produced by LIMS when a galactic chemical evolutionary code is not available.

  14. Role of Analytical Chemistry in Defense Strategies Against Chemical and Biological Attack

    NASA Astrophysics Data System (ADS)

    Janata, Jiri

    2009-07-01

    Analytical chemistry plays a role in the two strategies of defense against chemical or biological weapons that are discussed in this review: the detect-to-protect and the prevent-and-detect strategies. The detect-to-protect method, which is based on detection of a known chemical agent with a specific chemical sensor designed for said agent, has serious flaws. I argue that this approach should be replaced with the prevent-and-detect strategy. Such a change in the defense paradigm would require reallocation of resources, but it is necessary for effective protection of enclosed civilians from chemical and/or biological attack.

  15. Carbon disulfide reagent allows the characterization of nonpolar analytes by atmospheric pressure chemical ionization mass spectrometry.

    PubMed

    Owen, Benjamin C; Gao, Jinshan; Borton, David J; Amundson, Lucas M; Archibold, Enada F; Tan, Xiaoli; Azyat, Khalid; Tykwinski, Rik; Gray, Murray; Kenttämaa, Hilkka I

    2011-07-30

    While atmospheric pressure ionization methodologies have revolutionized the mass spectrometric analysis of nonvolatile analytes, limitations native to the chemistry of these methodologies hinder or entirely inhibit the analysis of certain analytes, specifically, many nonpolar compounds. Examination of various analytes, including asphaltene and lignin model compounds as well as saturated hydrocarbons, demonstrates that atmospheric pressure chemical ionization (APCI) using CS(2) as the reagent produces an abundant and stable molecular ion (M(+•)) for all model compounds studied, with the exception of completely saturated aliphatic hydrocarbons and the two amino acids tested, arginine and phenylalanine. This reagent substantially broadens the applicability of mass spectrometry to nonvolatile nonpolar analytes and also facilitates the examination of radical cation chemistry by mass spectrometry. PMID:21698674

  16. Do multiple herbivores maintain chemical diversity of Scots pine monoterpenes?

    PubMed Central

    Iason, Glenn R.; O'Reilly-Wapstra, Julianne M.; Brewer, Mark J.; Summers, Ron W.; Moore, Ben D.

    2011-01-01

    A central issue in our understanding of the evolution of the diversity of plant secondary metabolites (PSMs) is whether or not compounds are functional, conferring an advantage to the plant, or non-functional. We examine the hypothesis that the diversity of monoterpene PSMs within a plant species (Scots pine Pinus sylvestris) may be explained by different compounds acting as defences against high-impact herbivores operating at different life stages. We also hypothesize that pairwise coevolution, with uncorrelated interactions, is more likely to result in greater PSM diversity, than diffuse coevolution. We tested whether up to 13 different monoterpenes in Scots pine were inhibitory to herbivory by slugs (Arion ater), bank voles (Clethrionomys glareolus), red deer (Cervus elaphus) and capercaillie (Tetrao urogallus), each of which attack trees at a different life stage. Plants containing more α-pinene were avoided by both slugs and capercaillie, which may act as reinforcing selective agents for this dominant defensive compound. Herbivory by red deer and capercaillie were, respectively, weakly negatively associated with δ3-carene, and strongly negatively correlated with the minor compound β-ocimene. Three of the four herbivores are probably contributory selective agents on some of the terpenes, and thus maintain some, but by no means all, of the phytochemical diversity in the species. The correlated defensive function of α-pinene against slugs and capercaillie is consistent with diffuse coevolutionary processes. PMID:21444308

  17. Can Chemical Diversity Provide a Link to Ecosystem Function?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biodiversity indices – whether to count or differentiate – reflect the purpose for which they are designed. Diversity in litter-mix experiments has been traditionally described by species or functional group richness. The lack of predictability in decomposition or mineralization response to these di...

  18. Chemical and Analytical Sciences Division progress report for the period January 1, 1993--December 31, 1994

    SciTech Connect

    Poutsma, M.L.

    1995-06-01

    This report provides brief summaries of progress in the Chemical and Analytical Sciences Division (CASD) during 1993 and 1994. The first four chapters, which cover the research mission, are organized to mirror the major organizational units of the division and indicate the scope of the research portfolio. These divisions are the Analytical Spectroscopy Section, Nuclear and Radiochemistry Section, Organic Chemistry Section, and Physical and Materials Chemistry Section. The fifth and sixth chapters summarize the support activities within CASD that are critical for research progress. Finally, the appendices indicate the productivity and recognition of the staff in terms of various forms of external publications, professional activities, and awards.

  19. Chemical multi-contamination drives benthic prokaryotic diversity in the anthropized Toulon Bay.

    PubMed

    Misson, Benjamin; Garnier, Cédric; Lauga, Béatrice; Dang, Duc Huy; Ghiglione, Jean-François; Mullot, Jean-Ulrich; Duran, Robert; Pringault, Olivier

    2016-06-15

    Investigating the impact of human activities on marine coastal ecosystems remains difficult because of the co-occurrence of numerous natural and human-induced gradients. Our aims were (i) to evaluate the links between the chemical environment as a whole and microbial diversity in the benthic compartment, and (ii) to compare the contributions of anthropogenic and natural chemical gradients to microbial diversity shifts. We studied surface sediments from 54 sampling sites in the semi-enclosed Toulon Bay (NW Mediterranean) exposed to high anthropogenic pressure. Previously published chemical data were completed by new measurements, resulting in an in depth geochemical characterization by 29 representative environmental variables. Bacterial and archaeal diversity was assessed by terminal restriction fragment length polymorphism profiling on a selection of samples distributed along chemical gradients. Multivariate statistical analyses explained from 45% to 80% of the spatial variation in microbial diversity, considering only the chemical variables. A selection of trace metals of anthropogenic origin appeared to be strong structural factors for both bacterial and archaeal communities. Bacterial terminal restriction fragment (T-RF) richness correlated strongly with both anthropogenic and natural chemical gradients, whereas archaeal T-RF richness demonstrated fewer links with chemical variables. No significant decrease in diversity was evidenced in relation to chemical contamination, suggesting a high adaptive potential of benthic microbial communities in Toulon Bay. PMID:27032072

  20. Chemical Diversity in Lippia alba (Mill.) N. E. Brown Germplasm

    PubMed Central

    Camêlo, Lídia Cristina Alves; Pinheiro, José Baldin; Andrade, Thiago Matos; Alves, Péricles Barreto

    2015-01-01

    The aim of this study was to perform chemical characterization of Lippia alba accessions from the Active Germplasm Bank of the Federal University of Sergipe. A randomized block experimental design with two replications was applied. The analysis of the chemical composition of the essential oils was conducted using a gas chromatograph coupled to a mass spectrometer. The chemical composition of the essential oils allowed the accessions to be allocated to the following six groups: group 1: linalool, 1,8-cineole, and caryophyllene oxide; group 2: linalool, geranial, neral, 1,8-cineol, and caryophyllene oxide; group 3: limonene, carvone, and sabinene; group 4: carvone, limonene, g-muurolene, and myrcene; group 5: neral, geranial, and caryophyllene oxide; and group 6: geranial, neral, o-cymene, limonene, and caryophyllene oxide. PMID:26075292

  1. 3D simulation and analytical model of chemical heating during silicon wet etching in microchannels

    NASA Astrophysics Data System (ADS)

    Konakov, S. A.; Krzhizhanovskaya, V. V.

    2016-02-01

    We investigate chemical heating of a Silicon-on-Glass (SOG) chip during a highly exothermic reaction of silicon etching in potassium hydroxide (KOH) solution in a microchannel of 100-micron width inside a 1x1 cm SOG chip. Two modeling approaches have been developed, implemented and compared. (1) A detailed 3D model is based on unsteady Navier-Stokes equations, heat and mass transfer equations of a laminar flow of viscous incompressible fluid in microchannel, coupled to the heat transfer equation in the solid chip. 3D simulation results predicted temperature distributions for different KOH flow rates and silicon etching areas. Microchannels of a small diameter do not heat the chip due to the insufficient chemical heating of the cold fluid, whereas large-area etching (large channel diameter and/or length) leads to local overheating that may have negative effects on the device performance and durability. (2) A simplified analytical model solves a thermal balance equation describing the heating by chemical reactions inside the microchannel and energy loss by free convection of air around the chip. Analytical results compare well with the 3D simulations of a single straight microchannel, therefore the analytical model is suitable for quick estimation of process parameters. For complex microstructures, this simplified approach may be used as the first approximation.

  2. Chemical diversity among populations of Mikania micrantha: geographic mosaic structure and herbivory.

    PubMed

    Bravo-Monzón, Angel Eliezer; Ríos-Vásquez, Eunice; Delgado-Lamas, Guillermo; Espinosa-García, Francisco J

    2014-01-01

    Populations of the same species vary in their secondary metabolite content. This variation has been attributed to biotic and abiotic environmental conditions as well as to historical factors. Some studies have focused on the geographic variation of chemical diversity in plant populations, but whether this structure conforms to a central-marginal model or a mosaic pattern remains unclear. Furthermore, assessing the chemical diversity of invasive plants in their native distribution facilitates the understanding of their relationships with natural enemies. We examined the geographic variation of chemical diversity in Mexican populations of the bittervine weed Mikania micrantha and its relationship to herbivore damage. The foliar volatile terpenoid blend was analyzed in 165 individuals of 14 populations in the Pacific and Gulf of Mexico tropical watersheds. A cluster analysis grouped individuals with similar terpenoid blends into 56 compositional types. Chemical diversity was measured using the number of compounds and their concentration within the blends for individuals, and the number and frequency of compositional types for populations. A stepwise multiple regression analysis performed with geographic, climatic, and chemical diversity variables explained herbivore damage. However, population-level chemical diversity was the only variable found to be significant (β = -0.79, P = 0.042) in the model (R(2) = 0.89). A Mantel test using Euclidean distances did not indicate any separation by geographic origin; however, four barriers were identified using Monmonier's algorithm. We conclude that variation in population-level chemical diversity follows a mosaic pattern in which geographic factors (i.e., natural barriers) have some effect and that variation is also associated with the local intensity of herbivore attack. PMID:23942983

  3. DIVERSITY OF TYPE Ia SUPERNOVAE IMPRINTED IN CHEMICAL ABUNDANCES

    SciTech Connect

    Tsujimoto, Takuji; Shigeyama, Toshikazu

    2012-12-01

    A time delay of Type Ia supernova (SN Ia) explosions hinders the imprint of their nucleosynthesis on stellar abundances. However, some occasional cases give birth to stars that avoid enrichment of their chemical compositions by massive stars and thereby exhibit an SN-Ia-like elemental feature including a very low [Mg/Fe] ( Almost-Equal-To - 1). We highlight the elemental feature of Fe-group elements for two low-Mg/Fe objects detected in nearby galaxies, and propose the presence of a class of SNe Ia that yield the low abundance ratios of [Cr, Mn, Ni/Fe]. Our novel models of chemical evolution reveal that our proposed class of SNe Ia (slow SNe Ia) is associated with ones exploding on a long timescale after their stellar birth and give a significant impact on the chemical enrichment in the Large Magellanic Cloud (LMC). In the Galaxy, on the other hand, this effect is unseen due to the overwhelming enrichment by the major class of SNe Ia that explode promptly (prompt SNe Ia) and eject a large amount of Fe-group elements. This nicely explains the different [Cr, Mn, Ni/Fe] features between the two galaxies as well as the puzzling feature seen in the LMC stars exhibiting very low Ca but normal Mg abundances. Furthermore, the corresponding channel of slow SN Ia is exemplified by performing detailed nucleosynthesis calculations in the scheme of SNe Ia resulting from a 0.8 + 0.6 M{sub Sun} white dwarf merger.

  4. Fast estimation of solvation free energies for diverse chemical species.

    PubMed

    Boyer, Robert D; Bryan, Richard L

    2012-03-29

    The free energy of solvation can play an important or even dominant role in the accurate prediction of binding affinities and various other molecular-scale interaction phenomena critical to the study of biochemical processes. Many research applications for solvation modeling, such as fragment-based drug design, require algorithms that are both accurate and computationally inexpensive. We have developed a calculation of solvation free energy which runs fast enough for interactive applications, functions for a wide range of chemical species relevant to simulating molecules for biological and pharmaceutical applications, and is readily extended when data for new species becomes available. We have also demonstrated that the incorporation of ab initio data provides necessary access to sufficient reference data for a broad range of chemical features. Our empirical model, including an electrostatic term and a different set of atom types, demonstrates improvements over a previous, solvent-accessible surface area-only model by Wang et al. when fit to identical training sets (mean absolute error of 0.513 kcal/mol versus the 0.538 kcal/mol reported by Wang). The incorporation of ab initio solvation free energies provides a significant increase in the breadth of chemical features for which the model can be applied by introducing classes of compounds for which little or no experimental data is available. The increased breadth and the speed of this solvation model allow for conformational minimization, conformational search, and ligand binding free energy calculations that economically account for the complex interplay of bonded, nonbonded, and solvation free energies as conformations with varying solvent-accessible surfaces are sampled. PMID:22339050

  5. Chemical diversity and antiviral potential in the pantropical Diospyros genus.

    PubMed

    Peyrat, Laure-Anne; Eparvier, Véronique; Eydoux, Cécilia; Guillemot, Jean-Claude; Stien, Didier; Litaudon, Marc

    2016-07-01

    A screening using a dengue replicon virus-cell-based assay was performed on 3563 ethyl acetate (EtOAc) extracts from different parts of 1500 plants. The screening led to the selection of species from the genus Diospyros (Ebenaceae), among which 25 species distributed in tropical areas showed significant inhibitory activity on dengue virus replication. A metabolic analysis was conducted from the UPLC-HRMS profiles of 33 biologically active and inactive plant extracts, and their metabolic proximity is presented in the form of a dendrogram. The results of the study showed that chemical similarity is not related to plant species or organ. Overall, metabolomic profiling allowed us to define large groups of extracts, comprising both active and inactive ones. Closely related profiles from active extracts might indicate that the common major components of these extracts were responsible for the antiviral activity, while the comparison of chemically similar active and inactive extracts, will permit to find compounds of interest. Eventually, the phytochemical investigation of Diospyros glans bark EtOAc extract afforded usnic acid and 7 known ursane- and lupane-type triterpenoids, among which 5 were found significantly active against dengue virus replication. The inhibitory potency of these compounds was also evaluated on a DENV-NS5 RNA-dependant RNA polymerase assay. PMID:27126897

  6. Liver-stage malaria parasites vulnerable to diverse chemical scaffolds

    PubMed Central

    Derbyshire, Emily R.; Prudêncio, Miguel; Mota, Maria M.; Clardy, Jon

    2012-01-01

    Human malaria infection begins with a one-time asymptomatic liver stage followed by a cyclic symptomatic blood stage. All high-throughput malaria drug discovery efforts have focused on the cyclic blood stage, which has limited potential for the prophylaxis, transmission blocking, and eradication efforts that will be needed in the future. To address these unmet needs, a high-throughput phenotypic liver-stage Plasmodium parasite screen was developed to systematically identify molecules with liver-stage efficacy. The screen recapitulates liver-stage infection by isolating luciferase-expressing Plasmodium berghei parasites directly from the salivary glands of infected mosquitoes, adding them to confluent human liver cells in 384-well plates, and measuring luciferase activity after a suitable incubation period. Screening 5,375 known bioactive compounds identified 37 liver-stage malaria inhibitors with diverse modes of action, as shown by inhibition time course experiments. Further analysis of the hits in the Food and Drug Administration-approved drug subset revealed compounds that seem to act specifically on the liver stage of infection, suggesting that this phase of the parasite’s life cycle presents a promising area for new drug discovery. Notably, many active compounds in this screen have molecular structures and putative targets distinctly different from those of known antimalarial agents. PMID:22586124

  7. Substrate Type Determines Metagenomic Profiles from Diverse Chemical Habitats

    PubMed Central

    Jeffries, Thomas C.; Seymour, Justin R.; Gilbert, Jack A.; Dinsdale, Elizabeth A.; Newton, Kelly; Leterme, Sophie S. C.; Roudnew, Ben; Smith, Renee J.; Seuront, Laurent; Mitchell, James G.

    2011-01-01

    Environmental parameters drive phenotypic and genotypic frequency variations in microbial communities and thus control the extent and structure of microbial diversity. We tested the extent to which microbial community composition changes are controlled by shifting physiochemical properties within a hypersaline lagoon. We sequenced four sediment metagenomes from the Coorong, South Australia from samples which varied in salinity by 99 Practical Salinity Units (PSU), an order of magnitude in ammonia concentration and two orders of magnitude in microbial abundance. Despite the marked divergence in environmental parameters observed between samples, hierarchical clustering of taxonomic and metabolic profiles of these metagenomes showed striking similarity between the samples (>89%). Comparison of these profiles to those derived from a wide variety of publically available datasets demonstrated that the Coorong sediment metagenomes were similar to other sediment, soil, biofilm and microbial mat samples regardless of salinity (>85% similarity). Overall, clustering of solid substrate and water metagenomes into discrete similarity groups based on functional potential indicated that the dichotomy between water and solid matrices is a fundamental determinant of community microbial metabolism that is not masked by salinity, nutrient concentration or microbial abundance. PMID:21966446

  8. Demonstrating Chemical and Analytical Concepts in the Undergraduate Laboratory Using Capillary Electrophoresis and Micellar Electrokinetic Chromatography

    NASA Astrophysics Data System (ADS)

    Palmer, Christopher P.

    1999-11-01

    This paper describes instrumental analysis laboratory exercises that utilize capillary electrophoresis and micellar electrokinetic chromatography to demonstrate several analytical and chemical principles. Alkyl parabens (4-hydroxy alkyl benzoates), which are common ingredients in cosmetic formulations, are separated by capillary electrophoresis. The electrophoretic mobilities of the parabens can be explained on the basis of their relative size. 3-Hydroxy ethylbenzoate is also separated to demonstrate the effect of substituent position on the acid dissociation constant and the effect this has on electrophoretic mobility. Homologous series of alkyl benzoates and alkyl phthalates (common plasticizers) are separated by micellar electrokinetic chromatography at four surfactant concentrations. This exercise demonstrates the separation mechanism of micellar electrokinetic chromatography, the concept of chromatographic phase ratio, and the concepts of micelle formation. A photodiode array detector is used in both exercises to demonstrate the advantages and limitations of the detector and to demonstrate the effect of pH and substituent position on the spectra of the analytes.

  9. An Analytical Investigation of Three General Methods of Calculating Chemical-Equilibrium Compositions

    NASA Technical Reports Server (NTRS)

    Zeleznik, Frank J.; Gordon, Sanford

    1960-01-01

    The Brinkley, Huff, and White methods for chemical-equilibrium calculations were modified and extended in order to permit an analytical comparison. The extended forms of these methods permit condensed species as reaction products, include temperature as a variable in the iteration, and permit arbitrary estimates for the variables. It is analytically shown that the three extended methods can be placed in a form that is independent of components. In this form the Brinkley iteration is identical computationally to the White method, while the modified Huff method differs only'slightly from these two. The convergence rates of the modified Brinkley and White methods are identical; and, further, all three methods are guaranteed to converge and will ultimately converge quadratically. It is concluded that no one of the three methods offers any significant computational advantages over the other two.

  10. Analytical technique to address terrorist threats by chemical weapons of mass destruction

    NASA Astrophysics Data System (ADS)

    Dempsey, Patrick M.

    1997-01-01

    Terrorism is no longer an issue without effect on the American mind. We now live with the same concerns and fears that have been commonplace in other developed and third world countries for a long time. Citizens of other countries have long lived with the specter of terrorism and now the U.S. needs to be concerned and prepared for terrorist activities.T he terrorist has the ability to cause great destructive effects by focusing their effort on unaware and unprepared civilian populations. Attacks can range from simple explosives to sophisticated nuclear, chemical and biological weapons. Intentional chemical releases of hazardous chemicals or chemical warfare agents pose a great threat because of their ready availability and/or ease of production, and their ability to cause widespread damage. As this battlefront changes from defined conflicts and enemies to unnamed terrorists, we must implement the proper analytical tools to provide a fast and efficient response. Each chemical uses in a terrorists weapon leaves behind a chemical signature that can be used to identify the materials involved and possibly lead investigators to the source and to those responsible. New tools to provide fast and accurate detection for battlefield chemical and biological agent attack are emerging. Gas chromatography/mass spectrometry (GC/MS) is one of these tools that has found increasing use by the military to respond to chemical agent attacks. As the technology becomes smaller and more portable, it can be used by law enforcement personnel to identify suspected terrorist releases and to help prepare the response; define contaminated areas for evacuation and safety concerns, identify the proper treatment of exposed or affected civilians, and suggest decontamination and cleanup procedures.

  11. Study of sensory diversity and redundancy to encode for chemical mixtures

    NASA Astrophysics Data System (ADS)

    Gutiérrez-Gálvez, Agustín; Fernandez, Luis; Marco, Santiago

    2011-09-01

    Inspired by sensory diversity and redundancy at the olfactory epithelium, we have built a large chemical sensor array based on commercial MOX sensors. Different sensor families along with temperature modulation accounts for sensory diversity, whereas sensors of the same family combined with different load resistors provide redundancy to the system. To study the encoding of odor mixtures, a data collection consisting on the response of the array to 3 binary mixtures of ethanol, acetone, and butanone with 18 different concentration ratios is obtained.

  12. The diverse biological properties of the chemically inert noble gases.

    PubMed

    Winkler, David A; Thornton, Aaron; Farjot, Géraldine; Katz, Ira

    2016-04-01

    The noble gases represent an intriguing scientific paradox. They are extremely inert chemically but display a remarkable spectrum of clinically useful biological properties. Despite a relative paucity of knowledge of their mechanisms of action, some of the noble gases have been used successfully in the clinic. Studies with xenon have suggested that the noble gases as a class may exhibit valuable biological properties such as anaesthesia; amelioration of ischemic damage; tissue protection prior to transplantation; analgesic properties; and a potentially wide range of other clinically useful effects. Xenon has been shown to be safe in humans, and has useful pharmacokinetic properties such as rapid onset, fast wash out etc. The main limitations in wider use are that: many of the fundamental biochemical studies are still lacking; the lighter noble gases are likely to manifest their properties only under hyperbaric conditions, impractical in surgery; and administration of xenon using convectional gaseous anaesthesia equipment is inefficient, making its use very expensive. There is nonetheless a significant body of published literature on the biochemical, pharmacological, and clinical properties of noble gases but no comprehensive reviews exist that summarize their properties and the existing knowledge of their models of action at the molecular (atomic) level. This review provides such an up-to-date summary of the extensive, useful biological properties of noble gases as drugs and prospects for wider application of these atoms. PMID:26896563

  13. Chemical-Functional Diversity in Cell-Penetrating Peptides

    PubMed Central

    Stalmans, Sofie; Wynendaele, Evelien; Bracke, Nathalie; Gevaert, Bert; D’Hondt, Matthias; Peremans, Kathelijne; Burvenich, Christian; De Spiegeleer, Bart

    2013-01-01

    Cell-penetrating peptides (CPPs) are a promising tool to overcome cell membrane barriers. They have already been successfully applied as carriers for several problematic cargoes, like e.g. plasmid DNA and (si)RNA, opening doors for new therapeutics. Although several hundreds of CPPs are already described in the literature, only a few commercial applications of CPPs are currently available. Cellular uptake studies of these peptides suffer from inconsistencies in used techniques and other experimental conditions, leading to uncertainties about their uptake mechanisms and structural properties. To clarify the structural characteristics influencing the cell-penetrating properties of peptides, the chemical-functional space of peptides, already investigated for cellular uptake, was explored. For 186 peptides, a new cell-penetrating (CP)-response was proposed, based upon the scattered quantitative results for cellular influx available in the literature. Principal component analysis (PCA) and a quantitative structure-property relationship study (QSPR), using chemo-molecular descriptors and our newly defined CP-response, learned that besides typical well-known properties of CPPs, i.e. positive charge and amphipathicity, the shape, structure complexity and the 3D-pattern of constituting atoms influence the cellular uptake capacity of peptides. PMID:23951237

  14. Genetic diversity and chemical polymorphism of some Thymus species.

    PubMed

    Rustaiee, Ali Reza; Yavari, Alireza; Nazeri, Vahideh; Shokrpour, Majid; Sefidkon, Fatemeh; Rasouli, Musa

    2013-06-01

    To ascertain whether there are chemical and genetic relationships among some Thymus species and also to determine correlation between these two sets of data, the essential-oil composition and genetic variability of six populations of Thymus including: T. daenensis ČELAK. (two populations), T. fallax FISCH. & C.A.MEY., T. fedtschenkoi RONNIGER, T. migricus KLOKOV & DES.-SHOST., and T. vulgaris L. were analyzed by GC and GC/MS, and also by randomly amplified polymorphic DNA (RAPD). Thus, 27 individuals were analyzed using 16 RAPD primers, which generated 264 polymorphic scorable bands and volatiles isolated by distillation extraction were subjected to GC and GC/MS analyses. The yields of oils ranged from 2.1 to 3.8% (v/w), and 34 components were identified, amounting to a total percentage of 97.8-99.9%. RAPD Markers allowed a perfect distinction between the different species based on their distinctive genetic background. However, they did not show identical clustering with the volatile-oil profiles. PMID:23776024

  15. Essential oils from neotropical Myrtaceae: chemical diversity and biological properties.

    PubMed

    Stefanello, Maria Élida Alves; Pascoal, Aislan C R F; Salvador, Marcos J

    2011-01-01

    Myrtaceae family (121 genera, 3800-5800 spp.) is one of the most important families in tropical forests. They are aromatic trees or shrubs, which frequently produce edible fruits. In the neotropics, ca. 1000 species were found. Several members of this family are used in folk medicine, mainly as an antidiarrheal, antimicrobial, antioxidant, cleanser, antirheumatic, and anti-inflammatory agent and to decrease the blood cholesterol. In addition, some fruits are eaten fresh or used to make juices, liqueurs, and sweets very much appreciated by people. The flavor composition of some fruits belonging to the Myrtaceae family has been extensively studied due to their pleasant and intense aromas. Most of the essential oils of neotropical Myrtaceae analyzed so far are characterized by predominance of sesquiterpenes, some with important biological properties. In the present work, chemical and pharmacological studies carried out on neotropical Myrtaceae species are reviewed, based on original articles published since 1980. The uses in folk medicine and chemotaxonomic importance of secondary metabolites are also briefly discussed. PMID:21259421

  16. Combinatorial Generation of Chemical Diversity by Redox Enzymes in Chaetoviridin Biosynthesis.

    PubMed

    Sato, Michio; Winter, Jaclyn M; Kishimoto, Shinji; Noguchi, Hiroshi; Tang, Yi; Watanabe, Kenji

    2016-03-18

    Chaetoviridins constitute a large family of structurally related secondary metabolites isolated from Chaetomium fungi. To elucidate the biosynthesis pathway and understand how the chemical diversity of chaetoviridins is generated, gene deletion and in vitro characterization of the four post-PKS modifications enzymes were undertaken. CazL and CazP were identified to have substrate promiscuity that facilitates the formation of nonchlorinated analogues. In addition, enzymatic oxidation and reduction combined with spontaneous dehydration and lactonization of the intermediates further expand the chemical diversity. PMID:26959241

  17. Evolution of Chemical Diversity in Echinocandin Lipopeptide Antifungal Metabolites

    PubMed Central

    Yue, Qun; Chen, Li; Zhang, Xiaoling; Li, Kuan; Sun, Jingzu; Liu, Xingzhong

    2015-01-01

    The echinocandins are a class of antifungal drugs that includes caspofungin, micafungin, and anidulafungin. Gene clusters encoding most of the structural complexity of the echinocandins provided a framework for hypotheses about the evolutionary history and chemical logic of echinocandin biosynthesis. Gene orthologs among echinocandin-producing fungi were identified. Pathway genes, including the nonribosomal peptide synthetases (NRPSs), were analyzed phylogenetically to address the hypothesis that these pathways represent descent from a common ancestor. The clusters share cooperative gene contents and linkages among the different strains. Individual pathway genes analyzed in the context of similar genes formed unique echinocandin-exclusive phylogenetic lineages. The echinocandin NRPSs, along with the NRPS from the inp gene cluster in Aspergillus nidulans and its orthologs, comprise a novel lineage among fungal NRPSs. NRPS adenylation domains from different species exhibited a one-to-one correspondence between modules and amino acid specificity that is consistent with models of tandem duplication and subfunctionalization. Pathway gene trees and Ascomycota phylogenies are congruent and consistent with the hypothesis that the echinocandin gene clusters have a common origin. The disjunct Eurotiomycete-Leotiomycete distribution appears to be consistent with a scenario of vertical descent accompanied by incomplete lineage sorting and loss of the clusters from most lineages of the Ascomycota. We present evidence for a single evolutionary origin of the echinocandin family of gene clusters and a progression of structural diversification in two fungal classes that diverged approximately 290 to 390 million years ago. Lineage-specific gene cluster evolution driven by selection of new chemotypes contributed to diversification of the molecular functionalities. PMID:26024901

  18. Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics

    PubMed Central

    2015-01-01

    Background The development of robust methods for chemical named entity recognition, a challenging natural language processing task, was previously hindered by the lack of publicly available, large-scale, gold standard corpora. The recent public release of a large chemical entity-annotated corpus as a resource for the CHEMDNER track of the Fourth BioCreative Challenge Evaluation (BioCreative IV) workshop greatly alleviated this problem and allowed us to develop a conditional random fields-based chemical entity recogniser. In order to optimise its performance, we introduced customisations in various aspects of our solution. These include the selection of specialised pre-processing analytics, the incorporation of chemistry knowledge-rich features in the training and application of the statistical model, and the addition of post-processing rules. Results Our evaluation shows that optimal performance is obtained when our customisations are integrated into the chemical entity recogniser. When its performance is compared with that of state-of-the-art methods, under comparable experimental settings, our solution achieves competitive advantage. We also show that our recogniser that uses a model trained on the CHEMDNER corpus is suitable for recognising names in a wide range of corpora, consistently outperforming two popular chemical NER tools. Conclusion The contributions resulting from this work are two-fold. Firstly, we present the details of a chemical entity recognition methodology that has demonstrated performance at a competitive, if not superior, level as that of state-of-the-art methods. Secondly, the developed suite of solutions has been made publicly available as a configurable workflow in the interoperable text mining workbench Argo. This allows interested users to conveniently apply and evaluate our solutions in the context of other chemical text mining tasks. PMID:25810777

  19. Acid-Base Chemistry of White Wine: Analytical Characterisation and Chemical Modelling

    PubMed Central

    Prenesti, Enrico; Berto, Silvia; Toso, Simona; Daniele, Pier Giuseppe

    2012-01-01

    A chemical model of the acid-base properties is optimized for each white wine under study, together with the calculation of their ionic strength, taking into account the contributions of all significant ionic species (strong electrolytes and weak one sensitive to the chemical equilibria). Coupling the HPLC-IEC and HPLC-RP methods, we are able to quantify up to 12 carboxylic acids, the most relevant substances responsible of the acid-base equilibria of wine. The analytical concentration of carboxylic acids and of other acid-base active substances was used as input, with the total acidity, for the chemical modelling step of the study based on the contemporary treatment of overlapped protonation equilibria. New protonation constants were refined (L-lactic and succinic acids) with respect to our previous investigation on red wines. Attention was paid for mixed solvent (ethanol-water mixture), ionic strength, and temperature to ensure a thermodynamic level to the study. Validation of the chemical model optimized is achieved by way of conductometric measurements and using a synthetic “wine” especially adapted for testing. PMID:22566762

  20. Can phylogeny predict chemical diversity and potential medicinal activity of plants? A case study of Amaryllidaceae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During evolution, plants and other organisms have developed a diversity of chemical defences, leading to the evolution of various groups of specialized metabolites selected for their endogenous biological function. A correlation between phylogeny and biosynthetic pathways could offer a predictive ap...

