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Sample records for coffea rubiaceae identifying

  1. Towards a Phylogeny for Coffea (Rubiaceae): Identifying Well-supported Lineages Based on Nuclear and Plastid DNA Sequences

    PubMed Central

    Maurin, Olivier; Davis, Aaron P.; Chester, Michael; Mvungi, Esther F.; Jaufeerally-Fakim, Yasmina; Fay, Michael F.

    2007-01-01

    Background and Aims The phylogenetic relationships between species of Coffea and Psilanthus remain poorly understood, owing to low levels of sequence variation recovered in previous studies, coupled with relatively limited species sampling. In this study, the relationships between Coffea and Psilanthus species are assessed based on substantially increased molecular sequence data and greatly improved species sampling. Method Phylogenetic relationships are assessed using parsimony, with sequence data from four plastid regions [trnL–F intron, trnL–F intergenic spacer (IGS), rpl16 intron and accD–psa1 IGS], and the internal transcribed spacer (ITS) region of nuclear rDNA (ITS 1/5·8S/ITS 2). Supported lineages in Coffea are discussed within the context of geographical correspondence, biogeography, morphology and systematics. Key Results Several major lineages with geographical coherence, as identified in previous studies based on smaller data sets, are supported. Other lineages with either geographical or ecological correspondence are recognized for the first time. Coffea subgenus Baracoffea is shown to be monophyletic, but Coffea subgenus Coffea is paraphyletic. Sequence data do not substantiate the monophyly of either Coffea or Psilanthus. Low levels of sequence divergence do not allow detailed resolution of relationships within Coffea, most notably for species of Coffea subgenus Coffea occurring in Madagascar. The origin of C. arabica by recent hybridization between C. canephora and C. eugenioides is supported. Phylogenetic separation resulting from the presence of the Dahomey Gap is inferred based on sequence data from Coffea. PMID:17956855

  2. An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

    PubMed Central

    2011-01-01

    Background Coffee is one of the world's most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency. Results Assembling the expressed sequence tags (ESTs) of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories. Conclusion We present the first comprehensive genome-wide transcript

  3. High-throughput metabolic profiling of diverse green Coffea arabica beans identified tryptophan as a universal discrimination factor for immature beans.

    PubMed

    Setoyama, Daiki; Iwasa, Keiko; Seta, Harumichi; Shimizu, Hiroaki; Fujimura, Yoshinori; Miura, Daisuke; Wariishi, Hiroyuki; Nagai, Chifumi; Nakahara, Koichi

    2013-01-01

    The maturity of green coffee beans is the most influential determinant of the quality and flavor of the resultant coffee beverage. However, the chemical compounds that can be used to discriminate the maturity of the beans remain uncharacterized. We herein analyzed four distinct stages of maturity (immature, semi-mature, mature and overripe) of nine different varieties of green Coffea arabica beans hand-harvested from a single experimental field in Hawaii. After developing a high-throughput experimental system for sample preparation and liquid chromatography-mass spectrometry (LC-MS) measurement, we applied metabolic profiling, integrated with chemometric techniques, to explore the relationship between the metabolome and maturity of the sample in a non-biased way. For the multivariate statistical analyses, a partial least square (PLS) regression model was successfully created, which allowed us to accurately predict the maturity of the beans based on the metabolomic information. As a result, tryptophan was identified to be the best contributor to the regression model; the relative MS intensity of tryptophan was higher in immature beans than in those after the semi-mature stages in all arabica varieties investigated, demonstrating a universal discrimination factor for diverse arabica beans. Therefore, typtophan, either alone or together with other metabolites, may be utilized for traders as an assessment standard when purchasing qualified trading green arabica bean products. Furthermore, our results suggest that the tryptophan metabolism may be tightly linked to the development of coffee cherries and/or beans. PMID:23936381

  4. High-throughput metabolic profiling of diverse green Coffea arabica beans identified tryptophan as a universal discrimination factor for immature beans.

    PubMed

    Setoyama, Daiki; Iwasa, Keiko; Seta, Harumichi; Shimizu, Hiroaki; Fujimura, Yoshinori; Miura, Daisuke; Wariishi, Hiroyuki; Nagai, Chifumi; Nakahara, Koichi

    2013-01-01

    The maturity of green coffee beans is the most influential determinant of the quality and flavor of the resultant coffee beverage. However, the chemical compounds that can be used to discriminate the maturity of the beans remain uncharacterized. We herein analyzed four distinct stages of maturity (immature, semi-mature, mature and overripe) of nine different varieties of green Coffea arabica beans hand-harvested from a single experimental field in Hawaii. After developing a high-throughput experimental system for sample preparation and liquid chromatography-mass spectrometry (LC-MS) measurement, we applied metabolic profiling, integrated with chemometric techniques, to explore the relationship between the metabolome and maturity of the sample in a non-biased way. For the multivariate statistical analyses, a partial least square (PLS) regression model was successfully created, which allowed us to accurately predict the maturity of the beans based on the metabolomic information. As a result, tryptophan was identified to be the best contributor to the regression model; the relative MS intensity of tryptophan was higher in immature beans than in those after the semi-mature stages in all arabica varieties investigated, demonstrating a universal discrimination factor for diverse arabica beans. Therefore, typtophan, either alone or together with other metabolites, may be utilized for traders as an assessment standard when purchasing qualified trading green arabica bean products. Furthermore, our results suggest that the tryptophan metabolism may be tightly linked to the development of coffee cherries and/or beans.

  5. Differential regulation of caffeine metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta).

    PubMed

    Perrois, Charlène; Strickler, Susan R; Mathieu, Guillaume; Lepelley, Maud; Bedon, Lucie; Michaux, Stéphane; Husson, Jwanro; Mueller, Lukas; Privat, Isabelle

    2015-01-01

    Caffeine is a metabolite of great economic importance, especially in coffee, where it influences the sensorial and physiological impacts of the beverage. Caffeine metabolism in the Coffea species begins with the degradation of purine nucleotides through three specific N-methyltransferases: XMT, MXMT and DXMT. A comparative analysis was performed to clarify the molecular reasons behind differences in caffeine accumulation in two Coffea species, namely Coffea arabica and Coffea canephora var. robusta. Three different genes encoding N-methyltransferase were amplified in the doubled haploid Coffea canephora: CcXMT1, CcMXMT1 and CcDXMT. Six genes were amplified in the haploid Coffea arabica: CaXMT1, CaXMT2, CaMXMT1, CaMXMT2, CaDXMT1, and CaDXMT2. A complete phylogenic analysis was performed to identify specific key amino acids defining enzymatic function for each protein identified. Furthermore, a quantitative gene-expression analysis was conducted on leaves and on maturing coffee beans, simultaneously analyzing caffeine content. In the different varieties analyzed, caffeine accumulation is higher in leaves than in the coffee bean maturation period, higher in Robusta than in Arabica. In Robusta, CcXMT1 and CcDXMT gene expressions are predominant and transcriptional activity is higher in leaves than in maturing beans, and is highly correlated to caffeine accumulation. In Arabica, the CaXMT1 expression level is high in leaves and CaDXMT2 as well to a lesser extent, while global transcriptional activity is weak during bean maturation, suggesting that the transcriptional control of caffeine-related genes differs within different organs and between Arabica and Robusta. These findings indicate that caffeine accumulation in Coffea species has been modulated by a combination of differential transcriptional regulation and genome evolution. PMID:25249475

  6. Differential regulation of caffeine metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta).

    PubMed

    Perrois, Charlène; Strickler, Susan R; Mathieu, Guillaume; Lepelley, Maud; Bedon, Lucie; Michaux, Stéphane; Husson, Jwanro; Mueller, Lukas; Privat, Isabelle

    2015-01-01

    Caffeine is a metabolite of great economic importance, especially in coffee, where it influences the sensorial and physiological impacts of the beverage. Caffeine metabolism in the Coffea species begins with the degradation of purine nucleotides through three specific N-methyltransferases: XMT, MXMT and DXMT. A comparative analysis was performed to clarify the molecular reasons behind differences in caffeine accumulation in two Coffea species, namely Coffea arabica and Coffea canephora var. robusta. Three different genes encoding N-methyltransferase were amplified in the doubled haploid Coffea canephora: CcXMT1, CcMXMT1 and CcDXMT. Six genes were amplified in the haploid Coffea arabica: CaXMT1, CaXMT2, CaMXMT1, CaMXMT2, CaDXMT1, and CaDXMT2. A complete phylogenic analysis was performed to identify specific key amino acids defining enzymatic function for each protein identified. Furthermore, a quantitative gene-expression analysis was conducted on leaves and on maturing coffee beans, simultaneously analyzing caffeine content. In the different varieties analyzed, caffeine accumulation is higher in leaves than in the coffee bean maturation period, higher in Robusta than in Arabica. In Robusta, CcXMT1 and CcDXMT gene expressions are predominant and transcriptional activity is higher in leaves than in maturing beans, and is highly correlated to caffeine accumulation. In Arabica, the CaXMT1 expression level is high in leaves and CaDXMT2 as well to a lesser extent, while global transcriptional activity is weak during bean maturation, suggesting that the transcriptional control of caffeine-related genes differs within different organs and between Arabica and Robusta. These findings indicate that caffeine accumulation in Coffea species has been modulated by a combination of differential transcriptional regulation and genome evolution.

  7. The Impact of Climate Change on Indigenous Arabica Coffee (Coffea arabica): Predicting Future Trends and Identifying Priorities

    PubMed Central

    Gole, Tadesse Woldemariam; Baena, Susana

    2012-01-01

    Precise modelling of the influence of climate change on Arabica coffee is limited; there are no data available for indigenous populations of this species. In this study we model the present and future predicted distribution of indigenous Arabica, and identify priorities in order to facilitate appropriate decision making for conservation, monitoring and future research. Using distribution data we perform bioclimatic modelling and examine future distribution with the HadCM3 climate model for three emission scenarios (A1B, A2A, B2A) over three time intervals (2020, 2050, 2080). The models show a profoundly negative influence on indigenous Arabica. In a locality analysis the most favourable outcome is a c. 65% reduction in the number of pre-existing bioclimatically suitable localities, and at worst an almost 100% reduction, by 2080. In an area analysis the most favourable outcome is a 38% reduction in suitable bioclimatic space, and the least favourable a c. 90% reduction, by 2080. Based on known occurrences and ecological tolerances of Arabica, bioclimatic unsuitability would place populations in peril, leading to severe stress and a high risk of extinction. This study establishes a fundamental baseline for assessing the consequences of climate change on wild populations of Arabica coffee. Specifically, it: (1) identifies and categorizes localities and areas that are predicted to be under threat from climate change now and in the short- to medium-term (2020–2050), representing assessment priorities for ex situ conservation; (2) identifies ‘core localities’ that could have the potential to withstand climate change until at least 2080, and therefore serve as long-term in situ storehouses for coffee genetic resources; (3) provides the location and characterization of target locations (populations) for on-the-ground monitoring of climate change influence. Arabica coffee is confimed as a climate sensitivite species, supporting data and inference that existing

  8. The impact of climate change on indigenous Arabica coffee (Coffea arabica): predicting future trends and identifying priorities.

    PubMed

    Davis, Aaron P; Gole, Tadesse Woldemariam; Baena, Susana; Moat, Justin

    2012-01-01

    Precise modelling of the influence of climate change on Arabica coffee is limited; there are no data available for indigenous populations of this species. In this study we model the present and future predicted distribution of indigenous Arabica, and identify priorities in order to facilitate appropriate decision making for conservation, monitoring and future research. Using distribution data we perform bioclimatic modelling and examine future distribution with the HadCM3 climate model for three emission scenarios (A1B, A2A, B2A) over three time intervals (2020, 2050, 2080). The models show a profoundly negative influence on indigenous Arabica. In a locality analysis the most favourable outcome is a c. 65% reduction in the number of pre-existing bioclimatically suitable localities, and at worst an almost 100% reduction, by 2080. In an area analysis the most favourable outcome is a 38% reduction in suitable bioclimatic space, and the least favourable a c. 90% reduction, by 2080. Based on known occurrences and ecological tolerances of Arabica, bioclimatic unsuitability would place populations in peril, leading to severe stress and a high risk of extinction. This study establishes a fundamental baseline for assessing the consequences of climate change on wild populations of Arabica coffee. Specifically, it: (1) identifies and categorizes localities and areas that are predicted to be under threat from climate change now and in the short- to medium-term (2020-2050), representing assessment priorities for ex situ conservation; (2) identifies 'core localities' that could have the potential to withstand climate change until at least 2080, and therefore serve as long-term in situ storehouses for coffee genetic resources; (3) provides the location and characterization of target locations (populations) for on-the-ground monitoring of climate change influence. Arabica coffee is confimed as a climate sensitivite species, supporting data and inference that existing plantations

  9. Phytoalexin induction in rubiaceae.

    PubMed

    Braga, M R; Claudia, M; Young, M; Dietrich, S M; Gottlieb, O R

    1991-06-01

    Phytoalexin responses were measured by modified drop-diffusate and facilitated diffusion techniques after fungal inoculation of leaves of 32 Rubiaceae species from Brazilian forest and savanna. Such responses presented a trend similar to that previously observed for a broad sample of dicotyledonous plants and are more frequently positive for the more primitive (or slower growing) trees than for the advanced (or faster growing) herbs. Fifteen of these species analyzed during a one-year period showed that positive phytoalexin responses are stronger for the rainy (and hotter) than for the dry (and cooler) season. Species that contain relatively large quantities of phenolics gave invariably negative responses. Positive responses are not necessarily associated with the appearance of new substances within leaf tissue and are thus caused by inhibitins rather than by phytoalexins. These results are discussed recognizing that the tested plants are subject to the multifarious influences of their natural environment and of a possible conjugate-caused compartmentation of plant metabolites. PMID:24259169

  10. Coffee (Coffea arabica L.).

    PubMed

    Déchamp, Eveline; Breitler, Jean-Christophe; Leroy, Thierry; Etienne, Hervé

    2015-01-01

    Coffee (Coffea sp.) is a perennial plant widely cultivated in many tropical countries. It is a cash crop for millions of small farmers in these areas. As for other tree species, coffee has long breeding cycles, which makes conventional breeding programs time-consuming. For that matter, genetic transformation can be an effective way to introduce a desired trait in elite varieties or for functional genomics. In this chapter, we describe two highly efficient and reliable Agrobacterium-mediated transformation techniques developed for the C. arabica cultivated species: (1) A. tumefaciens to study and introduce genes conferring resistance/tolerance to biotic (coffee leaf rust, insects) and abiotic stress (drought, heat, seed desiccation) in fully transformed plants and (2) A. rhizogenes to study candidate gene expression for nematode resistance in transformed roots.

