Sample records for target chemical species

  1. Target organs in chronic bioassays of 533 chemical carcinogens

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gold, L.S.; Slone, T.H.; Manley, N.B.

    1991-06-01

    A compendium of carcinogenesis bioassay results organized by target organ is presented for 533 chemicals that are carcinogenic in at least one species. This compendium is based primarily on experiments in rats or mice; results in hamsters, nonhuman primates, and dogs are also reported. The compendium can be used to identify chemicals that induce tumors at particular sites, and to determine whether target sites are the same for chemicals positive in more than one species. The Carcinogenic Potency Database (CPDB), which includes results of 3969 experiments, is used in the analysis. The published CPDB includes details on each test, andmore » literature references. Chemical carcinogens are reported for 35 different target organs in rats or mice. More than 80% of the carcinogens in each of these species are positive in at least one of the 8 most frequent target sites; liver, lung, mammary gland, stomach, vascular system, kidney, hematopoietic system, and urinary bladder. An analysis is presented of how well one can predict the carcinogenic response in mice from results in rats, or vice versa. Among chemicals tested in both species, 76% of rat carcinogens are positive in mice, and 71% of mouse carcinogens are positive in rats. Prediction is less accurate to the same target site: 52% of rat carcinogens are positive in the same site in mice, and 48% of mouse carcinogens are positive in the same site in rats. The liver is the most frequent site in common between rats and mice.« less

  2. SeqAPASS: Predicting chemical susceptibility to threatened/endangered species

    EPA Science Inventory

    Conservation of a molecular target across species can be used as a line-of-evidence to predict the likelihood of chemical susceptibility. The web-based Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS; https://seqapass.epa.gov/seqapass/) application was devel...

  3. Laser-Beam-Absorption Chemical-Species Monitor

    NASA Technical Reports Server (NTRS)

    Gersh, Michael; Goldstein, Neil; Lee, Jamine; Bien, Fritz; Richtsmeier, Steven

    1996-01-01

    Apparatus measures concentration of chemical species in fluid medium (e.g., gaseous industrial process stream). Directs laser beam through medium, and measures intensity of beam after passage through medium. Relative amount of beam power absorbed in medium indicative of concentration of chemical species; laser wavelength chosen to be one at which species of interest absorbs.

  4. Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS): A web-based tool for addressing the challenges of cross-species extrapolation of chemical toxicity

    EPA Science Inventory

    Conservation of a molecular target across species can be used as a line-of-evidence to predict the likelihood of chemical susceptibility. The web-based Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed to simplify, streamline, and quantitat...

  5. Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease

    NASA Astrophysics Data System (ADS)

    Beck, Michael W.; Derrick, Jeffrey S.; Kerr, Richard A.; Oh, Shin Bi; Cho, Woo Jong; Lee, Shin Jung C.; Ji, Yonghwan; Han, Jiyeon; Tehrani, Zahra Aliakbar; Suh, Nayoung; Kim, Sujeong; Larsen, Scott D.; Kim, Kwang S.; Lee, Joo-Yong; Ruotolo, Brandon T.; Lim, Mi Hee

    2016-10-01

    The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal-Aβ, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs.

  6. Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease.

    PubMed

    Beck, Michael W; Derrick, Jeffrey S; Kerr, Richard A; Oh, Shin Bi; Cho, Woo Jong; Lee, Shin Jung C; Ji, Yonghwan; Han, Jiyeon; Tehrani, Zahra Aliakbar; Suh, Nayoung; Kim, Sujeong; Larsen, Scott D; Kim, Kwang S; Lee, Joo-Yong; Ruotolo, Brandon T; Lim, Mi Hee

    2016-10-13

    The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal-Aβ, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs.

  7. Model reduction for stochastic chemical systems with abundant species.

    PubMed

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-07

    Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. We first identify the rate constant limits under which the concentrations of a given set of species will tend to infinity (the abundant species) while the concentrations of all other species remains constant (the non-abundant species). Subsequently, we prove that, in this limit, the fluctuations in the molecule numbers of non-abundant species are accurately described by a hybrid stochastic description consisting of a chemical master equation coupled to deterministic rate equations. This is a reduced description when compared to the conventional chemical master equation which describes the fluctuations in both abundant and non-abundant species. We show that the reduced master equation can be solved exactly for a number of biochemical networks involving gene expression and enzyme catalysis, whose conventional chemical master equation description is analytically impenetrable. We use the linear noise approximation to obtain approximate expressions for the difference between the variance of fluctuations in the non-abundant species as predicted by the hybrid approach and by the conventional chemical master equation. Furthermore, we show that surprisingly, irrespective of any separation in the mean molecule numbers of various species, the conventional and hybrid master equations exactly agree for a class of chemical systems.

  8. Molecular target sequence similarity as a basis for species extrapolation to assess the ecological risk of chemicals with known modes of action

    EPA Science Inventory

    In practice, it is neither feasible nor ethical to conduct toxicity tests with all species that may be impacted by chemical exposures. Therefore, cross-species extrapolation is fundamental to human health and ecological risk assessment. The extensive chemical universe for which w...

  9. Model reduction for stochastic chemical systems with abundant species

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-07

    Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. We first identify the rate constant limits under which the concentrations of a given set of species will tend to infinity (the abundant species) while the concentrations of all other species remains constant (the non-abundant species). Subsequently, we prove that, in this limit, the fluctuations in the molecule numbers of non-abundant species are accurately described by a hybrid stochastic description consisting of a chemical master equation coupled to deterministic rate equations. This is a reduced description when compared to the conventional chemical master equationmore » which describes the fluctuations in both abundant and non-abundant species. We show that the reduced master equation can be solved exactly for a number of biochemical networks involving gene expression and enzyme catalysis, whose conventional chemical master equation description is analytically impenetrable. We use the linear noise approximation to obtain approximate expressions for the difference between the variance of fluctuations in the non-abundant species as predicted by the hybrid approach and by the conventional chemical master equation. Furthermore, we show that surprisingly, irrespective of any separation in the mean molecule numbers of various species, the conventional and hybrid master equations exactly agree for a class of chemical systems.« less

  10. Predictions of Chemical Species via Diode Laser Spectroscopy

    NASA Technical Reports Server (NTRS)

    Chen, Shin-Juh; Silver, Joel A.; Dahm, Werner J. A.; Piltch, Nancy D.; Salzman, Jack (Technical Monitor)

    2001-01-01

    A technique to predict temperature and chemical species in flames from absorbance measurement of one chemical species is presented. Predicted temperature and mole fractions of methane and water agreed well with measured and published results.

  11. Target sites for chemical regulation of strigolactone signaling

    PubMed Central

    Nakamura, Hidemitsu; Asami, Tadao

    2014-01-01

    Demands for plant growth regulators (PGRs; chemicals that control plant growth) are increasing globally, especially in developing countries. Both positive and negative PGRs are widely used to enhance crop production and to suppress unwanted shoot growth, respectively. Strigolactones (SLs) are multifunctional molecules that function as phytohormones, inhibiting shoot branching and also functioning in the rhizospheric communication with symbiotic fungi and parasitic weeds. Therefore, it is anticipated that chemicals that regulate the functions of SLs will be widely used in agricultural applications. Although the SL biosynthetic pathway is not fully understood, it has been demonstrated that β-carotene isomerases, carotenoid cleavage dioxygenases (CCDs), and a cytochrome P450 monooxygenase are involved in strigolactone biosynthesis. A CCD inhibitor, abamine, which is also an inhibitor of abscisic acid biosynthesis, reduces the levels of SL in several plant species and reduces the germination rate of Orobanche minor seeds grown with tobacco. On the basis of the structure of abamine, several chemicals have been designed to specifically inhibit CCDs during SL synthesis. Cytochrome P450 monooxygenase is another target enzyme in the development of SL biosynthesis inhibitors, and the triazole-derived TIS series of chemicals is known to include SL biosynthesis inhibitors, although their target enzyme has not been identified. Recently, DWARF14 (D14) has been shown to be a receptor for SLs, and the D-ring moiety of SL is essential for its recognition by D14. A variety of SL agonists are currently under development and most agonists commonly contain the D-ring or a D-ring-like moiety. Several research groups have also resolved the crystal structure of D14 in the last two years. It is expected that this information on the D14 structure will be invaluable not only for developing SL agonists with novel structures but also in the design of inhibitors of SL receptors. PMID:25414720

  12. Molecular Target Homology as a Basis for Species Extrapolation to Assess the Ecological Risk of Veterinary Drugs

    EPA Science Inventory

    Increased identification of veterinary pharmaceutical contaminants in aquatic environments has raised concerns regarding potential adverse effects of these chemicals on non-target organisms. The purpose of this work was to develop a method for predictive species extrapolation ut...

  13. Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens

    PubMed Central

    Lo, Yu-Chen; Senese, Silvia; Li, Chien-Ming; Hu, Qiyang; Huang, Yong; Damoiseaux, Robert; Torres, Jorge Z.

    2015-01-01

    Target identification is one of the most critical steps following cell-based phenotypic chemical screens aimed at identifying compounds with potential uses in cell biology and for developing novel disease therapies. Current in silico target identification methods, including chemical similarity database searches, are limited to single or sequential ligand analysis that have limited capabilities for accurate deconvolution of a large number of compounds with diverse chemical structures. Here, we present CSNAP (Chemical Similarity Network Analysis Pulldown), a new computational target identification method that utilizes chemical similarity networks for large-scale chemotype (consensus chemical pattern) recognition and drug target profiling. Our benchmark study showed that CSNAP can achieve an overall higher accuracy (>80%) of target prediction with respect to representative chemotypes in large (>200) compound sets, in comparison to the SEA approach (60–70%). Additionally, CSNAP is capable of integrating with biological knowledge-based databases (Uniprot, GO) and high-throughput biology platforms (proteomic, genetic, etc) for system-wise drug target validation. To demonstrate the utility of the CSNAP approach, we combined CSNAP's target prediction with experimental ligand evaluation to identify the major mitotic targets of hit compounds from a cell-based chemical screen and we highlight novel compounds targeting microtubules, an important cancer therapeutic target. The CSNAP method is freely available and can be accessed from the CSNAP web server (http://services.mbi.ucla.edu/CSNAP/). PMID:25826798

  14. Open access chemical probes for epigenetic targets

    PubMed Central

    Brown, Peter J; Müller, Susanne

    2015-01-01

    Background High attrition rates in drug discovery call for new approaches to improve target validation. Academia is filling gaps, but often lacks the experience and resources of the pharmaceutical industry resulting in poorly characterized tool compounds. Discussion The SGC has established an open access chemical probe consortium, currently encompassing ten pharmaceutical companies. One of its mandates is to create well-characterized inhibitors (chemical probes) for epigenetic targets to enable new biology and target validation for drug development. Conclusion Epigenetic probe compounds have proven to be very valuable and have not only spurred a plethora of novel biological findings, but also provided starting points for clinical trials. These probes have proven to be critical complementation to traditional genetic targeting strategies and provided sometimes surprising results. PMID:26397018

  15. Chemical Ecology of Chemosensation in Asteroidea: Insights Towards Management Strategies of Pest Species.

    PubMed

    Motti, Cherie A; Bose, Utpal; Roberts, Rebecca E; McDougall, Carmel; Smith, Meaghan K; Hall, Michael R; Cummins, Scott F

    2018-02-01

    Within the Phylum Echinodermata, the class Asteroidea, commonly known as starfish and sea stars, encompasses a large number of benthos inhabiting genera and species with various feeding modalities including herbivores, carnivores, omnivores and detritivores. The Asteroidea rely on chemosensation throughout their life histories including hunting prey, avoiding or deterring predators, in the formation of spawning aggregations, synchronizing gamete release and targeting appropriate locations for larval settlement. The identities of many of the chemical stimuli that mediate these physiological and behavioural processes remain unresolved even though evidence indicates they play pivotal roles in the functionality of benthic communities. Aspects of chemosensation, as well as putative chemically-mediated behaviours and the molecular mechanisms of chemoreception, within the Asteroidea are reviewed here, with particular reference to the coral reef pest the Crown-of-Thorns starfish Acanthaster planci species complex, in the context of mitigation of population outbreaks.

  16. Target Fishing for Chemical Compounds using Target-Ligand Activity data and Ranking based Methods

    PubMed Central

    Wale, Nikil; Karypis, George

    2009-01-01

    In recent years the development of computational techniques that identify all the likely targets for a given chemical compound, also termed as the problem of Target Fishing, has been an active area of research. Identification of likely targets of a chemical compound helps to understand problems such as toxicity, lack of efficacy in humans, and poor physical properties associated with that compound in the early stages of drug discovery. In this paper we present a set of techniques whose goal is to rank or prioritize targets in the context of a given chemical compound such that most targets that this compound may show activity against appear higher in the ranked list. These methods are based on our extensions to the SVM and Ranking Perceptron algorithms for this problem. Our extensive experimental study shows that the methods developed in this work outperform previous approaches by 2% to 60% under different evaluation criterions. PMID:19764745

  17. Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology

    PubMed Central

    Galdeano, Carles; Ciulli, Alessio

    2017-01-01

    Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity. PMID:27193077

  18. Malaria Elimination: Time to Target All Species.

    PubMed

    Lover, Andrew A; Baird, J Kevin; Gosling, Roly; Price, Ric

    2018-05-14

    Important strides have been made within the past decade toward malaria elimination in many regions, and with this progress, the feasibility of eradication is once again under discussion. If the ambitious goal of eradication is to be achieved by 2040, all species of Plasmodium infecting humans will need to be targeted with evidence-based and concerted interventions. In this perspective, the potential barriers to achieving global malaria elimination are discussed with respect to the related diversities in host, parasite, and vector populations. We argue that control strategies need to be reorientated from a sequential attack on each species, dominated by Plasmodium falciparum to one that targets all species in parallel. A set of research themes is proposed to mitigate the potential setbacks on the pathway to a malaria-free world.

  19. Chemical warfare agents. Classes and targets.

    PubMed

    Schwenk, Michael

    2018-09-01

    Synthetic toxic chemicals (toxicants) and biological poisons (toxins) have been developed as chemical warfare agents in the last century. At the time of their initial consideration as chemical weapon, only restricted knowledge existed about their mechanisms of action. There exist two different types of acute toxic action: nonspecific cytotoxic mechanisms with multiple chemo-biological interactions versus specific mechanisms that tend to have just a single or a few target biomolecules. TRPV1- and TRPA-receptors are often involved as chemosensors that induce neurogenic inflammation. The present work briefly surveys classes and toxicologically relevant features of chemical warfare agents and describes mechanisms of toxic action. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Cross-species malaria immunity induced by chemically attenuated parasites

    PubMed Central

    Good, Michael F.; Reiman, Jennifer M.; Rodriguez, I. Bibiana; Ito, Koichi; Yanow, Stephanie K.; El-Deeb, Ibrahim M.; Batzloff, Michael R.; Stanisic, Danielle I.; Engwerda, Christian; Spithill, Terry; Hoffman, Stephen L.; Lee, Moses; McPhun, Virginia

    2013-01-01

    Vaccine development for the blood stages of malaria has focused on the induction of antibodies to parasite surface antigens, most of which are highly polymorphic. An alternate strategy has evolved from observations that low-density infections can induce antibody-independent immunity to different strains. To test this strategy, we treated parasitized red blood cells from the rodent parasite Plasmodium chabaudi with seco-cyclopropyl pyrrolo indole analogs. These drugs irreversibly alkylate parasite DNA, blocking their ability to replicate. After administration in mice, DNA from the vaccine could be detected in the blood for over 110 days and a single vaccination induced profound immunity to different malaria parasite species. Immunity was mediated by CD4+ T cells and was dependent on the red blood cell membrane remaining intact. The human parasite, Plasmodium falciparum, could also be attenuated by treatment with seco-cyclopropyl pyrrolo indole analogs. These data demonstrate that vaccination with chemically attenuated parasites induces protective immunity and provide a compelling rationale for testing a blood-stage parasite-based vaccine targeting human Plasmodium species. PMID:23863622

  1. Chemically mediated species recognition in closely related Podarcis wall lizards.

    PubMed

    Barbosa, Diana; Font, Enrique; Desfilis, Ester; Carretero, Miguel A

    2006-07-01

    In many animals, chemical signals play an important role in species recognition and may contribute to reproductive isolation and speciation. The Iberian lizards of the genus Podarcis, with up to nine currently recognized lineages that are often sympatric, are highly chemosensory and provide an excellent model for the study of chemically mediated species recognition in closely related taxa. In this study, we tested the ability of male and female lizards of two sister species with widely overlapping distribution ranges (Podarcis bocagei and P. hispanica type 1) to discriminate between conspecific and heterospecific mates by using only substrate-borne chemical cues. We scored the number of tongue flicks directed at the paper substrate by each individual in a terrarium previously occupied by a conspecific or a heterospecific lizard of the opposite sex. Results show that males of P. bocagei and P. hispanica type 1 are capable of discriminating chemically between conspecifics and heterospecifics of the opposite sex, but females are not. These results suggest that differences in female, but not male, chemical cues may underlie species recognition and contribute to reproductive isolation in these species. The apparent inability of females to discriminate conspecific from heterospecific males, which is not because of reduced baseline exploration rates, is discussed in the context of sexual selection theory and species discrimination.

  2. Chemical Structural Novelty: On-Targets and Off-Targets

    PubMed Central

    Yera, Emmanuel R.; Cleves, Ann. E.; Jain, Ajay N.

    2011-01-01

    Drug structures may be quantitatively compared based on 2D topological structural considerations and based on 3D characteristics directly related to binding. A framework for combining multiple similarity computations is presented along with its systematic application to 358 drugs with overlapping pharmacology. Given a new molecule along with a set of molecules sharing some biological effect, a single score based on comparison to the known set is produced, reflecting either 2D similarity, 3D similarity, or their combination. For prediction of primary targets, the benefit of 3D over 2D was relatively small, but for prediction of off-targets, the added benefit was large. In addition to assessing prediction, the relationship between chemical similarity and pharmacological novelty was studied. Drug pairs that shared high 3D similarity but low 2D similarity (i.e. a novel scaffold) were shown to be much more likely to exhibit pharmacologically relevant differences in terms of specific protein target modulation. PMID:21916467

  3. Targeted predation of extrafloral nectaries by insects despite localized chemical defences

    PubMed Central

    Gish, Moshe; Mescher, Mark C.; De Moraes, Consuelo M.

    2015-01-01

    Extrafloral (EF) nectaries recruit carnivorous arthropods that protect plants from herbivory, but they can also be exploited by nectar thieves. We studied the opportunistic, targeted predation (and destruction) of EF nectaries by insects, and the localized chemical defences that plants presumably use to minimize this effect. In field and laboratory experiments, we identified insects that were possibly responsible for EF nectary predation in Vicia faba (fava bean) and determined the extent and accuracy of the feeding damage done to the EF nectaries by these insects. We also performed biochemical analyses of plant tissue samples in order to detect microscale distribution patterns of chemical defences in the area of the EF nectary. We observed selective, targeted feeding on EF nectaries by several insect species, including some that are otherwise not primarily herbivorous. Biochemical analyses revealed high concentrations of l-3,4-dihydroxyphenylalanine, a non-protein amino acid that is toxic to insects, near and within the EF nectaries. These results suggest that plants allocate defences to the protection of EF nectaries from predation, consistent with expectations of optimal defence theory, and that this may not be entirely effective, as insects limit their exposure to these defences by consuming only the secreting tissue of the nectary. PMID:26446809

  4. Progress in the Visualization and Mining of Chemical and Target Spaces.

    PubMed

    Medina-Franco, José L; Aguayo-Ortiz, Rodrigo

    2013-12-01

    Chemogenomics is a growing field that aims to integrate the chemical and target spaces. As part of a multi-disciplinary effort to achieve this goal, computational methods initially developed to visualize the chemical space of compound collections and mine single-target structure-activity relationships, are being adapted to visualize and mine complex relationships in chemogenomics data sets. Similarly, the growing evidence that clinical effects are many times due to the interaction of single or multiple drugs with multiple targets, is encouraging the development of novel methodologies that are integrated in multi-target drug discovery endeavors. Herein we review advances in the development and application of approaches to generate visual representations of chemical space with particular emphasis on methods that aim to explore and uncover relationships between chemical and target spaces. Also, progress in the data mining of the structure-activity relationships of sets of compounds screened across multiple targets are discussed in light of the concept of activity landscape modeling. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Targeting Conserved Genes in Fusarium Species.

    PubMed

    Gil-Serna, Jéssica; Patiño, Belén; Jurado, Miguel; Mirete, Salvador; Vázquez, Covadonga; González-Jaén, M Teresa

    2017-01-01

    Fumonisins are important mycotoxins contaminating foods and feeds which are mainly produced by F. verticillioides and F. proliferatum. Additionally, both are pathogens of maize and other cereals. We describe two highly sensitive, rapid, and species-specific PCR protocols which enable detection and discrimination of these closely related species in cereal flour or grain samples. The specific primer pairs of these assays were based on the intergenic spacer region of the multicopy rDNA unit which highly improves the sensitivity of the PCR assay in comparison with single-copy target regions.

  6. Nature and Analysis of Chemical Species.

    ERIC Educational Resources Information Center

    Shuman, Mark S.; Fogleman, Wavell W.

    1978-01-01

    Presents a literature review of the nature and analysis of chemical species in water, covering publications of 1976-77. This review is concerned with inorganics, and it covers: (1) electrochemical analysis; (2) spectroscopy; (3) neutron activation, radiochemical analysis, and isotope dilution. A list of 262 references is also presented. (HM)

  7. Mesophotic depths as refuge areas for fishery-targeted species on coral reefs

    NASA Astrophysics Data System (ADS)

    Lindfield, Steven J.; Harvey, Euan S.; Halford, Andrew R.; McIlwain, Jennifer L.

    2016-03-01

    Coral reefs are subjected to unprecedented levels of disturbance with population growth and climate change combining to reduce standing coral cover and stocks of reef fishes. Most of the damage is concentrated in shallow waters (<30 m deep) where humans can comfortably operate and where physical disturbances are most disruptive to marine organisms. Yet coral reefs can extend to depths exceeding 100 m, potentially offering refuge from the threats facing shallower reefs. We deployed baited remote underwater stereo-video systems (stereo-BRUVs) at depths of 10-90 m around the southern Mariana Islands to investigate whether fish species targeted by fishing in the shallows may be accruing benefits from being at depth. We show that biomass, abundance and species richness of fishery-targeted species increased from shallow reef areas to a depth of 60 m, whereas at greater depths, a lack of live coral habitat corresponded to lower numbers of fish. The majority of targeted species were found to have distributions that ranged from shallow depths (10 m) to depths of at least 70 m, emphasising that habitat, not depth, is the limiting factor in their vertical distribution. While the gradient of abundance and biomass versus depth was steepest for predatory species, the first species usually targeted by fishing, we also found that fishery-targeted herbivores prevailed in similar biomass and species richness to 60 m. Compared to shallow marine protected areas, there was clearly greater biomass of fishery-targeted species accrued in mesophotic depths. Particularly some species typically harvested by depth-limited fishing methods (e.g., spearfishing), such as the endangered humphead wrasse Cheilinus undulatus, were found in greater abundance on deeper reefs. We conclude that mesophotic depths provide essential fish habitat and refuge for fishery-targeted species, representing crucial zones for fishery management and research into the resilience of disturbed coral reef ecosystems.

  8. Chemical proteomics approaches for identifying the cellular targets of natural products

    PubMed Central

    Sieber, S. A.

    2016-01-01

    Covering: 2010 up to 2016 Deconvoluting the mode of action of natural products and drugs remains one of the biggest challenges in chemistry and biology today. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to understand protein function. In the context of natural products, chemical proteomics can be used to identify the protein binding partners or targets of small molecules in live cells. Here, we highlight recent examples of chemical probes based on natural products and their application for target identification. The review focuses on probes that can be covalently linked to their target proteins (either via intrinsic chemical reactivity or via the introduction of photocrosslinkers), and can be applied “in situ” – in living systems rather than cell lysates. We also focus here on strategies that employ a click reaction, the copper-catalysed azide–alkyne cycloaddition reaction (CuAAC), to allow minimal functionalisation of natural product scaffolds with an alkyne or azide tag. We also discuss ‘competitive mode’ approaches that screen for natural products that compete with a well-characterised chemical probe for binding to a particular set of protein targets. Fuelled by advances in mass spectrometry instrumentation and bioinformatics, many modern strategies are now embracing quantitative proteomics to help define the true interacting partners of probes, and we highlight the opportunities this rapidly evolving technology provides in chemical proteomics. Finally, some of the limitations and challenges of chemical proteomics approaches are discussed. PMID:27098809

  9. Chemical proteomics approaches for identifying the cellular targets of natural products.

    PubMed

    Wright, M H; Sieber, S A

    2016-05-04

    Covering: 2010 up to 2016Deconvoluting the mode of action of natural products and drugs remains one of the biggest challenges in chemistry and biology today. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to understand protein function. In the context of natural products, chemical proteomics can be used to identify the protein binding partners or targets of small molecules in live cells. Here, we highlight recent examples of chemical probes based on natural products and their application for target identification. The review focuses on probes that can be covalently linked to their target proteins (either via intrinsic chemical reactivity or via the introduction of photocrosslinkers), and can be applied "in situ" - in living systems rather than cell lysates. We also focus here on strategies that employ a click reaction, the copper-catalysed azide-alkyne cycloaddition reaction (CuAAC), to allow minimal functionalisation of natural product scaffolds with an alkyne or azide tag. We also discuss 'competitive mode' approaches that screen for natural products that compete with a well-characterised chemical probe for binding to a particular set of protein targets. Fuelled by advances in mass spectrometry instrumentation and bioinformatics, many modern strategies are now embracing quantitative proteomics to help define the true interacting partners of probes, and we highlight the opportunities this rapidly evolving technology provides in chemical proteomics. Finally, some of the limitations and challenges of chemical proteomics approaches are discussed.

  10. Application of chemical biology in target identification and drug discovery.

    PubMed

    Zhu, Yue; Xiao, Ting; Lei, Saifei; Zhou, Fulai; Wang, Ming-Wei

    2015-09-01

    Drug discovery and development is vital to the well-being of mankind and sustainability of the pharmaceutical industry. Using chemical biology approaches to discover drug leads has become a widely accepted path partially because of the completion of the Human Genome Project. Chemical biology mainly solves biological problems through searching previously unknown targets for pharmacologically active small molecules or finding ligands for well-defined drug targets. It is a powerful tool to study how these small molecules interact with their respective targets, as well as their roles in signal transduction, molecular recognition and cell functions. There have been an increasing number of new therapeutic targets being identified and subsequently validated as a result of advances in functional genomics, which in turn led to the discovery of numerous active small molecules via a variety of high-throughput screening initiatives. In this review, we highlight some applications of chemical biology in the context of drug discovery.

  11. Chemical structure determines target organ carcinogenesis in rats

    PubMed Central

    Carrasquer, C. A.; Malik, N.; States, G.; Qamar, S.; Cunningham, S.L.; Cunningham, A.R.

    2012-01-01

    SAR models were developed for 12 rat tumour sites using data derived from the Carcinogenic Potency Database. Essentially, the models fall into two categories: Target Site Carcinogen – Non-Carcinogen (TSC-NC) and Target Site Carcinogen – Non-Target Site Carcinogen (TSC-NTSC). The TSC-NC models were composed of active chemicals that were carcinogenic to a specific target site and inactive ones that were whole animal non-carcinogens. On the other hand, the TSC-NTSC models used an inactive category also composed of carcinogens but to any/all other sites but the target site. Leave one out validations produced an overall average concordance value for all 12 models of 0.77 for the TSC-NC models and 0.73 for the TSC-NTSC models. Overall, these findings suggest that while the TSC-NC models are able to distinguish between carcinogens and non-carcinogens, the TSC-NTSC models are identifying structural attributes that associate carcinogens to specific tumour sites. Since the TSC-NTSC models are composed of active and inactive compounds that are genotoxic and non-genotoxic carcinogens, the TSC-NTSC models may be capable of deciphering non-genotoxic mechanisms of carcinogenesis. Together, models of this type may also prove useful in anticancer drug development since they essentially contain chemicals moieties that target specific tumour site. PMID:23066888

  12. Chemical probes targeting epigenetic proteins: Applications beyond oncology

    PubMed Central

    Ackloo, Suzanne; Brown, Peter J.; Müller, Susanne

    2017-01-01

    ABSTRACT Epigenetic chemical probes are potent, cell-active, small molecule inhibitors or antagonists of specific domains in a protein; they have been indispensable for studying bromodomains and protein methyltransferases. The Structural Genomics Consortium (SGC), comprising scientists from academic and pharmaceutical laboratories, has generated most of the current epigenetic chemical probes. Moreover, the SGC has shared about 4 thousand aliquots of these probes, which have been used primarily for phenotypic profiling or to validate targets in cell lines or primary patient samples cultured in vitro. Epigenetic chemical probes have been critical tools in oncology research and have uncovered mechanistic insights into well-established targets, as well as identify new therapeutic starting points. Indeed, the literature primarily links epigenetic proteins to oncology, but applications in inflammation, viral, metabolic and neurodegenerative diseases are now being reported. We summarize the literature of these emerging applications and provide examples where existing probes might be used. PMID:28080202

  13. Singular vector-based targeted observations of chemical constituents: description and first application of the EURAD-IM-SVA v1.0

    NASA Astrophysics Data System (ADS)

    Goris, N.; Elbern, H.

    2015-12-01

    Measurements of the large-dimensional chemical state of the atmosphere provide only sparse snapshots of the state of the system due to their typically insufficient temporal and spatial density. In order to optimize the measurement configurations despite those limitations, the present work describes the identification of sensitive states of the chemical system as optimal target areas for adaptive observations. For this purpose, the technique of singular vector analysis (SVA), which has proven effective for targeted observations in numerical weather prediction, is implemented in the EURAD-IM (EURopean Air pollution and Dispersion - Inverse Model) chemical transport model, yielding the EURAD-IM-SVA v1.0. Besides initial values, emissions are investigated as critical simulation controlling targeting variables. For both variants, singular vectors are applied to determine the optimal placement for observations and moreover to quantify which chemical compounds have to be observed with preference. Based on measurements of the airship based ZEPTER-2 campaign, the EURAD-IM-SVA v1.0 has been evaluated by conducting a comprehensive set of model runs involving different initial states and simulation lengths. For the sake of brevity, we concentrate our attention on the following chemical compounds, O3, NO, NO2, HCHO, CO, HONO, and OH, and focus on their influence on selected O3 profiles. Our analysis shows that the optimal placement for observations of chemical species is not entirely determined by mere transport and mixing processes. Rather, a combination of initial chemical concentrations, chemical conversions, and meteorological processes determines the influence of chemical compounds and regions. We furthermore demonstrate that the optimal placement of observations of emission strengths is highly dependent on the location of emission sources and that the benefit of including emissions as target variables outperforms the value of initial value optimization with growing

  14. Using habitat suitability models to target invasive plant species surveys.

    PubMed

    Crall, Alycia W; Jarnevich, Catherine S; Panke, Brendon; Young, Nick; Renz, Mark; Morisette, Jeffrey

    2013-01-01

    Managers need new tools for detecting the movement and spread of nonnative, invasive species. Habitat suitability models are a popular tool for mapping the potential distribution of current invaders, but the ability of these models to prioritize monitoring efforts has not been tested in the field. We tested the utility of an iterative sampling design (i.e., models based on field observations used to guide subsequent field data collection to improve the model), hypothesizing that model performance would increase when new data were gathered from targeted sampling using criteria based on the initial model results. We also tested the ability of habitat suitability models to predict the spread of invasive species, hypothesizing that models would accurately predict occurrences in the field, and that the use of targeted sampling would detect more species with less sampling effort than a nontargeted approach. We tested these hypotheses on two species at the state scale (Centaurea stoebe and Pastinaca sativa) in Wisconsin (USA), and one genus at the regional scale (Tamarix) in the western United States. These initial data were merged with environmental data at 30-m2 resolution for Wisconsin and 1-km2 resolution for the western United States to produce our first iteration models. We stratified these initial models to target field sampling and compared our models and success at detecting our species of interest to other surveys being conducted during the same field season (i.e., nontargeted sampling). Although more data did not always improve our models based on correct classification rate (CCR), sensitivity, specificity, kappa, or area under the curve (AUC), our models generated from targeted sampling data always performed better than models generated from nontargeted data. For Wisconsin species, the model described actual locations in the field fairly well (kappa = 0.51, 0.19, P < 0.01), and targeted sampling did detect more species than nontargeted sampling with less

  15. Vesicle-based method for collecting, manipulating, and chemically processing trace macromolecular species

    DOEpatents

    Davalos, Rafael V [Oakland, CA; Ellis, Christopher R. B. [Oakland, CA

    2010-08-17

    Disclosed is an apparatus and method for inserting one or several chemical or biological species into phospholipid containers that are controlled within a microfluidic network, wherein individual containers are tracked and manipulated by electric fields and wherein the contained species may be chemically processed.

  16. Fluidic conduits for highly efficient purification of target species in EWOD-driven droplet microfluidics.

    PubMed

    Shah, Gaurav J; Kim, Chang-Jin Cj

    2009-08-21

    Due to the lack of continuous flows that would wash unwanted specifies and impurities off from a target location, droplet microfluidics commonly employs a long serial dilution process to purify target species. In this work, we achieve high-purity separation for the case of electrowetting-on-dielectric (EWOD) based droplet microfluidics by introducing a "fluidic conduit" between a sample droplet and a buffer droplet. The long and slender fluidic path minimizes the diffusion and fluidic mixing between the two droplets (thus eliminating non-specific transport) but provides a conduit between them for actively transported particles (thus allowing the specific transport). The conduit is purely fluidic, stabilized chemically (e.g. using surfactants) and controlled by EWOD. The effectiveness of the technique is demonstrated by eliminating approximately 97% non-magnetic beads in just one purification step, while maintaining high collection efficiency (>99%) of magnetic beads.

  17. Chemical similarity and local community assembly in the species rich tropical genus Piper.

    PubMed

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

    2016-11-01

    Community ecologists have strived to find mechanisms that mediate the assembly of natural communities. Recent evidence suggests that natural enemies could play an important role in the assembly of hyper-diverse tropical plant systems. Classic ecological theory predicts that in order for coexistence to occur, species differences must be maximized across biologically important niche dimensions. For plant-herbivore interactions, it has been recently suggested that, within a particular community, plant species that maximize the difference in chemical defense profiles compared to neighboring taxa will have a relative competitive advantage. Here we tested the hypothesis that plant chemical diversity can affect local community composition in the hyper-diverse genus Piper at a lowland wet forest location in Costa Rica. We first characterized the chemical composition of 27 of the most locally abundant species of Piper. We then tested whether species with different chemical compositions were more likely to coexist. Finally, we assessed the degree to which Piper phylogenetic relationships are related to differences in secondary chemical composition and community assembly. We found that, on average, co-occurring species were more likely to differ in chemical composition than expected by chance. Contrary to expectations, there was no phylogenetic signal for overall secondary chemical composition. In addition we found that species in local communities were, on average, more phylogenetically closely related than expected by chance, suggesting that functional traits other than those measured here also influence local assembly. We propose that selection by herbivores for divergent chemistries between closely related species facilitates the coexistence of a high diversity of congeneric taxa via apparent competition. © 2016 by the Ecological Society of America.

  18. Efficacy and Ecotoxicity of Novel Anti-Fouling Nanomaterials in Target and Non-Target Marine Species.

    PubMed

    Avelelas, Francisco; Martins, Roberto; Oliveira, Tânia; Maia, Frederico; Malheiro, Eliana; Soares, Amadeu M V M; Loureiro, Susana; Tedim, João

    2017-04-01

    Biofouling is a global problem that affects virtually all the immersed structures. Currently, several novel environmentally friendly approaches are being tested worldwide to decrease the toxicity of biocides in non-fouling species, such as the encapsulation/immobilization of commercially available biocides, in order to achieve control over the leaching rate. The present study addresses the toxicity of two widely used booster biocides, zinc pyrithione (ZnPT) and copper pyrithione (CuPT), in its free and incorporated forms in order to assess their toxicity and anti-fouling efficacy in target and non-target species. To achieve this goal, the following marine organisms were tested; the green microalgae Tetraselmis chuii (non-target species) and both target species, the diatom Phaeodactylum tricornutum and the mussel Mytilus edulis. Organisms were exposed to both biocides, two unloaded nanostructured materials and nanomaterials loaded with biocides, from 10 μg/L to 100 mg/L total weight, following standard protocols. The most eco-friendly and simultaneously efficient anti-fouling solution against the two photosynthetic species (nanoclays loaded with ZnPT) was then tested on mussels to assess its lethal efficacy (LC 50  = 123 μg/L) and compared with free biocide (LC 50  = 211 μg/L) and unloaded material (LC 50  > 1000 μg/L). A second exposure test with sub-lethal concentrations (lower than 100 μg/L), using mussels, was carried out to assess biochemical changes caused by the tested compounds. Oxidative stress, detoxification and neurotransmission markers were not responsive; however, different antioxidant patterns were found with free ZnPT and loaded nanoclay exposures. Thus, the immobilization of the biocide ZnPT into nanoclays proved to be a promising efficient and eco-friendly anti-fouling strategy.

  19. Treatment of biomass to obtain a target chemical

    DOEpatents

    Dunson, Jr., James B.; Tucker, III, Melvin P.; Elander, Richard T.; Hennessey, Susan Marie

    2010-08-24

    Target chemicals were produced using biocatalysts that are able to ferment sugars derived from treated biomass. Sugars were obtained by pretreating biomass under conditions of high solids and low ammonia concentration, followed by saccharification.

  20. Chemical fractionation resulting from the hypervelocity impact process on metallic targets

    NASA Astrophysics Data System (ADS)

    Libourel, Guy; Ganino, Clément; Michel, Patrick; Nakamura, Akiko

    2016-10-01

    In a regime of hypervelocity impact cratering, the internal energy deposited in target + projectile region is large enough to melt and/or vaporize part of the material involved, which expands rapidly away from the impact site. Fast and energetic impact processes have therefore important chemical consequences on the projectile and target rock transformations during major impact events. Several physical and chemical processes occurred indeed in the short duration of the impact, e.g., melting, coating, mixing, condensation, crystallization, redox reactions, quenching, etc., all concurring to alter both projectile and target composition on the irreversible way.In order to document such hypervelocity impact chemical fractionation, we have started a program of impact experiments by shooting doped (27 trace elements) millimeter-sized basalt projectiles on metallic target using a two stages light gas gun. With impact velocity in the range from 0.25 to 7 km.s-1, these experiments are aimed i) to characterize chemically and texturally all the post-mortem materials (e.g., target, crater, impact melt, condensates, and ejectas), in order ii) to make a chemical mass balance budget of the process, and iii) to relate it to the kinetic energy involved in the hypervelocity impacts for scaling law purpose. Irrespective of the incident velocities, our preliminary results show the importance of redox processes, the significant changes in the ejecta composition (e.g., iron enrichment) and the systematic coating of the crater by the impact melt [1]. On the target side, characterizations of the microstructure of the shocked iron alloys to better constrain the shielding processes. We also show how these results have great implications in our understanding on the current surface properties of small bodies, and chiefly in the case of M-type asteroids. [1] Ganino C, Libourel G, Nakamura AM & Michel P (2015) Goldschmidt Abstracts, 2015 990.

  1. Climate warming increases biological control agent impact on a non-target species

    PubMed Central

    Lu, Xinmin; Siemann, Evan; He, Minyan; Wei, Hui; Shao, Xu; Ding, Jianqing

    2015-01-01

    Climate change may shift interactions of invasive plants, herbivorous insects and native plants, potentially affecting biological control efficacy and non-target effects on native species. Here, we show how climate warming affects impacts of a multivoltine introduced biocontrol beetle on the non-target native plant Alternanthera sessilis in China. In field surveys across a latitudinal gradient covering their full distributions, we found beetle damage on A. sessilis increased with rising temperature and plant life history changed from perennial to annual. Experiments showed that elevated temperature changed plant life history and increased insect overwintering, damage and impacts on seedling recruitment. These results suggest that warming can shift phenologies, increase non-target effect magnitude and increase non-target effect occurrence by beetle range expansion to additional areas where A. sessilis occurs. This study highlights the importance of understanding how climate change affects species interactions for future biological control of invasive species and conservation of native species. PMID:25376303

  2. Using habitat suitability models to target invasive plant species surveys

    USGS Publications Warehouse

    Crall, Alycia W.; Jarnevich, Catherine S.; Panke, Brendon; Young, Nick; Renz, Mark; Morisette, Jeffrey

    2013-01-01

    Managers need new tools for detecting the movement and spread of nonnative, invasive species. Habitat suitability models are a popular tool for mapping the potential distribution of current invaders, but the ability of these models to prioritize monitoring efforts has not been tested in the field. We tested the utility of an iterative sampling design (i.e., models based on field observations used to guide subsequent field data collection to improve the model), hypothesizing that model performance would increase when new data were gathered from targeted sampling using criteria based on the initial model results. We also tested the ability of habitat suitability models to predict the spread of invasive species, hypothesizing that models would accurately predict occurrences in the field, and that the use of targeted sampling would detect more species with less sampling effort than a nontargeted approach. We tested these hypotheses on two species at the state scale (Centaurea stoebe and Pastinaca sativa) in Wisconsin (USA), and one genus at the regional scale (Tamarix) in the western United States. These initial data were merged with environmental data at 30-m2 resolution for Wisconsin and 1-km2 resolution for the western United States to produce our first iteration models. We stratified these initial models to target field sampling and compared our models and success at detecting our species of interest to other surveys being conducted during the same field season (i.e., nontargeted sampling). Although more data did not always improve our models based on correct classification rate (CCR), sensitivity, specificity, kappa, or area under the curve (AUC), our models generated from targeted sampling data always performed better than models generated from nontargeted data. For Wisconsin species, the model described actual locations in the field fairly well (kappa = 0.51, 0.19, P 2) = 47.42, P < 0.01). From these findings, we conclude that habitat suitability models can be

  3. Cross-species extrapolation of chemical effects: Challenges and new insights

    EPA Science Inventory

    One of the greatest uncertainties in chemical risk assessment is extrapolation of effects from tested to untested species. While this undoubtedly is a challenge in the human health arena, species extrapolation is a particularly daunting task in ecological assessments, where it is...

  4. Wood Chemical Composition in Species of Cactaceae: The Relationship between Lignification and Stem Morphology

    PubMed Central

    Canché-Escamilla, Gonzalo; Soto-Hernández, Marcos

    2015-01-01

    In Cactaceae, wood anatomy is related to stem morphology in terms of the conferred support. In species of cacti with dimorphic wood, a unique process occurs in which the cambium stops producing wide-band tracheids (WBTs) and produces fibers; this is associated with the aging of individuals and increases in size. Stem support and lignification have only been studied in fibrous tree-like species, and studies in species with WBTs or dimorphic wood are lacking. In this study, we approach this process with a chemical focus, emphasizing the role of wood lignification. We hypothesized that the degree of wood lignification in Cactaceae increases with height of the species and that its chemical composition varies with wood anatomy. To test this, we studied the chemical composition (cellulose, hemicellulose, and lignin content) in 13 species (2 WBTs wood, 3 dimorphic, and 8 fibrous) with contrasting growth forms. We also analyzed lignification in dimorphic and fibrous species to determine the chemical features of WBTs and fibers and their relationship with stem support. The lignin contents were characterized by Fourier transform infrared spectroscopy and high performance liquid chromatography. We found that 11 species have a higher percentage (>35%) of lignin in their wood than other angiosperms or gymnosperms. The lignin chemical composition in fibrous species is similar to that of other dicots, but it is markedly heterogeneous in non-fibrous species where WBTs are abundant. The lignification in WBTs is associated with the resistance to high water pressure within cells rather than the contribution to mechanical support. Dimorphic wood species are usually richer in syringyl lignin, and tree-like species with lignified rays have more guaiacyl lignin. The results suggest that wood anatomy and lignin distribution play an important role in the chemical composition of wood, and further research is needed at the cellular level. PMID:25880223

  5. Wood chemical composition in species of Cactaceae: the relationship between lignification and stem morphology.

    PubMed

    Reyes-Rivera, Jorge; Canché-Escamilla, Gonzalo; Soto-Hernández, Marcos; Terrazas, Teresa

    2015-01-01

    In Cactaceae, wood anatomy is related to stem morphology in terms of the conferred support. In species of cacti with dimorphic wood, a unique process occurs in which the cambium stops producing wide-band tracheids (WBTs) and produces fibers; this is associated with the aging of individuals and increases in size. Stem support and lignification have only been studied in fibrous tree-like species, and studies in species with WBTs or dimorphic wood are lacking. In this study, we approach this process with a chemical focus, emphasizing the role of wood lignification. We hypothesized that the degree of wood lignification in Cactaceae increases with height of the species and that its chemical composition varies with wood anatomy. To test this, we studied the chemical composition (cellulose, hemicellulose, and lignin content) in 13 species (2 WBTs wood, 3 dimorphic, and 8 fibrous) with contrasting growth forms. We also analyzed lignification in dimorphic and fibrous species to determine the chemical features of WBTs and fibers and their relationship with stem support. The lignin contents were characterized by Fourier transform infrared spectroscopy and high performance liquid chromatography. We found that 11 species have a higher percentage (>35%) of lignin in their wood than other angiosperms or gymnosperms. The lignin chemical composition in fibrous species is similar to that of other dicots, but it is markedly heterogeneous in non-fibrous species where WBTs are abundant. The lignification in WBTs is associated with the resistance to high water pressure within cells rather than the contribution to mechanical support. Dimorphic wood species are usually richer in syringyl lignin, and tree-like species with lignified rays have more guaiacyl lignin. The results suggest that wood anatomy and lignin distribution play an important role in the chemical composition of wood, and further research is needed at the cellular level.

  6. Differential Sharing of Chemical Cues by Social Parasites Versus Social Mutualists in a Three-Species Symbiosis.

    PubMed

    Emery, Virginia J; Tsutsui, Neil D

    2016-04-01

    Chemical recognition systems are crucial for maintaining the unity of social insect colonies. It has been proposed that colonies form a common chemical signature, called the gestalt odor, which is used to distinguish colony members and non-members. This chemical integration is achieved actively through social interactions such as trophallaxis and allogrooming, or passively such as through exposure to common nest material. When colonies are infiltrated by social parasites, the intruders often use some form of chemical mimicry. However, it is not always clear how this chemical mimicry is accomplished. Here, we used a three-species nesting symbiosis to test the differences in chemical integration of mutualistic (parabiotic) and parasitic ant species. We found that the parasite (Solenopsis picea) obtains chemical cues from both of the two parabiotic host ant species. However, the two parabiotic species (Crematogaster levior and Camponotus femoratus) maintain species-specific cues, and do not acquire compounds from the other species. Our findings suggest that there is a fundamental difference in how social mutualists and social parasites use chemicals to integrate themselves into colonies.

  7. Chemical changes with maturation of the bamboo species phyllostachys pubescens

    Treesearch

    X.B. Li; T.F. Shupe; G.F. Peter; C.Y. Hse; T.L. Eberhardt

    2007-01-01

    Chemical changes with maturation of the bamboo species Phyllostachys pubescens. Bamboo chemical properties were measured at three different heights from one-, three- and five-year-old plants and at three different radial positions from the thre-year-old culms of Phyllostachys pubescenssouth-eastern USA. Small but significant...

  8. The role of targeted chemical proteomics in pharmacology

    PubMed Central

    Sutton, Chris W

    2012-01-01

    Traditionally, proteomics is the high-throughput characterization of the global complement of proteins in a biological system using cutting-edge technologies (robotics and mass spectrometry) and bioinformatics tools (Internet-based search engines and databases). As the field of proteomics has matured, a diverse range of strategies have evolved to answer specific problems. Chemical proteomics is one such direction that provides the means to enrich and detect less abundant proteins (the ‘hidden’ proteome) from complex mixtures of wide dynamic range (the ‘deep’ proteome). In pharmacology, chemical proteomics has been utilized to determine the specificity of drugs and their analogues, for anticipated known targets, only to discover other proteins that bind and could account for side effects observed in preclinical and clinical trials. As a consequence, chemical proteomics provides a valuable accessory in refinement of second- and third-generation drug design for treatment of many diseases. However, determining definitive affinity capture of proteins by a drug immobilized on soft gel chromatography matrices has highlighted some of the challenges that remain to be addressed. Examples of the different strategies that have emerged using well-established drugs against pharmaceutically important enzymes, such as protein kinases, metalloproteases, PDEs, cytochrome P450s, etc., indicate the potential opportunity to employ chemical proteomics as an early-stage screening approach in the identification of new targets. PMID:22074351

  9. In Silico Studies of the Toxcast Chemicals Interacting with Biomolecular targets

    EPA Science Inventory

    Molecular docking, a structure-based in silico tool for chemical library pre-screening in drug discovery, can be used to explore the potential toxicity of environmental chemicals acting at specific biomelcular targets.

  10. Climate warming increases biological control agent impact on a non-target species.

    PubMed

    Lu, Xinmin; Siemann, Evan; He, Minyan; Wei, Hui; Shao, Xu; Ding, Jianqing

    2015-01-01

    Climate change may shift interactions of invasive plants, herbivorous insects and native plants, potentially affecting biological control efficacy and non-target effects on native species. Here, we show how climate warming affects impacts of a multivoltine introduced biocontrol beetle on the non-target native plant Alternanthera sessilis in China. In field surveys across a latitudinal gradient covering their full distributions, we found beetle damage on A. sessilis increased with rising temperature and plant life history changed from perennial to annual. Experiments showed that elevated temperature changed plant life history and increased insect overwintering, damage and impacts on seedling recruitment. These results suggest that warming can shift phenologies, increase non-target effect magnitude and increase non-target effect occurrence by beetle range expansion to additional areas where A. sessilis occurs. This study highlights the importance of understanding how climate change affects species interactions for future biological control of invasive species and conservation of native species. © 2014 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.

  11. Reproductive Impacts of Endocrine-Disrupting Chemicals on Wildlife Species: Implications for Conservation of Endangered Species.

    PubMed

    Tubbs, Christopher W; McDonough, Caitlin E

    2018-02-15

    Wildlife have proven valuable to our understanding of the potential effects of endocrine-disrupting chemicals (EDCs) on human health by contributing considerably to our understanding of the mechanisms and consequences of EDC exposure. But the threats EDCs present to populations of wildlife species themselves are significant, particularly for endangered species whose existence is vulnerable to any reproductive perturbation. However, few studies address the threats EDCs pose to endangered species owing to challenges associated with their study. Here, we highlight those barriers and review the available literature concerning EDC effects on endangered species. Drawing from other investigations into nonthreatened wildlife species, we highlight opportunities for new approaches to advance our understanding and potentially mitigate the effects of EDCs on endangered species to enhance their fertility.

  12. Can species-specific prey responses to chemical cues explain prey susceptibility to predation?

    PubMed

    Šmejkal, Marek; Ricard, Daniel; Sajdlová, Zuzana; Čech, Martin; Vejřík, Lukáš; Blabolil, Petr; Vejříková, Ivana; Prchalová, Marie; Vašek, Mojmír; Souza, Allan T; Brönmark, Christer; Peterka, Jiří

    2018-05-01

    The perception of danger represents an essential ability of prey for gaining an informational advantage over their natural enemies. Especially in complex environments or at night, animals strongly rely on chemoreception to avoid predators. The ability to recognize danger by chemical cues and subsequent adaptive responses to predation threats should generally increase prey survival. Recent findings suggest that European catfish ( Silurus glanis ) introduction induce changes in fish community and we tested whether the direction of change can be attributed to differences in chemical cue perception. We tested behavioral response to chemical cues using three species of freshwater fish common in European water: rudd ( Scardinius erythrophthalmus ), roach ( Rutilus rutilus ), and perch ( Perca fluviatilis ). Further, we conducted a prey selectivity experiment to evaluate the prey preferences of the European catfish. Roach exhibited the strongest reaction to chemical cues, rudd decreased use of refuge and perch did not alter any behavior in the experiment. These findings suggest that chemical cue perception might be behind community data change and we encourage collecting more community data of tested prey species before and after European catfish introduction to test the hypothesis. We conclude that used prey species can be used as a model species to verify whether chemical cue perception enhances prey survival.

  13. Multi-wavelength differential absorption measurements of chemical species

    NASA Astrophysics Data System (ADS)

    Brown, David M.

    The probability of accurate detection and quantification of airborne species is enhanced when several optical wavelengths are used to measure the differential absorption of molecular spectral features. Characterization of minor atmospheric constituents, biological hazards, and chemical plumes containing multiple species is difficult when using current approaches because of weak signatures and the use of a limited number of wavelengths used for identification. Current broadband systems such as Differential Optical Absorption Spectroscopy (DOAS) have either limitations for long-range propagation, or require transmitter power levels that are unsafe for operation in urban environments. Passive hyperspectral imaging systems that utilize absorption of solar scatter at visible and infrared wavelengths, or use absorption of background thermal emission, have been employed routinely for detection of airborne chemical species. Passive approaches have operational limitations at various ranges, or under adverse atmospheric conditions because the source intensity and spectrum is often an unknown variable. The work presented here describes a measurement approach that uses a known source of a low transmitted power level for an active system, while retaining the benefits of broadband and extremely long-path absorption operations. An optimized passive imaging system also is described that operates in the 3 to 4 mum window of the mid-infrared. Such active and passive instruments can be configured to optimize the detection of several hydrocarbon gases, as well as many other species of interest. Measurements have provided the incentive to develop algorithms for the calculations of atmospheric species concentrations using multiple wavelengths. These algorithms are used to prepare simulations and make comparisons with experimental results from absorption data of a supercontinuum laser source. The MODTRAN model is used in preparing the simulations, and also in developing additional

  14. Combining functional genomics and chemical biology to identify targets of bioactive compounds.

    PubMed

    Ho, Cheuk Hei; Piotrowski, Jeff; Dixon, Scott J; Baryshnikova, Anastasia; Costanzo, Michael; Boone, Charles

    2011-02-01

    Genome sequencing projects have revealed thousands of suspected genes, challenging researchers to develop efficient large-scale functional analysis methodologies. Determining the function of a gene product generally requires a means to alter its function. Genetically tractable model organisms have been widely exploited for the isolation and characterization of activating and inactivating mutations in genes encoding proteins of interest. Chemical genetics represents a complementary approach involving the use of small molecules capable of either inactivating or activating their targets. Saccharomyces cerevisiae has been an important test bed for the development and application of chemical genomic assays aimed at identifying targets and modes of action of known and uncharacterized compounds. Here we review yeast chemical genomic assays strategies for drug target identification. Copyright © 2010 Elsevier Ltd. All rights reserved.

  15. Target identification of small molecules based on chemical biology approaches.

    PubMed

    Futamura, Yushi; Muroi, Makoto; Osada, Hiroyuki

    2013-05-01

    Recently, a phenotypic approach-screens that assess the effects of compounds on cells, tissues, or whole organisms-has been reconsidered and reintroduced as a complementary strategy of a target-based approach for drug discovery. Although the finding of novel bioactive compounds from large chemical libraries has become routine, the identification of their molecular targets is still a time-consuming and difficult process, making this step rate-limiting in drug development. In the last decade, we and other researchers have amassed a large amount of phenotypic data through progress in omics research and advances in instrumentation. Accordingly, the profiling methodologies using these datasets expertly have emerged to identify and validate specific molecular targets of drug candidates, attaining some progress in current drug discovery (e.g., eribulin). In the case of a compound that shows an unprecedented phenotype likely by inhibiting a first-in-class target, however, such phenotypic profiling is invalid. Under the circumstances, a photo-crosslinking affinity approach should be beneficial. In this review, we describe and summarize recent progress in both affinity-based (direct) and phenotypic profiling (indirect) approaches for chemical biology target identification.

  16. Vesicle-based method and apparatus for collecting, manipulating, and chemically processing trace macromolecular species

    DOEpatents

    Davalos, Rafael V [Oakland, CA; Ellis, Christopher R. B. [Oakland, CA

    2008-03-04

    Disclosed is an apparatus and method for inserting one or several chemical or biological species into phospholipid containers that are controlled within a microfluidic network, wherein individual containers are tracked and manipulated by electric fields and wherein the contained species may be chemically processed.

  17. A cell-free testing platform to screen chemicals of potential neurotoxic concern across twenty vertebrate species.

    PubMed

    Arini, Adeline; Mittal, Krittika; Dornbos, Peter; Head, Jessica; Rutkiewicz, Jennifer; Basu, Niladri

    2017-11-01

    There is global demand for new in vitro testing tools for ecological risk assessment. The objective of the present study was to apply a set of cell-free neurochemical assays to screen many chemicals across many species in a relatively high-throughput manner. The platform assessed 7 receptors and enzymes that mediate neurotransmission of γ-aminobutyric acid, dopamine, glutamate, and acetylcholine. Each assay was optimized to work across 20 vertebrate species (5 fish, 5 birds, 7 mammalian wildlife, 3 biomedical species including humans). We tested the screening assay platform against 80 chemicals (23 pharmaceuticals and personal care products, 20 metal[loid]s, 22 polycyclic aromatic hydrocarbons and halogenated organic compounds, 15 pesticides). In total, 10 800 species-chemical-assay combinations were tested, and significant differences were found in 4041 cases. All 7 assays were significantly affected by at least one chemical in each species tested. Among the 80 chemicals tested, nearly all resulted in a significant impact on at least one species and one assay. The 5 most active chemicals were prochloraz, HgCl 2 , Sn, benzo[a]pyrene, and vinclozolin. Clustering analyses revealed groupings according to chemicals, species, and chemical-assay combinations. The results show that cell-free assays can screen a large number of samples in a short period of time in a cost-effective manner in a range of animals not easily studied using traditional approaches. Strengths and limitations of this approach are discussed, as well as next steps. Environ Toxicol Chem 2017;36:3081-3090. © 2017 SETAC. © 2017 SETAC.

  18. Diffusion of multi-isotopic chemical species in molten silicates

    NASA Astrophysics Data System (ADS)

    Watkins, James M.; Liang, Yan; Richter, Frank; Ryerson, Frederick J.; DePaolo, Donald J.

    2014-08-01

    Diffusion experiments in a simplified Na2O-CaO-SiO2 liquid system are used to develop a general formulation for the fractionation of Ca isotopes during liquid-phase diffusion. Although chemical diffusion is a well-studied process, the mathematical description of the effects of diffusion on the separate isotopes of a chemical element is surprisingly underdeveloped and uncertain. Kinetic theory predicts a mass dependence on isotopic mobility, but it is unknown how this translates into a mass dependence on effective binary diffusion coefficients, or more generally, the chemical diffusion coefficients that are housed in a multicomponent diffusion matrix. Our experiments are designed to measure Ca mobility, effective binary diffusion coefficients, the multicomponent diffusion matrix, and the effects of chemical diffusion on Ca isotopes in a liquid of single composition. We carried out two chemical diffusion experiments and one self-diffusion experiment, all at 1250 °C and 0.7 GPa and using a bulk composition for which other information is available from the literature. The self-diffusion experiment is used to determine the mobility of Ca in the absence of diffusive fluxes of other liquid components. The chemical diffusion experiments are designed to determine the effect on Ca isotope fractionation of changing the counter-diffusing component from fast-diffusing Na2O to slow-diffusing SiO2. When Na2O is the main counter-diffusing species, CaO diffusion is fast and larger Ca isotopic effects are generated. When SiO2 is the main counter-diffusing species, CaO diffusion is slow and smaller Ca isotopic effects are observed. In both experiments, the liquid is initially isotopically homogeneous, and during the experiment Ca isotopes become fractionated by diffusion. The results are used as a test of a new general expression for the diffusion of isotopes in a multicomponent liquid system that accounts for both self diffusion and the effects of counter-diffusing species. Our

  19. The difference between temperate and tropical saltwater species' acute sensitivity to chemicals is relatively small.

    PubMed

    Wang, Zhen; Kwok, Kevin W H; Lui, Gilbert C S; Zhou, Guang-Jie; Lee, Jae-Seong; Lam, Michael H W; Leung, Kenneth M Y

    2014-06-01

    Due to a lack of saltwater toxicity data in tropical regions, toxicity data generated from temperate or cold water species endemic to North America and Europe are often adopted to derive water quality guidelines (WQG) for protecting tropical saltwater species. If chemical toxicity to most saltwater organisms increases with water temperature, the use of temperate species data and associated WQG may result in under-protection to tropical species. Given the differences in species composition and environmental attributes between tropical and temperate saltwater ecosystems, there are conceivable uncertainties in such 'temperate-to-tropic' extrapolations. This study aims to compare temperate and tropical saltwater species' acute sensitivity to 11 chemicals through a comprehensive meta-analysis, by comparing species sensitivity distributions (SSDs) between the two groups. A 10 percentile hazardous concentration (HC10) is derived from each SSD, and then a temperate-to-tropic HC10 ratio is computed for each chemical. Our results demonstrate that temperate and tropical saltwater species display significantly different sensitivity towards all test chemicals except cadmium, although such differences are small with the HC10 ratios ranging from 0.094 (un-ionised ammonia) to 2.190 (pentachlorophenol) only. Temperate species are more sensitive to un-ionised ammonia, chromium, lead, nickel and tributyltin, whereas tropical species are more sensitive to copper, mercury, zinc, phenol and pentachlorophenol. Through comparison of a limited number of taxon-specific SSDs, we observe that there is a general decline in chemical sensitivity from algae to crustaceans, molluscs and then fishes. Following a statistical analysis of the results, we recommend an extrapolation factor of two for deriving tropical WQG from temperate information. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. High-performance metabolic profiling of plasma from seven mammalian species for simultaneous environmental chemical surveillance and bioeffect monitoring.

    PubMed

    Park, Youngja H; Lee, Kichun; Soltow, Quinlyn A; Strobel, Frederick H; Brigham, Kenneth L; Parker, Richard E; Wilson, Mark E; Sutliff, Roy L; Mansfield, Keith G; Wachtman, Lynn M; Ziegler, Thomas R; Jones, Dean P

    2012-05-16

    High-performance metabolic profiling (HPMP) by Fourier-transform mass spectrometry coupled to liquid chromatography gives relative quantification of thousands of chemicals in biologic samples but has had little development for use in toxicology research. In principle, the approach could be useful to detect complex metabolic response patterns to toxicologic exposures and to detect unusual abundances or patterns of potentially toxic chemicals. As an initial study to develop these possible uses, we applied HPMP and bioinformatics analysis to plasma of humans, rhesus macaques, marmosets, pigs, sheep, rats and mice to determine: (1) whether more chemicals are detected in humans living in a less controlled environment than captive species and (2) whether a subset of plasma chemicals with similar inter-species and intra-species variation could be identified for use in comparative toxicology. Results show that the number of chemicals detected was similar in humans (3221) and other species (range 2537-3373). Metabolite patterns were most similar within species and separated samples according to family and order. A total of 1485 chemicals were common to all species; 37% of these matched chemicals in human metabolomic databases and included chemicals in 137 out of 146 human metabolic pathways. Probability-based modularity clustering separated 644 chemicals, including many endogenous metabolites, with inter-species variation similar to intra-species variation. The remaining chemicals had greater inter-species variation and included environmental chemicals as well as GSH and methionine. Together, the data suggest that HPMP provides a platform that can be useful within human populations and controlled animal studies to simultaneously evaluate environmental exposures and biological responses to such exposures. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  1. Dual Ion Species Plasma Expansion from Isotopically Layered Cryogenic Targets

    NASA Astrophysics Data System (ADS)

    Scott, G. G.; Carroll, D. C.; Astbury, S.; Clarke, R. J.; Hernandez-Gomez, C.; King, M.; Alejo, A.; Arteaga, I. Y.; Dance, R. J.; Higginson, A.; Hook, S.; Liao, G.; Liu, H.; Mirfayzi, S. R.; Rusby, D. R.; Selwood, M. P.; Spindloe, C.; Tolley, M. K.; Wagner, F.; Zemaityte, E.; Borghesi, M.; Kar, S.; Li, Y.; Roth, M.; McKenna, P.; Neely, D.

    2018-05-01

    A dual ion species plasma expansion scheme from a novel target structure is introduced, in which a nanometer-thick layer of pure deuterium exists as a buffer species at the target-vacuum interface of a hydrogen plasma. Modeling shows that by controlling the deuterium layer thickness, a composite H+/D+ ion beam can be produced by target normal sheath acceleration (TNSA), with an adjustable ratio of ion densities, as high energy proton acceleration is suppressed by the acceleration of a spectrally peaked deuteron beam. Particle in cell modeling shows that a (4.3 ±0.7 ) MeV per nucleon deuteron beam is accelerated, in a directional cone of half angle 9°. Experimentally, this was investigated using state of the art cryogenic targetry and a spectrally peaked deuteron beam of (3.4 ±0.7 ) MeV per nucleon was measured in a cone of half angle 7°-9°, while maintaining a significant TNSA proton component.

  2. Various chemical strategies to deceive ants in three Arhopala species (lepidoptera: Lycaenidae) exploiting Macaranga myrmecophytes.

    PubMed

    Inui, Yoko; Shimizu-Kaya, Usun; Okubo, Tadahiro; Yamsaki, Eri; Itioka, Takao

    2015-01-01

    Macaranga myrmecophytes (ant-plants) are generally well protected from herbivore attacks by their symbiotic ants (plant-ants). However, larvae of Arhopala (Lepidoptera: Lycaenidae) species survive and develop on specific Macaranga ant-plant species without being attacked by the plant-ants of their host species. We hypothesized that Arhopala larvae chemically mimic or camouflage themselves with the ants on their host plant so that the larvae are accepted by the plant-ant species of their host. Chemical analyses of cuticular hydrocarbons showed that chemical congruency varied among Arhopala species; A. dajagaka matched well the host plant-ants, A. amphimuta did not match, and unexpectedly, A. zylda lacked hydrocarbons. Behaviorally, the larvae and dummies coated with cuticular chemicals of A. dajagaka were well attended by the plant-ants, especially by those of the host. A. amphimuta was often attacked by all plant-ants except for the host plant-ants toward the larvae, and those of A. zylda were ignored by all plant-ants. Our results suggested that conspicuous variations exist in the chemical strategies used by the myrmecophilous butterflies that allow them to avoid ant attack and be accepted by the plant-ant colonies.

  3. Various Chemical Strategies to Deceive Ants in Three Arhopala Species (Lepidoptera: Lycaenidae) Exploiting Macaranga Myrmecophytes

    PubMed Central

    Inui, Yoko; Shimizu-kaya, Usun; Okubo, Tadahiro; Yamsaki, Eri; Itioka, Takao

    2015-01-01

    Macaranga myrmecophytes (ant-plants) are generally well protected from herbivore attacks by their symbiotic ants (plant-ants). However, larvae of Arhopala (Lepidoptera: Lycaenidae) species survive and develop on specific Macaranga ant-plant species without being attacked by the plant-ants of their host species. We hypothesized that Arhopala larvae chemically mimic or camouflage themselves with the ants on their host plant so that the larvae are accepted by the plant-ant species of their host. Chemical analyses of cuticular hydrocarbons showed that chemical congruency varied among Arhopala species; A. dajagaka matched well the host plant-ants, A. amphimuta did not match, and unexpectedly, A. zylda lacked hydrocarbons. Behaviorally, the larvae and dummies coated with cuticular chemicals of A. dajagaka were well attended by the plant-ants, especially by those of the host. A. amphimuta was often attacked by all plant-ants except for the host plant-ants toward the larvae, and those of A. zylda were ignored by all plant-ants. Our results suggested that conspicuous variations exist in the chemical strategies used by the myrmecophilous butterflies that allow them to avoid ant attack and be accepted by the plant-ant colonies. PMID:25853675

  4. Chemical biology 2012: from drug targets to biological systems and back.

    PubMed

    Socher, Elke; Grossmann, Tom N

    2013-01-02

    Multiple sites sharing a common target: This year's EMBO conference on chemical biology encouraged over 340 researchers to come to Heidelberg, Germany, and discuss the use of diverse chemical strategies and tools to investigate biological questions and better understand cellular processes. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Sequence Alignment to Predict Across Species Susceptibility ...

    EPA Pesticide Factsheets

    Conservation of a molecular target across species can be used as a line-of-evidence to predict the likelihood of chemical susceptibility. The web-based Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed to simplify, streamline, and quantitatively assess protein sequence/structural similarity across taxonomic groups as a means to predict relative intrinsic susceptibility. The intent of the tool is to allow for evaluation of any potential protein target, so it is amenable to variable degrees of protein characterization, depending on available information about the chemical/protein interaction and the molecular target itself. To allow for flexibility in the analysis, a layered strategy was adopted for the tool. The first level of the SeqAPASS analysis compares primary amino acid sequences to a query sequence, calculating a metric for sequence similarity (including detection of candidate orthologs), the second level evaluates sequence similarity within selected domains (e.g., ligand-binding domain, DNA binding domain), and the third level of analysis compares individual amino acid residue positions identified as being of importance for protein conformation and/or ligand binding upon chemical perturbation. Each level of the SeqAPASS analysis provides increasing evidence to apply toward rapid, screening-level assessments of probable cross species susceptibility. Such analyses can support prioritization of chemicals for further ev

  6. Comparison of Brassicaceae species for phytotoxicity testing

    EPA Science Inventory

    We compared four Brassicaceae species for potential use as test species in the EPAs Series 850 vegetative vigor test and other phytotoxicity tests to determine effects of chemicals on non-target plants. Arabidopsis thaliana var. Columbia is commonly used in plant molecular and p...

  7. Phytotoxicity of cardoon (Cynara cardunculus) allelochemicals on standard target species and weeds.

    PubMed

    Rial, Carlos; Novaes, Paula; Varela, Rosa M; Molinillo, José M G; Macias, Francisco A

    2014-07-16

    Cardoon (Cynara cardunculus L.) is a native plant to the Iberian Peninsula and the European Atlantic coast and invasive in American environments. Different solvents were used to perform cardoon extracts that were tested in phytotoxic bioassays. The ethyl acetate extract had the highest inhibitory activity so this was tested on the germination and growth of standard target species (lettuce, watercress, tomato, and onion) and weeds (barnyardgrass and brachiaria). The ethyl acetate extract was very active on root growth in both standard target species and weeds and it was therefore fractionated by chromatography. The spectroscopic data showed that the major compounds were sesquiterpene lactones. Aguerin B, grosheimin, and cynaropicrin were very active on etiolated wheat coleoptile, standard target species, and weed growth. The presence of these compounds explains the bioactivity of the ethyl acetate extract. The strong phytotoxicity of these compounds on important weeds shows the potential of these compounds as natural herbicide models.

  8. Chemical and biological sensing using liquid crystals

    PubMed Central

    Carlton, Rebecca J.; Hunter, Jacob T.; Miller, Daniel S.; Abbasi, Reza; Mushenheim, Peter C.; Tan, Lie Na; Abbott, Nicholas L.

    2014-01-01

    The liquid crystalline state of matter arises from orientation-dependent, non-covalent interaction between molecules within condensed phases. Because the balance of intermolecular forces that underlies formation of liquid crystals is delicate, this state of matter can, in general, be easily perturbed by external stimuli (such as an electric field in a display). In this review, we present an overview of recent efforts that have focused on exploiting the responsiveness of liquid crystals as the basis of chemical and biological sensors. In this application of liquid crystals, the challenge is to design liquid crystalline systems that undergo changes in organization when perturbed by targeted chemical and biological species of interest. The approaches described below revolve around the design of interfaces that selectively bind targeted species, thus leading to surface-driven changes in the organization of the liquid crystals. Because liquid crystals possess anisotropic optical and dielectric properties, a range of different methods can be used to read out the changes in organization of liquid crystals that are caused by targeted chemical and biological species. This review focuses on principles for liquid crystal-based sensors that provide an optical output. PMID:24795857

  9. Quantum chemical study of methane oxidation species

    NASA Technical Reports Server (NTRS)

    Jackels, Charles F.

    1993-01-01

    The research funded by this project has focused on quantum chemical investigations of molecular species thought to be important in the chemistry of the earth's upper and lower atmospheres. The body of this report contains brief discussions of the results of the several phases of this investigation. In many instances these results have been presented at scientific meetings and/or published in refereed journals. Those bibliographic references are given. In addition to the study of specific chemical systems, there were several phases during the course of this investigation where much of the effort went into the development and modification of computer codes necessary to carry out these calculations on the wide range of computer equipment used during this study. This type of code maintenance and development work did not generally result in publications and presentations, but a brief review is given.

  10. Chemical Probes for Molecular Imaging and Detection of Hydrogen Sulfide and Reactive Sulfur Species in Biological Systems

    PubMed Central

    2014-01-01

    Hydrogen sulfide (H2S), a gaseous species produced by both bacteria and higher eukaryotic organisms, including mammalian vertebrates, has attracted attention in recent years for its contributions to human health and disease. H2S has been proposed as a cytoprotectant and gasotransmitter in many tissue types, including mediating vascular tone in blood vessels as well as neuromodulation in the brain. The molecular mechanisms dictating how H2S affects cellular signaling and other physiological events remain insufficiently understood. Furthermore, the involvement of H2S in metal-binding interactions and formation of related RSS such as sulfane sulfur may contribute to other distinct signaling pathways. Owing to its widespread biological roles and unique chemical properties, H2S is an appealing target for chemical biology approaches to elucidate its production, trafficking, and downstream function. In this context, reaction-based fluorescent probes offer a versatile set of screening tools to visualize H2S pools in living systems. Three main strategies used in molecular probe development for H2S detection include azide and nitro group reduction, nucleophilic attack, and CuS precipitation. Each of these approaches exploit the strong nucleophilicity and reducing potency of H2S to achieve selectivity over other biothiols. In addition, a variety of methods have been developed for the detection of other reactive sulfur species (RSS), including sulfite and bisulfite, as well as sulfane sulfur species and related modifications such as S-nitrosothiols. Access to this growing chemical toolbox of new molecular probes for H2S and related RSS sets the stage for applying these developing technologies to probe reactive sulfur biology in living systems. PMID:25474627

  11. Stock assessment of fishery target species in Lake Koka, Ethiopia.

    PubMed

    Tesfaye, Gashaw; Wolff, Matthias

    2015-09-01

    Effective management is essential for small-scale fisheries to continue providing food and livelihoods for households, particularly in developing countries where other options are often limited. Studies on the population dynamics and stock assessment on fishery target species are thus imperative to sustain their fisheries and the benefits for the society. In Lake Koka (Ethiopia), very little is known about the vital population parameters and exploitation status of the fishery target species: tilapia Oreochromis niloticus, common carp Cyprinus carpio and catfish Clarias gariepinus. Our study, therefore, aimed at determining the vital population parameters and assessing the status of these target species in Lake Koka using length frequency data collected quarterly from commercial catches from 2007-2012. A total of 20,097 fish specimens (distributed as 7,933 tilapia, 6,025 catfish and 6,139 common carp) were measured for the analysis. Von Bertalarffy growth parameters and their confidence intervals were determined from modal progression analysis using ELEFAN I and applying the jackknife technique. Mortality parameters were determined from length-converted catch curves and empirical models. The exploitation status of these target species were then assessed by computing exploitation rates (E) from mortality parameters as well as from size indicators i.e., assessing the size distribution of fish catches relative to the size at maturity (Lm), the size that provides maximum cohort biomass (Lopt) and the abundance of mega-spawners. The mean value of growth parameters L∞, K and the growth performance index ø' were 44.5 cm, 0.41/year and 2.90 for O. niloticus, 74.1 cm, 0.28/year and 3.19 for C. carpio and 121.9 cm, 0.16/year and 3.36 for C. gariepinus, respectively. The 95 % confidence intervals of the estimates were also computed. Total mortality (Z) estimates were 1.47, 0.83 and 0.72/year for O. niloticus, C. carpio and C. gariepinus, respectively. Our study suggest that

  12. Chemical approaches to targeted protein degradation through modulation of the ubiquitin-proteasome pathway.

    PubMed

    Collins, Ian; Wang, Hannah; Caldwell, John J; Chopra, Raj

    2017-03-15

    Manipulation of the ubiquitin-proteasome system to achieve targeted degradation of proteins within cells using chemical tools and drugs has the potential to transform pharmacological and therapeutic approaches in cancer and other diseases. An increased understanding of the molecular mechanism of thalidomide and its analogues following their clinical use has unlocked small-molecule modulation of the substrate specificity of the E3 ligase cereblon (CRBN), which in turn has resulted in the advancement of new immunomodulatory drugs (IMiDs) into the clinic. The degradation of multiple context-specific proteins by these pleiotropic small molecules provides a means to uncover new cell biology and to generate future drug molecules against currently undruggable targets. In parallel, the development of larger bifunctional molecules that bring together highly specific protein targets in complexes with CRBN, von Hippel-Lindau, or other E3 ligases to promote ubiquitin-dependent degradation has progressed to generate selective chemical compounds with potent effects in cells and in vivo models, providing valuable tools for biological target validation and with future potential for therapeutic use. In this review, we survey recent breakthroughs achieved in these two complementary methods and the discovery of new modes of direct and indirect engagement of target proteins with the proteasome. We discuss the experimental characterisation that validates the use of molecules that promote protein degradation as chemical tools, the preclinical and clinical examples disclosed to date, and the future prospects for this exciting area of chemical biology. © 2017 The Author(s).

  13. Plant Species Rather Than Climate Greatly Alters the Temporal Pattern of Litter Chemical Composition During Long-Term Decomposition

    NASA Astrophysics Data System (ADS)

    Li, Yongfu; Chen, Na; Harmon, Mark E.; Li, Yuan; Cao, Xiaoyan; Chappell, Mark A.; Mao, Jingdong

    2015-10-01

    A feedback between decomposition and litter chemical composition occurs with decomposition altering composition that in turn influences the decomposition rate. Elucidating the temporal pattern of chemical composition is vital to understand this feedback, but the effects of plant species and climate on chemical changes remain poorly understood, especially over multiple years. In a 10-year decomposition experiment with litter of four species (Acer saccharum, Drypetes glauca, Pinus resinosa, and Thuja plicata) from four sites that range from the arctic to tropics, we determined the abundance of 11 litter chemical constituents that were grouped into waxes, carbohydrates, lignin/tannins, and proteins/peptides using advanced 13C solid-state NMR techniques. Decomposition generally led to an enrichment of waxes and a depletion of carbohydrates, whereas the changes of other chemical constituents were inconsistent. Inconsistent convergence in chemical compositions during decomposition was observed among different litter species across a range of site conditions, whereas one litter species converged under different climate conditions. Our data clearly demonstrate that plant species rather than climate greatly alters the temporal pattern of litter chemical composition, suggesting the decomposition-chemistry feedback varies among different plant species.