  1. Using the gini coefficient to measure the chemical diversity of small-molecule libraries.

    PubMed

    Weidlich, Iwona E; Filippov, Igor V

    2016-08-15

    Modern databases of small organic molecules contain tens of millions of structures. The size of theoretically available chemistry is even larger. However, despite the large amount of chemical information, the "big data" moment for chemistry has not yet provided the corresponding payoff of cheaper computer-predicted medicine or robust machine-learning models for the determination of efficacy and toxicity. Here, we present a study of the diversity of chemical datasets using a measure that is commonly used in socioeconomic studies. We demonstrate the use of this diversity measure on several datasets that were constructed to contain various congeneric subsets of molecules as well as randomly selected molecules. We also apply our method to a number of well-known databases that are frequently used for structure-activity relationship modeling. Our results show the poor diversity of the common sources of potential lead compounds compared to actual known drugs. © 2016 Wiley Periodicals, Inc. PMID:27353971

  2. Chemical enhancement of SA7 virus transformation of hamster embryo cells: evaluation by interlaboratory testing of diverse chemicals.

    PubMed

    Hatch, G G; Anderson, T M; Lubet, R A; Kouri, R E; Putman, D L; Cameron, J W; Nims, R W; Most, B; Spalding, J W; Tennant, R W

    1986-01-01

    Twelve chemicals from diverse structural classes were tested under code for their capacity to enhance the transformation of Syrian hamster embryo cells by simian adenovirus SA7 in two independent laboratories. Pretreatment of hamster cells with eight of those chemicals (reserpine, dichlorvos, methapyrilene hydrochloride, benzidine dihydrochloride, diphenylhydantoin, cinnamyl anthranilate, 11-aminoundecanoic acid, and 4,4'-oxydianiline) produced repeatable enhancement of SA7 transformation at two or more consecutive dose levels, which constitutes clear evidence of enhancing activity in this assay. Both toxic and nontoxic doses of each of these chemicals caused enhancement of virus transformation. Two chemicals (2,6-dichloro-p-phenylenediamine and cinnamaldehyde) produced some evidence of enhancing activity (repeatable transformation enhancement at one dose). Dose ranges for cytotoxicity and enhancement of SA7 transformation were similar in both laboratories for all chemicals producing activity. The final two chemicals, chloramphenicol sodium succinate and ethylene thiourea, failed to reproducibly demonstrate either significant cytotoxicity or enhancement of SA7 transformation at concentrations up to 10-20 mM. The test results for these 12 chemicals were combined with the test results for 9 known carcinogens and noncarcinogens in order to evaluate relationships between activity, dose response, and lowest effective enhancing concentration for these compounds, as well as to correlate them with rodent carcinogenesis classifications. The Syrian hamster embryo cell-SA7 system demonstrated reproducible test responses in both intra- and interlaboratory studies and detected 13 out of 15 known rodent carcinogens. PMID:3732194

  3. Predicting carcinogenicity of diverse chemicals using probabilistic neural network modeling approaches

    SciTech Connect

    Singh, Kunwar P.; Gupta, Shikha; Rai, Premanjali

    2013-10-15

    Robust global models capable of discriminating positive and non-positive carcinogens; and predicting carcinogenic potency of chemicals in rodents were developed. The dataset of 834 structurally diverse chemicals extracted from Carcinogenic Potency Database (CPDB) was used which contained 466 positive and 368 non-positive carcinogens. Twelve non-quantum mechanical molecular descriptors were derived. Structural diversity of the chemicals and nonlinearity in the data were evaluated using Tanimoto similarity index and Brock–Dechert–Scheinkman statistics. Probabilistic neural network (PNN) and generalized regression neural network (GRNN) models were constructed for classification and function optimization problems using the carcinogenicity end point in rat. Validation of the models was performed using the internal and external procedures employing a wide series of statistical checks. PNN constructed using five descriptors rendered classification accuracy of 92.09% in complete rat data. The PNN model rendered classification accuracies of 91.77%, 80.70% and 92.08% in mouse, hamster and pesticide data, respectively. The GRNN constructed with nine descriptors yielded correlation coefficient of 0.896 between the measured and predicted carcinogenic potency with mean squared error (MSE) of 0.44 in complete rat data. The rat carcinogenicity model (GRNN) applied to the mouse and hamster data yielded correlation coefficient and MSE of 0.758, 0.71 and 0.760, 0.46, respectively. The results suggest for wide applicability of the inter-species models in predicting carcinogenic potency of chemicals. Both the PNN and GRNN (inter-species) models constructed here can be useful tools in predicting the carcinogenicity of new chemicals for regulatory purposes. - Graphical abstract: Figure (a) shows classification accuracies (positive and non-positive carcinogens) in rat, mouse, hamster, and pesticide data yielded by optimal PNN model. Figure (b) shows generalization and predictive

  4. The vanilloid receptor as a putative target of diverse chemicals in multiple chemical sensitivity.

    PubMed

    Pall, Martin L; Anderson, Julius H

    2004-07-01

    The vanilloid receptor (TRPV1 or VR1), widely distributed in the central and peripheral nervous system, is activated by a broad range of chemicals similar to those implicated in Multiple Chemical Sensitivity (MCS) Syndrome. The vanilloid receptor is reportedly hyperresponsive in MCS and can increase nitric oxide levels and stimulate N-methyl-D-aspartate (NMDA) receptor activity, both of which are important features in the previously proposed central role of nitric oxide and NMDA receptors in MCS. Vanilloid receptor activity is markedly altered by multiple mechanisms, possibly providing an explanation for the increased activity in MCS and symptom masking by previous chemical exposure. Activation of this receptor by certain mycotoxins may account for some cases of sick building syndrome, a frequent precursor of MCS. Twelve types of evidence implicate the vanilloid receptor as the major target of chemicals, including volatile organic solvents (but not pesticides) in MCS. PMID:16241041

  5. Analytical Capability of Defocused µ-SORS in the Chemical Interrogation of Thin Turbid Painted Layers

    PubMed Central

    Realini, Marco; Botteon, Alessandra; Colombo, Chiara; Noll, Sarah; Elliott, Stephen R.; Matousek, Pavel

    2016-01-01

    A recently developed micrometer-scale spatially offset Raman spectroscopy (μ-SORS) method provides a new analytical capability for investigating non-destructively the chemical composition of sub-surface, micrometer-scale thickness, diffusely scattering layers at depths beyond the reach of conventional confocal Raman microscopy. Here, we demonstrate experimentally, for the first time, the capability of μ-SORS to determine whether two detected chemical components originate from two separate layers or whether the two components are mixed together in a single layer. Such information is important in a number of areas, including conservation of cultural heritage objects, and is not available, for highly turbid media, from conventional Raman microscopy, where axial (confocal) scanning is not possible due to an inability to facilitate direct imaging within the highly scattering sample. This application constitutes an additional capability for μ-SORS in addition to its basic capacity to determine the overall chemical make-up of layers in a turbid system. PMID:26767641

  6. Analytical Capability of Defocused µ-SORS in the Chemical Interrogation of Thin Turbid Painted Layers.

    PubMed

    Conti, Claudia; Realini, Marco; Botteon, Alessandra; Colombo, Chiara; Noll, Sarah; Elliott, Stephen R; Matousek, Pavel

    2016-01-01

    A recently developed micrometer-scale spatially offset Raman spectroscopy (μ-SORS) method provides a new analytical capability for investigating non-destructively the chemical composition of sub-surface, micrometer-scale thickness, diffusely scattering layers at depths beyond the reach of conventional confocal Raman microscopy. Here, we demonstrate experimentally, for the first time, the capability of μ-SORS to determine whether two detected chemical components originate from two separate layers or whether the two components are mixed together in a single layer. Such information is important in a number of areas, including conservation of cultural heritage objects, and is not available, for highly turbid media, from conventional Raman microscopy, where axial (confocal) scanning is not possible due to an inability to facilitate direct imaging within the highly scattering sample. This application constitutes an additional capability for μ-SORS in addition to its basic capacity to determine the overall chemical make-up of layers in a turbid system. PMID:26767641

  7. Phylogenetic and chemical diversity of fungal endophytes isolated from Silybum marianum (L) Gaertn. (milk thistle)

    PubMed Central

    Raja, Huzefa A.; Kaur, Amninder; El-Elimat, Tamam; Figueroa, Mario; Kumar, Rahul; Deep, Gagan; Agarwal, Rajesh; Faeth, Stanley H.; Cech, Nadja B.; Oberlies, Nicholas H.

    2015-01-01

    Use of the herb milk thistle (Silybum marianum) is widespread, and its chemistry has been studied for over 50 years. However, milk thistle endophytes have not been studied previously for their fungal and chemical diversity. We examined the fungal endophytes inhabiting this medicinal herb to determine: (1) species composition and phylogenetic diversity of fungal endophytes; (2) chemical diversity of secondary metabolites produced by these organisms; and (3) cytotoxicity of the pure compounds against the human prostate carcinoma (PC-3) cell line. Forty-one fungal isolates were identified from milk thistle comprising 25 operational taxonomic units based on BLAST search via GenBank using published authentic sequences from nuclear ribosomal internal transcribed spacer sequence data. Maximum likelihood analyses of partial 28S rRNA gene showed that these endophytes had phylogenetic affinities to four major classes of Ascomycota, the Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes. Chemical studies of solid–substrate fermentation cultures led to the isolation of four new natural products. In addition, 58 known secondary metabolites, representing diverse biosynthetic classes, were isolated and characterized using a suite of nuclear magnetic resonance and mass spectrometry techniques. Selected pure compounds were tested against the PC-3 cell line, where six compounds displayed cytotoxicity. PMID:26000195

  8. Diversity-oriented synthetic strategies applied to cancer chemical biology and drug discovery.

    PubMed

    Collins, Ian; Jones, Alan M

    2014-01-01

    How can diversity-oriented strategies for chemical synthesis provide chemical tools to help shape our understanding of complex cancer pathways and progress anti-cancer drug discovery efforts? This review (surveying the literature from 2003 to the present) considers the applications of diversity-oriented synthesis (DOS), biology-oriented synthesis (BIOS) and associated strategies to cancer biology and drug discovery, summarising the syntheses of novel and often highly complex scaffolds from pluripotent or synthetically versatile building blocks. We highlight the role of diversity-oriented synthetic strategies in producing new chemical tools to interrogate cancer biology pathways through the assembly of relevant libraries and their application to phenotypic and biochemical screens. The use of diversity-oriented strategies to explore structure-activity relationships in more advanced drug discovery projects is discussed. We show how considering appropriate and variable focus in library design has provided a spectrum of DOS approaches relevant at all stages in anti-cancer drug discovery. PMID:25350364

  9. Multiple component analysis of cigarette smoke using THz spectroscopy, comparison with standard chemical analytical methods

    NASA Astrophysics Data System (ADS)

    Bigourd, D.; Cuisset, A.; Hindle, F.; Matton, S.; Bocquet, R.; Mouret, G.; Cazier, F.; Dewaele, D.; Nouali, H.

    2007-03-01

    Terahertz time domain spectroscopy and photomixing have been used alongside one another for the detection and the quantification of small polar species in mainstream cigarette smoke. The broadband submillimeter source used in time domain spectroscopy allowed a rapid and simultaneous detection of several pure rotational transitions of hydrogen cyanide (HCN) and carbon monoxide (CO) in realistic conditions of pressure and temperature. The spectral purity of the continuous wave terahertz source produced by photomixing, permitted the concentrations of these molecules to be measured at pressures of tens of hPa. Moreover, at lower pressure, traces of formaldehyde (H2CO) have been unambiguously identified at frequencies above 1 THz. A comparison with chemical analytical methods has been completed for each molecule highlighting the advantages of the direct measurement by THz spectroscopy.

  10. Chiral Separation of G-type Chemical Warfare Nerve Agents via Analytical Supercritical Fluid Chromatography

    PubMed Central

    Kasten, Shane A; Zulli, Steven; Jones, Jonathan L; Dephillipo, Thomas; Cerasoli, Douglas M

    2014-01-01

    Chemical warfare nerve agents (CWNAs) are extremely toxic organophosphorus compounds that contain a chiral phosphorus center. Undirected synthesis of G-type CWNAs produces stereoisomers of tabun, sarin, soman, and cyclosarin (GA, GB, GD, and GF, respectively). Analytical-scale methods were developed using a supercritical fluid chromatography (SFC) system in tandem with a mass spectrometer for the separation, quantitation, and isolation of individual stereoisomers of GA, GB, GD, and GF. Screening various chiral stationary phases (CSPs) for the capacity to provide full baseline separation of the CWNAs revealed that a Regis WhelkO1 (SS) column was capable of separating the enantiomers of GA, GB, and GF, with elution of the P(+) enantiomer preceding elution of the corresponding P(–) enantiomer; two WhelkO1 (SS) columns had to be connected in series to achieve complete baseline resolution. The four diastereomers of GD were also resolved using two tandem WhelkO1 (SS) columns, with complete baseline separation of the two P(+) epimers. A single WhelkO1 (RR) column with inverse stereochemistry resulted in baseline separation of the GD P(–) epimers. The analytical methods described can be scaled to allow isolation of individual stereoisomers to assist in screening and development of countermeasures to organophosphorus nerve agents. Chirality 26:817–824, 2014. © 2014 The Authors. Chirality published by John Wiley Periodicals, Inc. PMID:25298066

  11. Chemical composition of inks of diverse marine molluscs suggests convergent chemical defenses.

    PubMed

    Derby, Charles D; Kicklighter, Cynthia E; Johnson, P M; Zhang, Xu

    2007-05-01

    Some marine molluscs, notably sea hares, cuttlefish, squid, and octopus, release ink when attacked by predators. The sea hare Aplysia californica releases secretions from the ink gland and opaline gland that protect individuals from injury or death from predatory spiny lobsters through a combination of mechanisms that include chemical deterrence, sensory disruption, and phagomimicry. The latter two mechanisms are facilitated by millimolar concentrations of free amino acids (FAA) in sea hare ink and opaline, which stimulate the chemosensory systems of predators, ultimately leading to escape by sea hares. We hypothesize that other inking molluscs use sensory disruption and/or phagomimicry as a chemical defense. To investigate this, we examined concentrations of 21 FAA and ammonium in the defensive secretions of nine species of inking molluscs: three sea hares (Aplysia californica, Aplysia dactylomela, Aplysia juliana) and six cephalopods (cuttlefish: Sepia officinalis; squid: Loligo pealei, Lolliguncula brevis, Dosidicus gigas; octopus: Octopus vulgaris, Octopus bimaculoides). We found millimolar levels of total FAA and ammonium in these secretions, and the FAA in highest concentration were taurine, aspartic acid, glutamic acid, alanine, and lysine. Crustaceans and fish, which are major predators of these molluscs, have specific receptor systems for these FAA. Our chemical analysis supports the hypothesis that inking molluscs have the potential to use sensory disruption and/or phagomimicry as a chemical defense. PMID:17393278

  12. Characterization of plutonium-bearing wastes by chemical analysis and analytical electron microscopy

    SciTech Connect

    Behrens, R.G.; Buck, E.C.; Dietz, N.L.; Bates, J.K.; Van Deventer, E.; Chaiko, D.J.

    1995-09-01

    This report summarizes the results of characterization studies of plutonium-bearing wastes produced at the US Department of Energy weapons production facilities. Several different solid wastes were characterized, including incinerator ash and ash heels from Rocky Flats Plant and Los Alamos National Laboratory; sand, stag, and crucible waste from Hanford; and LECO crucibles from the Savannah River Site. These materials were characterized by chemical analysis and analytical electron microscopy. The results showed the presence of discrete PuO{sub 2}PuO{sub 2{minus}x}, and Pu{sub 4}O{sub 7} phases, of about 1{mu}m or less in size, in all of the samples examined. In addition, a number of amorphous phases were present that contained plutonium. In all the ash and ash heel samples examined, plutonium phases were found that were completely surrounded by silicate matrices. Consequently, to achieve optimum plutonium recovery in any chemical extraction process, extraction would have to be coupled with ultrafine grinding to average particle sizes of less than 1 {mu}m to liberate the plutonium from the surrounding inert matrix.

  13. An analytic model of axisymmetric mantle plume due to thermal and chemical diffusion

    NASA Technical Reports Server (NTRS)

    Liu, Mian; Chase, Clement G.

    1990-01-01

    An analytic model of axisymmetric mantle plumes driven by either thermal diffusion or combined diffusion of both heat and chemical species from a point source is presented. The governing equations are solved numerically in cylindrical coordinates for a Newtonian fluid with constant viscosity. Instead of starting from an assumed plume source, constraints on the source parameters, such as the depth of the source regions and the total heat input from the plume sources, are deduced using the geophysical characteristics of mantle plumes inferred from modelling of hotspot swells. The Hawaiian hotspot and the Bermuda hotspot are used as examples. Narrow mantle plumes are expected for likely mantle viscosities. The temperature anomaly and the size of thermal plumes underneath the lithosphere can be sensitive indicators of plume depth. The Hawaiian plume is likely to originate at a much greater depth than the Bermuda plume. One suggestive result puts the Hawaiian plume source at a depth near the core-mantle boundary and the source of the Bermuda plume in the upper mantle, close to the 700 km discontinuity. The total thermal energy input by the source region to the Hawaiian plume is about 5 x 10(10) watts. The corresponding diameter of the source region is about 100 to 150 km. Chemical diffusion from the same source does not affect the thermal structure of the plume.

  14. Chemical and mineralogical characterizations of LD converter steel slags: A multi-analytical techniques approach

    SciTech Connect

    Waligora, J.; Bulteel, D.; Degrugilliers, P.; Damidot, D.; Potdevin, J.L.; Measson, M.

    2010-01-15

    The use of LD converter steel slags (coming from Linz-Donawitz steelmaking process) as aggregates in road construction can in certain cases lead to dimensional damage due to a macroscopic swelling that is the consequence of chemical reactions. The aim of this study was to couple several analytical techniques in order to carefully undertake chemical and mineralogical characterizations of LD steel slags and identify the phases that are expected to be responsible for their instability. Optical microscopy, scanning electron microscopy and electron probe microanalyses revealed that LD steel slags mainly contain calcium silicates, dicalcium ferrites, iron oxides and lime. However, as a calcium silicate phase is heterogeneous, Raman microspectrometry and transmitted electron microscopy had to be used to characterize it more precisely. Results showed that lime is present under two forms in slag grains: some nodules observed in the matrix whose size ranges from 20 to 100 {mu}m and some micro-inclusions, enclosed in the heterogeneous calcium silicate phase whose size ranges from 1 to 3 {mu}m. It was also established that without the presence of magnesia, lime is expected to be the only phase responsible for LD steel slags instability. Nevertheless, the distribution of lime between nodules and micro-inclusions may play a major role and could explain that similar amounts of lime can induce different instabilities. Thus, it appears that lime content of LD steel slags is not the only parameter to explain their instability.

  15. Predicting binding affinities of diverse pharmaceutical chemicals to human serum plasma proteins using QSPR modelling approaches.

    PubMed

    Basant, N; Gupta, S; Singh, K P

    2016-01-01

    The prediction of the plasma protein binding (PPB) affinity of chemicals is of paramount significance in the drug development process. In this study, ensemble machine learning-based QSPR models have been established for a four-category classification and PPB affinity prediction of diverse compounds using a large PPB dataset of 930 compounds and in accordance with the OECD guidelines. The structural diversity of the chemicals was tested by the Tanimoto similarity index. The external predictive power of the developed QSPR models was evaluated through internal and external validations. In the QSPR models, XLogP was the most important descriptor. In the test data, the classification QSPR models rendered an accuracy of >93%, while the regression QSPR models yielded r(2) of >0.920 between the measured and predicted PPB affinities, with the root mean squared error <9.77. Values of statistical coefficients derived for the test data were above their threshold limits, thus put a high confidence in this analysis. The QSPR models in this study performed better than any of the previous studies. The results suggest that the developed QSPR models are reliable for predicting the PPB affinity of structurally diverse chemicals. They can be useful for initial screening of candidate molecules in the drug development process. PMID:26854728

  16. Quantile regression model for a diverse set of chemicals: application to acute toxicity for green algae.

    PubMed

    Villain, Jonathan; Lozano, Sylvain; Halm-Lemeille, Marie-Pierre; Durrieu, Gilles; Bureau, Ronan

    2014-12-01

    The potential of quantile regression (QR) and quantile support vector machine regression (QSVMR) was analyzed for the definitions of quantitative structure-activity relationship (QSAR) models associated with a diverse set of chemicals toward a particular endpoint. This study focused on a specific sensitive endpoint (acute toxicity to algae) for which even a narcosis QSAR model is not actually clear. An initial dataset including more than 401 ecotoxicological data for one species of algae (Selenastrum capricornutum) was defined. This set corresponds to a large sample of chemicals ranging from classical organic chemicals to pesticides. From this original data set, the selection of the different subsets was made in terms of the notion of toxic ratio (TR), a parameter based on the ratio between predicted and experimental values. The robustness of QR and QSVMR to outliers was clearly observed, thus demonstrating that this approach represents a major interest for QSAR associated with a diverse set of chemicals. We focused particularly on descriptors related to molecular surface properties. PMID:25431186

  17. Formation of Metal-Adducted Analyte Ions by Flame-Induced Atmospheric Pressure Chemical Ionization Mass Spectrometry.

    PubMed

    Cheng, Sy-Chyi; Wang, Chin-Hsiung; Shiea, Jentaie

    2016-05-17

    A flame-induced atmospheric pressure chemical ionization (FAPCI) source, consisting of a miniflame, nebulizer, and heated tube, was developed to ionize analytes. The ionization was performed by reacting analytes with a charged species generated in a flame. A stainless steel needle deposited with saturated alkali chloride solution was introduced into the mini oxyacetylene flame to generate alkali ions, which were reacted with analytes (M) generated in a heated nebulizer. The alkali-adducted 18-crown-6 ether ions, including (M + Li)(+), (M + Na)(+), (M + K)(+), (M + Rb)(+), and (M + Cs)(+), were successfully detected on the FAPCI mass spectra when the corresponding alkali chloride solutions were separately introduced to the flame. When an alkali chloride mixture was introduced, all alkali-adducted analyte ions were simultaneously detected. Their intensity order was as follows: (M + Cs)(+) > (M + Rb)(+) > (M + K)(+) > (M + Na)(+) > (M + Li)(+), and this trend agreed with the lattice energies of alkali chlorides. Besides alkali ions, other transition metal ions such as Ni(+), Cu(+), and Ag(+) were generated in a flame for analyte ionization. Other than metal ions, the reactive species generated in the fossil fuel flame could also be used to ionize analytes, which formed protonated analyte ions (M + H)(+) in positive ion mode and deprotonated analyte ions (M - H)(-) in negative ion mode. PMID:27093572

  18. Analytical/Operational Requirements for the In Situ Chemical Analysis of Cometary and Planetary Environments Using GC-IMS

    NASA Technical Reports Server (NTRS)

    Kojiro, Daniel R.; Stimac, Robert M.; Kaye, William J.; Takeuchi, Norishige; DeVincenizi, D. (Technical Monitor)

    2002-01-01

    Exobiology flight experiments require highly sensitive instrumentation for the in situ analysis of the volatile chemical species that occur in the atmospheres and surfaces of various bodies within the solar system. The complex mixtures encountered place a heavy burden on the analytical instrumentation to detect and identify all species present. The minimal resources available onboard for such missions mandate that the instruments provide maximum analytical capabilities with minimal requirements of volume, weight and consumables. The miniCIDEX instrument was developed for the chemical analysis of a cemetery environment. It combined a Gas Chromatograph (GC) with a helium based Ion Mobility Spectrometer (IMS) to fulfill the analytical requirements of a cemetery exobiology mission: universal response; ppb sensitivity; low mass, volume and consumable MiniCIDEX is now a candidate for the chemical analysis instrument of a Titan Aero-rover Mission. The complexity of the analyses will be similar to the comet application with a heavier emphasis on organic molecules. Because the Titan Aero-Rover will be a balloon powered rover, much more attention is placed on the total mass of the instrument package. The GC will likely be a Micro-Electro-Mechanical-System (MEMS) design, smaller than the initial miniCIDEX GC by a factor of ten (with a similar reduction in consumable use). Similar miniaturization of the helium-based IMS will be necessary while maintaining the analytical capabilities. The two mission applications, the analytical requirements, and the evolution of the IMS design to accommodate these requirements will be presented.

  19. Predicting acute aquatic toxicity of structurally diverse chemicals in fish using artificial intelligence approaches.

    PubMed

    Singh, Kunwar P; Gupta, Shikha; Rai, Premanjali

    2013-09-01

    The research aims to develop global modeling tools capable of categorizing structurally diverse chemicals in various toxicity classes according to the EEC and European Community directives, and to predict their acute toxicity in fathead minnow using set of selected molecular descriptors. Accordingly, artificial intelligence approach based classification and regression models, such as probabilistic neural networks (PNN), generalized regression neural networks (GRNN), multilayer perceptron neural network (MLPN), radial basis function neural network (RBFN), support vector machines (SVM), gene expression programming (GEP), and decision tree (DT) were constructed using the experimental toxicity data. Diversity and non-linearity in the chemicals' data were tested using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. Predictive and generalization abilities of various models constructed here were compared using several statistical parameters. PNN and GRNN models performed relatively better than MLPN, RBFN, SVM, GEP, and DT. Both in two and four category classifications, PNN yielded a considerably high accuracy of classification in training (95.85 percent and 90.07 percent) and validation data (91.30 percent and 86.96 percent), respectively. GRNN rendered a high correlation between the measured and model predicted -log LC50 values both for the training (0.929) and validation (0.910) data and low prediction errors (RMSE) of 0.52 and 0.49 for two sets. Efficiency of the selected PNN and GRNN models in predicting acute toxicity of new chemicals was adequately validated using external datasets of different fish species (fathead minnow, bluegill, trout, and guppy). The PNN and GRNN models showed good predictive and generalization abilities and can be used as tools for predicting toxicities of structurally diverse chemical compounds. PMID:23764236

  20. Odor intensity and characterization of jet exhaust and chemical analytical measurements

    NASA Technical Reports Server (NTRS)

    Kendall, D. A.; Levins, P. L.

    1973-01-01

    Odor and chemical analyses were carried out on the exhaust samples from a J-57 combustor can operated over a range of inlet conditions, and with several fuel types and nozzle modifications. The odor characteristics and total intensity of odor for each exhaust were determined over a range of dilutions to allow for a least squares determination of the intensity at 1,000 to 1 dilutions. Analytical measures included the concentration of total hydrocarbons and the concentrations of aromatic organic species and oxygenated organic species from collected samples which were taken concurrently. A correlation was found between the concentration of the odorous oxygenated fraction and the total intensity of aroma. Inlet operating conditions and nozzle modifications which increase the efficiency of combustion as measured by exhaust gas analyses reduce the odor intensity and the quantity of oxygenates in the exhaust. The type of fuel burned altered the intensity of odor in relation to the quantity of oxygenates produced and, in some instances, changed the odor character.

  1. EVALUATION OF AN ESCA (ELECTRON SPECTROSCOPY FOR CHEMICAL ANALYSIS)/LEACHATE ANALYTICAL SCHEME TO CHARACTERIZE PROCESS STREAM WASTES

    EPA Science Inventory

    The report gives results of an evaluation of the ability of an ESCA/leachate analytical scheme to characterize solid waste from combustion processes and hazardous waste incinerators. Samples were analyzed for surface elemental composition by electron spectroscopy for chemical ana...

  2. The antimicrobial potential of ionic liquids: A source of chemical diversity for infection and biofilm control.

    PubMed

    Pendleton, Jack Norman; Gilmore, Brendan F

    2015-08-01

    Although described almost a century ago, interest in ionic liquids has flourished in the last two decades, with significant advances in the understanding of their chemical, physical and biological property sets driving their widespread application across multiple and diverse research areas. Significant progress has been made through the contributions of numerous research groups detailing novel libraries of ionic liquids, often 'task-specific' designer solvents for application in areas as diverse as separation technology, catalysis and bioremediation. Basic antimicrobial screening has often been included as a surrogate indication of the environmental impact of these compounds widely regarded as 'green' solvents. Obviating the biological properties, specifically toxicity, of these compounds has obstructed their potential application as sophisticated designer biocides. A recent tangent in ionic liquids research now aims to harness tuneable biological properties of these compounds in the design of novel potent antimicrobials, recognising their unparalleled flexibility for chemical diversity in a severely depleted antimicrobial arsenal. This review concentrates primarily on the antimicrobial potential of ionic liquids and aims to consolidate contemporary microbiological background information, assessment protocols and future considerations necessary to advance the field in light of the urgent need for antimicrobial innovation. PMID:25907139

  3. Can phylogeny predict chemical diversity and potential medicinal activity of plants? A case study of amaryllidaceae

    PubMed Central

    2012-01-01

    Background During evolution, plants and other organisms have developed a diversity of chemical defences, leading to the evolution of various groups of specialized metabolites selected for their endogenous biological function. A correlation between phylogeny and biosynthetic pathways could offer a predictive approach enabling more efficient selection of plants for the development of traditional medicine and lead discovery. However, this relationship has rarely been rigorously tested and the potential predictive power is consequently unknown. Results We produced a phylogenetic hypothesis for the medicinally important plant subfamily Amaryllidoideae (Amaryllidaceae) based on parsimony and Bayesian analysis of nuclear, plastid, and mitochondrial DNA sequences of over 100 species. We tested if alkaloid diversity and activity in bioassays related to the central nervous system are significantly correlated with phylogeny and found evidence for a significant phylogenetic signal in these traits, although the effect is not strong. Conclusions Several genera are non-monophyletic emphasizing the importance of using phylogeny for interpretation of character distribution. Alkaloid diversity and in vitro inhibition of acetylcholinesterase (AChE) and binding to the serotonin reuptake transporter (SERT) are significantly correlated with phylogeny. This has implications for the use of phylogenies to interpret chemical evolution and biosynthetic pathways, to select candidate taxa for lead discovery, and to make recommendations for policies regarding traditional use and conservation priorities. PMID:22978363

  4. Importance of Genetic Diversity Assessment in Crop Plants and Its Recent Advances: An Overview of Its Analytical Perspectives

    PubMed Central

    Govindaraj, M.; Vetriventhan, M.; Srinivasan, M.

    2015-01-01

    The importance of plant genetic diversity (PGD) is now being recognized as a specific area since exploding population with urbanization and decreasing cultivable lands are the critical factors contributing to food insecurity in developing world. Agricultural scientists realized that PGD can be captured and stored in the form of plant genetic resources (PGR) such as gene bank, DNA library, and so forth, in the biorepository which preserve genetic material for long period. However, conserved PGR must be utilized for crop improvement in order to meet future global challenges in relation to food and nutritional security. This paper comprehensively reviews four important areas; (i) the significance of plant genetic diversity (PGD) and PGR especially on agriculturally important crops (mostly field crops); (ii) risk associated with narrowing the genetic base of current commercial cultivars and climate change; (iii) analysis of existing PGD analytical methods in pregenomic and genomic era; and (iv) modern tools available for PGD analysis in postgenomic era. This discussion benefits the plant scientist community in order to use the new methods and technology for better and rapid assessment, for utilization of germplasm from gene banks to their applied breeding programs. With the advent of new biotechnological techniques, this process of genetic manipulation is now being accelerated and carried out with more precision (neglecting environmental effects) and fast-track manner than the classical breeding techniques. It is also to note that gene banks look into several issues in order to improve levels of germplasm distribution and its utilization, duplication of plant identity, and access to database, for prebreeding activities. Since plant breeding research and cultivar development are integral components of improving food production, therefore, availability of and access to diverse genetic sources will ensure that the global food production network becomes more sustainable

  5. Reflectance Infrared Spectroscopy on Operating Surface Acoustic Wave Chemical Sensors During Exposure to Gas-Phase Analytes

    SciTech Connect

    Hierlemann, A.; Hill, M.; Ricco, A.J.; Staton, A.W.; Thomas, R.C.