  11. Identification of novel and conserved microRNAs in Coffea canephora and Coffea arabica

    PubMed Central

    Loss-Morais, Guilherme; Ferreira, Daniela C.R.; Margis, Rogério; Alves-Ferreira, Márcio; Corrêa, Régis L.

    2014-01-01

    As microRNAs (miRNAs) are important regulators of many biological processes, a series of small RNAomes from plants have been produced in the last decade. However, miRNA data from several groups of plants are still lacking, including some economically important crops. Here microRNAs from Coffea canephora leaves were profiled and 58 unique sequences belonging to 33 families were found, including two novel microRNAs that have never been described before in plants. Some of the microRNA sequences were also identified in Coffea arabica that, together with C. canephora, correspond to the two major sources of coffee production in the world. The targets of almost all miRNAs were also predicted on coffee expressed sequences. This is the first report of novel miRNAs in the genus Coffea, and also the first in the plant order Gentianales. The data obtained establishes the basis for the understanding of the complex miRNA-target network on those two important crops. PMID:25505842

  12. Secondary metabolites from Rubiaceae species.

    PubMed

    Martins, Daiane; Nunez, Cecilia Veronica

    2015-07-22

    This study describes some characteristics of the Rubiaceae family pertaining to the occurrence and distribution of secondary metabolites in the main genera of this family. It reports the review of phytochemical studies addressing all species of Rubiaceae, published between 1990 and 2014. Iridoids, anthraquinones, triterpenes, indole alkaloids as well as other varying alkaloid subclasses, have shown to be the most common. These compounds have been mostly isolated from the genera Uncaria, Psychotria, Hedyotis, Ophiorrhiza and Morinda. The occurrence and distribution of iridoids, alkaloids and anthraquinones point out their chemotaxonomic correlation among tribes and subfamilies. From an evolutionary point of view, Rubioideae is the most ancient subfamily, followed by Ixoroideae and finally Cinchonoideae. The chemical biosynthetic pathway, which is not so specific in Rubioideae, can explain this and large amounts of both iridoids and indole alkaloids are produced. In Ixoroideae, the most active biosysthetic pathway is the one that produces iridoids; while in Cinchonoideae, it produces indole alkaloids together with other alkaloids. The chemical biosynthetic pathway now supports this botanical conclusion.

  13. Identification of Ramie Genes in Response to Pratylenchus coffeae Infection Challenge by Digital Gene Expression Analysis.

    PubMed

    Yu, Yongting; Zeng, Liangbin; Yan, Zhun; Liu, Touming; Sun, Kai; Zhu, Taotao; Zhu, Aiguo

    2015-09-11

    Root lesion disease, caused by Pratylenchus coffeae, seriously impairs the growth and yield of ramie, an important natural fiber crop. The ramie defense mechanism against P. coffeae infection is poorly understood, which hinders efforts to improve resistance via breeding programs. In this study, the transcriptome of the resistant ramie cultivar Qingdaye was characterized using Illumina sequence technology. About 46.3 million clean pair end (PE) reads were generated and assembled into 40,826 unigenes with a mean length of 830 bp. Digital gene expression (DGE) analysis was performed on both the control roots (CK) and P. coffeae-challenged roots (CH), and the differentially expressed genes (DEGs) were identified. Approximately 10.16 and 8.07 million cDNA reads in the CK and CH cDNA libraries were sequenced, respectively. A total of 137 genes exhibited different transcript abundances between the two libraries. Among them, the expressions of 117 and 20 DEGs were up- and down-regulated in P. coffeae-challenged ramie, respectively. The expression patterns of 15 candidate genes determined by qRT-PCR confirmed the results of DGE analysis. Time-course expression profiles of eight defense-related genes in susceptible and resistant ramie cultivars were different after P. coffeae inoculation. The differential expression of protease inhibitors, pathogenesis-related proteins (PRs), and transcription factors in resistant and susceptible ramie during P. coffeae infection indicated that cystatin likely plays an important role in nematode resistance.

  14. Identification of Ramie Genes in Response to Pratylenchus coffeae Infection Challenge by Digital Gene Expression Analysis

    PubMed Central

    Yu, Yongting; Zeng, Liangbin; Yan, Zhun; Liu, Touming; Sun, Kai; Zhu, Taotao; Zhu, Aiguo

    2015-01-01

    Root lesion disease, caused by Pratylenchus coffeae, seriously impairs the growth and yield of ramie, an important natural fiber crop. The ramie defense mechanism against P. coffeae infection is poorly understood, which hinders efforts to improve resistance via breeding programs. In this study, the transcriptome of the resistant ramie cultivar Qingdaye was characterized using Illumina sequence technology. About 46.3 million clean pair end (PE) reads were generated and assembled into 40,826 unigenes with a mean length of 830 bp. Digital gene expression (DGE) analysis was performed on both the control roots (CK) and P. coffeae-challenged roots (CH), and the differentially expressed genes (DEGs) were identified. Approximately 10.16 and 8.07 million cDNA reads in the CK and CH cDNA libraries were sequenced, respectively. A total of 137 genes exhibited different transcript abundances between the two libraries. Among them, the expressions of 117 and 20 DEGs were up- and down-regulated in P. coffeae-challenged ramie, respectively. The expression patterns of 15 candidate genes determined by qRT-PCR confirmed the results of DGE analysis. Time-course expression profiles of eight defense-related genes in susceptible and resistant ramie cultivars were different after P. coffeae inoculation. The differential expression of protease inhibitors, pathogenesis-related proteins (PRs), and transcription factors in resistant and susceptible ramie during P. coffeae infection indicated that cystatin likely plays an important role in nematode resistance. PMID:26378527

  15. Analysis of Phosphorus Use Efficiency Traits in Coffea Genotypes Reveals Coffea arabica and Coffea canephora Have Contrasting Phosphorus Uptake and Utilization Efficiencies

    PubMed Central

    Neto, Ana P.; Favarin, José L.; Hammond, John P.; Tezotto, Tiago; Couto, Hilton T. Z.

    2016-01-01

    Background and Aims: Phosphate (Pi) is one of the most limiting nutrients for agricultural production in Brazilian soils due to low soil Pi concentrations and rapid fixation of fertilizer Pi by adsorption to oxidic minerals and/or precipitation by iron and aluminum ions. The objectives of this study were to quantify phosphorus (P) uptake and use efficiency in cultivars of the species Coffea arabica L. and Coffea canephora L., and group them in terms of efficiency and response to Pi availability. Methods: Plants of 21 cultivars of C. arabica and four cultivars of C. canephora were grown under contrasting soil Pi availabilities. Biomass accumulation, tissue P concentration and accumulation and efficiency indices for P use were measured. Key Results: Coffee plant growth was significantly reduced under low Pi availability, and P concentration was higher in cultivars of C. canephora. The young leaves accumulated more P than any other tissue. The cultivars of C. canephora had a higher root/shoot ratio and were significantly more efficient in P uptake, while the cultivars of C. arabica were more efficient in P utilization. Agronomic P use efficiency varied among coffee cultivars and E16 Shoa, E22 Sidamo, Iêmen and Acaiá cultivars were classified as the most efficient and responsive to Pi supply. A positive correlation between P uptake efficiency and root to shoot ratio was observed across all cultivars at low Pi supply. These data identify Coffea genotypes better adapted to low soil Pi availabilities, and the traits that contribute to improved P uptake and use efficiency. These data could be used to select current genotypes with improved P uptake or utilization efficiencies for use on soils with low Pi availability and also provide potential breeding material and targets for breeding new cultivars better adapted to the low Pi status of Brazilian soils. This could ultimately reduce the use of Pi fertilizers in tropical soils, and contribute to more sustainable coffee

  16. Chemical partitioning and antioxidant capacity of green coffee (Coffea arabica and Coffea canephora) of different geographical origin.

    PubMed

    Babova, Oxana; Occhipinti, Andrea; Maffei, Massimo E

    2016-03-01

    Green coffee beans of Coffea arabica and Coffea canephora accessions from different geographical origin (Brazil, Colombia, Ethiopia, Honduras, Kenya, Mexico, Peru, Uganda and Vietnam) were extracted and the extracts analyzed by HPLC-ESI-MS/MS for the identification and quantification of chlorogenic acids and caffeine content. Principal component and cluster analyses were used to identify chemical patterns separating the different species and accessions based on their geographical origin. C. canephora showed always a higher caffeine content with respect to C. arabica, whereas the C. arabica accessions from Kenya showed a higher chlorogenic acids and a lower caffeine content. The antioxidant capacity of green coffee extracts was assayed by the reducing power and DPPH assays. The antioxidant capacity correlated with the chlorogenic acids content. The results show that the C. arabica from Kenya possesses the highest chlorogenic acids/caffeine ratio and, among the C. arabica accessions, the highest antioxidant capacity. Therefore, the C. arabica from Kenya is the most suitable green coffee source for nutraceutical applications because of its high antioxidant capacity and low caffeine content. PMID:26837609

  17. Chemical partitioning and antioxidant capacity of green coffee (Coffea arabica and Coffea canephora) of different geographical origin.

    PubMed

    Babova, Oxana; Occhipinti, Andrea; Maffei, Massimo E

    2016-03-01

    Green coffee beans of Coffea arabica and Coffea canephora accessions from different geographical origin (Brazil, Colombia, Ethiopia, Honduras, Kenya, Mexico, Peru, Uganda and Vietnam) were extracted and the extracts analyzed by HPLC-ESI-MS/MS for the identification and quantification of chlorogenic acids and caffeine content. Principal component and cluster analyses were used to identify chemical patterns separating the different species and accessions based on their geographical origin. C. canephora showed always a higher caffeine content with respect to C. arabica, whereas the C. arabica accessions from Kenya showed a higher chlorogenic acids and a lower caffeine content. The antioxidant capacity of green coffee extracts was assayed by the reducing power and DPPH assays. The antioxidant capacity correlated with the chlorogenic acids content. The results show that the C. arabica from Kenya possesses the highest chlorogenic acids/caffeine ratio and, among the C. arabica accessions, the highest antioxidant capacity. Therefore, the C. arabica from Kenya is the most suitable green coffee source for nutraceutical applications because of its high antioxidant capacity and low caffeine content.

  18. Differential regulation of grain sucrose accumulation and metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta) revealed through gene expression and enzyme activity analysis.

    PubMed

    Privat, Isabelle; Foucrier, Séverine; Prins, Anneke; Epalle, Thibaut; Eychenne, Magali; Kandalaft, Laurianne; Caillet, Victoria; Lin, Chenwei; Tanksley, Steve; Foyer, Christine; McCarthy, James

    2008-01-01

    * Coffea arabica (Arabica) and Coffea canephora (Robusta) are the two main cultivated species used for coffee bean production. Arabica genotypes generally produce a higher coffee quality than Robusta genotypes. Understanding the genetic basis for sucrose accumulation during coffee grain maturation is an important goal because sucrose is an important coffee flavor precursor. * Nine new Coffea genes encoding sucrose metabolism enzymes have been identified: sucrose phosphate synthase (CcSPS1, CcSPS2), sucrose phosphate phosphatase (CcSP1), cytoplasmic (CaInv3) and cell wall (CcInv4) invertases and four invertase inhibitors (CcInvI1, 2, 3, 4). * Activities and mRNA abundance of the sucrose metabolism enzymes were compared at different developmental stages in Arabica and Robusta grains, characterized by different sucrose contents in mature grain. * It is concluded that Robusta accumulates less sucrose than Arabica for two reasons: Robusta has higher sucrose synthase and acid invertase activities early in grain development - the expression of CcSS1 and CcInv2 appears to be crucial at this stage and Robusta has a lower SPS activity and low CcSPS1 expression at the final stages of grain development and hence has less capacity for sucrose re-synthesis. Regulation of vacuolar invertase CcInv2 activity by invertase inhibitors CcInvI2 and/or CcInvI3 during Arabica grain development is considered. PMID:18384509

  19. Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes

    PubMed Central

    Guyot, Romain; de la Mare, Marion; Viader, Véronique; Hamon, Perla; Coriton, Olivier; Bustamante-Porras, José; Poncet, Valérie; Campa, Claudine; Hamon, Serge; de Kochko, Alexandre

    2009-01-01

    Background Coffea canephora, also called Robusta, belongs to the Rubiaceae, the fourth largest angiosperm family. This diploid species (2x = 2n = 22) has a fairly small genome size of ≈ 690 Mb and despite its extreme economic importance, particularly for developing countries, knowledge on the genome composition, structure and evolution remain very limited. Here, we report the 160 kb of the first C. canephora Bacterial Artificial Chromosome (BAC) clone ever sequenced and its fine analysis. Results This clone contains the CcEIN4 gene, encoding an ethylene receptor, and twenty other predicted genes showing a high gene density of one gene per 7.8 kb. Most of them display perfect matches with C. canephora expressed sequence tags or show transcriptional activities through PCR amplifications on cDNA libraries. Twenty-three transposable elements, mainly Class II transposon derivatives, were identified at this locus. Most of these Class II elements are Miniature Inverted-repeat Transposable Elements (MITE) known to be closely associated with plant genes. This BAC composition gives a pattern similar to those found in gene rich regions of Solanum lycopersicum and Medicago truncatula genomes indicating that the CcEIN4 regions may belong to a gene rich region in the C. canephora genome. Comparative sequence analysis indicated an extensive conservation between C. canephora and most of the reference dicotyledonous genomes studied in this work, such as tomato (S. lycopersicum), grapevine (V. vinifera), barrel medic M. truncatula, black cottonwood (Populus trichocarpa) and Arabidopsis thaliana. The higher degree of microcollinearity was found between C. canephora and V. vinifera, which belong respectively to the Asterids and Rosids, two clades that diverged more than 114 million years ago. Conclusion This study provides a first glimpse of C. canephora genome composition and evolution. Our data revealed a remarkable conservation of the microcollinearity between C. canephora and V

  20. Botanical and geographical characterization of green coffee (Coffea arabica and Coffea canephora): chemometric evaluation of phenolic and methylxanthine contents.