  14. Plant Species Rather Than Climate Greatly Alters the Temporal Pattern of Litter Chemical Composition During Long-Term Decomposition

    PubMed Central

    Li, Yongfu; Chen, Na; Harmon, Mark E.; Li, Yuan; Cao, Xiaoyan; Chappell, Mark A.; Mao, Jingdong

    2015-01-01

    A feedback between decomposition and litter chemical composition occurs with decomposition altering composition that in turn influences the decomposition rate. Elucidating the temporal pattern of chemical composition is vital to understand this feedback, but the effects of plant species and climate on chemical changes remain poorly understood, especially over multiple years. In a 10-year decomposition experiment with litter of four species (Acer saccharum, Drypetes glauca, Pinus resinosa, and Thuja plicata) from four sites that range from the arctic to tropics, we determined the abundance of 11 litter chemical constituents that were grouped into waxes, carbohydrates, lignin/tannins, and proteins/peptides using advanced 13C solid-state NMR techniques. Decomposition generally led to an enrichment of waxes and a depletion of carbohydrates, whereas the changes of other chemical constituents were inconsistent. Inconsistent convergence in chemical compositions during decomposition was observed among different litter species across a range of site conditions, whereas one litter species converged under different climate conditions. Our data clearly demonstrate that plant species rather than climate greatly alters the temporal pattern of litter chemical composition, suggesting the decomposition-chemistry feedback varies among different plant species. PMID:26515033

  15. Assessing risks to non-target species during poison baiting programs for feral cats.

    PubMed

    Buckmaster, Tony; Dickman, Christopher R; Johnston, Michael J

    2014-01-01

    Poison baiting is used frequently to reduce the impacts of pest species of mammals on agricultural and biodiversity interests. However, baiting may not be appropriate if non-target species are at risk of poisoning. Here we use a desktop decision tree approach to assess the risks to non-target vertebrate species in Australia that arise from using poison baits developed to control feral house cats (Felis catus). These baits are presented in the form of sausages with toxicant implanted in the bait medium within an acid-soluble polymer capsule (hard shell delivery vehicle, or HSDV) that disintegrates after ingestion. Using criteria based on body size, diet and feeding behaviour, we assessed 221 of Australia's 3,769 native vertebrate species as likely to consume cat-baits, with 47 of these likely to ingest implanted HSDVs too. Carnivorous marsupials were judged most likely to consume both the baits and HSDVs, with some large-bodied and ground-active birds and reptiles also consuming them. If criteria were relaxed, a further 269 species were assessed as possibly able to consume baits and 343 as possibly able to consume HSDVs; most of these consumers were birds. One threatened species, the Tasmanian devil (Sarcophilus harrisii) was judged as definitely able to consume baits with implanted HSDVs, whereas five threatened species of birds and 21 species of threatened mammals were rated as possible consumers. Amphibia were not considered to be at risk. We conclude that most species of native Australian vertebrates would not consume surface-laid baits during feral cat control programs, and that significantly fewer would be exposed to poisoning if HSDVs were employed. However, risks to susceptible species should be quantified in field or pen trials prior to the implementation of a control program, and minimized further by applying baits at times and in places where non-target species have little access.

  16. Assessing Risks to Non-Target Species during Poison Baiting Programs for Feral Cats

    PubMed Central

    Buckmaster, Tony; Dickman, Christopher R.; Johnston, Michael J.

    2014-01-01

    Poison baiting is used frequently to reduce the impacts of pest species of mammals on agricultural and biodiversity interests. However, baiting may not be appropriate if non-target species are at risk of poisoning. Here we use a desktop decision tree approach to assess the risks to non-target vertebrate species in Australia that arise from using poison baits developed to control feral house cats (Felis catus). These baits are presented in the form of sausages with toxicant implanted in the bait medium within an acid-soluble polymer capsule (hard shell delivery vehicle, or HSDV) that disintegrates after ingestion. Using criteria based on body size, diet and feeding behaviour, we assessed 221 of Australia's 3,769 native vertebrate species as likely to consume cat-baits, with 47 of these likely to ingest implanted HSDVs too. Carnivorous marsupials were judged most likely to consume both the baits and HSDVs, with some large-bodied and ground-active birds and reptiles also consuming them. If criteria were relaxed, a further 269 species were assessed as possibly able to consume baits and 343 as possibly able to consume HSDVs; most of these consumers were birds. One threatened species, the Tasmanian devil (Sarcophilus harrisii) was judged as definitely able to consume baits with implanted HSDVs, whereas five threatened species of birds and 21 species of threatened mammals were rated as possible consumers. Amphibia were not considered to be at risk. We conclude that most species of native Australian vertebrates would not consume surface-laid baits during feral cat control programs, and that significantly fewer would be exposed to poisoning if HSDVs were employed. However, risks to susceptible species should be quantified in field or pen trials prior to the implementation of a control program, and minimized further by applying baits at times and in places where non-target species have little access. PMID:25229348

  17. Chemical genetics-based development of small molecules targeting hepatitis C virus.

    PubMed

    Jin, Guanghai; Lee, Jisu; Lee, Kyeong

    2017-09-01

    Hepatitis C virus (HCV) infection is a major worldwide problem that has emerged as one of the most significant diseases affecting humans. There are currently no vaccines or efficient therapies without side effects, despite today's advanced medical technology. Currently, the common therapy for most patients (i.e. genotype 1) is combination of HCV-specific direct-acting antivirals (DAAs). Up to 2011, the standard of care (SOC) was a combination of peg-IFNα with ribavirin (RBV). After approval of NS3/4A protease inhibitor, SOC was peg-IFNα and RBV with either the first-generation DAAs boceprevir or telaprevir. In the past several years, various novel small molecules have been discovered and some of them (i.e., HCV polymerase, protease, helicase and entry inhibitors) have undergone clinical trials. Between 2013 and 2016, the second-generation DAA drugs simeprevir, asunaprevir, daclatasvir, dasabuvir, sofosbuvir, and elbasvir were approved, as well as the combinational drugs Harvoni ® , Zepatier ® , Technivie ® , and Epclusa ® . A number of reviews have been recently published describing the structure-activity relationship (SAR) in the development of HCV inhibitors and outlining current therapeutic approaches to hepatitis C infection. Target identification involves studying a drug's mechanism of action (MOA), and a variety of target identification methods have been developed in the past few years. Chemical biology has emerged as a powerful tool for studying biological processes using small molecules. The use of chemical genetic methods is a valuable strategy for studying the molecular mechanisms of the viral lifecycle and screening for anti-viral agents. Two general screening approaches have been employed: forward and reverse chemical genetics. This review reveals information on the small molecules in HCV drug discovery by using chemical genetics for targeting the HCV protein and describes successful examples of targets identified with these methods.

  18. Validation of N-myristoyltransferase as an antimalarial drug target using an integrated chemical biology approach

    NASA Astrophysics Data System (ADS)

    Wright, Megan H.; Clough, Barbara; Rackham, Mark D.; Rangachari, Kaveri; Brannigan, James A.; Grainger, Munira; Moss, David K.; Bottrill, Andrew R.; Heal, William P.; Broncel, Malgorzata; Serwa, Remigiusz A.; Brady, Declan; Mann, David J.; Leatherbarrow, Robin J.; Tewari, Rita; Wilkinson, Anthony J.; Holder, Anthony A.; Tate, Edward W.

    2014-02-01

    Malaria is an infectious disease caused by parasites of the genus Plasmodium, which leads to approximately one million deaths per annum worldwide. Chemical validation of new antimalarial targets is urgently required in view of rising resistance to current drugs. One such putative target is the enzyme N-myristoyltransferase, which catalyses the attachment of the fatty acid myristate to protein substrates (N-myristoylation). Here, we report an integrated chemical biology approach to explore protein myristoylation in the major human parasite P. falciparum, combining chemical proteomic tools for identification of the myristoylated and glycosylphosphatidylinositol-anchored proteome with selective small-molecule N-myristoyltransferase inhibitors. We demonstrate that N-myristoyltransferase is an essential and chemically tractable target in malaria parasites both in vitro and in vivo, and show that selective inhibition of N-myristoylation leads to catastrophic and irreversible failure to assemble the inner membrane complex, a critical subcellular organelle in the parasite life cycle. Our studies provide the basis for the development of new antimalarials targeting N-myristoyltransferase.

  19. Setting realistic recovery targets for two interacting endangered species, sea otter and northern abalone.

    PubMed

    Chadès, Iadine; Curtis, Janelle M R; Martin, Tara G

    2012-12-01

    Failure to account for interactions between endangered species may lead to unexpected population dynamics, inefficient management strategies, waste of scarce resources, and, at worst, increased extinction risk. The importance of species interactions is undisputed, yet recovery targets generally do not account for such interactions. This shortcoming is a consequence of species-centered legislation, but also of uncertainty surrounding the dynamics of species interactions and the complexity of modeling such interactions. The northern sea otter (Enhydra lutris kenyoni) and one of its preferred prey, northern abalone (Haliotis kamtschatkana), are endangered species for which recovery strategies have been developed without consideration of their strong predator-prey interactions. Using simulation-based optimization procedures from artificial intelligence, namely reinforcement learning and stochastic dynamic programming, we combined sea otter and northern abalone population models with functional-response models and examined how different management actions affect population dynamics and the likelihood of achieving recovery targets for each species through time. Recovery targets for these interacting species were difficult to achieve simultaneously in the absence of management. Although sea otters were predicted to recover, achieving abalone recovery targets failed even when threats to abalone such as predation and poaching were reduced. A management strategy entailing a 50% reduction in the poaching of northern abalone was a minimum requirement to reach short-term recovery goals for northern abalone when sea otters were present. Removing sea otters had a marginally positive effect on the abalone population but only when we assumed a functional response with strong predation pressure. Our optimization method could be applied more generally to any interacting threatened or invasive species for which there are multiple conservation objectives. © 2012 Society for

  20. Anopheline larval habitats seasonality and species distribution: a prerequisite for effective targeted larval habitats control programmes.

    PubMed

    Kweka, Eliningaya J; Zhou, Guofa; Munga, Stephen; Lee, Ming-Chieh; Atieli, Harrysone E; Nyindo, Mramba; Githeko, Andrew K; Yan, Guiyun

    2012-01-01

    Larval control is of paramount importance in the reduction of malaria vector abundance and subsequent disease transmission reduction. Understanding larval habitat succession and its ecology in different land use managements and cropping systems can give an insight for effective larval source management practices. This study investigated larval habitat succession and ecological parameters which influence larval abundance in malaria epidemic prone areas of western Kenya. A total of 51 aquatic habitats positive for anopheline larvae were surveyed and visited once a week for a period of 85 weeks in succession. Habitats were selected and identified. Mosquito larval species, physico-chemical parameters, habitat size, grass cover, crop cycle and distance to nearest house were recorded. Polymerase chain reaction revealed that An. gambiae s.l was the most dominant vector species comprised of An.gambiae s.s (77.60%) and An.arabiensis (18.34%), the remaining 4.06% had no amplification by polymerase chain reaction. Physico-chemical parameters and habitat size significantly influenced abundance of An. gambiae s.s (P = 0.024) and An. arabiensis (P = 0.002) larvae. Further, larval species abundance was influenced by crop cycle (P≤0.001), grass cover (P≤0.001), while distance to nearest houses significantly influenced the abundance of mosquito species larvae (r = 0.920;P≤0.001). The number of predator species influenced mosquito larval abundance in different habitat types. Crop weeding significantly influenced with the abundance of An.gambiae s.l (P≤0.001) when preceded with fertilizer application. Significantly higher anopheline larval abundance was recorded in habitats in pasture compared to farmland (P = 0.002). When habitat stability and habitat types were considered, hoof print were the most productive followed by disused goldmines. These findings suggest that implementation of effective larval control programme should be targeted with larval habitats

  1. Chemical communication threatened by endocrine-disrupting chemicals.

    PubMed Central

    Fox, Jennifer E

    2004-01-01

    Communication on a cellular level--defined as chemical signaling, sensing, and response--is an essential and universal component of all living organisms and the framework that unites all ecosystems. Evolutionarily conserved signaling "webs," existing both within an organism and between organisms, rely on efficient and accurate interpretation of chemical signals by receptors. Therefore, endocrine-disrupting chemicals (EDCs), which have been shown to disrupt hormone signaling in laboratory animals and exposed wildlife, may have broader implications for disrupting signaling webs that have yet to be identified as possible targets. In this article, I explore common evolutionary themes of chemical signaling (e.g., estrogen signaling in vertebrates and phytoestrogen signaling from plants to symbiotic soil bacteria) and show that such signaling systems are targets of disruption by EDCs. Recent evolutionary phylogenetic data have shown that the estrogen receptor (ER) is the ancestral receptor from which all other steroid receptors have evolved. In addition to binding endogenous estrogens, ERs also bind phytoestrogens, an ability shared in common with nodulation D protein (NodD) receptors found in Rhizobium soil bacteria. Recent data have shown that many of the same synthetic and natural environmental chemicals that disrupt endocrine signaling in vertebrates also disrupt phytoestrogen-NodD receptor signaling in soil bacteria, which is necessary for nitrogen-fixing symbiosis. Bacteria-plant symbiosis is an unexpected target of EDCs, and other unexpected nontarget species may also be vulnerable to EDCs found in the environment. PMID:15121505

  2. Chemical profiles of body surfaces and nests from six Bornean stingless bee species.

    PubMed

    Leonhardt, Sara Diana; Blüthgen, Nico; Schmitt, Thomas

    2011-01-01

    Stingless bees (Apidae: Meliponini) are the most diverse group of Apid bees and represent common pollinators in tropical ecosystems. Like honeybees they live in large eusocial colonies and rely on complex chemical recognition and communication systems. In contrast to honeybees, their ecology and especially their chemical ecology have received only little attention, particularly in the Old World. We previously have analyzed the chemical profiles of six paleotropical stingless bee species from Borneo and revealed the presence of species-specific cuticular terpenes- an environmentally derived compound class so far unique among social insects. Here, we compared the bees' surface profiles to the chemistry of their nest material. Terpenes, alkanes, and alkenes were the dominant compound groups on both body surfaces and nest material. However, bee profiles and nests strongly differed in their chemical composition. Body surfaces thus did not merely mirror nests, rendering a passive compound transfer from nests to bees unlikely. The difference between nests and bees was particularly pronounced when all resin-derived compounds (terpenes) were excluded and only genetically determined compounds were considered. When terpenes were included, bee profiles and nest material still differed, because whole groups of terpenes (e.g., sesquiterpenes) were found in nest material of some species, but missing in their chemical profile, indicating that bees are able to influence the terpene composition both in their nests and on their surfaces.

  3. Analysis of chemical constituents in Cistanche species.

    PubMed

    Jiang, Yong; Tu, Peng-Fei

    2009-03-13

    Species of the genus of Cistanche (Rou Cong Rong in Chinese) are perennial parasite herbs, and are mainly distributed in arid lands and warm deserts. As a superior tonic for the treatment of kidney deficiency, impotence, female infertility, morbid leucorrhea, profuse metrorrhagia and senile constipation, Cistanche herbs earned the honor of "Ginseng of the desert". Recently, there has been increasing scientific attention on Herba Cistanche for its remarkable bioactivities including antioxidation, neuroprotection, and anti-aging. The chemical constituents of Cistanche plants mainly include volatile oils and non-volatile phenylethanoid glycosides (PhGs), iridoids, lignans, alditols, oligosaccharides and polysaccharides. Pharmacological studies show that PhGs are the main active components for curing kidney deficiency, antioxidation and neuroprotection; galactitol and oligosaccharides are the representatives for the treatment of senile constipation, while polysaccharides are responsible for improving body immunity. In this paper, the advances on the chemical constituents of Cistanche plants and their corresponding analyses are reviewed.

  4. In vitro Perturbations of Targets in Cancer Hallmark Processes Predict Rodent Chemical Carcinogenesis

    EPA Science Inventory

    Thousands of untested chemicals in the environment require efficient characterization of carcinogenic potential in humans. A proposed solution is rapid testing of chemicals using in vitro high-throughput screening (HTS) assays for targets in pathways linked to disease processes ...

  5. Secondary targets of nitrite-derived reactive nitrogen species: nitrosation/nitration pathways, antioxidant defense mechanisms and toxicological implications.

    PubMed

    d'Ischia, Marco; Napolitano, Alessandra; Manini, Paola; Panzella, Lucia

    2011-12-19

    Nitrite, the primary metabolite of nitric oxide (NO) and a widely diffused component of human diet, plays distinct and increasingly appreciated roles in human physiology. However, when exposed to acidic environments, typically in the stomach, or under oxidative stress conditions, it may be converted to a range of reactive nitrogen species (RNS) which in turn can target a variety of biomolecules. Typical consequences of toxicological relevance include protein modification, DNA base deamination and the formation of N-nitrosamines, among the most potent mutagenic and carcinogenic compounds for humans. Besides primary biomolecules, nitrite can cause structural modifications to a variety of endogenous and exogenous organic compounds, ranging from polyunsaturated fatty acids to estrogens, tocopherol, catecholamines, furans, retinoids, dietary phenols, and a range of xenobiotics. The study of the interactions between nitrite and key food components, including phenolic antioxidants, has therefore emerged as an area of great promise for delineating innovative strategies in cancer chemoprevention. Depending on substrates and conditions, diverse reaction pathways may compete to determine product features and distribution patterns. These include nitrosation and nitration but also oxidation, via electron transfer to nitrosonium ion or nitrogen dioxide. This contribution aims to provide an overview of the main classes of compounds that can be targeted by nitrite and to discuss at chemical levels the possible reaction mechanisms under conditions that model those occurring in the stomach. The toxicological implications of the nitrite-modified molecules are finally addressed, and a rational chemical approach to the design of potent antinitrosing agents is illustrated. © 2011 American Chemical Society

  6. Marine chemical technology and sensors for marine waters: potentials and limits.

    PubMed

    Moore, Tommy S; Mullaugh, Katherine M; Holyoke, Rebecca R; Madison, Andrew S; Yücel, Mustafa; Luther, George W

    2009-01-01

    A significant need exists for in situ sensors that can measure chemical species involved in the major processes of primary production (photosynthesis and chemosynthesis) and respiration. Some key chemical species are O2, nutrients (N and P), micronutrients (metals), pCO2, dissolved inorganic carbon (DIC), pH, and sulfide. Sensors need to have excellent detection limits, precision, selectivity, response time, a large dynamic concentration range, low power consumption, robustness, and less variation of instrument response with temperature and pressure, as well as be free from fouling problems (biological, physical, and chemical). Here we review the principles of operation of most sensors used in marine waters. We also show that some sensors can be used in several different oceanic environments to detect the target chemical species, whereas others are useful in only one environment because of various limitations. Several sensors can be used truly in situ, whereas many others involve water brought into a flow cell via tubing to the analyzer in the environment or aboard ship. Multi-element sensors that measure many chemical species in the same water mass should be targeted for further development.

  7. Some inconvenient truths about biosignatures involving two chemical species on Earth-like exoplanets.

    PubMed

    Rein, Hanno; Fujii, Yuka; Spiegel, David S

    2014-05-13

    The detection of strong thermochemical disequilibrium in the atmosphere of an extrasolar planet is thought to be a potential biosignature. In this article we present a previously unidentified kind of false positive that can mimic a disequilibrium or any other biosignature that involves two chemical species. We consider a scenario where the exoplanet hosts a moon that has its own atmosphere and neither of the atmospheres is in chemical disequilibrium. Our results show that the integrated spectrum of the planet and the moon closely resembles that of a single object in strong chemical disequilibrium. We derive a firm limit on the maximum spectral resolution that can be obtained for both directly imaged and transiting planets. The spectral resolution of even idealized space-based spectrographs that might be achievable in the next several decades is in general insufficient to break the degeneracy. Both chemical species can only be definitively confirmed in the same object if absorption features of both chemicals can be unambiguously identified and their combined depth exceeds 100%.

  8. Some inconvenient truths about biosignatures involving two chemical species on Earth-like exoplanets

    PubMed Central

    Rein, Hanno; Fujii, Yuka; Spiegel, David S.

    2014-01-01

    The detection of strong thermochemical disequilibrium in the atmosphere of an extrasolar planet is thought to be a potential biosignature. In this article we present a previously unidentified kind of false positive that can mimic a disequilibrium or any other biosignature that involves two chemical species. We consider a scenario where the exoplanet hosts a moon that has its own atmosphere and neither of the atmospheres is in chemical disequilibrium. Our results show that the integrated spectrum of the planet and the moon closely resembles that of a single object in strong chemical disequilibrium. We derive a firm limit on the maximum spectral resolution that can be obtained for both directly imaged and transiting planets. The spectral resolution of even idealized space-based spectrographs that might be achievable in the next several decades is in general insufficient to break the degeneracy. Both chemical species can only be definitively confirmed in the same object if absorption features of both chemicals can be unambiguously identified and their combined depth exceeds 100%. PMID:24778224

  9. Important sources and chemical species of ambient fine particles related to adverse health effects

    NASA Astrophysics Data System (ADS)

    Heo, J.

    2017-12-01

    Although many epidemiological studies have reported that exposure to ambient fine particulate matter (PM2.5) has been linked to increases in mortality and mobidity health outcomes, the key question of which chemical species and sources of PM2.5 are most harmful to public health remains unanswered in the air pollution research area. This study was designed to address the key question with evaluating the risks of exposure to chemical species and source-specific PM2.5 mass on morbidity. Hourly measurements of PM2.5 mass and its major chemical species, including organic carbon, elemental carbon, ions, and trace elements, were observed from January 1 to December 31, 2013 at four of the PM2.5 supersites in urban environments in Korea and the reuslts were used in a positive matrix factorization to estimate source contributions to PM2.5 mass. Nine sources, including secondary sulfate, secondary nitrate, mobile, biomass burning, roadway emission, industry, oil combustion, soil, and aged sea salt, were identified and secondary inorganic aerosol factors (i.e. secondary sulfalte, and secondary nitrate) were the dominant sources contributing to 40% of the total PM2.5 mass in the study region. In order to evaluate the risks of exposure to chemical species and sources of PM2.5 on morbidity, emergency room visits for cardivascular disease and respiratory disease were considered. Hourly health outcomes were compared with hourly measurments of the PM2.5 chemical species and sources using a poission generalized linear model incorporating natural splines, as well as time-stratified case-crossover design. The PM2.5 mass and speveral chemical components, such as organic carbon, elemetal carbon, zinc, and potassium, were strongly associated with morbidity. Source-apporitionmened PM2.5 mass derived from biomass burning, and mobile sources, was significantly associated with cardiovascular and respiratory diseases. The findings represent that local combustion may be particularly important

  10. A hybrid computer program for rapidly solving flowing or static chemical kinetic problems involving many chemical species

    NASA Technical Reports Server (NTRS)

    Mclain, A. G.; Rao, C. S. R.

    1976-01-01

    A hybrid chemical kinetic computer program was assembled which provides a rapid solution to problems involving flowing or static, chemically reacting, gas mixtures. The computer program uses existing subroutines for problem setup, initialization, and preliminary calculations and incorporates a stiff ordinary differential equation solution technique. A number of check cases were recomputed with the hybrid program and the results were almost identical to those previously obtained. The computational time saving was demonstrated with a propane-oxygen-argon shock tube combustion problem involving 31 chemical species and 64 reactions. Information is presented to enable potential users to prepare an input data deck for the calculation of a problem.

  11. Extracting sets of chemical substructures and protein domains governing drug-target interactions.

    PubMed

    Yamanishi, Yoshihiro; Pauwels, Edouard; Saigo, Hiroto; Stoven, Véronique

    2011-05-23

    The identification of rules governing molecular recognition between drug chemical substructures and protein functional sites is a challenging issue at many stages of the drug development process. In this paper we develop a novel method to extract sets of drug chemical substructures and protein domains that govern drug-target interactions on a genome-wide scale. This is made possible using sparse canonical correspondence analysis (SCCA) for analyzing drug substructure profiles and protein domain profiles simultaneously. The method does not depend on the availability of protein 3D structures. From a data set of known drug-target interactions including enzymes, ion channels, G protein-coupled receptors, and nuclear receptors, we extract a set of chemical substructures shared by drugs able to bind to a set of protein domains. These two sets of extracted chemical substructures and protein domains form components that can be further exploited in a drug discovery process. This approach successfully clusters protein domains that may be evolutionary unrelated but that bind a common set of chemical substructures. As shown in several examples, it can also be very helpful for predicting new protein-ligand interactions and addressing the problem of ligand specificity. The proposed method constitutes a contribution to the recent field of chemogenomics that aims to connect the chemical space with the biological space.

  12. Single and fused transgenic Bacillus thuringiensis rice alter the species-specific responses of non-target planthoppers to elevated carbon dioxide and temperature.

    PubMed

    Wan, Guijun; Dang, Zhihao; Wu, Gang; Parajulee, Megha N; Ge, Feng; Chen, Fajun

    2014-05-01

    The approval of transgenic Bacillus thuringiensis (Bt) rice by China was momentous for biotech crops, although it has yet to be approved for commercial production. Non-target pest problems in rice paddies, such as the three ecologically similar species of planthoppers Nilaparvata lugens, Laodelphax striatellus and Sogatella furcifera, could become increasingly serious under global climate change. Fused (Cry1Ab/Cry1Ac) and single (Cry1Ab) transgenic Bt rice were evaluated for effects on species-specific responses of planthoppers to elevated carbon dioxide (CO2) and temperature. Transgenic Bt rice lines significantly modified species-specific responses of the planthoppers to elevated CO2 and temperature. High temperature appears to favour outbreaks of S. furcifera relative to N. lugens and L. striatellus when feeding upon fused transgenic Bt rice, especially at elevated CO2 . Elevated CO2 at high temperature appears to be a factor reducing S. furcifera occurrence when feeding upon single transgenic Bt rice. Different types of transgenic Bt rice alter the species-specific responses of non-target planthoppers to elevated CO2 and temperature. Compared with their non-transgenic parental lines, the single transgenic Bt rice shows better performance in controlling the non-target planthopper S. furcifera by comparison with the fused transgenic Bt rice under elevated CO2 and temperature. It is suggested that multitypes of transgenic Bt rice be used in the field simultaneously in order to take advantage of high transgenic diversity for optimal performance against all pests in paddy fields. © 2013 Society of Chemical Industry.

  13. Chemical, Bioactive, and Antioxidant Potential of Twenty Wild Culinary Mushroom Species

    PubMed Central

    Sharma, S. K.; Gautam, N.

    2015-01-01

    The chemical, bioactive, and antioxidant potential of twenty wild culinary mushroom species being consumed by the people of northern Himalayan regions has been evaluated for the first time in the present study. Nutrients analyzed include protein, crude fat, fibres, carbohydrates, and monosaccharides. Besides, preliminary study on the detection of toxic compounds was done on these species. Bioactive compounds evaluated are fatty acids, amino acids, tocopherol content, carotenoids (β-carotene, lycopene), flavonoids, ascorbic acid, and anthocyanidins. Fruitbodies extract of all the species was tested for different types of antioxidant assays. Although differences were observed in the net values of individual species all the species were found to be rich in protein, and carbohydrates and low in fat. Glucose was found to be the major monosaccharide. Predominance of UFA (65–70%) over SFA (30–35%) was observed in all the species with considerable amounts of other bioactive compounds. All the species showed higher effectiveness for antioxidant capacities. PMID:26199938

  14. Chemical, Bioactive, and Antioxidant Potential of Twenty Wild Culinary Mushroom Species.

    PubMed

    Sharma, S K; Gautam, N

    2015-01-01

    The chemical, bioactive, and antioxidant potential of twenty wild culinary mushroom species being consumed by the people of northern Himalayan regions has been evaluated for the first time in the present study. Nutrients analyzed include protein, crude fat, fibres, carbohydrates, and monosaccharides. Besides, preliminary study on the detection of toxic compounds was done on these species. Bioactive compounds evaluated are fatty acids, amino acids, tocopherol content, carotenoids (β-carotene, lycopene), flavonoids, ascorbic acid, and anthocyanidins. Fruitbodies extract of all the species was tested for different types of antioxidant assays. Although differences were observed in the net values of individual species all the species were found to be rich in protein, and carbohydrates and low in fat. Glucose was found to be the major monosaccharide. Predominance of UFA (65-70%) over SFA (30-35%) was observed in all the species with considerable amounts of other bioactive compounds. All the species showed higher effectiveness for antioxidant capacities.

  15. In silico models for predicting vector control chemicals targeting Aedes aegypti

    PubMed Central

    Devillers, J.; Lagneau, C.; Lattes, A.; Garrigues, J.C.; Clémenté, M.M.; Yébakima, A.

    2014-01-01

    Human arboviral diseases have emerged or re-emerged in numerous countries worldwide due to a number of factors including the lack of progress in vaccine development, lack of drugs, insecticide resistance in mosquitoes, climate changes, societal behaviours, and economical constraints. Thus, Aedes aegypti is the main vector of the yellow fever and dengue fever flaviviruses and is also responsible for several recent outbreaks of the chikungunya alphavirus. As for the other mosquito species, the A. aegypti control relies heavily on the use of insecticides. However, because of increasing resistance to the different families of insecticides, reduction of Aedes populations is becoming increasingly difficult. Despite the unquestionable utility of insecticides in fighting mosquito populations, there are very few new insecticides developed and commercialized for vector control. This is because the high cost of the discovery of an insecticide is not counterbalanced by the ‘low profitability’ of the vector control market. Fortunately, the use of quantitative structure–activity relationship (QSAR) modelling allows the reduction of time and cost in the discovery of new chemical structures potentially active against mosquitoes. In this context, the goal of the present study was to review all the existing QSAR models on A. aegypti. The homology and pharmacophore models were also reviewed. Specific attention was paid to show the variety of targets investigated in Aedes in relation to the physiology and ecology of the mosquito as well as the diversity of the chemical structures which have been proposed, encompassing man-made and natural substances. PMID:25275884

  16. In vitro perturbations of targets in cancer hallmark processes predict rodent chemical carcinogenesis.

    PubMed

    Kleinstreuer, Nicole C; Dix, David J; Houck, Keith A; Kavlock, Robert J; Knudsen, Thomas B; Martin, Matthew T; Paul, Katie B; Reif, David M; Crofton, Kevin M; Hamilton, Kerry; Hunter, Ronald; Shah, Imran; Judson, Richard S

    2013-01-01

    Thousands of untested chemicals in the environment require efficient characterization of carcinogenic potential in humans. A proposed solution is rapid testing of chemicals using in vitro high-throughput screening (HTS) assays for targets in pathways linked to disease processes to build models for priority setting and further testing. We describe a model for predicting rodent carcinogenicity based on HTS data from 292 chemicals tested in 672 assays mapping to 455 genes. All data come from the EPA ToxCast project. The model was trained on a subset of 232 chemicals with in vivo rodent carcinogenicity data in the Toxicity Reference Database (ToxRefDB). Individual HTS assays strongly associated with rodent cancers in ToxRefDB were linked to genes, pathways, and hallmark processes documented to be involved in tumor biology and cancer progression. Rodent liver cancer endpoints were linked to well-documented pathways such as peroxisome proliferator-activated receptor signaling and TP53 and novel targets such as PDE5A and PLAUR. Cancer hallmark genes associated with rodent thyroid tumors were found to be linked to human thyroid tumors and autoimmune thyroid disease. A model was developed in which these genes/pathways function as hypothetical enhancers or promoters of rat thyroid tumors, acting secondary to the key initiating event of thyroid hormone disruption. A simple scoring function was generated to identify chemicals with significant in vitro evidence that was predictive of in vivo carcinogenicity in different rat tissues and organs. This scoring function was applied to an external test set of 33 compounds with carcinogenicity classifications from the EPA's Office of Pesticide Programs and successfully (p = 0.024) differentiated between chemicals classified as "possible"/"probable"/"likely" carcinogens and those designated as "not likely" or with "evidence of noncarcinogenicity." This model represents a chemical carcinogenicity prioritization tool supporting targeted

  17. Targeted modulation of reactive oxygen species in the vascular endothelium.

    PubMed

    Shuvaev, Vladimir V; Muzykantov, Vladimir R

    2011-07-15

    'Endothelial cells lining vascular luminal surface represent an important site of signaling and injurious effects of reactive oxygen species (ROS) produced by other cells and endothelium itself in ischemia, inflammation and other pathological conditions. Targeted delivery of ROS modulating enzymes conjugated with antibodies to endothelial surface molecules (vascular immunotargeting) provides site-specific interventions in the endothelial ROS, unattainable by other formulations including PEG-modified enzymes. Targeting of ROS generating enzymes (e.g., glucose oxidase) provides ROS- and site-specific models of endothelial oxidative stress, whereas targeting of antioxidant enzymes SOD and catalase offers site-specific quenching of superoxide anion and H(2)O(2). These targeted antioxidant interventions help to clarify specific role of endothelial ROS in vascular and pulmonary pathologies and provide basis for design of targeted therapeutics for treatment of these pathologies. In particular, antibody/catalase conjugates alleviate acute lung ischemia/reperfusion injury, whereas antibody/SOD conjugates inhibit ROS-mediated vasoconstriction and inflammatory endothelial signaling. Encapsulation in protease-resistant, ROS-permeable carriers targeted to endothelium prolongs protective effects of antioxidant enzymes, further diversifying the means for targeted modulation of endothelial ROS. Copyright © 2011 Elsevier B.V. All rights reserved.

  18. Origin and maintenance of chemical diversity in a species-rich tropical tree lineage.

    PubMed

    Salazar, Diego; Lokvam, John; Mesones, Italo; Vásquez Pilco, Magno; Ayarza Zuñiga, Jacqueline Milagros; de Valpine, Perry; Fine, Paul V A

    2018-06-01

    Plant secondary metabolites play important ecological and evolutionary roles, most notably in the deterrence of natural enemies. The classical theory explaining the evolution of plant chemical diversity is that new defences arise through a pairwise co-evolutionary arms race between plants and their specialized natural enemies. However, plant species are bombarded by dozens of different herbivore taxa from disparate phylogenetic lineages that span a wide range of feeding strategies and have distinctive physiological constraints that interact differently with particular plant metabolites. How do plant defence chemicals evolve under such multiple and potentially contrasting selective pressures imposed by diverse herbivore communities? To tackle this question, we exhaustively characterized the chemical diversity and insect herbivore fauna from 31 sympatric species of Amazonian Protieae (Burseraceae) trees. Using a combination of phylogenetic, metabolomic and statistical learning tools, we show that secondary metabolites that were associated with repelling herbivores (1) were more frequent across the Protieae phylogeny and (2) were found in average higher abundance than other compounds. Our findings suggest that generalist herbivores can play an important role in shaping plant chemical diversity and support the hypothesis that chemical diversity can also arise from the cumulative outcome of multiple diffuse interactions.

  19. Target Abundance-Based Fitness Screening (TAFiS) Facilitates Rapid Identification of Target-Specific and Physiologically Active Chemical Probes

    PubMed Central

    Butts, Arielle; DeJarnette, Christian; Peters, Tracy L.; Parker, Josie E.; Kerns, Morgan E.; Eberle, Karen E.; Kelly, Steve L.

    2017-01-01

    ABSTRACT Traditional approaches to drug discovery are frustratingly inefficient and have several key limitations that severely constrain our capacity to rapidly identify and develop novel experimental therapeutics. To address this, we have devised a second-generation target-based whole-cell screening assay based on the principles of competitive fitness, which can rapidly identify target-specific and physiologically active compounds. Briefly, strains expressing high, intermediate, and low levels of a preselected target protein are constructed, tagged with spectrally distinct fluorescent proteins (FPs), and pooled. The pooled strains are then grown in the presence of various small molecules, and the relative growth of each strain within the mixed culture is compared by measuring the intensity of the corresponding FP tags. Chemical-induced population shifts indicate that the bioactivity of a small molecule is dependent upon the target protein’s abundance and thus establish a specific functional interaction. Here, we describe the molecular tools required to apply this technique in the prevalent human fungal pathogen Candida albicans and validate the approach using two well-characterized drug targets—lanosterol demethylase and dihydrofolate reductase. However, our approach, which we have termed target abundance-based fitness screening (TAFiS), should be applicable to a wide array of molecular targets and in essentially any genetically tractable microbe. IMPORTANCE Conventional drug screening typically employs either target-based or cell-based approaches. The first group relies on biochemical assays to detect modulators of a purified target. However, hits frequently lack drug-like characteristics such as membrane permeability and target specificity. Cell-based screens identify compounds that induce a desired phenotype, but the target is unknown, which severely restricts further development and optimization. To address these issues, we have developed a second

  20. Fast, sensitive, and selective gas chromatography tandem mass spectrometry method for the target analysis of chemical secretions from femoral glands in lizards.

    PubMed

    Sáiz, Jorge; García-Roa, Roberto; Martín, José; Gómara, Belén

    2017-09-08

    Chemical signaling is a widespread mode of communication among living organisms that is used to establish social organization, territoriality and/or for mate choice. In lizards, femoral and precloacal glands are important sources of chemical signals. These glands protrude chemical secretions used to mark territories and also, to provide valuable information from the bearer to other individuals. Ecologists have studied these chemical secretions for decades in order to increase the knowledge of chemical communication in lizards. Although several studies have focused on the chemical analysis of these secretions, there is a lack of faster, more sensitive and more selective analytical methodologies for their study. In this work a new GC coupled to tandem triple quadrupole MS (GC-QqQ (MS/MS)) methodology is developed and proposed for the target study of 12 relevant compounds often found in lizard secretions (i.e. 1-hexadecanol, palmitic acid, 1-octadecanol, oleic acid, stearic acid, 1-tetracosanol, squalene, cholesta-3,5-diene, α-tocopherol, cholesterol, ergosterol and campesterol). The method baseline-separated the analytes in less than 7min, with instrumental limits of detection ranging from 0.04 to 6.0ng/mL. It was possible to identify differences in the composition of the samples from the lizards analyzed, which depended on the species, the habitat occupied and the diet of the individuals. Moreover, α-tocopherol has been determined for the first time in a lizard species, which was thought to lack its expression in chemical secretions. Globally, the methodology has been proven to be a valuable alternative to other published methods with important improvements in terms of analysis time, sensitivity, and selectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Start codon targeted (SCoT) and target region amplification polymorphism (TRAP) for evaluating the genetic relationship of Dendrobium species.

    PubMed

    Feng, Shangguo; He, Refeng; Yang, Sai; Chen, Zhe; Jiang, Mengying; Lu, Jiangjie; Wang, Huizhong

    2015-08-10

    Two molecular marker systems, start codon targeted (SCoT) and target region amplification polymorphism (TRAP), were used for genetic relationship analysis of 36 Dendrobium species collected from China. Twenty-two selected SCoT primers produced 337 loci, of which 324 (96%) were polymorphic, whereas 13 TRAP primer combinations produced a total of 510 loci, with 500 (97.8%) of them being polymorphic. An average polymorphism information content of 0.953 and 0.983 was detected using the SCoT and TRAP primers, respectively, showing that a high degree of genetic diversity exists among Chinese Dendrobium species. The partition of clusters in the unweighted pair group method with arithmetic mean dendrogram and principal coordinate analysis plot based on the SCoT and TRAP markers was similar and clustered the 36 Dendrobium species into four main groups. Our results will provide useful information for resource protection and will also be useful to improve the current Dendrobium breeding programs. Our results also demonstrate that SCoT and TRAP markers are informative and can be used to evaluate genetic relationships between Dendrobium species. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Optical detection of chemical warfare agents and toxic industrial chemicals

    NASA Astrophysics Data System (ADS)

    Webber, Michael E.; Pushkarsky, Michael B.; Patel, C. Kumar N.

    2004-12-01

    We present an analytical model evaluating the suitability of optical absorption based spectroscopic techniques for detection of chemical warfare agents (CWAs) and toxic industrial chemicals (TICs) in ambient air. The sensor performance is modeled by simulating absorption spectra of a sample containing both the target and multitude of interfering species as well as an appropriate stochastic noise and determining the target concentrations from the simulated spectra via a least square fit (LSF) algorithm. The distribution of the LSF target concentrations determines the sensor sensitivity, probability of false positives (PFP) and probability of false negatives (PFN). The model was applied to CO2 laser based photoacosutic (L-PAS) CWA sensor and predicted single digit ppb sensitivity with very low PFP rates in the presence of significant amount of interferences. This approach will be useful for assessing sensor performance by developers and users alike; it also provides methodology for inter-comparison of different sensing technologies.

  3. Molecular Target Homology as a Basis for Species Extrapolation to Assess the Ecological Risk of Pharmaceuticals

    EPA Science Inventory

    Adverse effects of many chemical contaminants, including human pharmaceuticals and other chemicals of emerging concern (CECs), are initiated through interactions with specific proteins within the cells of effected organisms. When protein targets of a given chemical are known--as ...

  4. Pathogenicity Tests on Nine Mosquito Species and Several Non-target Organisms with Strelkovimermis spiculatus (Nemata Mermithidae).

    PubMed

    Becnel, J J; Johnson, M A

    1998-12-01

    Nine species of mosquitoes and several species of non-target aquatic organisms were tested for susceptibility to the mernaithid nematode, Strelkovimermis spiculatus. All species of Anopheles, Aedes, Culex, and Toxorhynchites exposed to S. spiculatus were susceptible. Of the nine mosquito species tested, C. pipiens quinquefasciatus had the greatest tolerance to initial invasion and the highest percent infection of those that survived. High levels of infection were also achieved with Aedes taeniorhynchus and A. albopictus, but these mosquitoes were significantly less tolerant to parasitism than C. pipiens quinquefasciatus. Strelkovimermis spiculatus did not infect or develop in any of the non-target hosts tested.

  5. An Unsolved Mystery: The Target-Recognizing RNA Species of MicroRNA Genes

    PubMed Central

    Chen, Chang-Zheng

    2013-01-01

    MicroRNAs (miRNAs) are an abundant class of endogenous ~ 21-nucleotide (nt) RNAs. These small RNAs are produced from long primary miRNA transcripts — pri-miRNAs — through sequential endonucleolytic maturation steps that yield precursor miRNA (pre-miRNA) intermediates and then the mature miRNAs. The mature miRNAs are loaded into the RNA-induced silencing complexes (RISC), and guide RISC to target mRNAs for cleavage and/or translational repression. This paradigm, which represents one of major discoveries of modern molecular biology, is built on the assumption that mature miRNAs are the only species produced from miRNA genes that recognize targets. This assumption has guided the miRNA field for more than a decade and has led to our current understanding of the mechanisms of target recognition and repression by miRNAs. Although progress has been made, fundamental questions remain unanswered with regard to the principles of target recognition and mechanisms of repression. Here I raise questions about the assumption that mature miRNAs are the only target-recognizing species produced from miRNA genes and discuss the consequences of working under an incomplete or incorrect assumption. Moreover, I present evolution-based and experimental evidence that support the roles of pri-/pre-miRNAs in target recognition and repression. Finally, I propose a conceptual framework that integrates the functions of pri-/pre-miRNAs and mature miRNAs in target recognition and repression. The integrated framework opens experimental enquiry and permits interpretation of fundamental problems that have so far been precluded. PMID:23685275

  6. Natural products used as a chemical library for protein-protein interaction targeted drug discovery.

    PubMed

    Jin, Xuemei; Lee, Kyungro; Kim, Nam Hee; Kim, Hyun Sil; Yook, Jong In; Choi, Jiwon; No, Kyoung Tai

    2018-01-01

    Protein-protein interactions (PPIs), which are essential for cellular processes, have been recognized as attractive therapeutic targets. Therefore, the construction of a PPI-focused chemical library is an inevitable necessity for future drug discovery. Natural products have been used as traditional medicines to treat human diseases for millennia; in addition, their molecular scaffolds have been used in diverse approved drugs and drug candidates. The recent discovery of the ability of natural products to inhibit PPIs led us to use natural products as a chemical library for PPI-targeted drug discovery. In this study, we collected natural products (NPDB) from non-commercial and in-house databases to analyze their similarities to small-molecule PPI inhibitors (iPPIs) and FDA-approved drugs by using eight molecular descriptors. Then, we evaluated the distribution of NPDB and iPPIs in the chemical space, represented by the molecular fingerprint and molecular scaffolds, to identify the promising scaffolds, which could interfere with PPIs. To investigate the ability of natural products to inhibit PPI targets, molecular docking was used. Then, we predicted a set of high-potency natural products by using the iPPI-likeness score based on a docking score-weighted model. These selected natural products showed high binding affinities to the PPI target, namely XIAP, which were validated in an in vitro experiment. In addition, the natural products with novel scaffolds might provide a promising starting point for further medicinal chemistry developments. Overall, our study shows the potency of natural products in targeting PPIs, which might help in the design of a PPI-focused chemical library for future drug discovery. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Artificial Chemical Reporter Targeting Strategy Using Bioorthogonal Click Reaction for Improving Active-Targeting Efficiency of Tumor.

    PubMed

    Yoon, Hong Yeol; Shin, Min Lee; Shim, Man Kyu; Lee, Sangmin; Na, Jin Hee; Koo, Heebeom; Lee, Hyukjin; Kim, Jong-Ho; Lee, Kuen Yong; Kim, Kwangmeyung; Kwon, Ick Chan

    2017-05-01

    Biological ligands such as aptamer, antibody, glucose, and peptide have been widely used to bind specific surface molecules or receptors in tumor cells or subcellular structures to improve tumor-targeting efficiency of nanoparticles. However, this active-targeting strategy has limitations for tumor targeting due to inter- and intraheterogeneity of tumors. In this study, we demonstrated an alternative active-targeting strategy using metabolic engineering and bioorthogonal click reaction to improve tumor-targeting efficiency of nanoparticles. We observed that azide-containing chemical reporters were successfully generated onto surface glycans of various tumor cells such as lung cancer (A549), brain cancer (U87), and breast cancer (BT-474, MDA-MB231, MCF-7) via metabolic engineering in vitro. In addition, we compared tumor targeting of artificial azide reporter with bicyclononyne (BCN)-conjugated glycol chitosan nanoparticles (BCN-CNPs) and integrin α v β 3 with cyclic RGD-conjugated CNPs (cRGD-CNPs) in vitro and in vivo. Fluorescence intensity of azide-reporter-targeted BCN-CNPs in tumor tissues was 1.6-fold higher and with a more uniform distribution compared to that of cRGD-CNPs. Moreover, even in the isolated heterogeneous U87 cells, BCN-CNPs could bind artificial azide reporters on tumor cells more uniformly (∼92.9%) compared to cRGD-CNPs. Therefore, the artificial azide-reporter-targeting strategy can be utilized for targeting heterogeneous tumor cells via bioorthogonal click reaction and may provide an alternative method of tumor targeting for further investigation in cancer therapy.

  8. Genotoxic chemical carcinogens target inducible genes in vivo

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hamilton, J.W.; McCaffrey, J.; Caron, R.M.

    1994-12-31

    Our laboratory is interested in whether carcinogen-induced DNA damage is distributed nonrandomly in the genome - that is, {open_quotes}targeted{close_quotes} to specific genes or gene regions in vivo. As an indirect measure of whether targeting occurs at the gene level, we have examined whether carcinogens differentially alter the expression of individual genes. We have compared the effects of model genotoxic carcinogens that principally induce either strand breaks, simple alkylations, bulky lesions, or DNA cross-links on the expression of several constitutive and inducible genes in a simple in vivo system, the chick embryo. Each agent was examined for its effects on genemore » expression over a 24 hour period corresponding to the period of maximal DNA damage and repair induced by each compound. The doses used in these studies represented the maximum doses that caused no overt toxicity over a 96 hour period but that induced significant levels of DNA damage. Our results demonstrate that inducible genes are targeted by chemical carcinogens. We hypothesize that such effects may be a result of DNA damage specifically altering DNA-protein interactions within the promoters of inducible genes.« less

  9. Chemical proteomics for target discovery of head-to-tail cyclized mini-proteins

    NASA Astrophysics Data System (ADS)

    Hellinger, Roland; Thell, Kathrin; Vasileva, Mina; Muhammad, Taj; Gunasekera, Sunithi; Kümmel, Daniel; Göransson, Ulf; Becker, Christian W.; Gruber, Christian W.

    2017-10-01

    Target deconvolution is one of the most challenging tasks in drug discovery, but a key step in drug development. In contrast to small molecules, there is a lack of validated and robust methodologies for target elucidation of peptides. In particular, it is difficult to apply these methods to cyclic and cysteine-stabilized peptides since they exhibit reduced amenability to chemical modification and affinity capture; however, such ribosomal synthesized and post-translationally modified peptide natural products are rich sources of promising drug candidates. For example, plant-derived circular peptides called cyclotides have recently attracted much attention due to their immunosuppressive effects and oral activity in the treatment of multiple sclerosis in mice, but their molecular target has hitherto not been reported. In this study a chemical proteomics approach using photo-affinity crosslinking was developed to determine a target of the circular peptide [T20K]kalata B1. Using this prototypic nature-derived peptide enabled the identification of a possible modulation of 14-3-3 proteins. This biochemical interaction was validated via competition pull down assays as well as a cellular reporter assay indicating an effect on 14-3-3-dependent transcriptional activity. As proof of concept, the presented approach may be applicable for target elucidation of various cyclic peptides and mini-proteins, in particular cyclotides, which represent a promising class of molecules in drug discovery and development.

  10. The influence of electrohydrodynamic flow on the distribution of chemical species in positive corona

    NASA Astrophysics Data System (ADS)

    Pontiga, Francisco; Yanallah, Khelifa; Bouazza, R.; Chen, Junhong

    2015-09-01

    A numerical simulation of positive corona discharge in air, including the effect of electrohydrodynamic (EHD) motion of the gas, has been carried out. Air flow is assumed to be confined between two parallel plates, and corona discharge is produced around a thin wire, midway between the plates. Therefore, fluid dynamics equations, including electrical forces, have been solved together with the continuity equation of each neutral species. The plasma chemical model included 24 chemical reactions and ten neutral species, in addition to electrons and positive ions. The results of the simulation have shown that the influence of EHD flow on the spatial distributions of the species is quite different depending on the species. Hence, reactive species like atomic oxygen and atomic nitrogen are confined to the vicinity of the wire, and they are weakly affected by the EHD gas motion. In contrast, nitrogen oxides and ozone are efficiently dragged outside the active region of the corona discharge by the EHD flow. This work was supported by the Spanish Government Agency ``Ministerio de Ciencia e Innovación'' under Contract No. FIS2011-25161.

  11. Chemical composition of Achillea schischkinii Sosn., an endemic species from Turkey

    USDA-ARS?s Scientific Manuscript database

    In this study, we investigated the chemical composition of an endemic species of Achillea schischkinii Sosn. (Asteraceae) collected from an eastern part of Turkey (Van). Air-dried aerial parts were subjected to water-distillation using a Clevenger-type system. The essential oil was analyzed by GC-MS...

  12. Systems Toxicology of Male Reproductive Development: Profiling 774 Chemicals for Molecular Targets and Adverse Outcomes

    PubMed Central

    Leung, Maxwell C.K.; Phuong, Jimmy; Baker, Nancy C.; Sipes, Nisha S.; Klinefelter, Gary R.; Martin, Matthew T.; McLaurin, Keith W.; Setzer, R. Woodrow; Darney, Sally Perreault; Judson, Richard S.; Knudsen, Thomas B.

    2015-01-01

    Background: Trends in male reproductive health have been reported for increased rates of testicular germ cell tumors, low semen quality, cryptorchidism, and hypospadias, which have been associated with prenatal environmental chemical exposure based on human and animal studies. Objective: In the present study we aimed to identify significant correlations between environmental chemicals, molecular targets, and adverse outcomes across a broad chemical landscape with emphasis on developmental toxicity of the male reproductive system. Methods: We used U.S. EPA’s animal study database (ToxRefDB) and a comprehensive literature analysis to identify 774 chemicals that have been evaluated for adverse effects on male reproductive parameters, and then used U.S. EPA’s in vitro high-throughput screening (HTS) database (ToxCastDB) to profile their bioactivity across approximately 800 molecular and cellular features. Results: A phenotypic hierarchy of testicular atrophy, sperm effects, tumors, and malformations, a composite resembling the human testicular dysgenesis syndrome (TDS) hypothesis, was observed in 281 chemicals. A subset of 54 chemicals with male developmental consequences had in vitro bioactivity on molecular targets that could be condensed into 156 gene annotations in a bipartite network. Conclusion: Computational modeling of available in vivo and in vitro data for chemicals that produce adverse effects on male reproductive end points revealed a phenotypic hierarchy across animal studies consistent with the human TDS hypothesis. We confirmed the known role of estrogen and androgen signaling pathways in rodent TDS, and importantly, broadened the list of molecular targets to include retinoic acid signaling, vascular remodeling proteins, G-protein coupled receptors (GPCRs), and cytochrome P450s. Citation: Leung MC, Phuong J, Baker NC, Sipes NS, Klinefelter GR, Martin MT, McLaurin KW, Setzer RW, Darney SP, Judson RS, Knudsen TB. 2016. Systems toxicology of male

  13. Chemical and mechanical changes during leaf expansion of four woody species of dry Restinga woodland.

    PubMed

    Schlindwein, C C D; Fett-Neto, A G; Dillenburg, L R

    2006-07-01

    Young leaves are preferential targets for herbivores, and plants have developed different strategies to protect them. This study aimed to evaluate different leaf attributes of presumed relevance in protection against herbivory in four woody species (Erythroxylum argentinum, Lithrea brasiliensis, Myrciaria cuspidata, and Myrsine umbellata), growing in a dry restinga woodland in southern Brazil. Evaluation of leaf parameters was made through single-point sampling of leaves (leaf mass per area and leaf contents of nitrogen, carbon, and pigments) at three developmental stages and through time-course sampling of expanding leaves (area and strength). Leaves of M. umbellata showed the highest leaf mass per area (LMA), the largest area, and the longest expansion period. On the other extreme, Myrc. cuspidata had the smallest LMA and leaf size, and the shortest expansion period. Similarly to L. brasiliensis, it displayed red young leaves. None of the species showed delayed-greening, which might be related to the high-irradiance growth conditions. Nitrogen contents reduced with leaf maturity and reached the highest values in the young leaves of E. argentinum and Myrc. cuspidata and the lowest in M. umbellata. Each species seems to present a different set of protective attributes during leaf expansion. Myrciaria cuspidata appears to rely mostly on chemical defences to protect its soft leaves, and anthocyanins might play this role at leaf youth, while M. umbellata seems to invest more on mechanical defences, even at early stages of leaf growth, as well as on a low allocation of nitrogen to the leaves. The other species display intermediate characteristics.

  14. Meat Species Identification using Loop-mediated Isothermal Amplification Assay Targeting Species-specific Mitochondrial DNA.

    PubMed

    Cho, Ae-Ri; Dong, Hee-Jin; Cho, Seongbeom

    2014-01-01

    Meat source fraud and adulteration scandals have led to consumer demands for accurate meat identification methods. Nucleotide amplification assays have been proposed as an alternative method to protein-based assays for meat identification. In this study, we designed Loop-mediated isothermal amplification (LAMP) assays targeting species-specific mitochondrial DNA to identify and discriminate eight meat species; cattle, pig, horse, goat, sheep, chicken, duck, and turkey. The LAMP primer sets were designed and the target genes were discriminated according to their unique annealing temperature generated by annealing curve analysis. Their unique annealing temperatures were found to be 85.56±0.07℃ for cattle, 84.96±0.08℃ for pig, and 85.99±0.05℃ for horse in the BSE-LAMP set (Bos taurus, Sus scrofa domesticus and Equus caballus); 84.91±0.11℃ for goat and 83.90±0.11℃ for sheep in the CO-LAMP set (Capra hircus and Ovis aries); and 86.31±0.23℃ for chicken, 88.66±0.12℃ for duck, and 84.49±0.08℃ for turkey in the GAM-LAMP set (Gallus gallus, Anas platyrhynchos and Meleagris gallopavo). No cross-reactivity was observed in each set. The limits of detection (LODs) of the LAMP assays in raw and cooked meat were determined from 10 pg/μL to 100 fg/μL levels, and LODs in raw and cooked meat admixtures were determined from 0.01% to 0.0001% levels. The assays were performed within 30 min and showed greater sensitivity than that of the PCR assays. These novel LAMP assays provide a simple, rapid, accurate, and sensitive technology for discrimination of eight meat species.

  15. Species diversity and chemical properties of litter influence non-additive effects of litter mixtures on soil carbon and nitrogen cycling

    PubMed Central

    Mao, Bing; Mao, Rong; Zeng, De-Hui

    2017-01-01

    Decomposition of litter mixtures generally cannot be predicted from the component species incubated in isolation. Therefore, such non-additive effects of litter mixing on soil C and N dynamics remain poorly understood in terrestrial ecosystems. In this study, litters of Mongolian pine and three dominant understory species and soil were collected from a Mongolian pine plantation in Northeast China. In order to examine the effects of mixed-species litter on soil microbial biomass N, soil net N mineralization and soil respiration, four single litter species and their mixtures consisting of all possible 2-, 3- and 4-species combinations were added to soils, respectively. In most instances, species mixing produced synergistic non-additive effects on soil microbial biomass N and soil respiration, but antagonistic non-additive effects on net N mineralization. Species composition rather than species richness explained the non-additive effects of species mixing on soil microbial biomass N and net N mineralization, due to the interspecific differences in litter chemical composition. Both litter species composition and richness explained non-additive soil respiration responses to mixed-species litter, while litter chemical diversity and chemical composition did not. Our study indicated that litter mixtures promoted soil microbial biomass N and soil respiration, and inhibited net N mineralization. Soil N related processes rather than soil respiration were partly explained by litter chemical composition and chemical diversity, highlighting the importance of functional diversity of litter on soil N cycling. PMID:28686660

  16. Species diversity and chemical properties of litter influence non-additive effects of litter mixtures on soil carbon and nitrogen cycling.

    PubMed

    Mao, Bing; Mao, Rong; Zeng, De-Hui

    2017-01-01

    Decomposition of litter mixtures generally cannot be predicted from the component species incubated in isolation. Therefore, such non-additive effects of litter mixing on soil C and N dynamics remain poorly understood in terrestrial ecosystems. In this study, litters of Mongolian pine and three dominant understory species and soil were collected from a Mongolian pine plantation in Northeast China. In order to examine the effects of mixed-species litter on soil microbial biomass N, soil net N mineralization and soil respiration, four single litter species and their mixtures consisting of all possible 2-, 3- and 4-species combinations were added to soils, respectively. In most instances, species mixing produced synergistic non-additive effects on soil microbial biomass N and soil respiration, but antagonistic non-additive effects on net N mineralization. Species composition rather than species richness explained the non-additive effects of species mixing on soil microbial biomass N and net N mineralization, due to the interspecific differences in litter chemical composition. Both litter species composition and richness explained non-additive soil respiration responses to mixed-species litter, while litter chemical diversity and chemical composition did not. Our study indicated that litter mixtures promoted soil microbial biomass N and soil respiration, and inhibited net N mineralization. Soil N related processes rather than soil respiration were partly explained by litter chemical composition and chemical diversity, highlighting the importance of functional diversity of litter on soil N cycling.

  17. Evidence for chemical interference effect of an allelopathic plant on neighboring plant species: A field study.

    PubMed

    Arroyo, Antonio I; Pueyo, Yolanda; Giner, M Luz; Foronda, Ana; Sanchez-Navarrete, Pedro; Saiz, Hugo; Alados, Concepción L

    2018-01-01

    Many studies have reported the phytotoxicity of allelopathic compounds under controlled conditions. However, more field studies are required to provide realistic evidences for the significance of allelopathic interference in natural communities. We conducted a 2-years field experiment in a semiarid plant community (NE Spain). Specifically, we planted juvenile individuals and sowed seeds of Salsola vermiculata L., Lygeum spartum L. and Artemisia herba-alba Asso. (three co-dominant species in the community) beneath adult individuals of the allelopathic shrub A. herba-alba, and assessed the growth, vitality, seed germination and seedling survival of those target species with and without the presence of chemical interference by the incorporation of activated carbon (AC) to the soil. In addition, juveniles and seeds of the same three target species were planted and sown beneath the canopy of adults of S. vermiculata (a shrub similar to A. herba-alba, but non-allelopathic) and in open bare soil to evaluate whether the allelopathic activity of A. herba-alba modulates the net outcome of its interactions with neighboring plants under contrasting abiotic stress conditions. We found that vitality of A. herba-alba juveniles was enhanced beneath A. herba-alba individuals when AC was present. Furthermore, we found that the interaction outcome in A. herba-alba microsite was neutral, whereas a positive outcome was found for S. vermiculata microsite, suggesting that allelopathy may limit the potential facilitative effects of the enhanced microclimatic conditions in A. herba-alba microsite. Yet, L. spartum juveniles were facilitated in A. herba-alba microsite. The interaction outcome in A. herba-alba microsite was positive under conditions of very high abiotic stress, indicating that facilitative interactions predominated over the interference of allelopathic plants under those conditions. These results highlight that laboratory studies can overestimate the significance of

  18. Evidence for chemical interference effect of an allelopathic plant on neighboring plant species: A field study

    PubMed Central

    Pueyo, Yolanda; Giner, M. Luz; Foronda, Ana; Sanchez-Navarrete, Pedro; Saiz, Hugo; Alados, Concepción L.

    2018-01-01

    Many studies have reported the phytotoxicity of allelopathic compounds under controlled conditions. However, more field studies are required to provide realistic evidences for the significance of allelopathic interference in natural communities. We conducted a 2-years field experiment in a semiarid plant community (NE Spain). Specifically, we planted juvenile individuals and sowed seeds of Salsola vermiculata L., Lygeum spartum L. and Artemisia herba-alba Asso. (three co-dominant species in the community) beneath adult individuals of the allelopathic shrub A. herba-alba, and assessed the growth, vitality, seed germination and seedling survival of those target species with and without the presence of chemical interference by the incorporation of activated carbon (AC) to the soil. In addition, juveniles and seeds of the same three target species were planted and sown beneath the canopy of adults of S. vermiculata (a shrub similar to A. herba-alba, but non-allelopathic) and in open bare soil to evaluate whether the allelopathic activity of A. herba-alba modulates the net outcome of its interactions with neighboring plants under contrasting abiotic stress conditions. We found that vitality of A. herba-alba juveniles was enhanced beneath A. herba-alba individuals when AC was present. Furthermore, we found that the interaction outcome in A. herba-alba microsite was neutral, whereas a positive outcome was found for S. vermiculata microsite, suggesting that allelopathy may limit the potential facilitative effects of the enhanced microclimatic conditions in A. herba-alba microsite. Yet, L. spartum juveniles were facilitated in A. herba-alba microsite. The interaction outcome in A. herba-alba microsite was positive under conditions of very high abiotic stress, indicating that facilitative interactions predominated over the interference of allelopathic plants under those conditions. These results highlight that laboratory studies can overestimate the significance of

  19. Generator-specific targets of mitochondrial reactive oxygen species.

    PubMed

    Bleier, Lea; Wittig, Ilka; Heide, Heinrich; Steger, Mirco; Brandt, Ulrich; Dröse, Stefan

    2015-01-01

    To understand the role of reactive oxygen species (ROS) in oxidative stress and redox signaling it is necessary to link their site of generation to the oxidative modification of specific targets. Here we have studied the selective modification of protein thiols by mitochondrial ROS that have been implicated as deleterious agents in a number of degenerative diseases and in the process of biological aging, but also as important players in cellular signal transduction. We hypothesized that this bipartite role might be based on different generator sites for "signaling" and "damaging" ROS and a directed release into different mitochondrial compartments. Because two main mitochondrial ROS generators, complex I (NADH:ubiquinone oxidoreductase) and complex III (ubiquinol:cytochrome c oxidoreductase; cytochrome bc1 complex), are known to predominantly release superoxide and the derived hydrogen peroxide (H2O2) into the mitochondrial matrix and the intermembrane space, respectively, we investigated whether these ROS generators selectively oxidize specific protein thiols. We used redox fluorescence difference gel electrophoresis analysis to identify redox-sensitive targets in the mitochondrial proteome of intact rat heart mitochondria. We observed that the modified target proteins were distinctly different when complex I or complex III was employed as the source of ROS. These proteins are potential targets involved in mitochondrial redox signaling and may serve as biomarkers to study the generator-dependent dual role of mitochondrial ROS in redox signaling and oxidative stress. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. Chemical defense and chemical variation in some tropical Pacific species of Halimeda (Halimedaceae; Chlorophyta)

    NASA Astrophysics Data System (ADS)

    Paul, Valerie J.; van Alstyne, Kathryn L.

    1988-03-01

    Over a dozen species of the genus Halimeda have been chemically investigated and found to produce the diterpenoid metabolites halimedatrial (1) and halimedatetraacetate (2) in varying concentrations. These meabolites have been proposed to play a role in chemical defense against herbivores based on their chemical structures and their demonstrated biological activities in laboratory and aquarium assays. We examined and compared the feeding deterrent effects of these two compounds tovard herbivorous fishes in field experiments on Guam reefs. Halimedatrial is a more effective feeding deterrent than halimedatetraacetate. It is the major secondary metabolite in young Halimeda macroloba and in the newly produced segments of growing plants. The organic extracts from young plants and new segments were significantly more deterrent than extracts from mature plant tissue. Some populations of Halimeda growing in reef-slope habitats, where herbivory is intense, also have high concentrations of halimedatrial. We compared extracts between reef slope and reef flat collections of Halimeda opuntia on Guam and Pohnpei (= Ponape), and H. discoidea and H. macroloba on Guam. We found that halimedtrial was the major metabolite in reef-slope collections of H. opuntia from Pohnpei and Pago Bay, Guam, and that halimedatetraacetate was the major metabolite a non-reef slope populations. In the cases examined, chemical defenses were greatest in (1) plant parts and (2) populations that were at greatest risk to herbivores.

  1. Lead discovery and chemical biology approaches targeting the ubiquitin proteasome system.

    PubMed

    Akinjiyan, Favour A; Carbonneau, Seth; Ross, Nathan T

    2017-10-15

    Protein degradation is critical for proteostasis, and the addition of polyubiquitin chains to a substrate is necessary for its recognition by the 26S proteasome. Therapeutic intervention in the ubiquitin proteasome system has implications ranging from cancer to neurodegeneration. Novel screening methods and chemical biology tools for targeting E1-activating, E2-conjugating and deubiquitinating enzymes will be discussed in this review. Approaches for targeting E3 ligase-substrate interactions as well as the proteasome will also be covered, with a focus on recently described approaches. Copyright © 2017. Published by Elsevier Ltd.

  2. Determining high-quality critical body residues for multiple species and chemicals by applying improved experimental design and data interpretation concepts.

    PubMed

    van der Heijden, Stephan A; Hermens, Joop L M; Sinnige, Theo L; Mayer, Philipp; Gilbert, Dorothea; Jonker, Michiel T O

    2015-02-03

    Ecotoxicological effect data are generally expressed as effective concentrations in the external exposure medium and do thus not account for differences in chemical uptake, bioavailability, and metabolism, which can introduce substantial data variation. The Critical Body Residue (CBR) concept provides clear advantages, because it links effects directly to the internal exposure. Using CBRs instead of external concentrations should therefore reduce variability. For compounds that act via narcosis even a constant CBR has been proposed. Despite the expected uniformity, CBR values for these compounds still show large variability, possibly due to biased and inconsistent experimental testing. In the present study we tested whether variation in CBR data can be substantially reduced when using an improved experimental design and avoiding confounding factors. The aim was to develop and apply a well-defined test protocol for accurately and precisely measuring CBR data, involving improved (passive) dosing, sampling, and processing of organisms. The chemicals 1,2,4-trichlorobenzene, 1,2,3,4-tetrachlorobenzene, 2,3,4-trichloroaniline, 2,3,5,6-tetrachloroaniline, 4-chloro-3-methylphenol, pentylbenzene, pyrene, and bromophos-methyl were tested on Lumbriculus variegatus (California blackworm), Hyalella azteca (scud), and Poecilia reticulata (guppy), which yielded a high-quality database of 348 individual CBR values. Medians of CBR values ranged from 2.1 to 16.1 mmol/kg wet weight (ww) within all combinations of chemicals and species, except for the insecticide bromophos-methyl, for which the median was 1.3 mmol/kg ww. The new database thus covers about one log unit, which is considerably less than in existing databases. Medians differed maximally by a factor of 8.4 between the 7 chemicals but within one species, and by a factor of 2.6 between the three species but for individual chemicals. Accounting for the chemicals' internal distribution to different partitioning domains and

  3. Investigation of potential targets of Porphyromonas CRISPRs among the genomes of Porphyromonas species

    PubMed Central

    Shibasaki, Masaki; Maruyama, Fumito; Sekizaki, Tsutomu; Nakagawa, Ichiro

    2017-01-01

    The oral bacterial species Porphyromonas gingivalis, a periodontal pathogen, has plastic genomes that may be driven by homologous recombination with exogenous deoxyribonucleic acid (DNA) that is incorporated by natural transformation and conjugation. However, bacteriophages and plasmids, both of which are main resources of exogenous DNA, do not exist in the known P. gingivalis genomes. This could be associated with an adaptive immunity system conferred by clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (cas) genes in P. gingivalis as well as innate immune systems such as a restriction-modification system. In a previous study, few immune targets were predicted for P. gingivalis CRISPR/Cas. In this paper, we analyzed 51 P. gingivalis genomes, which were newly sequenced, and publicly available genomes of 13 P. gingivalis and 46 other Porphyromonas species. We detected 6 CRISPR/Cas types (classified by sequence similarity of repeat) in P. gingivalis and 12 other types in the remaining species. The Porphyromonas CRISPR spacers with potential targets in the genus Porphyromonas were approximately 23 times more abundant than those with potential targets in other genus taxa (1,720/6,896 spacers vs. 74/6,896 spacers). Porphyromonas CRISPR/Cas may be involved in genome plasticity by exhibiting selective interference against intra- and interspecies nucleic acids. PMID:28837670

  4. The Unculturables: targeted isolation of bacterial species associated with canine periodontal health or disease from dental plaque.

    PubMed

    Davis, Ian J; Bull, Christopher; Horsfall, Alexander; Morley, Ian; Harris, Stephen

    2014-08-01

    The current inability to culture the entirety of observed bacteria is well known and with the advent of ever more powerful molecular tools, that can survey bacterial communities at previously unattainable depth, the gap in our capacity to culture and define all of these species increases exponentially. This gap has essentially become the rate limiting step in determining how the knowledge of which species are present in a sample can be applied to understand the role of these species in an ecosystem or disease process. A case in point is periodontal disease, which is the most widespread oral disease in dogs. If untreated the disease results in significant pain, eventual loss of the dentition and potentially an increased risk of systemic diseases. Previous molecular based studies have identified the bacterial species associated with periodontal disease in dogs; however without cultured strains from many of these species it has not been possible to study whether they play a role in the disease process. Using a quantitative polymerase chain reaction (qPCR) directed approach a range of microbiological media were screened and optimized to enrich for previously uncultivated target species. A systematic screening methodology was then employed to isolate the species of interest. In cases where the target species were not cultivable in isolation, helper strains grown underneath a nitrocellulose membrane were used to provide the necessary growth factors. This guided media optimization approach enabled the purification of 14 species, 8 of which we had previously been unable to cultivate in isolation. It is also applicable to the targeted isolation of isolates from species that have previously been cultured (for example to study intra-species variation) as demonstrated by the successful isolation of 6 targeted isolates of already cultured species. To our knowledge this is the first time this combination of qPCR guided media optimization, strategic screening and helper strain

  5. Light-Addressable Potentiometric Sensors for Quantitative Spatial Imaging of Chemical Species.

    PubMed

    Yoshinobu, Tatsuo; Miyamoto, Ko-Ichiro; Werner, Carl Frederik; Poghossian, Arshak; Wagner, Torsten; Schöning, Michael J

    2017-06-12

    A light-addressable potentiometric sensor (LAPS) is a semiconductor-based chemical sensor, in which a measurement site on the sensing surface is defined by illumination. This light addressability can be applied to visualize the spatial distribution of pH or the concentration of a specific chemical species, with potential applications in the fields of chemistry, materials science, biology, and medicine. In this review, the features of this chemical imaging sensor technology are compared with those of other technologies. Instrumentation, principles of operation, and various measurement modes of chemical imaging sensor systems are described. The review discusses and summarizes state-of-the-art technologies, especially with regard to the spatial resolution and measurement speed; for example, a high spatial resolution in a submicron range and a readout speed in the range of several tens of thousands of pixels per second have been achieved with the LAPS. The possibility of combining this technology with microfluidic devices and other potential future developments are discussed.

  6. Epigenetic targeting of the Nanog pathway and signaling networks during chemical carcinogenesis.

    PubMed

    Tommasi, Stella; Zheng, Albert; Yoon, Jae-In; Besaratinia, Ahmad

    2014-08-01

    Chemical carcinogenesis has long been synonymous with genotoxicity, which entails DNA damage, genetic mutations and chromosomal abnormalities. The present study investigates a paradigm-shifting model in which epigenetic changes are key contributors to chemical carcinogenesis. Using genome-wide microarray-based analysis followed by conventional validation assays, we have progressively chronicled changes in the epigenetic landscape, as reflected in the patterns of DNA methylation, in the target organ of tumorigenesis in mice treated in vivo with a prototype chemical carcinogen (benzo[a]pyrene). Here, we demonstrate characteristic CpG island gain/loss of methylation and demethylation of repetitive DNA elements in carcinogen-treated mice, dependent on tumor progression. Alterations of the DNA methylome are accompanied by silencing of major DNA methyltransferases. Members of the Nanog pathway that establishes and maintains pluripotency in embryonic stem cells and possibly triggers uncontrolled proliferation of neoplastic cells are preferential targets of aberrant DNA methylation and concomitant gene dysregulation during chemical carcinogenesis. Several components of the MEK/ERK, JAK/STAT3, PI3K/AKT, WNT/β- catenin and Shh signaling cascades, which are known to modulate Nanog expression, also show concurrent changes in the patterns of DNA methylation and gene expression. Our data support an epigenetic model of chemical carcinogenesis and suggest that surveillance of the epigenetic landscape, particularly at the loci and in the pathways identified in this study, may have utility for early detection and monitoring of the progression of malignancy. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  7. Chemical Proteomic Approaches Targeting Cancer Stem Cells: A Review of Current Literature.

    PubMed

    Jung, Hye Jin

    2017-01-01

    Cancer stem cells (CSCs) have been proposed as central drivers of tumor initiation, progression, recurrence, and therapeutic resistance. Therefore, identifying stem-like cells within cancers and understanding their properties is crucial for the development of effective anticancer therapies. Recently, chemical proteomics has become a powerful tool to efficiently determine protein networks responsible for CSC pathophysiology and comprehensively elucidate molecular mechanisms of drug action against CSCs. This review provides an overview of major methodologies utilized in chemical proteomic approaches. In addition, recent successful chemical proteomic applications targeting CSCs are highlighted. Future direction of potential CSC research by integrating chemical genomic and proteomic data obtained from a single biological sample of CSCs are also suggested in this review. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  8. Astrochem: Abundances of chemical species in the interstellar medium

    NASA Astrophysics Data System (ADS)

    Maret, Sébastien; Bergin, Edwin A.

    2015-07-01

    Astrochem computes the abundances of chemical species in the interstellar medium, as function of time. It studies the chemistry in a variety of astronomical objects, including diffuse clouds, dense clouds, photodissociation regions, prestellar cores, protostars, and protostellar disks. Astrochem reads a network of chemical reactions from a text file, builds up a system of kinetic rates equations, and solves it using a state-of-the-art stiff ordinary differential equation (ODE) solver. The Jacobian matrix of the system is computed implicitly, so the resolution of the system is extremely fast: large networks containing several thousands of reactions are usually solved in a few seconds. A variety of gas phase process are considered, as well as simple gas-grain interactions, such as the freeze-out and the desorption via several mechanisms (thermal desorption, cosmic-ray desorption and photo-desorption). The computed abundances are written in a HDF5 file, and can be plotted in different ways with the tools provided with Astrochem. Chemical reactions and their rates are written in a format which is meant to be easy to read and to edit. A tool to convert the chemical networks from the OSU and KIDA databases into this format is also provided. Astrochem is written in C, and its source code is distributed under the terms of the GNU General Public License (GPL).

  9. Assessing contaminant sensitivity of endangered and threatened aquatic species: Part I. Acute toxicity of five chemicals

    USGS Publications Warehouse

    Dwyer, F.J.; Mayer, F.L.; Sappington, L.C.; Buckler, D.R.; Bridges, C.M.; Greer, I.E.; Hardesty, D.K.; Henke, C.E.; Ingersoll, C.G.; Kunz, J.L.; Whites, D.W.; Augspurger, T.; Mount, D.R.; Hattala, K.; Neuderfer, G.N.

    2005-01-01

    Assessment of contaminant impacts to federally identified endangered, threatened and candidate, and state-identified endangered species (collectively referred to as "listed" species) requires understanding of a species' sensitivities to particular chemicals. The most direct approach would be to determine the sensitivity of a listed species to a particular contaminant or perturbation. An indirect approach for aquatic species would be application of toxicity data obtained from standard test procedures and species commonly used in laboratory toxicity tests. Common test species (fathead minnow, Pimephales promelas; sheepshead minnow, Cyprinodon variegatus; and rainbow trout, Oncorhynchus mykiss) and 17 listed or closely related species were tested in acute 96-hour water exposures with five chemicals (carbaryl, copper, 4-nonylphenol, pentachlorophenol, and permethrin) representing a broad range of toxic modes of action. No single species was the most sensitive to all chemicals. For the three standard test species evaluated, the rainbow trout was more sensitive than either the fathead minnow or sheepshead minnow and was equal to or more sensitive than listed and related species 81% of the time. To estimate an LC50 for a listed species, a factor of 0.63 can be applied to the geometric mean LC50 of rainbow trout toxicity data, and more conservative factors can be determined using variance estimates (0.46 based on 1 SD of the mean and 0.33 based on 2 SD of the mean). Additionally, a low- or no-acute effect concentration can be estimated by multiplying the respective LC50 by a factor of approximately 0.56, which supports the United States Environmental Protection Agency approach of multiplying the final acute value by 0.5 (division by 2). When captive or locally abundant populations of listed fish are available, consideration should be given to direct testing. When direct toxicity testing cannot be performed, approaches for developing protective measures using common test

  10. The effect of the electric wind on the spatial distribution of chemical species in the positive corona discharge

    NASA Astrophysics Data System (ADS)

    Yanallah, K.; Pontiga, F.; Bouazza, M. R.; Chen, J. H.

    2017-08-01

    The electrohydrodynamic air flow generated by a positive corona discharge, and its effect on the spatial distribution of chemical species within a wire-plate corona reactor, have been numerically simulated. The computational model is based on the solutions of the Navier-Stokes equation and the continuity equation of each chemical species generated by the electrical discharge. A simplified analytical expression of the electric force density, which only requires the current density as the input parameter, has been used in the Navier-Stokes equation to obtain the velocity field. For the solution of the continuity equations, a plasma chemistry model that includes the most important reactions between electrons, atoms and molecules in air has been used. Similar to the electric force, the electron density distribution has been approximated by using a semi-analytical expression appropriate for the electrode geometry. The results of the study show that the spatial distribution of chemical species can be very different, and depends on the interplay between the electrohydrodynamic flow, the chemical kinetics of the species and its characteristic lifetime.

  11. A Qualitative Comparison of Porcine and Rodent Thyroperoxidase -Effects of Environmental Chemicals.

    EPA Science Inventory

    A wide variety of environmental chemicals alter the function of the thyroid system in many animal species. Thyroperoxidase (TPO), the enzyme that synthesizes thyroid hormone, is one of the known biochemical targets for thyroid disrupting chemicals (TDC). The majority of the in vi...

  12. Systems Toxicology of Male Reproductive Development: Profiling 774 Chemicals for Molecular Targets and Adverse Outcomes

    EPA Pesticide Factsheets

    Background: Trends in male reproductive health have been reported for increased rates of testicular germ cell tumors, low semen quality, cryptorchidism, and hypospadias, which have been associated with prenatal environmental chemical exposure based on human and animal studies.Objective: In the present study we aimed to identify significant correlations between environmental chemicals, molecular targets, and adverse outcomes across a broad chemical landscape with emphasis on developmental toxicity of the male reproductive system.Methods: We used U.S. EPA??s animal study database (ToxRefDB) and a comprehensive literature analysis to identify 774 chemicals that have been evaluated for adverse effects on male reproductive parameters, and then used U.S. EPA??s in vitro high-throughput screening (HTS) database (ToxCastDB) to profile their bioactivity across approximately 800 molecular and cellular features. Results: A phenotypic hierarchy of testicular atrophy, sperm effects, tumors, and malformations, a composite resembling the human testicular dysgenesis syndrome (TDS) hypothesis, was observed in 281 chemicals. A subset of 54 chemicals with male developmental consequences had in vitro bioactivity on molecular targets that could be condensed into 156 gene annotations in a bipartite network. Conclusion: Computational modeling of available in vivo and in vitro data for chemicals that produce adverse effects on male reproductive end points revealed a phenotypic hierarch

  13. Chemical biology based on target-selective degradation of proteins and carbohydrates using light-activatable organic molecules.