    1999-01-11

    We have developed instrumentation to enable the combination of surface acoustic wave (SAW) sensor measurements with direct, in-situ molecular spectroscopic measurements to understand the response of the SAW sensors with respect to the interfacial chemistry of surface-confined sensing films interacting with gas-phase analytes. Specifically, the instrumentation and software was developed to perform in-situ Fourier-transform infrared external-reflectance spectroscopy (FTIR-ERS) on operating SAW devices during dosing of their chemically modified surfaces with analytes. By probing the surface with IR spectroscopy during gas exposure, it is possible to understand in unprecedented detail the interaction processes between the sorptive SAW coatings and the gaseous analyte molecules. In this report, we provide details of this measurement system, and also demonstrate the utility of these combined measurements by characterizing the SAW and FTIR-ERS responses of organic thin-film sensor coatings interacting with gas-phase analytes.

  6. Is parasite pressure a driver of chemical cue diversity in ants?

    PubMed

    Martin, Stephen J; Helanterä, Heikki; Drijfhout, Falko P

    2011-02-22

    Parasites and pathogens are possibly key evolutionary forces driving recognition systems. However, empirical evidence remains sparse. The ubiquitous pioneering ant Formica fusca is exploited by numerous socially parasitic ant species. We compared the chemical cue diversity, egg and nest mate recognition abilities in two Finnish and two UK populations where parasite pressure is high or absent, respectively. Finnish populations had excellent egg and nest mate discrimination abilities, which were lost in the UK populations. The loss of discrimination behaviour correlates with a loss in key recognition compounds (C(25)-dimethylalkanes). This was not owing to genetic drift or different ecotypes since neutral gene diversity was the same in both countries. Furthermore, it is known that the cuticular hydrocarbon profiles of non-host ant species remain stable between Finland and the UK. The most parsimonious explanation for the striking difference in the cue diversity (number of C(25)-dimethylalkanes isomers) between the UK and Finland populations is the large differences in parasite pressure experienced by F. fusca in the two countries. These results have strong parallels with bird (cuckoo) studies and support the hypothesis that parasites are driving recognition cue diversity. PMID:20610426

  7. [Chemical and genetic diversity of Ligularia plants collected in the Hengduan Mountains, China].

    PubMed

    Saito, Yoshinori

    2012-01-01

    The Hengduan Mountains area of China is rich in plant resources. The Ligularia species, which belong to Senecioneae and Asteraceae, distributed in this area are highly diversified and contain 6 sections and over 100 species, and are considered to be in on-going evolution and diversification. To understand the inter- and intra-specific diversity of these plants and to elucidate the mechanism of diversification, we analyzed Ligularia plants by chemical, genetic, geographical, ecological, and morphological approaches. We investigated 4 species, and isolated 26 novel compounds. Based on the chemical composition of root extract as well as nucleotide sequence variations in internal transcribed spacers (ITS), we obtained 3 findings. (i) L. virgaurea is classified into two groups, ligularol type and virgaurenone type from the view point of chemical constituents, which are phylogenetically distinguished from each other, (ii) L. subspicata and L. lamarum have an overlapped chemical spectrum, but showed no clear genetic correlation, and (iii) L. cyathiceps showed no significant variations in either chemical constituents or nucleotide sequences. PMID:23208053

  8. Chemically Diverse Toxicants Converge on Fyn and c-Cbl to Disrupt Precursor Cell Function

    PubMed Central

    Li, Zaibo; Dong, Tiefei; Pröschel, Chris; Noble, Mark

    2007-01-01

    Identification of common mechanistic principles that shed light on the action of the many chemically diverse toxicants to which we are exposed is of central importance in understanding how toxicants disrupt normal cellular function and in developing more effective means of protecting against such effects. Of particular importance is identifying mechanisms operative at environmentally relevant toxicant exposure levels. Chemically diverse toxicants exhibit striking convergence, at environmentally relevant exposure levels, on pathway-specific disruption of receptor tyrosine kinase (RTK) signaling required for cell division in central nervous system (CNS) progenitor cells. Relatively small toxicant-induced increases in oxidative status are associated with Fyn kinase activation, leading to secondary activation of the c-Cbl ubiquitin ligase. Fyn/c-Cbl pathway activation by these pro-oxidative changes causes specific reductions, in vitro and in vivo, in levels of the c-Cbl target platelet-derived growth factor receptor-α and other c-Cbl targets, but not of the TrkC RTK (which is not a c-Cbl target). Sequential Fyn and c-Cbl activation, with consequent pathway-specific suppression of RTK signaling, is induced by levels of methylmercury and lead that affect large segments of the population, as well as by paraquat, an organic herbicide. Our results identify a novel regulatory pathway of oxidant-mediated Fyn/c-Cbl activation as a shared mechanism of action of chemically diverse toxicants at environmentally relevant levels, and as a means by which increased oxidative status may disrupt mitogenic signaling. These results provide one of a small number of general mechanistic principles in toxicology, and the only such principle integrating toxicology, precursor cell biology, redox biology, and signaling pathway analysis in a predictive framework of broad potential relevance to the understanding of pro-oxidant–mediated disruption of normal development. PMID:17298174

  9. Creation and manipulation of common functional groups en route to a skeletally diverse chemical library

    PubMed Central

    Cui, Jiayue; Hao, Jason; Ulanovskaya, Olesya A.; Dundas, Joseph; Liang, Jie; Kozmin, Sergey A.

    2011-01-01

    We have developed an efficient strategy to a skeletally diverse chemical library, which entailed a sequence of enyne cycloisomerization, [4 + 2] cycloaddition, alkene dihydroxylation, and diol carbamylation. Using this approach, only 16 readily available building blocks were needed to produce a representative 191-member library, which displayed broad distribution of molecular shapes and excellent physicochemical properties. This library further enabled identification of a small molecule, which effectively suppressed glycolytic production of ATP and lactate in CHO-K1 cell line, representing a potential lead for the development of a new class of glycolytic inhibitors. PMID:21383124

  10. Bioluminescence in the Ocean: Origins of Biological, Chemical, and Ecological Diversity

    NASA Astrophysics Data System (ADS)

    Widder, E. A.

    2010-05-01

    From bacteria to fish, a remarkable variety of marine life depends on bioluminescence (the chemical generation of light) for finding food, attracting mates, and evading predators. Disparate biochemical systems and diverse phylogenetic distribution patterns of light-emitting organisms highlight the ecological benefits of bioluminescence, with biochemical and genetic analyses providing new insights into the mechanisms of its evolution. The origins and functions of some bioluminescent systems, however, remain obscure. Here, I review recent advances in understanding bioluminescence in the ocean and highlight future research efforts that will unite molecular details with ecological and evolutionary relationships.

  11. The influence of chemical chaperones on enzymatic activity under thermal and chemical stresses: common features and variation among diverse chemical families.

    PubMed

    Levy-Sakin, Michal; Berger, Or; Feibish, Nir; Sharon, Noa; Schnaider, Lee; Shmul, Guy; Amir, Yaniv; Buzhansky, Ludmila; Gazit, Ehud

    2014-01-01

    Molecular and chemical chaperones are key components of the two main mechanisms that ensure structural stability and activity under environmental stresses. Yet, chemical chaperones are often regarded only as osmolytes and their role beyond osmotic regulation is not fully understood. Here, we systematically studied a large group of chemical chaperones, representatives of diverse chemical families, for their protective influence under either thermal or chemical stresses. Consistent with previous studies, we observed that in spite of the structural similarity between sugars and sugar alcohols, they have an apparent difference in their protective potential. Our results support the notion that the protective activity is mediated by the solvent and the presence of water is essential. In the current work we revealed that i) polyols and sugars have a completely different profile of protective activity toward trifluoroethanol and thermal stress; ii) minor changes in solvent composition that do not affect enzyme activity, yet have a great effect on the ability of osmolytes to act as protectants and iii) increasing the number of active groups of carbohydrates makes them better protectants while increasing the number of active groups of methylamines does not, as revealed by attempts to synthesize de novo designed methylamines with multiple functional groups. PMID:24520396

  12. The Influence of Chemical Chaperones on Enzymatic Activity under Thermal and Chemical Stresses: Common Features and Variation among Diverse Chemical Families

    PubMed Central

    Feibish, Nir; Sharon, Noa; Schnaider, Lee; Shmul, Guy; Amir, Yaniv; Buzhansky, Ludmila; Gazit, Ehud

    2014-01-01

    Molecular and chemical chaperones are key components of the two main mechanisms that ensure structural stability and activity under environmental stresses. Yet, chemical chaperones are often regarded only as osmolytes and their role beyond osmotic regulation is not fully understood. Here, we systematically studied a large group of chemical chaperones, representatives of diverse chemical families, for their protective influence under either thermal or chemical stresses. Consistent with previous studies, we observed that in spite of the structural similarity between sugars and sugar alcohols, they have an apparent difference in their protective potential. Our results support the notion that the protective activity is mediated by the solvent and the presence of water is essential. In the current work we revealed that i) polyols and sugars have a completely different profile of protective activity toward trifluoroethanol and thermal stress; ii) minor changes in solvent composition that do not affect enzyme activity, yet have a great effect on the ability of osmolytes to act as protectants and iii) increasing the number of active groups of carbohydrates makes them better protectants while increasing the number of active groups of methylamines does not, as revealed by attempts to synthesize de novo designed methylamines with multiple functional groups. PMID:24520396

  13. Chemical diversity of microbial volatiles and their potential for plant growth and productivity

    PubMed Central

    Kanchiswamy, Chidananda Nagamangala; Malnoy, Mickael; Maffei, Massimo E.

    2015-01-01

    Microbial volatile organic compounds (MVOCs) are produced by a wide array of microorganisms ranging from bacteria to fungi. A growing body of evidence indicates that MVOCs are ecofriendly and can be exploited as a cost-effective sustainable strategy for use in agricultural practice as agents that enhance plant growth, productivity, and disease resistance. As naturally occurring chemicals, MVOCs have potential as possible alternatives to harmful pesticides, fungicides, and bactericides as well as genetic modification. Recent studies performed under open field conditions demonstrate that efficiently adopting MVOCs may contribute to sustainable crop protection and production. We review here the chemical diversity of MVOCs by describing microbial–plants and microbial–microbial interactions. Furthermore, we discuss MVOCs role in inducing phenotypic plant responses and their potential physiological effects on crops. Finally, we analyze potential and actual limitations for MVOC use and deployment in field conditions as a sustainable strategy for improving productivity and reducing pesticide use. PMID:25821453

  14. Structural diversity and chemical synthesis of peroxide and peroxide-derived polyketide metabolites from marine sponges.

    PubMed

    Norris, Matthew D; Perkins, Michael V

    2016-07-28

    Covering: up to early 2016Marine sponges are widely known as a rich source of natural products, especially of polyketide origin, with a wealth of chemical diversity. Within this vast collection, peroxide and peroxide-derived secondary metabolites have attracted significant interest in the fields of natural product isolation and chemical synthesis for their structural distinction and promising in vitro antimicrobial and anticancer properties. In this review, peroxide and peroxide-derived polyketide metabolites isolated from marine sponges in the past 35 years are summarised. Efforts toward their synthesis are detailed with a focus on methods that utilise or attempt to elucidate the complex biosynthetic interrelationships of these compounds beyond enzymatic polyketide synthesis. Recent isolations, advances in synthetic methodology and theories of biogenesis are highlighted and critically evaluated. PMID:27163115

  15. Microbial community diversity and physical-chemical features of the Southwestern Atlantic Ocean.

    PubMed

    Alves Junior, Nelson; Meirelles, Pedro Milet; de Oliveira Santos, Eidy; Dutilh, Bas; Silva, Genivaldo G Z; Paranhos, Rodolfo; Cabral, Anderson S; Rezende, Carlos; Iida, Tetsuya; de Moura, Rodrigo L; Kruger, Ricardo Henrique; Pereira, Renato C; Valle, Rogério; Sawabe, Tomoo; Thompson, Cristiane; Thompson, Fabiano

    2015-03-01

    Microbial oceanography studies have demonstrated the central role of microbes in functioning and nutrient cycling of the global ocean. Most of these former studies including at Southwestern Atlantic Ocean (SAO) focused on surface seawater and benthic organisms (e.g., coral reefs and sponges). This is the first metagenomic study of the SAO. The SAO harbors a great microbial diversity and marine life (e.g., coral reefs and rhodolith beds). The aim of this study was to characterize the microbial community diversity of the SAO along the depth continuum and different water masses by means of metagenomic, physical-chemical and biological analyses. The microbial community abundance and diversity appear to be strongly influenced by the temperature, dissolved organic carbon, and depth, and three groups were defined [1. surface waters; 2. sub-superficial chlorophyll maximum (SCM) (48-82 m) and 3. deep waters (236-1,200 m)] according to the microbial composition. The microbial communities of deep water masses [South Atlantic Central water, Antarctic Intermediate water and Upper Circumpolar Deep water] are highly similar. Of the 421,418 predicted genes for SAO metagenomes, 36.7 % had no homologous hits against 17,451,486 sequences from the North Atlantic, South Atlantic, North Pacific, South Pacific and Indian Oceans. From these unique genes from the SAO, only 6.64 % had hits against the NCBI non-redundant protein database. SAO microbial communities share genes with the global ocean in at least 70 cellular functions; however, more than a third of predicted SAO genes represent a unique gene pool in global ocean. This study was the first attempt to characterize the taxonomic and functional community diversity of different water masses at SAO and compare it with the microbial community diversity of the global ocean, and SAO had a significant portion of endemic gene diversity. Microbial communities of deep water masses (236-1,200 m) are highly similar, suggesting that these water

  16. Analytical methods for the quantification of bisphenol A, alkylphenols, phthalate esters, and perfluoronated chemicals in biological samples.

    PubMed

    Nakazawa, Hiroyuki; Iwasaki, Yusuke; Ito, Rie

    2014-01-01

    Our modern society has created a large number of chemicals that are used for the production of everyday commodities including toys, food packaging, cosmetic products, and building materials. We enjoy a comfortable and convenient lifestyle with access to these items. In addition, in specialized areas, such as experimental science and various medical fields, laboratory equipment and devices that are manufactured using a wide range of chemical substances are also extensively employed. The association between human exposure to trace hazardous chemicals and an increased incidence of endocrine disease has been recognized. However, the evaluation of human exposure to such endocrine disrupting chemicals is therefore imperative, and the determination of exposure levels requires the analysis of human biological materials, such as blood and urine. To obtain as much information as possible from limited sample sizes, highly sensitive and reliable analytical methods are also required for exposure assessments. The present review focuses on effective analytical methods for the quantification of bisphenol A (BPA), alkylphenols (APs), phthalate esters (PEs), and perfluoronated chemicals (PFCs), which are chemicals used in the production of everyday commodities. Using data obtained from liquid chromatography/mass spectrometry (LC/MS) and LC/MS/MS analyses, assessments of the risks to humans were also presented based on the estimated levels of exposure to PFCs. PMID:24420241

  17. Consequences of plant-chemical diversity for domestic goat food preference in Mediterranean forests

    NASA Astrophysics Data System (ADS)

    Baraza, Elena; Hódar, José A.; Zamora, Regino

    2009-01-01

    The domestic goat, a major herbivore in the Mediterranean basin, has demonstrated a strong ability to adapt its feeding behaviour to the chemical characteristics of food, selecting plants according to their nutritive quality. In this study, we determine some chemical characteristics related to plant nutritional quality and its variability among and within five tree species, these being the main components of the mountain forests of SE Spain, with the aim of determining their influence on food selection by this generalist herbivore. We analyse nitrogen, total phenols, condensed tannins and fibre concentration as an indicator of the nutritive value of the different trees. To determine the preference by the domestic goat, we performed two types of feeding-choice assays, where goats had to select between different species or between branches of the same species but from trees of different nutritional quality. The analysis of the plant nutritional quality showed significant differences in the chemical characteristics between species, and a high variability within species. However, when faced with different tree species, the domestic goat selected some of them but showed striking individual differences between goats. When selecting between trees of the same species, the goats showed no differential selection. This limited effect of chemical plant characteristics, together with the variability in foraging behaviour, resulted in a widespread consumption of diverse plant species, which can potentially modulate the effect of the goat on vegetation composition, and open the way for the conservation of traditional livestock grazing on natural protected areas.

  18. Plant Community Diversity Influences Allocation to Direct Chemical Defence in Plantago lanceolata

    PubMed Central

    Mraja, Anne; Unsicker, Sybille B.; Reichelt, Michael; Gershenzon, Jonathan; Roscher, Christiane

    2011-01-01

    Background Forecasting the consequences of accelerating rates of changes in biodiversity for ecosystem functioning requires a mechanistic understanding of the relationships between the structure of biological communities and variation in plant functional characteristics. So far, experimental data of how plant species diversity influences the investment of individual plants in direct chemical defences against herbivores and pathogens is lacking. Methodology/Principal Findings We used Plantago lanceolata as a model species in experimental grasslands differing in species richness and composition (Jena Experiment) to investigate foliar concentrations of the iridoid glycosides (IG), catalpol and its biosynthetic precursor aucubin. Total IG and aucubin concentrations decreased, while catalpol concentrations increased with increasing plant diversity in terms of species or functional group richness. Negative plant diversity effects on total IG and aucubin concentrations correlated with increasing specific leaf area of P. lanceolata, suggesting that greater allocation to light acquisition reduced the investment into these carbon-based defence components. In contrast, increasing leaf nitrogen concentrations best explained increasing concentrations of the biosynthetically more advanced IG, catalpol. Observed levels of leaf damage explained a significant proportion of variation in total IG and aucubin concentrations, but did not account for variance in catalpol concentrations. Conclusions/Significance Our results clearly show that plants growing in communities of varying species richness and composition differ in their defensive chemistry, which may modulate plant susceptibility to enemy attack and consequently their interactions with higher trophic level organisms. PMID:22174766

  19. Comparison of physico-chemical parameters and zooplankton diversity in two perennial ponds at Aligarh, India.

    PubMed

    Parveen, Saltanat; Abdel Mola, Hesham R

    2013-07-01

    Investigations were carried out on the diversity of zooplankton in relation to physico-chemical parameters of two perennial ponds (Chautal Pond and Medical Pond) of Aligarh, India. Thirty nine species of holoplankton were identified belonging to copepoda (2 species), rotifera (28 species), cladocera (6 species) and protozoa (3 species). Other forms; like as meroplankton (insects) and tychoplankton (nematodes and ostracodes) were also recorded. Higher values of physico-chemical parameters and low zooplankton diversity were recorded in the Chautal Pond, whereas low values of physico-chemical parameters and high diversity were recorded in the Medical Pond. Ostracods considered to be the most dominant group in Medical Pond (32.16% of the total zooplankton) while Cladocerans are considered to be the most dominant group in Chautal Pond (38.83% of the total zooplankton). Rotifera contributed more in Medical Pond (16.42%) as compared to Chautal Pond (15.81%). Five species of Brachionus was recorded during study. Out of five, four Brachionus species were recorded in Chautal Pond while only two species were recorded in Medical pond. This indicates that Chautal Pond is more eutrophic than Medical pond. In addition, higher carbon dioxide values (37-105 mg l(-1)), low dissolved oxygen (0.7-3.3 mg I(-1)) and higher electrical conductivity values (1069-1691 mg l(-1)) were also indicative of eutrophic nature of Chautal Pond. Present study also revealed that total zooplankton species, species richness and diversity indices (Evenness, Shannon-Winner and Simpson) were comparatively higher in Medical pond. The rotifer species Philodina roseola (146 Org. l(-1)) and Monstyla closterocerca (109 Org. l(-1)) was dominated in Medical Pond while the rotifers Brachionus urceolaris (512 Org. l(-1)) and the cladocern species Ceriodaphnia cornuta (1540 Org. l(-1)) dominated in Chautal Pond during post-monsoon season. This might be due to the effect of rain water which played an important role in

  20. Zooplankton diversity of Chikkadevarayana canal in relation to physico-chemical characteristics.

    PubMed

    Smitha; Shivashankar, P; Venkataramana, G V

    2013-07-01

    Plankton diversity and physico-chemical parameters are an important criterion for evaluating the suitability of water for irrigation and drinking purposes. In this study, we tried to assess zooplankton species richness, diversity and evenness to predict the state of Chickadevarayana canal water of Cauvery River according to physico-chemical parameters. A total of 51 taxa were recorded with 22 rotifers, 5 copepods, 6 cladocerans, 1 ostracoda and 17 protozoans. More number of zooplankton species were recorded in Darasaguppe (30) followed by Edmuri (26), Kennala (20), Pandavpura (19) and Gendehosahalli (16). Among the rotifers, Euchlanis sp. species was abundant (194). Acantholeberis curvirostris was predominant among cladocerans (970). Among copepods, numerical superiorities were found in the case Cyclops sp. Cypris sp. was recorded in the ostracoda. Centropyxis aculeate repeated abundance in protozoans (412). The water samples analyzed for temperature, pH, electrical conductivity, alkalinity, hardness, dissolved oxygen, phosphate, sulphate and nitrate did not indicate variation. The occurrence of Asplanchna herricki, Lacrymaria sp, Brachionus pala and Monostyla lunaris showed highest similarity of occurrence reaching above 90%. The study revealed that the presence of certain species like Monostyla, Lepadella, Leydigia, Keratella, Branchionus and Cypris species can be considered as a biological indicator for eutrophication. PMID:24640263

  1. Co-Cultivation—A Powerful Emerging Tool for Enhancing the Chemical Diversity of Microorganisms

    PubMed Central

    Marmann, Andreas; Aly, Amal H.; Lin, Wenhan; Wang, Bingui; Proksch, Peter

    2014-01-01

    Marine-derived bacteria and fungi are promising sources of novel bioactive compounds that are important for drug discovery programs. However, as encountered in terrestrial microorganisms there is a high rate of redundancy that results in the frequent re-discovery of known compounds. Apparently only a part of the biosynthetic genes that are harbored by fungi and bacteria are transcribed under routine laboratory conditions which involve cultivation of axenic microbial strains. Many biosynthetic genes remain silent and are not expressed in vitro thereby seriously limiting the chemical diversity of microbial compounds that can be obtained through fermentation. In contrast to this, co-cultivation (also called mixed fermentation) of two or more different microorganisms tries to mimic the ecological situation where microorganisms always co-exist within complex microbial communities. The competition or antagonism experienced during co-cultivation is shown to lead to a significantly enhanced production of constitutively present compounds and/or to an accumulation of cryptic compounds that are not detected in axenic cultures of the producing strain. This review highlights the power of co-cultivation for increasing the chemical diversity of bacteria and fungi drawing on published studies from the marine and from the terrestrial habitat alike. PMID:24549204

  2. Relationship between microbial diversity and chemical contamination along a 50-year-old sediment core

    NASA Astrophysics Data System (ADS)

    Berthe, T.; Petit, F.; Boust, D.; Lesueur, P.; Roose-Amsaleg, C.; Cécillon, S.; Kaci-Benaicha, A.

    2013-12-01

    The purpose of this study was to evaluate the potential use of sediment microbial diversity (community structure) as an indicator of the impact of anthropogenic activities within an estuarine ecosystem. The diversity of microbial communities was investigated along a 5-m-long sediment core collected in an anthropized European estuary (Seine, France), giving an evolution of trace metal, polycyclic aromatic hydrocarbons (PAHs), and polychlorinated biphenyls (PCBs) concentrations over the last 50 years. An increase of trace metal and PCB concentrations are observed with depth, with an enrichment of these contaminants in the 1970s. The concentration profiles of light, intermediate and heavy PAHs showed distinct peaks, but the highest total PAH concentration was also detected in the sediment from the 1970s. We first investigated the bacterial community resistant to cobalt, zinc and cadmium by analyzing the diversity of the czcA gene encoding an RND efflux pump (Heavy Metal Efflux-RND) in 5-year and 33-year-old sediment samples displaying contrasted concentrations in these trace metals. The diversity of the czcA gene was reduced in the 33-year-old and more contaminated sediments suggesting a selection of resistant bacterial species. A molecular fingerprinting method (DGGE) was used to study the evolution of total microbial (Bacteria and Archaea) community structures for samples selected along the sediment core. A correlation is observed between the bacterial community structures, the sediment age, the trace metal and PAH concentrations. The metabolically active and total microbial communities were further characterized by a microarray approach (Phylochips) in sediment samples selected according to the DGGE results. Bacterial diversity was found dominated by Proteobacteria, Actinobacteria, and Firmicutes in all analyzed samples. Diversity of phylotypes corresponds to changes in PAH and trace metal concentrations in sediment, suggesting that chemical contaminants have

  3. Standardization of chemical analytical techniques for pyrolysis bio-oil: history, challenges, and current status of methods

    DOE PAGESBeta

    Ferrell, Jack R.; Olarte, Mariefel V.; Christensen, Earl D.; Padmaperuma, Asanga B.; Connatser, Raynella M.; Stankovikj, Filip; Meier, Dietrich; Paasikallio, Ville

    2016-07-05

    Here, we discuss the standardization of analytical techniques for pyrolysis bio-oils, including the current status of methods, and our opinions on future directions. First, the history of past standardization efforts is summarized, and both successful and unsuccessful validation of analytical techniques highlighted. The majority of analytical standardization studies to-date has tested only physical characterization techniques. In this paper, we present results from an international round robin on the validation of chemical characterization techniques for bio-oils. Techniques tested included acid number, carbonyl titrations using two different methods (one at room temperature and one at 80 °C), 31P NMR for determination ofmore » hydroxyl groups, and a quantitative gas chromatography–mass spectrometry (GC-MS) method. Both carbonyl titration and acid number methods have yielded acceptable inter-laboratory variabilities. 31P NMR produced acceptable results for aliphatic and phenolic hydroxyl groups, but not for carboxylic hydroxyl groups. As shown in previous round robins, GC-MS results were more variable. Reliable chemical characterization of bio-oils will enable upgrading research and allow for detailed comparisons of bio-oils produced at different facilities. Reliable analytics are also needed to enable an emerging bioenergy industry, as processing facilities often have different analytical needs and capabilities than research facilities. We feel that correlations in reliable characterizations of bio-oils will help strike a balance between research and industry, and will ultimately help to -determine metrics for bio-oil quality. Lastly, the standardization of additional analytical methods is needed, particularly for upgraded bio-oils.« less

  4. Chromatographic elution profile of an analyte involved in reversible chemical reaction of the type A + B <--> AB.

    PubMed

    Kanatyeva, A Yu

    2007-05-25

    The chromatographic peak profile of the analyte involved in a chemical reaction of the type A + B <--> AB is considered using method of the apparent adsorption isotherm. The apparent isotherms derived are nonlinear even under assumption of Henry isotherms of individual solutes. Nonlinearity of apparent adsorption isotherm results in peak distortion. The resulted chromatographic peak profile depends on several factors such as the equilibrium constant K(mob) and Henry constants of the solutes. Simulated peak profiles of solutes involved in the chemical reaction are presented as illustration of influence of various factors. PMID:16965781

  5. Effect of widespread agricultural chemical use on butterfly diversity across Turkish provinces.

    PubMed

    Pekin, Burak K

    2013-12-01

    Although agricultural intensification is thought to pose a significant threat to species, little is known about its role in driving biodiversity loss at regional scales. I assessed the effects of a major component of agricultural intensification, agricultural chemical use, and land-cover and climatic variables on butterfly diversity across 81 provinces in Turkey, where agriculture is practiced extensively but with varying degrees of intensity. I determined butterfly species presence in each province from data on known butterfly distributions and calculated agricultural chemical use as the proportion of agricultural households that use chemical fertilizers and pesticides. I used constrained correspondence analyses and regression-based multimodel inference to determine the effect of environmental variables on species composition and richness, respectively. The variation in butterfly species composition across the provinces was largely explained (78%) by the combination of agricultural chemical use, particularly pesticides, and climatic and land-cover variables. Although overall butterfly richness was primarily explained by climatic and land-cover variables, such as the area of natural vegetation cover, threatened butterfly richness and the relative number of threatened butterfly species decreased substantially as the proportion of agricultural households using pesticides increased. These findings suggest that widespread use of agricultural chemicals, or other components of agricultural intensification that may be collinear with pesticide use, pose an imminent threat to the biodiversity of Turkey. Accordingly, policies that mitigate agricultural intensification and promote low-input farming practices are crucial for protecting threatened species from extinction in rapidly industrializing nations such as Turkey. Efectos del Uso Extensivo de Agroquímicos sobre la Diversidad de Mariposas en Provincias Turcas. PMID:23869856

  6. The radial dependence of pebble accretion rates: A source of diversity in planetary systems. I. Analytical formulation

    NASA Astrophysics Data System (ADS)

    Ida, S.; Guillot, T.; Morbidelli, A.

    2016-06-01

    Context. The classical planetesimal accretion scenario for the formation of planets has recently evolved with the idea that pebbles, centimeter- to meter-sized icy grains migrating in protoplanetary disks, can control planetesimal and/or planetary growth. Aims: We investigate how pebble accretion depends on disk properties and affects the formation of planetary systems. Methods: We construct analytical models of pebble accretion onto planetary embryos that consistently account for the mass and orbital evolution of the pebble flow and reflect disk structure. Results: We derive simple formulas for pebble accretion rates in the so-called settling regime for planetary embryos that are more than 100 km in size. For relatively smaller embryos or in outer disk regions, the accretion mode is three-dimensional (3D), meaning that the thickness of the pebble flow must be taken into account, and resulting in an accretion rate that is independent of the embryo mass. For larger embryos or in inner regions, the accretion is in a two-dimensional (2D) mode, i.e., the pebble disk may be considered infinitely thin. We show that the radial dependence of the pebble accretion rate is different (even the sign of the power-law exponent changes) for different disk conditions such as the disk heating source (viscous heating or stellar irradiation), drag law (Stokes or Epstein, and weak or strong coupling), and in the 2D or 3D accretion modes. We also discuss the effect of the sublimation and destruction of icy pebbles inside the snow line. Conclusions: Pebble accretion easily produces a large diversity of planetary systems. In other words, to infer the results of planet formation through pebble accretion correctly, detailed prescriptions of disk evolution and pebble growth, sublimation, destruction and migration are required.

  7. Fluid Diversion and Sweep Improvement with Chemical Gels in Oil Recovery Processes

    SciTech Connect

    Seright, R.S.; Martin, F.D.

    1991-11-01

    This report describes progress made during the second year of the three-year project, Fluid diversion and Sweep Improvement with Chemical Gels in Oil Recovery Processes.'' The objectives of this project are to identify the mechanisms by which gel treatments divert fluids in reservoirs and to establish where and how gel treatments are best applied. Several different types of gelants are being examined. This research is directed at gel applications in water injection wells, in production wells, and in high-pressure gasfloods. The work examines how the flow properties of gels and gelling agents are influenced by permeability, lithology, and wettability. Other goals include determining the proper placement of gelants, the stability of in-place gels, and the types of gels required for the various oil recovery processes and for different scales of reservoir heterogeneity. 93 refs., 39 figs., 43 tabs.