    PubMed

    Alonso-Salces, Rosa M; Serra, Francesca; Reniero, Fabiano; Héberger, Károly

    2009-05-27

    Green coffee beans of the two main commercial coffee varieties, Coffea arabica (Arabica) and Coffea canephora (Robusta), from the major growing regions of America, Africa, Asia, and Oceania were studied. The contents of chlorogenic acids, cinnamoyl amides, cinnamoyl glycosides, free phenolic acids, and methylxanthines of green coffee beans were analyzed by liquid chromatography coupled with UV spectrophotometry to determine their botanical and geographical origins. The analysis of caffeic acid, 3-feruloylquinic acid, 5-feruloylquinic acid, 4-feruloylquinic acid, 3,4-dicaffeoylquinic acid, 3-caffeoyl-5-feruloylquinic acid, 3-caffeoyl-4-feruloylquinic acid, 3-p-coumaroyl-4-caffeoylquinic acid, 3-caffeoyl-4-dimethoxycinnamoylquinic acid, 3-caffeoyl-5-dimethoxycinnamoylquinic acid, p-coumaroyl-N-tryptophan, feruloyl-N-tryptophan, caffeoyl-N-tryptophan, and caffeine enabled the unequivocal botanical characterization of green coffee beans. Moreover, some free phenolic acids and cinnamate conjugates of green coffee beans showed great potential as means for the geographical characterization of coffee. Thus, p-coumaroyl-N-tyrosine, caffeoyl-N-phenylalanine, caffeoyl-N-tyrosine, 3-dimethoxycinnamoyl-5-feruloylquinic acid, and dimethoxycinnamic acid were found to be characteristic markers for Ugandan Robusta green coffee beans. Multivariate data analysis of the phenolic and methylxanthine profiles provided preliminary results that allowed showing their potential for the determination of the geographical origin of green coffees. Linear discriminant analysis (LDA) and partial least-squares discriminant analysis (PLS-DA) provided classification models that correctly identified all authentic Robusta green coffee beans from Cameroon and Vietnam and 94% of those from Indonesia. Moreover, PLS-DA afforded independent models for Robusta samples from these three countries with sensitivities and specificities of classifications close to 100% and for Arabica samples from America and

  1. Chemical descriptors for sensory and parental origin of commercial Coffea genotypes.

    PubMed

    Bicho, Natalina Cavaco; Leitão, António Eduardo; Ramalho, José Cochicho; Lidon, Fernando Cebola

    2012-11-01

    To attain chemical descriptors responsible for sensory characteristics linked to the botanical origin of five Brazilian coffee genotypes, a chemical survey was carried out. Highest and lowest amounts of caffeine were found in Apoatã and Obatã. Coffea dewevrei showed the lowest contents of 5-CQA and 3-CQA. 3,5-diCQA was higher for Apoatã and minimum values were detected in Icatu. Apoatã showed the highest contents of 3,4-diCQA and 4,5-diCQA, Catuaí, Icatu and Obatã revealed lower values of 4,5-diCQA. Among hydroxycinnamic acids ferulic acid prevailed in all genotypes, with lower values in Icatu and Obatã. 3,4-DCA remained significantly higher in Apoatã, C. dewevrei and Catuaí. Caffeic acid and p-coumaric acid did not vary significantly. It was concluded that Apoatã was most adequate for the decaffeinated industry; Catuaí, Icatu and Obatã were identified as producers of good beverages. Apoatã and C. dewevrei seemed to share closer parental origins to Coffea canephora cv. Robusta, whereas Icatu, Obatã and Catuaí showed higher similarities to Coffea arabica.

  2. Spiradiclis longanensis, a new species of Rubiaceae from China

    PubMed Central

    Wen, Haizhen; Wang, Ruijiang; Deng, Shujun

    2015-01-01

    Abstract A new species of Spiradiclis (Rubiaceae) was found during our field trip to Guangxi, China, and is described here as Spiradiclis longanensis R. J. Wang. This species is readily distinguishable from other prostrate and decumbent species of the genus described previously by dense pubescence all over the plant, 5–20 small flowers per cymose, linear calyx lobes, and tubular corolla. The conservation status of VU was preliminarily assessed according to IUCN categories and criteria. PMID:26312046

  3. Sommera cusucoana, a new species of Rubiaceae from Honduras

    PubMed Central

    Lorence, David H.; Dietzsch, Anke C.; Kelly, Daniel L.

    2015-01-01

    Abstract Sommera cusucoana Lorence, D. Kelly & A. Dietzsch, sp. nov., (Rubiaceae), a new species from Honduras, differs from the other Mesoamerican Sommera species by the combination of large, obovate leaves with long red petioles, glabrous or glabrate intervenal areas, red stipules, lax, sparsely pubescent inflorescences with red axes, flowers with red hypanthium and calyx, long fruiting pedicels, and dark red mature fruits. It is known only from the type locality in Cusuco National Park. PMID:26751914

  4. Sommera cusucoana, a new species of Rubiaceae from Honduras.

    PubMed

    Lorence, David H; Dietzsch, Anke C; Kelly, Daniel L

    2015-01-01

    Sommera cusucoana Lorence, D. Kelly & A. Dietzsch, sp. nov., (Rubiaceae), a new species from Honduras, differs from the other Mesoamerican Sommera species by the combination of large, obovate leaves with long red petioles, glabrous or glabrate intervenal areas, red stipules, lax, sparsely pubescent inflorescences with red axes, flowers with red hypanthium and calyx, long fruiting pedicels, and dark red mature fruits. It is known only from the type locality in Cusuco National Park.

  5. Sommera cusucoana, a new species of Rubiaceae from Honduras.

    PubMed

    Lorence, David H; Dietzsch, Anke C; Kelly, Daniel L

    2015-01-01

    Sommera cusucoana Lorence, D. Kelly & A. Dietzsch, sp. nov., (Rubiaceae), a new species from Honduras, differs from the other Mesoamerican Sommera species by the combination of large, obovate leaves with long red petioles, glabrous or glabrate intervenal areas, red stipules, lax, sparsely pubescent inflorescences with red axes, flowers with red hypanthium and calyx, long fruiting pedicels, and dark red mature fruits. It is known only from the type locality in Cusuco National Park. PMID:26751914

  6. Rubipodanin A, the First Natural N-Desmonomethyl Rubiaceae-Type Cyclopeptide from Rubia podantha, Indicating an Important Role of the N9-Methyl Group in the Conformation and Bioactivity.

    PubMed

    Wang, Zhe; Zhao, Si-Meng; Zhao, Li-Mei; Chen, Xiao-Qiang; Zeng, Guang-Zhi; Tan, Ning-Hua

    2015-01-01

    One new cyclic hexapeptide named rubipodanin A (1), which is the first identified natural N-desmonomethyl Rubiaceae-type cyclopeptide, together with six known Rubiaceae-type cyclopeptides (2-7) were obtained using the TLC cyclopeptide protosite detection method with ninhydrin from the roots and rhizomes of Rubia podantha. The cyclopeptide structures were elucidated by extensive spectroscopic analysis, including 1D-NMR, 2D-NMR, IR, UV and MS. The solution conformation and biological activities of 1 and RA-V (4) were evaluated, and the results demonstrated that the N9-methyl group plays a vital role in the maintenance of the conformation and bioactivity. PMID:26694544

  7. New Insights on Coffea miRNAs: Features and Evolutionary Conservation.

    PubMed

    Chaves, S S; Fernandes-Brum, C N; Silva, G F F; Ferrara-Barbosa, B C; Paiva, L V; Nogueira, F T S; Cardoso, T C S; Amaral, L R; de Souza Gomes, M; Chalfun-Junior, A

    2015-10-01

    Small RNAs influence the gene expression at the post-transcriptional level by guiding messenger RNA (mRNA) cleavage, translational repression, and chromatin modifications. In addition to model plants, the microRNAs (miRNAs) have been identified in different crop species. In this work, we developed a specific pipeline to search for coffee miRNA homologs on expressed sequence tags (ESTs) and genome survey sequences (GSS) databases. As a result, 36 microRNAs were identified and a total of 616 and 362 potential targets for Coffea arabica and Coffea canephora, respectively. The evolutionary analyses of these molecules were performed by comparing the primary and secondary structures of precursors and mature miRNAs with their orthologs. Moreover, using a stem-loop RT-PCR assay, we evaluated the accumulation of mature miRNAs in genomes with different ploidy levels, detecting an increase in the miRNAs accumulation according to the ploidy raising. Finally, a 5' RACE (Rapid Amplification of cDNA Ends) assay was performed to verify the regulation of auxin responsive factor 8 (ARF8) by MIR167 in coffee plants. The great variety of target genes indicates the functional plasticity of these molecules and reinforces the importance of understanding the RNAi-dependent regulatory mechanisms. Our results expand the study of miRNAs and their target genes in this crop, providing new challenges to understand the biology of these species. PMID:26277190

  8. New Insights on Coffea miRNAs: Features and Evolutionary Conservation.

    PubMed

    Chaves, S S; Fernandes-Brum, C N; Silva, G F F; Ferrara-Barbosa, B C; Paiva, L V; Nogueira, F T S; Cardoso, T C S; Amaral, L R; de Souza Gomes, M; Chalfun-Junior, A

    2015-10-01

    Small RNAs influence the gene expression at the post-transcriptional level by guiding messenger RNA (mRNA) cleavage, translational repression, and chromatin modifications. In addition to model plants, the microRNAs (miRNAs) have been identified in different crop species. In this work, we developed a specific pipeline to search for coffee miRNA homologs on expressed sequence tags (ESTs) and genome survey sequences (GSS) databases. As a result, 36 microRNAs were identified and a total of 616 and 362 potential targets for Coffea arabica and Coffea canephora, respectively. The evolutionary analyses of these molecules were performed by comparing the primary and secondary structures of precursors and mature miRNAs with their orthologs. Moreover, using a stem-loop RT-PCR assay, we evaluated the accumulation of mature miRNAs in genomes with different ploidy levels, detecting an increase in the miRNAs accumulation according to the ploidy raising. Finally, a 5' RACE (Rapid Amplification of cDNA Ends) assay was performed to verify the regulation of auxin responsive factor 8 (ARF8) by MIR167 in coffee plants. The great variety of target genes indicates the functional plasticity of these molecules and reinforces the importance of understanding the RNAi-dependent regulatory mechanisms. Our results expand the study of miRNAs and their target genes in this crop, providing new challenges to understand the biology of these species.

  9. Identification of Putative Molecular Markers Associated with Root Traits in Coffea canephora Pierre ex Froehner

    PubMed Central

    Achar, Devaraja; Awati, Mallikarjuana G.; Udayakumar, M.; Prasad, T. G.

    2015-01-01

    Coffea canephora exhibit poor root system and are very sensitive to drought stress that affects growth and production. Deeper root system has been largely empirical as better avoidance to soil water limitation in drought condition. The present study aimed to identify molecular markers linked to high root types in Coffea canephora using molecular markers. Contrasting parents, L1 valley with low root and S.3334 with high root type, were crossed, and 134 F1 individuals were phenotyped for root and associated physiological traits (29 traits) and genotyped with 41 of the 320 RAPD and 9 of the 55 SSR polymorphic primers. Single marker analysis was deployed for detecting the association of markers linked to root associated traits by SAS software. There were 13 putative RAPD markers associated with root traits such as root length, secondary roots, root dry weight, and root to shoot ratio, in which root length associated marker OPS1850 showed high phenotypic variance of 6.86%. Two microsatellite markers linked to root length (CPCM13400) and root to shoot ratio (CM211300). Besides, 25 markers were associated with more than one trait and few of the markers were associated with positively related physiological traits and can be used in marker assisted trait selection. PMID:25821599

  10. Lipid transfer proteins in coffee: isolation of Coffea orthologs, Coffea arabica homeologs, expression during coffee fruit development and promoter analysis in transgenic tobacco plants.

    PubMed

    Cotta, Michelle G; Barros, Leila M G; de Almeida, Juliana D; de Lamotte, Fréderic; Barbosa, Eder A; Vieira, Natalia G; Alves, Gabriel S C; Vinecky, Felipe; Andrade, Alan C; Marraccini, Pierre

    2014-05-01

    The aim of the present study was to perform a genomic analysis of non-specific lipid-transfer proteins (nsLTPs) in coffee. Several nsLTPs-encoding cDNA and gene sequences were cloned from Coffea arabica and Coffea canephora species. In this work, their analyses revealed that coffee nsLTPs belong to Type II LTP characterized under their mature forms by a molecular weight of around 7.3 kDa, a basic isoelectric points of 8.5 and the presence of typical CXC pattern, with X being an hydrophobic residue facing towards the hydrophobic cavity. Even if several single nucleotide polymorphisms were identified in these nsLTP-coding sequences, 3D predictions showed that they do not have a significant impact on protein functions. Northern blot and RT-qPCR experiments revealed specific expression of Type II nsLTPs-encoding genes in coffee fruits, mainly during the early development of endosperm of both C. arabica and C. canephora. As part of our search for tissue-specific promoters in coffee, an nsLTP promoter region of around 1.2 kb was isolated. It contained several DNA repeats including boxes identified as essential for grain specific expression in other plants. The whole fragment, and a series of 5' deletions, were fused to the reporter gene β-glucuronidase (uidA) and analyzed in transgenic Nicotiana tabacum plants. Histochemical and fluorimetric GUS assays showed that the shorter (345 bp) and medium (827 bp) fragments of nsLTP promoter function as grain-specific promoters in transgenic tobacco plants. PMID:24469961

  11. Phylogenetic position of Guihaiothamnus (Rubiaceae): its evolutionary and ecological implications.

    PubMed

    Xie, Peiwu; Tu, Tieyao; Razafimandimbison, Sylvain G; Zhu, Chengjie; Zhang, Dianxiang

    2014-09-01

    Guihaiothamnus (Rubiaceae) is an enigmatic, monotypic genus endemic to southwestern China. Its generic status has never been doubted because it is morphologically unique by having rosette habit, showy, long-corolla-tubed flowers, and multi-seeded indehiscent berry-like fruits. The genus has been postulated to be a relict in the broad-leaved forests of China, and to be related to the genus Wendlandia, which was placed in the subfamily Cinchonoideae and recently classified in the tribe Augusteae of the subfamily Dialypetalanthoideae. Using combined evidence from palynology, cytology, and DNA sequences of nuclear ITS and four plastid markers (rps16, trnT-F, ndhF, rbcL), we assessed the phylogenetic position of Guihaiothamnus in Rubiaceae. Our molecular phylogenetic analyses placed the genus deeply nested within Wendlandia. This relationship is corroborated by evidence from palynology and cytology. Using a relaxed molecular clock method based on five fossil records, we dated the stem age of Wendlandia to be 17.46 my and, the split between G. acaulis and related Wendlandia species in southwestern China to be 2.11mya. This young age, coupled with the derived position in Wendlandia, suggests an evolutionary derivation rather than an evolutionary relict of G. acaulis. Its rosette habit and large showy flowers, which are very distinctive from other Wendlandias, are interpreted as a result of recent rapid adaptation to rock and cliff habitats.