    PubMed

    Toshima, Kazunobu

    2013-05-01

    Proteins and carbohydrates play crucial roles in a wide range of biological processes, including serious diseases. The development of novel and innovative methods for selective control of specific proteins and carbohydrates functions has attracted much attention in the field of chemical biology. In this account article, the development of novel chemical tools, which can degrade target proteins and carbohydrates by irradiation with a specific wavelength of light under mild conditions without any additives, is introduced. This novel class of photochemical agents promise bright prospects for finding not only molecular-targeted bioprobes for understanding of the structure-activity relationships of proteins and carbohydrates but also novel therapeutic drugs targeting proteins and carbohydrates.

  14. Plant seed species identification from chemical fingerprints: a high-throughput application of direct analysis in real time mass spectrometry.

    PubMed

    Lesiak, Ashton D; Cody, Robert B; Dane, A John; Musah, Rabi A

    2015-09-01

    Plant species identification based on the morphological features of plant parts is a well-established science in botany. However, species identification from seeds has largely been unexplored, despite the fact that the seeds contain all of the genetic information that distinguishes one plant from another. Using seeds of genus Datura plants, we show here that the mass spectrum-derived chemical fingerprints for seeds of the same species are similar. On the other hand, seeds from different species within the same genus display distinct chemical signatures, even though they may contain similar characteristic biomarkers. The intraspecies chemical signature similarities on the one hand, and interspecies fingerprint differences on the other, can be processed by multivariate statistical analysis methods to enable rapid species-level identification and differentiation. The chemical fingerprints can be acquired rapidly and in a high-throughput manner by direct analysis in real time mass spectrometry (DART-MS) analysis of the seeds in their native form, without use of a solvent extract. Importantly, knowledge of the identity of the detected molecules is not required for species level identification. However, confirmation of the presence within the seeds of various characteristic tropane and other alkaloids, including atropine, scopolamine, scopoline, tropine, tropinone, and tyramine, was accomplished by comparison of the in-source collision-induced dissociation (CID) fragmentation patterns of authentic standards, to the fragmentation patterns observed in the seeds when analyzed under similar in-source CID conditions. The advantages, applications, and implications of the chemometric processing of DART-MS derived seed chemical signatures for species level identification and differentiation are discussed.

  15. A Miniaturized Chemical Proteomic Approach for Target Profiling of Clinical Kinase Inhibitors in Tumor Biopsies

    PubMed Central

    Chamrád, Ivo; Rix, Uwe; Stukalov, Alexey; Gridling, Manuela; Parapatics, Katja; Müller, André C.; Altiok, Soner; Colinge, Jacques; Superti-Furga, Giulio; Haura, Eric B.; Bennett, Keiryn L.

    2014-01-01

    While targeted therapy based on the idea of attenuating the activity of a preselected, therapeutically relevant protein has become one of the major trends in modern cancer therapy, no truly specific targeted drug has been developed and most clinical agents have displayed a degree of polypharmacology. Therefore, the specificity of anticancer therapeutics has emerged as a highly important but severely underestimated issue. Chemical proteomics is a powerful technique combining postgenomic drug-affinity chromatography with high-end mass spectrometry analysis and bioinformatic data processing to assemble a target profile of a desired therapeutic molecule. Due to high demands on the starting material, however, chemical proteomic studies have been mostly limited to cancer cell lines. Herein, we report a down-scaling of the technique to enable the analysis of very low abundance samples, as those obtained from needle biopsies. By a systematic investigation of several important parameters in pull-downs with the multikinase inhibitor bosutinib, the standard experimental protocol was optimized to 100 µg protein input. At this level, more than 30 well-known targets were detected per single pull-down replicate with high reproducibility. Moreover, as presented by the comprehensive target profile obtained from miniaturized pull-downs with another clinical drug, dasatinib, the optimized protocol seems to be extendable to other drugs of interest. Sixty distinct human and murine targets were finally identified for bosutinib and dasatinib in chemical proteomic experiments utilizing core needle biopsy samples from xenotransplants derived from patient tumor tissue. Altogether, the developed methodology proves robust and generic and holds many promises for the field of personalized health care. PMID:23901793

  16. Initiated chemical vapor deposition polymers for high peak-power laser targets

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Baxamusa, Salmaan H.; Lepro, Xavier; Lee, Tom

    2016-12-05

    Here, we report two examples of initiated chemical vapor deposition (iCVD) polymers being developed for use in laser targets for high peak-power laser systems. First, we show that iCVD poly(divinylbenzene) is more photo-oxidatively stable than the plasma polymers currently used in laser targets. Thick layers (10–12 μm) of this highly crosslinked polymer can be deposited with near-zero intrinsic film stress. Second, we show that iCVD epoxy polymers can be crosslinked after deposition to form thin adhesive layers for assembling precision laser targets. The bondlines can be made as thin as ~ 1 μm, approximately a factor of 2 thinner thanmore » achievable using viscous resin-based adhesives. These bonds can withstand downstream coining and stamping processes.« less

  17. Phytotoxic Activity and Chemical Composition of Aqueous Volatile Fractions from Eucalyptus Species

    PubMed Central

    Zhang, Jinbiao; An, Min; Wu, Hanwen; Liu, De Li; Stanton, Rex

    2014-01-01

    The essential oils from four Eucalyptus species (E. spathulata, E. salubris, E. brockwayii and E. dundasii) have been previously confirmed to have stronger inhibitory effects on germination and seedling growth of silverleaf nightshade (Solanum elaeagnifolium Cav.). The aqueous volatile fractions (AVFs) were the water soluble volatile fractions produced together with the essential oils (water insoluble fractions) during the steam distillation process. The aim of this study was to further assess the phytotoxicity of AVFs from the four Eucalyptus species and their chemical composition. The fresh leaves of the four Eucalyptus species were used for the extraction of AVFs. The AVFs were tested for their phytotoxic effects on the perennial weed, silverleaf nightshade under laboratory conditions. The chemical compositions of the AVFs were determined by gas chromatograph–mass spectrometry (GC-MS). Our results showed that the AVFs had strong inhibition on the germination and seedling growth of silverleaf nightshade. The inhibition index increased with the increasing concentrations of AVFs. The inhibitory effects of the AVFs varied between different Eucalyptus species. The AVF from E. salubris demonstrated the highest inhibitory activity on the weed tested, with complete inhibition on germination and seedling growth at a concentration of 75%. The GC-MS analysis revealed that 1,8-cineole, isopentyl isovalerate, isomenthol, pinocarvone, trans-pinocarveol, alpha-terpineol and globulol were the main compounds in the AVFs. These results indicated that all AVFs tested had differential inhibition on the germination and seedling growth of silverleaf nightshade, which could be due to the joint effects of compounds present in the AVFs as these compounds were present in different quantities and ratio between Eucalyptus species. PMID:24681490

  18. In silico site-directed mutagenesis informs species-specific predictions of chemical susceptibility derived from the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool

    EPA Science Inventory

    The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed to address needs for rapid, cost effective methods of species extrapolation of chemical susceptibility. Specifically, the SeqAPASS tool compares the primary sequence (Level 1), functiona...

  19. Selective whole genome amplification for resequencing target microbial species from complex natural samples.

    PubMed

    Leichty, Aaron R; Brisson, Dustin

    2014-10-01

    Population genomic analyses have demonstrated power to address major questions in evolutionary and molecular microbiology. Collecting populations of genomes is hindered in many microbial species by the absence of a cost effective and practical method to collect ample quantities of sufficiently pure genomic DNA for next-generation sequencing. Here we present a simple method to amplify genomes of a target microbial species present in a complex, natural sample. The selective whole genome amplification (SWGA) technique amplifies target genomes using nucleotide sequence motifs that are common in the target microbe genome, but rare in the background genomes, to prime the highly processive phi29 polymerase. SWGA thus selectively amplifies the target genome from samples in which it originally represented a minor fraction of the total DNA. The post-SWGA samples are enriched in target genomic DNA, which are ideal for population resequencing. We demonstrate the efficacy of SWGA using both laboratory-prepared mixtures of cultured microbes as well as a natural host-microbe association. Targeted amplification of Borrelia burgdorferi mixed with Escherichia coli at genome ratios of 1:2000 resulted in >10(5)-fold amplification of the target genomes with <6.7-fold amplification of the background. SWGA-treated genomic extracts from Wolbachia pipientis-infected Drosophila melanogaster resulted in up to 70% of high-throughput resequencing reads mapping to the W. pipientis genome. By contrast, 2-9% of sequencing reads were derived from W. pipientis without prior amplification. The SWGA technique results in high sequencing coverage at a fraction of the sequencing effort, thus allowing population genomic studies at affordable costs. Copyright © 2014 by the Genetics Society of America.

  20. Detection of Apoptosis in Early Life Stages as a Tool to Evaluate Chemical Control of Invasive Species

    DTIC Science & Technology

    2007-08-01

    ERDC/TN ANSRP-07-2 August 2007 Detection of Apoptosis in Early Life Stages as a Tool to Evaluate Chemical Control of Invasive Species by J...4. TITLE AND SUBTITLE Detection of Apoptosis in Early Life Stages as a Tool to Evaluate Chemical Control of Invasive Species 5a. CONTRACT NUMBER 5b...heralding apoptosis . Data analysis. An apoptotic index (API) was established by calculating the percentage of embryos in each life stage with

  1. Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression

    PubMed Central

    2009-01-01

    Background Pulmonary metastasis continues to be the most common cause of death in osteosarcoma. Indeed, the 5-year survival for newly diagnosed osteosarcoma patients has not significantly changed in over 20 years. Further understanding of the mechanisms of metastasis and resistance for this aggressive pediatric cancer is necessary. Pet dogs naturally develop osteosarcoma providing a novel opportunity to model metastasis development and progression. Given the accelerated biology of canine osteosarcoma, we hypothesized that a direct comparison of canine and pediatric osteosarcoma expression profiles may help identify novel metastasis-associated tumor targets that have been missed through the study of the human cancer alone. Results Using parallel oligonucleotide array platforms, shared orthologues between species were identified and normalized. The osteosarcoma expression signatures could not distinguish the canine and human diseases by hierarchical clustering. Cross-species target mining identified two genes, interleukin-8 (IL-8) and solute carrier family 1 (glial high affinity glutamate transporter), member 3 (SLC1A3), which were uniformly expressed in dog but not in all pediatric osteosarcoma patient samples. Expression of these genes in an independent population of pediatric osteosarcoma patients was associated with poor outcome (p = 0.020 and p = 0.026, respectively). Validation of IL-8 and SLC1A3 protein expression in pediatric osteosarcoma tissues further supported the potential value of these novel targets. Ongoing evaluation will validate the biological significance of these targets and their associated pathways. Conclusions Collectively, these data support the strong similarities between human and canine osteosarcoma and underline the opportunities provided by a comparative oncology approach as a means to improve our understanding of cancer biology and therapies. PMID:20028558

  2. Assessment of local wood species used for the manufacture of cookware and the perception of chemical benefits and chemical hazards associated with their use in Kumasi, Ghana.

    PubMed

    Mensah, John Kenneth; Adei, Evans; Adei, Dina; Owusu Ansah, Gwendolyn

    2012-12-18

    Historical proven wood species have no reported adverse health effect associated with its past use. Different historical proven species have traditionally been used to manufacture different wooden food contact items. This study uses survey questionnaires to assess suppliers', manufacturers', retailers' and consumers' (end-users') preferences for specific wood species, to examine the considerations that inform these preferences and to investigate the extent of awareness of the chemical benefits and chemical hazards associated with wooden food contact material use. Through the combined use of a cross sectional approach and a case study design, 25 suppliers, 25 manufacturers, 25 retailers and 125 consumers (end-users) of wooden food contact materials in four suburbs in Kumasi Metropolitan Area (Anloga junction, Ahinsan Bus Stop, Ahwia-Pankrono and Race Course) and Ashanti Akyim Agogo in the Ashanti Akyim North District of the Ashanti Region were administered with closed ended questionnaires. The questionnaires were prepared in English, but local language, Twi, was used to translate and communicate the content of the questionnaire where necessary. Suppliers', manufacturers' and retailers' preferences for specific wood species for most wooden cookware differed from that of consumers (end-users). But all respondent groups failed to indicate any awareness of chemical benefits or chemical hazards associated with either the choice of specific wood species for specific wooden cookware or with the general use of wooden food contact materials. The lack of appreciation of chemical benefits or hazards associated with active principles of wooden cookware led to heavy reliance of consumers (end-users) on the wood density, price, attractive grain pattern and colour or on the judgement of retailers in their choice of specific species for a wooden cookware. This study contributes some practical suggestions to guide national policy development on improvement in quality of available

  3. Assessment of local wood species used for the manufacture of cookware and the perception of chemical benefits and chemical hazards associated with their use in Kumasi, Ghana

    PubMed Central

    2012-01-01

    Background Historical proven wood species have no reported adverse health effect associated with its past use. Different historical proven species have traditionally been used to manufacture different wooden food contact items. This study uses survey questionnaires to assess suppliers’, manufacturers’, retailers’ and consumers’ (end-users’) preferences for specific wood species, to examine the considerations that inform these preferences and to investigate the extent of awareness of the chemical benefits and chemical hazards associated with wooden food contact material use. Methods Through the combined use of a cross sectional approach and a case study design, 25 suppliers, 25 manufacturers, 25 retailers and 125 consumers (end-users) of wooden food contact materials in four suburbs in Kumasi Metropolitan Area (Anloga junction, Ahinsan Bus Stop, Ahwia-Pankrono and Race Course) and Ashanti Akyim Agogo in the Ashanti Akyim North District of the Ashanti Region were administered with closed ended questionnaires. The questionnaires were prepared in English, but local language, Twi, was used to translate and communicate the content of the questionnaire where necessary. Results Suppliers’, manufacturers’ and retailers’ preferences for specific wood species for most wooden cookware differed from that of consumers (end-users). But all respondent groups failed to indicate any awareness of chemical benefits or chemical hazards associated with either the choice of specific wood species for specific wooden cookware or with the general use of wooden food contact materials. The lack of appreciation of chemical benefits or hazards associated with active principles of wooden cookware led to heavy reliance of consumers (end-users) on the wood density, price, attractive grain pattern and colour or on the judgement of retailers in their choice of specific species for a wooden cookware. Conclusion This study contributes some practical suggestions to guide national policy

  4. Chemical exposure-response relationship between air pollutants and reactive oxygen species in the human respiratory tract

    NASA Astrophysics Data System (ADS)

    Lakey, P. S. J.; Berkemeier, T.; Tong, H.; Arangio, A. M.; Lucas, K.; Poeschl, U.; Shiraiwa, M.

    2016-12-01

    The inhalation of air pollutants such as O3 and particulate matter can lead to the formation of reactive oxygen species (ROS) which can cause damage to biosurfaces such as the lung epithelium unless they are effectively scavenged. Although the chemical processes that lead to ROS formation within the ELF upon inhalation of pollutants are well understood qualitatively, ROS concentrations within the ELF have hardly been quantified so far. The kinetic multi-layer model of surface and bulk chemistry in the epithelial lining fluid (KM-SUB-ELF) has been developed to describe chemical reactions and mass transport and to quantify ROS production rates and concentrations within the epithelial lining fluid. KM-SUB-ELF simulations suggest that O3 will rapidly saturate the ELF whereas antioxidants and surfactant species are effective scavengers of OH. High ambient concentrations of O3 can lead to the depletion of surfactants and antioxidants within the ELF, potentially leading to oxidative stress. KM-SUB-ELF reproduced measurements for the formation of H2O2 and OH due to the presence of iron, copper and quinones in surrogate lung lining fluid. This enabled ROS production rates and concentrations in the ELF to be quantified. We found that in polluted megacities the ROS concentration in the ELF due to inhalation of pollutants was at least as high as the concentrations in the ELF of patients suffering from respiratory diseases. Cu and Fe are found to be the most important redox-active aerosol components for ROS production upon inhalation of PM2.5 in polluted regions. Therefore, a reduction in the emission of Cu and Fe should be major targets of air pollution control. Chemical exposure-response relations provide a quantitative basis for assessing the relative importance of specific air pollutants in different regions of the world, showing that aerosol-induced epithelial ROS levels in polluted megacity air can be several orders of magnitude higher than in pristine rainforest air.

  5. Contribution of species-specific chemical signatures to soil organic matter in Kohala, HI.

    NASA Astrophysics Data System (ADS)

    Stewart, C. E.; Amatangelo, K.; Neff, J. C.

    2008-12-01

    Soil organic matter (SOM) inherits much of its chemical structure from the dominant vegetation, including phenolic (lignin-derived), aromatic, and aliphatic (cutin and wax-derived) compounds. The Hawaiian fern species Dicranopteris decomposes more slowly than the angiosperm, Cheirodendron due to high concentrations of recalcitrant C compounds. These aliphatic fern leaf waxes are well-preserved and may comprise a large portion of the recalcitrant organic matter in these soils. Our objective was to determine the chemical signature of fern and angiosperm vegetation types and trace the preservation or loss of those compounds into the soil. We collected live tissue, litter, roots, and soil (<53 μm) from five dominant vegetation types including two angiosperms Cheirodendron and Metrosideros, two basal ferns Dicranopteris and Cibotium and a polypod fern Diplazium in Kohala, HI. We characterized them via TMAH-pyrolysis-gas chromatography-mass spectrometry. We found distinct chemical differences between angiosperm and fern vegetation; angiosperm contained more G- and S-derived lignin structures and the fern species contained greater relative abundances of P-derived lignin and tannin-derivatives. There was a general decrease of lignin-derived phenolic compounds from live to litter to soils and an increase in more recalcitrant, aromatic and aliphatic C. Recalcitrant fern-derived cutin and leaf waxes (alkene and alkanes structures) were evident in the soils, but clear species differences were not observed. Although ferns contain distinct lipid and wax-derived compounds, soils developed under fern do not appear to accumulate these compounds in SOM.

  6. Spectroscopy of reactive species produced by low-energy atmospheric-pressure plasma on conductive target material surface

    NASA Astrophysics Data System (ADS)

    Yamada, Hiromasa; Sakakita, Hajime; Kato, Susumu; Kim, Jaeho; Kiyama, Satoru; Fujiwara, Masanori; Itagaki, Hirotomo; Okazaki, Toshiya; Ikehara, Sanae; Nakanishi, Hayao; Shimizu, Nobuyuki; Ikehara, Yuzuru

    2016-10-01

    A method for blood coagulation using low-energy atmospheric-pressure plasma (LEAPP) is confirmed as an alternative procedure to reduce tissue damage caused by heat. Blood coagulation using LEAPP behaves differently depending on working gas species; helium is more effective than argon in promoting fast coagulation. To analyse the difference in reactive species produced by helium and argon plasma, spectroscopic measurements were conducted without and with a target material. To compare emissions, blood coagulation experiments using LEAPP for both plasmas were performed under almost identical conditions. Although many kinds of reactive species such as hydroxyl radicals and excited nitrogen molecules were observed with similar intensity in both plasmas, intensities of nitrogen ion molecules and nitric oxide molecules were extremely strong in the helium plasma. It is considered that nitrogen ion molecules were mainly produced by penning ionization by helium metastable. Near the target, a significant increase in the emissions of reactive species is observed. There is a possibility that electron acceleration was induced in a local electric field formed on the surface. However, in argon plasma, emissions from nitrogen ion were not measured even near the target surface. These differences between the two plasmas may be producing the difference in blood coagulation behaviour. To control the surrounding gas of the plasma, a gas-component-controllable chamber was assembled. Filling the chamber with O2/He or N2/He gas mixtures selectively produces either reactive oxygen species or reactive nitrogen species. Through selective treatments, this chamber would be useful in studying the effects of specific reactive species on blood coagulation.

  7. Concordant Chemical Reaction Networks and the Species-Reaction Graph

    PubMed Central

    Shinar, Guy; Feinberg, Martin

    2015-01-01

    In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies within the very broad and natural weakly monotonic class. In particular, multiple equilibria are precluded, as are degenerate positive equilibria. Moreover, under certain circumstances, also related to concordance, all real eigenvalues associated with a positive equilibrium are negative. Although concordance of a reaction network can be decided by readily available computational means, we show here that, when a nondegenerate network’s Species-Reaction Graph satisfies certain mild conditions, concordance and its dynamical consequences are ensured. These conditions are weaker than earlier ones invoked to establish kinetic system injectivity, which, in turn, is just one ramification of network concordance. Because the Species-Reaction Graph resembles pathway depictions often drawn by biochemists, results here expand the possibility of inferring significant dynamical information directly from standard biochemical reaction diagrams. PMID:22940368

  8. 3D flexible alignment using 2D maximum common substructure: dependence of prediction accuracy on target-reference chemical similarity.

    PubMed

    Kawabata, Takeshi; Nakamura, Haruki

    2014-07-28

    A protein-bound conformation of a target molecule can be predicted by aligning the target molecule on the reference molecule obtained from the 3D structure of the compound-protein complex. This strategy is called "similarity-based docking". For this purpose, we develop the flexible alignment program fkcombu, which aligns the target molecule based on atomic correspondences with the reference molecule. The correspondences are obtained by the maximum common substructure (MCS) of 2D chemical structures, using our program kcombu. The prediction performance was evaluated using many target-reference pairs of superimposed ligand 3D structures on the same protein in the PDB, with different ranges of chemical similarity. The details of atomic correspondence largely affected the prediction success. We found that topologically constrained disconnected MCS (TD-MCS) with the simple element-based atomic classification provides the best prediction. The crashing potential energy with the receptor protein improved the performance. We also found that the RMSD between the predicted and correct target conformations significantly correlates with the chemical similarities between target-reference molecules. Generally speaking, if the reference and target compounds have more than 70% chemical similarity, then the average RMSD of 3D conformations is <2.0 Å. We compared the performance with a rigid-body molecular alignment program based on volume-overlap scores (ShaEP). Our MCS-based flexible alignment program performed better than the rigid-body alignment program, especially when the target and reference molecules were sufficiently similar.

  9. Applied Genomics: Data Mining Reveals Species-Specific Malaria Diagnostic Targets More Sensitive than 18S rRNA▿†‡

    PubMed Central

    Demas, Allison; Oberstaller, Jenna; DeBarry, Jeremy; Lucchi, Naomi W.; Srinivasamoorthy, Ganesh; Sumari, Deborah; Kabanywanyi, Abdunoor M.; Villegas, Leopoldo; Escalante, Ananias A.; Kachur, S. Patrick; Barnwell, John W.; Peterson, David S.; Udhayakumar, Venkatachalam; Kissinger, Jessica C.

    2011-01-01

    Accurate and rapid diagnosis of malaria infections is crucial for implementing species-appropriate treatment and saving lives. Molecular diagnostic tools are the most accurate and sensitive method of detecting Plasmodium, differentiating between Plasmodium species, and detecting subclinical infections. Despite available whole-genome sequence data for Plasmodium falciparum and P. vivax, the majority of PCR-based methods still rely on the 18S rRNA gene targets. Historically, this gene has served as the best target for diagnostic assays. However, it is limited in its ability to detect mixed infections in multiplex assay platforms without the use of nested PCR. New diagnostic targets are needed. Ideal targets will be species specific, highly sensitive, and amenable to both single-step and multiplex PCRs. We have mined the genomes of P. falciparum and P. vivax to identify species-specific, repetitive sequences that serve as new PCR targets for the detection of malaria. We show that these targets (Pvr47 and Pfr364) exist in 14 to 41 copies and are more sensitive than 18S rRNA when utilized in a single-step PCR. Parasites are routinely detected at levels of 1 to 10 parasites/μl. The reaction can be multiplexed to detect both species in a single reaction. We have examined 7 P. falciparum strains and 91 P. falciparum clinical isolates from Tanzania and 10 P. vivax strains and 96 P. vivax clinical isolates from Venezuela, and we have verified a sensitivity and specificity of ∼100% for both targets compared with a nested 18S rRNA approach. We show that bioinformatics approaches can be successfully applied to identify novel diagnostic targets and improve molecular methods for pathogen detection. These novel targets provide a powerful alternative molecular diagnostic method for the detection of P. falciparum and P. vivax in conventional or multiplex PCR platforms. PMID:21525225

  10. Predicting the sensitivity of populations from individual exposure to chemicals: the role of ecological interactions.

    PubMed

    Gabsi, Faten; Schäffer, Andreas; Preuss, Thomas G

    2014-07-01

    Population responses to chemical stress exposure are influenced by nonchemical, environmental processes such as species interactions. A realistic quantification of chemical toxicity to populations calls for the use of methodologies that integrate these multiple stress effects. The authors used an individual-based model for Daphnia magna as a virtual laboratory to determine the influence of ecological interactions on population sensitivity to chemicals with different modes of action on individuals. In the model, hypothetical chemical toxicity targeted different vital individual-level processes: reproduction, survival, feeding rate, or somatic growth rate. As for species interactions, predatory and competition effects on daphnid populations were implemented following a worst-case approach. The population abundance was simulated at different food levels and exposure scenarios, assuming exposure to chemical stress solely or in combination with either competition or predation. The chemical always targeted one vital endpoint. Equal toxicity-inhibition levels differently affected the population abundance with and without species interactions. In addition, population responses to chemicals were highly sensitive to the environmental stressor (predator or competitor) and to the food level. Results show that population resilience cannot be attributed to chemical stress only. Accounting for the relevant ecological interactions would reduce uncertainties when extrapolating effects of chemicals from individuals to the population level. Validated population models should be used for a more realistic risk assessment of chemicals. © 2014 SETAC.

  11. Rapid assessment of target species: Byssate bivalves in a large tropical port.

    PubMed

    Minchin, Dan; Olenin, Sergej; Liu, Ta-Kang; Cheng, Muhan; Huang, Sheng-Chih

    2016-11-15

    Rapid assessment sampling for target species is a fast cost-effective method aimed at determining the presence, abundance and distribution of alien and native harmful aquatic organisms and pathogens that may have been introduced by shipping. In this study, the method was applied within a large tropical port expected to have a high species diversity. The port of Kaohsiung was sampled for bivalve molluscan species that attach using a byssus. Such species, due to their biological traits, are spread by ships to ports worldwide. We estimated the abundance and distribution range of one dreissenid (Mytilopsis sallei) and four mytilids (Brachidontes variabilis, Arcuatula senhousa, Mytilus galloprovincialis, Perna viridis) known to be successful invaders and identified as potential pests, or high-risk harmful native or non-native species. We conclude that a rapid assessment of their abundance and distribution within a port, and its vicinity, is efficient and can provide sufficient information for decision making by port managers where IMO port exemptions may be sought. Copyright © 2016. Published by Elsevier Ltd.

  12. Target materials for exotic ISOL beams

    NASA Astrophysics Data System (ADS)

    Gottberg, A.

    2016-06-01

    The demand for intensity, purity, reliability and availability of short-lived isotopes far from stability is steadily high, and considerably exceeding the supply. In many cases the ISOL (Isotope Separation On-Line) method can provide beams of high intensity and purity. Limitations in terms of accessible chemical species and minimum half-life are driven mainly by chemical reactions and physical processes inside of the thick target. A wide range of materials are in use, ranging from thin metallic foils and liquids to refractory ceramics, while poly-phasic mixed uranium carbides have become the reference target material for most ISOL facilities world-wide. Target material research and development is often complex and especially important post-irradiation analyses are hindered by the high intrinsic radiotoxicity of these materials. However, recent achievements have proven that these investigations are possible if the effort of different facilities is combined, leading to the development of new material matrices that can supply new beams of unprecedented intensity and beam current stability.

  13. Application of a framework for extrapolating chemical effects across species in pathways controlled by estrogen receptor-á

    EPA Science Inventory

    Cross-species extrapolation of toxicity data from limited surrogate test organisms to all wildlife with potential of chemical exposure remains a key challenge in ecological risk assessment. A number of factors affect extrapolation, including the chemical exposure, pharmacokinetic...

  14. Graphene Chemical Sensor for Heliophysics Applications

    NASA Technical Reports Server (NTRS)

    Sultana, Mahmooda; Herrero, Fred; Khazanov, George

    2013-01-01

    Graphene is a single layer of carbon atoms that offer a unique set of advantages as a chemical sensor due to a number of its inherent properties. Graphene has been explored as a gas sensor for a variety of gases, and molecular sensitivity has been demonstrated by measuring the change in electrical properties due to the adsorption of target species. In this paper, we discuss the development of an array of chemical sensors based on graphene and its relevance to plasma physics due to its sensitivity to radical species such as oxonium, hydron and the corresponding neutrals. We briefly discuss the great impact such sensors will have on a number of heliophysics applications such as ground-based manifestations of space weather.

  15. Effects of the herbicide glyphosate on non-target plant native species from Chaco forest (Argentina).

    PubMed

    Florencia, Ferreira María; Carolina, Torres; Enzo, Bracamonte; Leonardo, Galetto

    2017-10-01

    Agriculture based on transgenic crops has expanded in Argentina into areas formerly occupied by Chaco forest. Even though glyphosate is the herbicide most widely used in the world, increasing evidence indicates severe ecotoxicological effects on non-target organisms as native plants. The aim of this work is to determine glyphosate effects on 23 native species present in the remaining Chaco forests immersed in agricultural matrices. This is a laboratory/greenhouse approach studying acute effects on seedlings after 21 days. A gradient of glyphosate rates (525, 1050, 2100, 4200, and 8400g ai/Ha; recommended field application rate (RFAR) = 2100g ai/Ha) was applied on four-week seedlings cultivated in a greenhouse and response variables (phytotoxicity, growth reduction, and sensitivity to the herbicide) were measured. This gradient of herbicide rates covers realistic rates of glyphosate applications in the crop field and also those that can reach vegetation of forest relicts by off-target drift and overspray. Testing was performed following guidelines for vegetative vigour (post-germination spray). All species showed lethal or sublethal effects after the application of the 25% of RFAR (50% of species showed severe phytotoxicity or death and 70% of species showed growth reduction). The results showed a gradient of sensitivity to glyphosate by which some of the studied species are very sensitive to glyphosate and seedlings died with 25% of RFAR while other species can be classified as herbicide-tolerant. Thus, the vegetation present in the forest relicts could be strongly affected by glyphosate application on crops. Lethal and sublethal effects of glyphosate on non-target plants could promote both the loss of biodiversity in native forest relicts immersed in the agroecosystems and the selection of new crop weeds considering that some biotypes are continuously exposed to low doses of glyphosate. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. A Multi-Receptor and Multi-Species Assay for Potential Endocrine Disruptor Targets (SLAS meeting)

    EPA Science Inventory

    Screening methods for detecting potential endocrine disrupting chemicals rely chiefly on transactivation assays targeting nuclear receptors such as the estrogen (ER) and androgen receptors (AR). These assays are predominately human-based; yet environmental exposure can affect div...

  17. Ion scattering and electron spectroscopy of the chemical species at a HF-prepared Si(211) surface

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jaime-Vasquez, M.; Martinka, M.; Groenert, M.

    2006-01-16

    The species and the nature of their chemical bonds at the surface of a hydrogen-terminated Si(211) wafer were characterized using temperature desorption spectroscopy, ion scattering spectroscopy, and electron spectroscopy. The surface region is dominated by monohydride species with dihydrides present in small amounts. Fluorine is distributed across the top layer as largely a physisorbed species to the Si substrate. Low-energy {sup 3}He{sup +} ions remove the H and F species with only minimal damage to the underlying region.

  18. Non-target effects of broadleaf herbicide on a native perennial forb: a demographic framework for assessing and minimizing impacts

    Treesearch

    Elizabeth E. Crone; Marilyn Marler; Dean E. Pearson

    2009-01-01

    Invasive species are one of the leading threats to biodiversity worldwide. Therefore, chemical herbicides are increasingly used to control invasive plants in natural and semi-natural areas. Little is known about the non-target impacts of these chemicals on native species. We conducted an experiment to test the demographic effects of the herbicide picloram on a native...

  19. Generation of Functional Human Retinal Ganglion Cells with Target Specificity from Pluripotent Stem Cells by Chemically Defined Recapitulation of Developmental Mechanism.

    PubMed

    Teotia, Pooja; Chopra, Divyan A; Dravid, Shashank Manohar; Van Hook, Matthew J; Qiu, Fang; Morrison, John; Rizzino, Angie; Ahmad, Iqbal

    2017-03-01

    Glaucoma is a complex group of diseases wherein a selective degeneration of retinal ganglion cells (RGCs) lead to irreversible loss of vision. A comprehensive approach to glaucomatous RGC degeneration may include stem cells to functionally replace dead neurons through transplantation and understand RGCs vulnerability using a disease in a dish stem cell model. Both approaches require the directed generation of stable, functional, and target-specific RGCs from renewable sources of cells, that is, the embryonic stem cells and induced pluripotent stem cells. Here, we demonstrate a rapid and safe, stage-specific, chemically defined protocol that selectively generates RGCs across species, including human, by recapitulating the developmental mechanism. The de novo generated RGCs from pluripotent cells are similar to native RGCs at the molecular, biochemical, functional levels. They also express axon guidance molecules, and discriminate between specific and nonspecific targets, and are nontumorigenic. Stem Cells 2017;35:572-585. © 2016 AlphaMed Press.

  20. Target strengths of two abundant mesopelagic fish species.

    PubMed

    Scoulding, Ben; Chu, Dezhang; Ona, Egil; Fernandes, Paul G

    2015-02-01

    Mesopelagic fish of the Myctophidae and Sternoptychidae families dominate the biomass of the oceanic deep scattering layers and, therefore, have important ecological roles within these ecosystems. Interest in the commercial exploitation of these fish is growing, so the development of techniques for estimating their abundance, distribution and, ultimately, sustainable exploitation are essential. The acoustic backscattering characteristics for two size classes of Maurolicus muelleri and Benthosema glaciale are reported here based on swimbladder morphology derived from digitized soft x-ray images, and empirical (in situ) measurements of target strength (TS) derived from an acoustic survey in a Norwegian Sea. A backscattering model based on a gas-filled prolate spheroid was used to predict the theoretical TS for both species across a frequency range between 0 and 250 kHz. Sensitivity analyses of the TS model to the modeling parameters indicate that TS is rather sensitive to the viscosity, swimbladder volume ratio, and tilt, which can result in substantial changes to the TS. Theoretical TS predictions close to the resonance frequency were in good agreement (±2 dB) with mean in situ TS derived from the areas acoustically surveyed that were spatially and temporally consistent with the trawl information for both species.

  1. The past and presence of gene targeting: from chemicals and DNA via proteins to RNA.

    PubMed

    Geel, T M; Ruiters, M H J; Cool, R H; Halby, L; Voshart, D C; Andrade Ruiz, L; Niezen-Koning, K E; Arimondo, P B; Rots, M G

    2018-06-05

    The ability to target DNA specifically at any given position within the genome allows many intriguing possibilities and has inspired scientists for decades. Early gene-targeting efforts exploited chemicals or DNA oligonucleotides to interfere with the DNA at a given location in order to inactivate a gene or to correct mutations. We here describe an example towards correcting a genetic mutation underlying Pompe's disease using a nucleotide-fused nuclease (TFO-MunI). In addition to the promise of gene correction, scientists soon realized that genes could be inactivated or even re-activated without inducing potentially harmful DNA damage by targeting transcriptional modulators to a particular gene. However, it proved difficult to fuse protein effector domains to the first generation of programmable DNA-binding agents. The engineering of gene-targeting proteins (zinc finger proteins (ZFPs), transcription activator-like effectors (TALEs)) circumvented this problem. The disadvantage of protein-based gene targeting is that a fusion protein needs to be engineered for every locus. The recent introduction of CRISPR/Cas offers a flexible approach to target a (fusion) protein to the locus of interest using cheap designer RNA molecules. Many research groups now exploit this platform and the first human clinical trials have been initiated: CRISPR/Cas has kicked off a new era of gene targeting and is revolutionizing biomedical sciences.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'. © 2018 The Author(s).

  2. Chemical composition, mineral content and amino acid and lipid profiles in bones from various fish species.

    PubMed

    Toppe, Jogeir; Albrektsen, Sissel; Hope, Britt; Aksnes, Anders

    2007-03-01

    The chemical composition, content of minerals and the profiles of amino acids and fatty acids were analyzed in fish bones from eight different species of fish. Fish bones varied significantly in chemical composition. The main difference was lipid content ranging from 23 g/kg in cod (Gadus morhua) to 509 g/kg in mackerel (Scomber scombrus). In general fatty fish species showed higher lipid levels in the bones compared to lean fish species. Similarly, lower levels of protein and ash were observed in bones from fatty fish species. Protein levels differed from 363 g/kg lipid free dry matter (dm) to 568 g/kg lipid free dm with a concomitant inverse difference in ash content. Ash to protein ratio differed from 0.78 to 1.71 with the lowest level in fish that naturally have highest swimming and physical activity. Saithe (Pollachius virens) and salmon (Salmo salar) were found to be significantly different in the levels of lipid, protein and ash, and ash/protein ratio in the bones. Only small differences were observed in the level of amino acids although species specific differences were observed. The levels of Ca and P in lipid free fish bones were about the same in all species analyzed. Fatty acid profile differed in relation to total lipid levels in the fish bones, but some minor differences between fish species were observed.

  3. Smells Like Home: Chemically Mediated Co-Habitation of Two Termite Species in a Single Nest.

    PubMed

    Jirošová, Anna; Sillam-Dussès, David; Kyjaková, Pavlína; Kalinová, Blanka; Dolejšová, Klára; Jančařík, Andrej; Majer, Pavel; Cristaldo, Paulo Fellipe; Hanus, Robert

    2016-10-01

    Termite nests often are referred to as the most elaborate constructions of animals. However, some termite species do not build a nest at all and instead found colonies inside the nests of other termites. Since these so-called inquilines do not need to be in direct contact with the host population, the two colonies usually live in separate parts of the nest. Adaptations of both the inquiline and its host are likely to occur to maintain the spatial exclusion and reduce the costs of potential conflicts. Among them, mutual avoidance, based on chemical cues, is expected. We investigated chemical aspects of cohabitation between Constrictotermes cavifrons (Nasutitermitinae) and its obligatory inquiline Inquilinitermes inquilinus (Termitinae). Inquiline soldiers produce in their frontal glands a blend of wax esters, consisting of the C 12 alcohols (3Z)-dodec enol, (3Z,6Z)-dodecadienol, and dodecanol, esterified with different fatty acids. The C 12 alcohols appear to be cleaved gradually from the wax esters, and they occur in the frontal gland, in soldier headspace, and in the walls of the inquiline part of the nest. Electrophysiological experiments revealed that (3Z)-dodecenol and (3Z,6Z)-dodecadienol are perceived by workers of both species. Bioassays indicated that inquiline soldier heads, as well as the two synthetic compounds, are attractive to conspecific workers and elicit an arresting behavior, while host soldiers and workers avoid these chemicals at biologically relevant amounts. These observations support the hypothesis that chemically mediated spatial separation of the host and the inquiline is an element of a conflict-avoidance strategy in these species.

  4. Size and chemical characterization of individual particles resulting from biomass burning of local southern California species

    Treesearch

    Philip J. Silva; Don-Yuan Liu; Christopher A. Noble; Kimberly A. Prather

    1999-01-01

    The chemical composition and size of individual particles derived from combustion products of several species found in Southern California were obtained using aerosol time-of-flight mass spectrometry. The major inorganic species observed in >90% of all biomass burning particles is potassium, indicated by the atomic ion, as well as clusters containing chloride,...

  5. Chemical preconcentrator

    DOEpatents

    Manginell, Ronald P.; Frye-Mason, Gregory C.

    2001-01-01

    A chemical preconcentrator is disclosed with applications to chemical sensing and analysis. The preconcentrator can be formed by depositing a resistive heating element (e.g. platinum) over a membrane (e.g. silicon nitride) suspended above a substrate. A coating of a sorptive material (e.g. a microporous hydrophobic sol-gel coating or a polymer coating) is formed on the suspended membrane proximate to the heating element to selective sorb one or more chemical species of interest over a time period, thereby concentrating the chemical species in the sorptive material. Upon heating the sorptive material with the resistive heating element, the sorbed chemical species are released for detection and analysis in a relatively high concentration and over a relatively short time period. The sorptive material can be made to selectively sorb particular chemical species of interest while not substantially sorbing other chemical species not of interest. The present invention has applications for use in forming high-sensitivity, rapid-response miniaturized chemical analysis systems (e.g. a "chem lab on a chip").

  6. Tree species traits influence soil physical, chemical, and biological properties in high elevation forests.

    PubMed

    Ayres, Edward; Steltzer, Heidi; Berg, Sarah; Wallenstein, Matthew D; Simmons, Breana L; Wall, Diana H

    2009-06-18

    Previous studies have shown that plants often have species-specific effects on soil properties. In high elevation forests in the Southern Rocky Mountains, North America, areas that are dominated by a single tree species are often adjacent to areas dominated by another tree species. Here, we assessed soil properties beneath adjacent stands of trembling aspen, lodgepole pine, and Engelmann spruce, which are dominant tree species in this region and are distributed widely in North America. We hypothesized that soil properties would differ among stands dominated by different tree species and expected that aspen stands would have higher soil temperatures due to their open structure, which, combined with higher quality litter, would result in increased soil respiration rates, nitrogen availability, and microbial biomass, and differences in soil faunal community composition. We assessed soil physical, chemical, and biological properties at four sites where stands of aspen, pine, and spruce occurred in close proximity to one-another in the San Juan Mountains, Colorado. Leaf litter quality differed among the tree species, with the highest nitrogen (N) concentration and lowest lignin:N in aspen litter. Nitrogen concentration was similar in pine and spruce litter, but lignin:N was highest in pine litter. Soil temperature and moisture were highest in aspen stands, which, in combination with higher litter quality, probably contributed to faster soil respiration rates from stands of aspen. Soil carbon and N content, ammonium concentration, and microbial biomass did not differ among tree species, but nitrate concentration was highest in aspen soil and lowest in spruce soil. In addition, soil fungal, bacterial, and nematode community composition and rotifer, collembolan, and mesostigmatid mite abundance differed among the tree species, while the total abundance of nematodes, tardigrades, oribatid mites, and prostigmatid mites did not. Although some soil characteristics were

  7. Systematic Approach to Calculate the Concentration of Chemical Species in Multi-Equilibrium Problems

    ERIC Educational Resources Information Center

    Baeza-Baeza, Juan Jose; Garcia-Alvarez-Coque, Maria Celia

    2011-01-01

    A general systematic approach is proposed for the numerical calculation of multi-equilibrium problems. The approach involves several steps: (i) the establishment of balances involving the chemical species in solution (e.g., mass balances, charge balance, and stoichiometric balance for the reaction products), (ii) the selection of the unknowns (the…

  8. Chemical Cues which Include Amino Acids Mediate Species-Specific Feeding Behavior in Invasive Filter-Feeding Bigheaded Carps.

    PubMed

    Claus, Aaron W; Sorensen, Peter W

    2017-04-01

    This study tested whether and how dissolved chemicals might assist food recognition in two filter-feeding fishes, the silver (Hypophthalmichthys molitrix) and the bighead carp (H. nobilis). These species evolved in Asia, are now invasive in the Mississippi River, and feed voraciously on microparticles including plankton. The food habits and biology of these carps are broadly similar to many filter-feeding fish, none of whose chemical ecology has been examined. We conducted five experiments. First, we demonstrated that buccal-pharngeal pumping (BPP), a behavior in which fish pump water into their buccal cavities, is responsible for sampling food: BPP activity in both silver and bighead carps was low and increased nearly 25-fold after exposure to a filtrate of a planktonic food mixture (P < 0.01) and over 35-fold when planktonic food was added (P < 0.001). Next, we showed that of nine food filtrates, the one containing chemicals released by spirulina, a type of cyanobacterium, was the most potent planktonic component for both species. The potency of filtrates varied between species in ways that reflected their different chemical compositions. While L-amino acids could explain about half of the activity of food filtrate, other unknown chemical stimuli were also implicated. Finally, occlusion experiments showed the olfactory sense has a very important, but not exclusive, role in bigheaded carp feeding behaviors and this might be exploited in both their control and culture.

  9. Discrimination and chemical phylogenetic study of seven species of Dendrobium using infrared spectroscopy combined with cluster analysis

    NASA Astrophysics Data System (ADS)

    Luo, Congpei; He, Tao; Chun, Ze

    2013-04-01

    Dendrobium is a commonly used and precious herb in Traditional Chinese Medicine. The high biodiversity of Dendrobium and the therapeutic needs require tools for the correct and fast discrimination of different Dendrobium species. This study investigates Fourier transform infrared spectroscopy followed by cluster analysis for discrimination and chemical phylogenetic study of seven Dendrobium species. Despite the general pattern of the IR spectra, different intensities, shapes, peak positions were found in the IR spectra of these samples, especially in the range of 1800-800 cm-1. The second derivative transformation and alcoholic extracting procedure obviously enlarged the tiny spectral differences among these samples. The results indicated each Dendrobium species had a characteristic IR spectra profile, which could be used to discriminate them. The similarity coefficients among the samples were analyzed based on their second derivative IR spectra, which ranged from 0.7632 to 0.9700, among the seven Dendrobium species, and from 0.5163 to 0.9615, among the ethanol extracts. A dendrogram was constructed based on cluster analysis the IR spectra for studying the chemical phylogenetic relationships among the samples. The results indicated that D. denneanum and D. crepidatum could be the alternative resources to substitute D. chrysotoxum, D. officinale and D. nobile which were officially recorded in Chinese Pharmacopoeia. In conclusion, with the advantages of high resolution, speediness and convenience, the experimental approach can successfully discriminate and construct the chemical phylogenetic relationships of the seven Dendrobium species.

  10. Initiated chemical vapor deposited nanoadhesive for bonding National Ignition Facility's targets

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lee, Tom

    Currently, the target fabrication scientists in National Ignition Facility Directorate at Lawrence Livermore National Laboratory (LLNL) is studying the propagation force resulted from laser impulses impacting a target. To best study this, they would like the adhesive used to glue the target substrates to be as thin as possible. The main objective of this research project is to create adhesive glue bonds for NIF’s targets that are ≤ 1 μm thick. Polyglycidylmethacrylate (PGMA) thin films were coated on various substrates using initiated chemical vapor deposition (iCVD). Film quality studies using white light interferometry reveal that the iCVD PGMA films weremore » smooth. The coated substrates were bonded at 150 °C under vacuum, with low inflow of Nitrogen. Success in bonding most of NIF’s mock targets at thicknesses ≤ 1 μm indicates that our process is feasible in bonding the real targets. Key parameters that are required for successful bonding were concluded from the bonding results. They include inert bonding atmosphere, sufficient contact between the PGMA films, and smooth substrates. Average bond strength of 0.60 MPa was obtained from mechanical shearing tests. The bonding failure mode of the sheared interfaces was observed to be cohesive. Future work on this project will include reattempt to bond silica aerogel to iCVD PGMA coated substrates, stabilize carbon nanotube forests with iCVD PGMA coating, and kinetics study of PGMA thermal crosslinking.« less

  11. Identification and Quantitative Measurements of Chemical Species by Mass Spectrometry

    NASA Technical Reports Server (NTRS)

    Zondlo, Mark A.; Bomse, David S.

    2005-01-01

    The development of a miniature gas chromatograph/mass spectrometer system for the measurement of chemical species of interest to combustion is described. The completed system is a fully-contained, automated instrument consisting of a sampling inlet, a small-scale gas chromatograph, a miniature, quadrupole mass spectrometer, vacuum pumps, and software. A pair of computer-driven valves controls the gas sampling and introduction to the chromatographic column. The column has a stainless steel exterior and a silica interior, and contains an adsorbent of that is used to separate organic species. The detection system is based on a quadrupole mass spectrometer consisting of a micropole array, electrometer, and a computer interface. The vacuum system has two miniature pumps to maintain the low pressure needed for the mass spectrometer. A laptop computer uses custom software to control the entire system and collect the data. In a laboratory demonstration, the system separated calibration mixtures containing 1000 ppm of alkanes and alkenes.

  12. Accumulation route and chemical form of mercury in mushroom species

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Minagawa, K.; Sasaki, T.; Takizawa, Y.

    1980-09-01

    Some papers were published on several species of fungi having more accumulating abilities of mercury than other land plants and a relatively small part of mercury being present as methylmercury in most species (Stegnar et al. 1973, Stijve and Roschnik 1974). But, little information is available regarding the routes of mercury in fungi, and also no report on mercury speciation (chemical form and complexation) in them have been published, apart from methylmercury. In order to evaluate accurately their biological characteristics such as absorption, excretion, accumulation and toxicity (The Task Group on Metal Interaction 1978), the mercury speciation present in mushrooms,more » regardless of edible or nonedible, should be identified. In this report, we present (1) contents of total and methylmercury in mushrooms near the acetaldehyde factory which had the mounds of sludge containing mercury, (2) data or exposure experiment of mercury vapor to raw mushrooms (Shiitake) on the market, and (3) data on mercury speciation of mercury other than methylmercury.« less

  13. Arbuscular mycorrhizal fungi alter above- and below-ground chemical defense expression differentially among Asclepias species.

    PubMed

    Vannette, Rachel L; Hunter, Mark D; Rasmann, Sergio

    2013-01-01

    Below-ground (BG) symbionts of plants can have substantial influence on plant growth and nutrition. Recent work demonstrates that mycorrhizal fungi can affect plant resistance to herbivory and the performance of above- (AG) and BG herbivores. Although these examples emerge from diverse systems, it is unclear if plant species that express similar defensive traits respond similarly to fungal colonization, but comparative work may inform this question. To examine the effects of arbuscular mycorrhizal fungi (AMF) on the expression of chemical resistance, we inoculated 8 species of Asclepias (milkweed)-which all produce toxic cardenolides-with a community of AMF. We quantified plant biomass, foliar and root cardenolide concentration and composition, and assessed evidence for a growth-defense tradeoff in the presence and absence of AMF. As expected, total foliar and root cardenolide concentration varied among milkweed species. Importantly, the effect of mycorrhizal fungi on total foliar cardenolide concentration also varied among milkweed species, with foliar cardenolides increasing or decreasing, depending on the plant species. We detected a phylogenetic signal to this variation; AMF fungi reduced foliar cardenolide concentrations to a greater extent in the clade including A. curassavica than in the clade including A. syriaca. Moreover, AMF inoculation shifted the composition of cardenolides in AG and BG plant tissues in a species-specific fashion. Mycorrhizal inoculation changed the relative distribution of cardenolides between root and shoot tissue in a species-specific fashion, but did not affect cardenolide diversity or polarity. Finally, a tradeoff between plant growth and defense in non-mycorrhizal plants was mitigated completely by AMF inoculation. Overall, we conclude that the effects of AMF inoculation on the expression of chemical resistance can vary among congeneric plant species, and ameliorate tradeoffs between growth and defense.

  14. Arbuscular mycorrhizal fungi alter above- and below-ground chemical defense expression differentially among Asclepias species

    PubMed Central

    Vannette, Rachel L.; Hunter, Mark D.; Rasmann, Sergio

    2013-01-01

    Below-ground (BG) symbionts of plants can have substantial influence on plant growth and nutrition. Recent work demonstrates that mycorrhizal fungi can affect plant resistance to herbivory and the performance of above- (AG) and BG herbivores. Although these examples emerge from diverse systems, it is unclear if plant species that express similar defensive traits respond similarly to fungal colonization, but comparative work may inform this question. To examine the effects of arbuscular mycorrhizal fungi (AMF) on the expression of chemical resistance, we inoculated 8 species of Asclepias (milkweed)—which all produce toxic cardenolides—with a community of AMF. We quantified plant biomass, foliar and root cardenolide concentration and composition, and assessed evidence for a growth-defense tradeoff in the presence and absence of AMF. As expected, total foliar and root cardenolide concentration varied among milkweed species. Importantly, the effect of mycorrhizal fungi on total foliar cardenolide concentration also varied among milkweed species, with foliar cardenolides increasing or decreasing, depending on the plant species. We detected a phylogenetic signal to this variation; AMF fungi reduced foliar cardenolide concentrations to a greater extent in the clade including A. curassavica than in the clade including A. syriaca. Moreover, AMF inoculation shifted the composition of cardenolides in AG and BG plant tissues in a species-specific fashion. Mycorrhizal inoculation changed the relative distribution of cardenolides between root and shoot tissue in a species-specific fashion, but did not affect cardenolide diversity or polarity. Finally, a tradeoff between plant growth and defense in non-mycorrhizal plants was mitigated completely by AMF inoculation. Overall, we conclude that the effects of AMF inoculation on the expression of chemical resistance can vary among congeneric plant species, and ameliorate tradeoffs between growth and defense. PMID:24065971

  15. The smell of change: warming affects species interactions mediated by chemical information.

    PubMed

    Sentis, Arnaud; Ramon-Portugal, Felipe; Brodeur, Jacques; Hemptinne, Jean-Louis

    2015-10-01

    Knowledge of how temperature influences an organism's physiology and behaviour is of paramount importance for understanding and predicting the impacts of climate change on species' interactions. While the behaviour of many organisms is driven by chemical information on which they rely on to detect resources, conspecifics, natural enemies and competitors, the effects of temperature on infochemical-mediated interactions remain largely unexplored. Here, we experimentally show that temperature strongly influences the emission of infochemicals by ladybeetle larvae, which, in turn, modifies the oviposition behaviour of conspecific females. Temperature also directly affects female perception of infochemicals and their oviposition behaviour. Our results suggest that temperature-mediated effects on chemical communication can influence flows across system boundaries (e.g. immigration and emigration) and thus alter the dynamics and stability of ecological networks. We therefore argue that investigating the effects of temperature on chemical communication is a crucial step towards a better understanding of the functioning of ecological communities facing rapid environmental changes. © 2015 John Wiley & Sons Ltd.

  16. Synthesis of mouse centromere-targeted polyamides and physico-chemical studies of their interaction with the target double-stranded DNA.

    PubMed

    Nozeret, Karine; Bonan, Marc; Yarmoluk, Serguiy M; Novopashina, Darya S; Boutorine, Alexandre S

    2015-09-01

    Synthetic minor groove-binding pyrrole-imidazole polyamides labeled by fluorophores are promising candidates for fluorescence imaging of double-stranded DNA in isolated chromosomes or fixed and living cells. We synthesized nine hairpin and two head-to-head tandem polyamides targeting repeated sequences from mouse major satellites. Their interaction with synthetic target dsDNA has been studied by physico-chemical methods in vitro before and after coupling to various fluorophores. Great variability in affinities and fluorescence properties reveals a conclusion that these properties do not only rely on recognition rules, but also on other known and unknown structural factors. Individual testing of each probe is needed before cellular applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Chemical properties in fruits of mulberry species from the Xinjiang province of China.

    PubMed

    Jiang, Yan; Nie, Wen-Jing

    2015-05-01

    Mulberries are a widely cultivated foodstuff both in China and worldwide. However, there are stark differences in the nutritional values of mulberry species. To better appreciate these differences, we here describe the chemical characteristics of white (Morus alba L.), Russian (M. alba var. tatarica L.), and black (Morus nigra L.) mulberry fruits cultivated in the Xinjiang province of China. The chemical composition analysis was performed by official methods procedures. The amino acids were analysed by the phenyl isothiocyanate method. The 2,6-dichloroindophenol titrimetric method, the aluminium chloride colorimetric method, and the pH differential method were also used in measuring the content of reduced ascorbic acid, total flavonoids, and total monomeric anthocyanins, respectively. The black mulberry fruits had the highest content of reduced ascorbic acid (48.4 mg/100 g fw), titratable acidity (47.1 mg/g fw), and Fe (11.9 mg/100 g fw) of these 3 species. The Russian mulberry fruits had the highest EAA/TAA (essential amino acid/total amino acid) ratio at 44% followed by the white mulberry (42%) and the black mulberry (29%). The black mulberry fruits had found to be richest in terms of total flavonoids and total monomeric anthocyanins. These results are helpful for selecting mulberry species with abundant nutrients and phytochemicals for commercial cultivation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Chemical signatures and new drug targets for gametocytocidal drug development

    NASA Astrophysics Data System (ADS)

    Sun, Wei; Tanaka, Takeshi Q.; Magle, Crystal T.; Huang, Wenwei; Southall, Noel; Huang, Ruili; Dehdashti, Seameen J.; McKew, John C.; Williamson, Kim C.; Zheng, Wei

    2014-01-01

    Control of parasite transmission is critical for the eradication of malaria. However, most antimalarial drugs are not active against P. falciparum gametocytes, responsible for the spread of malaria. Consequently, patients can remain infectious for weeks after the clearance of asexual parasites and clinical symptoms. Here we report the identification of 27 potent gametocytocidal compounds (IC50 < 1 μM) from screening 5,215 known drugs and compounds. All these compounds were active against three strains of gametocytes with different drug sensitivities and geographical origins, 3D7, HB3 and Dd2. Cheminformatic analysis revealed chemical signatures for P. falciparum sexual and asexual stages indicative of druggability and suggesting potential targets. Torin 2, a top lead compound (IC50 = 8 nM against gametocytes in vitro), completely blocked oocyst formation in a mouse model of transmission. These results provide critical new leads and potential targets to expand the repertoire of malaria transmission-blocking reagents.

  19. Substantial equivalence analysis in fruits from three Theobroma species through chemical composition and protein profiling.

    PubMed

    Pérez-Mora, Walter; Jorrin-Novo, Jesús V; Melgarejo, Luz Marina

    2018-02-01

    Substantial equivalence studies were performed in three Theobroma spp., cacao, bicolor and grandiflorum through chemical composition analysis and protein profiling of fruit (pulp juice and seeds). Principal component analysis of sugar, organic acid, and phenol content in pulp juice revealed equivalence among the three species, with differences in some of the compounds that may result in different organoleptic properties. Proteins were extracted from seeds and pulp juice, resolved by two dimensional electrophoresis and major spots subjected to mass spectrometry analysis and identification. The protein profile, as revealed by principal component analysis, was variable among the three species in both seed and pulp, with qualitative and quantitative differences in some of protein species. The functional grouping of the identified proteins correlated with the biological role of each organ. Some of the identified proteins are of interest, being minimally discussed, including vicilin, a protease inhibitor, and a flavonol synthase/flavanone 3-hydroxylase. Theobroma grandiflorum and Theobroma bicolor are endemic Amazonian plants that are poorly traded at the local level. As close relatives of Theobroma cacao, they may provide a good alternative for human consumption and industrial purposes. In this regard, we performed equivalence studies by conducting a comparative biochemical and proteomics analysis of the fruit, pulp juice and seeds of these three species. The results indicated equivalent chemical compositions and variable protein profiles with some differences in the content of the specific compounds or protein species that may result in variable organoleptic properties between the species and can be exploited for traceability purposes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Soil chemical factors and grassland species density in Emas National Park (central Brazil).

    PubMed

    Amorim, P K; Batalha, M A

    2008-05-01

    Studies of grasslands on specific soil types suggest that different nutrients can limit biomass production and, hence, species composition and number. The Brazilian cerrado is the major savanna region in America and once covered about 2 million km(2), mainly in the Brazilian Central Plateau, under seasonal climate, with wet summer and dry winter. In view of the importance of soil chemical factors in the distribution of the vegetation forms within the Cerrado domain and which may influence the number of species, we analyzed some soil characteristics in three herbaceous vegetation forms -- hyperseasonal cerrado, seasonal cerrado, and wet grassland -- in Emas National Park, a core cerrado site, to investigate the relationship between number of species and soil characteristics. We collected vegetation and soil samples in these three vegetation forms and submitted the obtained data to multiple linear regression. We found out that aluminum and pH were the best predictors of species density, the former positively related to species density and the latter negatively related. Since the predictable variation in species density is important in determining areas of conservation, we can postulate that these two soil factors are indicators of high species density areas in tropical grasslands, which could be used in selecting priority sites for conservation.

  1. A chemodynamic approach for estimating losses of target organic chemicals from water during sample holding time

    USGS Publications Warehouse

    Capel, P.D.; Larson, S.J.

    1995-01-01

    Minimizing the loss of target organic chemicals from environmental water samples between the time of sample collection and isolation is important to the integrity of an investigation. During this sample holding time, there is a potential for analyte loss through volatilization from the water to the headspace, sorption to the walls and cap of the sample bottle; and transformation through biotic and/or abiotic reactions. This paper presents a chemodynamic-based, generalized approach to estimate the most probable loss processes for individual target organic chemicals. The basic premise is that the investigator must know which loss process(es) are important for a particular analyte, based on its chemodynamic properties, when choosing the appropriate method(s) to prevent loss.

  2. Rational design of chemical genetic probes of RNA function and lead therapeutics targeting repeating transcripts.

    PubMed

    Disney, Matthew D

    2013-12-01

    RNA is an important yet vastly underexploited target for small molecule chemical probes or lead therapeutics. Small molecules have been used successfully to modulate the function of the bacterial ribosome, viral RNAs and riboswitches. These RNAs are either highly expressed or can be targeted using substrate mimicry, a mainstay in the design of enzyme inhibitors. However, most cellular RNAs are neither highly expressed nor have a lead small molecule inhibitor, a significant challenge for drug discovery efforts. Herein, I describe the design of small molecules targeting expanded repeating transcripts that cause myotonic muscular dystrophy (DM). These test cases illustrate the challenges of designing small molecules that target RNA and the advantages of targeting repeating transcripts. Lastly, I discuss how small molecules might be more advantageous than oligonucleotides for targeting RNA. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects

    PubMed Central

    Bramsen, Jesper B.; Pakula, Malgorzata M.; Hansen, Thomas B.; Bus, Claus; Langkjær, Niels; Odadzic, Dalibor; Smicius, Romualdas; Wengel, Suzy L.; Chattopadhyaya, Jyoti; Engels, Joachim W.; Herdewijn, Piet; Wengel, Jesper; Kjems, Jørgen

    2010-01-01

    Small interfering RNAs (siRNAs) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent miRNA-like behavior. Such off-target effects are primarily mediated by the sequence-specific interaction between the siRNA seed regions (position 2–8 of either siRNA strand counting from the 5′-end) and complementary sequences in the 3′UTR of (off-) targets. It was previously shown that chemical modification of siRNAs can reduce off-targeting but only very few modifications have been tested leaving more to be identified. Here we developed a luciferase reporter-based assay suitable to monitor siRNA off-targeting in a high throughput manner using stable cell lines. We investigated the impact of chemically modifying single nucleotide positions within the siRNA seed on siRNA function and off-targeting using 10 different types of chemical modifications, three different target sequences and three siRNA concentrations. We found several differently modified siRNAs to exercise reduced off-targeting yet incorporation of the strongly destabilizing unlocked nucleic acid (UNA) modification into position 7 of the siRNA most potently reduced off-targeting for all tested sequences. Notably, such position-specific destabilization of siRNA–target interactions did not significantly reduce siRNA potency and is therefore well suited for future siRNA designs especially for applications in vivo where siRNA concentrations, expectedly, will be low. PMID:20453030

  4. Mars 2020 Rover SHERLOC Calibration Target

    NASA Technical Reports Server (NTRS)

    Graff, Trevor; Fries, Marc; Burton, Aaron; Ross, Amy; Larson, Kristine; Garrison, Dan; Calaway, Mike; Tran, Vinh; Bhartia, Roh; Beegle, Luther

    2016-01-01

    The Scanning Habitable Environments with Raman & Luminescence for Organics & Chemicals (SHERLOC) instrument is a deep ultraviolet (UV) Raman Fluorescence instrument selected as part of the Mars 2020 rover instrument suite. SHERLOC will be mounted on the rover arm and its primary role is to identify carbonaceous species in martian samples. The SHERLOC instrument requires a calibration target which is being designed and fabricated at JSC as part of our continued science participation in Mars robotic missions. The SHERLOC calibration target will address a wide range of NASA goals to include basic science of interest to both the Science Mission Directorate and Human Exploration and Operations Mission Directorate.

  5. Simpler is better: fewer nontarget insects trapped with a 4-component chemical lure versus a chemically more complex food-type bait for Drosophila suzukii

    USDA-ARS?s Scientific Manuscript database

    As baits, fermented food products are generally attractive to many types of insects, making it difficult to sort through nontarget insects to monitor a pest species of interest. We test the hypothesis that a chemically simpler and more defined attractant developed for a target insect is more specifi...

  6. Chemical species of sulfur in prostate cancer cells studied by XANES spectroscopy

    NASA Astrophysics Data System (ADS)

    Czapla, Joanna; Kwiatek, Wojciech M.; Lekki, Janusz; Dulińska-Litewka, Joanna; Steininger, Ralph; Göttlicher, Jörg

    2013-12-01

    The role of sulfur in prostate cancer progression may be significant for understanding the process of carcinogenesis. This work, based on X-ray Absorption Near Edge Structure (XANES) spectroscopy, is focused on determination of sulfur chemical species occurring in prostate cancer cell lines. The experimental material consisted of four commercially available cell lines: three from metastasized prostate cancer (PC3, LNCaP, and DU145) and one, used as a control, from the non-tumourigenic peripheral zone of the prostate (PZ-HPV-7). The experiment was performed at the SUL-X beamline of the synchrotron radiation source ANKA, Karlsruhe (Germany). The K-edge XANES spectra of sulfur were analyzed by deconvolution in order to establish sulfur species that occur in prostate cancer cells and to find out whether there are any differences in their content between various cell lines. Experimental spectra were fitted in two ways: with two Gaussian peaks and one arctangent step function, and additionally by a Linear Combination Fit with spectra of reference compounds in order to obtain quantitative chemical information. All fitting procedures were performed with the Athena code (Ravel and Newville, 2005) and the results of deconvolution were used to determine the fraction of each sulfur form. The results of data analysis showed that cell lines from different metastasis had different ratio of reduced to oxidized sulfur species. The LCF analysis demonstrated that the highest content of GSH, one of the most important sulfur-bearing compounds in cells, was observed in DU145 cells. These findings may confirm the hypothesis of changes in redox balance in case of cancer initiation and progression.

  7. The action of chemical and mechanical stresses on single and dual species biofilm removal of drinking water bacteria.

    PubMed

    Gomes, I B; Lemos, M; Mathieu, L; Simões, M; Simões, L C

    2018-08-01

    The presence of biofilms in drinking water distribution systems (DWDS) is a global public health concern as they can harbor pathogenic microorganisms. Sodium hypochlorite (NaOCl) is the most commonly used disinfectant for microbial growth control in DWDS. However, its effect on biofilm removal is still unclear. This work aims to evaluate the effects of the combination of chemical (NaOCl) and mechanical stresses on the removal of single and dual species biofilms of two bacteria isolated from DWDS and considered opportunistic, Acinectobacter calcoaceticus and Stenotrophomonas maltophilia. A rotating cylinder reactor was successfully used for the first time in drinking water biofilm studies with polyvinyl chloride as substratum. The single and dual species biofilms presented different characteristics in terms of metabolic activity, mass, density, thickness and content of proteins and polysaccharides. Their complete removal was not achieved even when a high NaOCl concentrations and an increasing series of shear stresses (from 2 to 23Pa) were applied. In general, NaOCl pre-treatment did not improve the impact of mechanical stress on biofilm removal. Dual species biofilms were colonized mostly by S. maltophilia and were more susceptible to chemical and mechanical stresses than these single species. The most efficient treatment (93% biofilm removal) was the combination of NaOCl at 175mg·l -1 with mechanical stress against dual species biofilms. Of concern was the high tolerance of S. maltophilia to chemical and mechanical stresses in both single and dual species biofilms. The overall results demonstrate the inefficacy of NaOCl on biofilm removal even when combined with high shear stresses. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. Algal bioremediation of waste waters from land-based aquaculture using ulva: selecting target species and strains.

    PubMed

    Lawton, Rebecca J; Mata, Leonardo; de Nys, Rocky; Paul, Nicholas A

    2013-01-01

    The optimised reduction of dissolved nutrient loads in aquaculture effluents through bioremediation requires selection of appropriate algal species and strains. The objective of the current study was to identify target species and strains from the macroalgal genus Ulva for bioremediation of land-based aquaculture facilities in Eastern Australia. We surveyed land-based aquaculture facilities and natural coastal environments across three geographic locations in Eastern Australia to determine which species of Ulva occur naturally in this region and conducted growth trials at three temperature treatments on a subset of samples from each location to determine whether local strains had superior performance under local environmental conditions. DNA barcoding using the markers ITS and tufA identified six species of Ulva, with U. ohnoi being the most common blade species and U. sp. 3 the most common filamentous species. Both species occurred at multiple land-based aquaculture facilities in Townsville and Brisbane and multiple strains of each species grew well in culture. Specific growth rates of U. ohnoi and U. sp. 3 were high (over 9% and 15% day(-1) respectively) across temperature treatments. Within species, strains of U. ohnoi had higher growth in temperatures corresponding to local conditions, suggesting that strains may be locally adapted. However, across all temperature treatments Townsville strains had the highest growth rates (11.2-20.4% day(-1)) and Sydney strains had the lowest growth rates (2.5-8.3% day(-1)). We also found significant differences in growth between strains of U. ohnoi collected from the same geographic location, highlighting the potential to isolate and cultivate fast growing strains. In contrast, there was no clearly identifiable competitive strain of filamentous Ulva, with multiple species and strains having variable performance. The fast growth rates and broad geographical distribution of U. ohnoi make this an ideal species to target for

  9. Erythrocyte membrane-coated gold nanocages for targeted photothermal and chemical cancer therapy

    NASA Astrophysics Data System (ADS)

    Zhu, Dao-Ming; Xie, Wei; Xiao, Yu-Sha; Suo, Meng; Zan, Ming-Hui; Liao, Qing-Quan; Hu, Xue-Jia; Chen, Li-Ben; Chen, Bei; Wu, Wen-Tao; Ji, Li-Wei; Huang, Hui-Ming; Guo, Shi-Shang; Zhao, Xing-Zhong; Liu, Quan-Yan; Liu, Wei

    2018-02-01

    Recently, red blood cell (RBC) membrane-coated nanoparticles have attracted much attention because of their excellent immune escapability; meanwhile, gold nanocages (AuNs) have been extensively used for cancer therapy due to their photothermal effect and drug delivery capability. The combination of the RBC membrane coating and AuNs may provide an effective approach for targeted cancer therapy. However, few reports have shown the utilization of combining these two technologies. Here, we design erythrocyte membrane-coated gold nanocages for targeted photothermal and chemical cancer therapy. First, anti-EpCam antibodies were used to modify the RBC membranes to target 4T1 cancer cells. Second, the antitumor drug paclitaxel (PTX) was encapsulated into AuNs. Then, the AuNs were coated with the modified RBC membranes. These new nanoparticles were termed EpCam-RPAuNs. We characterized the capability of the EpCam-RPAuNs for selective tumor targeting via exposure to near-infrared irradiation. The experimental results demonstrate that EpCam-RPAuNs can effectively generate hyperthermia and precisely deliver the antitumor drug PTX to targeted cells. We also validated the biocompatibility of the EpCam-RAuNs in vitro. By combining the molecularly modified targeting RBC membrane and AuNs, our approach provides a new way to design biomimetic nanoparticles to enhance the surface functionality of nanoparticles. We believe that EpCam-RPAuNs can be potentially applied for cancer diagnoses and therapies.

  10. Cross-Species Extrapolation of Uptake and Disposition of Neutral Organic Chemicals in Fish Using a Multispecies Physiologically-Based Toxicokinetic Model Framework.

    PubMed

    Brinkmann, Markus; Schlechtriem, Christian; Reininghaus, Mathias; Eichbaum, Kathrin; Buchinger, Sebastian; Reifferscheid, Georg; Hollert, Henner; Preuss, Thomas G

    2016-02-16

    The potential to bioconcentrate is generally considered to be an unwanted property of a substance. Consequently, chemical legislation, including the European REACH regulations, requires the chemical industry to provide bioconcentration data for chemicals that are produced or imported at volumes exceeding 100 tons per annum or if there is a concern that a substance is persistent, bioaccumulative, and toxic. For the filling of the existing data gap for chemicals produced or imported at levels that are below this stipulated volume, without the need for additional animal experiments, physiologically-based toxicokinetic (PBTK) models can be used to predict whole-body and tissue concentrations of neutral organic chemicals in fish. PBTK models have been developed for many different fish species with promising results. In this study, we developed PBTK models for zebrafish (Danio rerio) and roach (Rutilus rutilus) and combined them with existing models for rainbow trout (Onchorhynchus mykiss), lake trout (Salvelinus namaycush), and fathead minnow (Pimephales promelas). The resulting multispecies model framework allows for cross-species extrapolation of the bioaccumulative potential of neutral organic compounds. Predictions were compared with experimental data and were accurate for most substances. Our model can be used for probabilistic risk assessment of chemical bioaccumulation, with particular emphasis on cross-species evaluations.

  11. Responses of three darter species (genus Etheostoma) to chemical alarm cues from conspecifics and congeners

    Treesearch

    Amy M. Commens-Carson; Alicia Mathis

    2007-01-01

    Several species of darters of the genus Etheostoma possess a chemical alarm substance, but it is not known how widespread this substance is within the genus. We performed behavioral bioassays on Fantail Darters (E. flabellare), Rainbow Darters (E. caeruleum), and Redfin Darters (E. whipplei)....

  12. Targeting Mitochondrial Calcium Handling and Reactive Oxygen Species in Heart Failure.

    PubMed

    Dietl, Alexander; Maack, Christoph

    2017-08-01

    In highly prevalent cardiac diseases, new therapeutic approaches are needed. Since the first description of oxidative stress in heart failure, reactive oxygen species (ROS) have been considered as attractive drug targets. Though clinical trials evaluating antioxidant vitamins as ROS-scavenging agents yielded neutral results in patients at cardiovascular risk, the knowledge of ROS as pathophysiological factors has considerably advanced in the past few years and led to novel treatment approaches. Here, we review recent new insights and current strategies in targeting mitochondrial calcium handling and ROS in heart failure. Mitochondria are an important ROS source, and more recently, drug development focused on targeting mitochondria (e.g. by SS-31 or MitoQ). Important advancement has also been made to decipher how the matching of energy supply and demand through calcium (Ca 2+ ) handling impacts on mitochondrial ROS production and elimination. This opens novel opportunities to ameliorate mitochondrial dysfunction in heart failure by targeting cytosolic and mitochondrial ion transporters to improve this matching process. According to this approach, highly specific substances as the preclinical CGP-37157, as well as the clinically used ranolazine and empagliflozin, provide promising results on different levels of evidence. Furthermore, the understanding of redox signalling relays, resembled by catalyst-mediated protein oxidation, is about to change former paradigms of ROS signalling. Novel methods, as redox proteomics, allow to precisely analyse key regulatory thiol switches, which may induce adaptive or maladaptive signalling. Additionally, the generation of genetically encoded probes increased the spatial and temporal resolution of ROS imaging and opened a new methodological window to subtle, formerly obscured processes. These novel insights may broaden our understanding of why previous attempts to target oxidative stress have failed, and at the same time provide us

  13. Sea Cucumber Glycosides: Chemical Structures, Producing Species and Important Biological Properties.

    PubMed

    Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Rahman, M Aminur; Islam, Mohamad Tofazzal

    2017-10-17

    Sea cucumbers belonging to echinoderm are traditionally used as tonic food in China and other Asian countries. They produce abundant biologically active triterpene glycosides. More than 300 triterpene glycosides have been isolated and characterized from various species of sea cucumbers, which are classified as holostane and nonholostane depending on the presence or absence of a specific structural unit γ(18,20)-lactone in the aglycone. Triterpene glycosides contain a carbohydrate chain up to six monosaccharide units mainly consisting of d-xylose, 3-O-methy-d-xylose, d-glucose, 3-O-methyl-d-glucose, and d-quinovose. Cytotoxicity is the common biological property of triterpene glycosides isolated from sea cucumbers. Besides cytotoxicity, triterpene glycosides also exhibit antifungal, antiviral and hemolytic activities. This review updates and summarizes our understanding on diverse chemical structures of triterpene glycosides from various species of sea cucumbers and their important biological activities. Mechanisms of action and structural-activity relationships (SARs) of sea cucumber glycosides are also discussed briefly.

  14. Sea Cucumber Glycosides: Chemical Structures, Producing Species and Important Biological Properties

    PubMed Central

    Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Rahman, M. Aminur; Islam, Mohamad Tofazzal

    2017-01-01

    Sea cucumbers belonging to echinoderm are traditionally used as tonic food in China and other Asian countries. They produce abundant biologically active triterpene glycosides. More than 300 triterpene glycosides have been isolated and characterized from various species of sea cucumbers, which are classified as holostane and nonholostane depending on the presence or absence of a specific structural unit γ(18,20)-lactone in the aglycone. Triterpene glycosides contain a carbohydrate chain up to six monosaccharide units mainly consisting of d-xylose, 3-O-methy-d-xylose, d-glucose, 3-O-methyl-d-glucose, and d-quinovose. Cytotoxicity is the common biological property of triterpene glycosides isolated from sea cucumbers. Besides cytotoxicity, triterpene glycosides also exhibit antifungal, antiviral and hemolytic activities. This review updates and summarizes our understanding on diverse chemical structures of triterpene glycosides from various species of sea cucumbers and their important biological activities. Mechanisms of action and structural–activity relationships (SARs) of sea cucumber glycosides are also discussed briefly. PMID:29039760

  15. Relative Sensitivity of Arctic Species to Physically and Chemically Dispersed Oil Determined from Three Hydrocarbon Measures of Aquatic Toxicity

    EPA Science Inventory

    The risks to Arctic species from oil releases is a global concern, but their sensitivity to chemically dispersed oil has not been assessed using a curated and standardized dataset from spiked declining tests. Species sensitivity to dispersed oil was determined by their position w...

  16. Chemical Diversity as a Function of Temperature in Six Northern Diatom Species

    PubMed Central

    Huseby, Siv; Degerlund, Maria; Eriksen, Gunilla K.; Ingebrigtsen, Richard A.; Eilertsen, Hans Chr.; Hansen, Espen

    2013-01-01

    In this study, we investigate how metabolic fingerprints are related to temperature. Six common northern temperate diatoms (Attheya longicornis, Chaetoceros socialis, Chaetoceros furcellatus, Porosira glacialis, Skeletonema marinoi, and Thalassiosira gravida) were cultivated at two different temperatures, 0.5 and 8.5 °C. To exclude metabolic variations due to differences in growth rates, the growth rates were kept similar by performing the experiments under light limited conditions but in exponential growth phase. Growth rates and maximum quantum yield of photosynthesis were measured and interpreted as physiological variables, and metabolic fingerprints were acquired by high-resolution mass spectrometry. The chemical diversity varied substantially between the two temperatures for the tested species, ranging from 31% similarity for C. furcellatus and P. glacialis to 81% similarity for A. longicornis. The chemical diversity was generally highest at the lowest temperature. PMID:24177671

  17. In vitro screening of environmental chemicals for targeted testing prioritization: the ToxCast project.

    PubMed

    Judson, Richard S; Houck, Keith A; Kavlock, Robert J; Knudsen, Thomas B; Martin, Matthew T; Mortensen, Holly M; Reif, David M; Rotroff, Daniel M; Shah, Imran; Richard, Ann M; Dix, David J

    2010-04-01

    Chemical toxicity testing is being transformed by advances in biology and computer modeling, concerns over animal use, and the thousands of environmental chemicals lacking toxicity data. The U.S. Environmental Protection Agency's ToxCast program aims to address these concerns by screening and prioritizing chemicals for potential human toxicity using in vitro assays and in silico approaches. This project aims to evaluate the use of in vitro assays for understanding the types of molecular and pathway perturbations caused by environmental chemicals and to build initial prioritization models of in vivo toxicity. We tested 309 mostly pesticide active chemicals in 467 assays across nine technologies, including high-throughput cell-free assays and cell-based assays, in multiple human primary cells and cell lines plus rat primary hepatocytes. Both individual and composite scores for effects on genes and pathways were analyzed. Chemicals displayed a broad spectrum of activity at the molecular and pathway levels. We saw many expected interactions, including endocrine and xenobiotic metabolism enzyme activity. Chemicals ranged in promiscuity across pathways, from no activity to affecting dozens of pathways. We found a statistically significant inverse association between the number of pathways perturbed by a chemical at low in vitro concentrations and the lowest in vivo dose at which a chemical causes toxicity. We also found associations between a small set of in vitro assays and rodent liver lesion formation. This approach promises to provide meaningful data on the thousands of untested environmental chemicals and to guide targeted testing of environmental contaminants.