  8. Soils of Sub-Antarctic tundras: diversity and basic chemical characteristics

    NASA Astrophysics Data System (ADS)

    Abakumov, Evgeny; Vlasov, Dmitry; Mukhametova, Nadezhda

    2014-05-01

    Antarctic peninsula is known as specific part of Antarctica, which is characterizes by humid and relatively warm climate of so-called sub Antarctic (maritime) zone. Annual precipitation and long above zero period provides the possibility of sustainable tundra's ecosystem formation. Therefore, the soil diversity of these tundra landscapes is maximal in the whole Antarctic. Moreover, the thickness of parent material debris's is also highest and achieves a 1 or 2 meters as highest. The presence of higher vascular plants Deshampsia antarctica which is considered as one of the main edificators provides the development of humus accumulation in upper solum. Penguins activity provides an intensive soil fertilization and development of plant communities with increased density. All these factors leads to formation of specific and quite diverse soil cover in sub Antarctic tundra's. These ecosystems are presented by following permafrost affected soils: Leptosols, Lithoosols, Crysols, Gleysols, Peats and Ornhitosols. Also the post Ornhitosols are widely spreaded in subantarcic ecosystems, they forms on the penguin rockeries during the plant succession development, leaching of nutrients and organic matter mineralization. "Amphibious" soils are specific for seasonal lakes, which evaporates in the end if Australian summer. These soils have specific features of bio sediments and soils as well. Soil chemical characteristic as well as organic matter features discussed in comparison with Antacrtic continental soil in presentation.

  9. Chemical Diversity and Biological Properties of Secondary Metabolites from Sea Hares of Aplysia Genus.

    PubMed

    Pereira, Renato B; Andrade, Paula B; Valentão, Patrícia

    2016-02-01

    The marine environment is an important source of structurally-diverse and biologically-active secondary metabolites. During the last two decades, thousands of compounds were discovered in marine organisms, several of them having inspired the development of new classes of therapeutic agents. Marine mollusks constitute a successful phyla in the discovery of new marine natural products (MNPs). Over a 50-year period from 1963, 116 genera of mollusks contributed innumerous compounds, Aplysia being the most studied genus by MNP chemists. This genus includes 36 valid species and should be distinguished from all mollusks as it yielded numerous new natural products. Aplysia sea hares are herbivorous mollusks, which have been proven to be a rich source of secondary metabolites, mostly of dietary origin. The majority of secondary metabolites isolated from sea hares of the genus Aplysia are halogenated terpenes; however, these animals are also a source of compounds from other chemical classes, such as macrolides, sterols and alkaloids, often exhibiting cytotoxic, antibacterial, antifungal, antiviral and/or antifeedant activities. This review focuses on the diverse structural classes of secondary metabolites found in Aplysia spp., including several compounds with pronounced biological properties. PMID:26907303

  10. Indole Alkaloids of the Stigonematales (Cyanophyta): Chemical Diversity, Biosynthesis and Biological Activity.

    PubMed

    Walton, Katherine; Berry, John P

    2016-04-01

    The cyanobacteria are well recognized as producers of a wide array of bioactive metabolites including toxins, and potential drug candidates. However, a limited number of taxa are generally considered with respect to both of these aspects. That said, the order Stigonematales, although largely overlooked in this regard, has become increasingly recognized as a source of bioactive metabolites relevant to both human and environmental health. In particular, the hapalindoles and related indole alkaloids (i.e., ambiguines, fischerindoles, welwitindolinones) from the order, represent a diverse, and phylogenetically characteristic, class of secondary metabolites with biological activity suggestive of potential as both environmental toxins, and promising drug discovery leads. The present review gives an overview of the chemical diversity of biologically active metabolites from the Stigonematales-and particularly the so-called hapalindole-type alkaloids-including their biosynthetic origins, and their pharmacologically and toxicologically relevant bioactivities. Taken together, the current evidence suggests that these alkaloids, and the associated cyanobacterial taxa from the order, warrant future consideration as both potentially harmful (i.e., "toxic") algae, and as promising leads for drug discovery. PMID:27058546

  11. Chemical Diversity and Biological Properties of Secondary Metabolites from Sea Hares of Aplysia Genus

    PubMed Central

    Pereira, Renato B.; Andrade, Paula B.; Valentão, Patrícia

    2016-01-01

    The marine environment is an important source of structurally-diverse and biologically-active secondary metabolites. During the last two decades, thousands of compounds were discovered in marine organisms, several of them having inspired the development of new classes of therapeutic agents. Marine mollusks constitute a successful phyla in the discovery of new marine natural products (MNPs). Over a 50-year period from 1963, 116 genera of mollusks contributed innumerous compounds, Aplysia being the most studied genus by MNP chemists. This genus includes 36 valid species and should be distinguished from all mollusks as it yielded numerous new natural products. Aplysia sea hares are herbivorous mollusks, which have been proven to be a rich source of secondary metabolites, mostly of dietary origin. The majority of secondary metabolites isolated from sea hares of the genus Aplysia are halogenated terpenes; however, these animals are also a source of compounds from other chemical classes, such as macrolides, sterols and alkaloids, often exhibiting cytotoxic, antibacterial, antifungal, antiviral and/or antifeedant activities. This review focuses on the diverse structural classes of secondary metabolites found in Aplysia spp., including several compounds with pronounced biological properties. PMID:26907303

  12. Indole Alkaloids of the Stigonematales (Cyanophyta): Chemical Diversity, Biosynthesis and Biological Activity

    PubMed Central

    Walton, Katherine; Berry, John P.

    2016-01-01

    The cyanobacteria are well recognized as producers of a wide array of bioactive metabolites including toxins, and potential drug candidates. However, a limited number of taxa are generally considered with respect to both of these aspects. That said, the order Stigonematales, although largely overlooked in this regard, has become increasingly recognized as a source of bioactive metabolites relevant to both human and environmental health. In particular, the hapalindoles and related indole alkaloids (i.e., ambiguines, fischerindoles, welwitindolinones) from the order, represent a diverse, and phylogenetically characteristic, class of secondary metabolites with biological activity suggestive of potential as both environmental toxins, and promising drug discovery leads. The present review gives an overview of the chemical diversity of biologically active metabolites from the Stigonematales—and particularly the so-called hapalindole-type alkaloids—including their biosynthetic origins, and their pharmacologically and toxicologically relevant bioactivities. Taken together, the current evidence suggests that these alkaloids, and the associated cyanobacterial taxa from the order, warrant future consideration as both potentially harmful (i.e., “toxic”) algae, and as promising leads for drug discovery. PMID:27058546

  13. CTEPP-OH DATA ANALYTICAL RESULTS ORGANIZED BY CHEMICAL AND MEDIA

    EPA Science Inventory

    This data set contains the field sample data by chemical and matrix for CTEPP-OH. The data is organized at the sample, chemical level.

    The Children’s Total Exposure to Persistent Pesticides and Other Persistent Pollutant (CTEPP) study was one of the largest aggregate exposure ...

  14. Combined physical and chemical nonequilibrium transport model: Analytical solution, moments, and application to colloids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The transport of solutes and colloids in porous media is influenced by a variety of physical and chemical nonequilibrium processes. A combined physical–chemical nonequilibrium (PCNE) model was therefore used to describe general mass transport. The model partitions the pore space into “mobile” and “i...

  15. Nanostructural and Chemical Characterization of Complex Oxide Catalysts by Analytical Electron Microscopy

    NASA Astrophysics Data System (ADS)

    Weng, Weihao

    Complex oxide catalysts are used as heterogeneous catalysts for producing various important organic chemicals. In this thesis, three types of complex oxide catalysts prepared using novel preparation methods have been studied. Each of them has been evaluated for its catalytic performance, namely (i) the selective oxidation of n-butane to maleic anhydride over vanadium phosphate (V-P-O) materials; (ii) the oxidative dehydrogenation (ODH) of ethane to ethylene over niobium phosphate (Nb-P-O) materials, and (iii) the oxidation of methanol to formaldehyde over iron molybdate (Fe-Mo-O) materials. Analytical electron microscopy, X-ray diffraction and other related characterization techniques have been used to provide useful information regarding the morphology, crystallography and chemical composition of these complex oxide catalysts. The underlying aim of this work is to uncover meaningful synthesis-structure-performance relationships for these three complex catalyst systems. Firstly, a standard methodology for generating V-P-O materials, i.e. the VPD route, has been revisited and modified. A variety of alkanes have been added during the alcohol reduction step of VOPO4·2H2O (dihydrate), which were found to have a remarkable influence on the morphology and structure of the V-P-O materials produced. Either VOHPO4·0.5H2O (hemihydrate) or VO(H2PO4)2 material can be produced depending on the precise alcohol:alkane volume ratio used in the reaction. In addition, the specific order in which the alkane and alcohol are added to VOPO 4·2H2O during the VPD route has a dramatic effect on the morphology of the resultant precursor. Through detailed electron microscopy studies we have been able to unveil the epitaxial relationship between the dihyrate and hemihydrate crystalline phases as being [001]dihydrate // [001]hemihydrate and [100]dihydrate // [110]hemihydrate. A two-step mechanism by which the topotactic transformation from dihydrate to hemihydrate occurs has been proposed

  16. ANALYTICAL METHODS NECESSARY TO IMPLEMENT RISK-BASED CRITERIA FOR CHEMICALS IN MUNICIPAL SLUDGE

    EPA Science Inventory

    The Ambient Water Quality Criteria that were promulgated by the U.S. Environmental Protection Agency in 1980 included water concentration levels which, for many pollutants, were so low as to be unmeasurable by standard analytical methods. Criteria for controlling toxics in munici...

  17. Chemical Diversity and Antimicrobial Activity of Salvia multicaulis Vahl Essential Oils.

    PubMed

    Fahed, Layal; Stien, Didier; Ouaini, Naïm; Eparvier, Véronique; El Beyrouthy, Marc

    2016-05-01

    The chemical compositions and antimicrobial activities of the essential oils (EOs) of aerial parts of Salvia multicaulis Vahl, collected during the same week from two different Lebanese regions, were investigated. The EOs were obtained by hydrodistillation using a Clevenger-type apparatus and characterized by GC and GC/MS analyses. The minimum inhibitory concentrations of these EOs were determined against one Gram-negative and two Gram-positive bacteria, one yeast, and five dermatophytes using the broth microdilution technique. One EO was notably active against Staphylococcus aureus, methicillin-resistant S. aureus, and all of the Trichophyton species tested. Nerolidol was found to be the major compound in the active oil; nerolidol was also absent from the inactive oil. This study demonstrated that nerolidol shows antimicrobial activity and therefore significantly contributes to the antimicrobial potential of the oil. The chemical diversity of worldwide S. multicaulis EOs was analyzed, revealing that the EOs of this study belong to two different chemotypes found in the literature. The nerolidol chemotype appears to be restricted to Lebanon, and it can be used as antimicrobial agent against external bacterial and fungal infections. PMID:27038067

  18. On the chemical diversity of the prebiotic ocean of early Earth

    NASA Astrophysics Data System (ADS)

    Canepa, Carlo

    2015-07-01

    This work investigates the consequences on the diverse number of chemical species in a pre-biotic terrestrial aqueous environment endowed with an amino acid source induced by the spontaneous build-up of catalytically active polypeptides from amino acid monomers. The assumed probability that a randomly formed polypeptide exhibits catalytic properties is dependent on constraining both the chemical identity and the position of a fraction of the amino acid residues. Within this hypothesis, and using values of the average length n of the catalytic polypeptides about one half of the present-day enzymes, the stationary-state concentration of the catalytically active polypeptides is ~10 - 30 -10 - 19 M, and the ratio of the concentration of a product of a catalytic process to the initial concentration of the corresponding substrate is predicted to be ~10 - 6-105. Matching the mean life of each catalytic polypeptide to the mean life of its substrate (λ ~ ω) is only possible by significantly raising the intensity of the source of the amino acid monomers. Under these hypothetical optimal conditions, the mean lives of the catalytic polypeptides and their substrates have values ω-1 ~ λ-1 ~10 yr and the asymptotic concentration of each product is of the same order of magnitude as the concentration of the substrate. In all cases the catalytic efficiency necessary to form the active peptides takes the typical values of present-day enzymes.

  19. Successful herbivore attack due to metabolic diversion of a plant chemical defense.

    PubMed

    Wittstock, Ute; Agerbirk, Niels; Stauber, Einar J; Olsen, Carl Erik; Hippler, Michael; Mitchell-Olds, Thomas; Gershenzon, Jonathan; Vogel, Heiko

    2004-04-01

    Plants protect themselves against herbivory with a diverse array of repellent or toxic secondary metabolites. However, many herbivorous insects have developed counteradaptations that enable them to feed on chemically defended plants without apparent negative effects. Here, we present evidence that larvae of the specialist insect, Pieris rapae (cabbage white butterfly, Lepidoptera: Pieridae), are biochemically adapted to the glucosinolate-myrosinase system, the major chemical defense of their host plants. The defensive function of the glucosinolate-myrosinase system results from the toxic isothiocyanates that are released when glucosinolates are hydrolyzed by myrosinases on tissue disruption. We show that the hydrolysis reaction is redirected toward the formation of nitriles instead of isothiocyanates if plant material is ingested by P. rapae larvae, and that the nitriles are excreted with the feces. The ability to form nitriles is due to a larval gut protein, designated nitrile-specifier protein, that by itself has no hydrolytic activity on glucosinolates and that is unrelated to any functionally characterized protein. Nitrile-specifier protein appears to be the key biochemical counteradaptation that allows P. rapae to feed with impunity on plants containing glucosinolates and myrosinases. This finding sheds light on the ecology and evolution of plant-insect interactions and suggests novel highly selective pest management strategies. PMID:15051878

  20. Evolution of chemical diversity by coordinated gene swaps in type II polyketide gene clusters

    PubMed Central

    Hillenmeyer, Maureen E.; Vandova, Gergana A.; Berlew, Erin E.; Charkoudian, Louise K.

    2015-01-01

    Natural product biosynthetic pathways generate molecules of enormous structural complexity and exquisitely tuned biological activities. Studies of natural products have led to the discovery of many pharmaceutical agents, particularly antibiotics. Attempts to harness the catalytic prowess of biosynthetic enzyme systems, for both compound discovery and engineering, have been limited by a poor understanding of the evolution of the underlying gene clusters. We developed an approach to study the evolution of biosynthetic genes on a cluster-wide scale, integrating pairwise gene coevolution information with large-scale phylogenetic analysis. We used this method to infer the evolution of type II polyketide gene clusters, tracing the path of evolution from the single ancestor to those gene clusters surviving today. We identified 10 key gene types in these clusters, most of which were swapped in from existing cellular processes and subsequently specialized. The ancestral type II polyketide gene cluster likely comprised a core set of five genes, a roster that expanded and contracted throughout evolution. A key C24 ancestor diversified into major classes of longer and shorter chain length systems, from which a C20 ancestor gave rise to the majority of characterized type II polyketide antibiotics. Our findings reveal that (i) type II polyketide structure is predictable from its gene roster, (ii) only certain gene combinations are compatible, and (iii) gene swaps were likely a key to evolution of chemical diversity. The lessons learned about how natural selection drives polyketide chemical innovation can be applied to the rational design and guided discovery of chemicals with desired structures and properties. PMID:26499248

  1. Chemical Diversity Along the Traverse of the Mer Rover Opportunity at Meridiani Planum, Mars

    NASA Astrophysics Data System (ADS)

    Gellert, R.; Arvidson, R. E.; Clark, B. C.; Squyres, S.; Yen, A. S.

    2012-12-01

    The APXS on board the MER rover Opportunity measured the chemical composition of some 200 samples over the 8 year mission and 34.6 km from Eagle Crater to the Rim of Endeavour Crater. Till reaching the rim of Endeavour the bedrock was found to be sulphate rich, very homogeneous with up to ~ 40 % sulphates by weight. Decreasing Mg-S trends were found downhill within all craters accompanied by up to 3 fold enrichment in Cl. At Cape York, a rim segment of the Noachian Crater, Endeavour, significant lower sulphate levels were found so far in the bedrock. Ejecta from secondary craters show significant signs of possible hydrothermal activity with drastically enriched Zn and Ni levels, accompanied by elevated P and Br values and changes in major chemistry. Many one inch wide bright veins with elevated Ca and S levels in good molar match for Calcium-sulphate were found and interpreted as Gypsum based on multi-spectral analysis of Pancam data. The soils consist of at least two end members, basaltic soil similar to the previous landing sites investigated with APXS or XRF and a Fe and Ni rich population of spherules and angular fragments, known to be rich in hematite from Moessbauer measurements. Comparisons with the first soil measurements in Gale Crater with the MSL APXS will be presented. Many erratics, Fe-Ni meteorites with chemical signs of surface alteration, basaltic ejecta, some identified stemming from Mars were measured by Opportunity, in addition to rocks identified as stony meteorites.. The diversity of the chemical composition is discussed under the aspect of changes in the alteration history and the environmental conditions of their formation. The comparison with mineralogical findings from orbital instruments will be discussed.

  2. ANALYTICAL STRATEGIES FOR ASSESSING CUMULATIVE EFFECTS OF CHEMICAL AND NONCHEMICAL STRESSORS

    EPA Science Inventory

    The project will assess the relative impact of community-level and individual-level stressors – including multiple chemical, social and psychosocial stressors -- on biologic markers of health effects across neighborhoods and vulnerable populations in Texas City, Texas...

  3. Analytical Methods for Chemical and Sensory Characterization of Scent-Markings in Large Wild Mammals: A Review

    PubMed Central

    Soso, Simone B.; Koziel, Jacek A.; Johnson, Anna; Lee, Young Jin; Fairbanks, W. Sue

    2014-01-01

    In conjoining the disciplines of “ethology” and “chemistry” the field of “Ethochemistry” has been instituted. Ethochemistry is an effective tool in conservation efforts of endangered species and the understanding of behavioral patterns across all species. Chemical constituents of scent-markings have an important, yet poorly understood function in territoriality, reproduction, dominance, and impact on evolutionary biology, especially in large mammals. Particular attention has recently been focused on scent-marking analysis of great cats (Kalahari leopards (Panthera pardus), puma (Puma concolor) snow leopard (Panthera uncia), African lions (Panthera leo), cheetahs (Acinonyx jubatus), and tigers (Panthera tigris)) for the purpose of conservation. Sensory analyses of scent-markings could address knowledge gaps in ethochemistry. The objective of this review is to summarize the current state-of-the art of both the chemical and sensory analyses of scent-markings in wild mammals. Specific focus is placed on sampling and sample preparation, chemical analysis, sensory analysis, and simultaneous chemical and sensory analyses. Constituents of exocrine and endocrine secretions have been most commonly studied with chromatography-based analytical separations. Odor analysis of scent-markings provides an insight into the animal's sensory perception. A limited number of articles have been published in the area of sensory characterization of scent marks. Simultaneous chemical and sensory analyses with chromatography-olfactometry hyphenation could potentially aid conservation efforts by linking perceived odor, compounds responsible for odor, and resulting behavior. PMID:24603639

  4. Analytical methods for chemical and sensory characterization of scent-markings in large wild mammals: a review.

    PubMed

    Soso, Simone B; Koziel, Jacek A; Johnson, Anna; Lee, Young Jin; Fairbanks, W Sue

    2014-01-01

    In conjoining the disciplines of "ethology" and "chemistry" the field of "Ethochemistry" has been instituted. Ethochemistry is an effective tool in conservation efforts of endangered species and the understanding of behavioral patterns across all species. Chemical constituents of scent-markings have an important, yet poorly understood function in territoriality, reproduction, dominance, and impact on evolutionary biology, especially in large mammals. Particular attention has recently been focused on scent-marking analysis of great cats (Kalahari leopards (Panthera pardus), puma (Puma concolor) snow leopard (Panthera uncia), African lions (Panthera leo), cheetahs (Acinonyx jubatus), and tigers (Panthera tigris)) for the purpose of conservation. Sensory analyses of scent-markings could address knowledge gaps in ethochemistry. The objective of this review is to summarize the current state-of-the art of both the chemical and sensory analyses of scent-markings in wild mammals. Specific focus is placed on sampling and sample preparation, chemical analysis, sensory analysis, and simultaneous chemical and sensory analyses. Constituents of exocrine and endocrine secretions have been most commonly studied with chromatography-based analytical separations. Odor analysis of scent-markings provides an insight into the animal's sensory perception. A limited number of articles have been published in the area of sensory characterization of scent marks. Simultaneous chemical and sensory analyses with chromatography-olfactometry hyphenation could potentially aid conservation efforts by linking perceived odor, compounds responsible for odor, and resulting behavior. PMID:24603639

  5. Transcriptional Regulation of Chemical Diversity in Aspergillus fumigatus by LaeA

    PubMed Central

    Perrin, Robyn M; Fedorova, Natalie D; Bok, Jin Woo; Cramer, Robert A; Wortman, Jennifer R; Kim, H. Stanley; Nierman, William C; Keller, Nancy P

    2007-01-01

    Secondary metabolites, including toxins and melanins, have been implicated as virulence attributes in invasive aspergillosis. Although not definitively proved, this supposition is supported by the decreased virulence of an Aspergillus fumigatus strain, ΔlaeA, that is crippled in the production of numerous secondary metabolites. However, loss of a single LaeA-regulated toxin, gliotoxin, did not recapitulate the hypovirulent ΔlaeA pathotype, thus implicating other toxins whose production is governed by LaeA. Toward this end, a whole-genome comparison of the transcriptional profile of wild-type, ΔlaeA, and complemented control strains showed that genes in 13 of 22 secondary metabolite gene clusters, including several A. fumigatus–specific mycotoxin clusters, were expressed at significantly lower levels in the ΔlaeA mutant. LaeA influences the expression of at least 9.5% of the genome (943 of 9,626 genes in A. fumigatus) but positively controls expression of 20% to 40% of major classes of secondary metabolite biosynthesis genes such as nonribosomal peptide synthetases (NRPSs), polyketide synthases, and P450 monooxygenases. Tight regulation of NRPS-encoding genes was highlighted by quantitative real-time reverse-transcription PCR analysis. In addition, expression of a putative siderophore biosynthesis NRPS (NRPS2/sidE) was greatly reduced in the ΔlaeA mutant in comparison to controls under inducing iron-deficient conditions. Comparative genomic analysis showed that A. fumigatus secondary metabolite gene clusters constitute evolutionarily diverse regions that may be important for niche adaptation and virulence attributes. Our findings suggest that LaeA is a novel target for comprehensive modification of chemical diversity and pathogenicity. PMID:17432932

  6. Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity.

    PubMed

    Wang, Liming; Zhang, Tianlu; Li, Panyun; Huang, Wanxia; Tang, Jinglong; Wang, Pengyang; Liu, Jing; Yuan, Qingxi; Bai, Ru; Li, Bai; Zhang, Kai; Zhao, Yuliang; Chen, Chunying

    2015-06-23

    To predict potential medical value or toxicity of nanoparticles (NPs), it is necessary to understand the chemical transformation during intracellular processes of NPs. However, it is a grand challenge to capture a high-resolution image of metallic NPs in a single cell and the chemical information on intracellular NPs. Here, by integrating synchrotron radiation-beam transmission X-ray microscopy (SR-TXM) and SR-X-ray absorption near edge structure (SR-XANES) spectroscopy, we successfully capture the 3D distribution of silver NPs (AgNPs) inside a single human monocyte (THP-1), associated with the chemical transformation of silver. The results reveal that the cytotoxicity of AgNPs is largely due to the chemical transformation of particulate silver from elemental silver (Ag(0))n, to Ag(+) ions and Ag-O-, then Ag-S- species. These results provide direct evidence in the long-lasting debate on whether the nanoscale or the ionic form dominates the cytotoxicity of silver nanoparticles. Further, the present approach provides an integrated strategy capable of exploring the chemical origins of cytotoxicity in metallic nanoparticles. PMID:25994391

  7. Analytic projection from plane-wave and PAW wavefunctions and application to chemical-bonding analysis in solids.

    PubMed

    Maintz, Stefan; Deringer, Volker L; Tchougréeff, Andrei L; Dronskowski, Richard

    2013-11-01

    Quantum-chemical computations of solids benefit enormously from numerically efficient plane-wave (PW) basis sets, and together with the projector augmented-wave (PAW) method, the latter have risen to one of the predominant standards in computational solid-state sciences. Despite their advantages, plane waves lack local information, which makes the interpretation of local densities-of-states (DOS) difficult and precludes the direct use of atom-resolved chemical bonding indicators such as the crystal orbital overlap population (COOP) and the crystal orbital Hamilton population (COHP) techniques. Recently, a number of methods have been proposed to overcome this fundamental issue, built around the concept of basis-set projection onto a local auxiliary basis. In this work, we propose a novel computational technique toward this goal by transferring the PW/PAW wavefunctions to a properly chosen local basis using analytically derived expressions. In particular, we describe a general approach to project both PW and PAW eigenstates onto given custom orbitals, which we then exemplify at the hand of contracted multiple-ζ Slater-type orbitals. The validity of the method presented here is illustrated by applications to chemical textbook examples-diamond, gallium arsenide, the transition-metal titanium-as well as nanoscale allotropes of carbon: a nanotube and the C60 fullerene. Remarkably, the analytical approach not only recovers the total and projected electronic DOS with a high degree of confidence, but it also yields a realistic chemical-bonding picture in the framework of the projected COHP method. PMID:24022911

  8. Modelling a flows in supply chain with analytical models: Case of a chemical industry

    NASA Astrophysics Data System (ADS)

    Benhida, Khalid; Azougagh, Yassine; Elfezazi, Said

    2016-02-01

    This study is interested on the modelling of the logistics flows in a supply chain composed on a production sites and a logistics platform. The contribution of this research is to develop an analytical model (integrated linear programming model), based on a case study of a real company operating in the phosphate field, considering a various constraints in this supply chain to resolve the planning problems for a better decision-making. The objectives of this model is to determine and define the optimal quantities of different products to route, to and from the various entities in the supply chain studied.

  9. Acidification in the Adirondacks: Defining the Biota in trophic Levels of 30 Chemically Diverse Acid-Impacted Lakes

    EPA Science Inventory

    The Adirondack Mountains in New York State have a varied surficial geology and chemically diverse surface waters that are among the most impacted by acid deposition in the U.S. No single Adirondack investigation has been comprehensive in defining the effects of acidification on ...

  10. Canopy spectral and chemical diversity from lowland to tree line in the Western Amazon using CAO-VSWIR

    NASA Astrophysics Data System (ADS)

    Martin, R. E.; Asner, G. P.

    2012-12-01

    Canopy chemistry and spectroscopy offer insight into community assembly and ecosystem processes in high-diversity tropical forests. Results from one lowland site in the Peruvian Amazon suggests both an environmental and an evolutionary component of canopy trait development however, the degree to which larger environmental differences influence diversity in canopy traits and their respective spectroscopic signatures across remains poorly understood. The spectranomics approach explicitly connects phylogenetic, chemical and spectral patterns in tropical canopies providing the basis for analysis, while high-fidelity, airborne remote sensing measurements extend plot-level data to landscape-scale, achieving a comprehensive view of the region. In 2011, the Carnegie Airborne Observatory (CAO) was used to sample a large region of the Western Amazon Basin in southeastern Peru, extending from lowlands to tree line in the Andean mountains. The CAO Visible-Shortwave Imaging Spectrometer (VSWIR) collected 480-band high-fidelity imaging spectroscopy data of the forest canopy, while its high-resolution LiDAR captured information on canopy structure and the underlying terrain. The data were used to quantify relationships between environmental gradients and canopy chemical and spectral diversity. Results suggest strong environmental control with additional phylogenetic influence over canopy spectral and chemical properties, particularly those related to structure, defense and metabolic function. Data from CAO-VSWIR extends the large range in canopy chemical and spectral diversity related to environmental factors across the Western Amazon Basin.

  11. Genetic Diversity and Structure of Populations of Annona crassiflora Mart. of Brazilian Savanna and Its Association with Chemical Variability.

    PubMed

    Egydio-Brandão, Anary Priscila Monteiro; Furlan, Claudia Maria; Dos Santos, Déborah Yara Alves Cursino

    2016-08-01

    Annona crassiflora Mart. is a native tree from Brazilian savanna. Isoquinoline alkaloids are characteristic of species of Annonaceae. This work aimed to assess the magnitude of genetic diversity among different populations of A. crassiflora using AFLP markers, and verify the existence of any correlation between the AFLP data and previous reported alkaloid composition. A. crassiflora from eight populations in the states of São Paulo, Goiás, Minas Gerais, and Distrito Federal were analyzed. The data suggest a low, moderate, and high level of genetic diversity from different populations of A. crassiflora. Concentration of alkaloids was significantly correlated with AFLP data, suggesting interaction between chemical and molecular markers in A. crassiflora. The data of association between the chemical and genetic differentiation of A. crassiflora may be useful to establish cultivation areas allowing the definition of strategies to preserve their genetic diversity with an interest in specific chemotypes for genetic improvement programs focused on sustainable utilization of this specie. PMID:27286480

  12. A Cluster Analytic Study of Clinical Orientations among Chemical Dependency Counselors.

    ERIC Educational Resources Information Center

    Thombs, Dennis L.; Osborn, Cynthia J.

    2001-01-01

    Three distinct clinical orientations were identified in a sample of chemical dependency counselors (N=406). Based on cluster analysis, the largest group, identified and labeled as "uniform counselors," endorsed a simple, moral-disease model with little interest in psychosocial interventions. (Contains 50 references and 4 tables.) (GCP)

  13. Model Analytical Development for Physical, Chemical, and Biological Characterization of Momordica charantia Vegetable Drug

    PubMed Central

    Guimarães, Geovani Pereira; Santos, Ravely Lucena; Júnior, Fernando José de Lima Ramos; da Silva, Karla Monik Alves; de Souza, Fabio Santos

    2016-01-01

    Momordica charantia is a species cultivated throughout the world and widely used in folk medicine, and its medicinal benefits are well documented, especially its pharmacological properties, including antimicrobial activities. Analytical methods have been used to aid in the characterization of compounds derived from plant drug extracts and their products. This paper developed a methodological model to evaluate the integrity of the vegetable drug M. charantia in different particle sizes, using different analytical methods. M. charantia was collected in the semiarid region of Paraíba, Brazil. The herbal medicine raw material derived from the leaves and fruits in different particle sizes was analyzed using thermoanalytical techniques as thermogravimetry (TG) and differential thermal analysis (DTA), pyrolysis coupled to gas chromatography/mass spectrometry (PYR-GC/MS), and nuclear magnetic resonance (1H NMR), in addition to the determination of antimicrobial activity. The different particle surface area among the samples was differentiated by the techniques. DTA and TG were used for assessing thermal and kinetic parameters and PYR-GC/MS was used for degradation products chromatographic identification through the pyrograms. The infusions obtained from the fruit and leaves of Momordica charantia presented antimicrobial activity. PMID:27579215

  14. Model Analytical Development for Physical, Chemical, and Biological Characterization of Momordica charantia Vegetable Drug.