  12. Revision of Coprosma (Rubiaceae, tribe Anthospermeae) in the Marquesas Islands

    PubMed Central

    Wagner, Warren L.; Lorence, David H.

    2011-01-01

    Abstract During the preparation of the Vascular Flora of the Marquesas Islands three new species of Coprosma (Rubiaceae, tribe Anthospermeae) have come to light and are described herein: Coprosma fatuhivaensis W. L. Wagner & Lorence, Coprosma meyeri W. L. Wagner & Lorence, and Coprosma temetiuensis W. L. Wagner & Lorence. Descriptions, illustrations, conservation status, and specimen citations are provided. Amended descriptions of three previously described Marquesan Coprosma species are also provided as well as a key to the species, four of which fall into the Critically Endangered (CR) and two into the Endangered (EN) category. With the description of these the new species, Coprosma becomes the sixth largest lineage in the Marquesas Islands with six species after Psychotria (one lineage which has 9 spp.), Cyrtandra (8 spp.), Bidens (8 spp.), Melicope (7 spp.), and Ixora (7 spp.). PMID:22171184

  13. Preliminary Characterization of Monofloral Coffea spp. Honey: Correlation between Potential Biomarkers and Pollen Content.

    PubMed

    Schievano, Elisabetta; Finotello, Claudia; Mammi, Stefano; Belci, Anna Illy; Colomban, Silvia; Navarini, Luciano

    2015-07-01

    To determine the botanical origin of Coffea honey, a new method using proton nuclear magnetic resonance ((1)H NMR) is proposed. Integration of the aromatic region of the NMR spectrum of Coffea honey diluted in deuterated water allowed us to simultaneously quantify caffeine, theobromine, and trigonelline, as well as other compounds. The amounts of the three markers listed are significantly higher than those previously reported for Citrus spp. honey: caffeine ranged from 15 to 98 mg/kg, theobromine from 25 to 160 mg/kg, and trigonelline from 23 to 86 mg/kg. The concurrent presence of these three substances is proposed as an indicator of the botanical origin of Coffea honey. Excellent correlation was found between these markers and the relative amounts of Coffea pollen measured in the same samples.

  14. The red spider mite, Oligonychus coffeae (Acari: Tetranychidae): its status, biology, ecology and management in tea plantations.

    PubMed

    Roy, Somnath; Muraleedharan, Narayanannair; Mukhopadhyay, Ananda

    2014-08-01

    Oligonychus coffeae Nietner (Acari: Tetranychidae), the red spider mite (RSM), is a major pest of tea (Camellia sinensis) in most tea-producing countries. Nymphs and adults of RSM lacerate cells, producing minute characteristic reddish brown marks on the upper surface of mature leaves, which turn red in severe cases of infestation, resulting in crop loss. The pest is present on tea all the year round, although numbers vary depending on season. Their number increases as the weather warms up and decreases markedly once rains set in. Under optimal conditions there may be 22 overlapping generations in a year. Parthenogenesis is known to occur; consequently, all mite stages can be found at a given time. Their infestation is mainly confined to the upper surface of the mature leaves and could readily be identified by the bronzing of the leaf. There are several naturally occurring insect predators, such as coccinellid and staphylinid larvae, lacewing larvae, and mite predators, most importantly species of the families Phytoseiidae and Stigmaeidae. Integrated management has been adopted to control this mite pest, involving cultural, mechanical, physical, biological and chemical methods. This review collates the most important works carried out on biology, ecology and management of O. coffeae. Also the scope of future studies for better management of this regular mite pest of tea is discussed. PMID:24705870

  15. The red spider mite, Oligonychus coffeae (Acari: Tetranychidae): its status, biology, ecology and management in tea plantations.

    PubMed

    Roy, Somnath; Muraleedharan, Narayanannair; Mukhopadhyay, Ananda

    2014-08-01

    Oligonychus coffeae Nietner (Acari: Tetranychidae), the red spider mite (RSM), is a major pest of tea (Camellia sinensis) in most tea-producing countries. Nymphs and adults of RSM lacerate cells, producing minute characteristic reddish brown marks on the upper surface of mature leaves, which turn red in severe cases of infestation, resulting in crop loss. The pest is present on tea all the year round, although numbers vary depending on season. Their number increases as the weather warms up and decreases markedly once rains set in. Under optimal conditions there may be 22 overlapping generations in a year. Parthenogenesis is known to occur; consequently, all mite stages can be found at a given time. Their infestation is mainly confined to the upper surface of the mature leaves and could readily be identified by the bronzing of the leaf. There are several naturally occurring insect predators, such as coccinellid and staphylinid larvae, lacewing larvae, and mite predators, most importantly species of the families Phytoseiidae and Stigmaeidae. Integrated management has been adopted to control this mite pest, involving cultural, mechanical, physical, biological and chemical methods. This review collates the most important works carried out on biology, ecology and management of O. coffeae. Also the scope of future studies for better management of this regular mite pest of tea is discussed.

  16. Melatonin and serotonin profiles in beans of Coffea species.

    PubMed

    Ramakrishna, Akula; Giridhar, Parvatam; Sankar, Kadimi Udaya; Ravishankar, Gokare Aswathanarayana

    2012-05-01

    A high-performance liquid chromatography (HPLC) and an electrospray ionization mass spectrometry (LC/ESI-MS) methods were applied to quantify the profiles of melatonin and serotonin (5-HT) in green and roasted beans of Coffea canephora (robusta) and Coffea arabica (arabica). Both melatonin and 5-HT were detected in green coffee beans (5.8±0.8μg/g dry weight (DW), 10.5±0.6μg/g DW) and also in roasted beans of C. canephora (8.0±0.9μg/g DW, 7.3±0.5μg/g DW). Melatonin (3.0±0.6μg/50mL) and 5-HT (4.0±0.7μg/50mL) were detected in coffee brew. In C. arabica, 5-HT was high in green beans (12.5±0.8μg/g DW) compared with roasted beans (8.7±0.4). The levels of melatonin were higher (9.6±0.8μg/g DW) in roasted beans compared with green beans (6.8±0.4μg/g DW). Both melatonin (3.9±0.2μg/50mL) and 5-HT (7.3±0.6μg/50mL) were detected in coffee brew. Because of the relevance of indoleamines as bioactive molecules with implications for food, nutritional sciences and human health, it was of interest to explore their levels in coffee, an important universal beverage.

  17. FISH using a gag-like fragment probe reveals a common Ty3-gypsy-like retrotransposon in genome of Coffea species.

    PubMed

    Yuyama, Priscila Mary; Pereira, Luiz Filipe Protasio; dos Santos, Tiago Benedito; Sera, Tumoru; Vilas-Boas, Laurival Antonio; Lopes, Fabrício Ramon; Carareto, Claudia Marcia Aparecida; Vanzela, André Luís Laforga

    2012-12-01

    The genus Coffea possesses about 100 species, and the most economically important are Coffea canephora and Coffea arabica. The latter is predominantly self-compatible with 2n = 4x = 44, while the others of the genus are diploid with 2n = 2x = 22 and mostly self-incompatible. Studies using molecular markers have been useful to detect differences between genomes in Coffea; however, molecular and cytogenetic studies have produced only limited information on the karyotypes organization. We used DOP-PCR to isolate repetitive elements from genome of Coffea arabica var. typica. The pCa06 clone, containing a fragment of 775 bp length, was characterized by sequencing and used as a probe in chromosomes of C. arabica and six other species: C. canephora, Coffea eugenioides, Coffea kapakata, Coffea liberica var. dewevrei, Coffea racemosa, and Coffea stenophylla. This insert shows similarities with a gag protein of the Ty3-gypsy-like super-family. Dot blot and FISH analyses demonstrated that pCa06 is differentially accumulated between species and chromosomes. Signals appeared scattered and clustered on the chromosomes and were also associated with heterochromatic regions. While the literature shows that there is a high karyotype similarity between Coffea species, our results point out differences in the accumulation and dispersion of this Ty3-gypsy-like retrotransposon during karyotype differentiation of Coffea. PMID:23231601

  18. The Structure of Colleters in Several Species of Simira (Rubiaceae)

    PubMed Central

    KLEIN, DENISE ESPELLET; MOREIRA GOMES, VALDIRENE; DA SILVA-NETO, SEBASTIÃO JOSÉ; DA CUNHA, MAURA

    2004-01-01

    • Background and Aims Colleters are secretory structures consisting of a parenchymatic middle axis surrounded by a layer of palisade-like epidermal cells. Colleters occur in a large number of rubiaceous species. Their function is to protect the developing shoot apex. They are also taxonomically useful in the Rubiaceae. This study characterized the structure of the colleters of Simira glaziovii, S. pikia and S. rubra and the biochemistry of secretions in S. glaziovii. • Methods Stipules of the shoot apices of the three species studied were collected at Barragem de Saracuruna, in Rio de Janeiro state, Brazil. The samples were fixed according to the usual methods for light and electron microscopy. Secretion stipules of S. glaziovii were washed with 0·1 m Tris–HCl plus 0·1 %Triton X-100 to extract proteins and carbohydrates. • Key Results Colleters in these species are located at the base of the stipule. Each species shows a different pattern of distribution. They form as emergentia from the stipules. Simira glaziovii was different from the other two species because it exhibited vascular traces. The epidermal cells of colleters have dense cytoplasm, nuclei, small vacuoles, endoplasmic reticulum, Golgi apparatus, mitochondria and extraplasmic spaces if they are secretory. The outer cell wall of the mature colleters differs from the outer cell wall of stipule cells and immature colleters. Both carbohydrates and proteins were found in secretions from the stipules of S. glaziovii. • Conclusions Few ultrastructural differences were noted among the three species. These secretory structures not only protect the shoot apex, but also have taxonomic importance below the genus level. PMID:15374836

  19. Protective Response Mechanisms to Heat Stress in Interaction with High [CO2] Conditions in Coffea spp.

    PubMed

    Martins, Madlles Q; Rodrigues, Weverton P; Fortunato, Ana S; Leitão, António E; Rodrigues, Ana P; Pais, Isabel P; Martins, Lima D; Silva, Maria J; Reboredo, Fernando H; Partelli, Fábio L; Campostrini, Eliemar; Tomaz, Marcelo A; Scotti-Campos, Paula; Ribeiro-Barros, Ana I; Lidon, Fernando J C; DaMatta, Fábio M; Ramalho, José C

    2016-01-01

    Modeling studies have predicted that coffee crop will be endangered by future global warming, but recent reports highlighted that high [CO2] can mitigate heat impacts on coffee. This work aimed at identifying heat protective mechanisms promoted by CO2 in Coffea arabica (cv. Icatu and IPR108) and Coffea canephora cv. Conilon CL153. Plants were grown at 25/20°C (day/night), under 380 or 700 μL CO2 L(-1), and then gradually submitted to 31/25, 37/30, and 42/34°C. Relevant heat tolerance up to 37/30°C for both [CO2] and all coffee genotypes was observed, likely supported by the maintenance or increase of the pools of several protective molecules (neoxanthin, lutein, carotenes, α-tocopherol, HSP70, raffinose), activities of antioxidant enzymes, such as superoxide dismutase (SOD), ascorbate peroxidase (APX), glutathione reductase (GR), catalase (CAT), and the upregulated expression of some genes (ELIP, Chaperonin 20). However, at 42/34°C a tolerance threshold was reached, mostly in the 380-plants and Icatu. Adjustments in raffinose, lutein, β-carotene, α-tocopherol and HSP70 pools, and the upregulated expression of genes related to protective (ELIPS, HSP70, Chape 20, and 60) and antioxidant (CAT, CuSOD2, APX Cyt, APX Chl) proteins were largely driven by temperature. However, enhanced [CO2] maintained higher activities of GR (Icatu) and CAT (Icatu and IPR108), kept (or even increased) the Cu,Zn-SOD, APX, and CAT activities, and promoted a greater upregulation of those enzyme genes, as well as those related to HSP70, ELIPs, Chaperonins in CL153, and Icatu. These changes likely favored the maintenance of reactive oxygen species (ROS) at controlled levels and contributed to mitigate of photosystem II photoinhibition at the highest temperature. Overall, our results highlighted the important role of enhanced [CO2] on the coffee crop acclimation and sustainability under predicted future global warming scenarios.

  20. Protective Response Mechanisms to Heat Stress in Interaction with High [CO2] Conditions in Coffea spp.

    PubMed

    Martins, Madlles Q; Rodrigues, Weverton P; Fortunato, Ana S; Leitão, António E; Rodrigues, Ana P; Pais, Isabel P; Martins, Lima D; Silva, Maria J; Reboredo, Fernando H; Partelli, Fábio L; Campostrini, Eliemar; Tomaz, Marcelo A; Scotti-Campos, Paula; Ribeiro-Barros, Ana I; Lidon, Fernando J C; DaMatta, Fábio M; Ramalho, José C

    2016-01-01

    Modeling studies have predicted that coffee crop will be endangered by future global warming, but recent reports highlighted that high [CO2] can mitigate heat impacts on coffee. This work aimed at identifying heat protective mechanisms promoted by CO2 in Coffea arabica (cv. Icatu and IPR108) and Coffea canephora cv. Conilon CL153. Plants were grown at 25/20°C (day/night), under 380 or 700 μL CO2 L(-1), and then gradually submitted to 31/25, 37/30, and 42/34°C. Relevant heat tolerance up to 37/30°C for both [CO2] and all coffee genotypes was observed, likely supported by the maintenance or increase of the pools of several protective molecules (neoxanthin, lutein, carotenes, α-tocopherol, HSP70, raffinose), activities of antioxidant enzymes, such as superoxide dismutase (SOD), ascorbate peroxidase (APX), glutathione reductase (GR), catalase (CAT), and the upregulated expression of some genes (ELIP, Chaperonin 20). However, at 42/34°C a tolerance threshold was reached, mostly in the 380-plants and Icatu. Adjustments in raffinose, lutein, β-carotene, α-tocopherol and HSP70 pools, and the upregulated expression of genes related to protective (ELIPS, HSP70, Chape 20, and 60) and antioxidant (CAT, CuSOD2, APX Cyt, APX Chl) proteins were largely driven by temperature. However, enhanced [CO2] maintained higher activities of GR (Icatu) and CAT (Icatu and IPR108), kept (or even increased) the Cu,Zn-SOD, APX, and CAT activities, and promoted a greater upregulation of those enzyme genes, as well as those related to HSP70, ELIPs, Chaperonins in CL153, and Icatu. These changes likely favored the maintenance of reactive oxygen species (ROS) at controlled levels and contributed to mitigate of photosystem II photoinhibition at the highest temperature. Overall, our results highlighted the important role of enhanced [CO2] on the coffee crop acclimation and sustainability under predicted future global warming scenarios. PMID:27446174

  1. Protective Response Mechanisms to Heat Stress in Interaction with High [CO2] Conditions in Coffea spp.

    PubMed Central

    Martins, Madlles Q.; Rodrigues, Weverton P.; Fortunato, Ana S.; Leitão, António E.; Rodrigues, Ana P.; Pais, Isabel P.; Martins, Lima D.; Silva, Maria J.; Reboredo, Fernando H.; Partelli, Fábio L.; Campostrini, Eliemar; Tomaz, Marcelo A.; Scotti-Campos, Paula; Ribeiro-Barros, Ana I.; Lidon, Fernando J. C.; DaMatta, Fábio M.; Ramalho, José C.