  18. Improving chemical species tomography of turbulent flows using covariance estimation.

    PubMed

    Grauer, Samuel J; Hadwin, Paul J; Daun, Kyle J

    2017-05-01

    Chemical species tomography (CST) experiments can be divided into limited-data and full-rank cases. Both require solving ill-posed inverse problems, and thus the measurement data must be supplemented with prior information to carry out reconstructions. The Bayesian framework formalizes the role of additive information, expressed as the mean and covariance of a joint-normal prior probability density function. We present techniques for estimating the spatial covariance of a flow under limited-data and full-rank conditions. Our results show that incorporating a covariance estimate into CST reconstruction via a Bayesian prior increases the accuracy of instantaneous estimates. Improvements are especially dramatic in real-time limited-data CST, which is directly applicable to many industrially relevant experiments.

  19. A GIS APPROACH FOR IDENTIFYING SPECIES AND LOCATIONS AT RISK FROM OFF-TARGET MOVEMENT OF PESTICIDES

    EPA Science Inventory

    In many countries, numerous tests are required prior to pesticide registration for the protection of human health and the environment from the unintended effects of chemical releases. Current methodology used by the US EPA for determining plant species at risk from off site movem...

  20. Organic Redox Species in Aqueous Flow Batteries: Redox Potentials, Chemical Stability and Solubility

    PubMed Central

    Wedege, Kristina; Dražević, Emil; Konya, Denes; Bentien, Anders

    2016-01-01

    Organic molecules are currently investigated as redox species for aqueous low-cost redox flow batteries (RFBs). The envisioned features of using organic redox species are low cost and increased flexibility with respect to tailoring redox potential and solubility from molecular engineering of side groups on the organic redox-active species. In this paper 33, mainly quinone-based, compounds are studied experimentially in terms of pH dependent redox potential, solubility and stability, combined with single cell battery RFB tests on selected redox pairs. Data shows that both the solubility and redox potential are determined by the position of the side groups and only to a small extent by the number of side groups. Additionally, the chemical stability and possible degradation mechanisms leading to capacity loss over time are discussed. The main challenge for the development of all-organic RFBs is to identify a redox pair for the positive side with sufficiently high stability and redox potential that enables battery cell potentials above 1 V. PMID:27966605

  1. Organic Redox Species in Aqueous Flow Batteries: Redox Potentials, Chemical Stability and Solubility

    NASA Astrophysics Data System (ADS)

    Wedege, Kristina; Dražević, Emil; Konya, Denes; Bentien, Anders

    2016-12-01

    Organic molecules are currently investigated as redox species for aqueous low-cost redox flow batteries (RFBs). The envisioned features of using organic redox species are low cost and increased flexibility with respect to tailoring redox potential and solubility from molecular engineering of side groups on the organic redox-active species. In this paper 33, mainly quinone-based, compounds are studied experimentially in terms of pH dependent redox potential, solubility and stability, combined with single cell battery RFB tests on selected redox pairs. Data shows that both the solubility and redox potential are determined by the position of the side groups and only to a small extent by the number of side groups. Additionally, the chemical stability and possible degradation mechanisms leading to capacity loss over time are discussed. The main challenge for the development of all-organic RFBs is to identify a redox pair for the positive side with sufficiently high stability and redox potential that enables battery cell potentials above 1 V.

  2. Organic Redox Species in Aqueous Flow Batteries: Redox Potentials, Chemical Stability and Solubility.

    PubMed

    Wedege, Kristina; Dražević, Emil; Konya, Denes; Bentien, Anders

    2016-12-14

    Organic molecules are currently investigated as redox species for aqueous low-cost redox flow batteries (RFBs). The envisioned features of using organic redox species are low cost and increased flexibility with respect to tailoring redox potential and solubility from molecular engineering of side groups on the organic redox-active species. In this paper 33, mainly quinone-based, compounds are studied experimentially in terms of pH dependent redox potential, solubility and stability, combined with single cell battery RFB tests on selected redox pairs. Data shows that both the solubility and redox potential are determined by the position of the side groups and only to a small extent by the number of side groups. Additionally, the chemical stability and possible degradation mechanisms leading to capacity loss over time are discussed. The main challenge for the development of all-organic RFBs is to identify a redox pair for the positive side with sufficiently high stability and redox potential that enables battery cell potentials above 1 V.

  3. Differential surface stress sensor for detection of chemical and biological species

    NASA Astrophysics Data System (ADS)

    Kang, K.; Nilsen-Hamilton, M.; Shrotriya, P.

    2008-10-01

    We report a sensor consisting of two micromachined cantilevers (a sensing/reference pair) that is suitable for detection of chemical and biological species. The sensing strategy involves coating the sensing cantilever with receptors that have high affinities for the analyte. The presence of analyte is detected by determining the differential surface stress associated with its adsorption/absorption to the sensing cantilever. An interferometric technique is utilized to measure the differential bending of the sensing cantilever with respect to reference. Surface stress associated with hybridization of single stranded DNA is measured to demonstrate the unique advantages of the sensor.

  4. Advances in identification and validation of protein targets of natural products without chemical modification.

    PubMed

    Chang, J; Kim, Y; Kwon, H J

    2016-05-04

    Covering: up to February 2016Identification of the target proteins of natural products is pivotal to understanding the mechanisms of action to develop natural products for use as molecular probes and potential therapeutic drugs. Affinity chromatography of immobilized natural products has been conventionally used to identify target proteins, and has yielded good results. However, this method has limitations, in that labeling or tagging for immobilization and affinity purification often result in reduced or altered activity of the natural product. New strategies have recently been developed and applied to identify the target proteins of natural products and synthetic small molecules without chemical modification of the natural product. These direct and indirect methods for target identification of label-free natural products include drug affinity responsive target stability (DARTS), stability of proteins from rates of oxidation (SPROX), cellular thermal shift assay (CETSA), thermal proteome profiling (TPP), and bioinformatics-based analysis of connectivity. This review focuses on and reports case studies of the latest advances in target protein identification methods for label-free natural products. The integration of newly developed technologies will provide new insights and highlight the value of natural products for use as biological probes and new drug candidates.

  5. Chemicals associated with site-specific neoplasia in 1394 long-term carcinogenesis experiments in laboratory rodents.

    PubMed Central

    Huff, J; Cirvello, J; Haseman, J; Bucher, J

    1991-01-01

    The carcinogenicity data base used for this paper originated in the late 1960s by the National Cancer Institute and since 1978 has been continued and made more comprehensive by the National Toxicology Program. The extensive files contain among other sets of information detailed pathology data on more than 400 long-term (most often 24 month) chemical carcinogenesis studies, comprised of nearly 1600 individual experiments having at least 10 million tissue sections that have been evaluated for toxicity and carcinogenicity. Using the current data set of 379 studies made up of 1394 experiments, we have compiled listings of chemicals having like carcinogenic target sites for each of the 34 organs or systems for which histopathology diagnoses have been recorded routinely. The most common tumor site is the liver (15% of all experiments), followed in rank order by: lung, hematopoietic system and kidneys, mammary glands, forestomach, thyroid glands, Zymbal glands, urinary bladder, skin and uterus/cervix, and circulatory system and adrenal glands. These compilations are most useful for maintaining a historic perspective when evaluating the carcinogenicity of contemporary experiments. Equally important, the chemical-tumor-organ connection permits an evaluation of how well chemically induced cancers in a particular organ in one sex or species will predict or correlate with the other sex or species. Using liver cancers as an example, the overall interspecies concordance is 80%. Likewise target site predictions can be made for chemicals selected for study that may be similar to those already evaluated; thereby experimental protocols could be adjusted to allow, for example, more extensive pathology on preselected target organs (i.e., serial sections of the kidney). Further from these observations, one could decide to use two strains of mice to evaluate a short-chain chlorinated aliphatic compound or to study a human carcinogen in a sex-species known to develop chemically induced

  6. Evaluation of an In Vitro Multi-Receptor and Multi-Species Assay for Potential Endocrine Disruptor Targets (SOT)

    EPA Science Inventory

    Receptor sequence conservation across species may be a key factor determining susceptibility to potential endocrine disrupting chemicals. Computational approaches that compare receptor sequence similarities (e.g. SeqAPASS; https://seqapass.epa.gov/seqapass/) have been proposed to...

  7. Subcellular Redox Targeting: Bridging in Vitro and in Vivo Chemical Biology.

    PubMed

    Long, Marcus J C; Poganik, Jesse R; Ghosh, Souradyuti; Aye, Yimon

    2017-03-17

    Networks of redox sensor proteins within discrete microdomains regulate the flow of redox signaling. Yet, the inherent reactivity of redox signals complicates the study of specific redox events and pathways by traditional methods. Herein, we review designer chemistries capable of measuring flux and/or mimicking subcellular redox signaling at the cellular and organismal level. Such efforts have begun to decipher the logic underlying organelle-, site-, and target-specific redox signaling in vitro and in vivo. These data highlight chemical biology as a perfect gateway to interrogate how nature choreographs subcellular redox chemistry to drive precision redox biology.

  8. Tuning reactivity of diphenylpropynone derivatives with metal-associated amyloid-β species via structural modifications.

    PubMed

    Liu, Yuzhong; Kochi, Akiko; Pithadia, Amit S; Lee, Sanghyun; Nam, Younwoo; Beck, Michael W; He, Xiaoming; Lee, Dongkuk; Lim, Mi Hee

    2013-07-15

    A diphenylpropynone derivative, DPP2, has been recently demonstrated to target metal-associated amyloid-β (metal-Aβ) species implicated in Alzheimer's disease (AD). DPP2 was shown to interact with metal-Aβ species and subsequently control Aβ aggregation (reactivity) in vitro; however, its cytotoxicity has limited further biological applications. In order to improve reactivity toward Aβ species and lower cytotoxicity, along with gaining an understanding of a structure-reactivity-cytotoxicity relationship, we designed, prepared, and characterized a series of small molecules (C1/C2, P1/P2, and PA1/PA2) as structurally modified DPP2 analogues. A similar metal binding site to that of DPP2 was contained in these compounds while their structures were varied to afford different interactions and reactivities with metal ions, Aβ species, and metal-Aβ species. Distinct reactivities of our chemical family toward in vitro Aβ aggregation in the absence and presence of metal ions were observed. Among our chemical series, the compound (C2) with a relatively rigid backbone and a dimethylamino group was observed to noticeably regulate both metal-free and metal-mediated Aβ aggregation to different extents. Using our compounds, cell viability was significantly improved, compared to that with DPP2. Lastly, modifications on the DPP framework maintained the structural properties for potential blood-brain barrier (BBB) permeability. Overall, our studies demonstrated that structural variations adjacent to the metal binding site of DPP2 could govern different metal binding properties, interactions with Aβ and metal-Aβ species, reactivity toward metal-free and metal-induced Aβ aggregation, and cytotoxicity of the compounds, establishing a structure-reactivity-cytotoxicity relationship. This information could help gain insight into structural optimization for developing nontoxic chemical reagents toward targeting metal-Aβ species and modulating their reactivity in biological

  9. Chemical genomics: characterizing target pathways for bioactive compounds using the endomembrane trafficking network.

    PubMed

    Rodriguez-Furlán, Cecilia; Hicks, Glenn R; Norambuena, Lorena

    2014-01-01

    The plant endomembrane trafficking system is a highly complex set of processes. This complexity presents a challenge for its study. Classical plant genetics often struggles with loss-of-function lethality and gene redundancy. Chemical genomics allows overcoming many of these issues by using small molecules of natural or synthetic origin to inhibit specific trafficking proteins thereby affecting the processes in a tunable and reversible manner. Bioactive chemicals identified by high-throughput phenotype screens must be characterized in detail starting with understanding of the specific trafficking pathways affected. Here, we describe approaches to characterize bioactive compounds that perturb vesicle trafficking. This should equip researchers with practical knowledge on how to identify endomembrane-specific trafficking pathways that may be perturbed by specific compounds and will help to eventually identify molecular targets for these small molecules.

  10. The spatial and temporal distribution of chemical species in Padaviya Reservoir, Sri Lanka.

    NASA Astrophysics Data System (ADS)

    Koliyabandara, S. M. P. A.; Siriwardhana, C.; Cooray, P. L. A. T.; Liyanage, S. S.

    2017-12-01

    Water is one of the most important assets for human life. Eutrophication and pollution are some of the major threats to many freshwater bodies. There are thousands of reservoirs exist in Sri Lanka; however, only a handful of them has been thoroughly monitored and studied. The main objective of this study is to investigate the temporal and spatial distribution of chemical species in Padaviya reservoir which is shallow man-made irrigation reservoir (8°49'30.6" N and 80°46'2.05"E) located in Sri Lanka constructed around 300 BC. The average depth is 8 m and 4 m in wet and dry seasons respectively. It has a catchment area of 270 km2. Water sampling was done at bi-monthly intervals for a period of one year staring from January 2016. Chemical analyses were conducted according to standard protocols. The maximum temperature difference between the surface and bottom waters of the reservoir was 2 °C throughout the year. The surface and bottom water conductivity varied between 175 ± 2.3 to 250 ± 3.0 μS cm-1 and 475 ± 3.7 to 600 ± 4.5 μScm-1 respectively. The average pH of surface and bottom waters varied between 8.5 ± 0.1 to 7.8 ± 0.2 and 7.2 ± 0.02 to 6.8 ± 0.2 respectively. The dissolved oxygen concentration showed a clinograde type distribution throughout the year where the surface waters were well oxygenated (DO ≈ 7.5 ppm) and the bottom waters were anoxic (DO ≈ 0.15 ppm). Ammonia concentration increased with the depth from surface concentration of 150 ± 50 to 300 ± 25 ppb at the bottom. Nitrite distribution was similar to ammonia and the surface concentration was 100 ± 25ppb throughtout the year and at the bottom it varied between 300 ± 30 to 4500 ± 30 ppb. Water soluble phosphate distribution was also similar to ammonia. The surface concentration was 200 ± 20 ppb throughtout the year and varied from 100 ± 20 to 2000 ±20 ppb at the bottom. Nitrate distribution was inverse of the ammonia. The surface concentration was 500 ± 30 to 900 ± 30 ppb

  11. Selection of focal earthworm species as non-target soil organisms for environmental risk assessment of genetically modified plants.

    PubMed

    van Capelle, Christine; Schrader, Stefan; Arpaia, Salvatore

    2016-04-01

    By means of a literature survey, earthworm species of significant relevance for soil functions in different biogeographical regions of Europe (Atlantic, Boreal, Mediterranean) were identified. These focal earthworm species, defined here according to the EFSA Guidance Document on the environmental risk assessment (ERA) of genetically modified plants, are typical for arable soils under crop rotations with maize and/or potatoes within the three regions represented by Ireland, Sweden and Spain, respectively. Focal earthworm species were selected following a matrix of four steps: Identification of functional groups, categorization of non-target species, ranking species on ecological criteria, and final selection of focal species. They are recommended as appropriate non-target organisms to assess environmental risks of genetically modified (GM) crops; in this case maize and potatoes. In total, 44 literature sources on earthworms in arable cropping systems including maize or potato from Ireland, Sweden and Spain were collected, which present information on species diversity, individual density and specific relevance for soil functions. By means of condensed literature data, those species were identified which (i) play an important functional role in respective soil systems, (ii) are well adapted to the biogeographical regions, (iii) are expected to occur in high abundances under cultivation of maize or potato and (iv) fulfill the requirements for an ERA test system based on life-history traits. First, primary and secondary decomposers were identified as functional groups being exposed to the GM crops. In a second step, anecic and endogeic species were categorized as potential species. In step three, eight anecic and endogeic earthworm species belonging to the family Lumbricidae were ranked as relevant species: Aporrectodea caliginosa, Aporrectodea rosea, Aporrectodea longa, Allolobophora chlorotica, Lumbricus terrestris, Lumbricus friendi, Octodrilus complanatus and

  12. The Reactive Species Interactome: Evolutionary Emergence, Biological Significance, and Opportunities for Redox Metabolomics and Personalized Medicine.

    PubMed

    Cortese-Krott, Miriam M; Koning, Anne; Kuhnle, Gunter G C; Nagy, Peter; Bianco, Christopher L; Pasch, Andreas; Wink, David A; Fukuto, Jon M; Jackson, Alan A; van Goor, Harry; Olson, Kenneth R; Feelisch, Martin

    2017-10-01

    Oxidative stress is thought to account for aberrant redox homeostasis and contribute to aging and disease. However, more often than not, administration of antioxidants is ineffective, suggesting that our current understanding of the underlying regulatory processes is incomplete. Recent Advances: Similar to reactive oxygen species and reactive nitrogen species, reactive sulfur species are now emerging as important signaling molecules, targeting regulatory cysteine redox switches in proteins, affecting gene regulation, ion transport, intermediary metabolism, and mitochondrial function. To rationalize the complexity of chemical interactions of reactive species with themselves and their targets and help define their role in systemic metabolic control, we here introduce a novel integrative concept defined as the reactive species interactome (RSI). The RSI is a primeval multilevel redox regulatory system whose architecture, together with the physicochemical characteristics of its constituents, allows efficient sensing and rapid adaptation to environmental changes and various other stressors to enhance fitness and resilience at the local and whole-organism level. To better characterize the RSI-related processes that determine fluxes through specific pathways and enable integration, it is necessary to disentangle the chemical biology and activity of reactive species (including precursors and reaction products), their targets, communication systems, and effects on cellular, organ, and whole-organism bioenergetics using system-level/network analyses. Understanding the mechanisms through which the RSI operates will enable a better appreciation of the possibilities to modulate the entire biological system; moreover, unveiling molecular signatures that characterize specific environmental challenges or other forms of stress will provide new prevention/intervention opportunities for personalized medicine. Antioxid. Redox Signal. 00, 000-000.

  13. Acute sensitivity of the vernal pool fairy shrimp, Branchinecta lynchi (Anostraca; Branchinectidae), and surrogate species to 10 chemicals

    USGS Publications Warehouse

    Ivey, Chris D.; Besser, John M.; Ingersoll, Christopher G.; Wang, Ning; Rogers, Christopher; Raimondo, Sandy; Bauer, Candice R.; Hammer, Edward J.

    2017-01-01

    Vernal pool fairy shrimp, Branchinecta lynchi, (Branchiopoda; Anostraca) and other fairy shrimp species have been listed as threatened or endangered under the US Endangered Species Act. Because few data exist about the sensitivity of Branchinecta spp. to toxic effects of contaminants, it is difficult to determine whether they are adequately protected by water quality criteria. A series of acute (24-h) lethality/immobilization tests was conducted with 3 species of fairy shrimp (B. lynchi, Branchinecta lindahli, and Thamnocephalus platyurus) and 10 chemicals with varying modes of toxic action: ammonia, potassium, chloride, sulfate, chromium(VI), copper, nickel, zinc, alachlor, and metolachlor. The same chemicals were tested in 48-h tests with other branchiopods (the cladocerans Daphnia magna and Ceriodaphnia dubia) and an amphipod (Hyalella azteca), and in 96-h tests with snails (Physa gyrina and Lymnaea stagnalis). Median effect concentrations (EC50s) for B. lynchi were strongly correlated (r2 = 0.975) with EC50s for the commercially available fairy shrimp species T. platyurus for most chemicals tested. Comparison of EC50s for fairy shrimp and EC50s for invertebrate taxa tested concurrently and with other published toxicity data indicated that fairy shrimp were relatively sensitive to potassium and several trace metals compared with other invertebrate taxa, although cladocerans, amphipods, and mussels had similar broad toxicant sensitivity. Interspecies correlation estimation models for predicting toxicity to fairy shrimp from surrogate species indicated that models with cladocerans and freshwater mussels as surrogates produced the best predictions of the sensitivity of fairy shrimp to contaminants. The results of these studies indicate that fairy shrimp are relatively sensitive to a range of toxicants, but Endangered Species Act-listed fairy shrimp of the genus Branchinecta were not consistently more sensitive than other fairy shrimp taxa. Environ Toxicol Chem

  14. Simultaneous identification and DNA barcoding of six Eimeria species infecting turkeys using PCR primers targeting the mitochondrial cytochrome c oxidase subunit I (mtCOI) locus.

    PubMed

    Hafeez, Mian A; Shivaramaiah, Srichaitanya; Dorsey, Kristi Moore; Ogedengbe, Mosun E; El-Sherry, Shiem; Whale, Julia; Cobean, Julie; Barta, John R

    2015-05-01

    Species-specific PCR primers targeting the mitochondrial cytochrome c oxidase subunit I (mtCOI) locus were generated that allow for the specific identification of the most common Eimeria species infecting turkeys (i.e., Eimeria adenoeides, Eimeria meleagrimitis, Eimeria gallopavonis, Eimeria meleagridis, Eimeria dispersa, and Eimeria innocua). PCR reaction chemistries were optimized with respect to divalent cation (MgCl2) and dNTP concentrations, as well as PCR cycling conditions (particularly anneal temperature for primers). Genomic DNA samples from single oocyst-derived lines of six Eimeria species were tested to establish specificity and sensitivity of these newly designed primer pairs. A mixed 60-ng total DNA sample containing 10 ng of each of the six Eimeria species was used as DNA template to demonstrate specific amplification of the correct product using each of the species-specific primer pairs. Ten nanograms of each of the five non-target Eimeria species was pooled to provide a non-target, control DNA sample suitable to test the specificity of each primer pair. The amplifications of the COI region with species-specific primer pairs from pooled samples yielded products of expected sizes (209 to 1,012 bp) and no amplification of non-target Eimeria sp. DNA was detected using the non-target, control DNA samples. These primer pairs specific for Eimeria spp. of turkeys did not amplify any of the seven Eimeria species infecting chickens. The newly developed PCR primers can be used as a diagnostic tool capable of specifically identifying six turkey Eimeria species; additionally, sequencing of the PCR amplification products yields sequence-based genotyping data suitable for identification and molecular phylogenetics.

  15. Characterization of homoionic Fe 2+-type montmorillonite: Potential chemical species of iron contaminant

    NASA Astrophysics Data System (ADS)

    Kozai, Naofumi; Inada, Koichi; Adachi, Yoshifusa; Kawamura, Sachi; Kashimoto, Yusuke; Kozaki, Tamotsu; Sato, Seichi; Ohnuki, Toshihiko; Sakai, Takuro; Sato, Takahiro; Oikawa, Masakazu; Esaka, Fumitaka; Mitamura, Hisayoshi

    2007-08-01

    Fe 2+-montmorillonite with Fe 2+ ions occupying cation exchange sites is an ideal transformation product in bentonite buffer material. In our previous study on preparation and characterization of Fe 2+-montmorillonite, the montmorillonite sample that adsorbed Fe 2+ ions on almost all of the cation exchange sites was prepared using a FeCl 2 solution under an inert gas condition [N. Kozai, Y. Adachi, S. Kawamura, K. Inada, T. Kozaki, S. Sato, H. Ohashi, T. Ohnuki, T. Banba, J. Nucl. Sci. Technol. 38 (2001) 1141]. In view of the unstable nature of iron(II) chemical species, this study attempted to determine the potential contaminant iron chemical species in the sample. Nondestructive elemental analysis revealed that a small amount of chloride ions remained dispersed throughout the clay particles. The chloride ion retention may be due to the adsorption of FeCl + ion pairs in the initial FeCl 2 solution and the subsequent containment of the Cl - ions that are dissociated from the FeCl + ion pairs during excess salt removal treatment. Two explanations are advanced for the second process: the slow release of the remaining Cl - ions from the collapsed interlayer of the montmorillonite, and the transformation of a minor fraction of the remaining FeCl + ion pairs to iron(III) hydroxide chloride complexes having low solubility.

  16. Identification of Vibrio parahaemolyticus Strains at the Species Level by PCR Targeted to the toxR Gene

    PubMed Central

    Kim, Yung Bu; Okuda, Jun; Matsumoto, Chiho; Takahashi, Naoki; Hashimoto, Satoru; Nishibuchi, Mitsuaki

    1999-01-01

    The DNA colony hybridization test with the polynucleotide probe for Vibrio parahaemolyticus toxR gene was performed. All 373 strains of V. parahaemolyticus gave positive results, and the strains belonging to four other Vibrio species including Vibrio alginolyticus gave weakly positive results, suggesting that toxR sequence variation may reflect the phylogenetic relationships of Vibrio species. We then established a toxR-targeted PCR protocol for the specific detection of V. parahaemolyticus. PMID:10074546

  17. Assessing the influence of biogeographical region and phylogenetic history on chemical defences and herbivory in Quercus species.

    PubMed

    Moreira, Xoaquín; Abdala-Roberts, Luis; Galmán, Andrea; Francisco, Marta; Fuente, María de la; Butrón, Ana; Rasmann, Sergio

    2018-06-07

    Biogeographical factors and phylogenetic history are key determinants of inter-specific variation in plant defences. However, few studies have conducted broad-scale geographical comparisons of plant defences while controlling for phylogenetic relationships, and, in doing so, none have separated constitutive from induced defences. This gap has limited our understanding of how historical or large-scale processes mediate biogeographical patterns in plant defences since these may be contingent upon shared evolutionary history and phylogenetic constraints. We conducted a phylogenetically-controlled experiment testing for differences in constitutive leaf chemical defences and their inducibility between Palearctic and Nearctic oak species (Quercus, total 18 species). We induced defences in one-year old plants by inflicting damage by gypsy moth larvae (Lymantria dispar), estimated the amount of leaf area consumed, and quantified various groups of phenolic compounds. There was no detectable phylogenetic signal for constitutive or induced levels of most defensive traits except for constitutive condensed tannins, as well as no phylogenetic signal in leaf herbivory. We did, however, find marked differences in defence levels between oak species from each region: Palearctic species had higher levels of constitutive condensed tannins, but less constitutive lignins and less constitutive and induced hydrolysable tannins compared with Nearctic species. Additionally, Palearctic species had lower levels of leaf damage compared with Nearctic species. These differences in leaf damage, lignins and hydrolysable (but not condensed) tannins were lost after accounting for phylogeny, suggesting that geographical structuring of phylogenetic relationships mediated biogeographical differences in defences and herbivore resistance. Together, these findings suggest that historical processes and large-scale drivers have shaped differences in allocation to constitutive defences (and in turn

  18. The influence of stream bed geomorphology on chemical species within the hyporheic zone over time and space

    NASA Astrophysics Data System (ADS)

    Quick, A. M.; Reeder, W. J.; Farrell, T. B.; Benner, S. G.; Tonina, D.; Feris, K. P.

    2017-12-01

    The hyporheic zone is well established as an important zone of biogeochemical activity in streams and rivers. Multiple large scale flume experiments were carried out to mimic bedform-controlled hyporheic zones in small streams. The laboratory setting allowed for geochemical measurement resolution and replicates that would not be possible in a natural setting. Two flume experiments that consisted of three small streams with variable sizes of bedform dunes were carried out in which chemical species were measured in the surface water and along hyporheic flow lines in the subsurface. The species measured included dissolved oxygen, pH, alkalinity, major cations (Na+, Mg2+, Ca2+, K+, Si4+, Al3+), anions (NO3-, NO2-, SO42-, PO43-, Cl-), and many trace elements (As, Sr, Co, Ni, Cu, Zn, Pb, U, V). Observed spatial and temporal trends reflect microbiological processes, changing redox conditions, and chemical weathering. In general, microbial respiration causes DO to decrease with residence time, leading to aerobic and anaerobic zones that influence redox-sensitive species and pH gradients that influence mineral solubility. Most other species concentrations, including those of major cations and trace elements, increase with residence time and generally decrease over time elapsed during the experiment. The different dune morphologies dictate flow velocities in the hyporheic zone; for most species, steeper dunes with higher velocities had lower concentrations at the end of the experiment, indicating the role of dune shape in the weathering rates of minerals in hyporheic sediment and the concentrations of dissolved species entering the surface water over time. Many of the observed trends can be applied, at least qualitatively, to understanding how these species will behave in natural settings. This insight will contribute to the understanding of many of the applications of the hyporheic zone (e.g. bioremediation, habitat, greenhouse gas emissions, etc.).

  19. Novel approach for the simultaneous detection of DNA from different fish species based on a nuclear target: quantification potential.

    PubMed

    Prado, Marta; Boix, Ana; von Holst, Christoph

    2012-07-01

    The development of DNA-based methods for the identification and quantification of fish in food and feed samples is frequently focused on a specific fish species and/or on the detection of mitochondrial DNA of fish origin. However, a quantitative method for the most common fish species used by the food and feed industry is needed for official control purposes, and such a method should rely on the use of a single-copy nuclear DNA target owing to its more stable copy number in different tissues. In this article, we report on the development of a real-time PCR method based on the use of a nuclear gene as a target for the simultaneous detection of fish DNA from different species and on the evaluation of its quantification potential. The method was tested in 22 different fish species, including those most commonly used by the food and feed industry, and in negative control samples, which included 15 animal species and nine feed ingredients. The results show that the method reported here complies with the requirements concerning specificity and with the criteria required for real-time PCR methods with high sensitivity.

  20. Comparison of two freshwater turtle species as monitors of radionuclide and chemical contamination: DNA damage and residue analysis

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Meyers-Schoene, L.; Shugart, L.R.; Beauchamp, J.J.

    1993-08-01

    Two species of turtles that occupy different ecological niches were compared for their usefulness as monitors of freshwater ecosystems where both low-level radioactive and nonradioactive contaminants are present. The pond slider (Trachemys scripta) and common snapping turtle (Chelydra serpentina) were analyzed for the presence of [sup 90]Sr, [sup 137]Cs, [sup 60]Co, and Hg, radionuclides and chemicals known to be present at the contaminated site, and single-strand breaks in liver DNA. The integrity of the DNA was examined by the alkaline unwinding assay, a technique that detects strand breaks as a biological marker of possible exposure to genotoxic agents. This measuremore » of DNA damage was significantly increased in both species of turtles at the contaminated site compared with turtles of the same species at a reference site, and shows that contaminant-exposed populations were under more severe genotoxic stress than those at the reference site. The level of strand breaks observed at the contaminated site was high and in the range reported for other aquatic species exposed to deleterious concentrations of genotoxic agents such as chemicals and ionizing radiation. Statistically significantly higher concentrations of radionuclides and Hg were detected in the turtles from the contaminated area. Mercury concentrations were significantly higher in the more carnivorous snapping turtle compared with the slider; however, both species were effective monitors of the contaminants.« less

  1. Chemical composition, antioxidant and antibacterial activities of two Spondias species from Northeastern Brazil.

    PubMed

    da Silva, Ana Raquel Araújo; de Morais, Selene Maia; Marques, Márcia Maria Mendes; de Oliveira, Danielle Ferreira; Barros, Caroline Costa; de Almeida, Raimundo Rafael; Vieira, Ícaro Gusmão Pinto; Guedes, Maria Izabel Florindo

    2012-06-01

    The leaves of Spondias tuberosa Arr. Cam. (Anacardiaceae) and Spondias mombin L. have been traditionally used for medicinal purposes. Some studies reveal their antibacterial, antimicrobial, and antiviral properties. Determine the chemical composition, antioxidant, and antimicrobial activities of Spondias species to justify its ethnopharmacological use. Spondias species extracts were prepared with methanol:water 80:20 and analyzed by silica gel column chromatography and reversed phase liquid chromatography (HPLC). The antioxidant activity was evaluated by scavenging the radicals 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) and 2,2-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS•+) and measuring antimicrobial activity (agar well diffusion method, minimum inhibitory concentration and minimum bactericidal concentrations). The HPLC analysis of Spondias extracts demonstrated the occurrence of high yield of flavonoids. Found in S. mombin were quercetin (2.36 ± 0.01 mg/g) and ellagic acid (41.56 ± 0.01 mg/g) and in S. tuberosa species rutin (53.38 ± 1.71 mg/g), quercetin (24.46 ± 0.87 mg/g), and ellagic acid (169.76 ± 0.17 mg/g). The antibacterial activity of the extracts against the various bacteria strains varied from 8.8 to 20.1 mm. MIC values from 62.5 to 125 µg/mL were satisfactory when compared with other plant products. Medium DPPH scavenging activity IC₅₀ for Spondias extracts varied from 0.042 to 0.558 mg/mL and for ABTS from 0.089 to 0.465 mg/mL. DPPH scavenging activity for constituent ellagic acid IC₅₀ = 0.042 mg/mL and for quercetin IC₅₀ = 0.081 mg/mL. The chemical study of Spondias leaf extracts showed the occurrence of quercetin, rutin and ellagic acid, substances with relevant antioxidant and antimicrobial activities.

  2. Targeting Conserved Genes in Penicillium Species.

    PubMed

    Peterson, Stephen W

    2017-01-01

    Polymerase chain reaction amplification of conserved genes and sequence analysis provides a very powerful tool for the identification of toxigenic as well as non-toxigenic Penicillium species. Sequences are obtained by amplification of the gene fragment, sequencing via capillary electrophoresis of dideoxynucleotide-labeled fragments or NGS. The sequences are compared to a database of validated isolates. Identification of species indicates the potential of the fungus to make particular mycotoxins.

  3. Cross-species comparison of in vivo PK/PD relationships for second-generation antisense oligonucleotides targeting apolipoprotein B-100.

    PubMed

    Yu, Rosie Z; Lemonidis, Kristina M; Graham, Mark J; Matson, John E; Crooke, Rosanne M; Tribble, Diane L; Wedel, Mark K; Levin, Arthur A; Geary, Richard S

    2009-03-01

    The in vivo pharmacokinetics/pharmacodynamics of 2'-O-(2-methoxyethyl) (2'-MOE) modified antisense oligonucleotides (ASOs), targeting apolipoprotein B-100 (apoB-100), were characterized in multiple species. The species-specific apoB antisense inhibitors demonstrated target apoB mRNA reduction in a drug concentration and time-dependent fashion in mice, monkeys, and humans. Consistent with the concentration-dependent decreases in liver apoB mRNA, reductions in serum apoB, and LDL-C, and total cholesterol were concurrently observed in animal models and humans. Additionally, the long duration of effect after cessation of dosing correlated well with the elimination half-life of 2'-MOE modified apoB ASOs studied in mice (t(1/2) congruent with 20 days) and humans (t(1/2) congruent with 30 days) following parental administrations. The plasma concentrations of ISIS 301012, observed in the terminal elimination phase of both mice and monkeys were in equilibrium with liver. The partition ratios between liver and plasma were similar, approximately 6000:1, across species, and thus provide a surrogate for tissue exposure in humans. Using an inhibitory E(max) model, the ASO liver EC(50s) were 101+/-32, 119+/-15, and 300+/-191 microg/g of ASO in high-fat-fed (HF) mice, transgenic mice containing the human apoB transgene, and monkeys, respectively. The estimated liver EC(50) in man, extrapolated from trough plasma exposure, was 81+/-122 microg/g. Therefore, extraordinary consistency of the exposure-response relationship for the apoB antisense inhibitor was observed across species, including human. The cross-species PK/PD relationships provide confidence in the use of pharmacology animal models to predict human dosing for second-generation ASOs targeting the liver.

  4. Antimicrobial Activity and Chemical Composition of Essential Oils from Verbenaceae Species Growing in South America.

    PubMed

    Pérez Zamora, Cristina M; Torres, Carola A; Nuñez, María B

    2018-03-01

    The Verbenaceae family includes 2600 species grouped into 100 genera with a pantropical distribution. Many of them are important elements of the floras of warm-temperature and tropical regions of America. This family is known in folk medicine, and its species are used as digestive, carminative, antipyretic, antitussive, antiseptic, and healing agents. This review aims to collect information about the essential oils from the most reported species of the Verbenaceae family growing in South America, focusing on their chemical composition, antimicrobial activity, and synergism with commercial antimicrobials. The information gathered comprises the last twenty years of research within the South American region and is summarized taking into consideration the most representative species in terms of their essential oils. These species belong to Aloysia , Lantana , Lippia , Phyla , and Stachytarpheta genera, and the main essential oils they contain are monoterpenes and sesquiterpenes, such as β-caryophyllene, thymol, citral, 1,8-cineole, carvone, and limonene. These compounds have been found to possess antimicrobial activities. The synergism of these essential oils with antibiotics is being studied by several research groups. It constitutes a resource of interest for the potential use of combinations of essential oils and antibiotics in infection treatments.

  5. Assessing environmental quality status by integrating chemical and biological effect data: The Cartagena coastal zone as a case.

    PubMed

    Martínez-Gómez, Concepción; Fernández, Beatriz; Robinson, Craig D; Campillo, J Antonio; León, Víctor M; Benedicto, José; Hylland, Ketil; Vethaak, A Dick

    2017-03-01

    Cartagena coastal zone (W Mediterranean) was chosen for a practical case study to investigate the suitability of an integrated indicator framework for marine monitoring and assessment of chemicals and their effects, which was developed by ICES and OSPAR. Red mullet (Mullus barbatus) and the Mediterranean mussel (Mytilus galloprovincialis) were selected as target species. Concentrations of contaminants in sediment and biota, and contaminant-related biomarkers were analysed. To assess environmental quality in the Cartagena coastal zone with respect to chemical pollution, data were assessed using available assessment criteria, and then integrated for different environmental matrices. A qualitative scoring method was used to rank the overall assessments into selected categories and to evaluate the confidence level of the final integrated assessment. The ICES/OSPAR integrated assessment framework, originally designed for the North Atlantic, was found to be applicable for Mediterranean species and environmental matrices. Further development of assessment criteria of chemical and biological parameters in sediments and target species from the Mediterranean will, however, be required before this framework can be fully applied for determining Good Environmental Status (GES) of the Marine Strategy Framework Directive in these regions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Chemical modification of projectile residues and target material in a MEMIN cratering experiment

    NASA Astrophysics Data System (ADS)

    Ebert, Matthias; Hecht, Lutz; Deutsch, Alexander; Kenkmann, Thomas

    2013-01-01

    In the context of the MEMIN project, a hypervelocity cratering experiment has been performed using a sphere of the iron meteorite Campo del Cielo as projectile accelerated to 4.56 km s-1, and a block of Seeberger sandstone as target material. The ejecta, collected in a newly designed catcher, are represented by (1) weakly deformed, (2) highly deformed, and (3) highly shocked material. The latter shows shock-metamorphic features such as planar deformation features (PDF) in quartz, formation of diaplectic quartz glass, partial melting of the sandstone, and partially molten projectile, mixed mechanically and chemically with target melt. During mixing of projectile and target melts, the Fe of the projectile is preferentially partitioned into target melt to a greater degree than Ni and Co yielding a Fe/Ni that is generally higher than Fe/Ni in the projectile. This fractionation results from the differing siderophile properties, specifically from differences in reactivity of Fe, Ni, and Co with oxygen during projectile-target interaction. Projectile matter was also detected in shocked quartz grains. The average Fe/Ni of quartz with PDF (about 20) and of silica glasses (about 24) are in contrast to the average sandstone ratio (about 422), but resembles the Fe/Ni-ratio of the projectile (about 14). We briefly discuss possible reasons of projectile melting and vaporization in the experiment, in which the calculated maximum shock pressure does not exceed 55 GPa.

  7. Susceptibility of non-target invertebrates to Brazilian microbial pest control agents.

    PubMed

    Oliveira-Filho, Eduardo Cyrino; Muniz, Daphne Heloisa Freitas; Freire, Ingrid Souza; Ramos, Felipe Rosa; Alves, Roberto Teixeira; Jonsson, Claudio Martin; Grisolia, Cesar Koppe; Monnerat, Rose Gomes

    2011-08-01

    Microbial pest control agents or entomopathogens have been considered an interesting alternative to use instead of chemical insecticides. Knowledge of ecotoxicity data is very important to predict the hazard of any product released in the environment and subsidize the regulation of these products by governmental agencies. In the present study four new Brazilian strains of Bacillus and one fungus were tested to evaluate their acute toxicity to the microcrustacean Daphnia similis, the snail Biomphalaria glabrata and the dung beetle Digitonthophagus gazella. The microcrustaceans and the snails were exposed to entomopathogens in synthetic softwater and the beetles were exposed directly in cattle dung. Obtained data reveal low susceptibility of the non-target species to tested microorganisms, with lethal concentrations being observed only at much higher concentrations than that effective against target insects. These results show that the tested strains are selective in their action mode and seem to be non-hazardous to non-target species.

  8. Targeting reactive oxygen species in development and progression of pancreatic cancer

    PubMed Central

    Durand, Nisha; Storz, Peter

    2017-01-01

    Introduction Pancreatic ductal adenocarcinoma (PDA) is characterized by expression of oncogenic KRas which drives all aspects of tumorigenesis. Oncogenic KRas induces the formation of reactive oxygen species (ROS) which have been implicated in initiation and progression of PDA. To facilitate tumor promoting levels and to avoid oncogene-induced senescence or cytotoxicity, ROS homeostasis in PDA cells is balanced by additional up-regulation of antioxidant systems. Areas Covered We examine the sources of ROS in PDA, the mechanisms by which ROS homeostasis is maintained, and the biological consequences of ROS in PDA. Additionally, we discuss the potential mechanisms for targeting ROS homoeostasis as a point of therapeutic intervention. An extensive review of the relevant literature as it relates to the topic was conducted using PubMed. Expert Commentary Even though oncogenic mutations in the KRAS gene have been detected in over 95% of human pancreatic adenocarcinoma, targeting its gene product, KRas, has been difficult. The dependency of PDA cells on balancing ROS homeostasis could be an angle for new prevention or treatment strategies. These include use of antioxidants to prevent formation or progression of precancerous lesions, or methods to increase ROS in tumor cells to toxic levels. PMID:27841037

  9. Polymers as directing agents for motions of chemical and biological species

    NASA Astrophysics Data System (ADS)

    Tanyeri, Nihan Yonet

    This thesis involves descriptions of solid surface modifications with various polymeric materials which were used as a guiding agent for motion of chemical and biological species. Quasi-two dimensional poly(oligoethylene glycol) acrylate polymer brush based molecular conduits have been designed with the goal of regulating and controlling the diffusive transport of molecular, e.g. organic dyes, and ionic species, e.g. AuCl4-, and Cu2+ ions, along predefined 2-D pathways. The transport of these chemical species has been examined by both fluorescence and dark field microscopy. The polymer brushes were formed through microcontact printing of an initiator, followed by surface-initiated Atom Transfer Radical Polymerization (SI-ATRP). SI-ATRP enables both 2-D patterning with a resolution of about 1 micrometer, and control over the resultant polymer brush thickness (which was varied from 10-100 nm). A hydrophilic poly(oligoethylene glycol) acrylate brushe was selected because of its potential to dissolve a wide range of hydrophilic species. The transport of fluorescent species can be directly followed. A non-lithographic fabrication method was developed for mufluidic devices used in the diffusion studies. Singular channel mufluidic device was utilized to study the directed organic dye diffusion. The AuCl4-, and Cu 2+ ion transport was studied by designing molecular devices with two mufluidic channels. We have demonstrated that the various species of interest diffuse much more rapidly along the predefined pathway than along the bare (polymer brush free) regions of the substrate, demonstrating that diffusive conduits for molecular transport can indeed be formed. The protein resistance of poly(N-isopropylacrylamide) (PNIPAM) brushes grafted from silicon wafers was investigated as a function of the chain molecular weight, grafting density, and temperature. Above the lower critical solution temperature (LCST) of 32°C, the collapse of the water swollen chains, determined by

  10. Relative sensitivity of Arctic species to physically and chemically dispersed oil determined from three hydrocarbon measures of aquatic toxicity.

    PubMed

    Bejarano, Adriana C; Gardiner, William W; Barron, Mace G; Word, Jack Q

    2017-09-15

    The risks to Arctic species from oil releases is a global concern, but their sensitivity to chemically dispersed oil has not been assessed using a curated and standardized dataset from spiked declining tests. Species sensitivity to dispersed oil was determined by their position within species sensitivity distributions (SSDs) using three measures of hydrocarbon toxicity: total petroleum hydrocarbons (TPH), polycyclic aromatic hydrocarbon (PAHs), and naphthalenes. Comparisons of SSDs with Arctic/sub-Arctic versus non-Arctic species, and across SSDs of compositionally similar oils, showed that Arctic and non-Arctic species have comparable sensitivities even with the variability introduced by combining data across studies and oils. Regardless of hydrocarbon measure, hazard concentrations across SSDs were protective of sensitive Arctic species. While the sensitivities of Arctic species to oil exposures resemble those of commonly tested species, PAH-based toxicity data are needed for a greater species diversity including sensitive Arctic species. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. The Reactive Species Interactome: Evolutionary Emergence, Biological Significance, and Opportunities for Redox Metabolomics and Personalized Medicine

    PubMed Central

    Koning, Anne; Kuhnle, Gunter G.C.; Nagy, Peter; Bianco, Christopher L.; Pasch, Andreas; Wink, David A.; Fukuto, Jon M.; Jackson, Alan A.; van Goor, Harry; Olson, Kenneth R.

    2017-01-01

    Abstract Significance: Oxidative stress is thought to account for aberrant redox homeostasis and contribute to aging and disease. However, more often than not, administration of antioxidants is ineffective, suggesting that our current understanding of the underlying regulatory processes is incomplete. Recent Advances: Similar to reactive oxygen species and reactive nitrogen species, reactive sulfur species are now emerging as important signaling molecules, targeting regulatory cysteine redox switches in proteins, affecting gene regulation, ion transport, intermediary metabolism, and mitochondrial function. To rationalize the complexity of chemical interactions of reactive species with themselves and their targets and help define their role in systemic metabolic control, we here introduce a novel integrative concept defined as the reactive species interactome (RSI). The RSI is a primeval multilevel redox regulatory system whose architecture, together with the physicochemical characteristics of its constituents, allows efficient sensing and rapid adaptation to environmental changes and various other stressors to enhance fitness and resilience at the local and whole-organism level. Critical Issues: To better characterize the RSI-related processes that determine fluxes through specific pathways and enable integration, it is necessary to disentangle the chemical biology and activity of reactive species (including precursors and reaction products), their targets, communication systems, and effects on cellular, organ, and whole-organism bioenergetics using system-level/network analyses. Future Directions: Understanding the mechanisms through which the RSI operates will enable a better appreciation of the possibilities to modulate the entire biological system; moreover, unveiling molecular signatures that characterize specific environmental challenges or other forms of stress will provide new prevention/intervention opportunities for personalized medicine. Antioxid. Redox

  12. Can a native rodent species limit the invasive potential of a non-native rodent species in tropical agroforest habitats?

    PubMed

    Stuart, Alexander M; Prescott, Colin V; Singleton, Grant R

    2016-06-01

    Little is known about native and non-native rodent species interactions in complex tropical agroecosystems. We hypothesised that the native non-pest rodent Rattus everetti may be competitively dominant over the invasive pest rodent Rattus tanezumi within agroforests. We tested this experimentally by using pulse removal for three consecutive months to reduce populations of R. everetti in agroforest habitat, and assessed over 6 months the response of R. tanezumi and other rodent species. Following removal, R. everetti individuals rapidly immigrated into removal sites. At the end of the study period, R. tanezumi were larger and there was a significant shift in their microhabitat use with respect to the use of ground vegetation cover following the perturbation of R. everetti. Irrespective of treatment, R. tanezumi selected microhabitat with less tree canopy cover, indicative of severely disturbed habitat, whereas R. everetti selected microhabitat with a dense canopy. Our results suggest that sustained habitat disturbance in agroforests favours R. tanezumi, while the regeneration of agroforests towards a more natural state would favour native species and may reduce pest pressure in adjacent crops. In addition, the rapid recolonisation of R. everetti suggests this species would be able to recover from non-target impacts of short-term rodent pest control. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

  13. Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species.

    PubMed

    Barik, Suvakanta; Kumar, Ashutosh; Sarkar Das, Shabari; Yadav, Sandeep; Gautam, Vibhav; Singh, Archita; Singh, Sharmila; Sarkar, Ananda K

    2015-10-13

    microRNAs (miRNAs), a class of endogenously produced small non-coding RNAs of 20-21 nt length, processed from precursor miRNAs, regulate many developmental processes by negatively regulating the target genes in both animals and plants. The coevolutionary pattern of a miRNA family and their targets underscores its functional conservation or diversification. The miR167 regulates various aspects of plant development in Arabidopsis by targeting ARF6 and ARF8. The evolutionary conservation or divergence of miR167s and their target genes are poorly understood till now. Here we show the evolutionary relationship among 153 MIR167 genes obtained from 33 diverse plant species. We found that out of the 153 of miR167 sequences retrieved from the "miRBase", 27 have been annotated to be processed from the 3' end, and have diverged distinctively from the other miR167s produced from 5' end. Our analysis reveals that gma-miR167h/i and mdm-miR167a are processed from 3' end and have evolved separately, diverged most resulting in novel targets other than their known ones, and thus led to functional diversification, especially in apple and soybean. We also show that mostly conserved miR167 sequences and their target AUXIN RESPONSE FACTORS (ARFs) have gone through parallel evolution leading to functional diversification among diverse plant species.

  14. A multi target approach to control chemical reactions in their inhomogeneous solvent environment

    NASA Astrophysics Data System (ADS)

    Keefer, Daniel; Thallmair, Sebastian; Zauleck, Julius P. P.; de Vivie-Riedle, Regina

    2015-12-01

    Shaped laser pulses offer a powerful tool to manipulate molecular quantum systems. Their application to chemical reactions in solution is a promising concept to redesign chemical synthesis. Along this road, theoretical developments to include the solvent surrounding are necessary. An appropriate theoretical treatment is helpful to understand the underlying mechanisms. In our approach we simulate the solvent by randomly selected snapshots from molecular dynamics trajectories. We use multi target optimal control theory to optimize pulses for the various arrangements of explicit solvent molecules simultaneously. This constitutes a major challenge for the control algorithm, as the solvent configurations introduce a large inhomogeneity to the potential surfaces. We investigate how the algorithm handles the new challenges and how well the controllability of the system is preserved with increasing complexity. Additionally, we introduce a way to statistically estimate the efficiency of the optimized laser pulses in the complete thermodynamical ensemble.

  15. Chemical composition and antibacterial activities of seven Eucalyptus species essential oils leaves.

    PubMed

    Sebei, Khaled; Sakouhi, Fawzi; Herchi, Wahid; Khouja, Mohamed Larbi; Boukhchina, Sadok

    2015-01-19

    In this paper, we have studied the essential oils chemical composition of the leaves of seven Eucalyptus species developed in Tunisia. Eucalyptus leaves were picked from trees growing in different arboretums in Tunisia. Choucha and Mrifeg arboretums located in Sedjnene, region of Bizerte (Choucha: E. maideni, E. astrengens et E. cinerea; Mrifeg : E. leucoxylon), Korbous arboretums located in the region of Nabeul, North East Tunisia with sub-humid bioclimate, (E. lehmani), Souiniet-Ain Drahem arboretum located in region of Jendouba (E. sideroxylon, E. bicostata). Essential oils were individually tested against a large panel of microorganisms including Staphylococcus aureus (ATCC 6539), Escherichia coli (ATCC 25922), Enterococcus faecalis (ATCC29212), Listeria ivanovii (RBL 30), Bacillus cereus (ATCC11778). The yield of essential oils ranged from 1.2% to 3% (w/w) for the different Eucalyptus species. All essential oils contain α-pinene, 1,8-cineol and pinocarveol-trans for all Eucalyptus species studied. The 1,8-cineol was the major compound in all species (49.07 to 83.59%). Diameter of inhibition zone of essential oils of Eucalyptus species varied from 10 to 29 mm. The largest zone of inhibition was obtained for Bacillus cereus (E. astrengens) and the lowest for Staphylococcus aureus (E. cinerea). The essential oils from E. maideni, E. astrengens, E. cinerea (arboretum of Bizerte), E. bicostata (arboretum of Aindraham) showed the highest antibacterial activity against Listeria ivanovii and Bacillus cereus. The major constituents of Eucalyptus leaves essential oils are 1,8-cineol (49.07 to 83.59%) and α-pinene (1.27 to 26.35%). The essential oils from E. maideni, E. astrengens, E. cinerea, E. bicostata showed the highest antibacterial activity against Listeria ivanovii and Bacillus cereus, they may have potential applications in food and pharmaceutical products.

  16. Chemical composition of some wild peanut species (Arachis L.) seeds.

    PubMed

    Grosso, N R; Nepote, V; Guzmán, C A

    2000-03-01

    Oil, protein, ash, and carbohydrate contents, iodine value, and fatty acid and sterol compositions were studied in seeds of Arachis trinitensis, A. chiquitana, A. kempff-mercadoi, A. diogoi, A. benensis, A. appressipila, A. valida, A. kretschmeri, A. helodes, A. kuhlmannii, A. williamsii, A. sylvestris, A. matiensis, A. pintoi, A. hoehnei, A. villosa, and A. stenosperma. Oil content was greatest in A.stenosperma (mean value = 51.8%). The protein level was higher in A. sylvestris (30.1%) and A. villosa (29.5%). Mean value of oleic acid varied between 30.6% (A. matiensis) and 46.8% (Arachis villosa), and linoleic acid oscillated between 34.1% (A. villosa) and 47.4% (A. appressipila). The better oleic-to-linoleic (O/L) ratio was exhibited by A. villosa (1.38). Some species showed higher concentration of behenic acid. The greatest level of this fatty acid was found in A. matiensis (6.2%). Iodine value was lower in A. valida (99.2). The sterol composition in the different peanut species showed higher concentration of beta-sitosterol (mean values oscillated between 55.7 and 60.2%) followed by campesterol (12.4-16. 5%), stigmasterol (9.7-13.3%), and Delta(5)-avenasterol (9.7-13.4%). The chemical quality and stability of oils (iodine value and O/L ratio) from wild peanut studied in this work are not better than those of cultivated peanut.

  17. Computational approach for elucidating interactions of cross-species miRNAs and their targets in Flaviviruses.

    PubMed

    Shinde, Santosh P; Banerjee, Amit Kumar; Arora, Neelima; Murty, U S N; Sripathi, Venkateswara Rao; Pal-Bhadra, Manika; Bhadra, Utpal

    2015-03-01

    Combating viral diseases has been a challenging task since time immemorial. Available molecular approaches are limited and not much effective for this daunting task. MicroRNA based therapies have shown promise in recent times. MicroRNAs are tiny non-coding RNAs that regulate translational repression of target mRNA in highly specific manner. In this study, we have determined the target regions for human and viral microRNAs in the conserved genomic regions of selected viruses of Flaviviridae family using miRanda and performed a comparative target selectivity analysis among them. Specific target regions were determined and they were compared extensively among themselves by exploring their position to determine the vicinity. Based on the multiplicity and cooperativity analysis, interaction maps were developed manually to represent the interactions between top-ranking miRNAs and genomes of the viruses considered in this study. Self-organizing map (SOM) was used to cluster the best-ranked microRNAs based on the vital physicochemical properties. This study will provide deep insight into the interrelation of the viral and human microRNAs interactions with the selected Flaviviridae genomes and will help to identify cross-species microRNA targets on the viral genome.

  18. A Review of Botany and Pharmacological Effect and Chemical Composition of Echinophora Species Growing in Iran.

    PubMed

    Hosseini, Zohreh; Lorigooini, Zahra; Rafieian-Kopaei, Mahmoud; Shirmardi, Hamzeh Ali; Solati, Kamal

    2017-01-01

    This review was conducted to investigate the botany, phytochemistry, and pharmacological properties of Echinophora species. The information of this review was obtained by searching for keywords Apiaceae , Echinophora , pharmacological effects, and traditional and modern medicine in scientific articles and books published in search engines Scopus, Google Scholar, Science Direct, PubMed, and Web of Science. The traditional uses of Echinophora and the existence of valuable phytochemicals in the plant have led to isolation and drug discovery of natural medicines such as antibiotic, analgesics, and anticancer drugs, and the beneficial effects of these plants can widely be used in healthcare. Echinophora species are medicinal and aromatic plants that are belong to Apiaceae family. This genus have four species in Iran. The botany, geographical distribution, traditional and pharmacological effects of Echinophora genus were described. Also, the major chemical constituents of the essential oil and extract of different species of Echinophora that have been reported. Overall, the existence of valuable phytochemicals purpose Echinophora species as novel candidate to isolation and drug discovery of natural medicines such as antibiotic, analgesics, and anticancer drugs.

  19. Cyprinid herpesvirus 3 as a potential biological control agent for carp (Cyprinus carpio) in Australia: susceptibility of non-target species.

    PubMed

    McColl, K A; Sunarto, A; Slater, J; Bell, K; Asmus, M; Fulton, W; Hall, K; Brown, P; Gilligan, D; Hoad, J; Williams, L M; Crane, M St J

    2017-09-01

    Carp (Cyprinus carpio L.) is a pest species in Australian waterways, and cyprinid herpesvirus 3 (CyHV-3) is being considered as a potential biological control (biocontrol) agent. An important consideration for any such agent is its target specificity. In this study, the susceptibility to CyHV-3 of a range of non-target species (NTS) was tested. The NTS were as follows: 13 native Australian, and one introduced, fish species; a lamprey species; a crustacean; two native amphibian species (tadpole and mature stages); two native reptilian species; chickens; and laboratory mice. Animals were exposed to 100-1000 times the approximate minimum amount of CyHV-3 required to cause disease in carp by intraperitoneal and/or bath challenge, and then examined clinically each day over the course of 28 days post-challenge. There were no clinical signs, mortalities or histological evidence consistent with a viral infection in a wide taxonomic range of NTS. Furthermore, there was no molecular evidence of infection with CyHV-3, and, in particular, all RT-PCRs for viral mRNA were negative. As a consequence, the results encourage further investigation of CyHV-3 as a potential biocontrol agent that is specific for carp. © 2016 John Wiley & Sons Ltd.

  20. Species-specific identification of Dekkera/Brettanomyces yeasts by fluorescently labeled DNA probes targeting the 26S rRNA.

    PubMed

    Röder, Christoph; König, Helmut; Fröhlich, Jürgen

    2007-09-01

    Sequencing of the complete 26S rRNA genes of all Dekkera/Brettanomyces species colonizing different beverages revealed the potential for a specific primer and probe design to support diagnostic PCR approaches and FISH. By analysis of the complete 26S rRNA genes of all five currently known Dekkera/Brettanomyces species (Dekkera bruxellensis, D. anomala, Brettanomyces custersianus, B. nanus and B. naardenensis), several regions with high nucleotide sequence variability yet distinct from the D1/D2 domains were identified. FISH species-specific probes targeting the 26S rRNA gene's most variable regions were designed. Accessibility of probe targets for hybridization was facilitated by the construction of partially complementary 'side'-labeled probes, based on secondary structure models of the rRNA sequences. The specificity and routine applicability of the FISH-based method for yeast identification were tested by analyzing different wine isolates. Investigation of the prevalence of Dekkera/Brettanomyces yeasts in the German viticultural regions Wonnegau, Nierstein and Bingen (Rhinehesse, Rhineland-Palatinate) resulted in the isolation of 37 D. bruxellensis strains from 291 wine samples.

  1. Cumulative Index to Chemicals and to Common and Scientific Names of Species Listed in Contaminant Hazard Reviews 1 through 34

    USGS Publications Warehouse

    Eisler, R.

    1999-01-01

    The Patuxent Wildlife Research Center Contaminant Hazard Reviews (CHR) series synthesizes ecotoxicological data of selected environmental contaminants, with emphasis on hazards to native species of flora and fauna. From 1985 through 1998 a total of 34 reviews were published in various Reports series of the U.S. Department of the Interior on agricultural pesticides (carbofuran, chlordane, chlorpyrifos, diazinon, diflubenzuron, fenvalerate, mirex, paraquat, toxaphene), herbicides (acrolein, atrazine), metals and metalloids (arsenic, boron, cadmium, chromium, copper, lead, mercury, molybdenum, nickel, selenium, silver, tin, zinc), predacides (sodium monofluoroacetate), organic industrial wastes (dioxins, pentachlorophenol), veterinary chemicals (famphur), polycyclic aromatic hydrocarbons, polychlorinated biphenyls, mining wastes (cyanide), and ionizing radiations. This report is a cumulative index to the common and scientific names of all biological species listed in the first 34 reports in the CHR series, with individual species cross-referenced by contaminant and corresponding page numbers. A similar index is shown for chemicals.

  2. Transcriptomics hit the target: Monitoring of ligand-activated and stress response pathways for chemical testing.

    PubMed

    Limonciel, Alice; Moenks, Konrad; Stanzel, Sven; Truisi, Germaine L; Parmentier, Céline; Aschauer, Lydia; Wilmes, Anja; Richert, Lysiane; Hewitt, Philip; Mueller, Stefan O; Lukas, Arno; Kopp-Schneider, Annette; Leonard, Martin O; Jennings, Paul

    2015-12-25

    High content omic methods provide a deep insight into cellular events occurring upon chemical exposure of a cell population or tissue. However, this improvement in analytic precision is not yet matched by a thorough understanding of molecular mechanisms that would allow an optimal interpretation of these biological changes. For transcriptomics (TCX), one type of molecular effects that can be assessed already is the modulation of the transcriptional activity of a transcription factor (TF). As more ChIP-seq datasets reporting genes specifically bound by a TF become publicly available for mining, the generation of target gene lists of TFs of toxicological relevance becomes possible, based on actual protein-DNA interaction and modulation of gene expression. In this study, we generated target gene signatures for Nrf2, ATF4, XBP1, p53, HIF1a, AhR and PPAR gamma and tracked TF modulation in a large collection of in vitro TCX datasets from renal and hepatic cell models exposed to clinical nephro- and hepato-toxins. The result is a global monitoring of TF modulation with great promise as a mechanistically based tool for chemical hazard identification. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Acute sensitivity of the vernal pool fairy shrimp, Branchinecta lynchi (Anostraca; Branchinectidae), and surrogate species to 10 chemicals.

    PubMed

    Ivey, Chris D; Besser, John M; Ingersoll, Chris G; Wang, Ning; Rogers, D Christopher; Raimondo, Sandy; Bauer, Candice R; Hammer, Edward J

    2017-03-01

    Vernal pool fairy shrimp, Branchinecta lynchi, (Branchiopoda; Anostraca) and other fairy shrimp species have been listed as threatened or endangered under the US Endangered Species Act. Because few data exist about the sensitivity of Branchinecta spp. to toxic effects of contaminants, it is difficult to determine whether they are adequately protected by water quality criteria. A series of acute (24-h) lethality/immobilization tests was conducted with 3 species of fairy shrimp (B. lynchi, Branchinecta lindahli, and Thamnocephalus platyurus) and 10 chemicals with varying modes of toxic action: ammonia, potassium, chloride, sulfate, chromium(VI), copper, nickel, zinc, alachlor, and metolachlor. The same chemicals were tested in 48-h tests with other branchiopods (the cladocerans Daphnia magna and Ceriodaphnia dubia) and an amphipod (Hyalella azteca), and in 96-h tests with snails (Physa gyrina and Lymnaea stagnalis). Median effect concentrations (EC50s) for B. lynchi were strongly correlated (r 2  = 0.975) with EC50s for the commercially available fairy shrimp species T. platyurus for most chemicals tested. Comparison of EC50s for fairy shrimp and EC50s for invertebrate taxa tested concurrently and with other published toxicity data indicated that fairy shrimp were relatively sensitive to potassium and several trace metals compared with other invertebrate taxa, although cladocerans, amphipods, and mussels had similar broad toxicant sensitivity. Interspecies correlation estimation models for predicting toxicity to fairy shrimp from surrogate species indicated that models with cladocerans and freshwater mussels as surrogates produced the best predictions of the sensitivity of fairy shrimp to contaminants. The results of these studies indicate that fairy shrimp are relatively sensitive to a range of toxicants, but Endangered Species Act-listed fairy shrimp of the genus Branchinecta were not consistently more sensitive than other fairy shrimp taxa. Environ Toxicol

  4. Acute toxicity of six freshwater mussel species (Glochidia) to six chemicals: Implications for daphnids and Utterbackia imbecillis as surrogates for protection of freshwater mussels (Unionidae)

    USGS Publications Warehouse

    Milam, C.D.; Farris, J.L.; Dwyer, F.J.; Hardesty, D.K.

    2005-01-01

    Acute (24-h) toxicity tests were used in this study to compare lethality responses in early life stages (glochidia) of six freshwater mussel species, Leptodea fragilis, U. imbecillis, Lampsilis cardium, Lampsilis siliquoidea, Megalonaias nervosa, and Ligumia subrostrata, and two standard test organisms, Ceriodaphnia dubia and Daphnia magna. Concentrations of carbaryl, copper, 4-nonylphenol, pentachlorophenol, permethrin, and 2,4-D were used in acute exposures to represent different chemical classes and modes of action. The relative sensitivities of species were evaluated by ranking their LC 50 values for each chemical. We used these ranks to determine the extent to which U. imbecillis (one of the most commonly used unionids in toxicity tests) was representative of the tolerances of other mussels. We also calculated geometric mean LC50s for the families Unionidae and Daphnidae. Rankings of these data were used to assess the extent to which Daphnidae can be used as surrogates for freshwater mussels relative to chemical sensitivity. While no single chemical elicited consistently high or low toxicity estimates, carbaryl and 2,4-D were generally the least toxic to all species tested. No species was always the most sensitive, and Daphnidae were generally protective of Unionidae. Utterbackia imbecillis, while often proposed as a standard unionid mussel test species, did not always qualify as a sufficient surrogate (i.e., a substitute organism that often elicits similar sensitivity responses to the same contaminant exposure) for other species of mussels, since it was usually one of the more tolerant species in our rankings. U. imbecillis should be used as a surrogate species only with this caution on its relative insensitivity. ?? 2005 Springer Science+Business Media, Inc.

  5. Chemical and physical properties of two-year short-rotation deciduous species. [Olea sp. , Populus deltoides, Platanus sp. , Alnus glutinosa, Paulownia tomentosa, Robina pseudoacacia, Acer saccharinum

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lee, C.S

    1982-01-01

    The following seven broadleaved species were tested: autumn olive (Olea sp.) eastern cottonwood (Populus deltoides), sycamore (Platanus species), black alder (Alnus glutinosa), royal paulownia (Paulownia tomentosa), black locust (Robina pseudoacacia) and silver maple (Acer saccharinum). The species and portions both significantly affected the chemical and the physical findings of the juvenile wood. The ages, which were tested in factorial combination with the species, also showed a significant effect on both the chemical and the physical properties of wood. All of the results indicated that both chemical and physical properties did vary with species, among the portions of the wood, andmore » according to the ages of the wood. From the portion standpoint, the bark had higher gross heat content, sulphur content, ash content and lignin content, and it was also higher in all three kinds of extractives contents. The wood portion was found to be rich in holocellulose, alpha-cellulose and pentosan. In considering the chemical and physical properties of juvenile wood among the species, eastern cottonwood was found to have the highest value for ash content and all of the three kinds of extractives content. Paulownia had the highest value for sulphur content. Black locust had highest gross heat content, holocellulose and alpha-cellulose contents. Silver maple had highest lignin content. Results from this study showed that these seven juvenile hardwood species can produce high biomass yields of fibre and energy when grown under intensive care in central and southern Illinois sites. The best species of these seven tested woods seem to be black locust, which could also serve as a raw material for the pulp and paper industry, as well as for a fuel for energy generation. However, further economic and energy efficiency analyses are needed before judging the feasibility of these short-rotation juvenile hardwood species.« less

  6. Chemical Proteomics Reveals Ferrochelatase as a Common Off-target of Kinase Inhibitors.

    PubMed

    Klaeger, Susan; Gohlke, Bjoern; Perrin, Jessica; Gupta, Vipul; Heinzlmeir, Stephanie; Helm, Dominic; Qiao, Huichao; Bergamini, Giovanna; Handa, Hiroshi; Savitski, Mikhail M; Bantscheff, Marcus; Médard, Guillaume; Preissner, Robert; Kuster, Bernhard

    2016-05-20

    Many protein kinases are valid drug targets in oncology because they are key components of signal transduction pathways. The number of clinical kinase inhibitors is on the rise, but these molecules often exhibit polypharmacology, potentially eliciting desired and toxic effects. Therefore, a comprehensive assessment of a compound's target space is desirable for a better understanding of its biological effects. The enzyme ferrochelatase (FECH) catalyzes the conversion of protoporphyrin IX into heme and was recently found to be an off-target of the BRAF inhibitor Vemurafenib, likely explaining the phototoxicity associated with this drug in melanoma patients. This raises the question of whether FECH binding is a more general feature of kinase inhibitors. To address this, we applied a chemical proteomics approach using kinobeads to evaluate 226 clinical kinase inhibitors for their ability to bind FECH. Surprisingly, low or submicromolar FECH binding was detected for 29 of all compounds tested and isothermal dose response measurements confirmed target engagement in cells. We also show that Vemurafenib, Linsitinib, Neratinib, and MK-2461 reduce heme levels in K562 cells, verifying that drug binding leads to a loss of FECH activity. Further biochemical and docking experiments identified the protoporphyrin pocket in FECH as one major drug binding site. Since the genetic loss of FECH activity leads to photosensitivity in humans, our data strongly suggest that FECH inhibition by kinase inhibitors is the molecular mechanism triggering photosensitivity in patients. We therefore suggest that a FECH assay should generally be part of the preclinical molecular toxicology package for the development of kinase inhibitors.

  7. The biological activities and chemical composition of Pereskia species (Cactaceae)--a review.

    PubMed

    Pinto, Nícolas de Castro Campos; Scio, Elita

    2014-09-01

    The exploration of nature as a source of sustainable, novel bioactive substances continues to grow as natural products play a significant role in the search for new therapeutic and agricultural agents. In this context, plants of the genus Pereskia (Cactaceae) have been studied for their biological activities, and are evolving as an interesting subject in the search for new, bioactive compounds. These species are commonly used as human foodstuffs and in traditional medicine to treat a variety of diseases. This review focuses on the bioactivity and chemical composition of the genus Pereskia, and aims to stimulate further studies on the chemistry and biological potential of the genus.

  8. Structural and Chemical Characterization of Hardwood from Tree Species with Applications as Bioenergy Feedstocks

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Çetinkol, Özgül Persil; Smith-Moritz, Andreia M.; Cheng, Gang

    2012-12-28

    Eucalypt species are a group of flowering trees widely used in pulp production for paper manufacture. For several decades, the wood pulp industry has focused research and development efforts on improving yields, growth rates and pulp quality through breeding and the genetic improvement of key tree species. Recently, this focus has shifted from the production of high quality pulps to the investigation of the use of eucalypts as feedstocks for biofuel production. Here the structure and chemical composition of the heartwood and sapwood of Eucalyptus dunnii, E. globulus, E. pillularis, E. urophylla, an E. urophylla-E. grandis cross, Corymbia citriodora ssp.more » variegata, and Acacia mangium were compared using nuclear magnetic resonance spectroscopy (NMR), X-ray diffraction (XRD) and biochemical composition analysis. Some trends relating to these compositions were also identified by Fourier transform near infrared (FT-NIR) spectroscopy. These results will serve as a foundation for a more comprehensive database of wood properties that will help develop criteria for the selection of tree species for use as biorefinery feedstocks.« less

  9. Structural and Chemical Characterization of Hardwood from Tree Species with Applications as Bioenergy Feedstocks

    PubMed Central

    Çetinkol, Özgül Persil; Smith-Moritz, Andreia M.; Cheng, Gang; Lao, Jeemeng; George, Anthe; Hong, Kunlun; Henry, Robert; Simmons, Blake A.; Heazlewood, Joshua L.; Holmes, Bradley M.

    2012-01-01

    Eucalypt species are a group of flowering trees widely used in pulp production for paper manufacture. For several decades, the wood pulp industry has focused research and development efforts on improving yields, growth rates and pulp quality through breeding and the genetic improvement of key tree species. Recently, this focus has shifted from the production of high quality pulps to the investigation of the use of eucalypts as feedstocks for biofuel production. Here the structure and chemical composition of the heartwood and sapwood of Eucalyptus dunnii, E. globulus, E. pillularis, E. urophylla, an E. urophylla-E. grandis cross, Corymbia citriodora ssp. variegata, and Acacia mangium were compared using nuclear magnetic resonance spectroscopy (NMR), X-ray diffraction (XRD) and biochemical composition analysis. Some trends relating to these compositions were also identified by Fourier transform near infrared (FT-NIR) spectroscopy. These results will serve as a foundation for a more comprehensive database of wood properties that will help develop criteria for the selection of tree species for use as biorefinery feedstocks. PMID:23300786

  10. Using a genetic algorithm as an optimal band selector in the mid and thermal infrared (2.5-14 μm) to discriminate vegetation species.

    PubMed

    Ullah, Saleem; Groen, Thomas A; Schlerf, Martin; Skidmore, Andrew K; Nieuwenhuis, Willem; Vaiphasa, Chaichoke

    2012-01-01

    Genetic variation between various plant species determines differences in their physio-chemical makeup and ultimately in their hyperspectral emissivity signatures. The hyperspectral emissivity signatures, on the one hand, account for the subtle physio-chemical changes in the vegetation, but on the other hand, highlight the problem of high dimensionality. The aim of this paper is to investigate the performance of genetic algorithms coupled with the spectral angle mapper (SAM) to identify a meaningful subset of wavebands sensitive enough to discriminate thirteen broadleaved vegetation species from the laboratory measured hyperspectral emissivities. The performance was evaluated using an overall classification accuracy and Jeffries Matusita distance. For the multiple plant species, the targeted bands based on genetic algorithms resulted in a high overall classification accuracy (90%). Concentrating on the pairwise comparison results, the selected wavebands based on genetic algorithms resulted in higher Jeffries Matusita (J-M) distances than randomly selected wavebands did. This study concludes that targeted wavebands from leaf emissivity spectra are able to discriminate vegetation species.

  11. Chemical Species in the Vapor Phase of Hanford Double-Shell Tanks: Potential Impacts on Waste Tank Corrosion Processes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Felmy, Andrew R.; Qafoku, Odeta; Arey, Bruce W.

    2010-09-22

    The presence of corrosive and inhibiting chemicals on the tank walls in the vapor space, arising from the waste supernatant, dictate the type and degree of corrosion that occurs there. An understanding of how waste chemicals are transported to the walls and the affect on vapor species from changing supernatant chemistry (e.g., pH, etc.), are basic to the evaluation of risks and impacts of waste changes on vapor space corrosion (VSC). In order to address these issues the expert panel workshop on double-shell tank (DST) vapor space corrosion testing (RPP-RPT-31129) participants made several recommendations on the future data and modelingmore » needs in the area of DST corrosion. In particular, the drying of vapor phase condensates or supernatants can form salt or other deposits at the carbon steel interface resulting in a chemical composition at the near surface substantially different from that observed directly in the condensates or the supernatants. As a result, over the past three years chemical modeling and experimental studies have been performed on DST supernatants and condensates to predict the changes in chemical composition that might occur as condensates or supernatants equilibrate with the vapor space species and dry at the carbon steel surface. The experimental studies included research on both the chemical changes that occurred as the supernatants dried as well as research on how these chemical changes impact the corrosion of tank steels. The chemical modeling and associated experimental studies were performed at the Pacific Northwest National Laboratory (PNNL) and the research on tank steel corrosion at the Savannah River National Laboratory (SRNL). This report presents a summary of the research conducted at PNNL with special emphasis on the most recent studies conducted in FY10. An overall summary of the project results as well as their broader implications for vapor space corrosion of the DST’s is given at the end of this report.« less

  12. Species identification in mixed tuna samples with next-generation sequencing targeting two short cytochrome b gene fragments.

    PubMed

    Kappel, Kristina; Haase, Ilka; Käppel, Christine; Sotelo, Carmen G; Schröder, Ute

    2017-11-01

    Conventional Sanger sequencing of PCR products is the gold standard for species authentication of seafood products. However, this method is inappropriate for the analysis of products that might contain mixtures of species, such as tinned tuna. The purpose of this study was to test whether next-generation sequencing (NGS) can be a solution for the authentication of mixed products. Nine tuna samples containing mixtures of up to four species were prepared and subjected to an NGS approach targeting two short cytochrome b gene (cytb) fragments on the Illumina MiSeq platform. Sequence recovery was precise and admixtures of as low as 1% could be identified, depending on the species composition of the mixtures. Duplicate samples as well as two individual NGS runs produced very similar results. A first test of three commercial tinned tuna samples indicated the presence of different species in the same tin, although this is forbidden by EU law. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Observational and modeling studies of chemical species concentrations as a function of raindrop size

    NASA Astrophysics Data System (ADS)

    Wai, K. M.; Tam, C. W. F.; Tanner, P. A.

    The Guttalgor method has been used to determine the chemical species concentrations in size-selected raindrops in nine rain events at Hong Kong from 1999 to 2001. The curve (concentration against raindrop radius) patterns for all the species are similar but depend on the starting time of sampling within a rain event. In these plots, the maximum concentration occurs at the same range of droplet radius, irrespective of the species, and this indicates the importance of coalescence and breakup processes. The maximum is located at a smaller droplet radius than was found in previous studies in Germany. All results show almost constant concentrations with size for large raindrops, and these indicate the in-cloud contributions. The pH of raindrops of similar size is linearly correlated with a function of the sulfate, nitrate, acetate, formate, calcium and ammonium ion species concentrations. Within a single raindrop, chloride depletion is not significant, and sulfate, ammonium and hydrogen ions are found in ratios compatible with the precursor solid-phase mixture of ammonium sulfate and ammonium bisulphate. When simulated by a below-cloud model, good agreement between the modeled and measured sodium and sulfate concentrations has been found. Below-cloud sulfur dioxide scavenging contributes at most 60% of the sulfate concentration in a single raindrop.