    PubMed

    Brandão, Deysiane Oliveira; Guimarães, Geovani Pereira; Santos, Ravely Lucena; Júnior, Fernando José de Lima Ramos; da Silva, Karla Monik Alves; de Souza, Fabio Santos; Macêdo, Rui Oliveira

    2016-01-01

    Momordica charantia is a species cultivated throughout the world and widely used in folk medicine, and its medicinal benefits are well documented, especially its pharmacological properties, including antimicrobial activities. Analytical methods have been used to aid in the characterization of compounds derived from plant drug extracts and their products. This paper developed a methodological model to evaluate the integrity of the vegetable drug M. charantia in different particle sizes, using different analytical methods. M. charantia was collected in the semiarid region of Paraíba, Brazil. The herbal medicine raw material derived from the leaves and fruits in different particle sizes was analyzed using thermoanalytical techniques as thermogravimetry (TG) and differential thermal analysis (DTA), pyrolysis coupled to gas chromatography/mass spectrometry (PYR-GC/MS), and nuclear magnetic resonance ((1)H NMR), in addition to the determination of antimicrobial activity. The different particle surface area among the samples was differentiated by the techniques. DTA and TG were used for assessing thermal and kinetic parameters and PYR-GC/MS was used for degradation products chromatographic identification through the pyrograms. The infusions obtained from the fruit and leaves of Momordica charantia presented antimicrobial activity. PMID:27579215

  15. Self-Aspirated Atmospheric Pressure Chemical Ionization Source for Direct Sampling of Analytes on Surfaces and in Liquid Solutions

    SciTech Connect

    Asano, Keiji G; Ford, Michael J; Tomkins, Bruce A; Van Berkel, Gary J

    2005-01-01

    A self-aspirating heated nebulizer probe is described and demonstrated for use in the direct analysis of analytes on surfaces and in liquid samples by atmospheric pressure chemical ionization (APCI) mass spectrometry. Functionality and performance of the probe as a self-aspirating APCI source is demonstrated using reserpine and progesterone as test compounds. The utility of the probe to sample analytes directly from surfaces was demonstrated first by scanning development lanes of a reversed-phase thin-layer chromatography plate in which a three-component dye mixture, viz., Fat Red 7B, Solvent Green 3, and Solvent Blue 35, was spotted and the components were separated. Development lanes were scanned by the sampling probe operated under computer control (x, y plane) while full-scan mass spectra were recorded using a quadrupole ion trap mass spectrometer. In addition, the ability to sample the surface of pharmaceutical tablets (viz., Extra Strength Tylenol(reg. sign) and Evista(reg. sign) tablets) and to detect the active ingredients (acetaminophen and raloxifene, respectively) selectively was demonstrated using tandem mass spectrometry (MS/MS). Finally, the capability to sample analyte solutions from the wells of a 384-well microtiter plate and to perform quantitative analyses using MS/MS detection was illustrated with cotinine standards spiked with cotinine-d{sub 3} as an internal standard.

  16. Analytical methods for the assessment of endocrine disrupting chemical exposure during human fetal and lactation stages: a review.

    PubMed

    Jiménez-Díaz, I; Vela-Soria, F; Rodríguez-Gómez, R; Zafra-Gómez, A; Ballesteros, O; Navalón, A

    2015-09-10

    In the present work, a review of the analytical methods developed in the last 15 years for the determination of endocrine disrupting chemicals (EDCs) in human samples related with children, including placenta, cord blood, amniotic fluid, maternal blood, maternal urine and breast milk, is proposed. Children are highly vulnerable to toxic chemicals in the environment. Among these environmental contaminants to which children are at risk of exposure are EDCs -substances able to alter the normal hormone function of wildlife and humans-. The work focuses mainly on sample preparation and instrumental techniques used for the detection and quantification of the analytes. The sample preparation techniques include, not only liquid-liquid extraction (LLE) and solid-phase extraction (SPE), but also modern microextraction techniques such as extraction with molecular imprinted polymers (MIPs), stir-bar sorptive extraction (SBSE), hollow-fiber liquid-phase microextraction (HF-LPME), dispersive liquid-liquid microextraction (DLLME), matrix solid phase dispersion (MSPD) or ultrasound-assisted extraction (UAE), which are becoming alternatives in the analysis of human samples. Most studies focus on minimizing the number of steps and using the lowest solvent amounts in the sample treatment. The usual instrumental techniques employed include liquid chromatography (LC), gas chromatography (GC) mainly coupled to tandem mass spectrometry. Multiresidue methods are being developed for the determination of several families of EDCs with one extraction step and limited sample preparation. PMID:26388473

  17. Different patterns of developmental toxicity in the rat following prenatal administration of structurally diverse chemicals

    SciTech Connect

    Simmons, D.L.; Valentine, D.M.; Bradshaw, W.S.

    1984-01-01

    Differences in the profiles of developmental toxicity for four structurally diverse chemical compounds have been defined following prenatal exposure in the rat. Diethylstilbestrol (DES), 3,4,3',4'-tetrachlorobiphenyl (4CB), zeranol, and cadmium were administered by gavage to Sprague-Dawley rats daily from d 6 through d 18 of gestation. Dams were sacrificed at four prenatal endpoints and the numbers of live and dead fetuses and resorbed embryos were counted. Additional dams were allowed to bring their litters to term, and their offspring were monitored until they reached adulthood. DES induced prenatal death primarily in early embryonic life, and also during parturition. 4CB increased mortality from late in gestation up to 24 h after birth, and altered the sex ratio of survivors by selectively acting against males in utero. Exposure to zeranol resulted in embryolethality only. Cadmium was not lethal to the conceptus at any dose below the dose that caused maternal mortality. Only 4CB had an obvious teratogenic effect, causing intestinal hemorrhage. All compounds produced transient perinatal decreases in the weight of the offspring. 30 references, 6 tables.

  18. An Exploration of the Physico-chemical Diversity of a Suite of Biochars

    NASA Astrophysics Data System (ADS)

    Amonette, J. E.; Dai, S. S.; Shaff, Z.; Russell, C. K.; Burton, S.; Arey, B.

    2008-12-01

    The production of biochar from biomass and its subsequent storage in soils offers a potential way of sequestering C and enhancing soil fertility while generating carbon-negative energy. Biochars, however, are highly diverse in their properties, and not all biochar is necessarily suitable for incorporation into soils. To help understand the factors that control the physico-chemical properties of biochars, a suite of biochars produced by a variety of processes including fast, slow, and flash pyrolysis, as well as hydrothermal carbonization were characterized. Properties measured include pH, specific surface by N2 adsorption, moisture sorption capacity, surface functional groups by Boehm titration, structural functional groups by 13C- NMR, crystallinity by X-ray diffraction, and micro-structure and composition by focused-ion-beam SEM. The results of these analyses demonstrate the heterogeneity of biochars in general, but also show that the process by which they are formed is more important than the feedstock in determining the majority of their properties.

  19. Fungal Diversity Is Not Determined by Mineral and Chemical Differences in Serpentine Substrates

    PubMed Central

    Daghino, Stefania; Murat, Claude; Sizzano, Elisa; Girlanda, Mariangela; Perotto, Silvia

    2012-01-01

    The physico-chemical properties of serpentine soils lead to strong selection of plant species. Whereas many studies have described the serpentine flora, little information is available on the fungal communities dwelling in these sites. Asbestos minerals, often associated with serpentine rocks, can be weathered by serpentine-isolated fungi, suggesting an adaptation to this substrate. In this study, we have investigated whether serpentine substrates characterized by the presence of rocks with distinct mineral composition could select for different fungal communities. Both fungal isolation and 454 pyrosequencing of amplicons obtained from serpentine samples following direct DNA extraction revealed some fungal taxa shared by the four ophiolitic substrates, but also highlighted several substrate-specific taxa. Bootstrap analysis of 454 OTU abundances indicated weak clustering of fungal assemblages from the different substrates, which did not match substrate classification based on exchangeable macronutrients and metals. Intra-substrate variability, as assessed by DGGE profiles, was similar across the four serpentine substrates, and comparable to inter-substrate variability. These findings indicate the absence of a correlation between the substrate (mineral composition and available cations) and the diversity of the fungal community. Comparison of culture-based and culture-independent methods supports the higher taxonomic precision of the former, as complementation of the better performance of the latter. PMID:23028507

  20. Sample handling in surface sensitive chemical and biological sensing: a practical review of basic fluidics and analyte transport.

    PubMed

    Orgovan, Norbert; Patko, Daniel; Hos, Csaba; Kurunczi, Sándor; Szabó, Bálint; Ramsden, Jeremy J; Horvath, Robert

    2014-09-01

    This paper gives an overview of the advantages and associated caveats of the most common sample handling methods in surface-sensitive chemical and biological sensing. We summarize the basic theoretical and practical considerations one faces when designing and assembling the fluidic part of the sensor devices. The influence of analyte size, the use of closed and flow-through cuvettes, the importance of flow rate, tubing length and diameter, bubble traps, pressure-driven pumping, cuvette dead volumes, and sample injection systems are all discussed. Typical application areas of particular arrangements are also highlighted, such as the monitoring of cellular adhesion, biomolecule adsorption-desorption and ligand-receptor affinity binding. Our work is a practical review in the sense that for every sample handling arrangement considered we present our own experimental data and critically review our experience with the given arrangement. In the experimental part we focus on sample handling in optical waveguide lightmode spectroscopy (OWLS) measurements, but the present study is equally applicable for other biosensing technologies in which an analyte in solution is captured at a surface and its presence is monitored. Explicit attention is given to features that are expected to play an increasingly decisive role in determining the reliability of (bio)chemical sensing measurements, such as analyte transport to the sensor surface; the distorting influence of dead volumes in the fluidic system; and the appropriate sample handling of cell suspensions (e.g. their quasi-simultaneous deposition). At the appropriate places, biological aspects closely related to fluidics (e.g. cellular mechanotransduction, competitive adsorption, blood flow in veins) are also discussed, particularly with regard to their models used in biosensing. PMID:24846752

  1. A novel analytical approach for visualizing and tracking organic chemicals in plants.

    PubMed

    Wild, Edward; Dent, John; Barber, Jonathan L; Thomas, Gareth O; Jones, Kevin C

    2004-08-01

    Vegetation plays a key role in the environmental fate of many organic chemicals, from pesticides applied to plants, to the air-vegetation exchange and global cycling of atmospheric organic contaminants. Our ability to locate such compounds in plants has traditionally relied on inferences being made from destructive chemical extraction techniques or methods with potential artifacts. Here, for the first time, two-photon excitation microscopy (TPEM) is coupled with plant autofluorescence to visualize and track trace levels of an organic contaminant in living plant tissue, without any form of sample modification or manipulation. Anthracene-a polynuclear aromatic hydrocarbon (PAH)-was selected for study in living maize (Zea mays) leaves. Anthracene was tracked over 96 h, where amounts as low as approximately 0.1-10 pg were visible, as it moved through the epicuticular wax and plant cuticle, and was observed reaching the cytoplasm of the epidermal cells. By this stage, anthracene was identifiable in five separate locations within the leaf: (1) as a thin (approximately 5 microm) diffuse layer, in the upper surface of the epicuticular wax; (2) as thick (approximately 28 microm) diffuse bands extending from the epicuticular wax through the cuticle, to the cell walls of the epidermal cells; (3) on the external surface of epidermal cell walls; (4) on the internal surface of epidermal cell walls; and (5) within the cytoplasm of the epidermal cells. This technique provides a powerful nonintrusive tool for visualizing and tracking the movement, storage locations, and degradation of organic chemicals within vegetation using only plant and compound autofluorescence. Many other applications are envisaged for TPEM, in visualizing organic chemicals within different matrixes. PMID:15352460

  2. [Analytical and on-site detection methods for chemical warfare agents].

    PubMed

    Seto, Yasuo

    2006-12-01

    Chemical warfare agents (CWAs) are fast acting and sometimes lethal, even at low levels, and can be classified into nerve gases, blister agents, choking agents, blood agents, vomit agents, tear gases, and incapacitating agents. As countermeasures against CWA terrorism, detection and identification are important. In crisis management, monitoring of CWAs in public places and security checks at territorial borders, big event venues, and executive facilities are performed for protection against terrorism. In consequence management, on-site detection by first responders and laboratory analysis after on-site sampling and transfer are performed for minimization of terrorism damage, leading to personal protection, initial investigation, and emergency lifesaving. In incident management, laboratory analysis is performed to provide evidence at court trials for the prevention of future crimes. Laboratory analysis consists of pretreatment of on-site and casualty samples and instrumental analysis using GC-MS. However, CWAs are easily degraded, and thus are difficult to detect. Instead, it is useful to detect their metabolites and degradation products using tert-butyldimethylsilyl derivatization GC-MS or direct LC-MS. Commercially available chemical detection equipment such as gas detection tubes and ion mobility spectrometers are used for on-site detection. We have evaluated the detection performance of such equipment and found that no equipment fulfills the required perfect performance of CWA detection sensitivity, accuracy, response time, return time, and operation. To overcome the drawbacks, we have adopted the monitoring tape method and counterflow introduction atmospheric pressure chemical ionization mass spectrometry and recommend the combination of commercial detection equipment and these new technologies for simultaneous, rapid detection of all CWAs. PMID:17139154

  3. Improving analytical methods for protein-protein interaction through implementation of chemically inducible dimerization

    PubMed Central

    Andersen, Tonni Grube; Nintemann, Sebastian J.; Marek, Magdalena; Halkier, Barbara A.; Schulz, Alexander; Burow, Meike

    2016-01-01

    When investigating interactions between two proteins with complementary reporter tags in yeast two-hybrid or split GFP assays, it remains troublesome to discriminate true- from false-negative results and challenging to compare the level of interaction across experiments. This leads to decreased sensitivity and renders analysis of weak or transient interactions difficult to perform. In this work, we describe the development of reporters that can be chemically induced to dimerize independently of the investigated interactions and thus alleviate these issues. We incorporated our reporters into the widely used split ubiquitin-, bimolecular fluorescence complementation (BiFC)- and Förster resonance energy transfer (FRET)- based methods and investigated different protein-protein interactions in yeast and plants. We demonstrate the functionality of this concept by the analysis of weakly interacting proteins from specialized metabolism in the model plant Arabidopsis thaliana. Our results illustrate that chemically induced dimerization can function as a built-in control for split-based systems that is easily implemented and allows for direct evaluation of functionality. PMID:27282591

  4. Improving analytical methods for protein-protein interaction through implementation of chemically inducible dimerization.

    PubMed

    Andersen, Tonni Grube; Nintemann, Sebastian J; Marek, Magdalena; Halkier, Barbara A; Schulz, Alexander; Burow, Meike

    2016-01-01

    When investigating interactions between two proteins with complementary reporter tags in yeast two-hybrid or split GFP assays, it remains troublesome to discriminate true- from false-negative results and challenging to compare the level of interaction across experiments. This leads to decreased sensitivity and renders analysis of weak or transient interactions difficult to perform. In this work, we describe the development of reporters that can be chemically induced to dimerize independently of the investigated interactions and thus alleviate these issues. We incorporated our reporters into the widely used split ubiquitin-, bimolecular fluorescence complementation (BiFC)- and Förster resonance energy transfer (FRET)- based methods and investigated different protein-protein interactions in yeast and plants. We demonstrate the functionality of this concept by the analysis of weakly interacting proteins from specialized metabolism in the model plant Arabidopsis thaliana. Our results illustrate that chemically induced dimerization can function as a built-in control for split-based systems that is easily implemented and allows for direct evaluation of functionality. PMID:27282591

  5. In situ analytical assessment and chemical imaging of historical buildings using a man-portable laser system.

    PubMed

    Fortes, F J; Cuñat, J; Cabalín, L M; Laserna, J J

    2007-05-01

    In this work, the capability of laser-induced breakdown spectrometry for the in situ analytical assessment and chemical mapping of the façade of the cathedral of Malaga (Spain) has been demonstrated. The task required the use of a portable laser analyzer that allowed real-time spectral acquisitions in the field. A man-portable laser, based on a Q-switched Nd:YAG laser operating at its fundamental wavelength, has been utilized to generate a LIBS plasma of the sample surface. A chemical characterization of the different materials employed in the construction of this building has been performed. The purpose of this study was to use LIBS spectrochemical analysis to qualitatively discriminate between sandstone, limestone, marble, and cement mortar, which are the main components used in this class of historical monument. The field analysis was performed in two zones: the northern façade and the "girola"; the total areas of analysis of the two regions were 250 m(2) and 650 m(2), respectively. Chemical images of Si/Ca and Ca/Mg ratios from both parts of the building were generated. During the measurement campaign, a protocol of analysis was chosen so as to achieve an accurate description of the building materials with respectable spatial resolutions. PMID:17555626

  6. One year of chemical diversity seen by ChemCam at Gale crater, Mars

    NASA Astrophysics Data System (ADS)

    Gasnault, Olivier; Wiens, Roger; Maurice, Sylvestre; Meslin, Pierre-Yves; Forni, Olivier; Leveillé, Richard; Bridges, Nathan; Lasue, Jérémie; Le Mouélic, Stéphane; Mangold, Nicolas; Sautter, Violaine

    2014-05-01

    ChemCam, the chemistry remote camera, has observed more than 300 different targets (rocks and soils) over the course of the first 360 Sols on Mars. This presentation gives an overview of the chemical variations revealed by ChemCam onboard the rover Curiosity. At the submillimeter scale, ChemCam identified two principal soil types: A fine-grained mafic type and a type made of coarse grains of diverse compositions [1]. The mafic soil component is similar to soils found at other landing sites, and may constitute a planet-wide reservoir. It possesses a ubiquitous hydration [2] in its amorphous phase, which may account for a significant fraction of the global hydration. The second soil component is made of pebbles, sometimes buried in the soil, and partly matches the diversity of chemical compositions found in the surrounding float rocks at the landing site [3]. The felsic end member appears to be specific to Gale crater, compared to other landing sites so far, and may be derived from coarse-grained intrusive rocks representing the ancient crust and transported from the crater rim [4]. Curiosity also came across many sedimentary rocks [5,6,7]. The 5 km deposits at the Yellowknife Bay formation testify prolonged aqueous activities relatively late in the history of early Mars, possibly in series of episodes: transport and sedimentation with little alteration, diagenesis partially into clays, and fluids circulation all along the unit formation through fractures, with a water activity more or less limited. Early diagenetic cracks in the lower most exposed unit appear to be filled with erosion-resistant raised ridges [8], that ChemCam has shown to be enriched in Mg- and Fe-rich clays [9]. The calcium sulfate veins (gypsum, bassanite) on the other hand are found all across the deposit and must have formed last [10]. In a large majority, rocks and coarse gravels encountered so far by Curiosity show little surface coatings but dust. However, some water-rock interaction

  7. Analytical characterization of plasma membrane-derived vesicles produced via osmotic and chemical vesiculation.

    PubMed

    Sarabipour, Sarvenaz; Chan, Robin B; Zhou, Bowen; Di Paolo, Gilbert; Hristova, Kalina

    2015-07-01

    Plasma membrane-derived vesicles are being used in biophysical and biochemical research as a simple, yet native-like model of the cellular membrane. Here we report on the characterization of vesicles produced via two different vesiculation methods from CHO and A431 cell lines. The first method is a recently developed method which utilizes chloride salts to induce osmotic vesiculation. The second is a well established chemical vesiculation method which uses DTT and formaldehyde. We show that both vesiculation methods produce vesicles which contain the lipid species previously reported in the plasma membrane of these cell lines. The two methods lead to small but statistically significant differences in two lipid species only; phosphatidylcholine (PC) and plasmalogen phosphatidylethanolamine (PEp). However, highly significant differences were observed in the degree of incorporation of a membrane receptor and in the degree of retention of soluble cytosolic proteins within the vesicles. PMID:25896659

  8. Real-Time Monitoring of Critical Care Analytes in the Bloodstream with Chemical Sensors: Progress and Challenges

    NASA Astrophysics Data System (ADS)

    Frost, Megan C.; Meyerhoff, Mark E.

    2015-07-01

    We review approaches and challenges in developing chemical sensor-based methods to accurately and continuously monitor levels of key analytes in blood related directly to the status of critically ill hospitalized patients. Electrochemical and optical sensor-based technologies have been pursued to measure important critical care species in blood [i.e., oxygen, carbon dioxide, pH, electrolytes (K+, Na+, Cl-, etc.), glucose, and lactate] in real-time or near real-time. The two main configurations examined to date for achieving this goal have been intravascular catheter sensors and patient attached ex vivo sensors with intermittent blood sampling via an attached indwelling catheter. We discuss the status of these configurations and the main issues affecting the accuracy of the measurements, including cell adhesion and thrombus formation on the surface of the sensors, sensor drift, sensor selectivity, etc. Recent approaches to mitigate these nagging performance issues that have prevented these technologies from clinical use are also discussed.

  9. Analytical Solution of Steady State Equations for Chemical Reaction Networks with Bilinear Rate Laws

    PubMed Central

    Halász, Ádám M.; Lai, Hong-Jian; McCabe, Meghan M.; Radhakrishnan, Krishnan; Edwards, Jeremy S.

    2014-01-01

    True steady states are a rare occurrence in living organisms, yet their knowledge is essential for quasi-steady state approximations, multistability analysis, and other important tools in the investigation of chemical reaction networks (CRN) used to describe molecular processes on the cellular level. Here we present an approach that can provide closed form steady-state solutions to complex systems, resulting from CRN with binary reactions and mass-action rate laws. We map the nonlinear algebraic problem of finding steady states onto a linear problem in a higher dimensional space. We show that the linearized version of the steady state equations obeys the linear conservation laws of the original CRN. We identify two classes of problems for which complete, minimally parameterized solutions may be obtained using only the machinery of linear systems and a judicious choice of the variables used as free parameters. We exemplify our method, providing explicit formulae, on CRN describing signal initiation of two important types of RTK receptor-ligand systems, VEGF and EGF-ErbB1. PMID:24334389

  10. Influence of chemical kinetics on postcolumn reaction in a capillary Taylor reactor with catechol analytes and photoluminescence following electron transfer.

    PubMed

    Jung, Moon Chul; Weber, Stephen G

    2005-02-15

    Postcolumn derivatization reactions can enhance detector sensitivity and selectivity, but their successful combination with capillary liquid chromatography has been limited because of the small peak volumes in capillary chromatography. A capillary Taylor reactor (CTR), developed in our laboratory, provides simple and effective mixing and reaction in a 25-microm-radius postcolumn capillary. Homogenization of reactant streams occurs by radial diffusion, and a chemical reaction follows. Three characteristic times for a given reaction process can be predicted using simple physical and chemical parameters. Two of these times are the homogenization time, which governs how long it takes the molecules in the analyte and reagent streams to mix, and the reaction time, which governs how long the molecules in a homogeneous solution take to react. The third characteristic time is an adjustment to the reaction time called the start time, which represents an estimate of the average time the analyte stream spends without exposure to reagent. In this study, laser-induced fluorescence monitored the extent of the postcolumn reaction (reduction of Os(bpy)3(3+) by analyte to the photoluminescent Os(bpy)3(2+)) in a CTR. The reaction time depends on the reaction rates. Analysis of product versus time data yielded second-order reaction rate constants between the PFET reagent, tris(2,2'-bipyridine)osmium, and standards ((ferrocenylmethyl)trimethylammonium cation and p-hydroquinone) or catechols (dopamine, epinephrine, norepinephrine, 3, 4-dihydroxyphenylacetic acid. The extent of the reactions in a CTR were then predicted from initial reaction conditions and compared to experimental results. Both the theory and experimental results suggested the reactions of catechols were generally kinetically controlled, while those of the standards were controlled by mixing time (1-2 s). Thus, the extent of homogenization can be monitored in a CTR using the relatively fast reaction of the reagent and p

  11. Understanding of the impact of chemicals on amphibians: a meta-analytic review

    PubMed Central

    Egea-Serrano, Andrés; Relyea, Rick A; Tejedo, Miguel; Torralva, Mar

    2012-01-01

    Many studies have assessed the impact of different pollutants on amphibians across a variety of experimental venues (laboratory, mesocosm, and enclosure conditions). Past reviews, using vote-counting methods, have described pollution as one of the major threats faced by amphibians. However, vote-counting methods lack strong statistical power, do not permit one to determine the magnitudes of effects, and do not compare responses among predefined groups. To address these challenges, we conducted a meta-analysis of experimental studies that measured the effects of different chemical pollutants (nitrogenous and phosphorous compounds, pesticides, road deicers, heavy metals, and other wastewater contaminants) at environmentally relevant concentrations on amphibian survival, mass, time to hatching, time to metamorphosis, and frequency of abnormalities. The overall effect size of pollutant exposure was a medium decrease in amphibian survival and mass and a large increase in abnormality frequency. This translates to a 14.3% decrease in survival, a 7.5% decrease in mass, and a 535% increase in abnormality frequency across all studies. In contrast, we found no overall effect of pollutants on time to hatching and time to metamorphosis. We also found that effect sizes differed among experimental venues and among types of pollutants, but we only detected weak differences among amphibian families. These results suggest that variation in sensitivity to contaminants is generally independent of phylogeny. Some publication bias (i.e., selective reporting) was detected, but only for mass and the interaction effect size among stressors. We conclude that the overall impact of pollution on amphibians is moderately to largely negative. This implies that pollutants at environmentally relevant concentrations pose an important threat to amphibians and may play a role in their present global decline. PMID:22957147

  12. Nature of the binding interaction for 50 structurally diverse chemicals with rat estrogen receptors

    EPA Science Inventory

    This study was conducted to characterize the estrogen receptor (ER)-binding affinities of 50 chemicals selected from among the high production volume chemicals under the U.S. EPA's (U.S. Environmental Protection Agency's) Toxic Substances Control Act inventory. The chemicals were...

  13. Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics Lecture: Broadband Rotational Spectroscopy for Chemical Kinetics, Molecular Structure, and Analytical Chemistry

    NASA Astrophysics Data System (ADS)

    Pate, Brooks

    2013-03-01

    Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Work

  14. EFFECTS OF CHEMICAL CONTAMINANTS ON GENETIC DIVERSITY IN NATURAL POPULATIONS: IMPLICATIONS FOR BIOMONITORING AND ECOTOXICOLOGY

    EPA Science Inventory

    The conservation of genetic diversity has emerged as one of the central issues in conservation biology. Although researchers in the areas of evolutionary biology, population management, and conservation biology routinely investigate genetic variability in natural populations, onl...

  15. [The analytical setting of rotary speed of centrifuge rotor and centrifugation time in chemical, biochemical and microbiological practice].

    PubMed

    Zolotarev, K V

    2012-08-01

    The researchers happen to face with suspensions in their chemical, biochemical and microbiological practice. The suspensions are the disperse systems with solid dispersed phase and liquid dispersion medium and with dispersed phase particle size > 100 nm (10-7 m). Quite often the necessity occurs to separate solid particles from liquid. To use for this purpose the precipitation in gravitation field can make the process to progress too long. In this respect an effective mode is the precipitation in the field of centrifugal forces--the centrifugation. The rotary speed of centrifuge rotor and centrifugation time can be set analytically using regularities of general dynamics and hydrodynamics. To this effect, should be written and transformed the equation of First and Second Newton Laws for suspension particle being in the field of centrifugal forces and forces of resistance of liquid and vessel wall. The force of liquid resistance depends on particle motion condition in liquid. To determine the regimen the Archimedes and Reynolds numerical dimensionless criteria are to be applied. The article demonstrates the results of these transformations as analytical inverse ratio dependence of centrifugation time from rotary speed. The calculation of series of "rate-time" data permits to choose the optimal data pair on the assumption of centrifuge capacity and practical reasonability. The results of calculations are validated by actual experimental data hence the physical mathematical apparatus can be considered as effective one. The setting progress depends both from parameter (Reynolds criterion) and data series calculation. So, the most convenient way to apply this operation is the programming approach. The article proposes to use the program Microsoft Excel and VBA programming language for this purpose. The possibility to download the file from Internet to use it for fast solution is proposed. PMID:23097986

  16. Analytical Method for the Detection of Ozone Depleting Chemicals (ODC) in Commercial Products Using a Gas Chromatograph with an Electron Capture Detector (GC-ECD)

    SciTech Connect

    Lee, Richard N.; Dockendorff, Brian P.; Wright, Bob W.

    2008-08-01

    This document describes an analytical procedure that was developed for the trace level detection of residual ozone depleting chemicals (ODC) associated with the manufacture of selected commercial products. To ensure the United States meets it obligation under the Montreal Protocol, Congress enacted legislation in 1989 to impose an excise tax on electronic goods imported into the United States that were produced with banned chemicals. This procedure was developed to technically determine if residual ODC chemicals could be detected on electronic circuit boards. The analytical method utilizes a “purge and trap” technique followed by gas chromatography with electron capture detection to capture and analyze the volatile chemicals associated with the matrix. The method describes the procedure, the hardware, operating conditions, calibration, and quality control measures in sufficient detail to allow the capability to be replicated. This document corresponds to internal Standard Operating Procedure (SOP) EFL-130A, Rev 4.

  17. Identification of improvised explosives residues using physical-chemical analytical methods under real conditions after an explosion

    NASA Astrophysics Data System (ADS)

    Kotrlý, Marek; Mareš, Bohumil; Turková, Ivana; Beroun, Ivo

    2016-05-01

    Within the analysis of cases relating to the use of explosives for crimes, we have experienced a shift from using industrial explosives towards substances made in amateur and illegal way. Availability of industrial explosives is increasingly limited to a narrow sphere of subjects with a relevant permission. Thus, on the part of perpetrators, terrorists, ever greater attention is paid to illegal production of explosives that are easily made from readily available raw materials. Another alarming fact is the availability of information found on the internet. Procedures of preparation are often very simple and do not require even a deeper professional knowledge. Explosive characteristics are not actually accessible for many of these substances (detonation velocity, sensitivity, working capacity, brisance, physical and chemical stability, etc.). Therefore, a project is being implemented, which on grounds of assessment of individual information available in literature and on the internet, aiming at choosing individual areas of potentially abusable substances (e.g. mixtures of nitric acid (98%) with organic substances, mixtures nitromethane and tetranitromethane with organic substances, mixtures of chlorates and perchlorates of alkali metals with organic substances, chemically individual compounds of organic base type of perchloric acid, azides, fulminates, acetylides, picrates, styphnates of heavy metals, etc.). It is directed towards preparation of these explosives also in non-stoichiometric mixtures, conducting test explosives, determination of explosive characteristics (if they are unknown) and analysis of both primary phases and post-blast residues through available analytical techniques, such as gas and liquid chromatography with mass detection, FTIR, micro-Raman spectrometry, electron microscopy with microanalysis and Raman microspectrometry directly in SEM chamber for analysis at the level of individual microparticles. The received characteristics will be used to

  18. Growth of Daphnia magna exposed to mixtures of chemicals with diverse modes of action

    SciTech Connect

    Deneer, J.W.; Seinen, W.; Hermens, J.L.

    1988-02-01

    Concentrations causing inhibition of growth of Daphnia magna after 16 days of exposure were determined for nine chemicals that presumably act through different modes of action. The joint toxic effect of a mixture of these chemicals is found to be nonadditive.

  19. Chemical diversity of organic volatiles among comets: An emerging taxonomy and implications for processes in the proto-planetary disk

    NASA Astrophysics Data System (ADS)

    Mumma, Michael J.

    2008-10-01

    As messengers from the early Solar System, comets contain key information from the time of planet formation and even earlier some may contain material formed in our natal interstellar cloud. Along with water, the cometary nucleus contains ices of natural gases (CH4, C2H6), alcohols (CH3OH), acids (HCOOH), embalming fluid (H2CO), and even anti-freeze (ethylene glycol). Comets today contain some ices that vaporize at temperatures near absolute zero (CO, CH4), demonstrating that their compositions remain largely unchanged after 4.5 billion years. By comparing their chemical diversity, several distinct cometary classes have been identified but their specific relation to chemical gradients in the proto-planetary disk remains murky. How does the compositional diversity of comets relate to nebular processes such as chemical processing, radial migration, and dynamical scattering? No current reservoir holds a unique class, but their fractional abundance can test emerging dynamical models for origins of the scattered Kuiper disk, the Oort cloud, and the (proposed) main-belt comets. I will provide a simplified overview emphasizing what we are learning, current issues, and their relevance to the subject of this Symposium.

  20. Role of vermicompost chemical composition, microbial functional diversity, and fungal community structure in their microbial respiratory response to three pesticides.