    2016-01-01

    Modeling studies have predicted that coffee crop will be endangered by future global warming, but recent reports highlighted that high [CO2] can mitigate heat impacts on coffee. This work aimed at identifying heat protective mechanisms promoted by CO2 in Coffea arabica (cv. Icatu and IPR108) and Coffea canephora cv. Conilon CL153. Plants were grown at 25/20°C (day/night), under 380 or 700 μL CO2 L−1, and then gradually submitted to 31/25, 37/30, and 42/34°C. Relevant heat tolerance up to 37/30°C for both [CO2] and all coffee genotypes was observed, likely supported by the maintenance or increase of the pools of several protective molecules (neoxanthin, lutein, carotenes, α-tocopherol, HSP70, raffinose), activities of antioxidant enzymes, such as superoxide dismutase (SOD), ascorbate peroxidase (APX), glutathione reductase (GR), catalase (CAT), and the upregulated expression of some genes (ELIP, Chaperonin 20). However, at 42/34°C a tolerance threshold was reached, mostly in the 380-plants and Icatu. Adjustments in raffinose, lutein, β-carotene, α-tocopherol and HSP70 pools, and the upregulated expression of genes related to protective (ELIPS, HSP70, Chape 20, and 60) and antioxidant (CAT, CuSOD2, APX Cyt, APX Chl) proteins were largely driven by temperature. However, enhanced [CO2] maintained higher activities of GR (Icatu) and CAT (Icatu and IPR108), kept (or even increased) the Cu,Zn-SOD, APX, and CAT activities, and promoted a greater upregulation of those enzyme genes, as well as those related to HSP70, ELIPs, Chaperonins in CL153, and Icatu. These changes likely favored the maintenance of reactive oxygen species (ROS) at controlled levels and contributed to mitigate of photosystem II photoinhibition at the highest temperature. Overall, our results highlighted the important role of enhanced [CO2] on the coffee crop acclimation and sustainability under predicted future global warming scenarios. PMID:27446174

  2. Expression patterns of three α-expansin isoforms in Coffea arabica during fruit development.

    PubMed

    Budzinski, I G F; Santos, T B; Sera, T; Pot, D; Vieira, L G E; Pereira, L F P

    2011-05-01

    As a first step towards understanding the physiological role and regulation of the expansin gene (EXP) family in Coffea arabica fruits during growth and maturation, we identified 11 expansin genes, nine belonging to the α-expansin family (EXPA), one EXLA and one EXLB, through in silico analysis of expressed sequence tags (ESTs). Within the α-expansin family, three isoforms were selected for detailed examination based on their high expression in coffee fruits or because they were specifically induced during different fruit developmental stages, according to the EST information. The expression patterns were analysed in different fruit tissues (perisperm, endosperm and pericarp) of C. arabica cv. IAPAR-59 and C. arabica cv. IAPAR-59 Graúdo, the latter being a closely related cultivar with a larger fruit size. Accumulation of CaEXPA1 and CaEXPA3 transcripts was high in the perisperm (tissue responsible for coffee bean size) and in the early stages of pericarp development. Transcripts of CaEXPA2 were detected only in the pericarp during the later stages of fruit maturation and ripening. There was no detectable transcription of the three EXPs analysed in the endosperm. The observed differences in mRNA expression levels of CaEXPA1 and CaEXP3 in the perisperm of IAPAR-59 and IAPAR-59 Graúdo suggest the participation of these two isoforms in the regulation of grain size.

  3. Looking for the physiological role of anthocyanins in the leaves of Coffea arabica.

    PubMed

    Domingues Júnior, Adilson Pereira; Shimizu, Milton Massao; Moura, Jullyana Cristina Magalhães Silva; Catharino, Rodrigo Ramos; Ramos, Rômulo Augusto; Ribeiro, Rafael Vasconcelos; Mazzafera, Paulo

    2012-01-01

    The aim of this study was to determine which anthocyanins are related to the purple coloration of young leaves in Coffea arabica var. Purpurascens and assess their impact on photosynthesis as compared to C. arabica var. Catuaí, with green leaves. Two delphinidin glicosides were identified and histological cross-sections showed they were located throughout the adaxial epidermis in young leaves, disappearing as the leaves mature. Regardless the irradiance level, the photosynthetic performance of Purpurascens leaves did not differ from that observed in leaves of the Catuaí variety, providing no evidence that anthocyanins improve photosynthetic performance in coffee plants. To analyze the photoprotective action of anthocyanins, we evaluated the isomerization process for chlorogenic acids (CGAs) in coffee leaves exposed to UV-B radiation. No differences were observed in the total concentration of phenolic compounds in either variety before or after the UV treatment; however, we observed less degradation of CGA isomers in the Purpurascens leaves and a relative increase of cis-5-caffeoylquinic acid, a positional isomer of one of the most abundant form of CQA in coffee leaves, trans-5-caffeoylquinic acid, suggesting a possible protective role for anthocyanins in this purple coffee variety. PMID:22372995

  4. Expression patterns of three α-expansin isoforms in Coffea arabica during fruit development.

    PubMed

    Budzinski, I G F; Santos, T B; Sera, T; Pot, D; Vieira, L G E; Pereira, L F P

    2011-05-01

    As a first step towards understanding the physiological role and regulation of the expansin gene (EXP) family in Coffea arabica fruits during growth and maturation, we identified 11 expansin genes, nine belonging to the α-expansin family (EXPA), one EXLA and one EXLB, through in silico analysis of expressed sequence tags (ESTs). Within the α-expansin family, three isoforms were selected for detailed examination based on their high expression in coffee fruits or because they were specifically induced during different fruit developmental stages, according to the EST information. The expression patterns were analysed in different fruit tissues (perisperm, endosperm and pericarp) of C. arabica cv. IAPAR-59 and C. arabica cv. IAPAR-59 Graúdo, the latter being a closely related cultivar with a larger fruit size. Accumulation of CaEXPA1 and CaEXPA3 transcripts was high in the perisperm (tissue responsible for coffee bean size) and in the early stages of pericarp development. Transcripts of CaEXPA2 were detected only in the pericarp during the later stages of fruit maturation and ripening. There was no detectable transcription of the three EXPs analysed in the endosperm. The observed differences in mRNA expression levels of CaEXPA1 and CaEXP3 in the perisperm of IAPAR-59 and IAPAR-59 Graúdo suggest the participation of these two isoforms in the regulation of grain size. PMID:21489097

  5. Looking for the physiological role of anthocyanins in the leaves of Coffea arabica.

    PubMed

    Domingues Júnior, Adilson Pereira; Shimizu, Milton Massao; Moura, Jullyana Cristina Magalhães Silva; Catharino, Rodrigo Ramos; Ramos, Rômulo Augusto; Ribeiro, Rafael Vasconcelos; Mazzafera, Paulo

    2012-01-01

    The aim of this study was to determine which anthocyanins are related to the purple coloration of young leaves in Coffea arabica var. Purpurascens and assess their impact on photosynthesis as compared to C. arabica var. Catuaí, with green leaves. Two delphinidin glicosides were identified and histological cross-sections showed they were located throughout the adaxial epidermis in young leaves, disappearing as the leaves mature. Regardless the irradiance level, the photosynthetic performance of Purpurascens leaves did not differ from that observed in leaves of the Catuaí variety, providing no evidence that anthocyanins improve photosynthetic performance in coffee plants. To analyze the photoprotective action of anthocyanins, we evaluated the isomerization process for chlorogenic acids (CGAs) in coffee leaves exposed to UV-B radiation. No differences were observed in the total concentration of phenolic compounds in either variety before or after the UV treatment; however, we observed less degradation of CGA isomers in the Purpurascens leaves and a relative increase of cis-5-caffeoylquinic acid, a positional isomer of one of the most abundant form of CQA in coffee leaves, trans-5-caffeoylquinic acid, suggesting a possible protective role for anthocyanins in this purple coffee variety.

  6. Toxigenic fungi associated with processed (green) coffee beans (Coffea arabica L.).

    PubMed

    Batista, Luis Roberto; Chalfoun, Sára Maria; Prado, Guilherme; Schwan, Rosane Freitas; Wheals, Alan E

    2003-08-25

    Processed (green) coffee beans from Coffea arabica in Brazil were assessed for the presence of Aspergillus and Penicillium species both before and after surface sterilisation, the aflatoxigenic and ochratoxigenic potential of the isolates and ochratoxin A levels. Contamination by Aspergillus and Penicillium species was found on 96% and 42%, respectively, of 45 samples from 11 localities. After disinfection with 1% sodium hypochlorite, the levels fell to 47% and 24%, respectively. One hundred and eighty isolates were identified to species level and comprised Aspergillus sections Circumdati (10 species), Flavi (3), Nigri (3), Versicolores (4), while two were teleomorphic species. Eight species of Penicillium were isolated. Within section Circumdati, 75% of the isolates produced ochratoxin A and all except Aspergillus elegans and Aspergillus insulicola have previously been reported to produce ochratoxin A. One-third of the 18 isolates of Aspergillus flavus produced aflatoxin B1 and B2. None of the isolates belonging to Aspergillus section Nigri or Penicillium produced ochratoxin A. Of the 40 bean samples analysed, 58% were infected with potentially ochratoxigenic fungi but only 22% of these were contaminated with ochratoxin A at levels that varied from 0.47 to 4.82 ng/g, with an average contamination level of 2.45 ng/g.

  7. Effects of shade on the development and sugar metabolism of coffee (Coffea arabica L.) fruits.

    PubMed

    Geromel, Clara; Ferreira, Lúcia Pires; Davrieux, Fabrice; Guyot, Bernard; Ribeyre, Fabienne; Brígida dos Santos Scholz, Maria; Protasio Pereira, Luiz Filipe; Vaast, Philippe; Pot, David; Leroy, Thierry; Androcioli Filho, Armando; Esteves Vieira, Luiz Gonzaga; Mazzafera, Paulo; Marraccini, Pierre

    2008-01-01

    Coffee fruits grown in shade are characterized by larger bean size than those grown under full-sun conditions. The present study assessed the effects of shade on bean characteristics and sugar metabolism by analyzing tissue development, sugar contents, activities of sucrose metabolizing enzymes and expression of sucrose synthase-encoding genes in fruits of coffee (Coffea arabica L.) plants submitted to full-sun (FS) and shade (SH) conditions. Evolution of tissue fresh weights measured in fruits collected regularly from flowering to maturation indicated that this increase is due to greater development of the perisperm tissue in the shade. The effects of light regime on sucrose and reducing sugar (glucose and fructose) contents were studied in fresh and dry coffee beans. Shade led to a significant reduction in sucrose content and to an increase in reducing sugars. In pericarp and perisperm tissues, higher activities of sucrose synthase (EC 2.4.1.13) and sucrose-phosphate synthase (SPS: EC 2.4.1.14) were detected at maturation in the shade compared with full sun. These two enzymes also had higher peaks of activities in developing endosperm under shade than in full sun. It was also noted that shade modified the expression of SUS-encoding genes in coffee beans; CaSUS2 gene transcripts levels were higher in SH than in FS. As no sucrose increase accompanied these changes, this suggests that sucrose metabolism was redirected to other metabolic pathways that need to be identified.

  8. Differentially expressed genes and proteins upon drought acclimation in tolerant and sensitive genotypes of Coffea canephora

    PubMed Central

    Marraccini, Pierre; Vinecky, Felipe; Alves, Gabriel S.C.; Ramos, Humberto J.O.; Elbelt, Sonia; Vieira, Natalia G.; Carneiro, Fernanda A.; Sujii, Patricia S.; Alekcevetch, Jean C.; Silva, Vânia A.; DaMatta, Fábio M.; Ferrão, Maria A.G.; Leroy, Thierry; Pot, David; Vieira, Luiz G.E.; da Silva, Felipe R.; Andrade, Alan C.

    2012-01-01

    The aim of this study was to investigate the molecular mechanisms underlying drought acclimation in coffee plants by the identification of candidate genes (CGs) using different approaches. The first approach used the data generated during the Brazilian Coffee expressed sequence tag (EST) project to select 13 CGs by an in silico analysis (electronic northern). The second approach was based on screening macroarrays spotted with plasmid DNA (coffee ESTs) with separate hybridizations using leaf cDNA probes from drought-tolerant and susceptible clones of Coffea canephora var. Conilon, grown under different water regimes. This allowed the isolation of seven additional CGs. The third approach used two-dimensional gel electrophoresis to identify proteins displaying differential accumulation in leaves of drought-tolerant and susceptible clones of C. canephora. Six of them were characterized by MALDI-TOF-MS/MS (matrix-assisted laser desorption-time of flight-tandem mass spectrometry) and the corresponding proteins were identified. Finally, additional CGs were selected from the literature, and quantitative real-time polymerase chain reaction (qPCR) was performed to analyse the expression of all identified CGs. Altogether, >40 genes presenting differential gene expression during drought acclimation were identified, some of them showing different expression profiles between drought-tolerant and susceptible clones. Based on the obtained results, it can be concluded that factors involved a complex network of responses probably involving the abscisic signalling pathway and nitric oxide are major molecular determinants that might explain the better efficiency in controlling stomata closure and transpiration displayed by drought-tolerant clones of C. canephora. PMID:22511801

  9. Dispersing towards Madagascar: Biogeography and evolution of the Madagascan endemics of the Spermacoceae tribe (Rubiaceae).