  14. NQO2 Is a Reactive Oxygen Species Generating Off-Target for Acetaminophen

    PubMed Central

    2014-01-01

    The analgesic and antipyretic compound acetaminophen (paracetamol) is one of the most used drugs worldwide. Acetaminophen overdose is also the most common cause for acute liver toxicity. Here we show that acetaminophen and many structurally related compounds bind quinone reductase 2 (NQO2) in vitro and in live cells, establishing NQO2 as a novel off-target. NQO2 modulates the levels of acetaminophen derived reactive oxygen species, more specifically superoxide anions, in cultured cells. In humans, NQO2 is highly expressed in liver and kidney, the main sites of acetaminophen toxicity. We suggest that NQO2 mediated superoxide production may function as a novel mechanism augmenting acetaminophen toxicity. PMID:25313982

  15. Using Molecular Docking to Compare Toxicity of Reactive Chemicals to Freshwater and Marine Luminous Bacteria.

    PubMed

    Gao, Ya; Lin, Zhifen; Chen, Rui; Wang, Ting; Liu, Shushen; Yao, Zhifeng; Yin, Daqiang

    2012-12-01

    Vibrio fischeri is a marine luminous bacterium that has been widely used in toxicity bioassays, while Vibrio qinghaiensis sp.-Q67 is a newly found freshwater species which is more suitable for the tests on freshwater samples. However, there is a sensitive difference between these two species due to the media, chemical modes of action and the tested species. It remains unclear how these factors induce toxicity changes in luminous bioassays. Therefore, by using molecular docking between reactive chemicals and the target proteins of Vibrio fischeri and Vibrio qinghaiensis sp.-Q67 respectively, the sensitive difference was explored from the angle of amino acid residues that involved in the interactions. Mutation of amino acid residues was performed to investigate the role of these amino acids in the interactions and the most important amino acid residues in toxicity effect were found. The results suggested tat the most important amino acid residues in toxicity effect would affect the binding affinity between chemicals and target proteins of Vibrio fischeri and Vibrio qinghaiensis sp.-Q67, and then induce distinct toxic effect on them. As there are fewer toxicity data for freshwater Vibrio qinghaiensis sp.-Q67 than for Vibrio fischeri, this study helps to take advantage of the plentiful toxicity data of Vibrio fischeri to predict toxicities of freshwater samples. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Aquatic plants: Test species sensitivity and minimum data requirement evaluations for chemical risk assessments and aquatic life criteria development for the USA

    EPA Science Inventory

    Phytotoxicity results from the publicly-available ECOTOX database were summarized for 20 chemicals and 188 aquatic plants to determine species sensitivities and the ability of a species-limited toxicity data set to serve as a surrogate for a larger data set. The lowest effect con...

  17. The Emory Chemical Biology Discovery Center: leveraging academic innovation to advance novel targets through HTS and beyond.

    PubMed

    Johns, Margaret A; Meyerkord-Belton, Cheryl L; Du, Yuhong; Fu, Haian

    2014-03-01

    The Emory Chemical Biology Discovery Center (ECBDC) aims to accelerate high throughput biology and translation of biomedical research discoveries into therapeutic targets and future medicines by providing high throughput research platforms to scientific collaborators worldwide. ECBDC research is focused at the interface of chemistry and biology, seeking to fundamentally advance understanding of disease-related biology with its HTS/HCS platforms and chemical tools, ultimately supporting drug discovery. Established HTS/HCS capabilities, university setting, and expertise in diverse assay formats, including protein-protein interaction interrogation, have enabled the ECBDC to contribute to national chemical biology efforts, empower translational research, and serve as a training ground for young scientists. With these resources, the ECBDC is poised to leverage academic innovation to advance biology and therapeutic discovery.

  18. Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species

    PubMed Central

    Barik, Suvakanta; Kumar, Ashutosh; Sarkar Das, Shabari; Yadav, Sandeep; Gautam, Vibhav; Singh, Archita; Singh, Sharmila; Sarkar, Ananda K.

    2015-01-01

    microRNAs (miRNAs), a class of endogenously produced small non-coding RNAs of 20–21 nt length, processed from precursor miRNAs, regulate many developmental processes by negatively regulating the target genes in both animals and plants. The coevolutionary pattern of a miRNA family and their targets underscores its functional conservation or diversification. The miR167 regulates various aspects of plant development in Arabidopsis by targeting ARF6 and ARF8. The evolutionary conservation or divergence of miR167s and their target genes are poorly understood till now. Here we show the evolutionary relationship among 153 MIR167 genes obtained from 33 diverse plant species. We found that out of the 153 of miR167 sequences retrieved from the “miRBase”, 27 have been annotated to be processed from the 3′ end, and have diverged distinctively from the other miR167s produced from 5′ end. Our analysis reveals that gma-miR167h/i and mdm-miR167a are processed from 3′ end and have evolved separately, diverged most resulting in novel targets other than their known ones, and thus led to functional diversification, especially in apple and soybean. We also show that mostly conserved miR167 sequences and their target AUXIN RESPONSE FACTORS (ARFs) have gone through parallel evolution leading to functional diversification among diverse plant species. PMID:26459056

  19. Microspectroscopic imaging of solution plasma: How do its physical properties and chemical species evolve in atmospheric-pressure water vapor bubbles?

    NASA Astrophysics Data System (ADS)

    Yui, Hiroharu; Banno, Motohiro

    2018-01-01

    In this article, we review the development of scientific instruments for obtaining information on the evolution of physical properties and chemical species of solution plasma (SP). When a pulsed high voltage is applied between electrodes immersed in an aqueous solution, SP is formed in water vapor bubbles transiently generated in the solution under atmospheric pressure. To clarify how SP emerges in water vapor bubbles and is sustained in solutions, an instrument with micrometer spatial resolution and nanosecond temporal resolution is required. To meet these requirements, a microscopic system with a custom-made optical discharge cell was newly developed, where the working distance between the SP and the microscopic objective lens was minimized. A hollow electrode equipped in the discharge cell also enabled us to control the chemical composition in water vapor bubbles. To study the spatial and temporal evolutions of chemical species in micrometer and nano- to microsecond regions, a streak camera with a spectrometer and a CCD detector with a time-gated electronic device were combined with the microscope system. The developed instrument is expected to contribute to providing a new means of developing new schemes for chemical reactions and material syntheses.

  20. Protectiveness of Species Sensitivity Distribution Hazard Concentrations for Acute Toxicity Used in Endangered Species Risk Assessment

    EPA Science Inventory

    A primary objective of threatened and endangered species conservation is to ensure that chemical contaminants and other stressors do not adversely affect listed species. Assessments of the ecological risks of chemical exposures to listed species often rely on the use of surrogate...

  1. Tau Antibody Targeting Pathological Species Blocks Neuronal Uptake and Interneuron Propagation of Tau in Vitro.

    PubMed

    Nobuhara, Chloe K; DeVos, Sarah L; Commins, Caitlin; Wegmann, Susanne; Moore, Benjamin D; Roe, Allyson D; Costantino, Isabel; Frosch, Matthew P; Pitstick, Rose; Carlson, George A; Hock, Christoph; Nitsch, Roger M; Montrasio, Fabio; Grimm, Jan; Cheung, Anne E; Dunah, Anthone W; Wittmann, Marion; Bussiere, Thierry; Weinreb, Paul H; Hyman, Bradley T; Takeda, Shuko

    2017-06-01

    The clinical progression of Alzheimer disease (AD) is associated with the accumulation of tau neurofibrillary tangles, which may spread throughout the cortex by interneuronal tau transfer. If so, targeting extracellular tau species may slow the spreading of tau pathology and possibly cognitive decline. To identify suitable target epitopes, we tested the effects of a panel of tau antibodies on neuronal uptake and aggregation in vitro. Immunodepletion was performed on brain extract from tau-transgenic mice and postmortem AD brain and added to a sensitive fluorescence resonance energy transfer-based tau uptake assay to assess blocking efficacy. The antibodies reduced tau uptake in an epitope-dependent manner: N-terminal (Tau13) and middomain (6C5 and HT7) antibodies successfully prevented uptake of tau species, whereas the distal C-terminal-specific antibody (Tau46) had little effect. Phosphorylation-dependent (40E8 and p396) and C-terminal half (4E4) tau antibodies also reduced tau uptake despite removing less total tau by immunodepletion, suggesting specific interactions with species involved in uptake. Among the seven antibodies evaluated, 6C5 most efficiently blocked uptake and subsequent aggregation. More important, 6C5 also blocked neuron-to-neuron spreading of tau in a unique three-chamber microfluidic device. Furthermore, 6C5 slowed down the progression of tau aggregation even after uptake had begun. Our results imply that not all antibodies/epitopes are equally robust in terms of blocking tau uptake of human AD-derived tau species. Copyright © 2017 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  2. New strategy for drug discovery by large-scale association analysis of molecular networks of different species.

    PubMed

    Zhang, Bo; Fu, Yingxue; Huang, Chao; Zheng, Chunli; Wu, Ziyin; Zhang, Wenjuan; Yang, Xiaoyan; Gong, Fukai; Li, Yuerong; Chen, Xiaoyu; Gao, Shuo; Chen, Xuetong; Li, Yan; Lu, Aiping; Wang, Yonghua

    2016-02-25

    The development of modern omics technology has not significantly improved the efficiency of drug development. Rather precise and targeted drug discovery remains unsolved. Here a large-scale cross-species molecular network association (CSMNA) approach for targeted drug screening from natural sources is presented. The algorithm integrates molecular network omics data from humans and 267 plants and microbes, establishing the biological relationships between them and extracting evolutionarily convergent chemicals. This technique allows the researcher to assess targeted drugs for specific human diseases based on specific plant or microbe pathways. In a perspective validation, connections between the plant Halliwell-Asada (HA) cycle and the human Nrf2-ARE pathway were verified and the manner by which the HA cycle molecules act on the human Nrf2-ARE pathway as antioxidants was determined. This shows the potential applicability of this approach in drug discovery. The current method integrates disparate evolutionary species into chemico-biologically coherent circuits, suggesting a new cross-species omics analysis strategy for rational drug development.

  3. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria.

    PubMed

    Browne, Patrick; Barret, Matthieu; O'Gara, Fergal; Morrissey, John P

    2010-11-25

    Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate nutritional status cues with the regulation

  4. Application of QSAR and shape pharmacophore modeling approaches for targeted chemical library design.

    PubMed

    Ebalunode, Jerry O; Zheng, Weifan; Tropsha, Alexander

    2011-01-01

    Optimization of chemical library composition affords more efficient identification of hits from biological screening experiments. The optimization could be achieved through rational selection of reagents used in combinatorial library synthesis. However, with a rapid advent of parallel synthesis methods and availability of millions of compounds synthesized by many vendors, it may be more efficient to design targeted libraries by means of virtual screening of commercial compound collections. This chapter reviews the application of advanced cheminformatics approaches such as quantitative structure-activity relationships (QSAR) and pharmacophore modeling (both ligand and structure based) for virtual screening. Both approaches rely on empirical SAR data to build models; thus, the emphasis is placed on achieving models of the highest rigor and external predictive power. We present several examples of successful applications of both approaches for virtual screening to illustrate their utility. We suggest that the expert use of both QSAR and pharmacophore models, either independently or in combination, enables users to achieve targeted libraries enriched with experimentally confirmed hit compounds.

  5. Targeted research to improve invasive species management: yellow crazy ant Anoplolepis gracilipes in Samoa.

    PubMed

    Hoffmann, Benjamin D; Auina, Saronna; Stanley, Margaret C

    2014-01-01

    Lack of biological knowledge of invasive species is recognised as a major factor contributing to eradication failure. Management needs to be informed by a site-specific understanding of the invasion system. Here, we describe targeted research designed to inform the potential eradication of the invasive yellow crazy ant Anoplolepis gracilipes on Nu'utele island, Samoa. First, we assessed the ant's impacts on invertebrate biodiversity by comparing invertebrate communities between infested and uninfested sites. Second, we investigated the timing of production of sexuals and seasonal variation of worker abundance and nest density. Third, we investigated whether an association existed between A. gracilipes and carbohydrate sources. Within the infested area there were few other ants larger than A. gracilipes, as well as fewer spiders and crabs, indicating that A. gracilipes is indeed a significant conservation concern. The timing of male reproduction appears to be consistent with places elsewhere in the world, but queen reproduction was outside of the known reproductive period for this species in the region, indicating that the timing of treatment regimes used elsewhere are not appropriate for Samoa. Worker abundance and nest density were among the highest recorded in the world, being greater in May than in October. These abundance and nest density data form baselines for quantifying treatment efficacy and set sampling densities for post-treatment assessments. The number of plants and insects capable of providing a carbohydrate supply to ants were greatest where A. gracilipes was present, but it is not clear if this association is causal. Regardless, indirectly controlling ant abundance by controlling carbohydrate supply appears to be promising avenue for research. The type of targeted, site-specific research such as that described here should be an integral part of any eradication program for invasive species to design knowledge-based treatment protocols and determine

  6. Mapping Asian anthropogenic emissions of non-methane volatile organic compounds to multiple chemical mechanisms

    NASA Astrophysics Data System (ADS)

    Li, M.; Zhang, Q.; Streets, D. G.; He, K. B.; Cheng, Y. F.; Emmons, L. K.; Huo, H.; Kang, S. C.; Lu, Z.; Shao, M.; Su, H.; Yu, X.; Zhang, Y.

    2014-06-01

    An accurate speciation mapping of non-methane volatile organic compounds (NMVOC) emissions has an important impact on the performance of chemical transport models (CTMs) in simulating ozone mixing ratios and secondary organic aerosols. Taking the INTEX-B Asian NMVOC emission inventory as the case, we developed an improved speciation framework to generate model-ready anthropogenic NMVOC emissions for various gas-phase chemical mechanisms commonly used in CTMs in this work, by using an explicit assignment approach and updated NMVOC profiles. NMVOC profiles were selected and aggregated from a wide range of new measurements and the SPECIATE database v.4.2. To reduce potential uncertainty from individual measurements, composite profiles were developed by grouping and averaging source profiles from the same category. The fractions of oxygenated volatile organic compounds (OVOC) were corrected during the compositing process for those profiles which used improper sampling and analyzing methods. Emissions of individual species were then lumped into species in different chemical mechanisms used in CTMs by applying mechanism-dependent species mapping tables, which overcomes the weakness of inaccurate mapping in previous studies. Emission estimates for individual NMVOC species differ between one and three orders of magnitude for some species when different sets of profiles are used, indicating that source profile is the most important source of uncertainties of individual species emissions. However, those differences are diminished in lumped species as a result of the lumping in the chemical mechanisms. Gridded emissions for eight chemical mechanisms at 30 min × 30 min resolution as well as the auxiliary data are available at target="_blank">http://mic.greenresource.cn/intex-b2006. The framework proposed in this work can be also used to develop speciated NMVOC emissions for other regions.

  7. Mapping Asian anthropogenic emissions of non-methane volatile organic compounds to multiple chemical mechanisms

    NASA Astrophysics Data System (ADS)

    Li, M.; Zhang, Q.; Streets, D. G.; He, K. B.; Cheng, Y. F.; Emmons, L. K.; Huo, H.; Kang, S. C.; Lu, Z.; Shao, M.; Su, H.; Yu, X.; Zhang, Y.

    2013-12-01

    An accurate speciation mapping of non-methane volatile organic compounds (NMVOC) emissions has an important impact on the performance of chemical transport models (CTMs) in simulating ozone mixing ratios and secondary organic aerosols. In this work, we developed an improved speciation framework to generate model-ready anthropogenic Asian NMVOC emissions for various gas-phase chemical mechanisms commonly used in CTMs by using an explicit assignment approach and updated NMVOC profiles, based on the total NMVOC emissions in the INTEX-B Asian inventory for the year 2006. NMVOC profiles were selected and aggregated from a wide range of new measurements and the SPECIATE database. To reduce potential uncertainty from individual measurements, composite profiles were developed by grouping and averaging source profiles from the same category. The fractions of oxygenated volatile organic compounds (OVOC) were corrected during the compositing process for those profiles which used improper sampling and analyzing methods. Emissions of individual species were then lumped into species in different chemical mechanisms used in CTMs by applying mechanism-dependent species mapping tables, which overcomes the weakness of inaccurate mapping in previous studies. Gridded emissions for eight chemical mechanisms are developed at 30 min × 30 min resolution using various spatial proxies and are provided through the website: target="_blank">http://mic.greenresource.cn/intex-b2006. Emission estimates for individual NMVOC species differ between one and three orders of magnitude for some species when different sets of profiles are used, indicating that source profile is the most important source of uncertainties of individual species emissions. However, those differences are diminished in lumped species as a result of the lumping in the chemical mechanisms.

  8. Chemically reactive species in liquids generated by atmospheric-pressure plasmas and their roles in plasma medicine

    NASA Astrophysics Data System (ADS)

    Hamaguchi, Satoshi

    2013-07-01

    Plasmas whose gas temperatures are close to room temperature may be generated in ambient air or a gas at atmospheric pressure with the use of low-frequency high voltage or low-power radio-frequency (RF) or microwave power applied to electrodes. Such plasmas can serve as a powerful source of free radicals and/or chemically reactive species that arise from atoms and molecules of the ambient gas. Recently use of such plasmas for medical purposes has attracted much attention as they can be implemented in possible medical devices that can cause blood coagulation, heal wounds, facilitate angiogenesis, sterilize surgical devices as well as living tissues without harming healthy cells, and selectively inactivate cancer cells. Especially of interest among reactive species generated by atmospheric-pressure plasmas (APP) are reactive oxygen species (ROS) and reactive nitrogen species (RNS) that are generated in liquid phase. Since most living tissues and cells are immersed in liquids (such as blood or culture media), reactive species generated by APPs in the gas phase are transported to the liquid phase and possibly converted to different types of reactive species therein before causing some influence on the tissues or cells. In this study, the rate equations are solved to evaluate concentrations of various reactive species in pure water that are originated by plasma reactions in atmosphere and possible effects of such species (including ROS/RNS) on living tissues and cells are discussed.

  9. In vitro activity of natural and chemical products on sporulation of Eimeria species oocysts of chickens.

    PubMed

    Gadelhaq, Sahar M; Arafa, Waleed M; Abolhadid, Shawky M

    2018-02-15

    This study was designed to investigate the ability of two herbal extracts and different chemical substances to inhibit or disrupt sporulation of Eimeria species oocysts of the chickens. The two herbal extracts were Allium sativum (garlic) and Moringa olifiera while the chemical substances included commercial disinfectants and diclazuril. Field isolates of Eimeria oocysts were propagated in chickens to obtain a continuous source of oocysts. The collected unsporulated oocysts (10 5 oocysts/5 ml) were dispensed into 5 cm Petri dish. Three replicates were used for each treatment. The treated oocysts were incubated for 48 h at 25-29 °C and 80% relative humidity. The results showed that herbal extracts, the commercial recommended dose of Dettol, TH4, Phenol, Virkon ® S, and Diclazuril 20% have no effect on the sporulation. While Sodium hypochlorite showed a significant degree of sporulation inhibition reached to 49.67%. Moreover, 70% ethanol, and 10% formalin showed 100% sporulation inhibition. It was concluded that 70% ethanol and 10% formalin are the most effective methods to inhibit Eimeria species sporulation. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Chemical proteomics reveals HSP70 1A as a target for the anticancer diterpene oridonin in Jurkat cells.

    PubMed

    Dal Piaz, Fabrizio; Cotugno, Roberta; Lepore, Laura; Vassallo, Antonio; Malafronte, Nicola; Lauro, Gianluigi; Bifulco, Giuseppe; Belisario, Maria Antonietta; De Tommasi, Nunziatina

    2013-04-26

    Oridonin, an ent-kaurane diterpene isolated from well known Chinese medicinal plant Isodon rubescens, has been shown to have multiple biological activities. Among them, the anticancer activity has been repeatedly reported by many research groups. The chemopreventive and antitumor effects of oridonin have been related to its ability to interfere with several pathways which are involved in cell proliferation, cell cycle arrest, apoptosis and/or autophagy. Despite the number of studies performed on this diterpene, the molecular mechanism underlying its cellular activity remains to be elucidated. Hence, we tried to mine target protein(s) of oridonin by employing a mass spectrometry-based chemical proteomics approach, providing evidences that oridonin is able to directly bind the multifunctional, stress-inducible heat shock protein 70 1A (HSP70 1A). Oridonin/HSP70 complex formation was confirmed in leukemia-derived Jurkat cells. The characterization of HSP70 inhibition by oridonin was performed using chemical and biological approaches. Moreover, the binding site of oridonin on the chaperone was identified by a mass-based approach combined with Molecular Dynamics simulations. Although natural products showed high efficiency and several of these agents have now entered in clinical trials, information concerning the mechanisms of action at a molecular level of many of them is very poor or completely missed. Nevertheless, the identification of the molecular target of a drug candidate has several advantages. The most significant is the ability to set up target-based assays and to allow structure-activity relationship studies to guide medicinal chemistry efforts towards lead optimization. The knowledge of drug targets can also facilitate the identification of potential toxicities or side effects, if there is any precedent of toxicities for the identified target. Achieving this in an effective, unbiased and efficient manner subsists as a significant challenge for the new era

  11. Effects of In Vivo Exposure to Tamoxifen on a Non-Target Species, the Marine Fish Cunner (Tautogolabrus adspersus)

    EPA Science Inventory

    Tamoxifen is an endocrine-active pharmaceutical that is used world-wide to treat certain breast cancers. Because tamoxifen has been detected in aquatic environments, a study was undertaken to investigate its biological effects in a non-target species, the marine fish cunner (Taut...

  12. Divergent Isoprenoid Biosynthesis Pathways in Staphylococcus Species Constitute a Drug Target for Treating Infections in Companion Animals

    PubMed Central

    Cain, Christine L.; Morris, Daniel O.; Rankin, Shelley C.

    2016-01-01

    ABSTRACT Staphylococcus species are a leading cause of skin and soft tissue infections in humans and animals, and the antibiotics used to treat these infections are often the same. Methicillin- and multidrug-resistant staphylococcal infections are becoming more common in human and veterinary medicine. From a “One Health” perspective, this overlap in antibiotic use and resistance raises concerns over the potential spread of antibiotic resistance genes. Whole-genome sequencing and comparative genomics analysis revealed that Staphylococcus species use divergent pathways to synthesize isoprenoids. Species frequently associated with skin and soft tissue infections in companion animals, including S. schleiferi and S. pseudintermedius, use the nonmevalonate pathway. In contrast, S. aureus, S. epidermidis, and S. lugdunensis use the mevalonate pathway. The antibiotic fosmidomycin, an inhibitor of the nonmevalonate pathway, was effective in killing canine clinical staphylococcal isolates but had no effect on the growth or survival of S. aureus and S. epidermidis. These data identify an essential metabolic pathway in Staphylococcus that differs among members of this genus and suggest that drugs such as fosmidomycin, which targets enzymes in the nonmevalonate pathway, may be an effective treatment for certain staphylococcal infections. IMPORTANCE Drug-resistant Staphylococcus species are a major concern in human and veterinary medicine. There is a need for new antibiotics that exhibit a selective effect in treating infections in companion and livestock animals and that would not be used to treat human bacterial infections. We have identified fosmidomycin as an antibiotic that selectively targets certain Staphylococcus species that are often encountered in skin infections in cats and dogs. These findings expand our understanding of Staphylococcus evolution and may have direct implications for treating staphylococcal infections in veterinary medicine. PMID:27704053

  13. Direct Detection and Differentiation of Pathogenic Leptospira Species Using a Multi-Gene Targeted Real Time PCR Approach

    PubMed Central

    Ferreira, Ana Sofia; Costa, Pedro; Rocha, Teresa; Amaro, Ana; Vieira, Maria Luísa; Ahmed, Ahmed; Thompson, Gertrude; Hartskeerl, Rudy A.; Inácio, João

    2014-01-01

    Leptospirosis is a growing public and veterinary health concern caused by pathogenic species of Leptospira. Rapid and reliable laboratory tests for the direct detection of leptospiral infections in animals are in high demand not only to improve diagnosis but also for understanding the epidemiology of the disease. In this work we describe a novel and simple TaqMan-based multi-gene targeted real-time PCR approach able to detect and differentiate Leptospira interrogans, L. kirschneri, L. borgpeteresenii and L. noguchii, which constitute the veterinary most relevant pathogenic species of Leptospira. The method uses sets of species-specific probes, and respective flanking primers, designed from ompL1 and secY gene sequences. To monitor the presence of inhibitors, a duplex amplification assay targeting both the mammal β-actin and the leptospiral lipL32 genes was implemented. The analytical sensitivity of all primer and probe sets was estimated to be <10 genome equivalents (GE) in the reaction mixture. Application of the amplification reactions on genomic DNA from a variety of pathogenic and non-pathogenic Leptospira strains and other non-related bacteria revealed a 100% analytical specificity. Additionally, pathogenic leptospires were successfully detected in five out of 29 tissue samples from animals (Mus spp., Rattus spp., Dolichotis patagonum and Sus domesticus). Two samples were infected with L. borgpetersenii, two with L. interrogans and one with L. kirschneri. The possibility to detect and identify these pathogenic agents to the species level in domestic and wildlife animals reinforces the diagnostic information and will enhance our understanding of the epidemiology of leptopirosis. PMID:25398140

  14. Chemical Form Matters: Differential Accumulation of Mercury Following Inorganic and Organic Mercury Exposures in Zebrafish Larvae

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Korbas, Malgorzata; MacDonald, Tracy C.; Pickering, Ingrid J.

    2013-04-08

    Mercury, one of the most toxic elements, exists in various chemical forms each with different toxicities and health implications. Some methylated mercury forms, one of which exists in fish and other seafood products, pose a potential threat, especially during embryonic and early postnatal development. Despite global concerns, little is known about the mechanisms underlying transport and toxicity of different mercury species. To investigate the impact of different mercury chemical forms on vertebrate development, we have successfully combined the zebrafish, a well-established developmental biology model system, with synchrotron-based X-ray fluorescence imaging. Our work revealed substantial differences in tissue-specific accumulation patterns ofmore » mercury in zebrafish larvae exposed to four different mercury formulations in water. Methylmercury species not only resulted in overall higher mercury burdens but also targeted different cells and tissues than their inorganic counterparts, thus revealing a significant role of speciation in cellular and molecular targeting and mercury sequestration. For methylmercury species, the highest mercury concentrations were in the eye lens epithelial cells, independent of the formulation ligand (chloride versus L-cysteine). For inorganic mercury species, in absence of L-cysteine, the olfactory epithelium and kidney accumulated the greatest amounts of mercury. However, with L-cysteine present in the treatment solution, mercuric bis-L-cysteineate species dominated the treatment, significantly decreasing uptake. Our results clearly demonstrate that the common differentiation between organic and inorganic mercury is not sufficient to determine the toxicity of various mercury species.« less

  15. Population Connectivity Measures of Fishery-Targeted Coral Reef Species to Inform Marine Reserve Network Design in Fiji.

    PubMed

    Eastwood, Erin K; López, Elora H; Drew, Joshua A

    2016-01-25

    Coral reef fish serve as food sources to coastal communities worldwide, yet are vulnerable to mounting anthropogenic pressures like overfishing and climate change. Marine reserve networks have become important tools for mitigating these pressures, and one of the most critical factors in determining their spatial design is the degree of connectivity among different populations of species prioritized for protection. To help inform the spatial design of an expanded reserve network in Fiji, we used rapidly evolving mitochondrial genes to investigate connectivity patterns of three coral reef species targeted by fisheries in Fiji: Epinephelus merra (Serranidae), Halichoeres trimaculatus (Labridae), and Holothuria atra (Holothuriidae). The two fish species, E. merra and Ha. trimaculatus, exhibited low genetic structuring and high amounts of gene flow, whereas the sea cucumber Ho. atra displayed high genetic partitioning and predominantly westward gene flow. The idiosyncratic patterns observed among these species indicate that patterns of connectivity in Fiji are likely determined by a combination of oceanographic and ecological characteristics. Our data indicate that in the cases of species with high connectivity, other factors such as representation or political availability may dictate where reserves are placed. In low connectivity species, ensuring upstream and downstream connections is critical.

  16. Ethnobiology of snappers (Lutjanidae): target species and suggestions for management

    PubMed Central

    2011-01-01

    In this study, we sought to investigate the biology (diet and reproduction) and ethnobiology (fishers knowledge and fishing spots used to catch snappers) of five species of snappers (Lutjanidae), including Lutjanus analis, Lutjanus synagris, Lutjanus vivanus, Ocyurus chrysurus, and Romboplites saliens at five sites along the northeast (Riacho Doce, Maceió in Alagoas State, and Porto do Sauípe, Entre Rios at Bahia State) and the southeast (SE) Brazilian coast (Paraty and Rio de Janeiro cities at Rio de Janeiro State, and Bertioga, at São Paulo State.). We collected 288 snappers and interviewed 86 fishermen. The stomach contents of each fish were examined and macroscopic gonad analysis was performed. Snappers are very important for the fisheries of NE Brazil, and our results indicated that some populations, such as mutton snapper (L. analis) and lane snapper (L. synagris), are being caught when they are too young, at early juvenile stages. Local knowledge has been shown to be a powerful tool for determining appropriate policies regarding management of target species, and artisanal fishermen can be included in management processes. Other suggestions for managing the fisheries are discussed, including proposals that could provide motivation for artisanal fishermen to participate in programs to conserve resources, such as co-management approaches that utilize local knowledge, the establishment of fishing seasons, and compensation of fishermen, through 'payment for environmental services'. These suggestions may enhance the participation of local artisanal fishermen in moving to a more realistic and less top-down management approach of the fish population. PMID:21410969

  17. Ethnobiology of snappers (Lutjanidae): target species and suggestions for management.

    PubMed

    Begossi, Alpina; Salivonchyk, Svetlana V; Araujo, Luciana G; Andreoli, Tainá B; Clauzet, Mariana; Martinelli, Claudia M; Ferreira, Allan G I; Oliveira, Luiz E C; Silvano, Renato A M

    2011-03-16

    In this study, we sought to investigate the biology (diet and reproduction) and ethnobiology (fishers knowledge and fishing spots used to catch snappers) of five species of snappers (Lutjanidae), including Lutjanus analis, Lutjanus synagris, Lutjanus vivanus, Ocyurus chrysurus, and Romboplites saliens at five sites along the northeast (Riacho Doce, Maceió in Alagoas State, and Porto do Sauípe, Entre Rios at Bahia State) and the southeast (SE) Brazilian coast (Paraty and Rio de Janeiro cities at Rio de Janeiro State, and Bertioga, at São Paulo State.).We collected 288 snappers and interviewed 86 fishermen. The stomach contents of each fish were examined and macroscopic gonad analysis was performed. Snappers are very important for the fisheries of NE Brazil, and our results indicated that some populations, such as mutton snapper (L. analis) and lane snapper (L. synagris), are being caught when they are too young, at early juvenile stages.Local knowledge has been shown to be a powerful tool for determining appropriate policies regarding management of target species, and artisanal fishermen can be included in management processes. Other suggestions for managing the fisheries are discussed, including proposals that could provide motivation for artisanal fishermen to participate in programs to conserve resources, such as co-management approaches that utilize local knowledge, the establishment of fishing seasons, and compensation of fishermen, through 'payment for environmental services'. These suggestions may enhance the participation of local artisanal fishermen in moving to a more realistic and less top-down management approach of the fish population.

  18. Chemical exposure-response relationship between air pollutants and reactive oxygen species in the human respiratory tract

    NASA Astrophysics Data System (ADS)

    Lakey, Pascale S. J.; Berkemeier, Thomas; Tong, Haijie; Arangio, Andrea M.; Lucas, Kurt; Pöschl, Ulrich; Shiraiwa, Manabu

    2016-09-01

    Air pollution can cause oxidative stress and adverse health effects such as asthma and other respiratory diseases, but the underlying chemical processes are not well characterized. Here we present chemical exposure-response relations between ambient concentrations of air pollutants and the production rates and concentrations of reactive oxygen species (ROS) in the epithelial lining fluid (ELF) of the human respiratory tract. In highly polluted environments, fine particulate matter (PM2.5) containing redox-active transition metals, quinones, and secondary organic aerosols can increase ROS concentrations in the ELF to levels characteristic for respiratory diseases. Ambient ozone readily saturates the ELF and can enhance oxidative stress by depleting antioxidants and surfactants. Chemical exposure-response relations provide a quantitative basis for assessing the relative importance of specific air pollutants in different regions of the world, showing that aerosol-induced epithelial ROS levels in polluted megacity air can be several orders of magnitude higher than in pristine rainforest air.

  19. Aerosol-halogen interaction: Change of physico-chemical properties of SOA by naturally released halogen species

    NASA Astrophysics Data System (ADS)

    Ofner, J.; Balzer, N.; Buxmann, J.; Grothe, H.; Krüger, H.; Platt, U.; Schmitt-Kopplin, P.; Zetzsch, C.

    2011-12-01

    Reactive halogen species are released by various sources like photo-activated sea-salt aerosol or salt pans and salt lakes. These heterogeneous release mechanisms have been overlooked so far, although their potential of interaction with organic aerosols like Secondary Organic Aerosol (SOA), Biomass Burning Organic Aerosol (BBOA) or Atmospheric Humic LIke Substances (HULIS) is completely unknown. Such reactions can constitute sources of gaseous organo-halogen compounds or halogenated organic particles in the atmospheric boundary layer. To study the interaction of organic aerosols with reactive halogen species (RHS), SOA was produced from α-pinene, catechol and guaiacol using an aerosol smog-chamber. The model SOAs were characterized in detail using a variety of physico-chemical methods (Ofner et al., 2011). Those aerosols were exposed to molecular halogens in the presence of UV/VIS irradiation and to halogens, released from simulated natural halogen sources like salt pans, in order to study the complex aerosol-halogen interaction. The heterogeneous reaction of RHS with those model aerosols leads to different gaseous species like CO2, CO and small reactive/toxic molecules like phosgene (COCl2). Hydrogen containing groups on the aerosol particles are destroyed to form HCl or HBr, and a significant formation of C-Br bonds could be verified in the particle phase. Carbonyl containing functional groups of the aerosol are strongly affected by the halogenation process. While changes of functional groups and gaseous species were visible using FTIR spectroscopy, optical properties were studied using Diffuse Reflectance UV/VIS spectroscopy. Overall, the optical properties of the processed organic aerosols are significantly changed. While chlorine causes a "bleaching" of the aerosol particles, bromine shifts the maximum of UV/VIS absorption to the red end of the UV/VIS spectrum. Further physico-chemical changes were recognized according to the aerosol size-distributions or the

  20. Effects of species and season on chemical composition and ruminal crude protein and organic matter degradability of some multi-purpose tree species by West African dwarf rams.

    PubMed

    Arigbede, O M; Anele, U Y; Südekum, K-H; Hummel, J; Oni, A O; Olanite, J A; Isah, A O

    2012-04-01

    Seasonal chemical composition and ruminal organic matter (OM) and crude protein (CP) degradabilities were determined in four tropical multi-purpose tree species (MPTS) namely; Pterocarpus santalinoides, Grewia pubescens, Enterolobium cyclocarpum and Leucaena leucocephala. Three West African dwarf (WAD) rams fitted with permanent rumen cannula were used for the degradability trials. Foliage samples were collected four times to represent seasonal variations as follows: January--mid dry; April--late dry; July--mid rainy and October--late rainy seasons. Leaf samples were randomly collected from the trees for estimation of dry matter (DM) and chemical composition. Ruminal in sacco OM and CP degradabilities were estimated from residues in nylon bags. All samples had high CP (161-259 g/kg DM) and moderate fibre concentrations [neutral detergent fibre (without residual ash], 300-501 g/kg DM; acid detergent fibre (without residual ash), 225-409 g/kg DM and acid detergent lignin, 87-179 g/kg DM across seasons. Interaction effects of species and season on chemical composition were highly significant (p = 0.001) except for trypsin inhibitor (p = 0.614). The MPTS recorded more than 60% OM and CP degradability at 24 h, which implied that they were all highly degradable in the rumen. Their incorporation into ruminant feeding systems as dry season forage supplements is therefore recommended. © 2011 Blackwell Verlag GmbH.

  1. Coatings with controlled porosity and chemical properties

    DOEpatents

    Frye, Gregory C.; Brinker, C. Jeffrey; Doughty, Daniel H.; Bein, Thomas; Moller, Karin

    1996-01-01

    Coatings and sensors having both steric and chemical selectivity. Controlled porosity provides the steric selectivity, whereas chemically tailored film properties, using controlled composition or modification by coupling agents, chemical species replacement, or chemical species within pores, provide the chemical selectivity. Single or multiple layers may be provided.

  2. Coatings with controlled porosity and chemical properties

    DOEpatents

    Frye, Gregory C.; Brinker, C. Jeffrey; Doughty, Daniel H.; Bein, Thomas; Moller, Karin

    1993-01-01

    Coatings and sensors having both steric and chemical selectivity. Controlled porosity provides the steric selectivity, whereas chemically tailored film properties, using controlled composition or modification by coupling agents, chemical species replacement, or chemical species within pores, provide the chemical selectivity. Single or multiple layers may be provided.

  3. Enantioselective Effects of Chiral Pesticides on their Primary Targets and Secondary Targets.

    PubMed

    Yang, Ye; Zhang, Jianyun; Yao, Yijun

    2017-01-01

    Enantioselectivity has been well recognized in the environmental fate and effects of chiral pesticides. Enantiospecific action of the optical enantiomers on the biological molecules establishes the mechanistic basis for the enantioselective toxicity of chiral pesticides to both target and non-target organisms. We undertook a structured search of bibliographic databases for research literature concerning the enantioselective effects of chiral pesticides, including insecticides, herbicides and fungicides, on biomolecules in various species by using some key words. The results of the relevant literatures were reviewed in the text and summarized in tables. Pesticides generally exert their activity on the target organisms via disrupting the primary target biomolecules. In non-target species, effects of pesticides on the secondary targets distinguished from the primary ones make great contribution to their toxicity. Recent investigations have provided convincing evidence of enantioselective toxicity of chiral pesticides to both target and non-target species which is recognized to result from their enantiospecific action on the primary or secondary targets in organisms. This review confirms that chiral pesticides have enantiospecific effects on both primary and secondary target biomolecules in organisms. Future studies regarding toxicological effects of chiral pesticides should focus on the relationship between the enantiomeric difference in the compound-biomolecules interaction and the enantioselectivity in their toxicity.

  4. Fe(+) chemical ionization of peptides.

    PubMed

    Speir, J P; Gorman, G S; Amster, I J

    1993-02-01

    Laser-desorbed peptide neutral molecules were allowed to react with Fe(+) in a Fourier transform mass spectrometer, using the technique of laser desorption/chemical ionization. The Fe(+) ions are formed by laser ablation of a steel target, as well as by dissociative charge-exchange ionization of ferrocene with Ne(+). Prior to reaction with laser-desorbed peptide molecules, Fe(+) ions undergo 20-100 thermalizin collisions with xenon to reduce the population of excited-state metal ion species. The Fe(+) ions that have not experienced thermalizing collisions undergo charge exchange with peptide molecules. Iron ions that undergo thermalizing collisions before they are allowed to react with peptides are found to undergo charge exchange and to form adduct species [M + Fe(+)] and fragment ions that result from the loss of small, stable molecules, such as H2O, CO, and CO2, from the metal ion-peptide complex.

  5. Coatings with controlled porosity and chemical properties

    DOEpatents

    Frye, G.C.; Brinker, C.J.; Doughty, D.H.; Bein, T.; Moller, K.

    1993-07-06

    Coatings and sensors are described having both steric and chemical selectivity. Controlled porosity provides the steric selectivity, whereas chemically tailored film properties, using controlled composition or modification by coupling agents, chemical species replacement, or chemical species within pores, provide the chemical selectivity. Single or multiple layers may be provided.

  6. Comparison of the chemical compositions and nutritive values of various pumpkin (Cucurbitaceae) species and parts

    PubMed Central

    Kim, Mi Young; Kim, Eun Jin; Kim, Young-Nam; Choi, Changsun

    2012-01-01

    Pumpkins have considerable variation in nutrient contents depending on the cultivation environment, species, or part. In this study, the general chemical compositions and some bioactive components, such as tocopherols, carotenoids, and β-sitosterol, were analyzed in three major species of pumpkin (Cucurbitaceae pepo, C. moschata, and C. maxima) grown in Korea and also in three parts (peel, flesh, and seed) of each pumpkin species. C. maxima had significantly more carbohydrate, protein, fat, and fiber than C. pepo or C. moschata (P < 0.05). The moisture content as well as the amino acid and arginine contents in all parts of the pumpkin was highest in C. pepo. The major fatty acids in the seeds were palmitic, stearic, oleic, and linoleic acids. C. pepo and C. moschata seeds had significantly more γ-tocopherol than C. maxima, whose seeds had the highest β-carotene content. C. pepo seeds had significantly more β-sitosterol than the others. Nutrient compositions differed considerably among the pumpkin species and parts. These results will be useful in updating the nutrient compositions of pumpkin in the Korean food composition database. Additional analyses of various pumpkins grown in different years and in different areas of Korea are needed. PMID:22413037

  7. Using existing data to predict and quantify the risks of GM forage to a population of a non-target invertebrate species: a New Zealand case study.

    PubMed

    O'Callaghan, Maureen; Soboleva, Tanya K; Barratt, Barbara I P

    2010-01-01

    Determining the effects of genetically modified (GM) crops on non-target organisms is essential as many non-target species provide important ecological functions. However, it is simply not possible to collect field data on more than a few potential non-target species present in the receiving environment of a GM crop. While risk assessment must be rigorous, new approaches are necessary to improve the efficiency of the process. Utilisation of published information and existing data on the phenology and population dynamics of test species in the field can be combined with limited amounts of experimental biosafety data to predict possible outcomes on species persistence. This paper presents an example of an approach where data from laboratory experiments and field studies on phenology are combined using predictive modelling. Using the New Zealand native weevil species Nicaeana cervina as a case study, we could predict that oviposition rates of the weevil feeding on a GM ryegrass could be reduced by up to 30% without threat to populations of the weevil in pastoral ecosystems. In addition, an experimentally established correlation between feeding level and oviposition led to the prediction that a consistent reduction in feeding of 50% or higher indicated a significant risk to the species and could potentially lead to local extinctions. This approach to biosafety risk assessment, maximising the use of pre-existing field and laboratory data on non-target species, can make an important contribution to informed decision-making by regulatory authorities and developers of new technologies. © ISBR, EDP Sciences, 2011.

  8. Chemical evolutionary games.

    PubMed

    Aristotelous, Andreas C; Durrett, Richard

    2014-05-01

    Inspired by the use of hybrid cellular automata in modeling cancer, we introduce a generalization of evolutionary games in which cells produce and absorb chemicals, and the chemical concentrations dictate the death rates of cells and their fitnesses. Our long term aim is to understand how the details of the interactions in a system with n species and m chemicals translate into the qualitative behavior of the system. Here, we study two simple 2×2 games with two chemicals and revisit the two and three species versions of the one chemical colicin system studied earlier by Durrett and Levin (1997). We find that in the 2×2 examples, the behavior of our new spatial model can be predicted from that of the mean field differential equation using ideas of Durrett and Levin (1994). However, in the three species colicin model, the system with diffusion does not have the coexistence which occurs in the lattices model in which sites interact with only their nearest neighbors. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Systematic Approach for Calculating the Concentrations of Chemical Species in Multiequilibrium Problems: Inclusion of the Ionic Strength Effects

    ERIC Educational Resources Information Center

    Baeza-Baeza, Juan J.; Garcia-Alvarez-Coque, M. Celia

    2012-01-01

    A general systematic approach including ionic strength effects is proposed for the numerical calculation of concentrations of chemical species in multiequilibrium problems. This approach extends the versatility of the approach presented in a previous article and is applied using the Solver option of the Excel spreadsheet to solve real problems…

  10. The Chemical Basis of Species, Sex, and Individual Recognition Using Feces in the Domestic Cat.

    PubMed

    Miyazaki, Masao; Miyazaki, Tamako; Nishimura, Takashi; Hojo, Wataru; Yamashita, Tetsuro

    2018-04-01

    Scents emitted from excretions provide important information about the owner. Volatile compounds with higher levels in a species and/or sex, or that vary among individuals could be odor cues for species and/or sex, or individual recognition. However, such compounds have been identified in only a few vertebrate species. In domestic cats (Felis silvestris catus), it is known that unburied cat feces are territorial markers asserting the border of their home range, but little was known which fecal compounds are scent cues for species, sex, and individual recognition in cats. In the present study, we demonstrated the chemical basis for species, sex, and individual recognition using feces of cats. For males, major contents were fatty acids and 3-mercapto-3-methyl-1-butanol (MMB), a derivative of the unusual amino acid, felinine. MMB emission levels from feces had sex-based differences (male > female) and dynamic temporal changes during aging. Cats distinguished fecal odors with and without MMB, and different fatty acid compositions among individuals. No cat-specific compound, such as MMB, was detectable from their anal odor emitting fatty acids. We concluded that fecal MMB is a male sex recognition pheromone in cats and also provides a temporal trace of the owner. After sensing MMB, they may distinguish individual differences of conspecific feces with variable subsets of fatty acids. In contrast to scent marks, since cats can obtain species information from visual cues before sniffing conspecific anal odors, they may use their efforts to distinguish individual differences of anal odors during sniffing.

  11. Standardized molecular diagnostic tool for the identification of cryptic species within the Bemisia tabaci complex.

    PubMed

    Elfekih, Samia; Tay, Wee Tek; Gordon, Karl; Court, Leon N; De Barro, Paul J

    2018-01-01

    The whitefly Bemisia tabaci complex harbours over 40 cryptic species that have been placed in 11 phylogenetically distinct clades based on the molecular characterization of partial mitochondrial DNA COI (mtCOI) gene region. Four cryptic species are currently within the invasive clade, i.e. MED, MEAM1, MEAM2 and IO. Correct identification of these species is a critical step towards implementing reliable measures for plant biosecurity and border protection; however, no standardized B. tabaci-specific primers are currently available which has caused inconsistencies in the species identification processes. We report three sets of polymerase chain reaction (PCR) primers developed to amplify the mtCOI region which can be used for genotyping MED, MEAM1 and IO species, and tested these primers on 91 MED, 35 MEAM1 and five IO individuals. PCR and sequencing of amplicons identified a total of 21, six and one haplotypes in MED, MEAM1 and IO respectively, of which six haplotypes were new to the B. tabaci database. These primer pairs enabled standardization and robust molecular species identification via mtCOI screening of the targeted invasive cryptic species and will improve quarantine decisions. Use of this diagnostic tool could be extended to other species within the complex. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  12. Enhanced permeability of blood-brain barrier and targeting function of brain via borneol-modified chemically solid lipid nanoparticle.

    PubMed

    Song, Hui; Wei, Man; Zhang, Nan; Li, He; Tan, Xiaochuan; Zhang, Yujia; Zheng, Wensheng

    2018-01-01

    The incidence of central nervous system disease has increased in recent years. However, the transportation of drug is restricted by the blood-brain barrier, contributing to the poor therapeutic effect in the brain. Therefore, the development of a new brain-targeting drug delivery system has become the hotspot of pharmacy. Borneol, a simple bicyclic monoterpene extracted from Dryobalanops aromatica , can direct drugs to the upper body parts according to the theory of traditional Chinese medicine. Dioleoyl phosphoethanolamine (DOPE) was chemically modified by borneol as one of the lipid materials of solid lipid nanoparticle (SLN) in the present study. The borneol-modified chemically solid lipid nanoparticle (BO-SLN/CM), borneol-modified physically solid lipid nanoparticle (BO-SLN/PM), and SLN have similar diameter (of about 87 nm) and morphological characteristics. However, BO-SLN/CM has a lower cytotoxicity, higher cell uptake, and better blood-brain barrier permeability compared with BO-SLN/PM and SLN. BO-SLN/CM has a remarkable targeting function to the brain, while BO-SLN/ PM and SLNs are concentrated at the lung. The present study provides an excellent drug delivery carrier, BO-SLN/CM, having the application potential of targeting to the brain and permeating to the blood-brain barrier.

  13. Target validation: linking target and chemical properties to desired product profile.

    PubMed

    Wyatt, Paul G; Gilbert, Ian H; Read, Kevin D; Fairlamb, Alan H

    2011-01-01

    The discovery of drugs is a lengthy, high-risk and expensive business taking at least 12 years and is estimated to cost upwards of US$800 million for each drug to be successfully approved for clinical use. Much of this cost is driven by the late phase clinical trials and therefore the ability to terminate early those projects destined to fail is paramount to prevent unwanted costs and wasted effort. Although neglected diseases drug discovery is driven more by unmet medical need rather than financial considerations, the need to minimise wasted money and resources is even more vital in this under-funded area. To ensure any drug discovery project is addressing the requirements of the patients and health care providers and delivering a benefit over existing therapies, the ideal attributes of a novel drug needs to be pre-defined by a set of criteria called a target product profile. Using a target product profile the drug discovery process, clinical study design, and compound characteristics can be defined all the way back through to the suitability or druggability of the intended biochemical target. Assessment and prioritisation of the most promising targets for entry into screening programmes is crucial for maximising chances of success.

  14. Surface Chemical Conversion of Organosilane Self-Assembled Monolayers with Active Oxygen Species Generated by Vacuum Ultraviolet Irradiation of Atmospheric Oxygen Molecules

    NASA Astrophysics Data System (ADS)

    Kim, Young-Jong; Lee, Kyung-Hwang; Sano, Hikaru; Han, Jiwon; Ichii, Takashi; Murase, Kuniaki; Sugimura, Hiroyuki

    2008-01-01

    The chemical conversion of the top surface of n-octadecyltrimethoxy silane self-assembled monolayers (ODS-SAMs) on oxide-covered Si substrates using active oxygen species generated from atmospheric oxygen molecules irradiated with vacuum ultraviolet (VUV) light at 172 nm in wavelength has been studied on the basis of water contact angle measurements, ellipsometry, X-ray photoelectron spectroscopy, and atomic force microscopy. An ODS-SAM whose water contact angle was 104° on average was prepared using chemical vapor deposition with substrate and vapor temperatures of 150 °C. The VUV treatment of an ODS-SAM sample was carried out by placing the sample in air and then irradiating the sample surface with a Xe-excimer lamp. The distance between the lamp and the sample was regulated so that the VUV light emitted from the lamp was almost entirely absorbed by atmospheric oxygen molecules to generate active oxygen species, such as ozone and atomic oxygen before reaching the sample surface. Hence, the surface chemical conversion of the ODS-SAM was primarily promoted through chemical reactions with the active oxygen species. Photochemical changes in the ODS-SAM were found to be the generation of polar functional groups, such as -COOH, -CHO, and -OH, on the surface and the subsequent etching of the monolayer. Irradiation parameters, such as irradiation time, were optimized to achieve a better functionalization of the SAM top surface while minimizing the etching depth of the ODS-SAM. The ability to graft another SAM onto the modified ODS-SAM bearing polar functional groups was demonstrated by the formation of alkylsilane bilayers.

  15. Coatings with controlled porosity and chemical properties

    DOEpatents

    Frye, G.C.; Brinker, C.J.; Doughty, D.H.; Bein, T.; Moller, K.

    1996-12-31

    Coatings and sensors are disclosed having both steric and chemical selectivity. Controlled porosity provides the steric selectivity, whereas chemically tailored film properties, using controlled composition or modification by coupling agents, chemical species replacement, or chemical species within pores, provide the chemical selectivity. Single or multiple layers may be provided. 7 figs.

  16. Sum over Histories Representation for Kinetic Sensitivity Analysis: How Chemical Pathways Change When Reaction Rate Coefficients Are Varied

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bai, Shirong; Davis, Michael J.; Skodje, Rex T.

    2015-11-12

    The sensitivity of kinetic observables is analyzed using a newly developed sum over histories representation of chemical kinetics. In the sum over histories representation, the concentrations of the chemical species are decomposed into the sum of probabilities for chemical pathways that follow molecules from reactants to products or intermediates. Unlike static flux methods for reaction path analysis, the sum over histories approach includes the explicit time dependence of the pathway probabilities. Using the sum over histories representation, the sensitivity of an observable with respect to a kinetic parameter such as a rate coefficient is then analyzed in terms of howmore » that parameter affects the chemical pathway probabilities. The method is illustrated for species concentration target functions in H-2 combustion where the rate coefficients are allowed to vary over their associated uncertainty ranges. It is found that large sensitivities are often associated with rate limiting steps along important chemical pathways or by reactions that control the branching of reactive flux« less

  17. Take time to smell the frogs: vocal sac glands of reed frogs (Anura: Hyperoliidae) contain species-specific chemical cocktails

    PubMed Central

    Starnberger, Iris; Poth, Dennis; Peram, Pardha Saradhi; Schulz, Stefan; Vences, Miguel; Knudsen, Jette; Barej, Michael F; Rödel, Mark-Oliver; Walzl, Manfred; Hödl, Walter

    2013-01-01

    Males of all reed frog species (Anura: Hyperoliidae) have a prominent, often colourful, gular patch on their vocal sac, which is particularly conspicuous once the vocal sac is inflated. Although the presence, shape, and form of the gular patch are well-known diagnostic characters for these frogs, its function remains unknown. By integrating biochemical and histological methods, we found strong evidence that the gular patch is a gland producing volatile compounds, which might be emitted while calling. Volatile compounds were confirmed by gas chromatography–mass spectrometry in the gular glands in 11 species of the hyperoliid genera Afrixalus, Heterixalus, Hyperolius, and Phlyctimantis. Comparing the gular gland contents of 17 specimens of four sympatric Hyperolius species yielded a large variety of 65 compounds in species-specific combinations. We suggest that reed frogs might use a complex combination of at least acoustic and chemical signals in species recognition and mate choice. PMID:24277973

  18. Development of chemical inhibitors of the SARS coronavirus: viral helicase as a potential target.

    PubMed

    Keum, Young-Sam; Jeong, Yong-Joo

    2012-11-15

    Severe acute respiratory syndrome (SARS) was the first pandemic in the 21st century to claim more than 700 lives worldwide. However, effective anti-SARS vaccines or medications are currently unavailable despite being desperately needed to adequately prepare for a possible SARS outbreak. SARS is caused by a novel coronavirus, and one of its components, a viral helicase, is emerging as a promising target for the development of chemical SARS inhibitors. In the following review, we describe the characterization, family classification, and kinetic movement mechanisms of the SARS coronavirus (SCV) helicase-nsP13. We also discuss the recent progress in the identification of novel chemical inhibitors of nsP13 in the context of our recent discovery of the strong inhibition of the SARS helicase by natural flavonoids, myricetin and scutellarein. These compounds will serve as important resources for the future development of anti-SARS medications. Copyright © 2012 Elsevier Inc. All rights reserved.

  19. Development of a New DNA Vaccine for Alzheimer Disease Targeting a Wide Range of Aβ Species and Amyloidogenic Peptides

    PubMed Central

    Matsumoto, Yoh; Niimi, Naoko; Kohyama, Kuniko

    2013-01-01

    It has recently been determined that not only Aβ oligomers, but also other Aβ species and amyloidogenic peptides are neurotoxic in Alzheimer disease (AD) and play a pivotal role in AD pathogenesis. In the present study, we attempted to develop new DNA vaccines targeting a wide range of Aβ species. For this purpose, we first performed in vitro assays with newly developed vaccines to evaluate Aβ production and Aβ secretion abilities and then chose an IgL-Aβx4-Fc-IL-4 vaccine (designated YM3711) for further studies. YM3711 was vaccinated to mice, rabbits and monkeys to evaluate anti-Aβ species antibody-producing ability and Aβ reduction effects. It was found that YM3711 vaccination induced significantly higher levels of antibodies not only to Aβ1-42 but also to AD-related molecules including AβpE3-42, Aβ oligomers and Aβ fibrils. Importantly, YM3711 significantly reduced these Aβ species in the brain of model mice. Binding and competition assays using translated YM3711 protein products clearly demonstrated that a large part of antibodies induced by YM3711 vaccination are directed at conformational epitopes of the Aβ complex and oligomers. Taken together, we demonstrate that YM3711 is a powerful DNA vaccine targeting a wide range of AD-related molecules and is worth examining in preclinical and clinical trials. PMID:24086465

  20. Chemical, computational and functional insights into the chemical stability of the Hedgehog pathway inhibitor GANT61.

    PubMed

    Calcaterra, Andrea; Iovine, Valentina; Botta, Bruno; Quaglio, Deborah; D'Acquarica, Ilaria; Ciogli, Alessia; Iazzetti, Antonia; Alfonsi, Romina; Lospinoso Severini, Ludovica; Infante, Paola; Di Marcotullio, Lucia; Mori, Mattia; Ghirga, Francesca

    2018-12-01

    This work aims at elucidating the mechanism and kinetics of hydrolysis of GANT61, the first and most-widely used inhibitor of the Hedgehog (Hh) signalling pathway that targets Glioma-associated oncogene homologue (Gli) proteins, and at confirming the chemical nature of its bioactive form. GANT61 is poorly stable under physiological conditions and rapidly hydrolyses into an aldehyde species (GANT61-A), which is devoid of the biological activity against Hh signalling, and a diamine derivative (GANT61-D), which has shown inhibition of Gli-mediated transcription. Here, we combined chemical synthesis, NMR spectroscopy, analytical studies, molecular modelling and functional cell assays to characterise the GANT61 hydrolysis pathway. Our results show that GANT61-D is the bioactive form of GANT61 in NIH3T3 Shh-Light II cells and SuFu -/- mouse embryonic fibroblasts, and clarify the structural requirements for GANT61-D binding to Gli1. This study paves the way to the design of GANT61 derivatives with improved potency and chemical stability.

  1. A mathematical analysis of multiple-target SELEX.

    PubMed

    Seo, Yeon-Jung; Chen, Shiliang; Nilsen-Hamilton, Marit; Levine, Howard A

    2010-10-01

    statement: For any initial pool of nucleic acids such that all N species are represented, the dynamical system defined by the multiple target SELEX process will converge to a unique subset of nucleic acids, each of whose concentrations depend only upon the total nucleic acid concentration, the initial fractional target distribution (both of which are assumed to be the same from round to round), and the overall limiting association constant. (The overall association constant is the equilibrium constant for the system of MN reactions when viewed as a composite single reaction). This condition is equivalent to the statement that every member of a certain family of chemical potentials at infinite target dilution can have at most one critical point. (The condition replaces the statement for single target SELEX that the dynamical system generated via the process always converges to a pool that contains only the nucleic acid that binds best to the target). This suggests that the effectiveness of multiple target SELEX as a separation procedure may not be as useful as single target SELEX unless the thermodynamic properties of these chemical potentials are well understood.

  2. Physical and chemical characterization of biochars produced from coppiced wood of thirteen tree species for use in horticultural substrates

    USDA-ARS?s Scientific Manuscript database

    Seven-year-old coppiced shoots from thirteen species of native and non-native trees and shrubs were harvested, dried, and were pyrolyzed to produce biochars for potential use in horticultural substrates. Several chemical and physical characteristics of the biochars were determined. There were slight...

  3. New applications in EPA’s ECOTOX Knowledge System: Assimilating relative potencies of metals across chemical and biological species from literature-based toxicity effects data.

    EPA Science Inventory

    Toxicity of metals in field settings can vary widely among ionic chemical species and across biological receptors. Thus, a challenge often found in developing TRVs for the risk assessment of metals is identifying the most appropriate metal and biological species combinations for...

  4. A chemical proteomics approach reveals Hsp27 as a target for proapoptotic clerodane diterpenes.

    PubMed

    Faiella, Laura; Piaz, Fabrizio Dal; Bisio, Angela; Tosco, Alessandra; De Tommasi, Nunziatina

    2012-10-01

    Clerodane diterpenoids are a class of naturally occurring molecules widely distributed in the Lamiaceae family. Neo-clerodane diterpenoids from Salvia ssp were recently described as compounds inhibiting the proliferation of human cancer cell lines. To gain new insights into molecular mechanism(s) underlying the antitumor potential of this class of compounds, we used a chemical proteomics approach to analyse the cellular interactome of hardwickiic acid (HAA) selected as a representative molecule. HAA was linked to an opportune 1,1'-carbonyldiimidazole modified by 1,12-dodecanediamine and then immobilized on a matrix support. The modified beads were then used as bait for fishing the potential partners of HAA in a U937 cell lysate. We identified heat shock protein 27 (Hsp27), an ATP-independent antiapoptotic chaperone characterized for its tumorigenic and metastatic properties and now referenced as a major therapeutic target in many types of cancer, as a major HAA partner. Here, we also report the study of HAA-Hsp27 interaction by means of a panel of chemical and biological approaches, including surface plasmon resonance measurements limited proteolysis, and biochemical assays. Our data suggest that HAA could provide a potential tool to develop strategies for the discovery of Hsp27 chemical inhibitors.

  5. Volatile Constituents from Baccharis spp. L. (Asteraceae): Chemical Support for the Conservation of Threatened Species in Uruguay.

    PubMed

    Minteguiaga, Manuel; González, Andrés; Cassel, Eduardo; Umpierrez, Noelia; Fariña, Laura; Dellacassa, Eduardo

    2018-05-01

    Chemical bioprospecting is an important tool for generating knowledge regarding local human-threatened floras and for conservation management. For Baccharis L. (Asteraceae), several volatile components have been reported for Brazil, Argentina, Bolivia, and Chile as a result of bioprospection, but not for Uruguayan flora, which is composed of more than 50 native species. In this work, through collection of aerial parts of different species and volatile simultaneous-distillation extraction and gas chromatography-mass spectrometry analyses, twelve native species of Baccharis were studied (B. articulata, B. cultrata, B. genistifolia, B. gibertii, B. gnaphalioides, B. ochracea, B. phyteumoides, B. punctulata, B. crispa, B. dracunculifolia, B. linearifolia subsp. linearifolia, and B. spicata). A detailed analysis of the male and female volatile composition was conducted for the last four species. The profiles of B. cultrata, B. genistifolia, B. gibertii, and B. gnaphalioides are reported for the first time. Because half of the species analyzed in this work are in Uruguay and are threatened or potentially threatened by human economic activities, the importance of their conservation as natural, sustainable resources is highlighted. © 2018 Wiley-VHCA AG, Zurich, Switzerland.

  6. Surrogate species selection for assessing potential adverse environmental impacts of genetically engineered insect-resistant plants on non-target organisms

    PubMed Central

    Carstens, Keri; Cayabyab, Bonifacio; De Schrijver, Adinda; Gadaleta, Patricia G; Hellmich, Richard L; Romeis, Jörg; Storer, Nicholas; Valicente, Fernando H; Wach, Michael

    2014-01-01

    Most regulatory authorities require that developers of genetically engineered insect-resistant (GEIR) crops evaluate the potential for these crops to have adverse impacts on valued non-target organisms (NTOs), i.e., organisms not intended to be controlled by the trait. In many cases, impacts to NTOs are assessed using surrogate species, and it is critical that the data derived from surrogates accurately predict any adverse impacts likely to be observed from the use of the crop in the agricultural context. The key is to select surrogate species that best represent the valued NTOs in the location where the crop is going to be introduced, but this selection process poses numerous challenges for the developers of GE crops who will perform the tests, as well as for the ecologists and regulators who will interpret the test results. These issues were the subject of a conference “Surrogate Species Selection for Assessing Potential Adverse Environmental Impacts of Genetically Engineered Plants on Non-Target Organisms” convened by the Center for Environmental Risk Assessment, ILSI Research Foundation. This report summarizes the proceedings of the conference, including the presentations, discussions and the points of consensus agreed to by the participants. PMID:24637519

  7. Surrogate species selection for assessing potential adverse environmental impacts of genetically engineered insect-resistant plants on non-target organisms.

    PubMed

    Carstens, Keri; Cayabyab, Bonifacio; De Schrijver, Adinda; Gadaleta, Patricia G; Hellmich, Richard L; Romeis, Jörg; Storer, Nicholas; Valicente, Fernando H; Wach, Michael

    2014-01-01

    Most regulatory authorities require that developers of genetically engineered insect-resistant (GEIR) crops evaluate the potential for these crops to have adverse impacts on valued non-target organisms (NTOs), i.e., organisms not intended to be controlled by the trait. In many cases, impacts to NTOs are assessed using surrogate species, and it is critical that the data derived from surrogates accurately predict any adverse impacts likely to be observed from the use of the crop in the agricultural context. The key is to select surrogate species that best represent the valued NTOs in the location where the crop is going to be introduced, but this selection process poses numerous challenges for the developers of GE crops who will perform the tests, as well as for the ecologists and regulators who will interpret the test results. These issues were the subject of a conference "Surrogate Species Selection for Assessing Potential Adverse Environmental Impacts of Genetically Engineered Plants on Non-Target Organisms" convened by the Center for Environmental Risk Assessment, ILSI Research Foundation. This report summarizes the proceedings of the conference, including the presentations, discussions and the points of consensus agreed to by the participants.

  8. Population Connectivity Measures of Fishery-Targeted Coral Reef Species to Inform Marine Reserve Network Design in Fiji

    PubMed Central

    Eastwood, Erin K.; López, Elora H.; Drew, Joshua A.

    2016-01-01

    Coral reef fish serve as food sources to coastal communities worldwide, yet are vulnerable to mounting anthropogenic pressures like overfishing and climate change. Marine reserve networks have become important tools for mitigating these pressures, and one of the most critical factors in determining their spatial design is the degree of connectivity among different populations of species prioritized for protection. To help inform the spatial design of an expanded reserve network in Fiji, we used rapidly evolving mitochondrial genes to investigate connectivity patterns of three coral reef species targeted by fisheries in Fiji: Epinephelus merra (Serranidae), Halichoeres trimaculatus (Labridae), and Holothuria atra (Holothuriidae). The two fish species, E. merra and Ha. trimaculatus, exhibited low genetic structuring and high amounts of gene flow, whereas the sea cucumber Ho. atra displayed high genetic partitioning and predominantly westward gene flow. The idiosyncratic patterns observed among these species indicate that patterns of connectivity in Fiji are likely determined by a combination of oceanographic and ecological characteristics. Our data indicate that in the cases of species with high connectivity, other factors such as representation or political availability may dictate where reserves are placed. In low connectivity species, ensuring upstream and downstream connections is critical. PMID:26805954

  9. Chemical sensor with oscillating cantilevered probe

    DOEpatents

    Adams, Jesse D

    2013-02-05

    The invention provides a method of detecting a chemical species with an oscillating cantilevered probe. A cantilevered beam is driven into oscillation with a drive mechanism coupled to the cantilevered beam. A free end of the oscillating cantilevered beam is tapped against a mechanical stop coupled to a base end of the cantilevered beam. An amplitude of the oscillating cantilevered beam is measured with a sense mechanism coupled to the cantilevered beam. A treated portion of the cantilevered beam is exposed to the chemical species, wherein the cantilevered beam bends when exposed to the chemical species. A second amplitude of the oscillating cantilevered beam is measured, and the chemical species is determined based on the measured amplitudes.

  10. Spatial distribution and temporal variation of chemical species in the bulk atmospheric aerosols collected at the Okinawa archipelago, Japan

    NASA Astrophysics Data System (ADS)

    Handa, D.; Somada, Y.; Ijyu, M.; Azechi, S.; Nakaema, F.; Arakaki, T.; Tanahara, A.

    2009-12-01

    The economic development and population growth in recent Asia have been increasing air pollution. A computer simulation study showed that air pollutants emitted from Asian continent could spread quickly within northern hemisphere. We initiated a study to elucidate the special distribution and chemical characterization of atmospheric aerosols around Okinawa archipelago, Japan. Okinawa Island is situated approximately 1500 km south of Tokyo, Japan, 2000 km southeast of Beijing, China, and 1000 km south of South Korea. Its location in Asia is well suited for studying long-range transport of air pollutants in East Asia because maritime air mass prevails during summer, while continental air mass dominates during fall, winter, and spring. The maritime air mass data can be seen as background and can be compared with continental air masses which have been affected by anthropogenic activities. We simultaneously collected bulk aerosol samples by using the same types of high volume air samplers at Cape Hedo Atmosphere and Aerosol Monitoring Station (CHAAMS, Okinawa Island), Kume Island (ca. 160 km south-west of CHAAMS) and Minami-daitou Island (ca. 320 km south-east of CHAAMS). We determined the concentrations of water-soluble anions, cations and dissolved organic carbon (DOC) using ion chromatography, atomic absorption spectrometry, and total organic carbon analyzer, respectively. We report and discuss spatial distribution and temporal variation of chemical species concentrations in bulk atmospheric aerosols collected during July, 2008 to July, 2009. We determine “background” concentration of chemical components in Okinawa archipelago. We then compare each chemical component among CHAAMS, Kume Island and Minami-daito Island to elucidate the influence of the long-range transport of chemical species from Asian continent.

  11. Snake (Colubridae: Thamnophis) predatory responses to chemical cues from native and introduced prey species

    USGS Publications Warehouse

    Mullin, S.J.; Imbert, H.; Fish, J.M.; Ervin, E.L.; Fisher, R.N.

    2004-01-01

    Several aquatic vertebrates have been introduced into freshwater systems in California over the past 100 years. Some populations of the two-striped garter snake (Thamnophis hammondii) have lived in sympatry with these species since their introduction; other populations have never encountered them. To assess the possible adaptation to a novel prey, we tested the predatory responses of T. hammondii from different populations to different chemosensory cues from native and introduced prey species. We presented chemical extracts from potential prey types and 2 control odors to individual snakes on cotton swabs and recorded the number of tongue flicks and attacks directed at each swab. Subject response was higher for prey odors than control substances. Odors from introduced centrarchid fish (Lepomis) elicited higher response levels than other prey types, including native anuran larvae (Pseudacris regilla). The pattern of response was similar for both populations of snakes (experienced and nai??ve, with respect to the introduced prey). We suggest that the generalist aquatic lifestyle of T. hammondii has allowed it to take advantage of increasing populations of introduced prey. Decisions on the management strategies for some of these introduced prey species should include consideration of how T. hammondii populations might respond in areas of sympatry.

  12. Use of anticoagulant rodenticides in outdoor urban areas: considerations and proposals for the protection of public health and non-target species.

    PubMed

    Dutto, M; Di Domenico, D; Rubbiani, M

    2018-01-01

    Rodent control operations represent an important tool for the prevention and management of infestations, in outdoor environments, by synanthropic rodents (Rattus rattus and R. norvegicus), which are a source of economic and environmental damage with significant sanitary implications. Although the use of anticoagulants is safer to humans and pets compared to the use of acute poisoning substances, an intrinsic hazard of the active ingredients exists, i.e. the possible poisoning of non-target organisms (e.g., children, pets and wildlife) following exposure. The risks arising from the use of anticoagulants for rodent control operations in anthropic contexts can therefore only be mitigated by a proper selection of the active ingredient, bait formulation and administration techniques, since an active ingredient with selective action towards non-target species does not currently exist on the market. This document lists practical proposals aimed at reducing the possibility of toxic exposure to anticoagulant rodenticides and mitigate the toxicological risk of human baits and non-target species.

  13. Future Needs and Recommendations in the Development of Species Sensitivity Distributions: Estimating Toxicity Thresholds for Aquatic Ecological Communities and Assessing Impacts of Chemical Exposures

    EPA Science Inventory

    A species sensitivity distribution (SSD) is a probability model of the variation of species sensitivities to a stressor, in particular chemical exposure. The SSD approach has been used as a decision support tool in environmental protection and management since the 1980s, and the ...

  14. Discovery: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria

    PubMed Central

    Joubert, Fourie; Harrison, Claudia M; Koegelenberg, Riaan J; Odendaal, Christiaan J; de Beer, Tjaart AP

    2009-01-01

    Background Up to half a billion human clinical cases of malaria are reported each year, resulting in about 2.7 million deaths, most of which occur in sub-Saharan Africa. Due to the over-and misuse of anti-malarials, widespread resistance to all the known drugs is increasing at an alarming rate. Rational methods to select new drug target proteins and lead compounds are urgently needed. The Discovery system provides data mining functionality on extensive annotations of five malaria species together with the human and mosquito hosts, enabling the selection of new targets based on multiple protein and ligand properties. Methods A web-based system was developed where researchers are able to mine information on malaria proteins and predicted ligands, as well as perform comparisons to the human and mosquito host characteristics. Protein features used include: domains, motifs, EC numbers, GO terms, orthologs, protein-protein interactions, protein-ligand interactions and host-pathogen interactions among others. Searching by chemical structure is also available. Results An in silico system for the selection of putative drug targets and lead compounds is presented, together with an example study on the bifunctional DHFR-TS from Plasmodium falciparum. Conclusion The Discovery system allows for the identification of putative drug targets and lead compounds in Plasmodium species based on the filtering of protein and chemical properties. PMID:19642978

  15. Integrative taxonomy: Combining morphological, molecular and chemical data for species delineation in the parthenogenetic Trhypochthonius tectorum complex (Acari, Oribatida, Trhypochthoniidae)

    PubMed Central

    2011-01-01

    Background There is a long-standing controversial about how parthenogenetic species can be defined in absence of a generally accepted species concept for this reproductive mode. An integrative approach was suggested, combining molecular and morphological data to identify distinct monophyletic entities. Using this approach, speciation of parthenogenetic lineages was recently demonstrated for groups of bdelloid rotifers and oribatid mites. Trhypochthonius tectorum, an oribatid mite from the entirely parthenogenetic desmonomatan family Trhypochthoniidae, is traditionally treated as a single species in Central Europe. However, two new morphological lineages were recently proposed for some Austrian populations of T. tectorum, and were described as novel subspecies (T. silvestris europaeus) or form (T. japonicus forma occidentalis). We used the morphological and morphometrical data which led to this separation, and added mitochondrial and nuclear DNA sequences and the chemical composition of complex exocrine oil gland secretions to test this taxonomical hypothesis. This is the first attempt to combine these three types of data for integrative taxonomical investigations of oribatid mites. Results We show that the previous European species T. tectorum represents a species complex consisting of three distinct lineages in Austria (T.tectorum, T. silvestris europaeus and T. japonicus forma occidentalis), each clearly separated by morphology, oil gland secretion profiles and mitochondrial cox1 sequences. This diversification happened in the last ten million years. In contrast to these results, no variation among the lineages was found in the nuclear 18S rDNA. Conclusions Our approach combined morphological, molecular and chemical data to investigate diversity and species delineation in a parthenogenetic oribatid mite species complex. To date, hypotheses of a general oribatid mite phylogeny are manifold, and mostly based on single-method approaches. Probably, the integrative

  16. Chemical characterization of 21 species of marine macroalgae common in Norwegian waters: benefits of and limitations to their potential use in food and feed.

    PubMed

    Biancarosa, Irene; Belghit, Ikram; Bruckner, Christian G; Liland, Nina S; Waagbø, Rune; Amlund, Heidi; Heesch, Svenja; Lock, Erik-Jan

    2018-03-01

    In the past few years, much effort has been invested into developing a new blue economy based on harvesting, cultivating and processing marine macroalgae in Norway. Macroalgae have high potential for a wide range of applications, e.g. as source of pharmaceuticals, production of biofuels or as food and feed. However, data on the chemical composition of macroalgae from Norwegian waters are scant. This study was designed to characterize the chemical composition of 21 algal species. Both macro- and micronutrients were analysed. Concentrations of heavy metals and the metalloid arsenic in the algae were also quantified. The results confirm that marine macroalgae contain nutrients which are relevant for both human and animal nutrition, the concentrations whereof are highly dependent on species. Although heavy metals and arsenic were detected in the algae studied, concentrations were mostly below maximum allowed levels set by food and feed legislation in the EU. This study provides chemical data on a wide range of algal species covering the three taxonomic groups (brown, red and green algae) and discusses both benefits of and potential limitations to their use for food and feed purposes. © 2017 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. © 2017 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

  17. Reduced chemical kinetics for propane combustion

    NASA Technical Reports Server (NTRS)

    Ying, Shuh-Jing; Nguyen, Hung Lee

    1990-01-01

    It is pointed out that a detailed chemical kinetics mechanism for the combustion of propane consists of 40 chemical species and 118 elementary chemical reactions. An attempt is made to reduce the number of chemical species and elementary chemical reactions so that the computer run times and storage requirements may be greatly reduced in three-dimensional gas turbine combustion flow calculations, while maintaining accurate predictions of the propane combustion and exhaust emissions. By way of a sensitivity analysis, the species of interest and chemical reactions are classified in descending order of importance. Nineteen species are chosen, and their pressure, temperature, and concentration profiles are presented for the reduced mechanisms, which are then compared with those from the full 118 reactions. It is found that 45 reactions involving 27 species have to be kept for comparable agreement. A comparison of the results obtained from the 45 reactions to that of the full 118 shows that the pressure and temperature profiles and concentrations of C3H8, O2, N2, H2O, CO, and CO2 are within 10 percent of maximum change.

  18. Extension of a hybrid particle-continuum method for a mixture of chemical species

    NASA Astrophysics Data System (ADS)

    Verhoff, Ashley M.; Boyd, Iain D.

    2012-11-01

    Due to the physical accuracy and numerical efficiency achieved by analyzing transitional, hypersonic flow fields with hybrid particle-continuum methods, this paper describes a Modular Particle-Continuum (MPC) method and its extension to include multiple chemical species. Considerations that are specific to a hybrid approach for simulating gas mixtures are addressed, including a discussion of the Chapman-Enskog velocity distribution function (VDF) for near-equilibrium flows, and consistent viscosity models for the individual CFD and DSMC modules of the MPC method. Representative results for a hypersonic blunt-body flow are then presented, where the flow field properties, surface properties, and computational performance are compared for simulations employing full CFD, full DSMC, and the MPC method.

  19. Unravelling chemical priming machinery in plants: the role of reactive oxygen-nitrogen-sulfur species in abiotic stress tolerance enhancement.

    PubMed

    Antoniou, Chrystalla; Savvides, Andreas; Christou, Anastasis; Fotopoulos, Vasileios

    2016-10-01

    Abiotic stresses severely limit crop yield and their detrimental effects are aggravated by climate change. Chemical priming is an emerging field in crop stress management. The exogenous application of specific chemical agents before stress events results in tolerance enhancement and reduction of stress impacts on plant physiology and growth. However, the molecular mechanisms underlying the remarkable effects of chemical priming on plant physiology remain to be elucidated. Reactive oxygen, nitrogen and sulfur species (RONSS) are molecules playing a vital role in the stress acclimation of plants. When applied as priming agents, RONSS improve stress tolerance. This review summarizes the recent knowledge on the role of RONSS in cell signalling and gene regulation contributing to abiotic stress tolerance enhancement. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Physico-chemical strategies to enhance stability and drug retention of polymeric micelles for tumor-targeted drug delivery

    PubMed Central

    Shi, Yang; Lammers, Twan; Storm, Gert; Hennink, Wim E.

    2017-01-01

    Polymeric micelles (PM) have been extensively used for tumor-targeted delivery of hydrophobic anti-cancer drugs. The lipophilic core of PM is naturally suitable for loading hydrophobic drugs and the hydrophilic shell endows them with colloidal stability and stealth properties. Decades of research on PM have resulted in tremendous numbers of PM-forming amphiphilic polymers, and approximately a dozen micellar nanomedicines have entered the clinic. The first generation of PM can be considered solubilizers of hydrophobic drugs, with short circulation times resulting from poor micelle stability and unstable drug entrapment. To more optimally exploit the potential of PM for targeted drug delivery, several physical (e.g. π-π stacking, stereocomplexation, hydrogen bonding, host-guest complexation and coordination interaction) and chemical (e.g. free radical polymerization, click chemistry, disulfide and hydrazone bonding) strategies have been developed to improve micelle stability and drug retention. In this review, we describe the most promising physico-chemical approaches to enhance micelle stability and drug retention, and we summarize how these strategies have resulted in systems with promising therapeutic efficacy in animal models, paving the way for clinical translation. PMID:27413999

  1. Gut Dysbiosis in Animals Due to Environmental Chemical Exposures

    PubMed Central

    Rosenfeld, Cheryl S.