    PubMed

    Fernández-Gómez, Manuel J; Nogales, Rogelio; Insam, Heribert; Romero, Esperanza; Goberna, Marta

    2011-10-01

    The relationships between vermicompost chemical features, enzyme activities, community-level physiological profiles (CLPPs), fungal community structures, and its microbial respiratory response to pesticides were investigated. Fungal community structure of vermicomposts produced from damaged tomato fruits (DT), winery wastes (WW), olive-mill waste and biosolids (OB), and cattle manure (CM) were determined by denaturing gradient gel electrophoresis of 18S rDNA. MicroResp™ was used for assessing vermicompost CLPPs and testing the microbial response to metalaxyl, imidacloprid, and diuron. Vermicompost enzyme activities and CLPPs indicated that WW, OB, and DT had higher microbial functional diversity than CM. The microbiota of the former tolerated all three pesticides whereas microbial respiration in CM was negatively affected by metalaxyl and imidacloprid. The response of vermicompost microbiota to the fungicide metalaxyl was correlated to its fungal community structure. The results suggest that vermicomposts with higher microbial functional diversity can be useful for the management of pesticide pollution in agriculture. PMID:21865033

  1. Material Characterization in the Electro-Analytic Approach for Applications in Chemical Mechanical Planarization and Electrochemical Energy Systems

    NASA Astrophysics Data System (ADS)

    Rock, Simon E.

    The work presented in this thesis covers electro-analytical characterization for multiple applications in material science. Electrochemical techniques were used to investigate soluble film formation on metals used in chemical mechanical planarization in order to better understand the removal rate process by studying new chemicals proposed by groups in industry. Second, an ionic liquid was used as an electrolyte in a lithium ion cathode half cell to show the essential functionality of the IL and the temperature advantage over traditional electrolytes. Lastly, a comprehensive measurement for charge recombination in dye-sensitized solar cells was performed using both open-circuit voltage decay and impedance spectroscopy, which may be used to better understand the limiting factors that affect the cell's efficiently. Electrochemical techniques were applied to new methods and materials to extend the development of material manufacturing and advance the measurement process. The fabrication of interconnect structures for semiconductor devices requires low down-pressure chemical mechanical planarization (CMP) of Ta barrier layers. Guanidine carbonate (GC) serves as an effective surface-complexing agent for such CMP applications, where the rate of Ta removal can be chemically controlled through pH-tuned selectivity with respect to the removal of Cu lines. Electrochemical techniques are employed in this work to study the surface-modifying roles of GC that make this chemical an attractive complexing agent for Ta CMP. In addition, the effects of including H2O2 (an oxidizer) and dodecyl benzene sulfonic acid (DBSA, a dissolution inhibitor for Cu) in GC-based CMP solutions are investigated to examine the selective CMP mechanisms of Ta and Cu in these solutions. The results suggest that the removal of Ta is supported in part by structurally weak guanidinium-tantalic-acid surface complexes formed on Ta/Ta2O5. The bicarbonate/carbonate anions of GC also facilitate Ta removal through

  2. An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes

    PubMed Central

    Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Masaki, Shunpei; Nakayama, Hiroshi; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

    2009-01-01

    We describe here a mass spectrometry (MS)-based analytical platform of RNA, which combines direct nano-flow reversed-phase liquid chromatography (RPLC) on a spray tip column and a high-resolution LTQ-Orbitrap mass spectrometer. Operating RPLC under a very low flow rate with volatile solvents and MS in the negative mode, we could estimate highly accurate mass values sufficient to predict the nucleotide composition of a ∼21-nucleotide small interfering RNA, detect post-transcriptional modifications in yeast tRNA, and perform collision-induced dissociation/tandem MS-based structural analysis of nucleolytic fragments of RNA at a sub-femtomole level. Importantly, the method allowed the identification and chemical analysis of small RNAs in ribonucleoprotein (RNP) complex, such as the pre-spliceosomal RNP complex, which was pulled down from cultured cells with a tagged protein cofactor as bait. We have recently developed a unique genome-oriented database search engine, Ariadne, which allows tandem MS-based identification of RNAs in biological samples. Thus, the method presented here has broad potential for automated analysis of RNA; it complements conventional molecular biology-based techniques and is particularly suited for simultaneous analysis of the composition, structure, interaction, and dynamics of RNA and protein components in various cellular RNP complexes. PMID:19740761

  3. Volatile chemicals released by Tephritid flies as a tool to understanding species diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It is clear that the Tephritids are a wonderfully diverse group of flies. However, as is evident from the current Coordinated Research Project many times clear species identifications are next to impossible using common systematic methods. Excellent examples of cryptic species are documented amon...

  4. Assessing metabolomic and chemical diversity of a soybean lineage representing 35 years of breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Information on crop genotype- and phenotype-metabolite associations can be of value to trait development as well as to food security and safety. The unique study presented here assessed seed metabolomic and ionomic diversity in a soybean lineage representing ~35 years of breeding (launch years 1972-...

  5. Chemical Analysis of a "Miller-Type" Complex Prebiotic Broth. Part I: Chemical Diversity, Oxygen and Nitrogen Based Polymers

    NASA Astrophysics Data System (ADS)

    Wollrab, Eva; Scherer, Sabrina; Aubriet, Frédéric; Carré, Vincent; Carlomagno, Teresa; Codutti, Luca; Ott, Albrecht

    2016-06-01

    In a famous experiment Stanley Miller showed that a large number of organic substances can emerge from sparking a mixture of methane, ammonia and hydrogen in the presence of water (Miller, Science 117:528-529, 1953). Among these substances Miller identified different amino acids, and he concluded that prebiotic events may well have produced many of Life's molecular building blocks. There have been many variants of the original experiment since, including different gas mixtures (Miller, J Am Chem Soc 77:2351-2361, 1955; Oró Nature 197:862-867, 1963; Schlesinger and Miller, J Mol Evol 19:376-382, 1983; Miyakawa et al., Proc Natl Acad Sci 99:14,628-14,631, 2002). Recently some of Miller's remaining original samples were analyzed with modern equipment (Johnson et al. Science 322:404-404, 2008; Parker et al. Proc Natl Acad Sci 108:5526-5531, 2011) and a total of 23 racemic amino acids were identified. To give an overview of the chemical variety of a possible prebiotic broth, here we analyze a "Miller type" experiment using state of the art mass spectrometry and NMR spectroscopy. We identify substances of a wide range of saturation, which can be hydrophilic, hydrophobic or amphiphilic in nature. Often the molecules contain heteroatoms, with amines and amides being prominent classes of molecule. In some samples we detect ethylene glycol based polymers. Their formation in water requires the presence of a catalyst. Contrary to expectations, we cannot identify any preferred reaction product. The capacity to spontaneously produce this extremely high degree of molecular variety in a very simple experiment is a remarkable feature of organic chemistry and possibly prerequisite for Life to emerge. It remains a future task to uncover how dedicated, organized chemical reaction pathways may have arisen from this degree of complexity.

  6. Chemical Analysis of a "Miller-Type" Complex Prebiotic Broth: Part I: Chemical Diversity, Oxygen and Nitrogen Based Polymers.

    PubMed

    Wollrab, Eva; Scherer, Sabrina; Aubriet, Frédéric; Carré, Vincent; Carlomagno, Teresa; Codutti, Luca; Ott, Albrecht

    2016-06-01

    In a famous experiment Stanley Miller showed that a large number of organic substances can emerge from sparking a mixture of methane, ammonia and hydrogen in the presence of water (Miller, Science 117:528-529, 1953). Among these substances Miller identified different amino acids, and he concluded that prebiotic events may well have produced many of Life's molecular building blocks. There have been many variants of the original experiment since, including different gas mixtures (Miller, J Am Chem Soc 77:2351-2361, 1955; Oró Nature 197:862-867, 1963; Schlesinger and Miller, J Mol Evol 19:376-382, 1983; Miyakawa et al., Proc Natl Acad Sci 99:14,628-14,631, 2002). Recently some of Miller's remaining original samples were analyzed with modern equipment (Johnson et al. Science 322:404-404, 2008; Parker et al. Proc Natl Acad Sci 108:5526-5531, 2011) and a total of 23 racemic amino acids were identified. To give an overview of the chemical variety of a possible prebiotic broth, here we analyze a "Miller type" experiment using state of the art mass spectrometry and NMR spectroscopy. We identify substances of a wide range of saturation, which can be hydrophilic, hydrophobic or amphiphilic in nature. Often the molecules contain heteroatoms, with amines and amides being prominent classes of molecule. In some samples we detect ethylene glycol based polymers. Their formation in water requires the presence of a catalyst. Contrary to expectations, we cannot identify any preferred reaction product. The capacity to spontaneously produce this extremely high degree of molecular variety in a very simple experiment is a remarkable feature of organic chemistry and possibly prerequisite for Life to emerge. It remains a future task to uncover how dedicated, organized chemical reaction pathways may have arisen from this degree of complexity. PMID:26508401

  7. Political and clinical developments in analytical psychology, 1972-2014: subjectivity, equality and diversity-inside and outside the consulting room.

    PubMed

    Samuels, Andrew

    2014-11-01

    Utilizing Jung's idea of theory as a 'personal confession', the author charts his own development as a theorist, establishing links between his personal history and his ideas. Such links include his relationship with both parents, his sexuality, his cultural heritage, and his fascination with Tricksters and with Hermes. There follows a substantial critical interrogation of what the author discerns as the two main lines of clinical theorizing in contemporary analytical psychotherapy: interpretation of transference-countertransference, and the relational approach. His conclusion is that neither is superior to the other and neither is in fact adequate as a basis for clinical work. The focus then shifts to explore a range of political and social aspects of the clinical project of analytical psychology: economic inequality, diversity within the professional field, and Jung's controversial ideas about Jews and Africans. The author calls for an apology from the 'Jungian community' for remarks about Africans analogous to the apology already issued for remarks about Jews. The paper is dedicated to the author's friend Fred Plaut (1913-2009). PMID:25331504

  8. Chemical fingerprinting of naphthenic acids and oil sands process waters-A review of analytical methods for environmental samples.

    PubMed

    Headley, J V; Peru, K M; Mohamed, M H; Frank, R A; Martin, J W; Hazewinkel, R R O; Humphries, D; Gurprasad, N P; Hewitt, L M; Muir, D C G; Lindeman, D; Strub, R; Young, R F; Grewer, D M; Whittal, R M; Fedorak, P M; Birkholz, D A; Hindle, R; Reisdorph, R; Wang, X; Kasperski, K L; Hamilton, C; Woudneh, M; Wang, G; Loescher, B; Farwell, A; Dixon, D G; Ross, M; Pereira, A Dos Santos; King, E; Barrow, M P; Fahlman, B; Bailey, J; McMartin, D W; Borchers, C H; Ryan, C H; Toor, N S; Gillis, H M; Zuin, L; Bickerton, G; Mcmaster, M; Sverko, E; Shang, D; Wilson, L D; Wrona, F J

    2013-01-01

    This article provides a review of the routine methods currently utilized for total naphthenic acid analyses. There is a growing need to develop chemical methods that can selectively distinguish compounds found within industrially derived oil sands process affected waters (OSPW) from those derived from the natural weathering of oil sands deposits. Attention is thus given to the characterization of other OSPW components such as oil sands polar organic compounds, PAHs, and heavy metals along with characterization of chemical additives such as polyacrylamide polymers and trace levels of boron species. Environmental samples discussed cover the following matrices: OSPW containments, on-lease interceptor well systems, on- and off-lease groundwater, and river and lake surface waters. There are diverse ranges of methods available for analyses of total naphthenic acids. However, there is a need for inter-laboratory studies to compare their accuracy and precision for routine analyses. Recent advances in high- and medium-resolution mass spectrometry, concomitant with comprehensive mass spectrometry techniques following multi-dimensional chromatography or ion-mobility separations, have allowed for the speciation of monocarboxylic naphthenic acids along with a wide range of other species including humics. The distributions of oil sands polar organic compounds, particularly the sulphur containing species (i.e., OxS and OxS2) may allow for distinguishing sources of OSPW. The ratios of oxygen- (i.e., Ox) and nitrogen-containing species (i.e., NOx, and N2Ox) are useful for differentiating organic components derived from OSPW from natural components found within receiving waters. Synchronous fluorescence spectroscopy also provides a powerful screening technique capable of quickly detecting the presence of aromatic organic acids contained within oil sands naphthenic acid mixtures. Synchronous fluorescence spectroscopy provides diagnostic profiles for OSPW and potentially impacted

  9. Using Secondary Data to Evaluate Diverse Groups of Chemical and Nonchemical Stressors in Cumulative Risk Assessment

    EPA Science Inventory

    A main impediment of performing cumulative risk assessments (CRAs) is having data for multiple chemical and nonchemical stressors in the same individuals or populations. Therefore, secondary data analysis can be utilized as a screening approach to integrate population characteri...

  10. Acidification in the Adirondacks: defining the biota in trophic levels of 30 chemically diverse acid-impacted lakes.

    PubMed

    Nierzwicki-Bauer, Sandra A; Boylen, Charles W; Eichler, Lawrence W; Harrison, James P; Sutherland, James W; Shaw, William; Daniels, Robert A; Charles, Donald F; Acker, Frank W; Sullivan, Timothy J; Momen, Bahram; Bukaveckas, Paul

    2010-08-01

    The Adirondack Mountains in New York State have a varied surficial geology and chemically diverse surface waters that are among the most impacted by acid deposition in the U.S. No single Adirondack investigation has been comprehensive in defining the effects of acidification on species diversity, from bacteria through fish, essential for understanding the full impact of acidification on biota. Baseline midsummer chemistry and community composition are presented for a group of chemically diverse Adirondack lakes. Species richness of all trophic levels except bacteria is significantly correlated with lake acid-base chemistry. The loss of taxa observed per unit pH was similar: bacterial genera (2.50), bacterial classes (1.43), phytoplankton (3.97), rotifers (3.56), crustaceans (1.75), macrophytes (3.96), and fish (3.72). Specific pH criteria were applied to the communities to define and identify acid-tolerant (pH<5.0), acid-resistant (pH 5.0-5.6), and acid-sensitive (pH>5.6) species which could serve as indicators. Acid-tolerant and acid-sensitive categories are at end-points along the pH scale, significantly different at P<0.05; the acid-resistant category is the range of pH between these end-points, where community changes continually occur as the ecosystem moves in one direction or another. The biota acid tolerance classification (batc) system described herein provides a clear distinction between the taxonomic groups identified in these subcategories and can be used to evaluate the impact of acid deposition on different trophic levels of biological communities. PMID:20614900

  11. Gustatory receptor neuron responds to chemically diverse insect repellents in the common malaria mosquito Anopheles quadrimaculatus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Female mosquitoes feed on blood from animal hosts to obtain nutritional resources used for egg production. These contacts facilitate the spread of harmful human diseases. Chemical repellents are used to disrupt mosquito host seeking and blood feeding behaviors; however, little is known about the g...

  12. Chemical and biological diversity of the volatiles of five Artemisia species from far east of Russia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aim of the present study was to investigate the chemical composition and biological activity of essential oils from aerial parts of Artemisia argyi, A. feddei, A. gmelinii, A. manshurica, A. olgensis (Asteraceae). Plants were collected in the Far East region (Primorski Krai) of the Russian Federatio...

  13. Chemically diverse microtubule stabilizing agents initiate distinct mitotic defects and dysregulated expression of key mitotic kinases.

    PubMed

    Rohena, Cristina C; Peng, Jiangnan; Johnson, Tyler A; Crews, Phillip; Mooberry, Susan L

    2013-04-15

    Microtubule stabilizers are some of the most successful drugs used in the treatment of adult solid tumors and yet the molecular events responsible for their antimitotic actions are not well defined. The mitotic events initiated by three structurally and biologically diverse microtubule stabilizers; taccalonolide AJ, laulimalide/fijianolide B and paclitaxel were studied. These microtubule stabilizers cause the formation of aberrant, but structurally distinct mitotic spindles leading to the hypothesis that they differentially affect mitotic signaling. Each microtubule stabilizer initiated different patterns of expression of key mitotic signaling proteins. Taccalonolide AJ causes centrosome separation and disjunction failure to a much greater extent than paclitaxel or laulimalide, which is consistent with the distinct defects in expression and activation of Plk1 and Eg5 caused by each stabilizer. Localization studies revealed that TPX2 and Aurora A are associated with each spindle aster formed by each stabilizer. This suggests a common mechanism of aster formation. However, taccalonolide AJ also causes pericentrin accumulation on every spindle aster. The presence of pericentrin at every spindle aster initiated by taccalonolide AJ might facilitate the maintenance and stability of the highly focused asters formed by this stabilizer. Laulimalide and paclitaxel cause completely different patterns of expression and activation of these proteins, as well as phenotypically different spindle phenotypes. Delineating how diverse microtubule stabilizers affect mitotic signaling pathways could identify key proteins involved in modulating sensitivity and resistance to the antimitotic actions of these compounds. PMID:23399639

  14. A three-tier QSAR modeling strategy for estimating eye irritation potential of diverse chemicals in rabbit for regulatory purposes.

    PubMed

    Basant, Nikita; Gupta, Shikha; Singh, Kunwar P

    2016-06-01

    Experimental determination of the eye irritation potential (EIP) of chemicals is not only tedious, time and resource intensive, it involves cruelty to test animals. In this study, we have established a three-tier QSAR modeling strategy for estimating the EIP of chemicals for the use of pharmaceutical industry and regulatory agencies. Accordingly, a qualitative (binary classification: irritating, non-irritating), semi-quantitative (four-category classification), and quantitative (regression) QSAR models employing the SDT, DTF, and DTB methods were developed for predicting the EIP of chemicals in accordance with the OECD guidelines. Structural features of chemicals responsible for eye irritation were extracted and used in QSAR analysis. The external predictive power of the developed QSAR models were evaluated through the internal and external validation procedures recommended in QSAR literature. In test data, the two and four category classification QSAR models (DTF, DTB) rendered accuracy of >93%, while the regression QSAR models (DTF, DTB) yielded correlation (R(2)) of >0.92 between the measured and predicted EIPs. Values of various statistical validation coefficients derived for the test data were above their respective threshold limits (except rm(2) in DTF), thus put a high confidence in this analysis. The applicability domain of the constructed QSAR models were defined using the descriptors range and leverage approaches. The QSAR models in this study performed better than any of the previous studies. The results suggest that the developed QSAR models can reliably predict the EIP of diverse chemicals and can be useful tools for screening of candidate molecules in the drug development process. PMID:27018829

  15. Predicting Toxicities of Diverse Chemical Pesticides in Multiple Avian Species Using Tree-Based QSAR Approaches for Regulatory Purposes.

    PubMed

    Basant, Nikita; Gupta, Shikha; Singh, Kunwar P

    2015-07-27

    A comprehensive safety evaluation of chemicals should require toxicity assessment in both the aquatic and terrestrial test species. Due to the application practices and nature of chemical pesticides, the avian toxicity testing is considered as an essential requirement in the risk assessment process. In this study, tree-based multispecies QSAR (quantitative-structure activity relationship) models were constructed for predicting the avian toxicity of pesticides using a set of nine descriptors derived directly from the chemical structures and following the OECD guidelines. Accordingly, the Bobwhite quail toxicity data was used to construct the QSAR models (SDT, DTF, DTB) and were externally validated using the toxicity data in four other test species (Mallard duck, Ring-necked pheasant, Japanese quail, House sparrow). Prior to the model development, the diversity in the chemical structures and end-point were verified. The external predictive power of the QSAR models was tested through rigorous validation deriving a wide series of statistical checks. Intercorrelation analysis and PCA methods provided information on the association of the molecular descriptors related to MW and topology. The S36 and MW were the most influential descriptors identified by DTF and DTB models. The DTF and DTB performed better than the SDT model and yielded a correlation (R(2)) of 0.945 and 0.966 between the measured and predicted toxicity values in test data array. Both these models also performed well in four other test species (R(2) > 0.918). ChemoTyper was used to identify the substructure alerts responsible for the avian toxicity. The results suggest for the appropriateness of the developed QSAR models to reliably predict the toxicity of pesticides in multiple avian test species and can be useful tools in screening the new chemical pesticides for regulatory purposes. PMID:26158470

  16. Secondary metabolites of seagrasses (Alismatales and Potamogetonales; Alismatidae): Chemical diversity, bioactivity, and ecological function.

    PubMed

    Zidorn, Christian

    2016-04-01

    Seagrasses are the only higher plants living in fully marine environments; they play a significant role in coastal ecosystems. Seagrasses inhabit the coastal shelves of all continents except Antarctica and can grow in depths of up to 90m. Because of their eminent ecological importance, innumerous studies have been dedicated to seagrasses and their ecology. However, the phytochemistry has not been equally well investigated yet and many of the existing studies in chemical ecology are only investigating the chemistry at the level of compound classes, e.g. phenolics, and not at the level of chemically defined metabolites. In the present review, the existing literature on secondary metabolites of seagrasses, their known source seagrasses, their bioactivity, and ecological function are compiled and critically assessed. Moreover, research gaps are highlighted and avenues for future research are discussed. Currently, a total of 154 chemically defined natural products have been reported from the about 70 seagrass species known worldwide. Compounds reported include simple phenols derivatives (four compounds), phenylmethane derivatives (14 compounds), phenylethane derivatives (four compounds), phenylpropane derivatives including their esters and dimers (20 compounds), chalkones (four compounds), flavonoids including catechins (57 compounds), phenylheptanoids (four compounds), one monoterpene derivative, one sesquiterpene, diterpenoids (13 compounds), steroids (31 compounds), and one alkaloid. Most of the existing bioactivity studies of seagrass metabolites and extracts have been directed to potential cytotoxic, antimicrobial, or antimacrofouling activity. Antimicrobial studies have been performed towards panels of both human pathogens and ecologically relevant pathogens. In the antimacrofouling studies, investigations of the potential of zosteric acid from the genus Zostera are the most numerous and have yielded so far the most interesting results. Studies on the chemical

  17. Chemical diversity among the essential oils of wild populations of Stachys lavandulifolia VAHL (Lamiaceae) from Iran.

    PubMed

    Aghaei, Yaqub; Hossein Mirjalili, Mohammad; Nazeri, Vahideh

    2013-02-01

    The variation of the essential-oil composition among ten wild populations of Stachys lavandulifolia VAHL (Lamiaceae), collected from different geographical regions of Iran, was assessed by GC-FID and GC/MS analyses, and their intraspecific chemical variability was determined. Altogether, 49 compounds were identified in the oils, and a relatively high variation in their contents was found. The major compounds of the essential oils were myrcene (0.0-26.2%), limonene (0.0-24.5%), germacrene D (4.2-19.3%), bicyclogermacrene (1.6-18.0%), δ-cadinene (6.5-16.0%), pulegone (0.0-15.1%), (Z)-hex-3-enyl tiglate (0.0-15.1%), (E)-caryophyllene (0.0-12.9), α-zingiberene (0.2-12.2%), and spathulenol (1.6-11.1%). For the determination of the chemotypes and the chemical variability, the essential-oil components were subjected to cluster analysis (CA). The five different chemotypes characterized were Chemotype I (germacrene D/bicyclogermacrene), Chemotype II (germacrene D/spathulenol), Chemotype III (limonene/δ-cadinene), Chemotype IV (pulegone), and Chemotype V (α-zingiberene). The high chemical variation among the populations according to their geographical and bioclimatic distribution imposes that conservation strategies of populations should be made appropriately, taking into account these factors. The in situ and ex situ conservation strategies should concern all populations representing the different chemotypes. PMID:23418173

  18. Invertebrate diversity in relation to chemical pollution in an Umbrian stream system (Italy).

    PubMed

    Pallottini, Matteo; Goretti, Enzo; Gaino, Elda; Selvaggi, Roberta; Cappelletti, David; Céréghino, Régis

    2015-07-01

    We used self-organizing maps (SOM, neural network) to bring out patterns of benthic macroinvertebrate diversity in relation to river pollution. Fourteen stations were sampled over various seasons in the Nestore drainage basin (Central Italy) and characterized for macroinvertebrate communities, nutrient and heavy metal concentrations. Physicochemical variables were introduced into a SOM previously trained with macroinvertebrate data. Patterns of communities matched spatial and seasonal changes in environmental conditions, including water chemistry related to economic activities in the catchment. Although our analyses did not allow us to establish the specific effect of any given environmental parameter upon macroinvertebrate community composition based on the field study, they enabled us to map the ecological health of river ecosystems in a readily interpretable manner. PMID:26043800

  19. Diverse mechanisms of hepatocellular injuries due to chemicals: evidence in rats administered carbon tetrachloride or dimethylnitrosamine.

    PubMed Central

    Nayak, N. C.; Chopra, P.; Dhar, A.; Das, P. K.

    1975-01-01

    Differences in acute hepatotoxicity of carbon tetrachloride (CCl4) and dimethylnitrosamine (DMN) have been tested in normal foetal, newborn and adult rats, foetal, newborn and adult rats pretreated with phenobarbitone and partially hepatectomized adult rats. While CCl4 is non-toxic to the foetal and newborn liver, DMN induces identical necrosis at all ages. Prior dosing with phenobarbitone augments CCl4 toxicity only in the adult and the newborn but the foetus continues to be resistant. Such pretreatment, on the other hand, significantly reduces the effects of DMN on liver in all animals. Partial hepatectomy makes the liver less susceptible to CCl4 and more so to DMN. Such diversities of hepatic response to the two toxins can be accounted for by the levels of the respective toxifying enzymes in the liver cell in different situations. Images Fig. 1 Fig. 2 Fig. 3 PMID:173382

  20. Comparison Between a Rapid Biological Screening Method (EPA 4425) for TCDDs/TCDFs and Chemical Analytical Methods

    SciTech Connect

    Anderson, Jack W.; Jones, Jennifer M.; McCoy, Daniel L.; Fujita, Akira; Yamamoto, Taichi; Iijima, Satoshi

    2003-08-01

    Seven polychlorinated dibenzo-p-dioxins (PCDDs), ten polychlorinated dibenzofurans (PCDFs) as well as twelve polychlorinated biphenyls (PCBs) are collectively referred to as dioxin-like compounds. The World Health Organization toxic equivalency factors (TEFs) for these persistent chlorinated organic compounds and their measured concentrations are used to produce the toxic equivalency quotient (TEQ) of a sample. TEF values are partially based on a common mechanism involving binding of the chemical to the aryl hydrocarbon receptor (AhR). Biological methods for the determination of TEQs are based on the assumption that all dioxin-related compounds act through the Ah receptor signal transduction pathway. Based on the biochemical response of CYP1A activation via the AhR, in vitro systems that utilize a reporter gene under transcriptional control of CYP1A have been developed. Several investigations have reported on the success of utilizing biological test systems to detect PCDDs, PCDFs, PCBs in environmental samples. The P450 Human Reporter Gene System assay (EPA Method 4425) utilizes a human hepatoma cell line (HepG2) in which a plasmid containing the human CYP1A1 promoter and 5'-flanking sequences with three xenobiotic responsive elements (XREs) fused to the luciferase reporter gene. The enzyme luciferase is produced in the presence of compounds that bind the XREs, and can be detected by a simple assay that measures relative light units with a luminometer. Method 4425, used by Columbia Analytical Services (CAS), has gained acceptance as a rapid and inexpensive approach for screening solvent extracts of environmental samples of soil, sediment, tissue, and water to detect compounds that activate the AhR. Investigations in the U. S. and Japan comparing the results of 4425 and standard high-resolution GC/MS (HRGC/HRMS) will be reported here. The purpose of making these comparisons is to determine if risk assessments for large dioxin sites both before and after remediation

  1. Physico-chemical parameters and Ichthyofauna diversity of Arasalar estuary in southeast coast of India

    NASA Astrophysics Data System (ADS)

    Raju, C.; Sridharan, G.; Mariappan, P.; Chelladurai, G.

    2015-01-01

    The physico-chemical changes may have the tendency to accumulate in the various organs of estuarine organisms, especially fish which may in turn enter into the human metabolism through consumption causing serious hazards. Hence, the present study was carried out to dete rmine the physico-chemical characteristics of water and Ichthyofauna in Arasalar estuary in southeast coast of India for the period of 1 year during September 2012-August 2013. The environmental parameters such as, temperature, pH, salinity, DO, silicate, nitrate and phosphate were observed from Department of Zoology, Rajah Serfoji Goverment College, Thanjavur, Tamil Nadu, India. During the period of study, air temperature varied from 28.8 to 35 °C. The surface water temperature also varied from 25 to 31.5 °C. The monthly mean values of hydrogen ion concentration of water varied from 7.1 to 8.2. The salinity of water varied from 5.5 ‰ to 34. Dissolved oxygen in Arasalar estuary was varied from 3.5 to 7.2 mg/l. The total phosphorus varied from 0.29 to 2.15 µg/1. The nitrate varied from 0.47 to 3.75 µg/l. The silicate content varied from 28.25 to 98.74 µg/l. Totally 866 fishes were collected belonging to 4 orders and 5 families. Mystus gulio was found to be the dominant species (25.40 %) in the study area.

  2. Analytical Evaluation of Bit Error Rate Performance of a Free-Space Optical Communication System with Receive Diversity Impaired by Pointing Error

    NASA Astrophysics Data System (ADS)

    Nazrul Islam, A. K. M.; Majumder, S. P.

    2015-06-01

    Analysis is carried out to evaluate the conditional bit error rate conditioned on a given value of pointing error for a Free Space Optical (FSO) link with multiple receivers using Equal Gain Combining (EGC). The probability density function (pdf) of output signal to noise ratio (SNR) is also derived in presence of pointing error with EGC. The average BER of a SISO and SIMO FSO links are analytically evaluated by averaging the conditional BER over the pdf of the output SNR. The BER performance results are evaluated for several values of pointing jitter parameters and number of IM/DD receivers. The results show that, the FSO system suffers significant power penalty due to pointing error and can be reduced by increasing in the number of receivers at a given value of pointing error. The improvement of receiver sensitivity over SISO is about 4 dB and 9 dB when the number of photodetector is 2 and 4 at a BER of 10-10. It is also noticed that, system with receive diversity can tolerate higher value of pointing error at a given BER and transmit power.

  3. Successions and diversity of humic-reducing microorganisms and their association with physical-chemical parameters during composting.