    PubMed

    Janssens, Steven B; Groeninckx, Inge; De Block, Petra J; Verstraete, Brecht; Smets, Erik F; Dessein, Steven

    2016-02-01

    Despite the close proximity of the African mainland, dispersal of plant lineages towards Madagascar remains intriguing. The composition of the Madagascan flora is rather mixed and shows besides African representatives, also floral elements of India, Southeast Asia, Australia, and the Neotropics. Due to its proportionally large number of Madagascan endemics, the taxonomically troublesome Spermacoceae tribe is an interesting group to investigate the origin and evolution of the herbaceous Rubiaceae endemic to Madagascar. The phylogenetic position of these endemics were inferred using four plastid gene markers. Age estimates were obtained by expanding the Spermacoceae dataset with representatives of all Rubiaceae tribes. This allowed incorporation of multiple fossil-based calibration points from the Rubiaceae fossil record. Despite the high morphological diversity of the endemic herbaceous Spermacoceae on Madagascar, only two colonization events gave rise to their current diversity. The first clade contains Lathraeocarpa, Phylohydrax and Gomphocalyx, whereas the second Madagascan clade includes the endemic genera Astiella, Phialiphora, Thamnoldenlandia and Amphistemon. The tribe Spermacoceae is estimated to have a Late Eocene origin, and diversified during Oligocene and Miocene. The two Madagascan clades of the tribe originated in the Oligocene and radiated in the Miocene. The origin of the Madagascan Spermacoceae cannot be explained by Gondwanan vicariance but only by means of Cenozoic long distance dispersal events. Interestingly, not only colonization from Africa occurred but also long distance dispersal from the Neotropics shaped the current diversity of the Spermacoceae tribe on Madagascar. PMID:26639100

  10. Aquaporins in Coffea arabica L.: Identification, expression, and impacts on plant water relations and hydraulics.

    PubMed

    Miniussi, Matilda; Del Terra, Lorenzo; Savi, Tadeja; Pallavicini, Alberto; Nardini, Andrea

    2015-10-01

    Plant aquaporins (AQPs) are involved in the transport of water and other small solutes across cell membranes, and thus play major roles in the regulation of plant water balance, as well as in growth regulation and response to abiotic stress factors. Limited information is currently available about the presence and role of AQPs in Coffea arabica L., despite the economic importance of the species and its vulnerability to drought stress. We identified candidate AQP genes by screening a proprietary C. arabica transcriptome database, resulting in the identification of nine putative aquaporins. A phylogenetic analysis based on previously characterized AQPs from Arabidopsis thaliana and Solanum tuberosum allowed to assign the putative coffee AQP sequences to the Tonoplast (TIP) and Plasma membrane (PIP) subfamilies. The possible functional role of coffee AQPs was explored by measuring hydraulic conductance and aquaporin gene expression on leaf and root tissues of two-year-old plants (C. arabica cv. Pacamara) subjected to different experimental conditions. In a first experiment, we tested plants for root and leaf hydraulic conductance both before dawn and at mid-day, to check the eventual impact of light on AQP activity and plant hydraulics. In a second experiment, we measured plant hydraulic responses to different water stress levels as eventually affected by changes in AQPs expression levels. Our results shed light on the possible roles of AQPs in the regulation of C. arabica hydraulics and water balance, opening promising research lines to improve the sustainability of coffee cultivation under global climate change scenarios.

  11. Aquaporins in Coffea arabica L.: Identification, expression, and impacts on plant water relations and hydraulics.

    PubMed

    Miniussi, Matilda; Del Terra, Lorenzo; Savi, Tadeja; Pallavicini, Alberto; Nardini, Andrea

    2015-10-01

    Plant aquaporins (AQPs) are involved in the transport of water and other small solutes across cell membranes, and thus play major roles in the regulation of plant water balance, as well as in growth regulation and response to abiotic stress factors. Limited information is currently available about the presence and role of AQPs in Coffea arabica L., despite the economic importance of the species and its vulnerability to drought stress. We identified candidate AQP genes by screening a proprietary C. arabica transcriptome database, resulting in the identification of nine putative aquaporins. A phylogenetic analysis based on previously characterized AQPs from Arabidopsis thaliana and Solanum tuberosum allowed to assign the putative coffee AQP sequences to the Tonoplast (TIP) and Plasma membrane (PIP) subfamilies. The possible functional role of coffee AQPs was explored by measuring hydraulic conductance and aquaporin gene expression on leaf and root tissues of two-year-old plants (C. arabica cv. Pacamara) subjected to different experimental conditions. In a first experiment, we tested plants for root and leaf hydraulic conductance both before dawn and at mid-day, to check the eventual impact of light on AQP activity and plant hydraulics. In a second experiment, we measured plant hydraulic responses to different water stress levels as eventually affected by changes in AQPs expression levels. Our results shed light on the possible roles of AQPs in the regulation of C. arabica hydraulics and water balance, opening promising research lines to improve the sustainability of coffee cultivation under global climate change scenarios. PMID:26241904

  12. A Revised Time Tree of the Asterids: Establishing a Temporal Framework For Evolutionary Studies of the Coffee Family (Rubiaceae)

    PubMed Central

    Wikström, Niklas; Kainulainen, Kent; Razafimandimbison, Sylvain G.; Smedmark, Jenny E. E.; Bremer, Birgitta

    2015-01-01

    Divergence time analyses in the coffee family (Rubiaceae) have all relied on the same Gentianales crown group age estimate, reported by an earlier analysis of the asterids, for defining the upper age bound of the root node in their analyses. However, not only did the asterid analysis suffer from several analytical shortcomings, but the estimate itself has been used in highly inconsistent ways in these Rubiaceae analyses. Based on the original data, we here reanalyze the divergence times of the asterids using relaxed-clock models and 14 fossil-based minimum age constraints. We also expand the data set to include an additional 67 taxa from Rubiaceae sampled across all three subfamilies recognized in the family. Three analyses are conducted: a separate analysis of the asterids, which completely mirrors the original asterid analysis in terms of taxon sample and data; a separate analysis of the Gentianales, where the result from the first analysis is used for defining a secondary root calibration point; and a combined analysis where all taxa are analyzed simultaneously. Results are presented in the form of a time-calibrated phylogeny, and age estimates for asterid groups, Gentianales, and major groups of Rubiaceae are compared and discussed in relation to previously published estimates. Our updated age estimates for major groups of Rubiaceae provide a significant step forward towards the long term goal of establishing a robust temporal framework for the divergence of this biologically diverse and fascinating group of plants. PMID:25996595

  13. Genome-wide analysis and differential expression of chitinases in banana against root lesion nematode (Pratylenchus coffeae) and eumusa leaf spot (Mycosphaerella eumusae) pathogens.

    PubMed

    Backiyarani, S; Uma, S; Nithya, S; Chandrasekar, A; Saraswathi, M S; Thangavelu, R; Mayilvaganan, M; Sundararaju, P; Singh, N K

    2015-04-01

    Knowledge on structure and conserved domain of Musa chitinase isoforms and their responses to various biotic stresses will give a lead to select the suitable chitinase isoform for developing biotic stress-resistant genotypes. Hence, in this study, chitinase sequences available in the Musa genome hub were analyzed for their gene structure, conserved domain, as well as intron and exon regions. To identify the Musa chitinase isoforms involved in Pratylenchus coffeae (root lesion nematode) and Mycosphaerella eumusae (eumusa leaf spot) resistant mechanisms, differential gene expression analysis was carried out in P. coffeae- and M. eumusae-challenged resistant and susceptible banana genotypes. This study revealed that more number of chitinase isoforms (CIs) were responses upon eumusa leaf spot stress than nematode stress. The nematode challenge studies revealed that class II chitinase (GSMUA_Achr9G16770_001) was significantly overexpressed with 6.75-fold (with high fragments per kilobase of exon per million fragments mapped (FPKM)) in resistant genotype (Karthobiumtham-ABB) than susceptible (Nendran-AAB) genotype, whereas when M. eumusae was challenge inoculated, two class III CIs (GSMUA_Achr9G25580_001 and GSMUA_Achr8G27880_001) were overexpressed in resistant genotype (Manoranjitham-AAA) than the susceptible genotype (Grand Naine-AAA). However, none of the CIs were found to be commonly overexpressed under both stress conditions. This study reiterated that the chitinase genes are responding differently to different biotic stresses in their respective resistant genotypes.

  14. A High-Throughput Data Mining of Single Nucleotide Polymorphisms in Coffea Species Expressed Sequence Tags Suggests Differential Homeologous Gene Expression in the Allotetraploid Coffea arabica1[W

    PubMed Central

    Vidal, Ramon Oliveira; Mondego, Jorge Maurício Costa; Pot, David; Ambrósio, Alinne Batista; Andrade, Alan Carvalho; Pereira, Luiz Filipe Protasio; Colombo, Carlos Augusto; Vieira, Luiz Gonzaga Esteves; Carazzolle, Marcelo Falsarella; Pereira, Gonçalo Amarante Guimarães

    2010-01-01

    Polyploidization constitutes a common mode of evolution in flowering plants. This event provides the raw material for the divergence of function in homeologous genes, leading to phenotypic novelty that can contribute to the success of polyploids in nature or their selection for use in agriculture. Mounting evidence underlined the existence of homeologous expression biases in polyploid genomes; however, strategies to analyze such transcriptome regulation remained scarce. Important factors regarding homeologous expression biases remain to be explored, such as whether this phenomenon influences specific genes, how paralogs are affected by genome doubling, and what is the importance of the variability of homeologous expression bias to genotype differences. This study reports the expressed sequence tag assembly of the allopolyploid Coffea arabica and one of its direct ancestors, Coffea canephora. The assembly was used for the discovery of single nucleotide polymorphisms through the identification of high-quality discrepancies in overlapped expressed sequence tags and for gene expression information indirectly estimated by the transcript redundancy. Sequence diversity profiles were evaluated within C. arabica (Ca) and C. canephora (Cc) and used to deduce the transcript contribution of the Coffea eugenioides (Ce) ancestor. The assignment of the C. arabica haplotypes to the C. canephora (CaCc) or C. eugenioides (CaCe) ancestral genomes allowed us to analyze gene expression contributions of each subgenome in C. arabica. In silico data were validated by the quantitative polymerase chain reaction and allele-specific combination TaqMAMA-based method. The presence of differential expression of C. arabica homeologous genes and its implications in coffee gene expression, ontology, and physiology are discussed. PMID:20864545

  15. Three new genera and three new species of Lasiopteridi (Diptera: Cecidomyiidae) on Rubiaceae from Guadeloupe, French West Indies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three new genera of Lasiopteridi (Diptera: Cecidomyiidae), Faramitella Gagné, Anapeza Gagné and Pellacara Gagné, each with one new species, are described. The new species are from leaf galls on Rubiaceae collected in Guadeloupe, F.W.I.: Faramitella planicauda Gagné, new species, was reared from Fara...

  16. (1) Request for a binding decision on whether Ferdinanda (Compositae) and Ferdinandea (Rubiaceae) are sufficiently alike to be confused

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Ferdinandusa is an attractive, widespread shrub in tropical America, a member of the family Rubiaceae, and is sometimes cultivated for its bright showy flowers. It is a later name for the genus Ferdinandea, which has been confused with the genus Ferdinanda. By officially establishing that ...

  17. A new species, of Aceria neopaederiae (Acari: Eriophyidae), infesting Paederia foetida L. (Rubiaceae) in Thailand, Hong Kong and Singapore

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aceria paederiae (Nalepa) infesting leaves of Paederia foetida L. (Family Rubiaceae) in Thailand, Hong Kong and Singapore is reported for the first time. The mite induces small, round galls on both leaf surfaces. The complete descriptions of both males and females, including line drawings and SEM ...

  18. Sub-Saharan Rubiaceae: a review of their traditional uses, phytochemistry and biological activities.

    PubMed

    Karou, Simplice D; Tchacondo, Tchadjobo; Ilboudo, Denise P; Simpore, Jacques

    2011-02-01

    Rubiaceae family is a large family of 630 genera and about 13000 species found worldwide, especially in tropical and warm regions. These plants are not only ornamental but they are also used in African folk medicine to treat several diseases. Based on online published data and library bibliographic research, we herein reported accumulated information related to their traditional usages in sub-Saharan traditional medicine, their chemical composition and the screened pharmacological activities. Indeed, more than 60 species are used for more than 70 medicinal indications including malaria, hepatitis, eczema, oedema, cough, hypertension, diabetes and sexual weakness. Through biological screening following leads supplied with traditional healers, many of these plants exhibited antimalarial, antimicrobial, antihypertension, antidiabetic, antioxidant and anti-inflammatory activities. Bioactive compounds including indole alkaloids, terpenoids and anthraquinones have been isolated from these bioguided fractionation studies. It is evidence that great attention has been paid to species such as Nauclea latifolia, Morinda lucida, Mitragyna inermis and Crossopteryx febrifuga; however, several compounds should be waiting to be discovered since none of these plants has been systematically investigated for its biochemical composition. According the current global health context with the recrudescence of HIV, much effort should be oriented towards this virus when screening Rubiaceae. PMID:21870639

  19. Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories.

    PubMed

    Guyot, Romain; Darré, Thibaud; Dupeyron, Mathilde; de Kochko, Alexandre; Hamon, Serge; Couturon, Emmanuel; Crouzillat, Dominique; Rigoreau, Michel; Rakotomalala, Jean-Jacques; Raharimalala, Nathalie E; Akaffou, Sélastique Doffou; Hamon, Perla

    2016-10-01

    The Coffea genus, 124 described species, has a natural distribution spreading from inter-tropical Africa, to Western Indian Ocean Islands, India, Asia and up to Australasia. Two cultivated species, C. arabica and C. canephora, are intensively studied while, the breeding potential and the genome composition of all the wild species remained poorly uncharacterized. Here, we report the characterization and comparison of the highly repeated transposable elements content of 11 Coffea species representatives of the natural biogeographic distribution. A total of 994 Mb from 454 reads were produced with a genome coverage ranging between 3.2 and 15.7 %. The analyses showed that highly repeated transposable elements, mainly LTR retrotransposons (LTR-RT), represent between 32 and 53 % of Coffea genomes depending on their biogeographic location and genome size. Species from West and Central Africa (Eucoffea) contained the highest LTR-RT content but with no strong variation relative to their genome size. At the opposite, for the insular species (Mascarocoffea), a strong variation of LTR-RT was observed suggesting differential dynamics of these elements in this group. Two LTR-RT lineages, SIRE and Del were clearly differentially accumulated between African and insular species, suggesting these lineages were associated to the genome divergence of Coffea species in Africa. Altogether, the information obtained in this study improves our knowledge and brings new data on the composition, the evolution and the divergence of wild Coffea genomes.