    2017-01-01

    The gut microbiome consists of over 103–104 microorganism inhabitants that together possess 150 times more genes that the human genome and thus should be considered an “organ” in of itself. Such communities of bacteria are in dynamic flux and susceptible to changes in host environment and body condition. In turn, gut microbiome disturbances can affect health status of the host. Gut dysbiosis might result in obesity, diabetes, gastrointestinal, immunological, and neurobehavioral disorders. Such host diseases can originate due to shifts in microbiota favoring more pathogenic species that produce various virulence factors, such as lipopolysaccharide. Bacterial virulence factors and metabolites may be transmitted to distal target sites, including the brain. Other potential mechanisms by which gut dysbiosis can affect the host include bacterial-produced metabolites, production of hormones and factors that mimic those produced by the host, and epimutations. All animals, including humans, are exposed daily to various environmental chemicals that can influence the gut microbiome. Exposure to such chemicals might lead to downstream systemic effects that occur secondary to gut microbiome disturbances. Increasing reports have shown that environmental chemical exposures can target both host and the resident gut microbiome. In this review, we will first consider the current knowledge of how endocrine disrupting chemicals (EDCs), heavy metals, air pollution, and nanoparticles can influence the gut microbiome. The second part of the review will consider how potential environmental chemical-induced gut microbiome changes might subsequently induce pathophysiological responses in the host, although definitive evidence for such effects is still lacking. By understanding how these chemicals result in gut dysbiosis, it may open up new remediation strategies in animals, including humans, exposed to such chemicals. PMID:28936425

  2. Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes.

    PubMed

    Schwiertz, A; Le Blay, G; Blaut, M

    2000-01-01

    Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E. hadrum, E. lentum, E. limosum, E. moniliforme, and E. ventriosum. The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none of the probes showed cross-hybridization under stringent conditions. The species-specific probes were applied to fecal samples obtained from 12 healthy volunteers. E. biforme, E. cylindroides, E. hadrum, E. lentum, and E. ventriosum could be determined. All other Eubacterium species for which probes had been designed were under the detection limit of 10(7) cells g (dry weight) of feces(-1). The cell counts obtained are essentially in accordance with the literature data, which are based on colony counts. This shows that whole-cell in situ hybridization with species-specific probes is a valuable tool for the enumeration of Eubacterium species in feces.

  3. Quantification of Different Eubacterium spp. in Human Fecal Samples with Species-Specific 16S rRNA-Targeted Oligonucleotide Probes

    PubMed Central

    Schwiertz, Andreas; Le Blay, Gwenaelle; Blaut, Michael

    2000-01-01

    Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E. hadrum, E. lentum, E. limosum, E. moniliforme, and E. ventriosum. The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none of the probes showed cross-hybridization under stringent conditions. The species-specific probes were applied to fecal samples obtained from 12 healthy volunteers. E. biforme, E. cylindroides, E. hadrum, E. lentum, and E. ventriosum could be determined. All other Eubacterium species for which probes had been designed were under the detection limit of 107 cells g (dry weight) of feces−1. The cell counts obtained are essentially in accordance with the literature data, which are based on colony counts. This shows that whole-cell in situ hybridization with species-specific probes is a valuable tool for the enumeration of Eubacterium species in feces. PMID:10618251

  4. The MIPAS2D: 2-D analysis of MIPAS observations of ESA target molecules and minor species

    NASA Astrophysics Data System (ADS)

    Arnone, E.; Brizzi, G.; Carlotti, M.; Dinelli, B. M.; Magnani, L.; Papandrea, E.; Ridolfi, M.

    2008-12-01

    Measurements from the MIPAS instrument onboard the ENVISAT satellite were analyzed with the Geofit Multi- Target Retrieval (GMTR) system to obtain 2-dimensional fields of pressure, temperature and volume mixing ratios of H2O, O3, HNO3, CH4, N2O, and NO2. Secondary target species relevant to stratospheric chemistry were also analysed and robust mixing ratios of N2O5, ClONO2, F11, F12, F14 and F22 were obtained. Other minor species with high uncertainties were not included in the database and will be the object of further studies. The analysis covers the original nominal observation mode from July 2002 to March 2004 and it is currently being extended to the ongoing reduced resolution mission. The GMTR algorithm was operated on a fixed 5 degrees latitudinal grid in order to ease the comparison with model calculations and climatological datasets. The generated database of atmospheric fields can be directly used for analyses based on averaging processes with no need of further interpolation. Samples of the obtained products are presented and discussed. The database of the retrieved quantities is made available to the scientific community.

  5. Rapid discrimination of different Apiaceae species based on HPTLC fingerprints and targeted flavonoids determination using multivariate image analysis.

    PubMed

    Shawky, Eman; Abou El Kheir, Rasha M

    2018-02-11

    Species of Apiaceae are used in folk medicine as spices and in officinal medicinal preparations of drugs. They are an excellent source of phenolics exhibiting antioxidant activity, which are of great benefit to human health. Discrimination among Apiaceae medicinal herbs remains an intricate challenge due to their morphological similarity. In this study, a combined "untargeted" and "targeted" approach to investigate different Apiaceae plants species was proposed by using the merging of high-performance thin layer chromatography (HPTLC)-image analysis and pattern recognition methods which were used for fingerprinting and classification of 42 different Apiaceae samples collected from Egypt. Software for image processing was applied for fingerprinting and data acquisition. HPTLC fingerprint assisted by principal component analysis (PCA) and hierarchical cluster analysis (HCA)-heat maps resulted in a reliable untargeted approach for discrimination and classification of different samples. The "targeted" approach was performed by developing and validating an HPTLC method allowing the quantification of eight flavonoids. The combination of quantitative data with PCA and HCA-heat-maps allowed the different samples to be discriminated from each other. The use of chemometrics tools for evaluation of fingerprints reduced expense and analysis time. The proposed method can be adopted for routine discrimination and evaluation of the phytochemical variability in different Apiaceae species extracts. Copyright © 2018 John Wiley & Sons, Ltd.

  6. Plasma-activation of tap water using DBD for agronomy applications: Identification and quantification of long lifetime chemical species and production/consumption mechanisms.

    PubMed

    Judée, F; Simon, S; Bailly, C; Dufour, T

    2018-04-15

    Cold atmospheric plasmas are weakly ionized gases that can be generated in ambient air. They produce energetic species (e.g. electrons, metastables) as well as reactive oxygen species, reactive nitrogen species, UV radiations and local electric field. Their interaction with a liquid such as tap water can hence change its chemical composition. The resulting "plasma-activated liquid" can meet many applications, including medicine and agriculture. Consequently, a complete experimental set of analytical techniques dedicated to the characterization of long lifetime chemical species has been implemented to characterize tap water treated using cold atmospheric plasma process and intended to agronomy applications. For that purpose, colorimetry and acid titrations are performed, considering acid-base equilibria, pH and temperature variations induced during plasma activation. 16 species are quantified and monitored: hydroxide and hydronium ions, ammonia and ammonium ions, orthophosphates, carbonate ions, nitrite and nitrate ions and hydrogen peroxide. The related consumption/production mechanisms are discussed. In parallel, a chemical model of electrical conductivity based on Kohlrausch's law has been developed to simulate the electrical conductivity of the plasma-activated tap water (PATW). Comparing its predictions with experimental measurements leads to a narrow fitting, hence supporting the self-sufficiency of the experimental set, I.e. the fact that all long lifetime radicals of interest present in PATW are characterized. Finally, to evaluate the potential of cold atmospheric plasmas for agriculture applications, tap water has been daily plasma-treated to irrigate lentils seeds. Then, seedlings lengths have been measured and compared with untreated tap water, showing an increase as high as 34.0% and 128.4% after 3 days and 6 days of activation respectively. The interaction mechanisms between plasma and tap water are discussed as well as their positive synergy on

  7. Identification of Aspergillus fumigatus and Related Species by Nested PCR Targeting Ribosomal DNA Internal Transcribed Spacer Regions

    PubMed Central

    Zhao, Jun; Kong, Fanrong; Li, Ruoyu; Wang, Xiaohong; Wan, Zhe; Wang, Duanli

    2001-01-01

    Aspergillus fumigatus is the most common species that causes invasive aspergillosis. In order to identify A. fumigatus, partial ribosomal DNA (rDNA) from two to six strains of five different Aspergillus species was sequenced. By comparing sequence data from GenBank, we designed specific primer pairs targeting rDNA internal transcribed spacer (ITS) regions of A. fumigatus. A nested PCR method for identification of other A. fumigatus-related species was established by using the primers. To evaluate the specificities and sensitivities of those primers, 24 isolates of A. fumigatus and variants, 8 isolates of Aspergillus nidulans, 7 isolates of Aspergillus flavus and variants, 8 isolates of Aspergillus terreus, 9 isolates of Aspergillus niger, 1 isolate each of Aspergillus parasiticus, Aspergillus penicilloides, Aspergillus versicolor, Aspergillus wangduanlii, Aspergillus qizutongii, Aspergillus beijingensis, and Exophiala dermatitidis, 4 isolates of Candida, 4 isolates of bacteria, and human DNA were used. The nested PCR method specifically identified the A. fumigatus isolates and closely related species and showed a high degree of sensitivity. Additionally, four A. fumigatus strains that were recently isolated from our clinic were correctly identified by this method. Our results demonstrate that these primers are useful for the identification of A. fumigatus and closely related species in culture and suggest further studies for the identification of Aspergillus fumigatus species in clinical specimens. PMID:11376067

  8. Chemical Diversity, Biological Activity, and Genetic Aspects of Three Ocotea Species from the Amazon

    PubMed Central

    da Silva, Joyce Kelly; da Trindade, Rafaela; Moreira, Edith Cibelle; Maia, José Guilherme S.; Dosoky, Noura S.; Miller, Rebecca S.; Cseke, Leland J.; Setzer, William N.

    2017-01-01

    Ocotea species present economic importance and biological activities attributed to their essential oils (EOs) and extracts. For this reason, various strategies have been developed for their conservation. The chemical compositions of the essential oils and matK DNA sequences of O. caudata, O. cujumary, and O. caniculata were subjected to comparison with data from O. floribunda, O. veraguensis, and O. whitei, previously reported. The multivariate analysis of chemical composition classified the EOs into two main clusters. Group I was characterized by the presence of α-pinene (9.8–22.5%) and β-pinene (9.7–21.3%) and it includes O. caudata, O. whitei, and O. floribunda. In group II, the oils of O. cujumary and O. caniculata showed high similarity due amounts of β-caryophyllene (22.2% and 18.9%, respectively). The EO of O. veraguensis, rich in p-cymene (19.8%), showed minor similarity among all samples. The oils displayed promising antimicrobial and cytotoxic activities against Escherichia coli (minimum inhibitory concentration (MIC) < 19.5 µg·mL−1) and MCF-7 cells (median inhibitory concentration (IC50) ≅ 65.0 µg·mL−1), respectively. The analysis of matK gene displayed a good correlation with the main class of chemical compounds present in the EOs. However, the matK gene data did not show correlation with specific compounds. PMID:28524091

  9. Toward systems metabolic engineering of Aspergillus and Pichia species for the production of chemicals and biofuels.

    PubMed

    Caspeta, Luis; Nielsen, Jens

    2013-05-01

    Recently genome sequence data have become available for Aspergillus and Pichia species of industrial interest. This has stimulated the use of systems biology approaches for large-scale analysis of the molecular and metabolic responses of Aspergillus and Pichia under defined conditions, which has resulted in much new biological information. Case-specific contextualization of this information has been performed using comparative and functional genomic tools. Genomics data are also the basis for constructing genome-scale metabolic models, and these models have helped in the contextualization of knowledge on the fundamental biology of Aspergillus and Pichia species. Furthermore, with the availability of these models, the engineering of Aspergillus and Pichia is moving from traditional approaches, such as random mutagenesis, to a systems metabolic engineering approach. Here we review the recent trends in systems biology of Aspergillus and Pichia species, highlighting the relevance of these developments for systems metabolic engineering of these organisms for the production of hydrolytic enzymes, biofuels and chemicals from biomass. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Protectiveness of species sensitivity distribution hazard concentrations for acute toxicity used in endangered species risk assessment.

    PubMed

    Raimondo, Sandy; Vivian, Deborah N; Delos, Charles; Barron, Mace G

    2008-12-01

    A primary objective of threatened and endangered species conservation is to ensure that chemical contaminants and other stressors do not adversely affect listed species. Assessments of the ecological risks of chemical exposures to listed species often rely on the use of surrogate species, safety factors, and species sensitivity distributions (SSDs) of chemical toxicity; however, the protectiveness of these approaches can be uncertain. We comprehensively evaluated the protectiveness of SSD first and fifth percentile hazard concentrations (HC1, HC5) relative to the application of safety factors using 68 SSDs generated from 1,482 acute (lethal concentration of 50%, or LC50) toxicity records for 291 species, including 24 endangered species (20 fish, four mussels). The SSD HC5s and HCls were lower than 97 and 99.5% of all endangered species mean acute LC50s, respectively. The HC5s were significantly less than the concentrations derived from applying safety factors of 5 and 10 to rainbow trout (Oncorhynchus mykiss) toxicity data, and the HCls were generally lower than the concentrations derived from a safety factor of 100 applied to rainbow trout toxicity values. Comparison of relative sensitivity (SSD percentiles) of broad taxonomic groups showed that crustaceans were generally the most sensitive taxa and taxa sensitivity was related to chemical mechanism of action. Comparison of relative sensitivity of narrow fish taxonomic groups showed that standard test fish species were generally less sensitive than salmonids and listed fish. We recommend the use of SSDs as a distribution-based risk assessment approach that is generally protective of listed species.

  11. Reduced biological control and enhanced chemical pest management in the evolution of fungus farming in ants

    PubMed Central

    Fernández-Marín, Hermógenes; Zimmerman, Jess K.; Nash, David R.; Boomsma, Jacobus J.; Wcislo, William T.

    2009-01-01

    To combat disease, most fungus-growing ants (Attini) use antibiotics from mutualistic bacteria (Pseudonocardia) that are cultured on the ants' exoskeletons and chemical cocktails from exocrine glands, especially the metapleural glands (MG). Previous work has hypothesized that (i) Pseudonocardia antibiotics are narrow-spectrum and control a fungus (Escovopsis) that parasitizes the ants' fungal symbiont, and (ii) MG secretions have broad-spectrum activity and protect ants and brood. We assessed the relative importance of these lines of defence, and their activity spectra, by scoring abundance of visible Pseudonocardia for nine species from five genera and measuring rates of MG grooming after challenging ants with disease agents of differing virulence. Atta and Sericomyrmex have lost or greatly reduced the abundance of visible bacteria. When challenged with diverse disease agents, including Escovopsis, they significantly increased MG grooming rates and expanded the range of targets. By contrast, species of Acromyrmex and Trachymyrmex maintain abundant Pseudonocardia. When challenged, these species had lower MG grooming rates, targeted primarily to brood. More elaborate MG defences and reduced reliance on mutualistic Pseudonocardia are correlated with larger colony size among attine genera, raising questions about the efficacy of managing disease in large societies with chemical cocktails versus bacterial antimicrobial metabolites. PMID:19324734

  12. BESMEX: Bering Sea marine mammal experiment. [with the primary target species being the walrus and bowhead whale

    NASA Technical Reports Server (NTRS)

    Ray, G. C.; Wartzok, D.

    1974-01-01

    Predictive ecological models are being studied for the management and conservation of the walrus, and the bowhead whale in the Bering Sea. The influence of sea ice on the distribution, and carrying capacity of the area for these two mammals is to be investigated with the primary target species being the walrus. Remote sensing and radio tracking is considered a requirement for assessing the walrus ecosystem.

  13. In Silico Investigations of Chemical Constituents of Clerodendrum colebrookianum in the Anti-Hypertensive Drug Targets: ROCK, ACE, and PDE5.

    PubMed

    Arya, Hemant; Syed, Safiulla Basha; Singh, Sorokhaibam Sureshkumar; Ampasala, Dinakar R; Coumar, Mohane Selvaraj

    2017-06-16

    Understanding the molecular mode of action of natural product is a key step for developing drugs from them. In this regard, this study is aimed to understand the molecular-level interactions of chemical constituents of Clerodendrum colebrookianum Walp., with anti-hypertensive drug targets using computational approaches. The plant has ethno-medicinal importance for the treatment of hypertension and reported to show activity against anti-hypertensive drug targets-Rho-associated coiled-coil protein kinase (ROCK), angiotensin-converting enzyme, and phosphodiesterase 5 (PDE5). Docking studies showed that three chemical constituents (acteoside, martinoside, and osmanthuside β6) out of 21 reported from the plant to interact with the anti-hypertensive drug targets with good glide score. In addition, they formed H-bond interactions with the key residues Met156/Met157 of ROCK I/ROCK II and Gln817 of PDE5. Further, molecular dynamics (MD) simulation of protein-ligand complexes suggest that H-bond interactions between acteoside/osmanthuside β6 and Met156/Met157 (ROCK I/ROCK II), acteoside and Gln817 (PDE5) were stable. The present investigation suggests that the anti-hypertensive activity of the plant is due to the interaction of acteoside and osmanthuside β6 with ROCK and PDE5 drug targets. The identified molecular mode of binding of the plant constituents could help to design new drugs to treat hypertension.

  14. Fiber-optic microarray for simultaneous detection of multiple harmful algal bloom species.

    PubMed

    Ahn, Soohyoun; Kulis, David M; Erdner, Deana L; Anderson, Donald M; Walt, David R

    2006-09-01

    Harmful algal blooms (HABs) are a serious threat to coastal resources, causing a variety of impacts on public health, regional economies, and ecosystems. Plankton analysis is a valuable component of many HAB monitoring and research programs, but the diversity of plankton poses a problem in discriminating toxic from nontoxic species using conventional detection methods. Here we describe a sensitive and specific sandwich hybridization assay that combines fiber-optic microarrays with oligonucleotide probes to detect and enumerate the HAB species Alexandrium fundyense, Alexandrium ostenfeldii, and Pseudo-nitzschia australis. Microarrays were prepared by loading oligonucleotide probe-coupled microspheres (diameter, 3 mum) onto the distal ends of chemically etched imaging fiber bundles. Hybridization of target rRNA from HAB cells to immobilized probes on the microspheres was visualized using Cy3-labeled secondary probes in a sandwich-type assay format. We applied these microarrays to the detection and enumeration of HAB cells in both cultured and field samples. Our study demonstrated a detection limit of approximately 5 cells for all three target organisms within 45 min, without a separate amplification step, in both sample types. We also developed a multiplexed microarray to detect the three HAB species simultaneously, which successfully detected the target organisms, alone and in combination, without cross-reactivity. Our study suggests that fiber-optic microarrays can be used for rapid and sensitive detection and potential enumeration of HAB species in the environment.

  15. Chemical characterization of 21 species of marine macroalgae common in Norwegian waters: benefits of and limitations to their potential use in food and feed

    PubMed Central

    Biancarosa, Irene; Belghit, Ikram; Bruckner, Christian G; Liland, Nina S; Waagbø, Rune; Amlund, Heidi; Heesch, Svenja

    2018-01-01

    Abstract BACKGROUND In the past few years, much effort has been invested into developing a new blue economy based on harvesting, cultivating and processing marine macroalgae in Norway. Macroalgae have high potential for a wide range of applications, e.g. as source of pharmaceuticals, production of biofuels or as food and feed. However, data on the chemical composition of macroalgae from Norwegian waters are scant. This study was designed to characterize the chemical composition of 21 algal species. Both macro‐ and micronutrients were analysed. Concentrations of heavy metals and the metalloid arsenic in the algae were also quantified. RESULTS The results confirm that marine macroalgae contain nutrients which are relevant for both human and animal nutrition, the concentrations whereof are highly dependent on species. Although heavy metals and arsenic were detected in the algae studied, concentrations were mostly below maximum allowed levels set by food and feed legislation in the EU. CONCLUSION This study provides chemical data on a wide range of algal species covering the three taxonomic groups (brown, red and green algae) and discusses both benefits of and potential limitations to their use for food and feed purposes. © 2017 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. PMID:29193189

  16. Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites.

    PubMed

    Grijseels, Sietske; Nielsen, Jens Christian; Randelovic, Milica; Nielsen, Jens; Nielsen, Kristian Fog; Workman, Mhairi; Frisvad, Jens Christian

    2016-10-14

    A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311 T  = IBT 12289 T ). The genome was sequenced and assembled into 33.7 Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases. Mining the genome for genes involved in secondary metabolite biosynthesis resulted in the identification of 62 putative biosynthetic gene clusters. Extracts of P. arizonense were analysed for secondary metabolites and austalides, pyripyropenes, tryptoquivalines, fumagillin, pseurotin A, curvulinic acid and xanthoepocin were detected. A comparative analysis against known pathways enabled the proposal of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential industrial applications for the new species P. arizonense. The description and availability of the genome sequence of P. arizonense, further provides the basis for biotechnological exploitation of this species.

  17. Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites

    PubMed Central

    Grijseels, Sietske; Nielsen, Jens Christian; Randelovic, Milica; Nielsen, Jens; Nielsen, Kristian Fog; Workman, Mhairi; Frisvad, Jens Christian

    2016-01-01

    A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311T = IBT 12289T). The genome was sequenced and assembled into 33.7 Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases. Mining the genome for genes involved in secondary metabolite biosynthesis resulted in the identification of 62 putative biosynthetic gene clusters. Extracts of P. arizonense were analysed for secondary metabolites and austalides, pyripyropenes, tryptoquivalines, fumagillin, pseurotin A, curvulinic acid and xanthoepocin were detected. A comparative analysis against known pathways enabled the proposal of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential industrial applications for the new species P. arizonense. The description and availability of the genome sequence of P. arizonense, further provides the basis for biotechnological exploitation of this species. PMID:27739446

  18. SPECIES DIFFERENCES IN ANDROGEN AND ESTROGEN RECEPTOR STRUCTURE AND FUNCTION AMONG VERTEBRATES AND INVERTEBRATES: INTERSPECIES EXTRAPOLATIONS REGARDING ENDOCRINE DISRUPTING CHEMICALS

    EPA Science Inventory

    Species Differences in Androgen and Estrogen Receptor Structure and Function Among Vertebrates and Invertebrates: Interspecies Extrapolations regarding Endocrine Disrupting Chemicals
    VS Wilson1, GT Ankley2, M Gooding 1,3, PD Reynolds 1,4, NC Noriega 1, M Cardon 1, P Hartig1,...

  19. Species-to-species rate coefficients for the H3+ + H2 reacting system

    NASA Astrophysics Data System (ADS)

    Sipilä, O.; Harju, J.; Caselli, P.

    2017-10-01

    Aims: We study whether or not rotational excitation can make a large difference to chemical models of the abundances of the H3+ isotopologs, including spin states, in physical conditions corresponding to starless cores and protostellar envelopes. Methods: We developed a new rate coefficient set for the chemistry of the H3+ isotopologs, allowing for rotational excitation, using previously published state-to-state rate coefficients. These new so-called species-to-species rate coefficients are compared with previously-used ground-state-to-species rate coefficients by calculating chemical evolution in variable physical conditions using a pseudo-time-dependent chemical code. Results: We find that the new species-to-species model produces different results to the ground state-to-species model at high density and toward increasing temperatures (T> 10 K). The most prominent difference is that the species-to-species model predicts a lower H3+ deuteration degree at high density owing to an increase of the rate coefficients of endothermic reactions that tend to decrease deuteration. For example at 20 K, the ground-state-to-species model overestimates the abundance of H2D+ by a factor of about two, while the abundance of D3+ can differ by up to an order of magnitude between the models. The spin-state abundance ratios of the various H3+ isotopologs are also affected, and the new model better reproduces recent observations of the abundances of ortho and para H2D+ and D2H+. The main caveat is that the applicability regime of the new rate coefficients depends on the critical densities of the various rotational transitions which vary with the abundances of the species and the temperature in dense clouds. Conclusions: The difference in the abundances of the H3+ isotopologs predicted by the species-to-species and ground state-to-species models is negligible at 10 K corresponding to physical conditions in starless cores, but inclusion of the excited states is very important in studies

  20. Investigation of sensory profiles and hedonic drivers of emerging aquaculture fish species.

    PubMed

    Alexi, Niki; Byrne, Derek V; Nanou, Evangelia; Grigorakis, Kriton

    2018-02-01

    The aquaculture sector needs to increase the diversity fish species and their processed products to cover rising consumer demands. Candidates for this diversification have been identified to be meagre, greater amberjack, pikeperch and wreckfish. Yet scientific knowledge on their sensory profiles and consumer hedonic responses is scarce. The aim of the current study was to investigate these aspects, since they are essential for product development and market targeting. Species exhibited different sensory profiles with the exception of the odor/flavor profiles of meagre and greater amberjack, which were similar. Texture was more important than odor/flavor in explaining interspecies differences. Yet the hedonic responses were equally related to texture and odor/flavor. None of the species received negative hedonic scores. Both positive and negative hedonic drivers were identified within the odor/flavor and texture modalities. The distinct profiles of meagre, greater amberjack, pikeperch and wreckfish make these fish species valuable first materials for new product development and for covering markets with different sensory preferences. Differences in fish texture are more easily perceivable, yet small variations in fish odor/flavor can have a great impact on consumers' hedonic responses. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  1. Myrmecochores can target high-quality disperser ants: variation in elaiosome traits and ant preferences for myrmecochorous Euphorbiaceae in Brazilian Caatinga.

    PubMed

    Leal, Laura Carolina; Lima Neto, Mário Correia; de Oliveira, Antônio Fernando Morais; Andersen, Alan N; Leal, Inara R

    2014-02-01

    Recent evidence suggests that the traditional view of myrmecochory as a highly diffuse interaction between diaspores and a wide range of ant species attracted to their elaiosomes may not be correct. The effectiveness of dispersal varies markedly among ant species, and combined with differential attractiveness of diaspores due to elaiosome size and composition, this raises the potential for myrmecochorous plants to target ant species that offer the highest quality dispersal services. We ask the question: Do particular physical and chemical traits of elaiosomes result in disproportionate removal of Euphorbiaceae diaspores by high-quality disperser ants in Caatinga vegetation of north-eastern Brazil? We offered seeds of five euphorb species that varied in morphological and chemical traits of elaiosomes to seed-dispersing ants. High-quality seed-disperser ants (species of Dinoponera, Ectatomma and Camponotus) were identified as those that rapidly collected and transported diaspores to their nests, often over substantial distances, whereas low-quality disperser ants (primarily species of Pheidole and Solenopsis) typically fed on elaiosomes in situ, and only ever transported diaspores very short distances. Low-quality disperser ants were equally attracted to the elaiosomes of all study species. However, high-quality dispersers showed a strong preference for diaspores with the highest elaiosome mass (and especially proportional mass). As far as we are aware, this is the first study to identify a mechanism of diaspore selection by high-quality ant dispersers based on elaiosome traits under field conditions. Our findings suggest that myrmecochorous plants can preferentially target high-quality seed-disperser ants through the evolution of particular elaiosome traits.

  2. Conserving rare species can have high opportunity costs for common species.

    PubMed

    Neeson, Thomas M; Doran, Patrick J; Ferris, Michael C; Fitzpatrick, Kimberly B; Herbert, Matthew; Khoury, Mary; Moody, Allison T; Ross, Jared; Yacobson, Eugene; McIntyre, Peter B

    2018-04-13

    Conservation practitioners face difficult choices in apportioning limited resources between rare species (to ensure their existence) and common species (to ensure their abundance and ecosystem contributions). We quantified the opportunity costs of conserving rare species of migratory fishes in the context of removing dams and retrofitting road culverts across 1,883 tributaries of the North American Great Lakes. Our optimization models show that maximizing total habitat gains across species can be very efficient in terms of benefits achieved per dollar spent, but disproportionately benefits common species. Conservation approaches that target rare species, or that ensure some benefits for every species (i.e., complementarity) enable strategic allocation of resources among species but reduce aggregate habitat gains. Thus, small habitat gains for the rarest species necessarily come at the expense of more than 20 times as much habitat for common ones. These opportunity costs are likely to occur in many ecosystems because range limits and conservation costs often vary widely among species. Given that common species worldwide are declining more rapidly than rare ones within major taxa, our findings provide incentive for triage among multiple worthy conservation targets. © 2018 John Wiley & Sons Ltd.

  3. Targeting efflux pumps to overcome antifungal drug resistance

    PubMed Central

    Holmes, Ann R; Cardno, Tony S; Strouse, J Jacob; Ivnitski-Steele, Irena; Keniya, Mikhail V; Lackovic, Kurt; Monk, Brian C; Sklar, Larry A; Cannon, Richard D

    2016-01-01

    Resistance to antifungal drugs is an increasingly significant clinical problem. The most common antifungal resistance encountered is efflux pump-mediated resistance of Candida species to azole drugs. One approach to overcome this resistance is to inhibit the pumps and chemosensitize resistant strains to azole drugs. Drug discovery targeting fungal efflux pumps could thus result in the development of azole-enhancing combination therapy. Heterologous expression of fungal efflux pumps in Saccharomyces cerevisiae provides a versatile system for screening for pump inhibitors. Fungal efflux pumps transport a range of xenobiotics including fluorescent compounds. This enables the use of fluorescence-based detection, as well as growth inhibition assays, in screens to discover compounds targeting efflux-mediated antifungal drug resistance. A variety of medium- and high-throughput screens have been used to identify a number of chemical entities that inhibit fungal efflux pumps. PMID:27463566

  4. On the stabilizing role of species diffusion in chemical enhanced oil recovery

    NASA Astrophysics Data System (ADS)

    Daripa, Prabir; Gin, Craig

    2015-11-01

    In this talk, the speaker will discuss a problem on the stability analysis related to the effect of species diffusion on stabilization of fingering in a Hele-Shaw model of chemical enhanced oil recovery. The formulation of the problem is motivated by a specific design principle of the immiscible interfaces in the hope that this will lead to significant stabilization of interfacial instabilities, there by improving oil recovery in the context of porous media flow. Testing the merits of this hypothesis poses some challenges which will be discussed along with some numerical results based on current formulation of this problem. Several open problems in this context will be discussed. This work is currently under progress. Supported by the grant NPRP 08-777-1-141 from the Qatar National Research Fund (a member of The Qatar Foundation).

  5. Construction of the first compendium of chemical-genetic profiles in the fission yeast Schizosaccharomyces pombe and comparative compendium approach

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Han, Sangjo; Lee, Minho; Chang, Hyeshik

    Highlights: •The first compendium of chemical-genetic profiles form fission yeast was generated. •The first HTS of drug mode-of-action in fission yeast was performed. •The first comparative chemical genetic analysis between two yeasts was conducted. -- Abstract: Genome-wide chemical genetic profiles in Saccharomyces cerevisiae since the budding yeast deletion library construction have been successfully used to reveal unknown mode-of-actions of drugs. Here, we introduce comparative approach to infer drug target proteins more accurately using two compendiums of chemical-genetic profiles from the budding yeast S. cerevisiae and the fission yeast Schizosaccharomyces pombe. For the first time, we established DNA-chip based growth defectmore » measurement of genome-wide deletion strains of S. pombe, and then applied 47 drugs to the pooled heterozygous deletion strains to generate chemical-genetic profiles in S. pombe. In our approach, putative drug targets were inferred from strains hypersensitive to given drugs by analyzing S. pombe and S. cerevisiae compendiums. Notably, many evidences in the literature revealed that the inferred target genes of fungicide and bactericide identified by such comparative approach are in fact the direct targets. Furthermore, by filtering out the genes with no essentiality, the multi-drug sensitivity genes, and the genes with less eukaryotic conservation, we created a set of drug target gene candidates that are expected to be directly affected by a given drug in human cells. Our study demonstrated that it is highly beneficial to construct the multiple compendiums of chemical genetic profiles using many different species. The fission yeast chemical-genetic compendium is available at (http://pombe.kaist.ac.kr/compendium)« less

  6. Active coherent laser spectrometer for remote detection and identification of chemicals

    NASA Astrophysics Data System (ADS)

    MacLeod, Neil A.; Weidmann, Damien

    2012-10-01

    Currently, there exists a capability gap for the remote detection and identification of threat chemicals. We report here on the development of an Active Coherent Laser Spectrometer (ACLaS) operating in the thermal infrared and capable of multi-species stand-off detection of chemicals at sub ppm.m levels. A bench top prototype of the instrument has been developed using distributed feedback mid-infrared quantum cascade lasers as spectroscopic sources. The instrument provides active eye-safe illumination of a topographic target and subsequent spectroscopic analysis through optical heterodyne detection of the diffuse backscattered field. Chemical selectivity is provided by the combination of the narrow laser spectral bandwidth (typically < 2 MHz) and frequency tunability that allows the recording of the full absorption spectrum of any species within the instrument line of sight. Stand-off detection at distances up to 12 m has been demonstrated on light molecules such as H2O, CH4 and N2O. A physical model of the stand-off detection scenario including ro-vibrational molecular absorption parameters was used in conjunction with a fitting algorithm to retrieve quantitative mixing ratio information on multiple absorbers.

  7. Comparison of the physico-chemical and phytochemical characteristics of the oil of two Plukenetia species.

    PubMed

    Chirinos, Rosana; Pedreschi, Romina; Domínguez, Gilberto; Campos, David

    2015-04-15

    A physico-chemical and phytochemical characterisation of the oil of two rich sources of polyunsaturated fatty acids, tocopherols and phytosterols is presented for two close species of Plukenetia, endemic to the Amazon Region of Peru. Plukenetia huayllabambana presented approximately 9% more oil yield than Plukenetia volubilis. Fatty acid profiles were pretty similar for both species but P. huayllabambana presented a significantly higher content of α-linolenic acid than P. volubilis (51.3 and 45.6 g/100 g oil, respectively). Important contents of γ- and δ-tocopherol were evidenced in both oils (127.6 and 84.0 and, 93.3 and 47.5 mg/100 g oil, for P. volubilis and P. huayllabambana, respectively). β-Sitosterol was the most important and representative phytosterol in both oils (∼127 mg/100 g oil). The results of this study indicate P. huayllabambana as an important dietary source of health promoting phytochemicals. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Studies on the origin and transformation of selenium and its chemical species along the process of petroleum refining

    NASA Astrophysics Data System (ADS)

    Stivanin de Almeida, Cibele M.; Ribeiro, Anderson S.; Saint'Pierre, Tatiana D.; Miekeley, Norbert

    2009-06-01

    Inductively coupled plasma optical emission spectrometry and mass spectrometry (ICPMS), the latter hyphenated to flow injection hydride generation, electrothermal vaporization or ion chromatography, have been applied to the chemical characterization of crude oil, aqueous process stream samples and wastewaters from a petroleum refinery, in order to get information on the behavior of selenium and its chemical species along effluent generation and treatment. Multielemental characterization of these effluents by ICPMS revealed a complex composition of most of them, with high salinity and potential spectral and non-spectral interferents present. For this reason, a critical re-assessment of the analytical techniques for the determination of total selenium and its species was performed. Methane was employed as gas in dynamic reaction cell ICPMS and cell parameters were optimized for a simulated brine matrix and for diluted aqueous solutions to match the expected process and treated wastewaters samples. The signal-to-background ratios for 78Se and 80Se were used as criteria in optimization, the first isotope resulting in better detection limits for the simulated brine matrix ( 78Se: 0.07 μg L - 1 , 80Se: 0.31 μg L - 1 ). A large variability in the concentration of selenium (from < 10 μg kg - 1 up to 960 μg kg - 1 ) was observed in 16 of the most frequently processed crude oil samples in the refinery here investigated, which may explain the pronounced concentrations changes of this element measured in aqueous process stream and wastewater samples. Highest concentrations of total selenium were analyzed in samples from the hydrotreater (up to about 1800 μg L - 1 ). The predominance of selenocyanate (SeCN -) was observed in most of the wastewaters so far investigated, but also other species were detected with retention times different from Se(IV), Se(VI) and SeCN -. Colloidal selenium (Se 0) was the only Se-species observed in samples from the atmospheric distillation

  9. How to tackle chemical communication? Relative proportions versus semiquantitative determination of compounds in lizard chemical secretions.

    PubMed

    García-Roa, Roberto; Sáiz, Jorge; Gómara, Belén; López, Pilar; Martín, José

    2018-02-01

    Knowledge about chemical communication in some vertebrates is still relatively limited. Squamates are a glaring example of this, even when recent evidences indicate that scents are involved in social and sexual interactions. In lizards, where our understanding of chemical communication has considerably progressed in the last few years, many questions about chemical interactions remain unanswered. A potential reason for this is the inherent complexity and technical limitations that some methodologies embody when analyzing the compounds used to convey information. We provide here a straightforward procedure to analyze lizard chemical secretions based on gas chromatography coupled to mass spectrometry that uses an internal standard for the semiquantification of compounds. We compare the results of this method with those obtained by the traditional procedure of calculating relative proportions of compounds. For such purpose, we designed two experiments to investigate if these procedures allowed revealing changes in chemical secretions 1) when lizards received previously a vitamin dietary supplementation or 2) when the chemical secretions were exposed to high temperatures. Our results show that the procedure based on relative proportions is useful to describe the overall chemical profile, or changes in it, at population or species levels. On the other hand, the use of the procedure based on semiquantitative determination can be applied when the target of study is the variation in one or more particular compounds of the sample, as it has proved more accurate detecting quantitative variations in the secretions. This method would reveal new aspects produced by, for example, the effects of different physiological and climatic factors that the traditional method does not show.

  10. An iterative and targeted sampling design informed by habitat suitability models for detecting focal plant species over extensive areas.

    PubMed

    Wang, Ophelia; Zachmann, Luke J; Sesnie, Steven E; Olsson, Aaryn D; Dickson, Brett G

    2014-01-01

    Prioritizing areas for management of non-native invasive plants is critical, as invasive plants can negatively impact plant community structure. Extensive and multi-jurisdictional inventories are essential to prioritize actions aimed at mitigating the impact of invasions and changes in disturbance regimes. However, previous work devoted little effort to devising sampling methods sufficient to assess the scope of multi-jurisdictional invasion over extensive areas. Here we describe a large-scale sampling design that used species occurrence data, habitat suitability models, and iterative and targeted sampling efforts to sample five species and satisfy two key management objectives: 1) detecting non-native invasive plants across previously unsampled gradients, and 2) characterizing the distribution of non-native invasive plants at landscape to regional scales. Habitat suitability models of five species were based on occurrence records and predictor variables derived from topography, precipitation, and remotely sensed data. We stratified and established field sampling locations according to predicted habitat suitability and phenological, substrate, and logistical constraints. Across previously unvisited areas, we detected at least one of our focal species on 77% of plots. In turn, we used detections from 2011 to improve habitat suitability models and sampling efforts in 2012, as well as additional spatial constraints to increase detections. These modifications resulted in a 96% detection rate at plots. The range of habitat suitability values that identified highly and less suitable habitats and their environmental conditions corresponded to field detections with mixed levels of agreement. Our study demonstrated that an iterative and targeted sampling framework can address sampling bias, reduce time costs, and increase detections. Other studies can extend the sampling framework to develop methods in other ecosystems to provide detection data. The sampling methods

  11. An Iterative and Targeted Sampling Design Informed by Habitat Suitability Models for Detecting Focal Plant Species over Extensive Areas

    PubMed Central

    Wang, Ophelia; Zachmann, Luke J.; Sesnie, Steven E.; Olsson, Aaryn D.; Dickson, Brett G.

    2014-01-01

    Prioritizing areas for management of non-native invasive plants is critical, as invasive plants can negatively impact plant community structure. Extensive and multi-jurisdictional inventories are essential to prioritize actions aimed at mitigating the impact of invasions and changes in disturbance regimes. However, previous work devoted little effort to devising sampling methods sufficient to assess the scope of multi-jurisdictional invasion over extensive areas. Here we describe a large-scale sampling design that used species occurrence data, habitat suitability models, and iterative and targeted sampling efforts to sample five species and satisfy two key management objectives: 1) detecting non-native invasive plants across previously unsampled gradients, and 2) characterizing the distribution of non-native invasive plants at landscape to regional scales. Habitat suitability models of five species were based on occurrence records and predictor variables derived from topography, precipitation, and remotely sensed data. We stratified and established field sampling locations according to predicted habitat suitability and phenological, substrate, and logistical constraints. Across previously unvisited areas, we detected at least one of our focal species on 77% of plots. In turn, we used detections from 2011 to improve habitat suitability models and sampling efforts in 2012, as well as additional spatial constraints to increase detections. These modifications resulted in a 96% detection rate at plots. The range of habitat suitability values that identified highly and less suitable habitats and their environmental conditions corresponded to field detections with mixed levels of agreement. Our study demonstrated that an iterative and targeted sampling framework can address sampling bias, reduce time costs, and increase detections. Other studies can extend the sampling framework to develop methods in other ecosystems to provide detection data. The sampling methods

  12. Non-target effects on songbirds from habitat manipulation for Greater Sage-Grouse: Implications for the umbrella species concept

    USGS Publications Warehouse

    Carlisle, Jason D.; Chalfoun, Anna D.; Smith, Kurt T.; Beck, Jeffery L.

    2018-01-01

    The “umbrella species” concept is a conservation strategy in which creating and managing reserve areas to meet the needs of one species is thought to benefit other species indirectly. Broad-scale habitat protections on behalf of an umbrella species are assumed to benefit co-occurring taxa, but targeted management actions to improve local habitat suitability for the umbrella species may produce unintended effects on other species. Our objective was to quantify the effects of a common habitat treatment (mowing of big sagebrush [Artemisia tridentata]) intended to benefit a high-profile umbrella species (Greater Sage-Grouse [Centrocercus urophasianus]) on 3 sympatric songbird species of concern. We used a before–after control-impact experimental design spanning 3 yr in Wyoming, USA, to quantify the effect of mowing on the abundance, nest-site selection, nestling condition, and nest survival of 2 sagebrush-obligate songbirds (Brewer's Sparrow [Spizella breweri] and Sage Thrasher [Oreoscoptes montanus]) and one open-habitat generalist songbird (Vesper Sparrow [Pooecetes gramineus]). Mowing was associated with lower abundance of Brewer's Sparrows and Sage Thrashers but higher abundance of Vesper Sparrows. We found no Brewer's Sparrows or Sage Thrashers nesting in the mowed footprint posttreatment, which suggests complete loss of nesting habitat for these species. Mowing was associated with higher nestling condition and nest survival for Vesper Sparrows but not for the sagebrush-obligate species. Management prescriptions that remove woody biomass within a mosaic of intact habitat may be tolerated by sagebrush-obligate songbirds but are likely more beneficial for open-habitat generalist species. By definition, umbrella species conservation entails habitat protections at broad spatial scales. We caution that habitat manipulations to benefit Greater Sage-Grouse could negatively affect nontarget species of conservation concern if implemented across large spatial extents.

  13. Combined chemical and physical transformation method with RbCl and sepiolite for the transformation of various bacterial species.

    PubMed

    Ren, Jun; Lee, Haram; Yoo, Seung Min; Yu, Myeong-Sang; Park, Hansoo; Na, Dokyun

    2017-04-01

    DNA transformation that delivers plasmid DNAs into bacterial cells is fundamental in genetic manipulation to engineer and study bacteria. Developed transformation methods to date are optimized to specific bacterial species for high efficiency. Thus, there is always a demand for simple and species-independent transformation methods. We herein describe the development of a chemico-physical transformation method that combines a rubidium chloride (RbCl)-based chemical method and sepiolite-based physical method, and report its use for the simple and efficient delivery of DNA into various bacterial species. Using this method, the best transformation efficiency for Escherichia coli DH5α was 4.3×10 6 CFU/μg of pUC19 plasmid, which is higher than or comparable to the reported transformation efficiencies to date. This method also allowed the introduction of plasmid DNAs into Bacillus subtilis (5.7×10 3 CFU/μg of pSEVA3b67Rb), Bacillus megaterium (2.5×10 3 CFU/μg of pSPAsp-hp), Lactococcus lactis subsp. lactis (1.0×10 2 CFU/μg of pTRKH3-ermGFP), and Lactococcus lactis subsp. cremoris (2.2×10 2 CFU/μg of pMSP3535VA). Remarkably, even when the conventional chemical and physical methods failed to generate transformed cells in Bacillus sp. and Enterococcus faecalis, E. malodoratus and E. mundtii, our combined method showed a significant transformation efficiency (2.4×10 4 , 4.5×10 2 , 2×10 1 , and 0.5×10 1 CFU/μg of plasmid DNA). Based on our results, we anticipate that our simple and efficient transformation method should prove usefulness for introducing DNA into various bacterial species without complicated optimization of parameters affecting DNA entry into the cell. Copyright © 2017. Published by Elsevier B.V.

  14. Identifying Metabolically Active Chemicals Using a Consensus ...

    EPA Pesticide Factsheets

    Traditional toxicity testing provides insight into the mechanisms underlying toxicological responses but requires a high investment in a large number of resources. The new paradigm of testing approaches involves rapid screening studies able to evaluate thousands of chemicals across hundreds of biological targets through use of in vitro assays. Endocrine disrupting chemicals (EDCs) are of concern due to their ability to alter neurodevelopment, behavior, and reproductive success of humans and other species. A recent integrated computational model examined results across 18 ER-related assays in the ToxCast in vitro screening program to eliminate chemicals that produce a false signal by possibly interfering with the technological attributes of an individual assay. However, in vitro assays can also lead to false negatives when the complex metabolic processes that render a chemical bioactive in a living system might be unable to be replicated in an in vitro environment. In the current study, the influence of metabolism was examined for over 1,400 chemicals considered inactive using the integrated computational model. Over 2,000 first-generation and over 4,000 second-generation metabolites were generated for the inactive chemicals using in silico techniques. Next, a consensus model comprised of individual structure activity relationship (SAR) models was used to predict ER-binding activity for each of the metabolites. Binding activity was predicted for 8-10% of the meta

  15. Construction Costs and Physico-chemical Properties of the Assimilatory Organs of Nepenthes Species in Northern Borneo

    PubMed Central

    Osunkoya, Olusegun O.; Daud, Siti Dayanawati; Di-Giusto, Bruno; Wimmer, Franz L.; Holige, Thippeswamy M.

    2007-01-01

    Background and Aims Species of the Nepenthaceae family are under-represented in studies of leaf traits and the consequent view of mineral nutrition and limitation in carnivorous plants. This study is aimed to complement existing data on leaf traits of carnivorous plants. Methods Physico-chemical properties, including construction costs (CC), of the assimilatory organs (leaf and pitcher) of a guild of lowland Nepenthes species inhabiting heath and/or peat swamp forests of Brunei, Northern Borneo were determined. Key Results Stoichiometry analyses indicate that Nepenthes species are nitrogen limited. Most traits vary appreciably across species, but greater variations exist between the assimilatory organs. Organ mass per unit area, dry matter tissue concentration (density), nitrogen (N), phosphorus (P), carbon, heat of combustion (Hc) and CC values were higher in the leaf relative to the pitcher, while organ thickness, potassium (K) and ash showed the opposite trend. Cross-species correlations indicate that joint rather than individual consideration of the leaf and the pitcher give better predictive relationships between variables, signalling tight coupling and functional interdependence of the two assimilatory organs. Across species, mass-based CC did not vary with N or P, but increases significantly with tissue density, carbon and Hc, and decreases with K and ash contents. Area-based CC gave the same trends (though weaker in strength) in addition to a significant positive correlation with tissue mass per unit area. Conclusions The lower CC value for the pitcher is in agreement with the concept of low marginal cost for carnivory relative to conventional autotrophy. The poor explanatory power of N, P or N : P ratio with CC suggests that factors other than production of expensive photosynthetic machinery (which calls for a high N input), including concentrations of lignin, wax/lipids or osmoregulatory ions like K+, may give a better explanation of the CC variation

  16. A Framework for Identifying Selective Chemical Applications for IPM in Dryland Agriculture

    PubMed Central

    Umina, Paul A.; Jenkins, Sommer; McColl, Stuart; Arthur, Aston; Hoffmann, Ary A.

    2015-01-01

    Shifts to Integrated Pest Management (IPM) in agriculture are assisted by the identification of chemical applications that provide effective control of pests relative to broad-spectrum pesticides but have fewer negative effects on natural enemy (beneficial) groups that assist in pest control. Here, we outline a framework for identifying such applications and apply this framework to field trials involving the crop establishment phase of Australian dryland cropping systems. Several chemicals, which are not presently available to farmers in Australia, were identified as providing moderate levels of pest control and seedling protection, with the potential to be less harmful to beneficial groups including predatory mites, predatory beetles and ants. This framework highlights the challenges involved in chemically controlling pests while maintaining non-target populations when pest species are present at damaging levels. PMID:26694469

  17. Epidemiological findings of major chemical attacks in the Syrian war are consistent with civilian targeting: a short report.

    PubMed

    Rodriguez-Llanes, Jose M; Guha-Sapir, Debarati; Schlüter, Benjamin-Samuel; Hicks, Madelyn Hsiao-Rei

    2018-01-01

    Evidence of use of toxic gas chemical weapons in the Syrian war has been reported by governmental and non-governmental international organizations since the war started in March 2011. To date, the profiles of victims of the largest chemical attacks in Syria remain unknown. In this study, we used descriptive epidemiological analysis to describe demographic characteristics of victims of the largest chemical weapons attacks in the Syrian war. We analysed conflict-related, direct deaths from chemical weapons recorded in non-government-controlled areas by the Violation Documentation Center, occurring from March 18, 2011 to April 10, 2017, with complete information on the victim's date and place of death, cause and demographic group. 'Major' chemical weapons events were defined as events causing ten or more direct deaths. As of April 10, 2017, a total of 1206 direct deaths meeting inclusion criteria were recorded in the dataset from all chemical weapons attacks regardless of size. Five major chemical weapons attacks caused 1084 of these documented deaths. Civilians comprised the majority ( n  = 1058, 97.6%) of direct deaths from major chemical weapons attacks in Syria and combatants comprised a minority of 2.4% ( n  = 26). In the first three major chemical weapons attacks, which occurred in 2013, children comprised 13%-14% of direct deaths, ranging in numbers from 2 deaths among 14 to 117 deaths among 923. Children comprised higher proportions of direct deaths in later major chemical weapons attacks, forming 21% ( n  = 7) of 33 deaths in the 2016 major attack and 34.8% ( n  = 32) of 92 deaths in the 2017 major attack. Our finding of an extreme disparity in direct deaths from major chemical weapons attacks in Syria, with 97.6% of victims being civilians and only 2.4% being combatants provides evidence that major chemical weapons attacks were indiscriminate or targeted civilians directly; both violations of International Humanitarian Law (IHL). Identifying and

  18. Setting conservation targets for sandy beach ecosystems

    NASA Astrophysics Data System (ADS)

    Harris, Linda; Nel, Ronel; Holness, Stephen; Sink, Kerry; Schoeman, David

    2014-10-01

    Representative and adequate reserve networks are key to conserving biodiversity. This begs the question, how much of which features need to be placed in protected areas? Setting specifically-derived conservation targets for most ecosystems is common practice; however, this has never been done for sandy beaches. The aims of this paper, therefore, are to propose a methodology for setting conservation targets for sandy beach ecosystems; and to pilot the proposed method using data describing biodiversity patterns and processes from microtidal beaches in South Africa. First, a classification scheme of valued features of beaches is constructed, including: biodiversity features; unique features; and important processes. Second, methodologies for setting targets for each feature under different data-availability scenarios are described. From this framework, targets are set for features characteristic of microtidal beaches in South Africa, as follows. 1) Targets for dune vegetation types were adopted from a previous assessment, and ranged 19-100%. 2) Targets for beach morphodynamic types (habitats) were set using species-area relationships (SARs). These SARs were derived from species richness data from 142 sampling events around the South African coast (extrapolated to total theoretical species richness estimates using previously-established species-accumulation curve relationships), plotted against the area of the beach (calculated from Google Earth imagery). The species-accumulation factor (z) was 0.22, suggesting a baseline habitat target of 27% is required to protect 75% of the species. This baseline target was modified by heuristic principles, based on habitat rarity and threat status, with final values ranging 27-40%. 3) Species targets were fixed at 20%, modified using heuristic principles based on endemism, threat status, and whether or not beaches play an important role in the species' life history, with targets ranging 20-100%. 4) Targets for processes and 5

  19. Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing

    PubMed Central

    Dasgupta, Modhumita Ghosh; Dharanishanthi, Veeramuthu; Agarwal, Ishangi; Krutovsky, Konstantin V.

    2015-01-01

    The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus. PMID:25602379

  20. Small Molecule Signaling Agents: The Integrated Chemistry and Biochemistry of Nitrogen Oxides, Oxides of Carbon, Dioxygen, Hydrogen Sulfide, and Their Derived Species

    PubMed Central

    Fukuto, Jon M.; Carrington, Samantha J.; Tantillo, Dean J.; Harrison, Jason G.; Ignarro, Louis J.; Freeman, Bruce A.; Chen, Andrew; Wink, David A.

    2014-01-01

    Several small molecule species formally known primarily as toxic gases have, over the past 20 years, been shown to be endogenously generated signaling molecules. The biological signaling associated with the small molecules NO, CO, H2S (and the nonendogenously generated O2), and their derived species have become a topic of extreme interest. It has become increasingly clear that these small molecule signaling agents form an integrated signaling web that affects/regulates numerous physiological processes. The chemical interactions between these species and each other or biological targets is an important factor in their roles as signaling agents. Thus, a fundamental understanding of the chemistry of these molecules is essential to understanding their biological/physiological utility. This review focuses on this chemistry and attempts to establish the chemical basis for their signaling functions. PMID:22263838

  1. CHEMICAL RISKS TO THREATENED AND ENDANGERED FISH SPECIES AT CONCENTRATIONS BELOW WATER QUALITY CRITERIA: IS IT FEASIBLE TO ENSURE PROTECTION OF INDIVIDUALS

    EPA Science Inventory

    The USGS Laboratory in Columbia, Missouri has evaluated the acute sensitivities of 17 threatened and endangered fish species (including three salmonids), to five different chemicals (carbaryl, copper, 4-nonylphenol, pentachlorophenol, and permethrin). The results of these studie...

  2. Chemical composition of various Ephedra species

    PubMed Central

    Ibragic, Saida; Sofić, Emin

    2015-01-01

    The medicinal significance of Ephedra is based on the sympathomimetic properties of ephedrine (E) alkaloids. Pharmacological effects depend on the phytocomposition of individual Ephedra species. The aim of this study was to measure the total alkaloids content (TAC), total phenolics content (TPC), and total flavonoids content (TFC) and determine their relationship in dry herb of Ephedra major, Ephedra distachya subsp. helvetica, Ephedra monosperma, Ephedra fragilis, Ephedra foeminea, Ephedra alata, Ephedra altissima and Ephedra foliata. Nowadays, medicinal use of Ephedrae herba is limited, but the abuse of its psychostimulants is rising. In this study, TAC, TPC and TFC were determined using spectrophotometric methods. For the first time, ultra-performance liquid chromatography with ultraviolet detection (UPLC-UV) was used for separation and quantification of E-type alkaloids of various Ephedra species. The highest TPC and TFC were found in E. alata (53.3 ± 0.1 mg Gallic acid equivalents/g dry weight, 2.8 mg quercetin equivalents/g dry weight, respectively). The total content of E and pseudoephedrine determined by UPLC-UV varied between 20.8 mg/g dry weight (E. distachya subsp. helvetica) and 34.7 mg/g dry weight (E. monosperma). The variable content and ratio between secondary metabolites determined in different Ephedra species reflects their metabolic activities. Utilization of UPLC-UV unveiled that this technique is sensitive, selective, and useful for separation and quantification of different alkaloids in complex biological matrixes. The limit of detection was 5 ng. Application of UPLC-UV can be recommended in quick analyses of E-type alkaloids in forensic medicine and quality control of pharmaceutical preparations. PMID:26295290

  3. BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemicals.

    PubMed

    Kim, Minsuk; Sun, Gwanggyu; Lee, Dong-Yup; Kim, Byung-Gee

    2017-01-01

    Modulation of regulatory circuits governing the metabolic processes is a crucial step for developing microbial cell factories. Despite the prevalence of in silico strain design algorithms, most of them are not capable of predicting required modifications in regulatory networks. Although a few algorithms may predict relevant targets for transcriptional regulator (TR) manipulations, they have limited reliability and applicability due to their high dependency on the availability of integrated metabolic/regulatory models. We present BeReTa (Beneficial Regulator Targeting), a new algorithm for prioritization of TR manipulation targets, which makes use of unintegrated network models. BeReTa identifies TR manipulation targets by evaluating regulatory strengths of interactions and beneficial effects of reactions, and subsequently assigning beneficial scores for the TRs. We demonstrate that BeReTa can predict both known and novel TR manipulation targets for enhanced production of various chemicals in Escherichia coli Furthermore, through a case study of antibiotics production in Streptomyces coelicolor, we successfully demonstrate its wide applicability to even less-studied organisms. To the best of our knowledge, BeReTa is the first strain design algorithm exclusively designed for predicting TR manipulation targets. MATLAB code is available at https://github.com/kms1041/BeReTa (github). byungkim@snu.ac.krSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Chemical sensors

    DOEpatents

    Lowell, Jr., James R.; Edlund, David J.; Friesen, Dwayne T.; Rayfield, George W.

    1991-01-01

    Sensors responsive to small changes in the concentration of chemical species are disclosed, comprising (a) a mechanochemically responsive polymeric film capable of expansion or contraction in response to a change in its chemical environment, operatively coupled to (b) a transducer capable of directly converting said expansion or contraction to a measurable electrical response.

  5. Identification of Direct Protein Targets of Small Molecules

    PubMed Central

    2010-01-01

    Small-molecule target identification is a vital and daunting task for the chemical biology community as well as for researchers interested in applying the power of chemical genetics to impact biology and medicine. To overcome this “target ID” bottleneck, new technologies are being developed that analyze protein–drug interactions, such as drug affinity responsive target stability (DARTS), which aims to discover the direct binding targets (and off targets) of small molecules on a proteome scale without requiring chemical modification of the compound. Here, we review the DARTS method, discuss why it works, and provide new perspectives for future development in this area. PMID:21077692

  6. Assessing Plausibility of Tentative Chemical Identifications from Suspect Screening Analyses via Chemical Function

    EPA Science Inventory

    Suspect screening (SSA) and non-targeted analysis (NTA) have become increasingly useful methods for identifying chemicals in indoor environments, which is where many chemical exposures occur. However, the tentative chemical identifications from these analyses must be confirmed. T...

  7. Patterns of chemical diversity in the marine ascidian Phallusia spp.: anti-tumor activity and metabolic pathway inhibiting steroid biosynthesis.

    PubMed

    Palanisamy, Satheesh Kumar; Arumugam, Velusamy; Peter, Magesh D; Sundaresan, Umamaheswari

    2018-05-01

    The complex nature of marine biodiversity is partially responsible for the lack of studies in Indian ascidian species, which often target a small number of novel biomolecules. We performed untargeted metabolomics using gas chromatography-mass spectrometry (GC-MS) in two invasive ascidian species to investigate the inter-specific chemical diversity of Phallusia nigra and P. arabica in search of drug-like properties and metabolic pathways. The chemical profiling of individual ascidian species was obtained using GC-MS, and the metabolites were determined by searching in NIST library and literature data. The principal component analysis of GC-MS mass spectral variables showed a clear discrimination of these two ascidian species based on the chemical composition and taxonomy. The metabolites, lipids, macrolides, and steroids contributed strongly to the discrimination of these two species. Results of this study confirmed that GC-MS-based chemical profiling could be utilized as a tool for chemotaxonomic classification of ascidian species. The extract of P. nigra showed promising anti-tumor activity against HT29 colon cancer 35 µM and MCF7-breast cancer (34.76 µM) cells compared to P. arabica . Of the more than 70 metabolites measured, 18 metabolites that mapped various pathways linked to three metabolic pathways being impacted and altered in steroid biosynthesis, primary bile acid biosynthesis, and steroid hormone biosynthesis were observed to have changed significantly ( p  > 0.004, FDR < 0.01). Also, higher expression of this pathway was associated with more significant cytotoxicity in breast and colon carcinoma cells.

  8. Method And Apparatus For Detecting Chemical Binding

    DOEpatents

    Warner, Benjamin P.; Havrilla, George J.; Miller, Thomasin C.; Wells, Cyndi A.

    2005-02-22

    The method for screening binding between a target binder and potential pharmaceutical chemicals involves sending a solution (preferably an aqueous solution) of the target binder through a conduit to a size exclusion filter, the target binder being too large to pass through the size exclusion filter, and then sending a solution of one or more potential pharmaceutical chemicals (preferably an aqueous solution) through the same conduit to the size exclusion filter after target binder has collected on the filter. The potential pharmaceutical chemicals are small enough to pass through the filter. Afterwards, x-rays are sent from an x-ray source to the size exclusion filter, and if the potential pharmaceutical chemicals form a complex with the target binder, the complex produces an x-ray fluorescence signal having an intensity that indicates that a complex has formed.

  9. Method and apparatus for detecting chemical binding

    DOEpatents

    Warner, Benjamin P [Los Alamos, NM; Havrilla, George J [Los Alamos, NM; Miller, Thomasin C [Los Alamos, NM; Wells, Cyndi A [Los Alamos, NM

    2007-07-10

    The method for screening binding between a target binder and potential pharmaceutical chemicals involves sending a solution (preferably an aqueous solution) of the target binder through a conduit to a size exclusion filter, the target binder being too large to pass through the size exclusion filter, and then sending a solution of one or more potential pharmaceutical chemicals (preferably an aqueous solution) through the same conduit to the size exclusion filter after target binder has collected on the filter. The potential pharmaceutical chemicals are small enough to pass through the filter. Afterwards, x-rays are sent from an x-ray source to the size exclusion filter, and if the potential pharmaceutical chemicals form a complex with the target binder, the complex produces an x-ray fluorescence signal having an intensity that indicates that a complex has formed.

  10. Understanding Release from Actinide Targets -- Recent Results from RIB Development

    NASA Astrophysics Data System (ADS)

    Kronenberg, Andreas; Carter, H. K.; Spejewski, E. H.; Stracener, D. W.

    2006-10-01

    Development of ion beams of short-lived isotopes is crucial for modern nuclear structure and nuclear astrophysics. The Holifield Radioactive Ion Beam Facility at Oak Ridge National Laboratory uses the ISOL (Isotope Separation Online) technique to provide radioactive ion beams. So far, uranium carbide has been used as a target to produce neutron-rich fission fragments. Thermodynamic calculations indicate the possibility of in-situ chemical side band formations of volatile species of refractory metals, such as V and Re. These elements release out of oxide targets after production in a nuclear reaction, and can occur only through in-situ formation of their volatile oxide. These have been confirmed experimentally. The results from recent, more detailed investigations of ThO2, UB4 and other actinide targets as well as conclusions from systematic studies will be presented. This research was sponsored by the NNSA under Stewardship Science Academic Alliance program through DOE Cooperative Agreement # DE-FC03-3NA00143.

  11. Phylogenetic and Chemical Diversity of Three Chemotypes of Bloom-Forming Lyngbya Species (Cyanobacteria: Oscillatoriales) from Reefs of Southeastern Florida▿

    PubMed Central

    Sharp, Koty; Arthur, Karen E.; Gu, Liangcai; Ross, Cliff; Harrison, Genelle; Gunasekera, Sarath P.; Meickle, Theresa; Matthew, Susan; Luesch, Hendrik; Thacker, Robert W.; Sherman, David H.; Paul, Valerie J.

    2009-01-01

    The cyanobacterial genus Lyngbya includes free-living, benthic, filamentous cyanobacteria that form periodic nuisance blooms in lagoons, reefs, and estuaries. Lyngbya spp. are prolific producers of biologically active compounds that deter grazers and help blooms persist in the marine environment. Here, our investigations reveal the presence of three distinct Lyngbya species on nearshore reefs in Broward County, FL, sampled in 2006 and 2007. With a combination of morphological measurements, molecular biology techniques, and natural products chemistry, we associated these three Lyngbya species with three distinct Lyngbya chemotypes. One species, identified as Lyngbya cf. confervoides via morphological measurements and 16S rRNA gene sequencing, produces a diverse array of bioactive peptides and depsipeptides. Our results indicate that the other two Lyngbya species produce either microcolins A and B or curacin D and dragonamides C and D. Results from screening for the biosynthetic capacity for curacin production among the three Lyngbya chemotypes in this study correlated that capacity with the presence of curacin D. Our work on these bloom-forming Lyngbya species emphasizes the significant phylogenetic and chemical diversity of the marine cyanobacteria on southern Florida reefs and identifies some of the genetic components of those differences. PMID:19270119

  12. RNA-Targeted Therapeutics.

    PubMed

    Crooke, Stanley T; Witztum, Joseph L; Bennett, C Frank; Baker, Brenda F

    2018-04-03

    RNA-targeted therapies represent a platform for drug discovery involving chemically modified oligonucleotides, a wide range of cellular RNAs, and a novel target-binding motif, Watson-Crick base pairing. Numerous hurdles considered by many to be impassable have been overcome. Today, four RNA-targeted therapies are approved for commercial use for indications as diverse as Spinal Muscular Atrophy (SMA) and reduction of low-density lipoprotein cholesterol (LDL-C) and by routes of administration including subcutaneous, intravitreal, and intrathecal delivery. The technology is efficient and supports approaching "undruggable" targets. Three additional agents are progressing through registration, and more are in clinical development, representing several chemical and structural classes. Moreover, progress in understanding the molecular mechanisms by which these drugs work has led to steadily better clinical performance and a wide range of mechanisms that may be exploited for therapeutic purposes. Here we summarize the progress, future challenges, and opportunities for this drug discovery platform. Copyright © 2018 Elsevier Inc. All rights reserved.

  13. Airborne mapping of chemical plumes in the aftermath of Hurricanes Katrina and Rita

    NASA Astrophysics Data System (ADS)

    Lewis, Paul E.; Thomas, Mark J.; Kroutil, Robert T.; Combs, Roger; Cummings, Alan S.; Miller, Dave; Curry, Tim; Shen, Sylvia S.

    2006-05-01

    Infrared airborne spectral measurements were collected over the Gulf Coast area during the aftermath of Hurricanes Katrina and Rita. These measurements allowed surveillance for potentially hazardous chemical vapor releases from industrial facilities caused by storm damage. Data was collected with a mid-longwave infrared multispectral imager and a hyperspectral Fourier transform infrared spectrometer operating in a low altitude aircraft. Signal processing allowed detection and identification of targeted spectral signatures in the presence of interferents, atmospheric contributions, and thermal clutter. Results confirmed the presence of a number of chemical vapors. All detection results were immediately passed along to emergency first responders on the ground. The chemical identification, location, and vapor species concentration information were used by the emergency response ground teams for identification of critical plume releases and subsequent mitigation.

  14. Chemical sensors

    DOEpatents

    Lowell, J.R. Jr.; Edlund, D.J.; Friesen, D.T.; Rayfield, G.W.

    1991-07-02

    Sensors responsive to small changes in the concentration of chemical species are disclosed. The sensors comprise a mechanochemically responsive polymeric film capable of expansion or contraction in response to a change in its chemical environment. They are operatively coupled to a transducer capable of directly converting the expansion or contraction to a measurable electrical response. 9 figures.

  15. Preparation of Ti species coating hydrotalcite by chemical vapor deposition for photodegradation of azo dye.

    PubMed

    Xiao, Gaofei; Zeng, HongYan; Xu, Sheng; Chen, ChaoRong; Zhao, Quan; Liu, XiaoJun

    2017-10-01

    TiO 2 in anatase crystal phase is a very effective catalyst in the photocatalytic oxidation of organic compounds in water. To improve its photocatalytic activity, the Ti-coating MgAl hydrotalcite (Ti-MgAl-LDH) was prepared by chemical vapor deposition (CVD) method. Response surface method (RSM) was employed to evaluate the effect of Ti species coating parameters on the photocatalytic activity, which was found to be affected by the furnace temperature, N 2 flow rate and influx time of precursor gas. Application of RSM successfully increased the photocatalytic efficiency of the Ti-MgAl-LDH in methylene blue photodegradation under UV irradiation, leading to improved economy of the process. According to the results from X-ray diffraction, scanning electron microscopy, Brunner-Emmet-Teller and Barrett-Joyner-Hallender, thermogravimetric and differential thermal analysis, UV-vis diffuse reflectance spectra analyses, the Ti species (TiO 2 or/and Ti 4+ ) were successfully coated on the MgAl-LDH matrix. The Ti species on the surface of the Ti-MgAl-LDH lead to a higher photocatalytic performance than commercial TiO 2 -P25. The results suggested that CVD method provided a new approach for the industrial preparation of Ti-coating MgAl-LDH material with good photocatalytic performances. Copyright © 2017. Published by Elsevier B.V.

  16. Chemically-functionalized microcantilevers for detection of chemical, biological and explosive material

    DOEpatents

    Pinnaduwage, Lal A [Knoxville, TN; Thundat, Thomas G [Knoxville, TN; Brown, Gilbert M [Knoxville, TN; Hawk, John Eric [Olive Branch, MS; Boiadjiev, Vassil I [Knoxville, TN

    2007-04-24

    A chemically functionalized cantilever system has a cantilever coated on one side thereof with a reagent or biological species which binds to an analyte. The system is of particular value when the analyte is a toxic chemical biological warfare agent or an explosive.

  17. DNA-based species detection capabilities using laser transmission spectroscopy

    PubMed Central

    Mahon, A. R.; Barnes, M. A.; Li, F.; Egan, S. P.; Tanner, C. E.; Ruggiero, S. T.; Feder, J. L.; Lodge, D. M.

    2013-01-01

    Early detection of invasive species is critical for effective biocontrol to mitigate potential ecological and economic damage. Laser transmission spectroscopy (LTS) is a powerful solution offering real-time, DNA-based species detection in the field. LTS can measure the size, shape and number of nanoparticles in a solution and was used here to detect size shifts resulting from hybridization of the polymerase chain reaction product to nanoparticles functionalized with species-specific oligonucleotide probes or with the species-specific oligonucleotide probes alone. We carried out a series of DNA detection experiments using the invasive freshwater quagga mussel (Dreissena bugensis) to evaluate the capability of the LTS platform for invasive species detection. Specifically, we tested LTS sensitivity to (i) DNA concentrations of a single target species, (ii) the presence of a target species within a mixed sample of other closely related species, (iii) species-specific functionalized nanoparticles versus species-specific oligonucleotide probes alone, and (iv) amplified DNA fragments versus unamplified genomic DNA. We demonstrate that LTS is a highly sensitive technique for rapid target species detection, with detection limits in the picomolar range, capable of successful identification in multispecies samples containing target and non-target species DNA. These results indicate that the LTS DNA detection platform will be useful for field application of target species. Additionally, we find that LTS detection is effective with species-specific oligonucleotide tags alone or when they are attached to polystyrene nanobeads and with both amplified and unamplified DNA, indicating that the technique may also have versatility for broader applications. PMID:23015524

  18. Evaluation of chemical and biological agents for control of Phytophthora species on intact plants or detached leaves of rhododendron and lilac

    Treesearch

    R.G. Linderman; E.A. Davis

    2006-01-01

    The recent incidence of Ramorum blight, caused by Phytophthora ramorum, on many nursery crops has focused attention on improving management strategies against Phytophthora diseases in nurseries. We evaluated several chemical agents that target Oomycete pathogens for their capacity to inhibit infection of rhododendron or lilac...

  19. Do water quality criteria based on nonnative species provide appropriate protection for native species?

    PubMed

    Jin, Xiaowei; Wang, Zijian; Wang, Yeyao; Lv, Yibing; Rao, Kaifeng; Jin, Wei; Giesy, John P; Leung, Kenneth M Y

    2015-08-01

    The potential use of toxicity data for nonnative species to derive water quality criteria is controversial because it is sometimes questioned whether criteria based on species from one geographical region provide appropriate protection for species in a different region. However, this is an important concept for the development of Chinese water quality criteria or standards. Data were assembled on 38 chemicals for which values were available for both native and nonnative species. Sensitivities of these organisms were compared based on the 5% hazardous concentration values and the species sensitivity distribution from a literature review. Results of the present study's analysis showed that there is approximately 74% certainty that use of nonnative species to generate water quality criteria would be sufficiently protective of aquatic ecosystems in China. Without applying any assessment factor to the water quality criteria generated from nonnative species, the uncertainty would be 26% when the native Chinese species might be under protection. Applying an assessment factor of 10 would offer adequate protection to native Chinese species for approximately 90% of tested chemicals and thus reduce the uncertainty from 26% to 10%. © 2015 SETAC.

  20. Leveraging 3D chemical similarity, target and phenotypic data in the identification of drug-protein and drug-adverse effect associations.

    PubMed

    Vilar, Santiago; Hripcsak, George

    2016-01-01

    Drug-target identification is crucial to discover novel applications for existing drugs and provide more insights about mechanisms of biological actions, such as adverse drug effects (ADEs). Computational methods along with the integration of current big data sources provide a useful framework for drug-target and drug-adverse effect discovery. In this article, we propose a method based on the integration of 3D chemical similarity, target and adverse effect data to generate a drug-target-adverse effect predictor along with a simple leveraging system to improve identification of drug-targets and drug-adverse effects. In the first step, we generated a system for multiple drug-target identification based on the application of 3D drug similarity into a large target dataset extracted from the ChEMBL. Next, we developed a target-adverse effect predictor combining targets from ChEMBL with phenotypic information provided by SIDER data source. Both modules were linked to generate a final predictor that establishes hypothesis about new drug-target-adverse effect candidates. Additionally, we showed that leveraging drug-target candidates with phenotypic data is very useful to improve the identification of drug-targets. The integration of phenotypic data into drug-target candidates yielded up to twofold precision improvement. In the opposite direction, leveraging drug-phenotype candidates with target data also yielded a significant enhancement in the performance. The modeling described in the current study is simple and efficient and has applications at large scale in drug repurposing and drug safety through the identification of mechanism of action of biological effects.

  1. Cultural and chemical characterization of CDC groups EO-2, M-5, and M-6, Moraxella (Moraxella) species, Oligella urethralis, Acinetobacter species, and Psychrobacter immobilis.

    PubMed

    Moss, C W; Wallace, P L; Hollis, D G; Weaver, R E

    1988-03-01

    We determined phenotypic characteristics, cellular fatty acid composition, and isoprenoid quinone content of representative strains of CDC groups EO-2, M-5, and M-6, Moraxella (Moraxella) species, Oligella urethralis, Acinetobacter species, and Psychrobacter immobilis. All organisms contained ubiquinone with eight isoprene units as the major isoprenolog, but distinct differences were observed in fatty acid composition. Twenty-eight of the original collection of CDC group EO-2 strains were further identified as P. immobilis, EO-2, or EO-3 by distinctive cellular fatty acid profiles, cellular morphology, and pigment production. The cellular fatty acid compositions of M-5 and M-6 were similar but were clearly different from those of other organisms. The genus Acinetobacter was differentiated from other organisms in the study by small amounts of 2-hydroxydodecanoic acid (2-OH-12:0), and P. immobilis was differentiated by small amounts of decanoic acid (10:0) and a branched-chain 17-carbon acid (i-17:0). All Moraxella species were distinguished by small amounts of decanoic acid (10:0) and the absence of i-17:0. M. bovis, M. nonliquefaciens, and some strains of M. lacunata formed a single fatty acid group, while M. osloensis, M. phenylpyruvica, M. atlantae, and other strains of M. lacunata (M. lacunata II) had species-specific fatty acid profiles. O. urethralis differed from Moraxella species by the presence of large amounts (49%) of cis-vaccenic acid (18:1 omega 7c), small amounts (1%) of 3-hydroxyhexadecanoate (3-OH-16:0), and the absence of 10:0 and 3-hydroxydodecanoate (3-OH-12:0). The combined use of chemical data and a small number of conventional tests permitted rapid identification and differentiation of these organisms from each other and from related organisms.

  2. Cultural and chemical characterization of CDC groups EO-2, M-5, and M-6, Moraxella (Moraxella) species, Oligella urethralis, Acinetobacter species, and Psychrobacter immobilis.

    PubMed Central

    Moss, C W; Wallace, P L; Hollis, D G; Weaver, R E

    1988-01-01

    We determined phenotypic characteristics, cellular fatty acid composition, and isoprenoid quinone content of representative strains of CDC groups EO-2, M-5, and M-6, Moraxella (Moraxella) species, Oligella urethralis, Acinetobacter species, and Psychrobacter immobilis. All organisms contained ubiquinone with eight isoprene units as the major isoprenolog, but distinct differences were observed in fatty acid composition. Twenty-eight of the original collection of CDC group EO-2 strains were further identified as P. immobilis, EO-2, or EO-3 by distinctive cellular fatty acid profiles, cellular morphology, and pigment production. The cellular fatty acid compositions of M-5 and M-6 were similar but were clearly different from those of other organisms. The genus Acinetobacter was differentiated from other organisms in the study by small amounts of 2-hydroxydodecanoic acid (2-OH-12:0), and P. immobilis was differentiated by small amounts of decanoic acid (10:0) and a branched-chain 17-carbon acid (i-17:0). All Moraxella species were distinguished by small amounts of decanoic acid (10:0) and the absence of i-17:0. M. bovis, M. nonliquefaciens, and some strains of M. lacunata formed a single fatty acid group, while M. osloensis, M. phenylpyruvica, M. atlantae, and other strains of M. lacunata (M. lacunata II) had species-specific fatty acid profiles. O. urethralis differed from Moraxella species by the presence of large amounts (49%) of cis-vaccenic acid (18:1 omega 7c), small amounts (1%) of 3-hydroxyhexadecanoate (3-OH-16:0), and the absence of 10:0 and 3-hydroxydodecanoate (3-OH-12:0). The combined use of chemical data and a small number of conventional tests permitted rapid identification and differentiation of these organisms from each other and from related organisms. Images PMID:3356788

  3. Magnetic microgels for drug targeting applications: Physical-chemical properties and cytotoxicity evaluation

    NASA Astrophysics Data System (ADS)

    Turcu, Rodica; Craciunescu, Izabell; Garamus, Vasil M.; Janko, Christina; Lyer, Stefan; Tietze, Rainer; Alexiou, Christoph; Vekas, Ladislau

    2015-04-01

    Magnetoresponsive microgels with high saturation magnetization values have been obtained by a strategy based on the miniemulsion method using high colloidal stability organic carrier ferrofluid as primary material. Hydrophobic nanoparticles Fe3O4/oleic acid are densely packed into well-defined spherical nanoparticle clusters coated with polymers with sizes in the range 40-350 nm. Physical-chemical characteristics of magnetic microgels were investigated by TEM, SAXS, XPS and VSM measurements with the focus on the structure-properties relationship. The impact of magnetic microgels loaded with anticancer drug mitoxantrone (MTO) on the non-adherent human T cell leukemia line Jurkat was investigated in multiparameter flow cytometry. We showed that both MTO and microgel-loaded MTO penetrate into cells and both induce apoptosis and later secondary necrosis in a time- and dose dependent manner. In contrast, microgels without MTO are not cytotoxic in the corresponding concentrations. Our results show that MTO-loaded microgels are promising structures for application in magnetic drug targeting.

  4. Targeted genotyping-by-sequencing permits cost-effective identification and discrimination of pasture grass species and cultivars.