    PubMed

    Xi, Beidou; Zhao, Xinyu; He, Xiaosong; Huang, Caihong; Tan, Wenbing; Gao, Rutai; Zhang, Hui; Li, Dan

    2016-11-01

    Humic-reducing microorganisms (HRMs) could utilize humic substances (HS) as terminal electron mediator to promote the biodegradation of recalcitrant pollutants. However, the dynamics of HRMs during composting has not been explored. Here, high throughput sequencing technology was applied to investigate the patterns of HRMs during three composting systems. A total of 30 main genera of HRMs were identified in three composts, with Proteobacteria being the largest phylum. HRMs were detected with increased diversity and abundance and distinct patterns during composting, which were significantly associated with dissolved organic carbon, dissolved organic nitrogen and germination index. Regulating key physical-chemical parameters is a process control of HRMs community composition, thus promoting the redox capability of the compost. The redox capability of HRMs were strengthened during composting, suggesting that HRMs of the compost may play an important role on pollutant degradation of the compost or when they are applied to the contaminated soils. PMID:27494101

  4. Strawberry flavor: diverse chemical compositions, a seasonal influence, and effects on sensory perception.

    PubMed

    Schwieterman, Michael L; Colquhoun, Thomas A; Jaworski, Elizabeth A; Bartoshuk, Linda M; Gilbert, Jessica L; Tieman, Denise M; Odabasi, Asli Z; Moskowitz, Howard R; Folta, Kevin M; Klee, Harry J; Sims, Charles A; Whitaker, Vance M; Clark, David G

    2014-01-01

    Fresh strawberries (Fragaria x ananassa) are valued for their characteristic red color, juicy texture, distinct aroma, and sweet fruity flavor. In this study, genetic and environmentally induced variation is exploited to capture biochemically diverse strawberry fruit for metabolite profiling and consumer rating. Analyses identify fruit attributes influencing hedonics and sensory perception of strawberry fruit using a psychophysics approach. Sweetness intensity, flavor intensity, and texture liking are dependent on sugar concentrations, specific volatile compounds, and fruit firmness, respectively. Overall liking is most greatly influenced by sweetness and strawberry flavor intensity, which are undermined by environmental pressures that reduce sucrose and total volatile content. The volatile profiles among commercial strawberry varieties are complex and distinct, but a list of perceptually impactful compounds from the larger mixture is better defined. Particular esters, terpenes, and furans have the most significant fits to strawberry flavor intensity. In total, thirty-one volatile compounds are found to be significantly correlated to strawberry flavor intensity, only one of them negatively. Further analysis identifies individual volatile compounds that have an enhancing effect on perceived sweetness intensity of fruit independent of sugar content. These findings allow for consumer influence in the breeding of more desirable fruits and vegetables. Also, this approach garners insights into fruit metabolomics, flavor chemistry, and a paradigm for enhancing liking of natural or processed products. PMID:24523895

  5. Actinomycetes from Red Sea Sponges: Sources for Chemical and Phylogenetic Diversity

    PubMed Central

    Abdelmohsen, Usama Ramadan; Yang, Chen; Horn, Hannes; Hajjar, Dina; Ravasi, Timothy; Hentschel, Ute

    2014-01-01

    The diversity of actinomycetes associated with marine sponges collected off Fsar Reef (Saudi Arabia) was investigated in the present study. Forty-seven actinomycetes were cultivated and phylogenetically identified based on 16S rRNA gene sequencing and were assigned to 10 different actinomycete genera. Eight putatively novel species belonging to genera Kocuria, Mycobacterium, Nocardia, and Rhodococcus were identified based on sequence similarity values below 98.2% to other 16S rRNA gene sequences available in the NCBI database. PCR-based screening for biosynthetic genes including type I and type II polyketide synthases (PKS-I, PKS-II) as well as nonribosomal peptide synthetases (NRPS) showed that 20 actinomycete isolates encoded each at least one type of biosynthetic gene. The organic extracts of nine isolates displayed bioactivity against at least one of the test pathogens, which were Gram-positive and Gram-negative bacteria, fungi, human parasites, as well as in a West Nile Virus protease enzymatic assay. These results emphasize that marine sponges are a prolific resource for novel bioactive actinomycetes with potential for drug discovery. PMID:24824024

  6. Chemical and morphological diversity in wild populations of Mentha longifolia in Israel.

    PubMed

    Segev, Daniel; Nitzan, Nadav; Chaimovitsh, David; Eshel, Amram; Dudai, Nativ

    2012-03-01

    Populations of Mentha longifolia, an endangered species in Israel, were tested for essential oil composition and conservational ability. In 2002-2003, 25 wild populations country-wide were tested, indicating population divergence into two chemotypes. Chemotype A was characterized by high levels of menthone and pulegone, and chemotype B by high levels of piperitenone oxide and piperitone oxide. Chemotype A was more abundant (22 of 25 populations) than chemotype B (11 of 25 populations). However, a chemotype/population interaction was not recorded (P > 0.05). In spring 2003, seven of the 25 wild populations were resampled, propagated, and cultivated at the Newe Ya'ar campus. Then, in 2004, the propagated plants were tested for essential oil composition. The propagated plants maintained the essential oil composition as well as the chemotype-frequency distribution of the original wild population from which they were obtained. Since a chemotype/population interaction was not recorded, and the cultivated plants displayed the wild population essential oil composition, it can be concluded that i) the chemotype diversity is genetically based, and ii) the M. longifolia populations sampled can be horticulturally conserved. PMID:22422525

  7. Studies on bio-chemical profiling of Indian gooseberry (Emblica officinalis) for genetic diversity.

    PubMed

    Pandey, G; Pandey, D; Tripathi, Mritynjay; Singh, Achal; Mishra, Maneesh

    2016-03-01

    Biochemical profiling of physiologically mature fruits of 51 diverse Indian gooseberry (Emblica officinalis Gaertn) germplasm accessions was collected from Vindhyan hill region of Madhya Pradesh, with a view to select nutraceutically rich genotypes based on important biochemical traits. The mean ascorbic acid and total phenol (tannin) content amongst different accessions was recorded as 496.47 mg 100 g⁻¹ and 4.88% with highest value found in CISH A-12 (654.50 mg 100 g⁻¹) and CISH A-30 (7.18%), respectively. Apart from the above, wide range of variability in the composition of other important biochemical attributes viz., total soluble solids (8.60-17.70°Brix), acidity (1.61-2.94%), total sugar (4.15-9.17), reducing sugar (2.19-4.45%) and TSS/acid ratio (3.89-8.33) was also recorded. Highest significant and positive correlation was observed between total sugar and TSS (0.895) followed by reducing sugar and TSS (0.882). Significant positive correlation between ascorbic acid and tannins (0.551) was an indication to be associated with binding capacity of ascorbic acid over a longer period of storage. PMID:27097435

  8. Chemical diversity in the essential oil of Indian valerian (Valeriana jatamansi Jones).

    PubMed

    Verma, Ram S; Verma, Rajesh K; Padalia, Rajendra C; Chauhan, Amit; Singh, Anand; Singh, Hemendra P

    2011-10-01

    To explore the diversity in the essential oil yield and composition of Valeriana jatamansi Jones (syn. V. wallichii DC) growing wild in Uttarakhand (Western Himalaya), 17 populations were collected from different locations and grown under similar conditions. Comparative results showed considerable variations in the essential oil yield and composition. The essential oil yield varied from 0.21 to 0.46% in the fresh roots and rhizomes of different populations of V. jatamansi. Analysis of the essential oils by GC (RI) and GC/MS and the subsequent classification by principal component analysis (PCA) resulted in six clusters with significant variations in their terpenoid composition. Major components in the essential oils of the different populations were patchouli alcohol (1; 13.4-66.7%), α-bulnesene (3; <0.05-23.5%), α-guaiene (4; 0.2-13.3%), guaiol (5; <0.05-12.2%), seychellene (6; 0.2-9.9%) viridiflorol (<0.05-7.3%), and β-gurjunene (7; 0.0-7.1%). V. jatamansi populations with contents of 1 higher than 60% may be utilized commercially in perfumery. PMID:22006721

  9. The Chemical Diversity of Lantana camara: Analyses of Essential Oil Samples from Cuba, Nepal, and Yemen.

    PubMed

    Satyal, Prabodh; Crouch, Rebecca A; Monzote, Lianet; Cos, Paul; Awadh Ali, Nasser A; Alhaj, Mehdi A; Setzer, William N

    2016-03-01

    The aerial parts of Lantana camara L. were collected from three different geographical locations: Artemisa (Cuba), Biratnagar (Nepal), and Sana'a (Yemen). The essential oils were obtained by hydrodistillation and analyzed by gas chromatography/mass spectrometry. A cluster analysis of 39 L. camara essential oil compositions revealed eight major chemotypes: β-caryophyllene, germacrene D, ar-curcumene/zingiberene, γ-curcumen-15-al/epi-β-bisabolol, (E)-nerolidol, davanone, eugenol/alloaromadendrene, and carvone. The sample from Cuba falls into the group dominated by (E)-nerolidol, the sample from Nepal is a davanone chemotype, and the sample from Yemen belongs to the β-caryophyllene chemotype. The chemical composition of L. camara oil plays a role in the biological activity; the β-caryophyllene and (E)-nerolidol chemotypes showed antimicrobial and cytotoxic activities. PMID:26917060

  10. Chemical diversity of Ziziphora clinopodioides: composition of the essential oil of Z. clinopodioides from Tajikistan.

    PubMed

    Sharopov, Farukh S; Setzer, William N

    2011-05-01

    The chemical composition of the essential oils of Ziziphora clinopodioides Lam. from the aerial flowering parts, collected during two different years, were obtained by hydrodistillation and analyzed by gas chromatography - mass spectrometry. Forty-five components representing 100% and 94.7% of the total oil were identified. The main constituents of the essential oils were pulegone (72.8 and 35.0%), neomenthol (6.5 and 23.1%), menthone (6.2 and 13.3%), p-menth-3-en-8-ol (1.7 and 3.5%), piperitenone (2.6 and 1.1%) and piperitone (0.7 and 1.2%). A cluster analysis was carried out on the essential oil compositions of Z. clinopodioides. PMID:21615034

  11. Phytoplankton communities of polar regions--Diversity depending on environmental conditions and chemical anthropopressure.

    PubMed

    Kosek, Klaudia; Polkowska, Żaneta; Żyszka, Beata; Lipok, Jacek

    2016-04-15

    The polar regions (Arctic and Antarctic) constitute up to 14% of the biosphere and offer some of the coldest and most arid Earth's environments. Nevertheless several oxygenic phototrophs including some higher plants, mosses, lichens, various algal groups and cyanobacteria, survive that harsh climate and create the base of the trophic relationships in fragile ecosystems of polar environments. Ecosystems in polar regions are characterized by low primary productivity and slow growth rates, therefore they are more vulnerable to disturbance, than those in temperate regions. From this reason, chemical contaminants influencing the growth of photoautotrophic producers might induce serious disorders in the integrity of polar ecosystems. However, for a long time these areas were believed to be free of chemical contamination, and relatively protected from widespread anthropogenic pressure, due their remoteness and extreme climate conditions. Nowadays, there is a growing amount of data that prove that xenobiotics are transported thousands of kilometers by the air and ocean currents and then they are deposed in colder regions and accumulate in many environments, including the habitats of marine and freshwater cyanobacteria. Cyanobacteria (blue green algae), as a natural part of phytoplankton assemblages, are globally distributed, but in high polar ecosystems they represent the dominant primary producers. These microorganisms are continuously exposed to various concentration levels of the compounds that are present in their habitats and act as nourishment or the factors influencing the growth and development of cyanobacteria in other way. The most common group of contaminants in Arctic and Antarctic are persistent organic pollutants (POPs), characterized by durability and resistance to degradation. It is important to determine their concentrations in all phytoplankton species cells and in their environment to get to know the possibility of contaminants to transfer to higher

  12. Chemical and genetic diversity of Zataria multiflora Boiss. accessions growing wild in Iran.

    PubMed

    Hadian, Javad; Ebrahimi, Samad Nejad; Mirjalili, Mohammad Hossein; Azizi, Ali; Ranjbar, Hamid; Friedt, Wolfgang

    2011-01-01

    Zataria multiflora Boiss. is an aromatic shrub belonging to the Lamiaceae family. Its aerial parts are used in the traditional medicine and in the pharmaceutical and food industries. The terpenoid and genetic profiles of 18 accessions of Z. multiflora, collected in different locations in Iran, have been analyzed by GC/FID and GC/MS or by AFLP (amplified fragment length polymorphism) analyses, respectively. Altogether, 56 compounds were identified in the essential oils, with the major constituents being thymol (6.0-54.9%), carvacrol (0.7-50.6%), linalool (1.2-46.8%), and p-cymene (1.6-14.8%). On the basis of the essential-oil composition, the 18 accessions were divided into four groups. The first group was characterized by a high content of carvacrol, thymol, and linalool, the second group was dominated by carvacrol, thymol, and p-cymene, the third group was characterized by a high concentration of thymol and a low content of carvacrol and p-cymene, and the forth group contained linalool and carvacrol as the main components. The AFLP results revealed that the average genetic similarity (GS) between the accessions was 0.61, ranging from 0.40 to 0.77. The UPGMA (unweighted pair-group method with arithmetic mean) cluster analysis divided all accessions into five groups at a similarity level of 0.60. The two clusters generated, the first based on the essential-oil compositions and the second on the AFLP data, showed a different pattern of relationships among the accessions. The knowledge of the Z. multiflora chemotype diversity, illustrated in this study, will allow an improvement of the homogeneity of the plant material for the production of different types of essential oils, depending on the demands of the pharmaceutical and food industries for specific uses. PMID:21259428

  13. Diversity of Ammonia-Oxidizing Archaea and Bacteria Across Physical-Chemical Gradients in San Francisco Bay Estuary Sediments

    NASA Astrophysics Data System (ADS)

    Mosier, A. C.; Francis, C. A.

    2006-12-01

    A combination of recent metagenomic analyses and the cultivation of a novel, ammonia-oxidizing, marine crenarchaeota revealed the first evidence for nitrification within the Archaeal domain. Further genetic and metagenomic studies demonstrated the presence of ammonia-oxidizing crenarchaea in diverse marine and terrestrial environments. These discoveries challenge the currently accepted view of the global nitrogen cycle and validate the need for further research on microbial diversity and function. In particular, it is imperative to reexamine the microbial communities involved in ammonia oxidation in marine and estuarine sediments, where this process plays a pivotal role in the cycling and removal of nitrogen. Using phylogenetic analyses of ammonia monooxygenase subunit A (amoA) gene sequences, we examined the distribution and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in San Francisco Bay, the largest estuary on the West coast of the United States. The highly impacted bay, encompassing nearly 178,000 km2, effectively connects two estuaries with varying physical-chemical characteristics to the Pacific Ocean. We recovered archaeal and bacterial amoA genes from 11 sites distributed throughout the bay, spanning the northern and southern estuaries and the central region where they connect to the ocean. Richness estimates varied considerably across all sites examined, with archaeal amoA estimates being generally higher than bacterial amoA. Several of the bacterial amoA libraries were represented by fewer than 3 genotypes. Archaeal amoA sequences were phylogenetically diverse and grouped within previously described sediment and soil/sediment clusters. Several sequences were closely related to the only cultivated AOA, Nitrosopumilus maritimus. Both the archaeal and bacterial amoA sequences showed significant regional specificity. Distinct populations exist in the northern and southern estuaries and sequences from the northernmost and southernmost sites

  14. Analytical Chemistry in Industry.

    ERIC Educational Resources Information Center

    Kaiser, Mary A.; Ullman, Alan H.

    1988-01-01

    Clarifies the roles of a practicing analytical chemist in industry: quality control, methods and technique development, troubleshooting, research, and chemical analysis. Lists criteria for success in industry. (ML)

  15. Chemical Diversity along the Traverse of the Rover Spirit at Gusev Crater

    NASA Technical Reports Server (NTRS)

    Gellert, R.; Brueckner, J.; Clark, B. C.; Dreibus, G.; d'Uston, C.; Economou, T.; Klingelhoefer, G.; Lugmair, G.; Ming, D. W.; Morris, R. V.; Rieder, R.; Squyres, S. W.; Wanke, H.; Yen, A.; Zipfel, J.

    2006-01-01

    The Alpha-Particle-X-ray Spectrometer (APXS) is part of the in situ payload of the Mars Exploration Rovers. It has determined the chemical composition of soils and rocks along the nearly 6 km long traverse of the rover Spirit. The measuring method a combination of PIXE and XRF using Cm244 sources - allowed the unambiguous identification of elemental compositions with high precision. Besides sample triage and quantification of saltforming elements as indicators for aqueous alteration, the APXS also delivered important constraints to mineralogy intruments (i.e., Mossbauer (MB), MiniTES, Pancam) on minerals and rock types. The mineralogy instruments on the other hand provided constraints on minerals used for APXS normative calculations and, e.g. allowed the attribution of S to sulfate, instead of sulfide or elemental sulfur. This abstract gives an updated overview of the data obtained up to our current rover position on sol 720 at the eastern base of the Columbia Hills. We will emphasize elemental correlations that imply the presence of certain minerals that can not be identified by the MER mineralogy instruments.

  16. Site-Specific Variability in the Chemical Diversity of the Antarctic Red Alga Plocamium cartilagineum

    PubMed Central

    Young, Ryan M.; von Salm, Jacqueline L.; Amsler, Margaret O.; Lopez-Bautista, Juan; Amsler, Charles D.; McClintock, James B.; Baker, Bill J.

    2013-01-01

    Plocamium cartilagineum is a common red alga on the benthos of Antarctica and can be a dominant understory species along the western Antarctic Peninsula. Algae from this region have been studied chemically, and like “P. cartilagineum” from other worldwide locations where it is common, it is rich in halogenated monoterpenes, some of which have been implicated as feeding deterrents toward sympatric algal predators. Secondary metabolites are highly variable in this alga, both qualitatively and quantitatively, leading us to probe individual plants to track the possible link of variability to genetic or other factors. Using cox1 and rbcL gene sequencing, we find that the Antarctic alga divides into two closely related phylogroups, but not species, each of which is further divided into one of five chemogroups. The chemogroups themselves, defined on the basis of Bray-Curtis similarity profiling of GC/QqQ chromatographic analyses, are largely site specific within a 10 km2 area. Thus, on the limited geographical range of this analysis, P. cartilagineum displays only modest genetic radiation, but its secondary metabolome was found to have experienced more extensive radiation. Such metabogenomic divergence demonstrated on the larger geographical scale of the Antarctic Peninsula, or perhaps even continent-wide, may contribute to the discovery of cryptic speciation. PMID:23771046

  17. Long-term effect on some chemical parameter and microbial diversity in a conifer forest soil

    NASA Astrophysics Data System (ADS)

    Iglesias, T.; Iglesias, M.; Francisco-Álvarez, R.; Ramírez, M.; Fernández-Bermejo, M. C.

    2009-04-01

    Soil microbiota are one of the soil components most affected by wildfires. The data from the present study were obtained from a conifer forest soil at Sierra de Gredos (Ávila, central Spain) twenty years after fire of low-to-moderate intensity. A set of soil characteristics indicated the extent to which the spontaneous recovery of the soil is produced as a result of vegetation regrowth. Ten months after fire a strong increase in soil pH, organic C and N, and exchangeable Ca and K, with respect the control soil. Eighteen years after this fire it was observed a decrease of soil organic C and N, whereas other variables such as pH, exchangeable Ca and K were slightly increased with respect to control soil. Is summe a change in soil microbiota was observed due to wildfire, with a decrease in fungi and bacteria population, Also some changes in microbial community was detected, Key words: Forest Fire, soil microbiology, chemical soil properties

  18. Chemical Diversity and Defence Metabolism: How Plants Cope with Pathogens and Ozone Pollution

    PubMed Central

    Iriti, Marcello; Faoro, Franco

    2009-01-01

    Chemical defences represent a main trait of the plant innate immune system. Besides regulating the relationship between plants and their ecosystems, phytochemicals are involved both in resistance against pathogens and in tolerance towards abiotic stresses, such as atmospheric pollution. Plant defence metabolites arise from the main secondary metabolic routes, the phenylpropanoid, the isoprenoid and the alkaloid pathways. In plants, antibiotic compounds can be both preformed (phytoanticipins) and inducible (phytoalexins), the former including saponins, cyanogenic glycosides and glucosinolates. Chronic exposure to tropospheric ozone (O3) stimulates the carbon fluxes from the primary to the secondary metabolic pathways to a great extent, inducing a shift of the available resources in favour of the synthesis of secondary products. In some cases, the plant defence responses against pathogens and environmental pollutants may overlap, leading to the unspecific synthesis of similar molecules, such as phenylpropanoids. Exposure to ozone can also modify the pattern of biogenic volatile organic compounds (BVOC), emitted from plant in response to herbivore feeding, thus altering the tritrophic interaction among plant, phytophagy and their natural enemies. Finally, the synthesis of ethylene and polyamines can be regulated by ozone at level of S-adenosylmethionine (SAM), the biosynthetic precursor of both classes of hormones, which can, therefore, mutually inhibit their own biosynthesis with consequence on plant phenotype. PMID:20111684

  19. Impacts of chemical modification on the toxicity of diverse nanocellulose materials to developing zebrafish

    PubMed Central

    Harper, Bryan J.; Clendaniel, Alicea; Sinche, Federico; Way, Daniel; Hughes, Michael; Schardt, Jenna; Simonsen, John; Stefaniak, Aleksandr B.

    2016-01-01

    Cellulose is an abundant and renewable resource currently being investigated for utility in nanomaterial form for various promising applications ranging from medical and pharmaceutical uses to mechanical reinforcement and biofuels. The utility of nanocellulose and wide implementation ensures increasing exposure to humans and the environment as nanocellulose-based technologies advance. Here, we investigate how differences in aspect ratio and changes to surface chemistry, as well as synthesis methods, influence the biocompatibility of nanocellulose materials using the embryonic zebrafish. Investigations into the toxicity of neutral, cationic and anionic surface functionalities revealed that surface chemistry had a minimal influence on the overall toxicity of nanocellulose materials. Higher aspect ratio cellulose nanofibers produced by mechanical homogenization were, in some cases, more toxic than other cellulose-based nanofibers or nanocrystals produced by chemical synthesis methods. Using fluorescently labeled nanocellulose we were able to show that nanocellulose uptake did occur in embryonic zebrafish during development. We conclude that the benign nature of nanocellulose materials makes them an ideal platform to systematically investigate the inherent surface features driving nanomaterial toxicity in order to create safer design principles for engineered nanoparticles. PMID:27468180

  20. Structural Plasticity of Malaria Dihydroorotate Dehydrogenase Allows Selective Binding of Diverse Chemical Scaffolds

    SciTech Connect

    Deng, Xiaoyi; Gujjar, Ramesh; El Mazouni, Farah; Kaminsky, Werner; Malmquist, Nicholas A.; Goldsmith, Elizabeth J.; Rathod, Pradipsinh K.; Phillips, Margaret A.

    2010-01-20

    Malaria remains a major global health burden and current drug therapies are compromised by resistance. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) was validated as a new drug target through the identification of potent and selective triazolopyrimidine-based DHODH inhibitors with anti-malarial activity in vivo. Here we report x-ray structure determination of PfDHODH bound to three inhibitors from this series, representing the first of the enzyme bound to malaria specific inhibitors. We demonstrate that conformational flexibility results in an unexpected binding mode identifying a new hydrophobic pocket on the enzyme. Importantly this plasticity allows PfDHODH to bind inhibitors from different chemical classes and to accommodate inhibitor modifications during lead optimization, increasing the value of PfDHODH as a drug target. A second discovery, based on small molecule crystallography, is that the triazolopyrimidines populate a resonance form that promotes charge separation. These intrinsic dipoles allow formation of energetically favorable H-bond interactions with the enzyme. The importance of delocalization to binding affinity was supported by site-directed mutagenesis and the demonstration that triazolopyrimidine analogs that lack this intrinsic dipole are inactive. Finally, the PfDHODH-triazolopyrimidine bound structures provide considerable new insight into species-selective inhibitor binding in this enzyme family. Together, these studies will directly impact efforts to exploit PfDHODH for the development of anti-malarial chemotherapy.

  1. Site-specific variability in the chemical diversity of the Antarctic red alga Plocamium cartilagineum.

    PubMed

    Young, Ryan M; von Salm, Jacqueline L; Amsler, Margaret O; Lopez-Bautista, Juan; Amsler, Charles D; McClintock, James B; Baker, Bill J

    2013-06-01

    Plocamium cartilagineum is a common red alga on the benthos of Antarctica and can be a dominant understory species along the western Antarctic Peninsula. Algae from this region have been studied chemically, and like "P. cartilagineum" from other worldwide locations where it is common, it is rich in halogenated monoterpenes, some of which have been implicated as feeding deterrents toward sympatric algal predators. Secondary metabolites are highly variable in this alga, both qualitatively and quantitatively, leading us to probe individual plants to track the possible link of variability to genetic or other factors. Using cox1 and rbcL gene sequencing, we find that the Antarctic alga divides into two closely related phylogroups, but not species, each of which is further divided into one of five chemogroups. The chemogroups themselves, defined on the basis of Bray-Curtis similarity profiling of GC/QqQ chromatographic analyses, are largely site specific within a 10 km² area. Thus, on the limited geographical range of this analysis, P. cartilagineum displays only modest genetic radiation, but its secondary metabolome was found to have experienced more extensive radiation. Such metabogenomic divergence demonstrated on the larger geographical scale of the Antarctic Peninsula, or perhaps even continent-wide, may contribute to the discovery of cryptic speciation. PMID:23771046

  2. Chemical Composition and Disruption of Quorum Sensing Signaling in Geographically Diverse United States Propolis

    PubMed Central

    Savka, Michael A.; Dailey, Lucas; Popova, Milena; Mihaylova, Ralitsa; Merritt, Benjamin; Masek, Marissa; Le, Phuong; Nor, Sharifah Radziah Mat; Ahmad, Muhammad; Hudson, André O.; Bankova, Vassya

    2015-01-01

    Propolis or bee glue has been used for centuries for various purposes and is especially important in human health due to many of its biological and pharmacological properties. In this work we showed quorum sensing inhibitory (QSI) activity of ten geographically distinct propolis samples from the United States using the acyl-homoserine lactone- (AHL-) dependent Chromobacterium violaceum strain CV026. Based on GC-MS chemical profiling the propolis samples can be classified into several groups that are as follows: (1) rich in cinnamic acid derivatives, (2) rich in flavonoids, and (3) rich in triterpenes. An in-depth analysis of the propolis from North Carolina led to the isolation and identification of a triterpenic acid that was recently isolated from Hondurian propolis (Central America) and ethyl ether of p-coumaric alcohol not previously identified in bee propolis. QSI activity was also observed in the second group US propolis samples which contained the flavonoid pinocembrin in addition to other flavonoid compounds. The discovery of compounds that are involved in QSI activity has the potential to facilitate studies that may lead to the development of antivirulence therapies that can be complementary and/or alternative treatments against antibiotic resistant bacterial pathogens and/or emerging pathogens that have yet to be identified. PMID:25960752

  3. An Analytical Framework for Studying Small-Number Effects in Catalytic Reaction Networks: A Probability Generating Function Approach to Chemical Master Equations

    PubMed Central

    Nakagawa, Masaki; Togashi, Yuichi

    2016-01-01

    Cell activities primarily depend on chemical reactions, especially those mediated by enzymes, and this has led to these activities being modeled as catalytic reaction networks. Although deterministic ordinary differential equations of concentrations (rate equations) have been widely used for modeling purposes in the field of systems biology, it has been pointed out that these catalytic reaction networks may behave in a way that is qualitatively different from such deterministic representation when the number of molecules for certain chemical species in the system is small. Apart from this, representing these phenomena by simple binary (on/off) systems that omit the quantities would also not be feasible. As recent experiments have revealed the existence of rare chemical species in cells, the importance of being able to model potential small-number phenomena is being recognized. However, most preceding studies were based on numerical simulations, and theoretical frameworks to analyze these phenomena have not been sufficiently developed. Motivated by the small-number issue, this work aimed to develop an analytical framework for the chemical master equation describing the distributional behavior of catalytic reaction networks. For simplicity, we considered networks consisting of two-body catalytic reactions. We used the probability generating function method to obtain the steady-state solutions of the chemical master equation without specifying the parameters. We obtained the time evolution equations of the first- and second-order moments of concentrations, and the steady-state analytical solution of the chemical master equation under certain conditions. These results led to the rank conservation law, the connecting state to the winner-takes-all state, and analysis of 2-molecules M-species systems. A possible interpretation of the theoretical conclusion for actual biochemical pathways is also discussed. PMID:27047384

  4. An Analytical Framework for Studying Small-Number Effects in Catalytic Reaction Networks: A Probability Generating Function Approach to Chemical Master Equations.

    PubMed

    Nakagawa, Masaki; Togashi, Yuichi

    2016-01-01

    Cell activities primarily depend on chemical reactions, especially those mediated by enzymes, and this has led to these activities being modeled as catalytic reaction networks. Although deterministic ordinary differential equations of concentrations (rate equations) have been widely used for modeling purposes in the field of systems biology, it has been pointed out that these catalytic reaction networks may behave in a way that is qualitatively different from such deterministic representation when the number of molecules for certain chemical species in the system is small. Apart from this, representing these phenomena by simple binary (on/off) systems that omit the quantities would also not be feasible. As recent experiments have revealed the existence of rare chemical species in cells, the importance of being able to model potential small-number phenomena is being recognized. However, most preceding studies were based on numerical simulations, and theoretical frameworks to analyze these phenomena have not been sufficiently developed. Motivated by the small-number issue, this work aimed to develop an analytical framework for the chemical master equation describing the distributional behavior of catalytic reaction networks. For simplicity, we considered networks consisting of two-body catalytic reactions. We used the probability generating function method to obtain the steady-state solutions of the chemical master equation without specifying the parameters. We obtained the time evolution equations of the first- and second-order moments of concentrations, and the steady-state analytical solution of the chemical master equation under certain conditions. These results led to the rank conservation law, the connecting state to the winner-takes-all state, and analysis of 2-molecules M-species systems. A possible interpretation of the theoretical conclusion for actual biochemical pathways is also discussed. PMID:27047384

  5. The role of autocatalysis on the chemical diversity of the prebiotic ocean of early Earth

    NASA Astrophysics Data System (ADS)

    Canepa, Carlo

    2016-01-01

    The spontaneous formation of catalytic polypeptides of various lengths in a primordial ocean endowed with a source of amino acids from micrometeorites was investigated and found to be sufficient to induce the transformation of potential substrates under the assumption of a high propensity of the environment to catalyse the formation of the peptide bond. This work aims to include in this picture the effect of autocatalysis, i.e. the ability of a polypeptide with a specific length to promote the formation of the peptide bond. Once the formation of an autocatalytic species is attained, the concentrations of the polypeptides, substrates and products of reaction exhibit a time-dependent rate of formation and undergo a catastrophic change. While in the absence of autocatalysis the concentrations of polypeptides are stationary and the formation of reaction products is limited by the proper frequency λ, autocatalysis induces a steady growth of the concentrations of polypeptides and a 100 - 105-fold increase of reaction products at t = ω-1<0.46 Gyr, with a subsequent linear growth in time according to the law u/z 0 = 1+s(ω-1+t)/z 0, provided the autocatalytic species be active with length fewer than 70 amino acid units. A relationship was found between the catalytic ability of the environment (expressed by the ratio η/ηh of the rate coefficient for peptide bond formation to the corresponding rate coefficient for hydrolysis) and the time of the sharp increase of the concentration of both the polypeptides and their products of transformation. Although the formation of autocatalytic polypeptides is able to rapidly induce a sharp increase in the concentration of both polypeptides and their products of transformation, the crucial formation of the first autocatalytic polypeptides relies on the ability of the environment to promote the formation of the peptide bond. The value of the ratio η/ηh, constrained by the available time for chemical evolution to values bordering the

  6. DEVELOPMENT AND VALIDATION OF ANALYTICAL METHODS FOR ENUMERATION OF FECAL INDICATORS AND EMERGING CHEMICAL CONTAMINANTS IN BIOSOLIDS

    EPA Science Inventory

    In 2002 the National Research Council (NRC) issued a report which identified a number of issues regarding biosolids land application practices and pointed out the need for improved and validated analytical techniques for regulated indicator organisms and pathogens. They also call...

  7. ANALYTICAL METHODS FOR A NATIONAL STUDY OF CHEMICAL RESIDUES IN FISH - I: POLYCHLORINATED DIBENZO-P-DIOXINS/DIBENZOFURANS

    EPA Science Inventory

    Analytical Methods were developed to determine the concentration of PCDD/PCDF in fish tissue for a national survey conducted by EPA. he method was designed to achieve a relatively low cost per sample while maintaining adequate quality control. t utilizes a Soxhlet extraction, aci...