  20. Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories.

    PubMed

    Guyot, Romain; Darré, Thibaud; Dupeyron, Mathilde; de Kochko, Alexandre; Hamon, Serge; Couturon, Emmanuel; Crouzillat, Dominique; Rigoreau, Michel; Rakotomalala, Jean-Jacques; Raharimalala, Nathalie E; Akaffou, Sélastique Doffou; Hamon, Perla

    2016-10-01

    The Coffea genus, 124 described species, has a natural distribution spreading from inter-tropical Africa, to Western Indian Ocean Islands, India, Asia and up to Australasia. Two cultivated species, C. arabica and C. canephora, are intensively studied while, the breeding potential and the genome composition of all the wild species remained poorly uncharacterized. Here, we report the characterization and comparison of the highly repeated transposable elements content of 11 Coffea species representatives of the natural biogeographic distribution. A total of 994 Mb from 454 reads were produced with a genome coverage ranging between 3.2 and 15.7 %. The analyses showed that highly repeated transposable elements, mainly LTR retrotransposons (LTR-RT), represent between 32 and 53 % of Coffea genomes depending on their biogeographic location and genome size. Species from West and Central Africa (Eucoffea) contained the highest LTR-RT content but with no strong variation relative to their genome size. At the opposite, for the insular species (Mascarocoffea), a strong variation of LTR-RT was observed suggesting differential dynamics of these elements in this group. Two LTR-RT lineages, SIRE and Del were clearly differentially accumulated between African and insular species, suggesting these lineages were associated to the genome divergence of Coffea species in Africa. Altogether, the information obtained in this study improves our knowledge and brings new data on the composition, the evolution and the divergence of wild Coffea genomes. PMID:27469896

  1. Ochratoxigenic fungi associated with green coffee beans (Coffea arabica L.) in conventional and organic cultivation in Brazil

    PubMed Central

    de Fátima Rezende, Elisângela; Borges, Josiane Gonçalves; Cirillo, Marcelo Ângelo; Prado, Guilherme; Paiva, Leandro Carlos; Batista, Luís Roberto

    2013-01-01

    The genera Aspergillus comprises species that produce mycotoxins such as aflatoxins, ochratoxins and patulin. These are cosmopolitan species, natural contaminants of agricultural products. In coffee grains, the most important Aspergillus species in terms of the risk of presenting mycotoxins belong to the genera Aspergillus Section Circumdati and Section Nigri. The purpose of this study was to assess the occurrence of isolated ochratoxigenic fungi of coffee grains from organic and conventional cultivation from the South of Minas Gerais, Brazil, as well as to evaluate which farming system presents higher contamination risk by ochratoxin A (OTA) produced by fungi. Thirty samples of coffee grains (Coffea arabica L.) were analysed, being 20 of them of conventional coffee grains and 10 of them organic. The microbiological analysis was done with the Direct Plating Technique in a Dichloran Rose Bengal Chloramphenicol Agar (DRBC) media. The identification was done based on the macro and micro morphological characteristics and on the toxigenic potential with the Plug Agar technique. From the 30 samples analysed, 480 filamentous fungi of the genera Aspergillus of the Circumdati and Nigri Sections were isolated. The ochratoxigenic species identified were: Aspergillus auricoumus, A. ochraceus, A. ostianus, A. niger and A. niger Aggregate. The most frequent species which produces ochratoxin A among the isolated ones was A. ochraceus, corresponding to 89.55%. There was no significant difference regarding the presence of ochratoxigenic A. ochreceus between the conventional and organic cultivation systems, which suggests that the contamination risk is similar for both cultivation systems. PMID:24294225

  2. Evolutionary Expansion of WRKY Gene Family in Banana and Its Expression Profile during the Infection of Root Lesion Nematode, Pratylenchus coffeae.

    PubMed

    Kaliyappan, Raja; Viswanathan, Sriram; Suthanthiram, Backiyarani; Subbaraya, Uma; Marimuthu Somasundram, Saraswathi; Muthu, Mayilvaganan

    2016-01-01

    The WRKY family of transcription factors orchestrate the reprogrammed expression of the complex network of defense genes at various biotic and abiotic stresses. Within the last 96 million years, three rounds of Musa polyploidization events had occurred from selective pressure causing duplication of MusaWRKYs with new activities. Here, we identified a total of 153 WRKY transcription factors available from the DH Pahang genome. Based on their phylogenetic relationship, the MusaWRKYs available with complete gene sequence were classified into the seven common WRKY sub-groups. Synteny analyses data revealed paralogous relationships, with 17 MusaWRKY gene pairs originating from the duplication events that had occurred within the Musa lineage. We also found 15 other MusaWRKY gene pairs originating from much older duplication events that had occurred along Arecales and Poales lineage of commelinids. Based on the synonymous and nonsynonymous substitution rates, the fate of duplicated MusaWRKY genes was predicted to have undergone sub-functionalization in which the duplicated gene copies retain a subset of the ancestral gene function. Also, to understand the regulatory roles of MusaWRKY during a biotic stress, Illumina sequencing was performed on resistant and susceptible cultivars during the infection of root lesion nematode, Pratylenchus coffeae. The differential WRKY gene expression analysis in nematode resistant and susceptible cultivars during challenged and unchallenged conditions had distinguished: 1) MusaWRKYs participating in general banana defense mechanism against P.coffeae common to both susceptible and resistant cultivars, 2) MusaWRKYs that may aid in the pathogen survival as suppressors of plant triggered immunity, 3) MusaWRKYs that may aid in the host defense as activators of plant triggered immunity and 4) cultivar specific MusaWRKY regulation. Mainly, MusaWRKY52, -69 and -92 are found to be P.coffeae specific and can act as activators or repressors in a

  3. Evolutionary Expansion of WRKY Gene Family in Banana and Its Expression Profile during the Infection of Root Lesion Nematode, Pratylenchus coffeae

    PubMed Central

    Suthanthiram, Backiyarani; Subbaraya, Uma; Marimuthu Somasundram, Saraswathi; Muthu, Mayilvaganan

    2016-01-01

    The WRKY family of transcription factors orchestrate the reprogrammed expression of the complex network of defense genes at various biotic and abiotic stresses. Within the last 96 million years, three rounds of Musa polyploidization events had occurred from selective pressure causing duplication of MusaWRKYs with new activities. Here, we identified a total of 153 WRKY transcription factors available from the DH Pahang genome. Based on their phylogenetic relationship, the MusaWRKYs available with complete gene sequence were classified into the seven common WRKY sub-groups. Synteny analyses data revealed paralogous relationships, with 17 MusaWRKY gene pairs originating from the duplication events that had occurred within the Musa lineage. We also found 15 other MusaWRKY gene pairs originating from much older duplication events that had occurred along Arecales and Poales lineage of commelinids. Based on the synonymous and nonsynonymous substitution rates, the fate of duplicated MusaWRKY genes was predicted to have undergone sub-functionalization in which the duplicated gene copies retain a subset of the ancestral gene function. Also, to understand the regulatory roles of MusaWRKY during a biotic stress, Illumina sequencing was performed on resistant and susceptible cultivars during the infection of root lesion nematode, Pratylenchus coffeae. The differential WRKY gene expression analysis in nematode resistant and susceptible cultivars during challenged and unchallenged conditions had distinguished: 1) MusaWRKYs participating in general banana defense mechanism against P.coffeae common to both susceptible and resistant cultivars, 2) MusaWRKYs that may aid in the pathogen survival as suppressors of plant triggered immunity, 3) MusaWRKYs that may aid in the host defense as activators of plant triggered immunity and 4) cultivar specific MusaWRKY regulation. Mainly, MusaWRKY52, -69 and -92 are found to be P.coffeae specific and can act as activators or repressors in a

  4. Validation of reference genes for normalization of qPCR gene expression data from Coffea spp. hypocotyls inoculated with Colletotrichum kahawae

    PubMed Central

    2013-01-01

    Background Coffee production in Africa represents a significant share of the total export revenues and influences the lives of millions of people, yet severe socio-economic repercussions are annually felt in result of the overall losses caused by the coffee berry disease (CBD). This quarantine disease is caused by the fungus Colletotrichum kahawae Waller and Bridge, which remains one of the most devastating threats to Coffea arabica production in Africa at high altitude, and its dispersal to Latin America and Asia represents a serious concern. Understanding the molecular genetic basis of coffee resistance to this disease is of high priority to support breeding strategies. Selection and validation of suitable reference genes presenting stable expression in the system studied is the first step to engage studies of gene expression profiling. Results In this study, a set of ten genes (S24, 14-3-3, RPL7, GAPDH, UBQ9, VATP16, SAND, UQCC, IDE and β-Tub9) was evaluated to identify reference genes during the first hours of interaction (12, 48 and 72 hpi) between resistant and susceptible coffee genotypes and C. kahawae. Three analyses were done for the selection of these genes considering the entire dataset and the two genotypes (resistant and susceptible), separately. The three statistical methods applied GeNorm, NormFinder, and BestKeeper, allowed identifying IDE as one of the most stable genes for all datasets analysed, and in contrast GADPH and UBQ9 as the least stable ones. In addition, the expression of two defense-related transcripts, encoding for a receptor like kinase and a pathogenesis related protein 10, were used to validate the reference genes selected. Conclusion Taken together, our results provide guidelines for reference gene(s) selection towards a more accurate and widespread use of qPCR to study the interaction between Coffea spp. and C. kahawae. PMID:24073624

  5. Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

    PubMed Central

    da Silva, Carlos R. M.; Andrade, Alan C.; Marraccini, Pierre; Teixeira, João B.; Carazzolle, Marcelo F.; Pereira, Gonçalo A. G.; Pereira, Luiz Filipe P.; Vanzela, André L. L.; Wang, Lu; Jordan, I. King; Carareto, Claudia M. A.

    2013-01-01

    Plant genomes are massively invaded by transposable elements (TEs), many of which are located near host genes and can thus impact gene expression. In flowering plants, TE expression can be activated (de-repressed) under certain stressful conditions, both biotic and abiotic, as well as by genome stress caused by hybridization. In this study, we examined the effects of these stress agents on TE expression in two diploid species of coffee, Coffea canephora and C. eugenioides, and their allotetraploid hybrid C. arabica. We also explored the relationship of TE repression mechanisms to host gene regulation via the effects of exonized TE sequences. Similar to what has been seen for other plants, overall TE expression levels are low in Coffea plant cultivars, consistent with the existence of effective TE repression mechanisms. TE expression patterns are highly dynamic across the species and conditions assayed here are unrelated to their classification at the level of TE class or family. In contrast to previous results, cell culture conditions per se do not lead to the de-repression of TE expression in C. arabica. Results obtained here indicate that differing plant drought stress levels relate strongly to TE repression mechanisms. TEs tend to be expressed at significantly higher levels in non-irrigated samples for the drought tolerant cultivars but in drought sensitive cultivars the opposite pattern was shown with irrigated samples showing significantly higher TE expression. Thus, TE genome repression mechanisms may be finely tuned to the ideal growth and/or regulatory conditions of the specific plant cultivars in which they are active. Analysis of TE expression levels in cell culture conditions underscored the importance of nonsense-mediated mRNA decay (NMD) pathways in the repression of Coffea TEs. These same NMD mechanisms can also regulate plant host gene expression via the repression of genes that bear exonized TE sequences. PMID:24244387

  6. Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species.

    PubMed

    Gomez, Céline; Despinoy, Marc; Hamon, Serge; Hamon, Perla; Salmon, Danyela; Akaffou, Doffou Sélastique; Legnate, Hyacinthe; de Kochko, Alexandre; Mangeas, Morgan; Poncet, Valérie

    2016-05-01

    The frequency of plant species introductions has increased in a highly connected world, modifying species distribution patterns to include areas outside their natural ranges. These introductions provide the opportunity to gain new insight into the importance of flowering phenology as a component of adaptation to a new environment. Three Coffea species, C. arabica, C. canephora (Robusta), and C. liberica, native to intertropical Africa have been introduced to New Caledonia. On this archipelago, a secondary contact zone has been characterized where these species coexist, persist, and hybridize spontaneously. We investigated the impact of environmental changes undergone by each species following its introduction in New Caledonia on flowering phenology and overcoming reproductive barriers between sister species. We developed species distribution models and compared both environmental envelopes and climatic niches between native and introduced hybrid zones. Flowering phenology was monitored in a population in the hybrid zone along with temperature and precipitation sequences recorded at a nearby weather station. The extent and nature of hybridization events were characterized using chloroplast and nuclear microsatellite markers. The three Coffea species encountered weak environmental suitability compared to their native ranges when introduced to New Caledonia, especially C. arabica and C. canephora. The niche of the New Caledonia hybrid zone was significantly different from all three species' native niches based on identity tests (I Similarity and D Schoener's Similarity Indexes). This area appeared to exhibit intermediate conditions between the native conditions of the three species for temperature-related variables and divergent conditions for precipitation-related ones. Flowering pattern in these Coffea species was shown to have a strong genetic component that determined the time between the triggering rain and anthesis (flower opening), specific to each species

  7. Diversity and communities of foliar endophytic fungi from different agroecosystems of Coffea arabica L. in two regions of Veracruz, Mexico.