    PubMed

    Pembleton, Luke W; Drayton, Michelle C; Bain, Melissa; Baillie, Rebecca C; Inch, Courtney; Spangenberg, German C; Wang, Junping; Forster, John W; Cogan, Noel O I

    2016-05-01

    A targeted amplicon-based genotyping-by-sequencing approach has permitted cost-effective and accurate discrimination between ryegrass species (perennial, Italian and inter-species hybrid), and identification of cultivars based on bulked samples. Perennial ryegrass and Italian ryegrass are the most important temperate forage species for global agriculture, and are represented in the commercial pasture seed market by numerous cultivars each composed of multiple highly heterozygous individuals. Previous studies have identified difficulties in the use of morphophysiological criteria to discriminate between these two closely related taxa. Recently, a highly multiplexed single nucleotide polymorphism (SNP)-based genotyping assay has been developed that permits accurate differentiation between both species and cultivars of ryegrasses at the genetic level. This assay has since been further developed into an amplicon-based genotyping-by-sequencing (GBS) approach implemented on a second-generation sequencing platform, allowing accelerated throughput and ca. sixfold reduction in cost. Using the GBS approach, 63 cultivars of perennial, Italian and interspecific hybrid ryegrasses, as well as intergeneric Festulolium hybrids, were genotyped. The genetic relationships between cultivars were interpreted in terms of known breeding histories and indistinct species boundaries within the Lolium genus, as well as suitability of current cultivar registration methodologies. An example of applicability to quality assurance and control (QA/QC) of seed purity is also described. Rapid, low-cost genotypic assays provide new opportunities for breeders to more fully explore genetic diversity within breeding programs, allowing the combination of novel unique genetic backgrounds. Such tools also offer the potential to more accurately define cultivar identities, allowing protection of varieties in the commercial market and supporting processes of cultivar accreditation and quality assurance.

  5. Functional kinomics identifies candidate therapeutic targets in head and neck cancer

    PubMed Central

    Moser, Russell; Xu, Chang; Kao, Michael; Annis, James; Lerma, Luisa Angelica; Schaupp, Christopher M.; Gurley, Kay E.; Jang, In Sock; Biktasova, Asel; Yarbrough, Wendell G.; Margolin, Adam A.; Grandori, Carla; Kemp, Christopher J.; Méndez, Eduardo

    2014-01-01

    Purpose To identify novel therapeutic drug targets for p53 mutant head and neck squamous cell carcinoma (HNSCC). Experimental Design RNAi kinome viability screens were performed on HNSCC cells including autologous pairs from primary tumor and recurrent/metastatic lesions, and in parallel on murine squamous cell carcinoma (MSCC) cells derived from tumors of inbred mice bearing germline mutations in Trp53, and p53 regulatory genes: Atm, Prkdc, and p19Arf. Cross-species analysis of cell lines stratified by p53 mutational status and metastatic phenotype was utilized to select 38 kinase targets. Both primary and secondary RNAi validation assays were performed on additional HNSCC cell lines to credential these kinase targets utilizing multiple phenotypic endpoints. Kinase targets were also examined via chemical inhibition utilizing a panel of kinase inhibitors. A preclinical study was conducted on the WEE1 kinase inhibitor, MK-1775. Results Our functional kinomics approach identified novel survival kinases in HNSCC involved in G2/M cell cycle checkpoint, SFK, PI3K and FAK pathways. RNAi mediated knockdown and chemical inhibition of the WEE1 kinase with a specific inhibitor, MK-1775, had a significant effect on both viability and apoptosis. Sensitivity to the MK-1775 kinase inhibitor is in part determined by p53 mutational status, and due to unscheduled mitotic entry. MK-1775 displays single-agent activity and potentiates the efficacy of cisplatin in a p53 mutant HNSCC xenograft model. Conclusions WEE1 kinase is a potential therapeutic drug target for HNSCC. This study supports the application of a functional kinomics strategy to identify novel therapeutic targets for cancer. PMID:25125259

  6. Functional kinomics identifies candidate therapeutic targets in head and neck cancer.

    PubMed

    Moser, Russell; Xu, Chang; Kao, Michael; Annis, James; Lerma, Luisa Angelica; Schaupp, Christopher M; Gurley, Kay E; Jang, In Sock; Biktasova, Asel; Yarbrough, Wendell G; Margolin, Adam A; Grandori, Carla; Kemp, Christopher J; Méndez, Eduardo

    2014-08-15

    To identify novel therapeutic drug targets for p53-mutant head and neck squamous cell carcinoma (HNSCC). RNAi kinome viability screens were performed on HNSCC cells, including autologous pairs from primary tumor and recurrent/metastatic lesions, and in parallel on murine squamous cell carcinoma (MSCC) cells derived from tumors of inbred mice bearing germline mutations in Trp53, and p53 regulatory genes: Atm, Prkdc, and p19(Arf). Cross-species analysis of cell lines stratified by p53 mutational status and metastatic phenotype was used to select 38 kinase targets. Both primary and secondary RNAi validation assays were performed on additional HNSCC cell lines to credential these kinase targets using multiple phenotypic endpoints. Kinase targets were also examined via chemical inhibition using a panel of kinase inhibitors. A preclinical study was conducted on the WEE1 kinase inhibitor, MK-1775. Our functional kinomics approach identified novel survival kinases in HNSCC involved in G2-M cell-cycle checkpoint, SFK, PI3K, and FAK pathways. RNAi-mediated knockdown and chemical inhibition of the WEE1 kinase with a specific inhibitor, MK-1775, had a significant effect on both viability and apoptosis. Sensitivity to the MK-1775 kinase inhibitor is in part determined by p53 mutational status, and due to unscheduled mitotic entry. MK-1775 displays single-agent activity and potentiates the efficacy of cisplatin in a p53-mutant HNSCC xenograft model. WEE1 kinase is a potential therapeutic drug target for HNSCC. This study supports the application of a functional kinomics strategy to identify novel therapeutic targets for cancer. ©2014 American Association for Cancer Research.

  7. Experimental and Quantum-Chemical Study of Electronically Excited States of Protolytic Isovanillin Species

    NASA Astrophysics Data System (ADS)

    Vusovich, O. V.; Tchaikovskaya, O. N.; Sokolova, I. V.; Vasil'eva, N. Yu.

    2014-05-01

    Methods of electronic spectroscopy and quantum chemistry are used to compare protolytic vanillin and isovanillin species. Three protolytic species: anion, cation, and neutral are distinguished in the ground state of the examined molecules. Vanillin and isovanillin in the ground state in water possess identical spectral characteristics: line positions and intensities in the absorption spectra coincide. Minima of the electrostatic potential demonstrate that the deepest isomer minimum is observed on the carbonyl oxygen atom. However, investigations of the fluorescence spectra show that the radiative properties of isomers differ. An analysis of results of quantum-chemical calculations demonstrate that the long-wavelength ππ* transition in the vanillin absorption spectra is formed due to electron charge transfer from the phenol part of the molecule to oxygen atoms of the methoxy and carbonyl groups, and in the isovanillin absorption spectra, it is formed only on the oxygen atom of the methoxy group. The presence of hydroxyl and carbonyl groups in the structure of the examined molecules leads to the fact that isovanillin in the ground S0 state, the same as vanillin, possesses acidic properties, whereas in the excited S1 state, they possess basic properties. A comparison of the рKа values of aqueous solutions demonstrates that vanillin possesses stronger acidic and basic properties in comparison with isovanillin.

  8. Chemical projectile-target interaction during hypervelocity cratering experiments (MEMIN project).

    NASA Astrophysics Data System (ADS)

    Ebert, M.; Hecht, L.; Deutsch, A.; Kenkmann, T.

    2012-04-01

    , Cr, Co and V (experiment with the steel projectile). An enrichment of W and Mo in the shocked quartzes could not be observed. It is suggested that two types of geochemical mixing processes between projectile and target occur during the impact process: (i) After shock compression with formation of PDF in Qtz and diaplectic quartz glass, up to about 1 % of projectile matter is added to these phases without detectable fractionation between the meteoritic tracer elements (except W and Mo). We suggest that projectile material was introduced to shocked quartz from a metallic vapour phase, which was formed near the projectile-target interface. The lack of W and Mo enrichment in shocked target material probably results from the relatively high melting and boiling points of these elements. (ii) In addition heterogeneous melting of sandstone and projectile and subsequent mixing of both melts inter-element fractionation occurred according to the chemical properties of the elements. Fractionation processes similar to our type (ii) are known from natural impactites [3]. We acknowledge support by the German Science Foundation (DFG FOR 887)

  9. Genetic and chemical diversity of high mucilaginous plants of Sida complex by ISSR markers and chemical fingerprinting.

    PubMed

    Thul, Sanjog T; Srivastava, Ankit K; Singh, Subhash C; Shanker, Karuna

    2011-09-01

    A method was developed based on multiple approaches wherein DNA and chemical analysis was carried out toward differentiation of important species of Sida complex that is being used for commercial preparation. Isolated DNA samples were successfully performed through PCR amplification using ISSR markers and degree of genetic diversity among the different species of Sida is compared with that of chemical diversity. For genetic fingerprint investigation, selected 10 ISSR primers generating reproducible banding patterns were used. Among the total of 63 amplicons, 62 were recorded as polymorphic, genetic similarity index deduced from ISSR profiles ranged from 12 to 51%. Based on similarity index, S. acuta and S. rhombifolia found to be most similar (51%). High number of species-specific bands played pivotal role to delineate species at genetic level. Investigation based on HPTLC fingerprints analysis revealed 23 bands representing to characteristic chemicals and similarity index ranged from 73 to 91%. Prominent distinguishable bands were observed only in S. acuta, while S. cordifolia and S. rhombifolia shared most bands making them difficult to identify on chemical fingerprint basis. This report summarizes the genotypic and chemotypic diversity and the use of profiles for authentication of species of Sida complex.

  10. Biological networks for predicting chemical hepatocarcinogenicity using gene expression data from treated mice and relevance across human and rat species.

    PubMed

    Thomas, Reuben; Thomas, Russell S; Auerbach, Scott S; Portier, Christopher J

    2013-01-01

    Several groups have employed genomic data from subchronic chemical toxicity studies in rodents (90 days) to derive gene-centric predictors of chronic toxicity and carcinogenicity. Genes are annotated to belong to biological processes or molecular pathways that are mechanistically well understood and are described in public databases. To develop a molecular pathway-based prediction model of long term hepatocarcinogenicity using 90-day gene expression data and to evaluate the performance of this model with respect to both intra-species, dose-dependent and cross-species predictions. Genome-wide hepatic mRNA expression was retrospectively measured in B6C3F1 mice following subchronic exposure to twenty-six (26) chemicals (10 were positive, 2 equivocal and 14 negative for liver tumors) previously studied by the US National Toxicology Program. Using these data, a pathway-based predictor model for long-term liver cancer risk was derived using random forests. The prediction model was independently validated on test sets associated with liver cancer risk obtained from mice, rats and humans. Using 5-fold cross validation, the developed prediction model had reasonable predictive performance with the area under receiver-operator curve (AUC) equal to 0.66. The developed prediction model was then used to extrapolate the results to data associated with rat and human liver cancer. The extrapolated model worked well for both extrapolated species (AUC value of 0.74 for rats and 0.91 for humans). The prediction models implied a balanced interplay between all pathway responses leading to carcinogenicity predictions. Pathway-based prediction models estimated from sub-chronic data hold promise for predicting long-term carcinogenicity and also for its ability to extrapolate results across multiple species.

  11. Entrainment in an electrochemical forced oscillator as a method of classification of chemical species-a new strategy to develop a chemical sensor

    NASA Astrophysics Data System (ADS)

    Nakata, S.; Yoshikawa, K.; Kawakami, H.

    1992-10-01

    We propose a new sensing method of varios chemical species based on information on the mode of entrainment in an electrochemically forced oscillator. It is demonstrated that the presence of one of the four basic taste compounds (salty, sweet, bitter, and sour) changes the mode of entrainment in a unique way. Thus a characteristics change of the entrainment allows us to obtain information on the properties of the electrochemical system. The response of the mode of entrainment to the taste compounds is related to the nonlinear properties of the studied electrochemical system, i.e., its voltage dependent capacitance and conductance. The experimental results are compared with computer simulations of a model system in which the capacitance is a nonlinear function of the voltage.

  12. The Atmospheric Tomography Mission (ATom): Comparing the Chemical Climatology of Reactive Species and Air Parcels from Measurements and Global Models

    NASA Astrophysics Data System (ADS)

    Prather, M. J.; Flynn, C.; Wennberg, P. O.; Kim, M. J.; Ryerson, T. B.; Hanisco, T. F.; Diskin, G. S.; Daube, B. C.; Commane, R.; McKain, K.; Apel, E. C.; Blake, N. J.; Blake, D. R.; Elkins, J. W.; Hall, S.; Steenrod, S.; Strahan, S. E.; Lamarque, J. F.; Fiore, A. M.; Horowitz, L. W.; Murray, L. T.; Mao, J.; Shindell, D. T.; Wofsy, S. C.

    2017-12-01

    The NASA Atmospheric Tomography Mission (ATom) is building a photochemical climatology of the remote troposphere based on objective sampling and profiling transects over the Pacific and Atlantic Oceans. These statistics provide direct tests of chemistry-climate models. The choice of species focuses on those controlling primary reactivity (a.k.a. oxidative state) of the troposphere, specifically chemical tendencies of O3 and CH4. These key species include, inter alia, O3, CH4, CO, C2H6, other alkanes, alkenes, aromatics, NOx, HNO3, HO2NO2, PAN, other organic nitrates, H2O, HCHO, H2O2, CH3OOH. Three of the four ATom deployments are now complete, and data from the first two (ATom-1 & -2) have been released as of this talk (see espoarchive.nasa.gov/archive/browse/atom). The statistical distributions of key species are presented as 1D and 2D probability densities (PDs) and we focus here on the tropical and mid-latitude regions of the Pacific during ATom-1 (Aug) and -2 (Feb). PDs are computed from ATom observations and 6 global chemistry models over the tropospheric depth (0-12 km) and longitudinal extent of the observations. All data are weighted to achieve equal mass-weighting by latitude regimes to account for spatial sampling biases. The models are used to calculate the reactivity in each ATom air parcel. Reweighting parcels with loss of CH4 or production of O3, for example, allows us to identify which air parcels are most influential, including assessment of the importance of fine pollution layers in the most remote troposphere. Another photochemical climatology developed from ATom, and used to test models, includes the effect of clouds on photolysis rates. The PDs and reactivity-weighted PDs reveal important seasonal differences and similarities between the two campaigns and also show which species may be most important in controlling reactivities. They clearly identify some very specific failings in the modeled climatologies and help us evaluate the chemical

  13. Agrobacterium tumefaciens-mediated transformation of oleaginous yeast Lipomyces species

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dai, Ziyu; Deng, Shuang; Culley, David E.

    Background: Because of interest in the production of renewable bio-hydrocarbon fuels, various living organisms have been explored for their potential use in producing fuels and chemicals. The oil-producing (oleaginous) yeast Lipomyces starkeyi is the subject of active research regarding the production of lipids using a wide variety of carbon and nutrient sources. The genome of L. starkeyi has been published, which opens the door to production strain improvements using the tools of synthetic biology and metabolic engineering. However, using these tools for strain improvement requires the establishment of effective and reliable transformation methods with suitable selectable markers (antibiotic resistance ormore » auxotrophic marker genes) and the necessary genetic elements (promoters and terminators) for expression of introduced genes. Chemical-based methods have been published, but suffer from low efficiency or the requirement for targeting to rRNA loci. To address these problems, Agrobacterium-mediated transformation was investigated as an alternative method for L. starkeyi and other Lipomyces species. Results: In this study, Agrobacterium-mediated transformation was demonstrated to be effective in the transformation of both L. starkeyi and other Lipomyces species and that the introduced DNA can be reliably integrated into the chromosomes of these species. The gene deletion of Ku70 and Pex10 was also demonstrated in L. starkeyi. In addition to the bacterial antibiotic selection marker gene hygromycin B phosphotransferase, the bacterial -glucuronidase reporter gene under the control of L. starkeyi translation elongation factor 1 promoter was also stably expressed in seven different Lipomyces species. Conclusion: The results from this study clearly demonstrate that Agrobacterium-mediated transformation is a reliable genetic tool for gene deletion and integration and expression of heterologous genes in L. starkeyi and other Lipomyces species.« less

  14. Preference and aversion for deterrent chemicals in two species of Peromyscus mouse.

    PubMed

    Glendinning, J I

    1993-07-01

    Deterrent chemicals such as quinine hydrochloride (QHC1) are generally considered to be aversive to mammals at all detectable concentrations. However, several species contain individuals that drink solutions containing low concentrations of deterrents in preference to plain water. The present study examines this paradoxical preference in two species of mouse, Peromyscus melanotis and P. aztecus. Preliminary findings had suggested that whereas some P. aztecus prefer low concentrations of QHC1, no P. melanotis prefer any concentration of QHC1. Experiment 1 tested the hypothesis that individual mice that prefer low concentrations of QHC1 would respond similarly to four other deterrents described by humans as bitter and/or astringent (ouabain, hop extract, sucrose octaacetate, and tannic acid) in 48-h, two-bottle choice tests. Peromyscus aztecus displayed a large amount of intraspecific variation in response to all five deterrents. Those P. aztecus that drank low concentrations of QHC1 in preference to plain water were significantly more likely to respond similarly to low concentrations of the other deterrents. No P. melanotis displayed a preference for any concentration of either deterrent. Experiment 2 examined the temporal stability of the response to 0.1 mM QHC1 in P. aztecus over six consecutive choice tests. Mice were divided into three groups based on their initial response to the QHC1 solution (preference, no response, or rejection) and then subjected to the 12-day test. The response of mice within each of the groups did not change significantly over time.(ABSTRACT TRUNCATED AT 250 WORDS)

  15. PEROXISOME-PROLIFERATOR ACTIVATED RECEPTORS AS A MACROMOLECULAR TARGET FOR CHEMICAL TOXICITY: MODELS OF THE INTERACTIONS OF PPARS WITH PERFLUORINATED ORGANIC COMPOUNDS-S

    EPA Science Inventory

    Many toxicological processes may be studied using the same paradigms as used in this study. As a result, methods applied here may have a far reaching effect for evaluating the risk of this and other classes of chemicals and other macromolecular targets.

  16. Impact of Environmentally Based Chemical Hardness on Uranium Speciation and Toxicity in Six Aquatic Species

    PubMed Central

    Goulet, Richard R; Thompson, Patsy A; Serben, Kerrie C; Eickhoff, Curtis V

    2015-01-01

    Treated effluent discharge from uranium (U) mines and mills elevates the concentrations of U, calcium (Ca), magnesium (Mg), and sulfate (SO42–) above natural levels in receiving waters. Many investigations on the effect of hardness on U toxicity have been experiments on the combined effects of changes in hardness, pH, and alkalinity, which do not represent water chemistry downstream of U mines and mills. Therefore, more toxicity studies with water chemistry encountered downstream of U mines and mills are necessary to support predictive assessments of impacts of U discharge to the environment. Acute and chronic U toxicity laboratory bioassays were realized with 6 freshwater species in waters of low alkalinity, circumneutral pH, and a range of chemical hardness as found in field samples collected downstream of U mines and mills. In laboratory-tested waters, speciation calculations suggested that free uranyl ion concentrations remained constant despite increasing chemical hardness. When hardness increased while pH remained circumneutral and alkalinity low, U toxicity decreased only to Hyalella azteca and Pseudokirchneriella subcapitata. Also, Ca and Mg did not compete with U for the same uptake sites. The present study confirms that the majority of studies concluding that hardness affected U toxicity were in fact studies in which alkalinity and pH were the stronger influence. The results thus confirm that studies predicting impacts of U downstream of mines and mills should not consider chemical hardness. PMID:25475484

  17. Tortuous path chemical preconcentrator

    DOEpatents

    Manginell, Ronald P.; Lewis, Patrick R.; Adkins, Douglas R.; Wheeler, David R.; Simonson, Robert J.

    2010-09-21

    A non-planar, tortuous path chemical preconcentrator has a high internal surface area having a heatable sorptive coating that can be used to selectively collect and concentrate one or more chemical species of interest from a fluid stream that can be rapidly released as a concentrated plug into an analytical or microanalytical chain for separation and detection. The non-planar chemical preconcentrator comprises a sorptive support structure having a tortuous flow path. The tortuosity provides repeated twists, turns, and bends to the flow, thereby increasing the interfacial contact between sample fluid stream and the sorptive material. The tortuous path also provides more opportunities for desorption and readsorption of volatile species. Further, the thermal efficiency of the tortuous path chemical preconcentrator is comparable or superior to the prior non-planar chemical preconcentrator. Finally, the tortuosity can be varied in different directions to optimize flow rates during the adsorption and desorption phases of operation of the preconcentrator.

  18. Suspect screening of maternal serum to identify new environmental chemical biomonitoring targets using liquid chromatography-quadrupole time-of-flight mass spectrometry.

    PubMed

    Gerona, Roy R; Schwartz, Jackie M; Pan, Janet; Friesen, Matthew M; Lin, Thomas; Woodruff, Tracey J

    2018-03-01

    The use and advantages of high-resolution mass spectrometry (MS) as a discovery tool for environmental chemical monitoring has been demonstrated for environmental samples but not for biological samples. We developed a method using liquid chromatography-quadrupole time-of-flight MS (LC-QTOF/MS) for discovery of previously unmeasured environmental chemicals in human serum. Using non-targeted data acquisition (full scan MS analysis) we were able to screen for environmental organic acids (EOAs) in 20 serum samples from second trimester pregnant women. We define EOAs as environmental organic compounds with at least one dissociable proton which are utilized in commerce. EOAs include environmental phenols, phthalate metabolites, perfluorinated compounds, phenolic metabolites of polybrominated diphenyl ethers and polychlorinated biphenyls, and acidic pesticides and/or predicted acidic pesticide metabolites. Our validated method used solid phase extraction, reversed-phase chromatography in a C18 column with gradient elution, electrospray ionization in negative polarity and automated tandem MS (MS/MS) data acquisition to maximize true positive rates. We identified "suspect EOAs" using Agilent MassHunter Qualitative Analysis software, to match chemical formulas generated from each sample run with molecular formulas in our unique database of 693 EOAs assembled from multiple environmental literature sources. We found potential matches for 282 (41%) of the EOAs in our database. Sixty-five of these suspect EOAs were detected in at least 75% of the samples; only 19 of these compounds are currently biomonitored in National Health and Nutrition Examination Survey. We confirmed two of three suspect EOAs by LC-QTOF/MS using a targeted method developed through LC-MS/MS, reporting the first confirmation of benzophenone-1 and bisphenol S in pregnant women's sera. Our suspect screening workflow provides an approach to comprehensively scan environmental chemical exposures in humans. This

  19. Chemical Composition and in-Vitro Evaluation of the Antimicrobial and Antioxidant Activities of Essential Oils Extracted from Seven Eucalyptus Species.

    PubMed

    Ghaffar, Abdul; Yameen, Muhammad; Kiran, Shumaila; Kamal, Shagufta; Jalal, Fatima; Munir, Bushra; Saleem, Sadaf; Rafiq, Naila; Ahmad, Aftab; Saba, Iram; Jabbar, Abdul

    2015-11-18

    Eucalyptus is well reputed for its use as medicinal plant around the globe. The present study was planned to evaluate chemical composition, antimicrobial and antioxidant activity of the essential oils (EOs) extracted from seven Eucalyptus species frequently found in South East Asia (Pakistan). EOs from Eucalyptus citriodora, Eucalyptus melanophloia, Eucalyptus crebra, Eucalyptus tereticornis, Eucalyptus globulus, Eucalyptus camaldulensis and Eucalyptus microtheca were extracted from leaves through hydrodistillation. The chemical composition of the EOs was determined through GC-MS-FID analysis. The study revealed presence of 31 compounds in E. citriodora and E. melanophloia, 27 compounds in E. crebra, 24 compounds in E. tereticornis, 10 compounds in E. globulus, 13 compounds in E. camaldulensis and 12 compounds in E. microtheca. 1,8-Cineole (56.5%), α-pinene (31.4%), citrinyl acetate (13.3%), eugenol (11.8%) and terpenene-4-ol (10.2%) were the highest principal components in these EOs. E. citriodora exhibited the highest antimicrobial activity against the five microbial species tested (Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Aspergillus niger and Rhizopus solani). Gram positive bacteria were found more sensitive than Gram negative bacteria to all EOs. The diphenyl-1-picrylhydazyl (DPPH) radical scavenging activity and percentage inhibition of linoleic acid oxidation were highest in E. citriodora (82.1% and 83.8%, respectively) followed by E. camaldulensis (81.9% and 83.3%, respectively). The great variation in chemical composition of EOs from Eucalyptus, highlight its potential for medicinal and nutraceutical applications.

  20. Analysis of pharmacology data and the prediction of adverse drug reactions and off-target effects from chemical structure.

    PubMed

    Bender, Andreas; Scheiber, Josef; Glick, Meir; Davies, John W; Azzaoui, Kamal; Hamon, Jacques; Urban, Laszlo; Whitebread, Steven; Jenkins, Jeremy L

    2007-06-01

    Preclinical Safety Pharmacology (PSP) attempts to anticipate adverse drug reactions (ADRs) during early phases of drug discovery by testing compounds in simple, in vitro binding assays (that is, preclinical profiling). The selection of PSP targets is based largely on circumstantial evidence of their contribution to known clinical ADRs, inferred from findings in clinical trials, animal experiments, and molecular studies going back more than forty years. In this work we explore PSP chemical space and its relevance for the prediction of adverse drug reactions. Firstly, in silico (computational) Bayesian models for 70 PSP-related targets were built, which are able to detect 93% of the ligands binding at IC(50) < or = 10 microM at an overall correct classification rate of about 94%. Secondly, employing the World Drug Index (WDI), a model for adverse drug reactions was built directly based on normalized side-effect annotations in the WDI, which does not require any underlying functional knowledge. This is, to our knowledge, the first attempt to predict adverse drug reactions across hundreds of categories from chemical structure alone. On average 90% of the adverse drug reactions observed with known, clinically used compounds were detected, an overall correct classification rate of 92%. Drugs withdrawn from the market (Rapacuronium, Suprofen) were tested in the model and their predicted ADRs align well with known ADRs. The analysis was repeated for acetylsalicylic acid and Benperidol which are still on the market. Importantly, features of the models are interpretable and back-projectable to chemical structure, raising the possibility of rationally engineering out adverse effects. By combining PSP and ADR models new hypotheses linking targets and adverse effects can be proposed and examples for the opioid mu and the muscarinic M2 receptors, as well as for cyclooxygenase-1 are presented. It is hoped that the generation of predictive models for adverse drug reactions is able

  1. Morphological and chemical variation of Stemona tuberosa from southern China - Evidence for heterogeneity of this medicinal plant species.

    PubMed

    Chen, G; Brecker, L; Felsinger, S; Cai, X-H; Kongkiatpaiboon, S; Schinnerl, J

    2017-09-01

    The occurrence of bioactive alkaloids and tocopherols was studied in 15 different provenances of Stemona tuberosa Lour. collected in southern China, to examine chemical variation of individuals that show notable differences in flower characteristics. Morphological variations stimulated examination of chemical characteristics of these individuals. Methanolic root extracts of 15 individuals of S. tuberosa were comparatively assessed with HPLC-UV-DAD/ELSD. Five of seven compounds were co-chromatographically identified. Two compounds were isolated and their structure elucidated using NMR and MS. Amounts of alkaloids and tocopherols were determined using HPLC-UV-DAD/ELSD with the external standard method. Five alkaloids, tuberostemonine (1), tuberostemonine A (2), neotuberostemonine (3), tuberostemonine N (4), stemoninine (5) and two 3,4-dehydrotocopherol derivatives were identified. Within S. tuberosa alkaloid accumulation tends either towards tuberostemonine (1) or stemoninine (5). All individuals show a notable co-occurrence of compounds 1 or 5 and 3,4-dehydro-δ-tocopherol (6). These results coincide with differences in flower morphology of S. tuberosa. Stemona tuberosa, as defined in the Flora of China, shows a remarkable variation in flower morphology and additionally in the accumulation of alkaloids. The obtained data show the need for future species delimitation to either species or subspecies level. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

  2. Development of a DNA microarray for species identification of quarantine aphids.

    PubMed

    Lee, Won Sun; Choi, Hwalran; Kang, Jinseok; Kim, Ji-Hoon; Lee, Si Hyeock; Lee, Seunghwan; Hwang, Seung Yong

    2013-12-01

    Aphid pests are being brought into Korea as a result of increased crop trading. Aphids exist on growth areas of plants, and thus plant growth is seriously affected by aphid pests. However, aphids are very small and have several sexual morphs and life stages, so it is difficult to identify species on the basis of morphological features. This problem was approached using DNA microarray technology. DNA targets of the cytochrome c oxidase subunit I gene were generated with a fluorescent dye-labelled primer and were hybridised onto a DNA microarray consisting of specific probes. After analysing the signal intensity of the specific probes, the unique patterns from the DNA microarray, consisting of 47 species-specific probes, were obtained to identify 23 aphid species. To confirm the accuracy of the developed DNA microarray, ten individual blind samples were used in blind trials, and the identifications were completely consistent with the sequencing data of all individual blind samples. A microarray has been developed to distinguish aphid species. DNA microarray technology provides a rapid, easy, cost-effective and accurate method for identifying aphid species for pest control management. © 2013 Society of Chemical Industry.

  3. Expanding the Species and Chemical Diversity of Penicillium Section Cinnamopurpurea

    PubMed Central

    Peterson, Stephen W.; Jurjević, Željko; Frisvad, Jens C.

    2015-01-01

    A set of isolates very similar to or potentially conspecific with an unidentified Penicillium isolate NRRL 735, was assembled using a BLAST search of ITS similarity among described (GenBank) and undescribed Penicillium isolates in our laboratories. DNA was amplified from six loci of the assembled isolates and sequenced. Two species in section Cinnamopurpurea are self-compatible sexual species, but the asexual species had polymorphic loci suggestive of sexual reproduction and variation in conidium size suggestive of ploidy level differences typical of heterothallism. Accordingly we use genealogical concordance analysis, a technique valid only in heterothallic organisms, for putatively asexual species. Seven new species were revealed in the analysis and are described here. Extrolite analysis showed that two of the new species, P. colei and P. monsserratidens produce the mycotoxin citreoviridin that has demonstrated pharmacological activity against human lung tumors. These isolates could provide leads in pharmaceutical research. PMID:25853891

  4. Bioaccessibility of selenium after human ingestion in relation to its chemical species and compartmentalization in maize.

    PubMed

    Mombo, Stéphane; Schreck, Eva; Dumat, Camille; Laplanche, Christophe; Pierart, Antoine; Longchamp, Mélanie; Besson, Philippe; Castrec-Rouelle, Maryse

    2016-06-01

    Selenium is a micronutrient needed by all living organisms including humans, but often present in low concentration in food with possible deficiency. From another side, at higher concentrations in soils as observed in seleniferous regions of the world, and in function of its chemical species, Se can also induce (eco)toxicity. Root Se uptake was therefore studied in function of its initial form for maize (Zea mays L.), a plant widely cultivated for human and animal food over the world. Se phytotoxicity and compartmentalization were studied in different aerial plant tissues. For the first time, Se oral human bioaccessibility after ingestion was assessed for the main Se species (Se(IV) and Se(VI)) with the BARGE ex vivo test in maize seeds (consumed by humans), and in stems and leaves consumed by animals. Corn seedlings were cultivated in hydroponic conditions supplemented with 1 mg L(-1) of selenium (Se(IV), Se(VI), Control) for 4 months. Biomass, Se concentration, and bioaccessibility were measured on harvested plants. A reduction in plant biomass was observed under Se treatments compared to control, suggesting its phytotoxicity. This plant biomass reduction was higher for selenite species than selenate, and seed was the main affected compartment compared to control. Selenium compartmentalization study showed that for selenate species, a preferential accumulation was observed in leaves, whereas selenite translocation was very limited toward maize aerial parts, except in the seeds where selenite concentrations are generally high. Selenium oral bioaccessibility after ingestion fluctuated from 49 to 89 % according to the considered plant tissue and Se species. Whatever the tissue, selenate appeared as the most human bioaccessible form. A potential Se toxicity was highlighted for people living in seleniferous regions, this risk being enhanced by the high Se bioaccessibility.

  5. Dose-dependent intracellular reactive oxygen and nitrogen species (ROS/RNS) production from particulate matter exposure: comparison to oxidative potential and chemical composition

    NASA Astrophysics Data System (ADS)

    Tuet, Wing Y.; Fok, Shierly; Verma, Vishal; Tagle Rodriguez, Marlen S.; Grosberg, Anna; Champion, Julie A.; Ng, Nga L.

    2016-11-01

    Elevated particulate matter (PM) concentrations have been associated with cardiopulmonary risks. In this study, alveolar macrophages and ventricular myocytes were exposed to PM extracts from 104 ambient filters collected in multiple rural and urban sites in the greater Atlanta area. PM-induced reactive oxygen/nitrogen species (ROS/RNS) were measured to investigate the effect of chemical composition and determine whether chemical assays are representative of cellular responses. For summer samples, the area under the ROS/RNS dose-response curve per volume of air (AUCvolume) was significantly correlated with dithiothreitol (DTT) activity, water-soluble organic carbon (WSOC), brown carbon, titanium, and iron, while a relatively flat response was observed for winter samples. EC50 was also correlated with max response for all filters investigated, which suggests that certain PM constituents may be involved in cellular protective pathways. Although few metal correlations were observed, exposure to laboratory-prepared metal solutions induced ROS/RNS production, indicating that a lack of correlation does not necessarily translate to a lack of response. Collectively, these results suggest that complex interactions may occur between PM species. Furthermore, the strong correlation between organic species and ROS/RNS response highlights a need to understand the contribution of organic aerosols, especially photochemically driven secondary organic aerosols (SOA), to PM-induced health effects.

  6. Analysis of Chemical Bioactivity through In Vitro Profiling ...

    EPA Pesticide Factsheets

    Safety assessment of drugs and environmental chemicals relies extensively on animal testing. However, the quantity of chemicals needing assessment and challenges of species extrapolation drive the development of alternative approaches. The EPA’s ToxCast and the multiagency Tox21 programs address this through use of an extensive in vitro screening program to generate data on a large library of important environmental chemicals. These in vitro assays encompass both cell-free, biochemical assays targeting proteins that may be potential molecular initiating events and cellular assays that provide coverage of critical signaling pathways and toxicity phenotypes. Effects on model organisms such as the developing zebrafish, are also part of the testing strategy. A variety of computational approaches are used to analyze the resulting complex data sets to gain insight in to inherent biological activity of chemicals and possible mechanisms of toxicity. Several case studies including identification of modulators of estrogen receptor and aromatic hydrocarbon receptor pathways with effects in primary human cell systems will be described. In addition, existing in vivo data from a subset of the chemicals was used to anchor predictive models using in vitro data for a number of adverse endpoints including reproductive and developmental toxicities. The strengths and weaknesses of this approach will be described. This work does not necessarily reflect official Agency policy. Pres

  7. Enumerating lepidopteran species associated with maize as a first step in risk assessment in the USA.

    PubMed

    Losey, John E; Hufbauer, Ruth A; Hartzler, Robert G

    2003-01-01

    Pest management can have substantial impacts on non-target species both within and outside the units being managed. Assessment of these impacts is hampered by the lack of even the most basic checklist of the species present in most systems. The maize agroecosytem is of particular interest because of the large area covered and the intensity of widely varying forms of pest management. In this study a database of lepidopteran species that occur within the maize agroecosystem in the United States was compiled. The process was initiated by developing a list of plants present in maize using published sources and the first-hand knowledge of "weed" experts. This list of plant species associated with maize was then cross-listed with lepidopteran host feeding records using published sources. Finally, phenological profiles and conservation rankings were added. Although our list is not exhaustive, we found 132 plant species in 33 families associated with maize, and 229 lepidopteran species in 21 families that feed on these plants. The database of plants and lepidopteran species can be a starting point for assessment of risk to non-target Lepidoptera in maize from chemical control, biological control, and the use of transgenic Bt maize. The lepidopteran species associated with maize were found to be significantly less imperiled, as measured by their conservation rankings, than lepidopteran species as a whole in all habitats. This finding suggests that rare or endangered lepidopteran species are unlikely to be impacted by pest management in maize. Based on the likely lack of impact of pest management in maize on individual species, future studies should focus on potential impacts on the ecological services that lepidopteran species provide.

  8. Metabolomic profiling reveals deep chemical divergence between two morphotypes of the zoanthid Parazoanthus axinellae

    NASA Astrophysics Data System (ADS)

    Cachet, Nadja; Genta-Jouve, Grégory; Ivanisevic, Julijana; Chevaldonné, Pierre; Sinniger, Frédéric; Culioli, Gérald; Pérez, Thierry; Thomas, Olivier P.

    2015-02-01

    Metabolomics has recently proven its usefulness as complementary tool to traditional morphological and genetic analyses for the classification of marine invertebrates. Among the metabolite-rich cnidarian order Zoantharia, Parazoanthus is a polyphyletic genus whose systematics and phylogeny remain controversial. Within this genus, one of the most studied species, Parazoanthus axinellae is prominent in rocky shallow waters of the Mediterranean Sea and the NE Atlantic Ocean. Although different morphotypes can easily be distinguished, only one species is recognized to date. Here, a metabolomic profiling approach has been used to assess the chemical diversity of two main Mediterranean morphotypes, the ``slender'' and ``stocky'' forms of P. axinellae. Targeted profiling of their major secondary metabolites revealed a significant chemical divergence between the morphotypes. While zoanthoxanthin alkaloids and ecdysteroids are abundant in both morphs, the ``slender'' morphotype is characterized by the presence of additional and bioactive 3,5-disubstituted hydantoin derivatives named parazoanthines. The absence of these specific compounds in the ``stocky'' morphotype was confirmed by spatial and temporal monitoring over an annual cycle. Moreover, specimens of the ``slender'' morphotype are also the only ones found as epibionts of several sponge species, particularly Cymbaxinella damicornis thus suggesting a putative ecological link.

  9. Biological Networks for Predicting Chemical Hepatocarcinogenicity Using Gene Expression Data from Treated Mice and Relevance across Human and Rat Species

    PubMed Central

    Thomas, Reuben; Thomas, Russell S.; Auerbach, Scott S.; Portier, Christopher J.

    2013-01-01

    Background Several groups have employed genomic data from subchronic chemical toxicity studies in rodents (90 days) to derive gene-centric predictors of chronic toxicity and carcinogenicity. Genes are annotated to belong to biological processes or molecular pathways that are mechanistically well understood and are described in public databases. Objectives To develop a molecular pathway-based prediction model of long term hepatocarcinogenicity using 90-day gene expression data and to evaluate the performance of this model with respect to both intra-species, dose-dependent and cross-species predictions. Methods Genome-wide hepatic mRNA expression was retrospectively measured in B6C3F1 mice following subchronic exposure to twenty-six (26) chemicals (10 were positive, 2 equivocal and 14 negative for liver tumors) previously studied by the US National Toxicology Program. Using these data, a pathway-based predictor model for long-term liver cancer risk was derived using random forests. The prediction model was independently validated on test sets associated with liver cancer risk obtained from mice, rats and humans. Results Using 5-fold cross validation, the developed prediction model had reasonable predictive performance with the area under receiver-operator curve (AUC) equal to 0.66. The developed prediction model was then used to extrapolate the results to data associated with rat and human liver cancer. The extrapolated model worked well for both extrapolated species (AUC value of 0.74 for rats and 0.91 for humans). The prediction models implied a balanced interplay between all pathway responses leading to carcinogenicity predictions. Conclusions Pathway-based prediction models estimated from sub-chronic data hold promise for predicting long-term carcinogenicity and also for its ability to extrapolate results across multiple species. PMID:23737943

  10. Differences in uptake and translocation of hexavalent and trivalent chromium by two species of willows.

    PubMed

    Yu, Xiao-Zhang; Gu, Ji-Dong; Xing, Li-Qun

    2008-11-01

    Uptake and translocation of chromium (Cr) by two willow species was investigated. Intact pre-rooted weeping willows (Salix babylonica L.) and hankow willows (Salix matsudana Koidz) were grown hydroponically and spiked with hexavalent chromium [Cr (VI)] or trivalent chromium [Cr (III)] at 25.0 +/- 0.5 degrees C for 120 h. Removal of leaves was also performed as a treatment to quantify the effect of transpiration on uptake and translocation of either of the Cr species. Although the two willow species were able to eliminate Cr (VI) and Cr (III) from the hydroponic solution, significant differences in the removal rate for both chemical species were observed between the two willows (p < 0.05): faster removal rate for Cr (III) than Cr (VI) was detected in both willow species; hankow willows showed higher removal potential for both chemical species than weeping willows. Remarkable decreases in the removal rates for both Cr species were detected in the willows with leaves removed (p < 0.05). The results from the treatments spiked with Cr (VI) also revealed that Cr was more mobile in plant materials of hankow willows than that in weeping willows (p < 0.01), while higher translocation efficiency of Cr was observed in weeping willows than hankow willows for the Cr (III) treated (p < 0.01). However, a convincing decrease in the translocation efficiency due to the removal of leaves was only observed in the treatments spiked with Cr (VI) (p < 0.05). Substantial differences existed in the distribution of Cr species in plant materials after exposure of either of the chemical forms: roots and lower stems were the major sites for accumulation in weeping willows exposed to Cr (VI) and Cr (III), respectively; in contrast roots were the only sink in hankow willows exposed to both chemical species. The capacity of willows to assimilate both Cr species was also evaluated using detached leaves and roots of both willow species in sealed glass vessels in vivo. The results indicated that

  11. Detection of Chemical Precursors of Explosives

    NASA Technical Reports Server (NTRS)

    Li, Jing

    2012-01-01

    Certain selected chemicals associated with terrorist activities are too unstable to be prepared in final form. These chemicals are often prepared as precursor components, to be combined at a time immediately preceding the detonation. One example is a liquid explosive, which usually requires an oxidizer, an energy source, and a chemical or physical mechanism to combine the other components. Detection of the oxidizer (e.g. H2O2) or the energy source (e.g., nitromethane) is often possible, but must be performed in a short time interval (e.g., 5 15 seconds) and in an environment with a very small concentration (e.g.,1 100 ppm), because the target chemical(s) is carried in a sealed container. These needs are met by this invention, which provides a system and associated method for detecting one or more chemical precursors (components) of a multi-component explosive compound. Different carbon nanotubes (CNTs) are loaded (by doping, impregnation, coating, or other functionalization process) for detecting of different chemical substances that are the chemical precursors, respectively, if these precursors are present in a gas to which the CNTs are exposed. After exposure to the gas, a measured electrical parameter (e.g. voltage or current that correlate to impedance, conductivity, capacitance, inductance, etc.) changes with time and concentration in a predictable manner if a selected chemical precursor is present, and will approach an asymptotic value promptly after exposure to the precursor. The measured voltage or current are compared with one or more sequences of their reference values for one or more known target precursor molecules, and a most probable concentration value is estimated for each one, two, or more target molecules. An error value is computed, based on differences of voltage or current for the measured and reference values, using the most probable concentration values. Where the error value is less than a threshold, the system concludes that the target

  12. Synergies and trade-offs in achieving global biodiversity targets.

    PubMed

    Di Marco, Moreno; Butchart, Stuart H M; Visconti, Piero; Buchanan, Graeme M; Ficetola, Gentile F; Rondinini, Carlo

    2016-02-01

    After their failure to achieve a significant reduction in the global rate of biodiversity loss by 2010, world governments adopted 20 new ambitious Aichi biodiversity targets to be met by 2020. Efforts to achieve one particular target can contribute to achieving others, but different targets may sometimes require conflicting solutions. Consequently, lack of strategic thinking might result, once again, in a failure to achieve global commitments to biodiversity conservation. We illustrate this dilemma by focusing on Aichi Target 11. This target requires an expansion of terrestrial protected area coverage, which could also contribute to reducing the loss of natural habitats (Target 5), reducing human-induced species decline and extinction (Target 12), and maintaining global carbon stocks (Target 15). We considered the potential impact of expanding protected areas to mitigate global deforestation and the consequences for the distribution of suitable habitat for >10,000 species of forest vertebrates (amphibians, birds, and mammals). We first identified places where deforestation might have the highest impact on remaining forests and then identified places where deforestation might have the highest impact on forest vertebrates (considering aggregate suitable habitat for species). Expanding protected areas toward locations with the highest deforestation rates (Target 5) or the highest potential loss of aggregate species' suitable habitat (Target 12) resulted in partially different protected area network configurations (overlapping with each other by about 73%). Moreover, the latter approach contributed to safeguarding about 30% more global carbon stocks than the former. Further investigation of synergies and trade-offs between targets would shed light on these and other complex interactions, such as the interaction between reducing overexploitation of natural resources (Targets 6, 7), controlling invasive alien species (Target 9), and preventing extinctions of native

  13. Host selection in the forest interior: cowbirds target ground-nesting species

    USGS Publications Warehouse

    Hahn, D.C.; Hatfield, J.S.

    2000-01-01

    We investigated patterns of cowbird host selection in a large (1300 ha), unfragmented forest in eastern New York in 1992-3 to determine whether cowbird parasitism rates can be attributed to species-specific traits or to other features associated with nest sites. Nest height was significantly associated with parasitism (P = 0.003) in this community of 23 species (n = 430 nests, 23% parasitized). Further analysis revealed that the difference in mean nest heights between parasitized and unparasitized nests was due to species identity, and within each species there was no difference in mean nest heights between parasitized and unparasitized nests. These results imply that during 1992-3 cowbirds in this forest specialized on species that have low nests and did not necessarily select low nests regardless of species. This was further supported by a negative association across all 23 species between mean nest height and parasitism rate (P = 0.03). Thus, although most of the forest-nesting species in this community experienced cowbird parasitism, there was a tendency for higher parasitism rates on low-nesting species such as the Ovenbird, Black-and-white Warbler, Louisiana Waterthrush, Veery, and Hermit Thrush. The Wood Thrush, a mid-range nester which is heavily parasitized in southern Illinois, experienced only 10% parasitism in our site and ranked 9th in parasitism rate, although it was the most abundant species in this forest in terms of the number of nests found. A long-term study is necessary to determine whether this cowbird population consistently parasitizes the ground-nesting species of this forest community more often than those nesting at higher levels or whether they periodically shift among hosts at different heights and in different habitats across the local landscape.

  14. Targeted Integration of RNA-Seq and Metabolite Data to Elucidate Curcuminoid Biosynthesis in Four Curcuma Species.

    PubMed

    Li, Donghan; Ono, Naoaki; Sato, Tetsuo; Sugiura, Tadao; Altaf-Ul-Amin, Md; Ohta, Daisaku; Suzuki, Hideyuki; Arita, Masanori; Tanaka, Ken; Ma, Zhiqiang; Kanaya, Shigehiko

    2015-05-01

    Curcuminoids, namely curcumin and its analogs, are secondary metabolites that act as the primary active constituents of turmeric (Curcuma longa). The contents of these curcuminoids vary among species in the genus Curcuma. For this reason, we compared two wild strains and two cultivars to understand the differences in the synthesis of curcuminoids. Because the fluxes of metabolic reactions depend on the amounts of their substrate and the activity of the catalysts, we analyzed the metabolite concentrations and gene expression of related enzymes. We developed a method based on RNA sequencing (RNA-Seq) analysis that focuses on a specific set of genes to detect expression differences between species in detail. We developed a 'selection-first' method for RNA-Seq analysis in which short reads are mapped to selected enzymes in the target biosynthetic pathways in order to reduce the effect of mapping errors. Using this method, we found that the difference in the contents of curcuminoids among the species, as measured by gas chromatography-mass spectrometry, could be explained by the changes in the expression of genes encoding diketide-CoA synthase, and curcumin synthase at the branching point of the curcuminoid biosynthesis pathway. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  15. Chromatographic speciation of Cr(III)-species, inter-species equilibrium isotope fractionation and improved chemical purification strategies for high-precision isotope analysis

    PubMed Central

    Larsen, K.K.; Wielandt, D.; Schiller, M.; Bizzarro, M.

    2016-01-01

    Chromatographic purification of chromium (Cr), which is required for high-precision isotope analysis, is complicated by the presence of multiple Cr-species with different effective charges in the acid digested sample aliquots. The differing ion exchange selectivity and sluggish reaction rates of these species can result in incomplete Cr recovery during chromatographic purification. Because of large mass-dependent inter-species isotope fractionation, incomplete recovery can affect the accuracy of high-precision Cr isotope analysis. Here, we demonstrate widely differing cation distribution coefficients of Cr(III)-species (Cr3+, CrCl2+ and CrCl2+) with equilibrium mass-dependent isotope fractionation spanning a range of ~1‰/amu and consistent with theory. The heaviest isotopes partition into Cr3+, intermediates in CrCl2+ and the lightest in CrCl2+/CrCl3°. Thus, for a typical reported loss of ~25% Cr (in the form of Cr3+) through chromatographic purification, this translates into 185 ppm/amu offset in the stable Cr isotope ratio of the residual sample. Depending on the validity of the mass-bias correction during isotope analysis, this further results in artificial mass-independent effects in the mass-bias corrected 53Cr/52Cr (μ53 Cr* of 5.2 ppm) and 54Cr/52Cr (μ54Cr* of 13.5 ppm) components used to infer chronometric and nucleosynthetic information in meteorites. To mitigate these fractionation effects, we developed strategic chemical sample pre-treatment procedures that ensure high and reproducible Cr recovery. This is achieved either through 1) effective promotion of Cr3+ by >5 days exposure to HNO3 —H2O2 solutions at room temperature, resulting in >~98% Cr recovery for most types of sample matrices tested using a cationic chromatographic retention strategy, or 2) formation of Cr(III)-Cl complexes through exposure to concentrated HCl at high temperature (>120 °C) for several hours, resulting in >97.5% Cr recovery using a chromatographic elution strategy that

  16. Potential secondary poisoning risks to non-targets from a sodium nitrite toxic bait for invasive wild pigs.

    PubMed

    Snow, Nathan P; Foster, Justin A; VanNatta, Eric H; Horak, Katherine E; Humphrys, Simon T; Staples, Linton D; Hewitt, David G; VerCauteren, Kurt C

    2018-01-01

    An acute and orally delivered toxic bait containing micro-encapsulated sodium nitrite (MESN), is under development to provide a novel and humane technology to help curtail damage caused by invasive wild pigs (Sus scrofa). We evaluated potential secondary risks for non-target species by: testing whether four different types of micro-encapsulation coatings could reduce vomiting by invasive wild pigs, testing the levels of residual sodium nitrite (SN) in tissues of invasive wild pigs, testing the environmental persistence of SN in vomitus, and conducting a risk assessment for scavengers. Micro-encapsulation coatings did not affect the frequency of vomiting. We identified no risk of secondary poisoning for non-target scavengers that consume muscle, eyes, and livers of invasive wild pig carcasses because residual SN from the toxic bait was not detected in those tissues. The risk of secondary poisoning from consuming vomitus appeared low because ∼90% of the SN was metabolized or broken down prior to vomiting, and continued to degrade after being exposed to the environment. Secondary poisoning could occur for common scavengers that consume approximately ≥15% of their daily dietary requirements of digestive tract tissues or undigested bait from carcasses of invasive wild pigs in a rapid, single-feeding event. The likelihood of this occurring in a natural setting is unknown. The digestive tracts of poisoned invasive wild pigs contained an average of ∼4.35 mg/g of residual SN. Data from this study suggest no risks of secondary poisoning for non-target species (including humans) that consume muscle, liver, or eyes of invasive wild pigs poisoned with a MESN toxic bait. More species-specific testing for scavengers that consume digestive tract tissues and undigested bait is needed to reduce uncertainty about these potential risks. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  17. Chemical sensors

    DOEpatents

    Lowell, J.R. Jr.; Edlund, D.J.; Friesen, D.T.; Rayfield, G.W.

    1992-06-09

    Sensors responsive to small changes in the concentration of chemical species are disclosed, comprising a mechanicochemically responsive polymeric film capable of expansion or contraction in response to a change in its chemical environment, either operatively coupled to a transducer capable of directly converting the expansion or contraction to a measurable electrical or optical response, or adhered to a second inert polymeric strip, or doped with a conductive material. 12 figs.

  18. Chemical sensors

    DOEpatents

    Lowell, Jr., James R.; Edlund, David J.; Friesen, Dwayne T.; Rayfield, George W.

    1992-01-01

    Sensors responsive to small changes in the concentration of chemical species are disclosed, comprising a mechanicochemically responsive polymeric film capable of expansion or contraction in response to a change in its chemical environment, either operatively coupled to a transducer capable of directly converting the expansion or contraction to a measurable electrical or optical response, or adhered to a second inert polymeric strip, or doped with a conductive material.

  19. Reaction of mutualistic and granivorous ants to ulex elaiosome chemicals.

    PubMed

    Gammans, Nicola; Bullock, James M; Gibbons, Hannah; Schönrogge, Karsten

    2006-09-01

    It has been proposed that chemicals on plant elaiosomes aid seed detection by seed-dispersing ants. We hypothesized that the chemical interaction between ants and elaiosomes is more intimate than a generic attraction, and that elaiosome chemicals will attract mutualistic but not granivorous ant species. We investigated this by using two gorse species, Ulex minor and U. europaeus, and two associated ant species from European heathlands, the mutualist Myrmica ruginodis and the granivore Tetramorium caespitum. Behavioral studies were conducted with laboratory nests and foraging arenas. Both ants will take Ulex seeds, but while M. ruginodis showed increased antennation toward ether extracts of elaiosome surface chemicals compared with controls, T. caespitum showed no response. Elaiosome extracts were separated into seven lipid fractions. M. ruginodis showed increased antennation only toward the diglyceride fractions of both Ulex species, whereas T. caespitum showed no consistent reaction. This indicates that M. ruginodis can detect the elaiosome by responding to its surface chemicals, but T. caespitum is unresponsive to these chemicals. Responses to surface chemicals could increase the rate of seed detection in the field, and so these results suggest that Ulex elaiosomes produce chemicals that facilitate attraction of mutualistic rather than granivorous ant species. This could reduce seed predation and increase Ulex fitness.

  20. Species-level assessment of secondary metabolite diversity among Hamigera species and a taxonomic note on the genus

    PubMed Central

    Igarashi, Yasuhiro; Hanafusa, Tomoaki; Gohda, Fumiya; Peterson, Stephen; Bills, Gerald

    2014-01-01

    Secondary metabolite phenotypes in nine species of the Hamigera clade were analysed to assess their correlations to a multi-gene species-level phylogeny. High-pressure-liquid-chromatography-based chemical analysis revealed three distinctive patterns of secondary metabolite production: (1) the nine species could be divided into two groups on the basis of production of the sesquiterpene tricinonoic acid; (2) the tricinonoic acid-producing group produced two cyclic peptides avellanins A and B; (3) the tricinonoic acid-non-producing group could be further divided into two groups according to the production of avellanins A and B. The chemical phenotype was consistent with the phylogeny of the species, although metabolite patterns were not diagnostic at the species level. In addition, the taxonomy of the Hamigera clade was updated with the new combination Hamigera ingelheimensis proposed for Merimbla ingelheimensis, so that all species in the clade are now in the same genus. PMID:25379334

  1. LC-MS/MS Identification of Species-Specific Muscle Peptides in Processed Animal Proteins.

    PubMed

    Marchis, Daniela; Altomare, Alessandra; Gili, Marilena; Ostorero, Federica; Khadjavi, Amina; Corona, Cristiano; Ru, Giuseppe; Cappelletti, Benedetta; Gianelli, Silvia; Amadeo, Francesca; Rumio, Cristiano; Carini, Marina; Aldini, Giancarlo; Casalone, Cristina

    2017-12-06

    An innovative analytical strategy has been applied to identify signature peptides able to distinguish among processed animal proteins (PAPs) derived from bovine, pig, fish, and milk products. Proteomics was first used to elucidate the proteome of each source. Starting from the identified proteins and using a funnel based approach, a set of abundant and well characterized peptides with suitable physical-chemical properties (signature peptides) and specific for each source was selected. An on-target LC-ESI-MS/MS method (MRM mode) was set up using standard peptides and was then applied to selectively identify the PAP source and also to distinguish proteins from bovine carcass and milk proteins. We believe that the method described meets the request of the European Commission which has developed a strategy for gradually lifting the "total ban" toward "species to species ban", therefore requiring official methods for species-specific discrimination in feed.

  2. Biological control via "ecological" damping: An approach that attenuates non-target effects.

    PubMed

    Parshad, Rana D; Quansah, Emmanuel; Black, Kelly; Beauregard, Matthew

    2016-03-01

    In this work we develop and analyze a mathematical model of biological control to prevent or attenuate the explosive increase of an invasive species population, that functions as a top predator, in a three-species food chain. We allow for finite time blow-up in the model as a mathematical construct to mimic the explosive increase in population, enabling the species to reach "disastrous", and uncontrollable population levels, in a finite time. We next improve the mathematical model and incorporate controls that are shown to drive down the invasive population growth and, in certain cases, eliminate blow-up. Hence, the population does not reach an uncontrollable level. The controls avoid chemical treatments and/or natural enemy introduction, thus eliminating various non-target effects associated with such classical methods. We refer to these new controls as "ecological damping", as their inclusion dampens the invasive species population growth. Further, we improve prior results on the regularity and Turing instability of the three-species model that were derived in Parshad et al. (2014). Lastly, we confirm the existence of spatiotemporal chaos. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Ion beam sputter target and method of manufacture

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Higdon, Clifton; Elmoursi, Alaa A.; Goldsmith, Jason

    A target for use in an ion beam sputtering apparatus made of at least two target tiles where at least two of the target tiles are made of different chemical compositions and are mounted on a main tile and geometrically arranged on the main tile to yield a desired chemical composition on a sputtered substrate. In an alternate embodiment, the tiles are of varied thickness according to the desired chemical properties of the sputtered film. In yet another alternate embodiment, the target is comprised of plugs pressed in a green state which are disposed in cavities formed in a mainmore » tile also formed in a green state and the assembly can then be compacted and then sintered.« less

  4. A framework for spatial risk assessments: Potential impacts of nonindigenous invasive species on native species

    USGS Publications Warehouse

    Allen, Craig R.; Johnson, A.R.; Parris, L.

    2006-01-01

    Many populations of wild animals and plants are declining and face increasing threats from habitat fragmentation and loss as well as exposure to stressors ranging from toxicants to diseases to invasive nonindigenous species. We describe and demonstrate a spatially explicit ecological risk assessment that allows for the incorporation of a broad array of information that may influence the distribution of an invasive species, toxicants, or other stressors, and the incorporation of landscape variables that may influence the spread of a species or substances. The first step in our analyses is to develop species models and quantify spatial overlap between stressor and target organisms. Risk is assessed as the product of spatial overlap and a hazard index based on target species vulnerabilities to the stressor of interest. We illustrate our methods with an example in which the stressor is the ecologically destructive nonindigenous ant, Solenopsis invicta, and the targets are two declining vertebrate species in the state of South Carolina, USA. A risk approach that focuses on landscapes and that is explicitly spatial is of particular relevance as remaining undeveloped lands become increasingly uncommon and isolated and more important in the management and recovery of species and ecological systems. Effective ecosystem management includes the control of multiple stressors, including invasive species with large impacts, understanding where those impacts may be the most severe, and implementing management strategies to reduce impacts. Copyright ?? 2006 by the author(s).

  5. Sequential chemical treatment of radium species in TENORM waste sludge produced from oil and natural gas production.

    PubMed

    El Afifi, E M; Awwad, N S; Hilal, M A

    2009-01-30

    This paper is dedicated to the treatment of sludge occurring in frame of the Egyptian produced from oil and gas production. The activity levels of three radium isotopes: Ra-226 (of U-series), Ra-228 and Ra-224 (of Th-series) in the solid TENORM waste (sludge) were first evaluated and followed by a sequential treatment for all radium species (fractions) presented in TENORM. The sequential treatment was carried out based on two approaches 'A' and 'B' using different chemical solutions. The results obtained indicate that the activity levels of all radium isotopes (Ra-226, Ra-228 and Ra-224) of the environmental interest in the TENORM waste sludge were elevated with regard to exemption levels established by IAEA [International Atomic Energy Agency (IAEA), International basic safety standards for the protection against ionizing radiation and for the safety of radiation sources. GOV/2715/Vienna, 1994]. Each approach of the sequential treatment was performed through four steps using different chemical solutions to reduce the activity concentration of radium in a large extent. Most of the leached radium was found as an oxidizable Ra species. The actual removal % leached using approach B was relatively efficient compared to A. It is observed that the actual removal percentages (%) of Ra-226, Ra-228 and Ra-224 using approach A are 78+/-2.8, 64.8+/-4.1 and 76.4+/-5.2%, respectively. Whereas in approach A, the overall removal % of Ra-226, Ra-228 and Ra-228 was increased to approximately 91+/-3.5, 87+/-4.1 and 90+/-6.2%, respectively.

  6. Quantitative Absorption and Kinetic Studies of Transient Species Using Gas Phase Optical Calorimetry

    NASA Astrophysics Data System (ADS)

    Melnik, Dmitry G.

    2014-06-01

    Quantitative measurements of the absorption cross-sections and reaction rates constants of free radicals by spectroscopic means requires the knowledge of the absolute concentration of the target species. We have demonstrated earlier that such information can be retrieved from absorption measurements of the well-known ``reporter" molecule, co-produced in radical synthesis. This method is limited to photochemical protocols allowing for production of ``reporters" stochiometrically with the target species. This limitation can be overcome by use of the optical calorimetry (OC) which measures heat signatures of a photochemical protocol. These heat signatures are directly related to the amount of species produced and the thermochemical data of the reactants and stable products whose accuracy is usually substantially higher than that of the absorption data for prospective ``reporters". The implementation of the OC method presented in this talk is based on the measurements of the frequency shift of the resonances due to the change in the optical density of the reactiove sample within a Fabry-Perot cavity caused by deposition of heat from the absorbed photolysis beam and subsequent chemical reactions. Preliminary results will be presented and future development of this experimental technique will be discussed. D. Melnik, R. Chhantyal-Pun and T. A. Miller, J. Phys. Chem. A, 114, 11583, (2010)

  7. A broad cocktail of environmental pollutants found in eggs of three seabird species from remote colonies in Norway.

    PubMed

    Huber, Sandra; Warner, Nicholas A; Nygård, Torgeir; Remberger, Mikael; Harju, Mikael; Uggerud, Hilde T; Kaj, Lennart; Hanssen, Linda

    2015-06-01

    Eggs of 3 seabird species, common eider (Somateria mollisima), European shag (Phalacrocorax aristotelis aristotelis), and European herring gull (Larus argentatus), were surveyed for a broad range of legacy and emerging pollutants to assess chemical mixture exposure profiles of seabirds from the Norwegian marine environment. In total, 201 chemical substances were targeted for analysis ranging from metals, organotin compounds, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and associated metabolites, chlorinated paraffins, chlorinated and nonchlorinated organic pesticides, per- and polyfluoroalkyl substances (PFAS), dechlorane plus, octachlorostyrene, brominated flame retardants (BFRs), organophosphorous compounds, brominated and alkyl phenols, cyclic siloxanes, and phthalates. Of the chemicals targeted, 149 substances were found above the detection limits, with metals dominating the contaminant profile and comprising 60% of the total contaminant load. Polychlorinated biphenyls, pesticides, organophosphorous compounds, and PFAS were the dominant contaminant classes of organic pollutants found within the seabird species, with the highest loads occurring in herring gulls, followed by shag, and common eider. New generation pollutants (e.g., PFAS, organophosphorous compounds, and alkylphenols) were detected at similar or higher concentrations than the legacy persistent organic pollutants (POPs). Time trends of reported concentrations of legacy POPs appear to have decreased in recent decades from the Norwegian coastal environment. Concentrations of detected pollutants do not appear to have a negative effect on seabird population development within the sampling area. Additional stress caused by pollutants, however, may affect seabird health more at the individual level. © 2015 SETAC.

  8. Protective mechanisms of helminths against reactive oxygen species are highly promising drug targets.

    PubMed

    Perbandt, Markus; Ndjonka, Dieudonne; Liebau, Eva

    2014-01-01

    Helminths that are the causative agents of numerous neglected tropical diseases continue to be a major problem for human global health. In the absence of vaccines, control relies solely on pharmacoprophylaxis and pharmacotherapy to reduce transmission and to relieve symptoms. There are only a few drugs available and resistance in helminths of lifestock has been observed to the same drugs that are also used to treat humans. Clearly there is an urgent need to find novel antiparasitic compounds. Not only are helminths confronted with their own metabolically derived toxic and redox-active byproducts but also with the production of reactive oxygen species (ROS) by the host immune system, adding to the overall oxidative burden of the parasite. Antioxidant enzymes of helminths have been identified as essential proteins, some of them biochemically distinct to their host counterpart and thus appealing drug targets. In this review we have selected a few enzymatic antioxidants of helminths that are thought to be druggable.

  9. Can ozone be used to control the spread of freshwater Aquatic Invasive Species?

    USGS Publications Warehouse

    Buley, Riley P.; Hasler, Caleb T.; Tix, John A.; Suski, Cory D.; Hubert, Terrance D.

    2017-01-01

    The introduction of aquatic invasive species to non-native habitats can cause negative ecological effects and also billions of dollars in economic damage to governments and private industries. Once aquatic invasive species are introduced, eradication may be difficult without adversely affecting native species and habitats, urging resource managers to find preventative methods to protect non-invaded areas. The use of ozone (O3) as a non-physical barrier has shown promise as it is lethal to a wide range of aquatic taxa, requires a short contact time, and is relatively environmentally safe in aquatic systems when compared to other chemicals. However, before O3 can be considered as an approach to prevent the spread of aquatic invasive species, its effects on non-target organisms and already established aquatic invasive species must be fully evaluated. A review of the current literature was conducted to summarize data regarding the effects of O3 on aquatic taxa including fish, macroinvertebrates, zooplankton, phytoplankton, microbes, and pathogens. In addition, we assessed the practicality of ozone applications to control the movement of aquatic invasive species, and identified data gaps concerning the use of O3 as a non-physical barrier in field applications.

  10. Deriving criteria to select arthropod species for laboratory tests to assess the ecological risks from cultivating arthropod-resistant genetically engineered crops.

    PubMed

    Romeis, Jörg; Raybould, Alan; Bigler, Franz; Candolfi, Marco P; Hellmich, Richard L; Huesing, Joseph E; Shelton, Anthony M

    2013-01-01

    Arthropods form a major part of the biodiversity in agricultural landscapes. Many species are valued because they provide ecosystem services, including biological control, pollination and decomposition, or because they are of conservation interest. Some arthropods reduce crop yield and quality, and conventional chemical pesticides, biological control agents and genetically engineered (GE) crops are used to control them. A common concern addressed in the ecological risk assessment (ERA) that precedes regulatory approval of these pest control methods is their potential to adversely affect valued non-target arthropods (NTAs). A key concept of ERA is early-tier testing using worst-case exposure conditions in the laboratory and surrogate test species that are most likely to reveal an adverse effect. If no adverse effects are observed in those species at high exposures, confidence of negligible ecological risk from the use of the pest control method is increased. From experience with chemical pesticides and biological control agents, an approach is proposed for selecting test species for early-tier ERA of GE arthropod-resistant crops. Surrogate species should be selected that most closely meet three criteria: (i) Potential sensitivity: species should be the most likely to be sensitive to the arthropod-active compound based on the known spectrum of activity of the active ingredient, its mode of action, and the phylogenetic relatedness of the test and target species; (ii) species should be representative of valued taxa or functional groups that are most likely to be exposed to the arthropod-active compound in the field; and (iii) Availability and reliability: suitable life-stages of the test species must be obtainable in sufficient quantity and quality, and validated test protocols must be available that allow consistent detection of adverse effects on ecologically relevant parameters. Our proposed approach ensures that the most suitable species are selected for testing

  11. Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum

    PubMed Central

    2012-01-01

    Background Hidden Markov Models (HMMs) are a powerful tool for protein domain identification. The Pfam database notably provides a large collection of HMMs which are widely used for the annotation of proteins in new sequenced organisms. In Pfam, each domain family is represented by a curated multiple sequence alignment from which a profile HMM is built. In spite of their high specificity, HMMs may lack sensitivity when searching for domains in divergent organisms. This is particularly the case for species with a biased amino-acid composition, such as P. falciparum, the main causal agent of human malaria. In this context, fitting HMMs to the specificities of the target proteome can help identify additional domains. Results Using P. falciparum as an example, we compare approaches that have been proposed for this problem, and present two alternative methods. Because previous attempts strongly rely on known domain occurrences in the target species or its close relatives, they mainly improve the detection of domains which belong to already identified families. Our methods learn global correction rules that adjust amino-acid distributions associated with the match states of HMMs. These rules are applied to all match states of the whole HMM library, thus enabling the detection of domains from previously absent families. Additionally, we propose a procedure to estimate the proportion of false positives among the newly discovered domains. Starting with the Pfam standard library, we build several new libraries with the different HMM-fitting approaches. These libraries are first used to detect new domain occurrences with low E-values. Second, by applying the Co-Occurrence Domain Discovery (CODD) procedure we have recently proposed, the libraries are further used to identify likely occurrences among potential domains with higher E-values. Conclusion We show that the new approaches allow identification of several domain families previously absent in the P. falciparum proteome

  12. Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum.

    PubMed

    Terrapon, Nicolas; Gascuel, Olivier; Maréchal, Eric; Bréhélin, Laurent

    2012-05-01

    Hidden Markov Models (HMMs) are a powerful tool for protein domain identification. The Pfam database notably provides a large collection of HMMs which are widely used for the annotation of proteins in new sequenced organisms. In Pfam, each domain family is represented by a curated multiple sequence alignment from which a profile HMM is built. In spite of their high specificity, HMMs may lack sensitivity when searching for domains in divergent organisms. This is particularly the case for species with a biased amino-acid composition, such as P. falciparum, the main causal agent of human malaria. In this context, fitting HMMs to the specificities of the target proteome can help identify additional domains. Using P. falciparum as an example, we compare approaches that have been proposed for this problem, and present two alternative methods. Because previous attempts strongly rely on known domain occurrences in the target species or its close relatives, they mainly improve the detection of domains which belong to already identified families. Our methods learn global correction rules that adjust amino-acid distributions associated with the match states of HMMs. These rules are applied to all match states of the whole HMM library, thus enabling the detection of domains from previously absent families. Additionally, we propose a procedure to estimate the proportion of false positives among the newly discovered domains. Starting with the Pfam standard library, we build several new libraries with the different HMM-fitting approaches. These libraries are first used to detect new domain occurrences with low E-values. Second, by applying the Co-Occurrence Domain Discovery (CODD) procedure we have recently proposed, the libraries are further used to identify likely occurrences among potential domains with higher E-values. We show that the new approaches allow identification of several domain families previously absent in the P. falciparum proteome and the Apicomplexa phylum, and

  13. Meaningful traits for grouping plant species across arid ecosystems.

    PubMed

    Bär Lamas, Marlene Ivonne; Carrera, A L; Bertiller, M B

    2016-05-01

    Grouping species may provide some degree of simplification to understand the ecological function of plants on key ecosystem processes. We asked whether groups of plant species based on morpho-chemical traits associated with plant persistence and stress/disturbance resistance reflect dominant plant growth forms in arid ecosystems. We selected twelve sites across an aridity gradient in northern Patagonia. At each site, we identified modal size plants of each dominant species and assessed specific leaf area (SLA), plant height, seed mass, N and soluble phenol concentration in green and senesced leaves at each plant. Plant species were grouped according with plant growth forms (perennial grasses, evergreen shrubs and deciduous shrubs) and plant morphological and/or chemical traits using cluster analysis. We calculated mean values of each plant trait for each species group and plant growth form. Plant growth forms significantly differed among them in most of the morpho-chemical traits. Evergreen shrubs were tall plants with the highest seed mass and soluble phenols in leaves, deciduous shrubs were also tall plants with high SLA and the highest N in leaves, and perennial grasses were short plants with high SLA and low concentration of N and soluble phenols in leaves. Grouping species by the combination of morpho-chemical traits yielded 4 groups in which species from one growth form prevailed. These species groups differed in soluble phenol concentration in senesced leaves and plant height. These traits were highly correlated. We concluded that (1) plant height is a relevant synthetic variable, (2) growth forms adequately summarize ecological strategies of species in arid ecosystems, and (3) the inclusion of plant morphological and chemical traits related to defenses against environmental stresses and herbivory enhanced the potential of species grouping, particularly within shrubby growth forms.

  14. Essential Oils of Myrtaceae Species Growing Wild in Tunisia: Chemical Variability and Antifungal Activity Against Biscogniauxia mediterranea, the Causative Agent of Charcoal Canker.

    PubMed

    Yangui, Islem; Zouaoui Boutiti, Meriem; Boussaid, Mohamed; Messaoud, Chokri

    2017-07-01

    The chemical composition of five Eucalyptus species and five Myrtus communis L. populations was investigated using GC/MS and GC-FID. For Eucalyptus essential oils, 32 compounds, representing 88.56 - 96.83% of the total oil according to species, were identified. The main compounds were 1,8-cineole, α-pinene, p-cymene, γ-gurjunene, α-aromadendrene, and β-phellandrene. For Myrtle essential oils, 26 compounds, representing 93.13 - 98.91% of the total oil were identified. α-Pinene, 1,8-cineole, linalool, and myrtenyl acetate were found to be the major compounds. Principal component analysis (PCA) showed chemical differentiation between Eucalyptus species and between Myrtle populations. Biscogniauxia mediterranea, the causative agent of charcoal canker, was identified according to its morphological and molecular characteristics. Essential oils of the investigated Eucalyptus species and Myrtle populations were tested for their antifungal capacity against this fungus. The antifungal activity varied according to the essential oil composition. Biscogniauxia mediterranea exhibited powerful resistance to some essential oils including them of Eucalyptus lehmannii and Eucalyptus sideroxylon but it was very sensitive to Eucalyptus camaldulensis oil (IC 50  = 3.83 mg/ml) and M. communis oil from Zaghouan (IC 50  = 1 mg/ml). This sensitivity was found to be correlated to some essential oil compounds such as p-cymene, carvacrol, cuminaldehyde, and linalool. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

  15. The Role of Diet in Shaping the Chemical Signal Design of Lacertid Lizards.

    PubMed

    Baeckens, Simon; García-Roa, Roberto; Martín, José; Van Damme, Raoul

    2017-09-01

    Lizards communicate with others via chemical signals, the composition of which may vary among species. Although the selective pressures and constraints affecting chemical signal diversity at the species level remain poorly understood, the possible role of diet has been largely neglected. The chemical signals of many lizards originate from the femoral glands that exude a mixture of semiochemicals, and may be used in a variety of contexts. We analyzed the lipophilic fraction of the glandular secretions of 45 species of lacertid lizard species by gas chromatography/mass spectrometry. The proportions of nine major chemical classes (alcohols, aldehydes, fatty acids, furanones, ketones, steroids, terpenoids, tocopherols and waxy esters), the relative contributions of these different classes ('chemical diversity'), and the total number of different lipophilic compounds ('chemical richness') varied greatly among species. We examined whether interspecific differences in these chemical variables could be coupled to interspecific variation in diet using data from the literature. In addition, we compared chemical signal composition among species that almost never, occasionally, or often eat plant material. We found little support for the hypothesis that the chemical profile of a given species' secretion depends on the type of food consumed. Diet breadth did not correlate with chemical diversity or richness. The amount of plants or ants consumed did not affect the relative contribution of any of the nine major chemical classes to the secretion. Chemical diversity did not differ among lizards with different levels of plant consumption; however, chemical richness was low in species with an exclusive arthropod diet, suggesting that incorporating plants in the diet enables lizards to increase the number of compounds allocated to secretions, likely because a (partly) herbivorous diet allows them to include compounds of plant origin that are unavailable in animal prey. Still, overall

  16. An oyster species-specific miRNA scaffold42648_5080 modulates haemocyte migration by targeting integrin pathway.

    PubMed

    Chen, Hao; Wang, Hao; Jiang, Shuai; Xu, Jiachao; Wang, Lingling; Qiu, Limei; Song, Linsheng

    2016-10-01

    miRNAs are important gene regulators at post-transcriptional level and can modulate diverse biological processes, including immune response. Dozens of species-specific miRNAs have been identified in oyster Crassostrea gigas while their functions remain largely unknown. In the present study, an oyster species-specific miRNA scaffold42648_5080 was found responsive to LPS stimulation and might target a total of 31 oyster genes possibly involved in cell communication, cellular localization and cellular response to stimulus. Besides, in gain-of-function assay of scaffold42648_5080 in vivo, the phagocytosis (30.90% in miRNA group verse 23.20% in miRNA control group), apoptosis (3.10% in miRNA group verse 5.30% in miRNA control group) and migration rate (13.88% in miRNA group verse 21.03% in miRNA control group) of oyster haemocytes were found significantly altered after the injection of scaffold42648_5080 mimics. Among the target genes, integrin-linked kinase (CgILK) was considered crucial in cell migration and its interaction with scaffold42648_5080 was then verified both in vitro and in vivo. Consequently, a significant decrease of relative luciferase ratio was observed in CgILK 3'-UTR luciferase reporter assay after transfection of scaffold42648_5080 mimics (0.70-fold of that in blank group, p < 0.01). Meanwhile, when scaffold42648_5080 was overexpressed in vivo (5.41-fold of miRNA control group, p < 0.01), the expression of CgILK declined significantly to 0.25-fold of miRNA control group (p < 0.01). Comparatively, a significant decrease of the haemocyte migration rate (19.76% verse 34.82% in siEGFP control group, p < 0.01) was observed after knock-down of CgILK in vivo. The present study, as far as we know, for the first time revealed the immunomodulation role of an oyster species-specific miRNA, which might provide new insights into miRNA-mediated adaptation mechanism of oysters. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. The Relevance of Marine Chemical Ecology to Plankton and Ecosystem Function: An Emerging Field

    PubMed Central

    Ianora, Adrianna; Bentley, Matthew G.; Caldwell, Gary S.; Casotti, Raffaella; Cembella, Allan D.; Engström-Öst, Jonna; Halsband, Claudia; Sonnenschein, Eva; Legrand, Catherine; Llewellyn, Carole A.; Paldavičienë, Aistë; Pilkaityte, Renata; Pohnert, Georg; Razinkovas, Arturas; Romano, Giovanna; Tillmann, Urban; Vaiciute, Diana

    2011-01-01

    Marine chemical ecology comprises the study of the production and interaction of bioactive molecules affecting organism behavior and function. Here we focus on bioactive compounds and interactions associated with phytoplankton, particularly bloom-forming diatoms, prymnesiophytes and dinoflagellates. Planktonic bioactive metabolites are structurally and functionally diverse and some may have multiple simultaneous functions including roles in chemical defense (antipredator, allelopathic and antibacterial compounds), and/or cell-to-cell signaling (e.g., polyunsaturated aldehydes (PUAs) of diatoms). Among inducible chemical defenses in response to grazing, there is high species-specific variability in the effects on grazers, ranging from severe physical incapacitation and/or death to no apparent physiological response, depending on predator susceptibility and detoxification capability. Most bioactive compounds are present in very low concentrations, in both the producing organism and the surrounding aqueous medium. Furthermore, bioactivity may be subject to synergistic interactions with other natural and anthropogenic environmental toxicants. Most, if not all phycotoxins are classic secondary metabolites, but many other bioactive metabolites are simple molecules derived from primary metabolism (e.g., PUAs in diatoms, dimethylsulfoniopropionate (DMSP) in prymnesiophytes). Producing cells do not seem to suffer physiological impact due to their synthesis. Functional genome sequence data and gene expression analysis will provide insights into regulatory and metabolic pathways in producer organisms, as well as identification of mechanisms of action in target organisms. Understanding chemical ecological responses to environmental triggers and chemically-mediated species interactions will help define crucial chemical and molecular processes that help maintain biodiversity and ecosystem functionality. PMID:22131962

  18. Cumulative index to chemicals and to common and scientific names of species listed in Contaminant Hazard Reviews 1 through 34

    USGS Publications Warehouse

    Eisler, Ronald

    1999-01-01

    The Contaminant Hazard Review (CHR) series--sponsored by the U.S. Geological Survey, Patuxent Wildlife Research Center--synthesizes ecotoxicological data for selected environmental contaminants, with emphasis on hazards to native species of flora and fauna. From 1985 through 1998, 34 reviews were published in various report series of the U.S. Department of the Interior on agricultural pesticides (acrolein, atrazine, carbofuran, chlordane, chlorpyrifos, diazinon, diflubenzuron, famphur, fenvalerate, mirex, paraquat, toxaphene), metals and metalloids (arsenic, boron, cadmium, chromium, copper, lead, mercury, molybdenum, nickel, selenium, silver, tin, zinc), mammalian biocides (sodium monofluoroacetate), organic industrial and municipal wastes (dioxins, pentachlorophenol, polycyclic aromatic hydrocarbons, polychlorinated biphenyls), minin wastes (cyanide), and ionizing radiations. This current report is a cumulative index to the common and scientific names of all biological species listed in the first 34 reports in the CHR series, with individual species cross-referenced with contaminant hazard review and corresponding page numbers. A similar index for chemicals is included.