  8. Analysis on Soil Seed Bank Diversity Characteristics and Its Relation with Soil Physical and Chemical Properties after Substrate Addition

    PubMed Central

    He, Mengxuan; Lv, Lingyue; Li, Hongyuan; Meng, Weiqing; Zhao, Na

    2016-01-01

    Aims Considered as an essential measure in the application of soil seed bank (SSB) projects, the mixing of substrate and surface soil can effectively improve soil condition. This research is aimed at exploring the diversity characteristics of SSBs and the relationships between SSBs and soil properties. Methods Canonical correspondence analysis (CCA) was adopted to describe the ordination of SSBs on soil properties’ gradients; multiple linear regressions were adopted to analyze the relationship between average growth height and soil properties, density and soil properties. Results Experimental groups of mixed substrate (the mixture of organic and inorganic substrates) had high diversity indexes, especially the Shannon-Wiener Index compared with those of single substrate. Meanwhile, a higher number of species and increased density were also noted in those of mixed substrate. The best test group, No.16, had the highest diversity indexes with a Shannon-Wiener of 1.898, Simpson of 0.633 and Pielou of 0.717, and also showed the highest density of 14000 germinants /m2 and 21 species. In addition, an improvement of the soil’s chemical and physical properties was noted when the substrates were mixed. The mixed substrate of turfy soil and perlite could effectively enhance the soil moisture content, whilst a mixed substrate of rice husk carbon and vermiculite could improve the content of available potassium (AK) and phosphorus (AP) and strengthen soil fertility. The germinated plants also reflected obvious regularities of ordination on soil factor gradients. Three distinct cluster groups were presented, of which the first cluster was distributed in an area with a relatively higher content of AK and AP; the second cluster was distributed at places with relatively higher soil moisture content; and the third cluster of plants didn’t show any obvious relationship with soil physical and chemical properties. Through CCA analysis, AK and AP were considered the most important

  9. Ability of structurally diverse natural products and synthetic chemicals to induce gene expression mediated by estrogen receptors from various species.

    PubMed

    Matthews, J B; Fertuck, K C; Celius, T; Huang, Y-W; Fong, C J; Zacharewski, T R

    2002-10-01

    The ability of 14 structurally diverse estrogenic compounds to induce reporter gene expression mediated by estrogen receptors (ERs) from different species was examined. MCF-7 cells were transiently transfected with a Gal4-regulated luciferase reporter gene (17m5-G-Luc) and Gal4-ER chimeric receptors containing the D, E and F domains of the human alpha (Gal4-hERalphadef), mouse alpha (Gal4-mERalphadef), mouse beta (Gal4-mERbetadef), chicken (Gal4-cERalphadef), green anole (Gal4-aERalphadef), Xenopus (Gal4-xERdef) or rainbow trout alpha ERs (Gal4-rtERalphadef). The efficacy of 17beta-estradiol (E2) in inducing reporter gene expression was similar among the different constructs overall, with EC(50) values ranging from 0.05 to 0.7nM. However, Gal4-rtERalphadef had an EC(50) value at 37 degrees C of 28nM, though at 20 degrees C an EC(50) value of 1nM was observed. Despite a similar response to E2 treatment among the ERs, many differences were observed in the magnitude of the response to other structurally diverse chemicals. For example, coumestrol induced Gal4-mERbetadef- and Gal4-aERdef-mediated reporter gene expression 164- and 8-fold greater, respectively, than mediated with the other Gal4-ERs. As well, in contrast to results with other Gal4-ERs, alpha-zearalenol consistently induced Gal4-rtERalphadef-mediated reporter gene activity at lower concentrations than did E2. Overall, the results demonstrate that selected estrogenic compounds exhibit a differential ability to induce reporter gene activity mediated by ERs from different vertebrate species. These data also highlight the importance of incubation temperature when examining rtERalpha-mediated activity. PMID:12477484

  10. Diverse Chemical Zoning Trends in Acapulco Chromites: How Many Sources for the Parental Materials?

    NASA Astrophysics Data System (ADS)

    El Goresy, A.; Janicke, J.

    1995-09-01

    Acapulco is considered to be a link between primitive chondritic meteorites and the differentiated achondrites. Its parent body presumably formed by accretion of material of chondritic compositions at an fO2 that lies between that of H- and enstatite chondrites [1]. The accreted chondritic material was subjected 4.557 Gyr ago to peak temperatures close to 1200 degrees C that lead to partial melting and extensive recrystallization [1, 2]. Seven morphologically different types of graphite with large variations in C- and N-isotopic compositions were recently reported from Acapulco [3, 4]. At least four distinct isotopic reservoirs are required to explain the C- and N-isotopic compositions of these graphites [3, 4]. While the silicate minerals in Acapulco have isotopically heavy N (delta^(15)N = + 15 per mil) chromites were found to be isotopically light (delta^(15)N = _ 75 to _ 82 per mil). Chromite occurs in Acapulco in six different assemblages: (1) as inclusions in silicates, (2) in FeNi, (3) in troilite, (4) with FeNi and troilite, (5) with FeNi and silicates, and (6) with troilite and silicates. It is also rarely present as small idiomorphic inclusions in plagioclase. Chromites in contact with silicates display no chemical zoning for Cr, Al, Ti, Fe, Mg, Mn, or Zn to the silicate borders thus indicating high degree of equilibration with the silicate neighbours. The MgO-contents of chromites in metals and troilites (4.74 to 7.2 %) are relatively lower and their compositional ranges are relatively wider than those in contact with silicates (6.1 to 7.69 %). Zoning profiles of MgO and FeO in chromites in all assemblages are quite flat. Chromites in contact with metals and troilite display a variety of zoning patterns of Cr, Al, Ti, and Zn. All these chromite types , however, depict the same MnO zoning trends with low MnO-contents in their cores (0.96 to 2.14 %) than in their rims to metal or troilite (1.7 to 3.1 %). With few exceptions, the zoning behaviour of Cr, Al

  11. [Book review] Epiphytic Lichen Diversity and its Dependence on Chemical Site Factors in Differently Elevated Dieback-affected Spruce Stands of the Harz Mountains, by Volker Hesse

    USGS Publications Warehouse

    Bennett, J.P.

    2002-01-01

    Review of: Epiphytic lichen diversity and its dependence on chemical site factors in differently elevated dieback-affected spruce stands of the Harz Mountains. (Dissertationes Botanicae, Band 354). Volker Hesse. 2002. 191 pages, 66 figures, 49 tables, 23x14cm, 390 g. ISBN 978-3-443-64266-2.

  12. Integrated sensing platform and method for improved quantitative and selective monitoring of chemical analytes in both liquid and gas phase

    DOEpatents

    Blair, Dianna S.; Frye-Mason, Gregory C.; Butler, Michael A.

    2000-01-01

    By measuring two or more physical parameters of a thin sensing film which are altered when exposed to chemicals, more effective discrimination between chemicals can be achieved. In using more than one sensor, the sensors are preferably integrated on the same substrate so that they may measure the same thin film. Even more preferably, the sensors are provided orthogonal to one another so that they may measure the same portion of the thin film. These provisions reduce problems in discrimination arising from variations in thin films.

  13. Analysis of soil samples for chemical warfare agents: Canadian contribution to a multinational round-robin analytical exercise. Memorandum report

    SciTech Connect

    D'Agostino, P.A.; Provost, L.R.; Sawyer, T.W.; Weiss, M.T.

    1990-04-01

    VX and two VX related compounds, diethyl methylphosphonate and bis(2-(diisopropylamino)ethyl) disulfide, were confirmed at the 2 to 40 micrograms/gram level as the principal components in three of four soil samples distributed by Finland as part of a multinational round robin exercise designed to evaluate laboratory methodologies. Several other compounds related to VX, were also identified in extracts of the soil samples. Keywords: Gas chromatography, Canada, Soil samples, Diethyl methylphosphonate, Mass spectrometry, Bis(2-(diisopropylamino)ethyl) disulfide, Bioassay, Defence research establishment suffield(dres), VX, Military chemical agents, International relations, Neuron, Tissue culture, Chemical agent detection.

  14. International organization for standardization (ISO) 9000 and chemical agent standard analytical reference material (SASARM) quality system development and implementation. Phase 1. Final report, April 1993-June 1994

    SciTech Connect

    Turley, S.D.

    1994-09-01

    U.S. Army Dugway Proving Ground (DPG) is in the process of developing an International Organization for Standardization (ISO) 9000 quality assurance (QA) system and a Chemical Agent Standard Analytical Reference Material (CASARM) QA program. Phase I of this process consisted of analyzing the current DPG QA system, defining the structure of the new QA system, determine how the ISO 9000 and the CASARM systems will interact, develop the new QA system and implementation plan, and develop the CASARM program and begin implementation. The initial phases of the system design and synthesis met the objectives established for Phase I of this methodology project. Phase II will complete the functional analysis, system design, and prototype implementation. The prototype will be analyzed for weaknesses in operation, personnel and equipment requirements, software, and cost effectiveness. The system will be modified, if needed, and implemented across the Materiel Test Directorate. The final stage of this methodology will be to achieve ISO 9000 registration. International Organization for Standardization(ISO) 9000, Chemical Agent Standard Analytical Reference Material(CASARM), Standardized Quality Assurance(QA), QA/Quality Control(QC).

  15. 3-Naphthoylindazoles and 2-naphthoylbenzoimidazoles as novel chemical groups of synthetic cannabinoids: chemical structure elucidation, analytical characteristics and identification of the first representatives in smoke mixtures.

    PubMed

    Shevyrin, Vadim; Melkozerov, Vladimir; Nevero, Alexander; Eltsov, Oleg; Morzherin, Yuri; Shafran, Yuri

    2014-09-01

    By means of gas chromatography with mass spectrometry detection (GC-MS), including high resolution mass spectrometry (GC-HRMS) together with ultra-high performance liquid chromatography in combination with high resolution tandem mass spectrometry (UHPLC-HRMS), nuclear magnetic resonance spectroscopy (NMR) and Fourier transform infrared spectroscopy (FT-IR), structure of novel synthetic cannabinoids, namely, 1-(5-fluoropentyl)-1H-indazol-3-yl(naphthalen-1-yl)methanone, naphthalen-1-yl(1-pentyl-1H-benzo[d]imidazol-2-yl)methanone and 1-(5-fluoropentyl)-1H-benzo[d]imidazol-2-yl(naphthalen-1-yl)methanone was established. Analytical data obtained in the paper enable reliable identification of these compounds during qualitative analysis of seizures, including smoke mixtures. PMID:25036783

  16. Automation of the γ-ray spectroscopy counting system at the Dow Chemical Company Analytical Sciences Laboratory

    NASA Astrophysics Data System (ADS)

    Romick, J. D.; Rigot, W. L.; Morabito, P. L.; Quinn, T. J.; Kocher, C. W.; Duke, D. J.

    1994-12-01

    The neutron activation analysis group within the Analytical Sciences Laboratory analyzes 3000-5000 samples annually for a wide variety of analytes. Due to the high sample load, it is imperative that the gamma spectroscopy counting system be automated to maximize the efficiency of the system while ensuring the accuracy of the analyses. Using a Zymark robotic system, Compumotor drives, and DEC-based Canberra/Nuclear Data software we have automated sample changing, detector positioning, and data acquisition. Automation of these functions has resulted in a more consistent counting geometry, minimized crosstalk between samples, and accurate repositioning of the detectors for standardless quantitative analysis. The Zymark robotic system currently controls two detector systems, but is designed to control up to three independent detector systems. Canberra/Nuclear Data software, operating on a Microvax 3100, issues commands to the Zymark controller to change samples when spectral acquisition is complete. Once a new sample is in place, the robot sends a signal to the Microvax to begin data acquisition. Up to 40 samples, with sizes between 1 and 20 ml, can be accommodated using customized sample racks and sample holders. The location of the sample racks relative to the detectors has eliminated noticeable crosstalk between samples in the racks and samples being counted. The two HPGe detectors for each detector system sit on motorized platforms controlled by programmable Compumotor drives. Programmed function keys move the detectors in or out at fixed increments to optimize sample/detector geometry. The high resolution of the stepper motors enables accurate repositioning of detectors so that previously acquired standard spectra can be compared with samples activated and counted under identical conditions but at different times.

  17. Ab initio quantum chemical investigation of arsenic sulfide molecular diversity from As4S6 and As4

    NASA Astrophysics Data System (ADS)

    Kyono, Atsushi

    2013-10-01

    The structural diversity of arsenic sulfide molecules in compositions between As4S6 and As4 was investigated using ab initio quantum chemical calculations. The As4S6 molecule consists of four trigonal pyramid coordinations of As atoms bonding to three S atoms. In the As4S5 composition, only one type of molecular configuration corresponds to an uzonite-type molecule. In the As4S4 composition, two molecular configurations exist with realgar-type and pararealgar-type molecules. Three molecular configurations are in the As4S3 composition. The first configuration comprises trigonal pyramidal As atom coordinations of two types: bonding to two S atoms and one As atom, and bonding to one S atom and two As atoms. The second is the molecular configuration of dimorphite. The third comprises trigonal pyramidal As atom coordinations of two types: bonding to three As atoms, and bonding to one As atom and two S atoms. The As4S2 composition allows molecular configurations of two types. One is comprised of trigonal pyramidal As atom configurations of one type bonding to two As atoms and one S atom. The other comprises trigonal pyramidal As atom coordinations of three types: bonding to two S atoms and one As atoms, bonding to one S atom and two As atoms, and bonding to three As atoms. The As4S molecule has trigonal pyramidal As atom coordinations of two types: bonding to one S atom and two As atoms, and bonding to three As atoms. The As4S composition permits only one molecular configuration, which suggests that the mineral duranusite comprises the As4S molecular geometry. In all, ten molecular configurations are predicted in the molecular hierarchy of the arsenic sulfide binary system. The simulated Raman spectral profiles are helpful in searching for undiscovered arsenic sulfide minerals.

  18. Elemental mapping of Neuromelanin organelles of human Substantia Nigra: correlative ultrastructural and chemical analysis by analytical transmission electron microscopy and nano-secondary ion mass spectrometry.

    PubMed

    Biesemeier, Antje; Eibl, Oliver; Eswara, Santhana; Audinot, Jean-Nicolas; Wirtz, Tom; Pezzoli, Gianni; Zucca, Fabio A; Zecca, Luigi; Schraermeyer, Ulrich

    2016-07-01

    Neuromelanin (NM) is a compound which highly accumulates mainly in catecholamine neurons of the substantia nigra (SN), and is contained in organelles (NM-containing organelles) with lipid bodies and proteins. These neurons selectively degenerate in Parkinson's disease and NM can play either a protective or toxic role. NM-containing organelles of SN were investigated by Analytical Electron Microscopy (AEM) and Nano-Secondary Ion Mass Spectrometry (NanoSIMS) within human tissue sections with respect to ultrastructure and elemental composition. Within the NM-containing organelle, the single NM granules and lipid bodies had sizes of about 200-600 nm. Energy-Dispersive X-ray microanalysis spectra of the NM granules and lipid bodies were acquired with 100 nm beam diameter in AEM, NanoSIMS yielded elemental maps with a lateral resolution of about 150 nm. AEM yielded the quantitative elemental composition of NM granules and bound metals, e.g., iron with a mole fraction of about 0.15 atomic percent. Chemical analyses by AEM and NanoSIMS were consistent at the subcellular level so that nanoSIMS measurements have been quantitated. In NM granules of SN from healthy subjects, a significant amount of S, Fe, and Cu was found. In lipid bodies an amount of P consistent with the presence of phospholipids was measured. The improved detection limits of nanoSIMS offer new possibilities for chemical mapping, high-sensitivity trace element detection, and reduced acquisition times. Variations between individual NM granules can now be investigated effectively and quantitatively by NanoSIMS mapping Cu and Fe. This should yield new insight into the changes in chemical composition of NM pigments during healthy aging and disease. Neuromelanin-containing organelles of dopamine neurons in normal human substantia nigra were investigated by analytical electron mircoscopy and secondary ion mass spectroscopy (NanoSIMS) yielding the ultrastructure and elemental composition. In neuromelanin

  19. Development of preparative and analytical methods of the hop bitter acid oxide fraction and chemical properties of its components.

    PubMed

    Taniguchi, Yoshimasa; Matsukura, Yasuko; Taniguchi, Harumi; Koizumi, Hideki; Katayama, Mikio

    2015-01-01

    The bitter acids in hops (Humulus lupulus L.) and beer, such as α-, β-, and iso-α-acids, are known to affect beer quality and display various physiological effects. However, these compounds readily oxidize, and the effect of the oxides on the properties of beer or their potential health benefits are not well understood. In this study, we developed a simple preparative method for the bitter acid oxide fraction derived from hops and designated the constituents as matured hop bitter acids (MHBA). HPLC-PDA-ESI/HRMS and MS(2) revealed that MHBA are primarily composed of α-acid-derived oxides, which possess a common β-tricarbonyl moiety in their structures similar to α-, β-, and iso-α-acids. We also developed a quantitative analytical method of whole MHBA by HPLC, which showed high precision and reproducibility. Using our newly developed method, the concentration of whole MHBA in several commercial beers was evaluated. Our results will promote the study of bitter acid oxides. PMID:25996959

  20. Analytical study of endocrine-disrupting chemicals in leachate treatment process of municipal solid waste (MSW) landfill sites.

    PubMed

    Asakura, Hiroshi; Matsuto, Toshihiko; Tanaka, Nobutoshi

    2007-01-01

    Influent and processed water were sampled at different points in the leachate treatment facilities of five municipal solid waste (MSW) landfill sites. Then, the concentrations of endocrine-disrupting chemicals (EDCs), namely, alkylphenols (APs), bisphenol A (BPA), phthalic acid esters (PAEs) and organotin compounds (OTs), in the treated leachate samples were determined and the behavior of the EDCs in the treatment processes was discussed. The concentrations of APs were as low as those in surface waters, and no OTs were detected (detection limit: 0.01 microg/L). Meanwhile, diethylhexyl phthalate (DEHP), which was the most abundant of the four substances measured as PAEs, and BPA were found in all of the influent samples. BPA was considerably degraded by aeration, except when the water temperature was low and the total organic carbon (TOC) was high. By contrast, aeration, biological treatment, and coagulation/sedimentation removed only a small amount of DEHP. PMID:17585294

  1. The Influence of Intense Chemical Pollution on the Community Composition, Diversity and Abundance of Anammox Bacteria in the Jiaojiang Estuary (China)

    PubMed Central

    Hu, Baolan; Shen, Lidong; Du, Ping; Zheng, Ping; Xu, Xiangyang; Zeng, Jiangning

    2012-01-01

    Continuous chemical pollution is one of the most serious environmental problems in the Jiaojiang Estuary of the East Sea (China). This chemical pollution has significantly changed the estuarine environmental conditions and may have profoundly influenced the distribution of anammox bacterial communities in this estuary. Here, we investigated the influence of chemical pollution on the community composition, diversity and abundance of anammox bacteria in Jiaojiang estuarine sediments. Phylogenetic analysis of 16S rRNA genes showed that the majority of anammox bacterial sequences retrieved from the estuarine intertidal sediments were associated with Kuenenia. In contrast, different anammox communities composed of Brocadia, Kuenenia, Scalindua and Jettenia were found in the estuarine subtidal sediments. Redundancy analysis (RDA) indicated that the sediment nitrobenzene and organic content had significant impacts on the distribution of anammox communities in the intertidal sediments. Pearson correlation analysis showed that the diversity of anammox bacteria in the intertidal sediments was positively correlated with the organic content. In contrast, RDA results showed that the nitrobenzene content, NO3− concentration and salinity significantly influenced the distribution of anammox communities in the subtidal sediments. The diversity and relative abundance of anammox bacteria in the subtidal sediments were positively correlated with NO3− concentration. PMID:22470481

  2. Fine Particle Sources and Cardiorespiratory Morbidity: An Application of Chemical Mass Balance and Factor Analytical Source-Apportionment Methods

    PubMed Central

    Sarnat, Jeremy A.; Marmur, Amit; Klein, Mitchel; Kim, Eugene; Russell, Armistead G.; Sarnat, Stefanie E.; Mulholland, James A.; Hopke, Philip K.; Tolbert, Paige E.

    2008-01-01

    Background Interest in the health effects of particulate matter (PM) has focused on identifying sources of PM, including biomass burning, power plants, and gasoline and diesel emissions that may be associated with adverse health risks. Few epidemiologic studies, however, have included source-apportionment estimates in their examinations of PM health effects. We analyzed a time-series of chemically speciated PM measurements in Atlanta, Georgia, and conducted an epidemiologic analysis using data from three distinct source-apportionment methods. Objective The key objective of this analysis was to compare epidemiologic findings generated using both factor analysis and mass balance source-apportionment methods. Methods We analyzed data collected between November 1998 and December 2002 using positive-matrix factorization (PMF), modified chemical mass balance (CMB-LGO), and a tracer approach. Emergency department (ED) visits for a combined cardiovascular (CVD) and respiratory disease (RD) group were assessed as end points. We estimated the risk ratio (RR) associated with same day PM concentrations using Poisson generalized linear models. Results There were significant, positive associations between same-day PM2.5 (PM with aero-dynamic diameter ≤ 2.5 μm) concentrations attributed to mobile sources (RR range, 1.018–1.025) and biomass combustion, primarily prescribed forest burning and residential wood combustion, (RR range, 1.024–1.033) source categories and CVD-related ED visits. Associations between the source categories and RD visits were not significant for all models except sulfate-rich secondary PM2.5 (RR range, 1.012–1.020). Generally, the epidemiologic results were robust to the selection of source-apportionment method, with strong agreement between the RR estimates from the PMF and CMB-LGO models, as well as with results from models using single-species tracers as surrogates of the source-apportioned PM2.5 values. Conclusions Despite differences among the

  3. A new six-dimensional analytical potential up to chemically significant energies for the electronic ground state of hydrogen peroxide

    NASA Astrophysics Data System (ADS)

    Kuhn, Bernd; Rizzo, Thomas R.; Luckhaus, David; Quack, Martin; Suhm, Martin A.

    1999-08-01

    We report calculations of the electronic ground state potential energy surface (PES) of hydrogen peroxide covering, in an almost global fashion, all six internal degrees of freedom by two different ab initio techniques. Density functional theory (DFT) calculations using the Becke 3 parameter Lee-Yang-Parr (B3LYP) hybrid functional and multiconfigurational second order perturbation theory (CASPT2) calculations, both using large basis sets, are performed for a wide range of geometries (8145 DFT and 5310 CASPT2 single-point energies). We use a combined data set of mostly DFT with additional CASPT2 ab initio points and the complete CASPT2 surface to fit a total of four different 6D analytical representations. The resulting potentials contain 70-76 freely adjusted parameters and represent the ground state PES up to 40000 cm-1 above the equilibrium energy with a standard deviation of 100-107 cm-1 without any important artifacts. One of the model surfaces is further empirically refined to match the bond dissociation energy D0 for HOOH→2OH . The potentials are designed for energy regions accessible by vibrational fundamental and overtone spectroscopy including the dissociation channel into hydroxyl radicals. Characteristic properties of the model surfaces are investigated by means of stationary point analyses, torsional barrier heights, harmonic frequencies, low-dimensional cuts and minimum energy paths for dissociation. Overall good agreement with high-level ab initio calculations, especially for the CASPT2 based potentials, is achieved. The drastic change in geometry at intermediate O-O distances, which reflects the transition from covalent to hydrogen bonding, is reproduced quantitatively. We calculate fully 6D anharmonic zero point energies and ground state torsional splittings with the diffusion quantum Monte Carlo method in perfect agreement, within statistical error bars, with experiment for the CASPT2 based potentials. Variational vibrational calculations in the

  4. Analytical chemical kinetic investigation of the effects of oxygen, hydrogen, and hydroxyl radicals on hydrogen-air combustion

    NASA Technical Reports Server (NTRS)

    Carson, G. T., Jr.

    1974-01-01

    Quantitative values were computed which show the effects of the presence of small amounts of oxygen, hydrogen, and hydroxyl radicals on the finite-rate chemical kinetics of premixed hydrogen-air mixtures undergoing isobaric autoignition and combustion. The free radicals were considered to be initially present in hydrogen-air mixtures at equivalence ratios of 0.2, 0.6, 1.0, and 1.2. Initial mixture temperatures were 1100 K, 1200 K, and 1500 K, and pressures were 0.5, 1.0, 2.0, and 4.0 atm. Of the radicals investigated, atomic oxygen was found to be the most effective for reducing induction time, defined as the time to 5 percent of the total combustion temperature rise. The reaction time, the time between 5 percent and 95 percent of the temperature rise, is not decreased by the presence of free radicals in the initial hydrogen-air mixture. Fuel additives which yield free radicals might be used to effect a compact supersonic combustor design for efficient operation in an otherwise reaction-limited combustion regime.

  5. Green Chemistry Metrics with Special Reference to Green Analytical Chemistry.

    PubMed

    Tobiszewski, Marek; Marć, Mariusz; Gałuszka, Agnieszka; Namieśnik, Jacek

    2015-01-01

    The concept of green chemistry is widely recognized in chemical laboratories. To properly measure an environmental impact of chemical processes, dedicated assessment tools are required. This paper summarizes the current state of knowledge in the field of development of green chemistry and green analytical chemistry metrics. The diverse methods used for evaluation of the greenness of organic synthesis, such as eco-footprint, E-Factor, EATOS, and Eco-Scale are described. Both the well-established and recently developed green analytical chemistry metrics, including NEMI labeling and analytical Eco-scale, are presented. Additionally, this paper focuses on the possibility of the use of multivariate statistics in evaluation of environmental impact of analytical procedures. All the above metrics are compared and discussed in terms of their advantages and disadvantages. The current needs and future perspectives in green chemistry metrics are also discussed. PMID:26076112

  6. Localization and chemical forms of cadmium in plant samples by combining analytical electron microscopy and X-ray spectromicroscopy

    NASA Astrophysics Data System (ADS)

    Isaure, Marie-Pierre; Fayard, Barbara; Sarret, Géraldine; Pairis, Sébastien; Bourguignon, Jacques

    2006-12-01

    Cadmium (Cd) is a metal of high toxicity for plants. Resolving its distribution and speciation in plants is essential for understanding the mechanisms involved in Cd tolerance, trafficking and accumulation. The model plant Arabidopsis thaliana was exposed to cadmium under controlled conditions. Elemental distributions in the roots and in the leaves were determined using scanning electron microscopy coupled with energy dispersive X-ray microanalysis (SEM-EDX), and synchrotron-based micro X-ray fluorescence (μ-XRF), which offers a better sensitivity. The chemical form(s) of cadmium was investigated using Cd L III-edge (3538 eV) micro X-ray absorption near edge structure (μ-XANES) spectroscopy. Plant μ-XANES spectra were fitted by linear combination of Cd reference spectra. Biological sample preparation and conditioning is a critical point because of possible artifacts. In this work we compared freeze-dried samples analyzed at ambient temperature and frozen hydrated samples analyzed at -170 °C. Our results suggest that in the roots Cd is localized in vascular bundles, and coordinated to S ligands. In the leaves, trichomes (epidermal hairs) represent the main compartment of Cd accumulation. In these specialized cells, μ-XANES results show that the majority of Cd is bound to O/N ligands likely provided by the cell wall, and a minor fraction could be bound to S-containing ligands. No significant difference in Cd speciation was observed between freeze-dried and frozen hydrated samples. This work illustrates the interest and the sensitivity of Cd L III-edge XANES spectroscopy, which is applied here for the first time to plant samples. Combining μ-XRF and Cd L III-edge μ-XANES spectroscopy offers promising tools to study Cd storage and trafficking mechanisms in plants and other biological samples.

  7. Process analytical technology: non-destructive assessment of anastrozole entrapment within PLGA microparticles by near infrared spectroscopy and chemical imaging.

    PubMed

    Zidan, A S; Sammour, O A; Hammad, M A; Megrab, N A; Habib, M J; Khan, M A

    2008-05-01

    The objective of this study was to evaluate near-infrared (NIR) spectroscopy and imaging as approaches to assess anastrozole entrapment within PLGA microparticles. By varying the polymer concentration, three batches containing the same amount of the drug were prepared. The spectral features that allow NIR drug quantitation were evaluated and compared with a best fit line algorithm. Actual entrapment efficiencies (EEF) determined via a destructive method were used for construction of calibration models using partial least square regression (PLS) or the algorithm. On the other hand, a chemical imaging system based on array detector technology was used to rapidly collect high contrast NIR images of the formulated microparticles. A quantitative measure of anastrozole entrapped was determined by calculating the percentage standard deviation of the distribution of pixel intensities in the PLS score images and histograms. Concerning conventional NIR analysis, both methods were equivalent for the prediction of EEF over the range of polymer levels studied. Correlation coefficients of more than 0.992 were obtained for either the calibration or prediction of EEF by the two methods; 0.392% and 0.374% were the standard errors of calibration and prediction (SEC and SEP) obtained for the prediction of EEF using the fit line, respectively, whereas the prediction of the EEF by the partial least square regression showed a SEC of 0.195% and SEP of 0.179%. As a result, the spectral best fit algorithm method compared favourably to the multivariate PLS method, but was easier to develop. In contrast, NIR spectral imaging was capable of clearly differentiating the three batches, both qualitatively and quantitatively. The percentage standard deviation increased progressively by increasing the ratio of drug-to-polymer concentrations. In conclusion, both NIR approaches were capable of accurate assessment of drug entrapment within microparticles. In addition, the NIR spectral imaging system

  8. DEVELOPMENT OF ANALYTICAL METHODS FOR THE QUANTIFICATION OF THE CHEMICAL FORMS OF MERCURY AND OTHER TARGET POLLUTANTS IN COAL-FIRED BOILER FLUE GAS

    SciTech Connect

    Terence J. McManus, Ph.D.

    1999-06-30

    . (ATS) as a secondary DOE contractor on this project, assessed the sampling and analytical plans and the emission reports of the five primary contractors to determine how successful the contractors were in satisfying their defined objectives. ATS identified difficulties and inconsistencies in a number of sampling and analytical methodologies in these studies. In particular there was uncertainty as to the validity of the sampling and analytical methods used to differentiate the chemical forms of mercury observed in coal flue gas. Considering the differences in the mercury species with regard to human toxicity, the rate of transport through the ecosystem and the design variations in possible emission control schemes, DOE sought an accurate and reliable means to identify and quantify the various mercury compounds emitted by coal-fired utility boilers. ATS, as a contractor for DOE, completed both bench- and pilot-scale studies on various mercury speciation methods. The final validation of the modified Ontario-Hydro Method, its acceptance by DOE and submission of the method for adoption by ASTM was a direct result of these studies carried out in collaboration with the University of North Dakota's Energy and Environmental Research Center (UNDEERC). This report presents the results from studies carried out at ATS in the development of analytical methods to identify and quantify various chemical species, particularly those of mercury, in coal derived flue gas. Laboratory- and pilot-scale studies, not only on mercury species, but also on other inorganics and organics present in coal combustion flue gas are reported.

  9. Process Analytical Chemistry.

    ERIC Educational Resources Information Center

    Callis, James B.; And Others

    1987-01-01

    Discusses process analytical chemistry as a discipline designed to supply quantitative and qualitative information about a chemical process. Encourages academic institutions to examine this field for employment opportunities for students. Describes the five areas of process analytical chemistry, including off-line, at-line, on-line, in-line, and…

  10. Validating Analytical Methods

    ERIC Educational Resources Information Center

    Ember, Lois R.

    1977-01-01

    The procedures utilized by the Association of Official Analytical Chemists (AOAC) to develop, evaluate, and validate analytical methods for the analysis of chemical pollutants are detailed. Methods validated by AOAC are used by the EPA and FDA in their enforcement programs and are granted preferential treatment by the courts. (BT)