  19. Chemical Synthesis of Proteins

    PubMed Central

    Nilsson, Bradley L.; Soellner, Matthew B.; Raines, Ronald T.

    2010-01-01

    Proteins have become accessible targets for chemical synthesis. The basic strategy is to use native chemical ligation, Staudinger ligation, or other orthogonal chemical reactions to couple synthetic peptides. The ligation reactions are compatible with a variety of solvents and proceed in solution or on a solid support. Chemical synthesis enables a level of control on protein composition that greatly exceeds that attainable with ribosome-mediated biosynthesis. Accordingly, the chemical synthesis of proteins is providing previously unattainable insight into the structure and function of proteins. PMID:15869385

  20. Steam sauna and mother roasting in Lao PDR: practices and chemical constituents of essential oils of plant species used in postpartum recovery

    PubMed Central

    2011-01-01

    Background Fundamental in traditional postpartum recovery in Lao PDR is the use of hotbeds, mother roasting, steam sauna and steam baths. During these treatments medicinal plants play a crucial role, but little has been published about how the treatments are carried out precisely, which species are used, the medicinal properties of these species, and the medicinal efficacy of their chemical constituents. Methods Sixty-five interviews, in 15 rural villages, with women of 4 different ethnic groups were conducted to survey confinement rituals, and postpartum plant use and salience. Essential oils from the main species used were extracted using steam distillation and the main chemical constituents characterized using gas chromatography-mass spectrometry (GC-MS). Results A total of 10 different species were used by three or more of the ethnic groups included in this study. All species were used in steam sauna and bath, but only 3 species were used in hotbed and mother roasting. Essential oils of Amomum villosum, Amomum microcarpum and Blumea balsamifera were found to contain significant amounts of the following terpenes: β-pinene, camphor, bornyl acetate, borneol, linalool, D-limonene, fenchone, terpinen-4-ol and α-terpinene. Conclusions Many of these terpenes have documented antimicrobial and analgesic properties, and some have also synergistic interactions with other terpenes. The mode of application in hotbed and mother roasting differs from the documented mechanisms of action of these terpenes. Plants in these two practices are likely to serve mainly hygienic purposes, by segregating the mother from infection sources such as beds, mats, stools, cloth and towels. Steam sauna medicinal plant use through inhalation of essential oils vapors can possibly have medicinal efficacy, but is unlikely to alleviate the ailments commonly encountered during postpartum convalescence. Steam sauna medicinal plant use through dermal condensation of essential oils, and steam bath

  1. An ambusher's arsenal: chemical crypsis in the puff adder (Bitis arietans)

    PubMed Central

    Miller, Ashadee Kay; Maritz, Bryan; McKay, Shannon; Glaudas, Xavier; Alexander, Graham J.

    2015-01-01

    Ambush foragers use a hunting strategy that places them at risk of predation by both visual and olfaction-oriented predators. Resulting selective pressures have driven the evolution of impressive visual crypsis in many ambushing species, and may have led to the development of chemical crypsis. However, unlike for visual crypsis, few studies have attempted to demonstrate chemical crypsis. Field observations of puff adders (Bitis arietans) going undetected by several scent-orientated predator and prey species led us to investigate chemical crypsis in this ambushing species. We trained dogs (Canis familiaris) and meerkats (Suricata suricatta) to test whether a canid and a herpestid predator could detect B. arietans using olfaction. We also tested for chemical crypsis in five species of active foraging snakes, predicted to be easily detectable. Dogs and meerkats unambiguously indicated active foraging species, but failed to correctly indicate puff adder, confirming that B. arietans employs chemical crypsis. This is the first demonstration of chemical crypsis anti-predatory behaviour, though the phenomenon may be widespread among ambushers, especially those that experience high mortality rates owing to predation. Our study provides additional evidence for the existence of an ongoing chemically mediated arms race between predator and prey species. PMID:26674950

  2. An ambusher's arsenal: chemical crypsis in the puff adder (Bitis arietans).

    PubMed

    Miller, Ashadee Kay; Maritz, Bryan; McKay, Shannon; Glaudas, Xavier; Alexander, Graham J

    2015-12-22

    Ambush foragers use a hunting strategy that places them at risk of predation by both visual and olfaction-oriented predators. Resulting selective pressures have driven the evolution of impressive visual crypsis in many ambushing species, and may have led to the development of chemical crypsis. However, unlike for visual crypsis, few studies have attempted to demonstrate chemical crypsis. Field observations of puff adders (Bitis arietans) going undetected by several scent-orientated predator and prey species led us to investigate chemical crypsis in this ambushing species. We trained dogs (Canis familiaris) and meerkats (Suricata suricatta) to test whether a canid and a herpestid predator could detect B. arietans using olfaction. We also tested for chemical crypsis in five species of active foraging snakes, predicted to be easily detectable. Dogs and meerkats unambiguously indicated active foraging species, but failed to correctly indicate puff adder, confirming that B. arietans employs chemical crypsis. This is the first demonstration of chemical crypsis anti-predatory behaviour, though the phenomenon may be widespread among ambushers, especially those that experience high mortality rates owing to predation. Our study provides additional evidence for the existence of an ongoing chemically mediated arms race between predator and prey species. © 2015 The Author(s).

  3. Bioactivity of compounds from Acmella oleracea against Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) and selectivity to two non-target species.

    PubMed

    Moreno, Shaiene C; Carvalho, Geraldo A; Picanço, Marcelo C; Morais, Elisangela G F; Pereira, Rogério M

    2012-03-01

    Tropical plants are recognised sources of bioactive compounds that can be used for pest control. The objective of this study was to evaluate the biological activity of compounds present in Acmella oleracea (Asteracea) against Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae), which is the main pest of tomato crops in Latin America. The selectivity of these compounds to the predator Solenopsis saevissima (Smith) (Hymenoptera: Formicidae) and to the pollinator Tetragonisca angustula (Latr.) (Hymenoptera: Apidae: Meliponinae) was also of interest. A bioassay screening with hexane and ethanol extracts from 23 plants was performed. The hexane extract of A. oleraceae was the most active of the extracts and was selected for further study. The following three alkamides were isolated from a hexane extract of the aerial parts of A. oleracea: spilanthol, (E)-N-isobutylundeca-2-en-8,10-diynamide and (R, E)-N-(2-methylbutyl)undeca-2-en-8,10-diynamide. All of the isolated compounds showed insecticidal activity, with spilanthol being the most active (LD(50) = 0.13 µg mg(-1) ) against T. absoluta. The alkamides were selective to both beneficial species studied. The crude hexane extract of A. oleraceae showed high insecticidal activity and can be used to control T. absoluta in organic or conventional crops. Quantification of LD(50) values of isolated compounds against T. absoluta showed that alkamides could serve as potent insecticides for T. absoluta control programmes. Spilanthol was the main alkamide active isolated. This alkamide is the most promising as it has the highest insecticidal activity and is selective to non-target organisms. Copyright © 2011 Society of Chemical Industry.

  4. Facultative slave-making ants Formica sanguinea label their slaves with own recognition cues instead of employing the strategy of chemical mimicry.

    PubMed

    Włodarczyk, Tomasz; Szczepaniak, Lech

    2017-01-01

    Slave-making ant species use the host workforce to ensure normal colony functioning. Slaves are robbed as pupae from their natal nest and after eclosion, assume the parasite colony as their own. A possible factor promoting the successful integration of slaves into a foreign colony is congruence with the slave-makers in terms of cuticular hydrocarbons, which are known to play the role of recognition cues in social insects. Such an adaptation is observed in the obligate slave-making ant species, which are chemically adjusted to their slaves. To date, however, no reports have been available on facultative slave-making species, which represent an earlier stage of the evolution of slavery. Such an example is Formica sanguinea, which exploit F. fusca colonies as their main source of a slave workforce. Our results show that F. sanguinea ants have a distinct cuticular hydrocarbon profile, which contains compounds not present in free-living F. fusca ants from potential target nests. Moreover, enslaved F. fusca ants acquire hydrocarbons from their slave-making nestmates to such an extent that they become chemically differentiated from free-living, conspecific ants. Our study shows that F. sanguinea ants promote their own recognition cues in their slaves, rather than employing the strategy of chemical mimicry. Possible reasons why F. sanguinea is not chemically well adjusted to its main host species are discussed in this paper. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Spreading the news: subcellular and organellar reactive oxygen species production and signalling.

    PubMed

    Mignolet-Spruyt, Lorin; Xu, Enjun; Idänheimo, Niina; Hoeberichts, Frank A; Mühlenbock, Per; Brosché, Mikael; Van Breusegem, Frank; Kangasjärvi, Jaakko

    2016-06-01

    As plants are sessile organisms that have to attune their physiology and morphology continuously to varying environmental challenges in order to survive and reproduce, they have evolved complex and integrated environment-cell, cell-cell, and cell-organelle signalling circuits that regulate and trigger the required adjustments (such as alteration of gene expression). Although reactive oxygen species (ROS) are essential components of this network, their pathways are not yet completely unravelled. In addition to the intrinsic chemical properties that define the array of interaction partners, mobility, and stability, ROS signalling specificity is obtained via the spatiotemporal control of production and scavenging at different organellar and subcellular locations (e.g. chloroplasts, mitochondria, peroxisomes, and apoplast). Furthermore, these cellular compartments may crosstalk to relay and further fine-tune the ROS message. Hence, plant cells might locally and systemically react upon environmental or developmental challenges by generating spatiotemporally controlled dosages of certain ROS types, each with specific chemical properties and interaction targets, that are influenced by interorganellar communication and by the subcellular location and distribution of the involved organelles, to trigger the suitable acclimation responses in association with other well-established cellular signalling components (e.g. reactive nitrogen species, phytohormones, and calcium ions). Further characterization of this comprehensive ROS signalling matrix may result in the identification of new targets and key regulators of ROS signalling, which might be excellent candidates for engineering or breeding stress-tolerant plants. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  6. Chemical scissors cut phosphorene nanostructures

    NASA Astrophysics Data System (ADS)

    Peng, Xihong; Wei, Qun

    2014-12-01

    Phosphorene, a recently fabricated two-dimensional puckered honeycomb structure of phosphorus, showed promising properties for applications in nano-electronics. In this work, we report a chemical scissors effect on phosphorene, using first-principles method. It was found that chemical species, such as H, OH, F, and Cl, can act as scissors to cut phosphorene. Phosphorus nanochains and nanoribbons can be obtained. The scissors effect results from the strong bonding between the chemical species and phosphorus atoms. Other species such as O, S and Se fail to cut phosphorene nanostructures due to their weak bonding with phosphorus. The electronic structures of the produced P-chains reveal that the hydrogenated chain is an insulator while the pristine chain is a one-dimensional Dirac material, in which the charge carriers are massless fermions travelling at an effective speed of light ˜8 × 105 m s-1. The obtained zigzag phosphorene nanoribbons show either metallic or semiconducting behaviors, depending on the treatment of the edge phosphorus atoms.

  7. Can species-specific differences in foliar chemistry influence leaf litter decomposition in grassland species?

    NASA Astrophysics Data System (ADS)

    Sanaullah, M.; Chabbi, A.; Rumpel, C.

    2009-04-01

    The influence of litter quality on its rate of decomposition is a crucial aspect of C cycle. In this study we concentrated on grassland ecosystems where leaf litter is one of the major sources of C input. To quantify the contribution of initial leaf chemistry within different plant species, the decomposition of chemically different leaf litter of three grassland species (Lolium perenne, Festuca arundinacea and Dactylis glomerata) was monitored, using the litter bag technique. Litter of different maturity stages i.e. green (fresh leaves) and brown litter (brown leaves were still attached to the plant), were incubated on bare soil surface. Samples were taken at different time intervals (0, 2, 4, 8, 20 and 44 weeks) and were analyzed for mass loss, organic C and N contents and stable isotopic signatures (C and N). Changes in litter chemistry were addressed by determining lignin-derived phenols after CuO oxidation and non-cellulosic polysaccharides after acid hydrolysis followed by gas chromatography. Green litter was chemically different from brown litter due to higher initial N and lower lignin contents. While in grassland species, both L. perenne and D. glomerata were similar in their initial chemical composition compared with F. arundinacea. Green litter showed higher rate of degradation. In green litter, Percent lignin remaining of initial (% OI) followed the similar decomposition pattern as of C remaining indicating lignin as controlling factor in decomposition. Constant Acid-to-Aldehyde ratios of lignin-derived phenols (vanillyl and syringyl) did not suggest any transformation in lignin structures. In green litter, increase in non-cellulosic polysaccharides ratios (C6/C5 and deoxy/C5) proposed microbial-derived sugars, while there was no significant increase in these ratios in brown litter. In conclusion, due to the differences in initial chemical composition (initial N and lignin contents), green litter decomposition was higher than brown litter in all

  8. SeqAPASS: Sequence alignment to predict across-species ...

    EPA Pesticide Factsheets

    Efforts to shift the toxicity testing paradigm from whole organism studies to those focused on the initiation of toxicity and relevant pathways have led to increased utilization of in vitro and in silico methods. Hence the emergence of high through-put screening (HTS) programs, such as U.S. EPA ToxCast, and application of the adverse outcome pathway (AOP) framework for identifying and defining biological key events triggered upon perturbation of molecular initiating events and leading to adverse outcomes occuring at a level of organization relevant for risk assessment [1]. With these recent initiatives to harness the power of “the pathway” in describing and evaluating toxicity comes the need to extrapolate data beyond the model species. Sequence alignment to predict across-species susceptibilty (SeqAPASS) is a web-based tool that allows the user to begin to understand how broadly HTS data or AOP constructs may plausibly be extrapolated across species, while describing the relative intrinsic susceptibiltiy of different taxa to chemicals with known modes of action (e.g., pharmaceuticals and pesticides). The tool rapidly and strategically assesses available molecular target information to describe protein sequence similarity at the primary amino acid sequence, conserved domain, and individual amino acid residue levels. This in silico approach to species extrapolation was designed to automate and streamline the relatively complex and time-consuming process of co

  9. Miscellaneous chemical toxins

    USGS Publications Warehouse

    Friend, M.

    1999-01-01

    The previous chapters provide information about some of the chemical toxins that have lethal effects on wild birds. The material presented in Section 7, Chemical Toxins, is far from comprehensive because wild birds are poisoned by a wide variety of toxic substances. Also, monitoring of wild bird mortality is not yet organized so that diagnostic findings can be extended to reflect the relative impacts among the types of toxins, within populations, or among species, geographic areas, and time. The data that are available are not collectively based on random sampling, nor do specimen collection and submission follow methodical assessment methods. Instead, most data simply document individual bird poisoning events. The inherent biases in this information include the species of birds observed dead (large birds in open areas are more likely to be observed dead than small forest birds); the species of birds likely to be submitted for analysis (bald eagles are more likely to be submitted than house sparrows); collection sites (agricultural fields are more likely to be observed than urban environments); geographic area of the country; season; reasons for submissions; and other variables. Nevertheless, findings from individual events reflect the causes of mortality associated with those events and collectively identify chemical toxins that repeatedly cause bird mortalities which result in carcass collection and sub

  10. Developing risk hypotheses and selecting species for assessing non-target impacts of GM trees with novel traits: the case of altered-lignin pine trees.

    PubMed

    Malone, Louise A; Todd, Jacqui H; Burgess, Elisabeth P J; Walter, Christian; Wagner, Armin; Barratt, Barbara I P

    2010-01-01

    A procedure is presented for developing environmental risk hypotheses associated with the deployment of forest trees genetically modified to have altered wood properties and for selecting non-target species to test these hypotheses. Altered-lignin Pinus radiata trees intended for use in New Zealand are used as a hypothetical case study to illustrate our approach. Firstly, environmental management goals (such as wood production, flood control or preservation of biodiversity) were identified and linked to the forest attributes they require. Necessary conditions for each attribute were listed and appropriate assessment endpoints for them developed. For example, biological control of pests may be one condition necessary for a forest to have healthy trees, and the diversity and abundance of natural enemy species in the forest could be an appropriate assessment endpoint for measuring this condition. A conceptual model describing the relationships between an altered-lignin GM pine tree and potentially affected invertebrates and micro-organisms in a plantation forest was used to develop a set of risk hypotheses describing how the GM trees might affect each assessment endpoint. Because purified lignin does not represent the properties it imparts to wood, maximum hazard dose tests with non-target organisms, as are used to inform toxin risk assessment, cannot be conducted. Alternative experiments, based on current knowledge of the responses of organisms to lignin, must be designed. A screening method was adapted and applied to a database of invertebrate species known to inhabit New Zealand pine forests to identify and prioritize non-target invertebrate species that could be used as experimental subjects for examining these hypotheses. The screening model and its application are presented, along with a set of recommendations for pre-release tests with GM pines and potentially affected invertebrates and micro-organisms. © ISBR, EDP Sciences, 2011.

  11. Chemical Composition of Selected Commercial Herbal Remedies in Relation to Geographical Origin and Inter-Species Diversity.

    PubMed

    Konieczynski, Pawel; Viapiana, Agnieszka; Lysiuk, Roman; Wesolowski, Marek

    2018-03-01

    Infusions prepared from medicinal herbs that are rich in flavonoids are very popular herbal remedies in societies of Eastern Europe. Therefore, the content of essential elements together with total flavonoids was analyzed in 65 commercially available samples of herbal drugs originating from Ukraine, Romania, and Belarus. The results showed that metallic elements (in mg kg -1 d.w.) have occurred in the following order: Fe > Mn > Zn > Cu, both for total and water-extractable species. Total flavonoids were determined in the range from 10.0 to 191.8 mg g -1 d.w. Several significant correlations have been found between the analytes, especially among water-extractable Fe with other metals, and total flavonoids and Fe, Zn, and Mn. Analysis of variance has revealed significant differences among studied samples due to their origin from different countries, especially between Belarussian samples and others. Differences owing to belonging to various plant species were also found, as it was noticed in the case of Polygoni aviculare herba in comparison with other botanical plant species. Moreover, multivariate statistical techniques, such as cluster analysis (CA) and principal component analysis (PCA) were used to gather herbal drugs based on similarity of chemical composition. CA grouped the samples into clusters with similar level of elements and total flavonoid contents, and PCA has indicated Hyperici herba, Tiliae flores, and Crataegi fructus as herbal remedies with close concentration of studied elements and flavonoids.

  12. Impact of environmentally based chemical hardness on uranium speciation and toxicity in six aquatic species.

    PubMed

    Goulet, Richard R; Thompson, Patsy A; Serben, Kerrie C; Eickhoff, Curtis V

    2015-03-01

    Treated effluent discharge from uranium (U) mines and mills elevates the concentrations of U, calcium (Ca), magnesium (Mg), and sulfate (SO4 (2-) ) above natural levels in receiving waters. Many investigations on the effect of hardness on U toxicity have been experiments on the combined effects of changes in hardness, pH, and alkalinity, which do not represent water chemistry downstream of U mines and mills. Therefore, more toxicity studies with water chemistry encountered downstream of U mines and mills are necessary to support predictive assessments of impacts of U discharge to the environment. Acute and chronic U toxicity laboratory bioassays were realized with 6 freshwater species in waters of low alkalinity, circumneutral pH, and a range of chemical hardness as found in field samples collected downstream of U mines and mills. In laboratory-tested waters, speciation calculations suggested that free uranyl ion concentrations remained constant despite increasing chemical hardness. When hardness increased while pH remained circumneutral and alkalinity low, U toxicity decreased only to Hyalella azteca and Pseudokirchneriella subcapitata. Also, Ca and Mg did not compete with U for the same uptake sites. The present study confirms that the majority of studies concluding that hardness affected U toxicity were in fact studies in which alkalinity and pH were the stronger influence. The results thus confirm that studies predicting impacts of U downstream of mines and mills should not consider chemical hardness. Environ Toxicol Chem 2015;34:562-574. © 2014 The Authors. Published by Wiley Periodicals, Inc. on behalf of SETAC. © 2014 The Authors. Published by Wiley Periodicals, Inc. on behalf of SETAC.

  13. Capacitive chemical sensor

    DOEpatents

    Manginell, Ronald P; Moorman, Matthew W; Wheeler, David R

    2014-05-27

    A microfabricated capacitive chemical sensor can be used as an autonomous chemical sensor or as an analyte-sensitive chemical preconcentrator in a larger microanalytical system. The capacitive chemical sensor detects changes in sensing film dielectric properties, such as the dielectric constant, conductivity, or dimensionality. These changes result from the interaction of a target analyte with the sensing film. This capability provides a low-power, self-heating chemical sensor suitable for remote and unattended sensing applications. The capacitive chemical sensor also enables a smart, analyte-sensitive chemical preconcentrator. After sorption of the sample by the sensing film, the film can be rapidly heated to release the sample for further analysis. Therefore, the capacitive chemical sensor can optimize the sample collection time prior to release to enable the rapid and accurate analysis of analytes by a microanalytical system.

  14. Detection of electrophilic and nucleophilic chemical agents

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    McElhanon, James R.; Shepodd, Timothy J.

    2014-08-12

    A "real time" method for detecting chemical agents generally and particularly electrophilic and nucleophilic species by employing tunable, precursor sensor materials that mimic the physiological interaction of these agents to form highly florescent berberine-type alkaloids that can be easily and rapidly detected. These novel precursor sensor materials can be tuned for reaction with both electrophilic (chemical species, toxins) and nucleophilic (proteins and other biological molecules) species. By bonding or otherwise attaching these precursor molecules to a surface or substrate they can be used in numerous applications.

  15. Performance of potential non-crop or wild species under OECD 208 testing guideline study conditions for terrestrial non-target plants.

    PubMed

    Pallett, Ken; Cole, Jon; Oberwalder, Christian; Porch, John

    2007-02-01

    The inclusion of 52 potential non-crop or wild species in new OECD guidelines for terrestrial non-target plant (TNTP) testing led to a ring test conducted by four laboratories experienced in regulatory testing. Species selected had shown potential to meet validity criteria of emergence for TNTP studies in a previous evaluation of the 52 species. OECD 208 guideline conditions were applied, with and without seed pretreatments recommended to enhance germination. These species were Abutilon theophrasti (L.) Medic., Avena fatua L., Fallopia convolvulus (L.) Adans., Galium aparine L., Ipomoea hederacea (L.) Jacq. and Veronica persica Poir. Only I. hederacea met the validity criterion of 70% emergence in all laboratories and showed a low variability in biomass. Of the other species, none led to 70% emergence in all four laboratories. The recommended pretreatments did not have a major impact on emergence. Biomass was also investigated with A. theophrasti, A. fatua, Centaurea cyanus L., I. hederacea and Rumex crispus L. Variability of biomass, a key parameter in TNTP regulatory studies, exceeded normal biomass variability of crop species used for TNTP studies. The addition of a thin layer of quartz sand to the soil surface resulted in improved emergence of C. cyanus, G. aparine and V. persica; however, such a procedure, while routine in screening studies to improve germination, is a deviation from the TNTP guidelines. These initial studies indicate that some species could meet the emergence criteria for TNTP testing. However, there is a need for further studies on seed source, seed quality and conditions for uniform emergence before their use in routine regulatory testing.

  16. High innate attractiveness to black targets in the blue blowfly, Calliphora vomitoria (L.) (Diptera: Calliphoridae).

    PubMed

    Benelli, Giovanni; Otranto, Domenico; Caselli, Alice; Romano, Donato; Remorini, Damiano; Di Giuseppe, Graziano; Stefanini, Cesare; Mele, Marcello; Canale, Angelo

    2018-06-01

    Calliphora vomitoria is a myiasis-causing fly in many animal species including humans. The control of blowflies is still anchored on the use of chemicals. However, mass trapping and lure-and-kill techniques represent a promising alternative to pesticides. Visual and olfactory cues are the main stimuli routing the fly's landing behavior. Notably, color attractiveness has been barely explored in flies of medical and veterinary importance, with special reference to blowflies. In this study, we investigated the innate color preferences in C. vomitoria adults, testing binary combinations of painted targets under laboratory conditions. The identity of tested species C. vomitoria was confirmed by DNA sequencing (18S and cox1 genes). C. vomitoria flies showed a significant preference for black colored targets in all tested binary color combinations, after 5, 15, 30 and 60 min of exposure. Black targets were significantly preferred over blue, red, yellow and white ones. Spectral characteristics of all tested color combinations were quantified and the innate attraction of blowflies towards black targets was discussed in relation to their behavioral ecology. To the best of our knowledge, this is the first report on innate color preferences in the Calliphora genus. Our findings can be useful to develop new, cheap and reliable monitoring traps as well as "lure and kill" tools to control blowfly pests. Copyright © 2018 Elsevier B.V. All rights reserved.

  17. Ionospheric chemical releases

    NASA Technical Reports Server (NTRS)

    Bernhardt, Paul A.; Scales, W. A.

    1990-01-01

    Ionospheric plasma density irregularities can be produced by chemical releases into the upper atmosphere. F-region plasma modification occurs by: (1) chemically enhancing the electron number density; (2) chemically reducing the electron population; or (3) physically convecting the plasma from one region to another. The three processes (production, loss, and transport) determine the effectiveness of ionospheric chemical releases in subtle and surprising ways. Initially, a chemical release produces a localized change in plasma density. Subsequent processes, however, can lead to enhanced transport in chemically modified regions. Ionospheric modifications by chemical releases excites artificial enhancements in airglow intensities by exothermic chemical reactions between the newly created plasma species. Numerical models were developed to describe the creation and evolution of large scale density irregularities and airglow clouds generated by artificial means. Experimental data compares favorably with theses models. It was found that chemical releases produce transient, large amplitude perturbations in electron density which can evolve into fine scale irregularities via nonlinear transport properties.

  18. Chemical fate and biological effects of several endocrine disrupters compounds in two echinoderm species.

    PubMed

    Sugni, Michela; Tremolada, Paolo; Porte, Cinta; Barbaglio, Alice; Bonasoro, Francesco; Carnevali, M Daniela Candia

    2010-03-01

    Two echinoderm species, the sea urchin Paracentrotus lividus and the feather star Antedon mediterranea, were exposed for 28 days to several EDCs: three putative androgenic compounds, triphenyltin (TPT), fenarimol (FEN), methyltestosterone (MET), and two putative antiandrogenic compounds, p,p'-DDE (DDE) and cyproterone acetate (CPA). The exposure nominal concentrations were from 10 to 3000 ng L(-1), depending on the compound. This paper is an attempt to join three different aspects coming from our ecotoxicological tests: (1) the chemical behaviour inside the experimental system; (2) the measured toxicological endpoints; (3) the biochemical responses, to which the measured endpoints may depend. The chemical fate of the different compounds was enquired by a modelling approach throughout the application of the 'Aquarium model'. An estimation of the day-to-day concentration levels in water and biota were obtained together with the amount assumed each day by each animal (uptake in microg animal(-1) d(-1) or ng g-wet weight(-1) d(-1)). The toxicological endpoints investigated deal with the reproductive potential (gonad maturation stage, gonad index and oocyte diameter) and with the regenerative potential (growth and histology). Almost all the compounds exerted some kind of effect at the tested concentrations, however TPT was the most effective in altering both reproductive and regenerative parameters (also at the concentration of few ng L(-1)). The biochemical analyses of testosterone (T) and 17beta-estradiol (E(2)) also showed the ability of the selected compounds to significantly alter endogenous steroid concentrations.

  19. Chromatographic speciation of Cr(III)-species, inter-species equilibrium isotope fractionation and improved chemical purification strategies for high-precision isotope analysis.

    PubMed

    Larsen, K K; Wielandt, D; Schiller, M; Bizzarro, M

    2016-04-22

    Chromatographic purification of chromium (Cr), which is required for high-precision isotope analysis, is complicated by the presence of multiple Cr-species with different effective charges in the acid digested sample aliquots. The differing ion exchange selectivity and sluggish reaction rates of these species can result in incomplete Cr recovery during chromatographic purification. Because of large mass-dependent inter-species isotope fractionation, incomplete recovery can affect the accuracy of high-precision Cr isotope analysis. Here, we demonstrate widely differing cation distribution coefficients of Cr(III)-species (Cr(3+), CrCl(2+) and CrCl2(+)) with equilibrium mass-dependent isotope fractionation spanning a range of ∼1‰/amu and consistent with theory. The heaviest isotopes partition into Cr(3+), intermediates in CrCl(2+) and the lightest in CrCl2(+)/CrCl3°. Thus, for a typical reported loss of ∼25% Cr (in the form of Cr(3+)) through chromatographic purification, this translates into 185 ppm/amu offset in the stable Cr isotope ratio of the residual sample. Depending on the validity of the mass-bias correction during isotope analysis, this further results in artificial mass-independent effects in the mass-bias corrected (53)Cr/(52)Cr (μ(53)Cr* of 5.2 ppm) and (54)Cr/(52)Cr (μ(54)Cr* of 13.5 ppm) components used to infer chronometric and nucleosynthetic information in meteorites. To mitigate these fractionation effects, we developed strategic chemical sample pre-treatment procedures that ensure high and reproducible Cr recovery. This is achieved either through 1) effective promotion of Cr(3+) by >5 days exposure to HNO3H2O2 solutions at room temperature, resulting in >∼98% Cr recovery for most types of sample matrices tested using a cationic chromatographic retention strategy, or 2) formation of Cr(III)-Cl complexes through exposure to concentrated HCl at high temperature (>120 °C) for several hours, resulting in >97.5% Cr recovery using a

  20. ESTIMATION OF CHEMICAL TOXICITY TO WILDLIFE SPECIES USING INTERSPECIES CORRELATION MODELS

    EPA Science Inventory

    Ecological risks to wildlife are typically assessed using toxicity data for relataively few species and with limited understanding of differences in species sensitivity to contaminants. Empirical interspecies correlation models were derived from LD50 values for 49 wildlife speci...

  1. The Redox Chemistry and Chemical Biology of H2S, Hydropersulfides and Derived Species: Implications to Their Possible Biological Activity and Utility

    PubMed Central

    Ono, Katsuhiko; Akaike, Takaake; Sawa, Tomohiro; Kumagai, Yoshito; Wink, David A.; Tantillo, Dean J.; Hobbs, Adrian J.; Nagy, Peter; Xian, Ming; Lin, Joseph; Fukuto, Jon M.

    2014-01-01

    Hydrogen sulfide (H2S) is an endogenously generated and putative signaling/effector molecule. In spite of its numerous reported functions, the chemistry by which it elicits its functions is not understood. Moreover, recent studies allude to the existence of other sulfur species besides H2S that may play critical physiological roles. Herein, the basic chemical biology of H2S as well as other related or derived species is discussed and reviewed. A particular focus of this review are the per- and poly-sulfides which are likely in equilibrium with free H2S and which may be important biological effectors themselves. PMID:25229186

  2. Bacterial colonization of the phyllosphere of mediterranean perennial species as influenced by leaf structural and chemical features.

    PubMed

    Yadav, R K P; Karamanoli, K; Vokou, D

    2005-08-01

    In this study, we assessed various leaf structural and chemical features as possible predictors of the size of the phyllosphere bacterial population in the Mediterranean environment. We examined eight perennial species, naturally occurring and coexisting in the same area, in Halkidiki (northern Greece). They are Arbutus unedo, Quercus coccifera, Pistacia lentiscus, and Myrtus communis (evergreen sclerophyllous species), Lavandula stoechas and Cistus incanus (drought semi-deciduous species), and Calamintha nepeta and Melissa officinalis (non-woody perennial species). M. communis, L. stoechas, C. nepeta, and M. officinalis produce essential oil in substantial quantities. We sampled summer leaves from these species and (1) estimated the size of the bacterial population of their phyllosphere, (2) estimated the concentration of different leaf constituents, and (3) studied leaf morphological and anatomical features and expressed them in a quantitative way. The aromatic plants are on average more highly colonized than the other species, whereas the non-woody perennials are more highly colonized than the woody species. The population size of epiphytic bacteria is positively correlated with glandular and non-glandular trichome densities, and with water and phosphorus contents; it is negatively correlated with total phenolics content and the thickness of the leaf, of the mesophyll, and of the abaxial epidermis. No correlation was found with the density of stomata, the nitrogen, and the soluble sugar contents. By regression tree analysis, we found that the leaf-microbe system can be effectively described by three leaf attributes with leaf water content being the primary explanatory attribute. Leaves with water content >73% are the most highly colonized. For leaves with water content <73%, the phosphorus content, with a critical value of 1.34 mg g(-1) d.w., is the next explanatory leaf attribute, followed by the thickness of the adaxial epidermis. Leaves higher in phosphorus

  3. Chemical antipredator defence is linked to higher extinction risk

    PubMed Central

    2016-01-01

    Many attributes of species may be linked to contemporary extinction risk, though some such traits remain untested despite suggestions that they may be important. Here, I test whether a trait associated with higher background extinction rates, chemical antipredator defence, is also associated with current extinction risk, using amphibians as a model system—a group facing global population declines. I find that chemically defended species are approximately 60% more likely to be threatened than species without chemical defence, although the severity of the contemporary extinction risk may not relate to chemical defence. The results confirm that background and contemporary extinction rates can be predicted from the same traits, at least in certain cases. This suggests that associations between extinction risk and phenotypic traits can be temporally stable over long periods. The results also provide novel insights into the relevance of antipredator defences for species subject to conservation concerns. PMID:28018657

  4. Metabolomic profiling reveals deep chemical divergence between two morphotypes of the zoanthid Parazoanthus axinellae

    PubMed Central

    Cachet, Nadja; Genta-Jouve, Grégory; Ivanisevic, Julijana; Chevaldonné, Pierre; Sinniger, Frédéric; Culioli, Gérald; Pérez, Thierry; Thomas, Olivier P.

    2015-01-01

    Metabolomics has recently proven its usefulness as complementary tool to traditional morphological and genetic analyses for the classification of marine invertebrates. Among the metabolite-rich cnidarian order Zoantharia, Parazoanthus is a polyphyletic genus whose systematics and phylogeny remain controversial. Within this genus, one of the most studied species, Parazoanthus axinellae is prominent in rocky shallow waters of the Mediterranean Sea and the NE Atlantic Ocean. Although different morphotypes can easily be distinguished, only one species is recognized to date. Here, a metabolomic profiling approach has been used to assess the chemical diversity of two main Mediterranean morphotypes, the “slender” and “stocky” forms of P. axinellae. Targeted profiling of their major secondary metabolites revealed a significant chemical divergence between the morphotypes. While zoanthoxanthin alkaloids and ecdysteroids are abundant in both morphs, the “slender” morphotype is characterized by the presence of additional and bioactive 3,5-disubstituted hydantoin derivatives named parazoanthines. The absence of these specific compounds in the “stocky” morphotype was confirmed by spatial and temporal monitoring over an annual cycle. Moreover, specimens of the “slender” morphotype are also the only ones found as epibionts of several sponge species, particularly Cymbaxinella damicornis thus suggesting a putative ecological link. PMID:25655432

  5. Chemical equilibrium of ablation materials including condensed species

    NASA Technical Reports Server (NTRS)

    Stroud, C. W.; Brinkley, K. L.

    1975-01-01

    Equilibrium is determined by finding chemical composition with minimum free energy. Method of steepest descent is applied to quadratic representation of free-energy surface. Solution is initiated by selecting arbitrary set of mole fractions, from which point on free-energy surface is computed.

  6. Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean

    PubMed Central

    Chappell, P. Dreux; Whitney, LeAnn P.; Haddock, Traci L.; Menden-Deuer, Susanne; Roy, Eric G.; Wells, Mark L.; Jenkins, Bethany D.

    2013-01-01

    Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here, we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a 3-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA) method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a 3-month-old Haida eddy remained largely (>80%) similar over a 2-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe) and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response. PMID:24065961

  7. Quantification of Human Fecal Bifidobacterium Species by Use of Quantitative Real-Time PCR Analysis Targeting the groEL Gene

    PubMed Central

    Junick, Jana

    2012-01-01

    Quantitative real-time PCR assays targeting the groEL gene for the specific enumeration of 12 human fecal Bifidobacterium species were developed. The housekeeping gene groEL (HSP60 in eukaryotes) was used as a discriminative marker for the differentiation of Bifidobacterium adolescentis, B. angulatum, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. gallicum, B. longum, B. pseudocatenulatum, B. pseudolongum, and B. thermophilum. The bifidobacterial chromosome contains a single copy of the groEL gene, allowing the determination of the cell number by quantification of the groEL copy number. Real-time PCR assays were validated by comparing fecal samples spiked with known numbers of a given Bifidobacterium species. Independent of the Bifidobacterium species tested, the proportion of groEL copies recovered from fecal samples spiked with 5 to 9 log10 cells/g feces was approximately 50%. The quantification limit was 5 to 6 log10 groEL copies/g feces. The interassay variability was less than 10%, and variability between different DNA extractions was less than 23%. The method developed was applied to fecal samples from healthy adults and full-term breast-fed infants. Bifidobacterial diversity in both adults and infants was low, with mostly ≤3 Bifidobacterium species and B. longum frequently detected. The predominant species in infant and adult fecal samples were B. breve and B. adolescentis, respectively. It was possible to distinguish B. catenulatum and B. pseudocatenulatum. We conclude that the groEL gene is a suitable molecular marker for the specific and accurate quantification of human fecal Bifidobacterium species by real-time PCR. PMID:22307308

  8. Using Temperature-Dependent Phenomena at Oxide Surfaces for Species Recognition in Chemical Sensing.

    NASA Astrophysics Data System (ADS)

    Semancik, Steve; Meier, Douglas; Evju, Jon; Benkstein, Kurt; Boger, Zvi; Montgomery, Chip

    2006-03-01

    Nanostructured films of SnO2 and TiO2 have been deposited on elements in MEMS arrays to fabricate solid state conductometric gas microsensors. The multilevel platforms within an array, called microhotplates, are individually addressable for localized temperature control and measurement of sensing film electrical conductance. Temperature variations of the microhotplates are employed in thermally-activated CVD oxide film growth, and for rapid temperature-programmed operation of the microsensors. Analytical information on environmental gas phase composition is produced temporally as purposeful thermal fluctuations provide energetic and kinetic control of surface reaction and adsorption/desorption phenomena. Resulting modulations of oxide adsorbate populations cause changing charge transfer behavior and measurable conductance responses. Rich data streams from different sensing films in the arrays have been analyzed by Artificial Neural Networks (ANN) to successfully recognize low concentration species in mixed gases. We illustrate capabilities of the approach and technology in the homeland security area, where dangerous chemicals (TICs, CWSs and CWAs) have been detected at 10-100 ppb levels in interference-spiked air backgrounds.

  9. Teaching the basics of reactive oxygen species and their relevance to cancer biology: Mitochondrial reactive oxygen species detection, redox signaling, and targeted therapies.

    PubMed

    Kalyanaraman, Balaraman; Cheng, Gang; Hardy, Micael; Ouari, Olivier; Bennett, Brian; Zielonka, Jacek

    2018-05-01

    Reactive oxygen species (ROS) have been implicated in tumorigenesis (tumor initiation, tumor progression, and metastasis). Of the many cellular sources of ROS generation, the mitochondria and the NADPH oxidase family of enzymes are possibly the most prevalent intracellular sources. In this article, we discuss the methodologies to detect mitochondria-derived superoxide and hydrogen peroxide using conventional probes as well as newly developed assays and probes, and the necessity of characterizing the diagnostic marker products with HPLC and LC-MS in order to rigorously identify the oxidizing species. The redox signaling roles of mitochondrial ROS, mitochondrial thiol peroxidases, and transcription factors in response to mitochondria-targeted drugs are highlighted. ROS generation and ROS detoxification in drug-resistant cancer cells and the relationship to metabolic reprogramming are discussed. Understanding the subtle role of ROS in redox signaling and in tumor proliferation, progression, and metastasis as well as the molecular and cellular mechanisms (e.g., autophagy) could help in the development of combination therapies. The paradoxical aspects of antioxidants in cancer treatment are highlighted in relation to the ROS mechanisms in normal and cancer cells. Finally, the potential uses of newly synthesized exomarker probes for in vivo superoxide and hydrogen peroxide detection and the low-temperature electron paramagnetic resonance technique for monitoring oxidant production in tumor tissues are discussed. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  10. Evolution of egg target size: an analysis of selection on correlated characters.

    PubMed

    Podolsky, R D

    2001-12-01

    In broadcast-spawning marine organisms, chronic sperm limitation should select for traits that improve chances of sperm-egg contact. One mechanism may involve increasing the size of the physical or chemical target for sperm. However, models of fertilization kinetics predict that increasing egg size can reduce net zygote production due to an associated decline in fecundity. An alternate method for increasing physical target size is through addition of energetically inexpensive external structures, such as the jelly coats typical of eggs in species from several phyla. In selection experiments on eggs of the echinoid Dendraster excentricus, in which sperm was used as the agent of selection, eggs with larger overall targets were favored in fertilization. Actual shifts in target size following selection matched quantitative predictions of a model that assumed fertilization was proportional to target size. Jelly volume and ovum volume, two characters that contribute to target size, were correlated both within and among females. A cross-sectional analysis of selection partitioned the independent effects of these characters on fertilization success and showed that they experience similar direct selection pressures. Coupled with data on relative organic costs of the two materials, these results suggest that, under conditions where fertilization is limited by egg target size, selection should favor investment in low-cost accessory structures and may have a relatively weak effect on the evolution of ovum size.

  11. A targeted gene expression platform allows for rapid analysis of chemical-induced antioxidant mRNA expression in zebrafish larvae.

    PubMed

    Mills, Margaret G; Gallagher, Evan P

    2017-01-01

    Chemical-induced oxidative stress and the biochemical pathways that protect against oxidative damage are of particular interest in the field of toxicology. To rapidly identify oxidative stress-responsive gene expression changes in zebrafish, we developed a targeted panel of antioxidant genes using the Affymetrix QuantiGene Plex (QGP) platform. The genes contained in our panel include eight putative Nrf2 (Nfe2l2a)-dependent antioxidant genes (hmox1a, gstp1, gclc, nqo1, prdx1, gpx1a, sod1, sod2), a stress response gene (hsp70), an inducible DNA damage repair gene (gadd45bb), and three reference genes (actb1, gapdh, hprt1). We tested this platform on larval zebrafish exposed to tert-butyl hydroperoxide (tBHP) and cadmium (Cd), two model oxidative stressors with different modes of action, and compared our results with those obtained using the more common quantitative PCR (qPCR) method. Both methods showed that exposure to tBHP and Cd induced expression of prdx1, gstp1, and hmox1a (2- to 12-fold increase via QGP), indicative of an activated Nrf2 response in larval zebrafish. Both compounds also elicited a general stress response as reflected by elevation of hsp70 and gadd45bb, with Cd being the more potent inducer. Transient changes were observed in sod2 and gpx1a expression, whereas nqo1, an Nrf2-responsive gene in mammalian cells, was minimally affected by either tBHP or Cd chemical exposures. Developmental expression analysis of the target genes by QGP revealed marked upregulation of sod2 between 0-96hpf, and to a lesser extent, of sod1 and gstp1. Once optimized, QGP analysis of these experiments was accomplished more rapidly, using far less tissue, and at lower total costs than qPCR analysis. In summary, the QGP platform as applied to higher-throughput zebrafish studies provides a reasonable cost-effective alternative to qPCR or more comprehensive transcriptomics approaches to rapidly assess the potential for chemicals to elicit oxidative stress as a mechanism of

  12. Latin American protected areas: Protected from chemical pollution?

    PubMed

    Rodríguez-Jorquera, Ignacio A; Siroski, Pablo; Espejo, Winfred; Nimptsch, Jorge; Choueri, Paloma Gusso; Choueri, Rodrigo Brasil; Moraga, Claudio A; Mora, Miguel; Toor, Gurpal S

    2017-03-01

    Protected areas (PAs) are critically important means to preserve species and maintain natural ecosystems. However, the potential impacts of chemical pollution on PAs are seldom mentioned in the scientific literature. Research on the extent of the occurrence of chemical pollution inside PAs and in-depth assessments of how chemical contaminants may adversely affect the maintenance of species abundance, species survival, and ecosystem functions are scarce to nonexistent. We investigated 1) the occurrence of chemical contaminants inside 119 PAs in Latin America from publically available databases, and 2) reviewed case studies of chemical contaminants and pollution in 4 Latin American PAs. Cases of chemical pollution and contamination inside Latin American PAs mostly originated from sources such as mining, oil, and gas extraction. To date, the focus of the research on chemical pollution research inside Latin American PAs has been primarily on the detection of contamination, typically limited to trace metals. Where management actions have occurred, they have been reactive rather than proactive. Protected areas established in wetlands are the most affected by chemical pollution. Based on the information from the pollution and/or contamination occurrence and the case studies analyzed, Latin American PAs are not well safeguarded from chemical pollution, resulting in both challenges and opportunities to conserve biodiversity and ecosystems. Integr Environ Assess Manag 2017;13:360-370. © 2016 SETAC. © 2016 SETAC.

  13. A review of reaction rates and thermodynamic and transport properties for an 11-species air model for chemical and thermal nonequilibrium calculations to 30000 K

    NASA Technical Reports Server (NTRS)

    Gupta, Roop N.; Yos, Jerrold M.; Thompson, Richard A.; Lee, Kam-Pui

    1990-01-01

    Reaction rate coefficients and thermodynamic and transport properties are reviewed and supplemented for the 11-species air model which can be used for analyzing flows in chemical and thermal nonequilibrium up to temperatures of 3000 K. Such flows will likely occur around currently planned and future hypersonic vehicles. Guidelines for determining the state of the surrounding environment are provided. Curve fits are given for the various species properties for their efficient computation in flowfield codes. Approximate and more exact formulas are provided for computing the properties of partially ionized air mixtures in a high energy environment. Limitations of the approximate mixing laws are discussed for a mixture of ionized species. An electron number-density correction for the transport properties of the charged species is obtained. This correction has been generally ignored in the literature.

  14. Biochemical Activities of 320 ToxCast Chemicals Evaluated Across 239 Functional Targets

    EPA Science Inventory

    EPA’s ToxCast research program is profiling chemical bioactivity in order to generate predictive signatures of toxicity. The present study evaluated 320 chemicals across 239 biochemical assays. ToxCast phase I chemicals include 309 unique structures, most of which are pesticide ...

  15. Target molecules detection by waveguiding in a photonic silicon membrane

    DOEpatents

    Letant, Sonia E [Livermore, CA; Van Buuren, Anthony [Livermore, CA; Terminello, Louis [Danville, CA; Hart, Bradley R [Brentwood, CA

    2006-12-26

    Disclosed herein is a porous silicon filter capable of binding and detecting biological and chemical target molecules in liquid or gas samples. A photonic waveguiding silicon filter with chemical and/or biological anchors covalently attached to the pore walls bind target molecules. The system uses transmission curve engineering principles to allow measurements to be made in situ and in real time to detect the presence of various target molecules and calculate the concentration of bound target.

  16. Target molecules detection by waveguiding in a photonic silicon membrane

    DOEpatents

    Letant, Sonia; Van Buuren, Anthony; Terminello, Louis

    2004-08-31

    Disclosed herein is a photonic silicon filter capable of binding and detecting biological and chemical target molecules in liquid or gas samples. A photonic waveguiding silicon filter with chemical and/or biological anchors covalently attached to the pore walls selectively bind target molecules. The system uses transmission curve engineering principles to allow measurements to be made in situ and in real time to detect the presence of various target molecules and determine the concentration of bound target.

  17. Evaluation of Chemical Composition and Antileishmanial and Antituberculosis Activities of Essential Oils of Piper Species.

    PubMed

    Bernuci, Karine Zanoli; Iwanaga, Camila Cristina; Fernadez-Andrade, Carla Maria Mariano; Lorenzetti, Fabiana Brusco; Torres-Santos, Eduardo Caio; Faiões, Viviane Dos Santos; Gonçalves, José Eduardo; do Amaral, Wanderlei; Deschamps, Cícero; Scodro, Regiane Bertin de Lima; Cardoso, Rosilene Fressatti; Baldin, Vanessa Pietrowski; Cortez, Diógenes Aparício Garcia

    2016-12-12

    Essential oils from fresh Piperaceae leaves were obtained by hydrodistillation and analyzed by gas chromatography mass spectrometry (GC-MS), and a total of 68 components were identified. Principal components analysis results showed a chemical variability between species, with sesquiterpene compounds predominating in the majority of species analyzed. The composition of the essential oil of Piper mosenii was described for the first time. The cytotoxicity of the essential oils was evaluated in peritoneal macrophages and the oils of P. rivinoides , P. arboretum , and P. aduncum exhibited the highest values, with cytotoxic concentration at 50% (CC 50 ) > 200 µg/mL. Both P. diospyrifolium and P. aduncum displayed activity against Leishmania amazonensis , and were more selective for the parasite than for the macrophages, with a selectivity index (SI) of 2.35 and >5.52, respectively. These SI values were greater than the 1 for the standard drug pentamidine. The antileishmanial activity of the essential oils of P. diospyrifolium and P. aduncum was described for the first time. P. rivinoides, P. cernuum , and P. diospyrifolium displayed moderate activity against the Mycobacterium tuberculosis H 37 Rv bacillus, with a minimum inhibitory concentration (MIC) of 125 µg/mL. These results are relevant and suggests their potential for therapeutic purposes. Nevertheless, further studies are required to explain the exact mechanism of action of these essential oils.

  18. Evaluation of the scientific underpinnings for identifying estrogenic chemicals in nonmammalian taxa using mammalian test systems.

    PubMed

    Ankley, Gerald T; LaLone, Carlie A; Gray, L Earl; Villeneuve, Daniel L; Hornung, Michael W

    2016-11-01

    The US Environmental Protection Agency has responsibility for assessing endocrine activity of more than 10 000 chemicals, a task that cannot reasonably be achieved solely through use of available mammalian and nonmammalian in vivo screening assays. Hence, it has been proposed that chemicals be prioritized for in vivo testing using data from in vitro high-throughput assays for specific endocrine system targets. Recent efforts focused on potential estrogenic chemicals-specifically those that activate estrogen receptor-alpha (ERα)-have broadly demonstrated feasibility of the approach. However, a major uncertainty is whether prioritization based on mammalian (primarily human) high-throughput assays accurately reflects potential chemical-ERα interactions in nonmammalian species. The authors conducted a comprehensive analysis of cross-species comparability of chemical-ERα interactions based on information concerning structural attributes of estrogen receptors, in vitro binding and transactivation data for ERα, and the effects of a range of chemicals on estrogen-signaling pathways in vivo. Overall, this integrated analysis suggests that chemicals with moderate to high estrogenic potency in mammalian systems also should be priority chemicals in nonmammalian vertebrates. However, the degree to which the prioritization approach might be applicable to invertebrates is uncertain because of a lack of knowledge of the biological role(s) of possible ERα orthologs found in phyla such as annelids. Further, comparative analysis of in vitro data for fish and reptiles suggests that mammalian-based assays may not effectively capture ERα interactions for low-affinity chemicals in all vertebrate classes. Environ Toxicol Chem 2016;35:2806-2816. Published 2016 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America. Published 2016 Wiley Periodicals Inc. on behalf of SETAC. This article is

  19. Chemical combination effects predict connectivity in biological systems

    PubMed Central

    Lehár, Joseph; Zimmermann, Grant R; Krueger, Andrew S; Molnar, Raymond A; Ledell, Jebediah T; Heilbut, Adrian M; Short, Glenn F; Giusti, Leanne C; Nolan, Garry P; Magid, Omar A; Lee, Margaret S; Borisy, Alexis A; Stockwell, Brent R; Keith, Curtis T

    2007-01-01

    Efforts to construct therapeutically useful models of biological systems require large and diverse sets of data on functional connections between their components. Here we show that cellular responses to combinations of chemicals reveal how their biological targets are connected. Simulations of pathways with pairs of inhibitors at varying doses predict distinct response surface shapes that are reproduced in a yeast experiment, with further support from a larger screen using human tumour cells. The response morphology yields detailed connectivity constraints between nearby targets, and synergy profiles across many combinations show relatedness between targets in the whole network. Constraints from chemical combinations complement genetic studies, because they probe different cellular components and can be applied to disease models that are not amenable to mutagenesis. Chemical probes also offer increased flexibility, as they can be continuously dosed, temporally controlled, and readily combined. After extending this initial study to cover a wider range of combination effects and pathway topologies, chemical combinations may be used to refine network models or to identify novel targets. This response surface methodology may even apply to non-biological systems where responses to targeted perturbations can be measured. PMID:17332758

  20. Ethnopharmacological and Chemical Characterization of Salvia Species Used in Valencian Traditional Herbal Preparations

    PubMed Central

    Martínez-Francés, Vanessa; Hahn, Emeline; Ríos, Segundo; Rivera, Diego; Reich, Eike; Vila, Roser; Cañigueral, Salvador

    2017-01-01

    In Valencia Region (Spain), some wild and cultivated sages are used for medicinal purposes. Among them, Salvia officinalis subsp. lavandulifolia (SL) is widely employed and known for production of Spanish sage oil and herbal products. Nevertheless, it shares the market with S. blancoana subsp. mariolensis (SB) and, to a lesser extent, with their hybrid S. x hegelmaieri (SH). The knowledge on these two species is far low and confusion between them is possible. The aim of the present paper is to improve the ethnopharmacological, morphological and chemical knowledge of these sages, and to contribute to setting up quality specifications for improving identification and distinction from other Salvia species, such as, S. officinalis subsp. officinalis, S. x auriculata and S. microphylla var. microphylla. Samples were collected in Valencia Region and surrounding mountain areas during the ethnopharmacological field work. Twenty-nine medicinal uses were reported for SL, 13 of them being also recorded for SB. Of particular interest is a homemade liquor, used as digestive and known as “salvieta,” which is mainly prepared with SB. The macro- and microscopic characters are insufficient for identification of cut, crushed or powdered material. The study of the essential oil and a HPTLC (High Performance Thin Layer Chromatography) fingerprint of their extracts could help to distinguish SB from the other sages. The essential oil from dried aerial parts of SB (content: 1.8–4.5%) was characterized by GC-FID (Gas Chromatography with Flame Ionization Detector) and GC-MS (Gas Chromatography coupled to Mass Spectrometry) showing a composition close to that currently accepted for Spanish sage essential oil in the European Pharmacopoeia, ISO (International Standard Organization) and UNE (Una Norma Española) standards, with 1,8-cineole (13.7–45.7%) and camphor (12.1–28.6%) as major constituents. HPTLC methods, based on the analysis of hydroalcoholic and dichloromethane extracts

  1. Agonists and Antagonists of Protease-Activated Receptor 2 Discovered within a DNA-Encoded Chemical Library Using Mutational Stabilization of the Target.

    PubMed

    Brown, Dean G; Brown, Giles A; Centrella, Paolo; Certel, Kaan; Cooke, Robert M; Cuozzo, John W; Dekker, Niek; Dumelin, Christoph E; Ferguson, Andrew; Fiez-Vandal, Cédric; Geschwindner, Stefan; Guié, Marie-Aude; Habeshian, Sevan; Keefe, Anthony D; Schlenker, Oliver; Sigel, Eric A; Snijder, Arjan; Soutter, Holly T; Sundström, Linda; Troast, Dawn M; Wiggin, Giselle; Zhang, Jing; Zhang, Ying; Clark, Matthew A

    2018-06-01

    The discovery of ligands via affinity-mediated selection of DNA-encoded chemical libraries is driven by the quality and concentration of the protein target. G-protein-coupled receptors (GPCRs) and other membrane-bound targets can be difficult to isolate in their functional state and at high concentrations, and therefore have been challenging for affinity-mediated selection. Here, we report a successful selection campaign against protease-activated receptor 2 (PAR2). Using a thermo-stabilized mutant of PAR2, we conducted affinity selection using our >100-billion-compound DNA-encoded library. We observed a number of putative ligands enriched upon selection, and subsequent cellular profiling revealed these ligands to comprise both agonists and antagonists. The agonist series shared structural similarity with known agonists. The antagonists were shown to bind in a novel allosteric binding site on the PAR2 protein. This report serves to demonstrate that cell-free affinity selection against GPCRs can be achieved with mutant stabilized protein targets.

  2. Flow method and apparatus for screening chemicals using micro x-ray fluorescence

    DOEpatents

    Warner, Benjamin P [Los Alamos, NM; Havrilla, George J [Los Alamos, NM; Miller, Thomasin C [Bartlesville, OK; Lewis, Cris [Los Alamos, NM; Mahan, Cynthia A [Los Alamos, NM; Wells, Cyndi A [Los Alamos, NM

    2009-04-14

    Method and apparatus for screening chemicals using micro x-ray fluorescence. A method for screening a mixture of potential pharmaceutical chemicals for binding to at least one target binder involves flow-separating a solution of chemicals and target binders into separated components, exposing them to an x-ray excitation beam, detecting x-ray fluorescence signals from the components, and determining from the signals whether or not a binding event between a chemical and target binder has occurred.

  3. Flow method and apparatus for screening chemicals using micro x-ray fluorescence

    DOEpatents

    Warner, Benjamin P [Los Alamos, NM; Havrilla, George J [Los Alamos, NM; Miller, Thomasin C [Bartlesville, OK; Lewis, Cris [Los Alamos, NM; Mahan, Cynthia A [Los Alamos, NM; Wells, Cyndi A [Los Alamos, NM

    2011-04-26

    Method and apparatus for screening chemicals using micro x-ray fluorescence. A method for screening a mixture of potential pharmaceutical chemicals for binding to at least one target binder involves flow separating a solution of chemicals and target binders into separated components, exposing them to an x-ray excitation beam, detecting x-ray fluorescence signals from the components, and determining from the signals whether or not a binding event between a chemical and target binder has occurred.

  4. Chemical analysis of bioactive substances in seven siberian Saussurea species

    NASA Astrophysics Data System (ADS)

    Avdeeva, Elena; Reshetov, Yaroslav; Shurupova, Margarita; Zibareva, Larisa; Borisova, Evgeniia; Belousov, Mikhail

    2017-11-01

    Main groups of biologically active substances of seven siberian Saussurea species (S. controversa DC., S. latifolia Ledeb., S. parviflora (Poir.) DC., S. frolowii Ledeb, S. amara (L.) DC., S. salicifolia (L.) DC. and S. daurica Adams) have been studied using paper, thin-layer, performance liquid chromatography, IR spectroscopy, spectrophotometry and mass spectrometry with inductively coupled plasma. Siberian Saussurea species have a rich elemental composition and contain a variety of phenolic compounds, amino acids, polysaccharides. The majority of polysaccharides are accumulated by S. controversa, S. salicifolia and S. frolowii. These plants contain a significant amount of calcium that may be a species characteristic. All plants contain quercetin and its glycosides, in some species luteolin, kaempferol, glycosides of apigenin and myricetin were revealed. Phenolic acids with predominant content of caffeic, chlorogenic and cinnamic acids were found in all the species. The maximum amount of phenolic acids and flavonoids was determined in the grass of S. latifolia, S. controversa and S. daurica. Characteristic absorption bands of lactone carbonyl of sesquiterpenoids in IR spectrum found in S. latifolia, S. controversa, S. daurica, S. amara and S. salicifolia. HPLC / UV analysis showed that peaks with absorption maxima of 242-246 nm due to the presence of α,β-unsaturated ketone group in the structure of ecdysteroids were found in S. salicifolia, S. controversa, S. daurica and S. latifolia.

  5. Species-level assessment of secondary metabolite diversity among Hamigera species and a taxonomic note on the genus

    USDA-ARS?s Scientific Manuscript database

    Secondary metabolite phenotypes in nine species of the Hamigera clade were analysed to assess their correlations to a multi-gene species-level phylogeny. High-pressure-liquid-chromatography-based chemical analysis revealed three distinctive patterns of secondary metabolite production: (1) the nine s...

  6. Targeted gene flow for conservation.

    PubMed

    Kelly, Ella; Phillips, Ben L

    2016-04-01

    Anthropogenic threats often impose strong selection on affected populations, causing rapid evolutionary responses. Unfortunately, these adaptive responses are rarely harnessed for conservation. We suggest that conservation managers pay close attention to adaptive processes and geographic variation, with an eye to using them for conservation goals. Translocating pre-adapted individuals into recipient populations is currently considered a potentially important management tool in the face of climate change. Targeted gene flow, which involves moving individuals with favorable traits to areas where these traits would have a conservation benefit, could have a much broader application in conservation. Across a species' range there may be long-standing geographic variation in traits or variation may have rapidly developed in response to a threatening process. Targeted gene flow could be used to promote natural resistance to threats to increase species resilience. We suggest that targeted gene flow is a currently underappreciated strategy in conservation that has applications ranging from the management of invasive species and their impacts to controlling the impact and virulence of pathogens. © 2015 Society for Conservation Biology.

  7. Molecular characterization of patulin producing and non-producing Penicillium species in apples from Morocco.

    PubMed

    Rharmitt, Sanae; Hafidi, Majida; Hajjaj, Hassan; Scordino, Fabio; Giosa, Domenico; Giuffrè, Letterio; Barreca, Davide; Criseo, Giuseppe; Romeo, Orazio

    2016-01-18

    The isolation of patulin-producing Penicillia in apples collected in different markets in four localities in Morocco is reported. Fungi were identified by β-tubulin sequencing and further characterized using a specific PCR-based method targeting the isoepoxydon dehydrogenase (IDH) gene to discriminate between patulin-producing and non-producing strains. Production of patulin was also evaluated using standard cultural and biochemical methods. Results showed that 79.5% of contaminant fungi belonged to the genus Penicillium and that Penicillium expansum was the most isolated species (83.9%) followed by Penicillium chrysogenum (~9.7%) and Penicillium crustosum (~6.4%). Molecular analysis revealed that 64.5% of the Penicillium species produced the expected IDH-amplicon denoting patulin production in these strains. However, patulin production was not chemically confirmed in all P. expansum strains. The isolation of IDH(-)/patulin(+) strains poses the hypothesis that gentisylaldehyde is not a direct patulin precursor, supporting previous observations that highlighted the importance of the gentisyl alcohol in the production of this mycotoxin. Total agreement between IDH-gene detection and cultural/chemical methods employed was observed in 58% of P. expansum strains and for 100% of the other species isolated. Overall the data reported here showed a substantial genetic variability within P. expansum population from Morocco. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Breeding for cuticle-associated traits in crop species: traits, targets, and strategies.

    PubMed

    Petit, Johann; Bres, Cécile; Mauxion, Jean-Philippe; Bakan, Bénédicte; Rothan, Christophe

    2017-11-09

    Improving crop productivity and quality while promoting sustainable agriculture have become major goals in plant breeding. The cuticle is a natural film covering the aerial organs of plants and consists of lipid polyesters covered and embedded with wax. The cuticle protects plants against water loss and pathogens and affects traits with strong impacts on crop quality such as, for horticultural crops, fruit brightness, cracking, russeting, netting, and shelf life. Here we provide an overview of the most important cuticle-associated traits that can be targeted for crop improvement. To date, most studies on cuticle-associated traits aimed at crop breeding have been done on fleshy fruits. Less information is available for staple crops such as rice, wheat or maize. Here we present new insights into cuticle formation and properties resulting from the study of genetic resources available for the various crop species. Our review also covers the current strategies and tools aimed at exploiting available natural and artificially induced genetic diversity and the technologies used to transfer the beneficial alleles affecting cuticle-associated traits to commercial varieties. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  9. Chemical and biochemical composition of caviar from different sturgeon species and origins.

    PubMed

    Wirth, M; Kirschbaum, F; Gessner, J; Krüger, A; Patriche, N; Billard, R

    2000-08-01

    The chemical and biochemical composition of caviar in 22 specimens of wild caught and of 2 farmed animals were measured. The results include grain size, protein and fat content, fatty acid composition of triglycerides and phospholipids, as well as the concentrations of relevant heavy metals and chlorinated hydrocarbons. The average protein content varied between 26.2 and 31.1% (wet weight) and fat from 10.9 to 19.4% (wet weight) with lowest values for caviar from farmed sturgeon. The triglycerides and phospholipids contained more n-3 fatty acids, especially eicosapentaenoic and docosahexaenoic acid than n-6 fatty acids. The copper and zinc concentrations varied between 1.20 and 1.69 and 10.3 and 12.4 mg/kg (wet weight), respectively. These values reflect the elevated requirement of sturgeons for these components. Lead content varied between 0.06 and 0.15 mg/kg (wet weight). The cadmium concentrations were less than 5 micrograms/kg (wet weight) leading to the conclusion that no accumulation took place in the eggs. The concentrations of sigma DDT and sigma PCB were extremely high in caviar from Huso huso compared to the samples of the other species thus reflecting the different food habits leading to increased bio-accumulation.

  10. Objective, Quantitative, Data-Driven Assessment of Chemical Probes.

    PubMed

    Antolin, Albert A; Tym, Joseph E; Komianou, Angeliki; Collins, Ian; Workman, Paul; Al-Lazikani, Bissan

    2018-02-15

    Chemical probes are essential tools for understanding biological systems and for target validation, yet selecting probes for biomedical research is rarely based on objective assessment of all potential compounds. Here, we describe the Probe Miner: Chemical Probes Objective Assessment resource, capitalizing on the plethora of public medicinal chemistry data to empower quantitative, objective, data-driven evaluation of chemical probes. We assess >1.8 million compounds for their suitability as chemical tools against 2,220 human targets and dissect the biases and limitations encountered. Probe Miner represents a valuable resource to aid the identification of potential chemical probes, particularly when used alongside expert curation. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. Role of reactive oxygen and nitrogen species in the vascular responses to inflammation

    PubMed Central

    Kvietys, Peter R.; Granger, D. Neil

    2012-01-01

    Inflammation is a complex and potentially life-threatening condition that involves the participation of a variety of chemical mediators, signaling pathways, and cell types. The microcirculation, which is critical for the initiation and perpetuation of an inflammatory response, exhibits several characteristic functional and structural changes in response to inflammation. These include vasomotor dysfunction (impaired vessel dilation and constriction), the adhesion and transendothelial migration of leukocytes, endothelial barrier dysfunction (increased vascular permeability), blood vessel proliferation (angiogenesis), and enhanced thrombus formation. These diverse responses of the microvasculature largely reflect the endothelial cell dysfunction that accompanies inflammation and the central role of these cells in modulating processes as varied as blood flow regulation, angiogenesis, and thrombogenesis. The importance of endothelial cells in inflammation-induced vascular dysfunction is also predicated on the ability of these cells to produce and respond to reactive oxygen and nitrogen species. Inflammation seems to upset the balance between nitric oxide and superoxide within (and surrounding) endothelial cells, which is necessary for normal vessel function. This review is focused on defining the molecular targets in the vessel wall that interact with reactive oxygen species and nitric oxide to produce the characteristic functional and structural changes that occur in response to inflammation. This analysis of the literature is consistent with the view that reactive oxygen and nitrogen species contribute significantly to the diverse vascular responses in inflammation and supports efforts that are directed at targeting these highly reactive species to maintain normal vascular health in pathological conditions that are associated with acute or chronic inflammation. PMID:22154653

  12. Comparison of two freshwater turtle species as monitors of environmental contamination

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Meyers-Schoene, L.; Walton, B.T.

    1990-04-01

    Two species of turtles that occupy different ecological niches were compared for their usefulness as monitors of contamination in freshwater ecosystems. Trachemys scripta (Agassiz) and Chelydra serpentina (Linnaeus) were selected for comparison based on species abundance and differences in food habits and sediment contact. A review of the literature on contaminants in turtles and results of preliminary surveys conducted at the field sites, which are included in this study, were used to direct and focus this research project. White Oak Lake, a settling basin for low-level radioactive and nonradioactive contaminants, and Bearden Creek Embayment, an uncontaminated reference site upriver, weremore » used as study sites in the investigation of turtles as indicators of chemical contamination. Turtles were analyzed for concentrations of strontium-90, cesium-137, cobalt 60, and mercury in specific target tissues, and for single-stranded DNA breaks, a non-specific indicator of possible exposure to genotoxic agents in the environment. 133 refs., 2 figs., 15 tabs.« less

  13. Species specificity of symbiosis and secondary metabolism in ascidians.

    PubMed

    Tianero, Ma Diarey B; Kwan, Jason C; Wyche, Thomas P; Presson, Angela P; Koch, Michael; Barrows, Louis R; Bugni, Tim S; Schmidt, Eric W

    2015-03-01

    Ascidians contain abundant, diverse secondary metabolites, which are thought to serve a defensive role and which have been applied to drug discovery. It is known that bacteria in symbiosis with ascidians produce several of these metabolites, but very little is known about factors governing these 'chemical symbioses'. To examine this phenomenon across a wide geographical and species scale, we performed bacterial and chemical analyses of 32 different ascidians, mostly from the didemnid family from Florida, Southern California and a broad expanse of the tropical Pacific Ocean. Bacterial diversity analysis showed that ascidian microbiomes are highly diverse, and this diversity does not correlate with geographical location or latitude. Within a subset of species, ascidian microbiomes are also stable over time (R=-0.037, P-value=0.499). Ascidian microbiomes and metabolomes contain species-specific and location-specific components. Location-specific bacteria are found in low abundance in the ascidians and mostly represent strains that are widespread. Location-specific metabolites consist largely of lipids, which may reflect differences in water temperature. By contrast, species-specific bacteria are mostly abundant sequenced components of the microbiomes and include secondary metabolite producers as major components. Species-specific chemicals are dominated by secondary metabolites. Together with previous analyses that focused on single ascidian species or symbiont type, these results reveal fundamental properties of secondary metabolic symbiosis. Different ascidian species have established associations with many different bacterial symbionts, including those known to produce toxic chemicals. This implies a strong selection for this property and the independent origin of secondary metabolite-based associations in different ascidian species. The analysis here streamlines the connection of secondary metabolite to producing bacterium, enabling further biological and

  14. Seasonal Variation of Chemical Species Associated With Short-Term Mortality Effects of PM2.5 in Xi’an, a Central City in China

    PubMed Central

    Huang, Wei; Cao, Junji; Tao, Yebin; Dai, Lingzhen; Lu, Shou-En; Hou, Bin; Wang, Zheng; Zhu, Tong

    2012-01-01

    The authors conducted a time-series analysis to examine seasonal variation of mortality risk in association with particulate matter less than 2.5 μm in aerodynamic diameter (PM2.5) and chemical species in Xi’an, China, using daily air pollution and all-cause and cause-specific mortality data (2004–2008). Poisson regression incorporating natural splines was used to estimate mortality risks of PM2.5 and its chemical components, adjusting for day of the week, time trend, and meteorologic effects. Increases of 2.29% (95% confidence interval: 0.83, 3.76) for all-cause mortality and 3.08% (95% confidence interval: 0.94, 5.26) for cardiovascular mortality were associated with an interquartile range increase of 103.0 μg/m3 in lagged 1–2 day PM2.5 exposure. Stronger effects were observed for the elderly (≥65 years), males, and cardiovascular diseases groups. Secondary components (sulfate and ammonium), combustion species (elemental carbon, sulfur, chlorine), and transition metals (chromium, lead, nickel, and zinc) appeared most responsible for increased risk, particularly in the cold months. The authors concluded that differential association patterns observed across species and seasons indicated that PM2.5-related effects might not be sufficiently explained by PM2.5 mass alone. Future research is needed to examine spatial and temporal varying factors that might play important roles in modifying the PM2.5–mortality association. PMID:22323403

  15. Macroevolutionary chemical escalation in an ancient plant-herbivore arms race.

    PubMed

    Becerra, Judith X; Noge, Koji; Venable, D Lawrence

    2009-10-27

    A central paradigm in the field of plant-herbivore interactions is that the diversity and complexity of secondary compounds in plants have intensified over evolutionary time, resulting in the great variety of secondary products that currently exists. Unfortunately, testing of this proposal has been very limited. We analyzed the volatile chemistry of 70 species of the tropical plant genus Bursera and used a molecular phylogeny to test whether the species' chemical diversity or complexity have escalated. The results confirm that as new species diverged over time they tended to be armed not only with more compounds/species, but also with compounds that could potentially be more difficult for herbivores to adapt to because they belong to an increasing variety of chemical pathways. Overall chemical diversity in the genus also increased, but not as fast as species diversity, possibly because of allopatric species gaining improved defense with compounds that are new locally, but already in existence elsewhere.

  16. Multi-target QSPR modeling for simultaneous prediction of multiple gas-phase kinetic rate constants of diverse chemicals

    NASA Astrophysics Data System (ADS)

    Basant, Nikita; Gupta, Shikha

    2018-03-01

    The reactions of molecular ozone (O3), hydroxyl (•OH) and nitrate (NO3) radicals are among the major pathways of removal of volatile organic compounds (VOCs) in the atmospheric environment. The gas-phase kinetic rate constants (kO3, kOH, kNO3) are thus, important in assessing the ultimate fate and exposure risk of atmospheric VOCs. Experimental data for rate constants are not available for many emerging VOCs and the computational methods reported so far address a single target modeling only. In this study, we have developed a multi-target (mt) QSPR model for simultaneous prediction of multiple kinetic rate constants (kO3, kOH, kNO3) of diverse organic chemicals considering an experimental data set of VOCs for which values of all the three rate constants are available. The mt-QSPR model identified and used five descriptors related to the molecular size, degree of saturation and electron density in a molecule, which were mechanistically interpretable. These descriptors successfully predicted three rate constants simultaneously. The model yielded high correlations (R2 = 0.874-0.924) between the experimental and simultaneously predicted endpoint rate constant (kO3, kOH, kNO3) values in test arrays for all the three systems. The model also passed all the stringent statistical validation tests for external predictivity. The proposed multi-target QSPR model can be successfully used for predicting reactivity of new VOCs simultaneously for their exposure risk assessment.

  17. Generation of quasi-monoenergetic protons from a double-species target driven by the radiation pressure of an ultraintense laser pulse

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pae, Ki Hong; Kim, Chul Min, E-mail: chulmin@gist.ac.kr; Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005

    In laser-driven proton acceleration, generation of quasi-monoenergetic proton beams has been considered a crucial feature of the radiation pressure acceleration (RPA) scheme, but the required difficult physical conditions have hampered its experimental realization. As a method to generate quasi-monoenergetic protons under experimentally viable conditions, we investigated using double-species targets of controlled composition ratio in order to make protons bunched in the phase space in the RPA scheme. From a modified optimum condition and three-dimensional particle-in-cell simulations, we showed by varying the ion composition ratio of proton and carbon that quasi-monoenergetic protons could be generated from ultrathin plane targets irradiated withmore » a circularly polarized Gaussian laser pulse. The proposed scheme should facilitate the experimental realization of ultrashort quasi-monoenergetic proton beams for unique applications in high field science.« less

  18. In Situ Infrared Spectroscopy of the Gaseous Species Present in a Diamond Chemical Vapor Deposition System

    NASA Technical Reports Server (NTRS)

    Morell, G.; Weiner, B. R.

    1998-01-01

    We interfaced a Hot-Filament Chemical Vapor Deposition (HFCVD) system to the emission port of an FT-IR spectrometer, in order to study the gas phase species present during the deposition of diamond thin films. The implementation of the infrared (IR) emission technique in situ allowed the study of various carbon-containing species believed to be crucial in diamond film growth. The two IR-active vibrational fundamentals of methane, v(3)(f2) and v(4)(f2), were observed at three different filament temperatures: 1000, 1500 and 2000 C. However, the net signal of v(3) was emission, while that of v(4) was absorption. These results indicate that the v(4) fundamental is excited beyond equilibrium, while the v(3) fundamental remains mostly in the ground state. This is due to the small concentration of methane, the low energy of v(4) compared to v(3) or to the Hz vibrational mode, and symmetry considerations that forbid interaction among the four fundamentals of methane. Thus, the excitation of v(3) is more likely than its decay under HFCVD conditions, producing a non-equilibrium population. At a filament temperature of 2000 C, the v(3) (sigma(+)(3)) fundamental of acetylene and a band at 1328 cm-l also ascribed to acetylene (v5 (pi(U)) + v4) appear in net absorption. This correlates well with the onset of molecular hydrogen breaking by the filament, which occurs at temperatures around 2000 C and above. The hydrogen atoms produced in this heterogeneous reaction give rise to a chain of reactions that lead to acetylene, among other carbonaceous species.

  19. Targeting proteasomes in infectious organisms to combat disease.

    PubMed

    Bibo-Verdugo, Betsaida; Jiang, Zhenze; Caffrey, Conor R; O'Donoghue, Anthony J

    2017-05-01

    Proteasomes are multisubunit, energy-dependent, proteolytic complexes that play an essential role in intracellular protein turnover. They are present in eukaryotes, archaea, and in some actinobacteria species. Inhibition of proteasome activity has emerged as a powerful strategy for anticancer therapy and three drugs have been approved for treatment of multiple myeloma. These compounds react covalently with a threonine residue located in the active site of a proteasome subunit to block protein degradation. Proteasomes in pathogenic organisms such as Mycobacterium tuberculosis and Plasmodium falciparum also have a nucleophilic threonine residue in the proteasome active site and are therefore sensitive to these anticancer drugs. This review summarizes efforts to validate the proteasome in pathogenic organisms as a therapeutic target. We describe several strategies that have been used to develop inhibitors with increased potency and selectivity for the pathogen proteasome relative to the human proteasome. In addition, we highlight a cell-based chemical screening approach that identified a potent, allosteric inhibitor of proteasomes found in Leishmania and Trypanosoma species. Finally, we discuss the development of proteasome inhibitors as anti-infective agents. © 2017 Federation of European Biochemical Societies.

  20. Synchronized chaotic targeting and acceleration of surface chemistry in prebiotic hydrothermal microenvironments

    PubMed Central

    Priye, Aashish; Yu, Yuncheng; Hassan, Yassin A.; Ugaz, Victor M.

    2017-01-01

    Porous mineral formations near subsea alkaline hydrothermal vents embed microenvironments that make them potential hot spots for prebiotic biochemistry. But, synthesis of long-chain macromolecules needed to support higher-order functions in living systems (e.g., polypeptides, proteins, and nucleic acids) cannot occur without enrichment of chemical precursors before initiating polymerization, and identifying a suitable mechanism has become a key unanswered question in the origin of life. Here, we apply simulations and in situ experiments to show how 3D chaotic thermal convection—flows that naturally permeate hydrothermal pore networks—supplies a robust mechanism for focused accumulation at discrete targeted surface sites. This interfacial enrichment is synchronized with bulk homogenization of chemical species, yielding two distinct processes that are seemingly opposed yet synergistically combine to accelerate surface reaction kinetics by several orders of magnitude. Our results suggest that chaotic thermal convection may play a previously unappreciated role in mediating surface-catalyzed synthesis in the prebiotic milieu. PMID:28119504