    PubMed

    Saucedo-García, Aurora; Anaya, Ana Luisa; Espinosa-García, Francisco J; González, María C

    2014-01-01

    Over the past 20 years, the biodiversity associated with shaded coffee plantations and the role of diverse agroforestry types in biodiversity conservation and environmental services have been topics of debate. Endophytic fungi, which are microorganisms that inhabit plant tissues in an asymptomatic manner, form a part of the biodiversity associated with coffee plants. Studies on the endophytic fungi communities of cultivable host plants have shown variability among farming regions; however, the variability in fungal endophytic communities of coffee plants among different coffee agroforestry systems is still poorly understood. As such, we analyzed the diversity and communities of foliar endophytic fungi inhabiting Coffea arabica plants growing in the rustic plantations and simple polycultures of two regions in the center of Veracruz, Mexico. The endophytic fungi isolates were identified by their morphological traits, and the majority of identified species correspond to species of fungi previously reported as endophytes of coffee leaves. We analyzed and compared the colonization rates, diversity, and communities of endophytes found in the different agroforestry systems and in the different regions. Although the endophytic diversity was not fully recovered, we found differences in the abundance and diversity of endophytes among the coffee regions and differences in richness between the two different agroforestry systems of each region. No consistent pattern of community similarity was found between the coffee agroforestry systems, but we found that rustic plantations shared the highest number of morphospecies. The results suggest that endophyte abundance, richness, diversity, and communities may be influenced predominantly by coffee region, and to a lesser extent, by the agroforestry system. Our results contribute to the knowledge of the relationships between agroforestry systems and biodiversity conservation and provide information regarding some endophytic fungi and

  8. Diversity and Communities of Foliar Endophytic Fungi from Different Agroecosystems of Coffea arabica L. in Two Regions of Veracruz, Mexico

    PubMed Central

    Saucedo-García, Aurora; Anaya, Ana Luisa; Espinosa-García, Francisco J.; González, María C.

    2014-01-01

    Over the past 20 years, the biodiversity associated with shaded coffee plantations and the role of diverse agroforestry types in biodiversity conservation and environmental services have been topics of debate. Endophytic fungi, which are microorganisms that inhabit plant tissues in an asymptomatic manner, form a part of the biodiversity associated with coffee plants. Studies on the endophytic fungi communities of cultivable host plants have shown variability among farming regions; however, the variability in fungal endophytic communities of coffee plants among different coffee agroforestry systems is still poorly understood. As such, we analyzed the diversity and communities of foliar endophytic fungi inhabiting Coffea arabica plants growing in the rustic plantations and simple polycultures of two regions in the center of Veracruz, Mexico. The endophytic fungi isolates were identified by their morphological traits, and the majority of identified species correspond to species of fungi previously reported as endophytes of coffee leaves. We analyzed and compared the colonization rates, diversity, and communities of endophytes found in the different agroforestry systems and in the different regions. Although the endophytic diversity was not fully recovered, we found differences in the abundance and diversity of endophytes among the coffee regions and differences in richness between the two different agroforestry systems of each region. No consistent pattern of community similarity was found between the coffee agroforestry systems, but we found that rustic plantations shared the highest number of morphospecies. The results suggest that endophyte abundance, richness, diversity, and communities may be influenced predominantly by coffee region, and to a lesser extent, by the agroforestry system. Our results contribute to the knowledge of the relationships between agroforestry systems and biodiversity conservation and provide information regarding some endophytic fungi and

  9. Diversity and communities of foliar endophytic fungi from different agroecosystems of Coffea arabica L. in two regions of Veracruz, Mexico.

    PubMed

    Saucedo-García, Aurora; Anaya, Ana Luisa; Espinosa-García, Francisco J; González, María C

    2014-01-01

    Over the past 20 years, the biodiversity associated with shaded coffee plantations and the role of diverse agroforestry types in biodiversity conservation and environmental services have been topics of debate. Endophytic fungi, which are microorganisms that inhabit plant tissues in an asymptomatic manner, form a part of the biodiversity associated with coffee plants. Studies on the endophytic fungi communities of cultivable host plants have shown variability among farming regions; however, the variability in fungal endophytic communities of coffee plants among different coffee agroforestry systems is still poorly understood. As such, we analyzed the diversity and communities of foliar endophytic fungi inhabiting Coffea arabica plants growing in the rustic plantations and simple polycultures of two regions in the center of Veracruz, Mexico. The endophytic fungi isolates were identified by their morphological traits, and the majority of identified species correspond to species of fungi previously reported as endophytes of coffee leaves. We analyzed and compared the colonization rates, diversity, and communities of endophytes found in the different agroforestry systems and in the different regions. Although the endophytic diversity was not fully recovered, we found differences in the abundance and diversity of endophytes among the coffee regions and differences in richness between the two different agroforestry systems of each region. No consistent pattern of community similarity was found between the coffee agroforestry systems, but we found that rustic plantations shared the highest number of morphospecies. The results suggest that endophyte abundance, richness, diversity, and communities may be influenced predominantly by coffee region, and to a lesser extent, by the agroforestry system. Our results contribute to the knowledge of the relationships between agroforestry systems and biodiversity conservation and provide information regarding some endophytic fungi and

  10. Proteomic analysis of apoplastic fluid of Coffea arabica leaves highlights novel biomarkers for resistance against Hemileia vastatrix

    PubMed Central

    Guerra-Guimarães, Leonor; Tenente, Rita; Pinheiro, Carla; Chaves, Inês; Silva, Maria do Céu; Cardoso, Fernando M. H.; Planchon, Sébastien; Barros, Danielle R.; Renaut, Jenny; Ricardo, Cândido P.

    2015-01-01

    A proteomic analysis of the apoplastic fluid (APF) of coffee leaves was conducted to investigate the cellular processes associated with incompatible (resistant) and compatible (susceptible) Coffea arabica-Hemileia vastatrix interactions, during the 24–96 hai period. The APF proteins were extracted by leaf vacuum infiltration and protein profiles were obtained by 2-DE. The comparative analysis of the gels revealed 210 polypeptide spots whose volume changed in abundance between samples (control, resistant and susceptible) during the 24–96 hai period. The proteins identified were involved mainly in protein degradation, cell wall metabolism and stress/defense responses, most of them being hydrolases (around 70%), particularly sugar hydrolases and peptidases/proteases. The changes in the APF proteome along the infection process revealed two distinct phases of defense responses, an initial/basal one (24–48 hai) and a late/specific one (72–96 hai). Compared to susceptibility, resistance was associated with a higher number of proteins, which was more evident in the late/specific phase. Proteins involved in the resistance response were mainly, glycohydrolases of the cell wall, serine proteases and pathogen related-like proteins (PR-proteins), suggesting that some of these proteins could be putative candidates for resistant markers of coffee to H. vastatrix. Antibodies were produced against chitinase, pectin methylesterase, serine carboxypeptidase, reticuline oxidase and subtilase and by an immunodetection assay it was observed an increase of these proteins in the resistant sample. With this methodology we have identified proteins that are candidate markers of resistance and that will be useful in coffee breeding programs to assist in the selection of cultivars with resistance to H. vastatrix. PMID:26175744

  11. The use of fatty acid profile as a potential marker for Brazilian coffee (Coffea arabica L.) for corn adulteration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fatty acid methyl ester (FAME) compositions of six coffee (Coffea arabica L.) varieties (Catuaí, Catuca, Burbourn, Mundo Novo, Rubí, and Topázio) known to produce good, intermediate and poor quality coffee were determined for the first time. Average area % of the FAMEs of the six varieties was: pa...

  12. Distribution of the cardiotoxin pavettamine in the coffee family (Rubiaceae) and its significance for gousiekte, a fatal poisoning of ruminants.

    PubMed

    Van Elst, Daan; Nuyens, Sarah; van Wyk, Braam; Verstraete, Brecht; Dessein, Steven; Prinsen, Els

    2013-06-01

    Gousiekte, a cardiac syndrome of ruminants in southern Africa, is caused by the ingestion of plants containing the polyamine pavettamine. All the six known gousiekte-causing plants are members of the Rubiaceae or coffee family and house endosymbiotic Burkholderia bacteria in their leaves. It was therefore hypothesized that these bacteria could be involved in the production of the toxin. The pavettamine level in the leaves of 82 taxa from 14 genera was determined. Included in the analyses were various nodulated and non-nodulated members of the Rubiaceae. This led to the discovery of other pavettamine producing Rubiaceae, namely Psychotria kirkii and Psychotria viridiflora. Our analysis showed that many plant species containing bacterial nodules in their leaves do not produce pavettamine. It is consequently unlikely that the endosymbiont alone can be accredited for the synthesis of the toxin. Until now the inconsistent toxicity of the gousiekte-causing plants have hindered studies that aimed at a better understanding of the disease. In vitro dedifferentiated plant cell cultures are a useful tool for the study of molecular processes. Plant callus cultures were obtained from pavettamine-positive species. Mass spectrometric analysis shows that these calli do not produce pavettamine but can produce common plant polyamines.

  13. Metabolic pathways in tropical dicotyledonous albuminous seeds: Coffea arabica as a case study

    PubMed Central

    Joët, Thierry; Laffargue, Andréina; Salmona, Jordi; Doulbeau, Sylvie; Descroix, Frédéric; Bertrand, Benoît; de Kochko, Alexandre; Dussert, Stéphane

    2009-01-01

    The genomic era facilitates the understanding of how transcriptional networks are interconnected to program seed development and filling. However, to date, little information is available regarding dicot seeds with a transient perisperm and a persistent, copious endosperm. Coffea arabica is the subject of increasing genomic research and is a model for nonorthodox albuminous dicot seeds of tropical origin. The aim of this study was to reconstruct the metabolic pathways involved in the biosynthesis of the main coffee seed storage compounds, namely cell wall polysaccharides, triacylglycerols, sucrose, and chlorogenic acids. For this purpose, we integrated transcriptomic and metabolite analyses, combining real-time RT-PCR performed on 137 selected genes (of which 79 were uncharacterized in Coffea) and metabolite profiling. Our map-drawing approach derived from model plants enabled us to propose a rationale for the peculiar traits of the coffee endosperm, such as its unusual fatty acid composition, remarkable accumulation of chlorogenic acid and cell wall polysaccharides. Comparison with the developmental features of exalbuminous seeds described in the literature revealed that the two seed types share important regulatory mechanisms for reserve biosynthesis, independent of the origin and ploidy level of the storage tissue. PMID:19207685

  14. Agrobacterium-mediated genetic transformation of Coffea arabica (L.) is greatly enhanced by using established embryogenic callus cultures

    PubMed Central

    2011-01-01

    Background Following genome sequencing of crop plants, one of the main challenges today is determining the function of all the predicted genes. When gene validation approaches are used for woody species, the main obstacle is the low recovery rate of transgenic plants from elite or commercial cultivars. Embryogenic calli have frequently been the target tissue for transformation, but the difficulty in producing or maintaining embryogenic tissues is one of the main problems encountered in genetic transformation of many woody plants, including Coffea arabica. Results We identified the conditions required for successful long-term proliferation of embryogenic cultures in C. arabica and designed a highly efficient and reliable Agrobacterium tumefaciens-mediated transformation method based on these conditions. The transformation protocol with LBA1119 harboring pBin 35S GFP was established by evaluating the effect of different parameters on transformation efficiency by GFP detection. Using embryogenic callus cultures, co-cultivation with LBA1119 OD600 = 0.6 for five days at 20 °C enabled reproducible transformation. The maintenance conditions for the embryogenic callus cultures, particularly a high auxin to cytokinin ratio, the age of the culture (optimum for 7-10 months of proliferation) and the use of a yellow callus phenotype, were the most important factors for achieving highly efficient transformation (> 90%). At the histological level, successful transformation was related to the number of proembryogenic masses present. All the selected plants were proved to be transformed by PCR and Southern blot hybridization. Conclusion Most progress in increasing transformation efficiency in coffee has been achieved by optimizing the production conditions of embryogenic cultures used as target tissues for transformation. This is the first time that a strong positive effect of the age of the culture on transformation efficiency was demonstrated. Our results make Agrobacterium

  15. In vitro anti-Herpes simplex virus activity of crude extract of the roots of Nauclea latifolia Smith (Rubiaceae)

    PubMed Central

    2013-01-01

    Background Nauclea latifolia Smith, a shrub belonging to the family Rubiaceae is a very popular medicinal plant in Cameroon and neighboring countries where it is used to treat jaundice, yellow fever, rheumatism, abdominal pains, hepatitis, diarrhea, dysentery, hypertension, as well as diabetes. The ethno-medicinal use against yellow fever, jaundice and diarrhea prompted us to investigate on the antiviral activity of the root bark of N. latifolia. In this study, HSV-2 was chosen as a viral model because of its strong impact on HIV transmission and acquisition. Methods The crude extract under study was prepared by maceration of air-dried and powdered roots barks of N. latifolia in CH2Cl2/MeOH (50:50) mixture for 48 hours, then it was subjected to filtration and evaporation under vacuum. A phytochemical analysis of the crude extract was performed by High Performance Liquid Chromatography coupled with a photodiode array and mass spectrometry (HPLC-PDA-ESI-qMS). The anti-HSV-2 activity was assayed in vitro by plaque reduction and virus yield assays and the major mechanism of action was investigated by virucidal and time of addition assays. Data values were compared using the Extra sum of squares F test of program GraphPad PRISM 4. Results The main components detected in the extract belong to the class of indole alkaloids characteristic of Nauclea genus. Strictosamide, vincosamide and pumiloside were tentatively identified together with quinovic acid glycoside. N. latifolia crude extract inhibited both acyclovir sensitive and acyclovir resistant HSV-2 strains, with IC50 values of 5.38 μg/ml for the former and 7.17 μg/ml for the latter. The extract was found to be most active when added post-infection, with IC50 of 3.63 μg/ml. Conclusion The results of this work partly justify the empirical use of N. latifolia in traditional medicine for the treatment of viral diseases. This extract could be a promising rough material for the development of a new and more effective

  16. The botanical origin of kratom (Mitragyna speciosa; Rubiaceae) available as abused drugs in the Japanese markets.

    PubMed

    Maruyama, Takuro; Kawamura, Maiko; Kikura-Hanajiri, Ruri; Takayama, Hiromitsu; Goda, Yukihiro

    2009-07-01

    Kratom is the leaves of Mitragyna speciosa (Rubiaceae). Recently, kratom has been sold in street shops or on the Internet in Japan for the purpose of abuse due to its opium-like effects. In this study, we investigated the botanical origin of the commercial kratom products using the internal transcribed spacer (ITS) sequence analysis of rDNA in preparation for future regulation of this product. In addition, a previously reported method to authenticate the plant, utilizing polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was applied to the same products in order to estimate the method's accuracy and utility. The ITS sequence analysis of the commercial kratoms revealed that most of them were derived from M. speciosa or closely related plants, while the others were made from the same tribe plant as M. speciosa. The reported PCR-RFLP method could clearly distinguish kratoms from the other psychoactive plants available in the Japanese markets and also from related plants. The authentication method is considered to be useful for the practical regulation of the plant due to its wide range of application, high accuracy and simplicity. PMID:19294483

  17. Crassulacean acid metabolism (CAM) in an epiphytic ant-plant, Myrmecodia beccarii Hook.f. (Rubiaceae).

    PubMed

    Tsen, Edward W J; Holtum, Joseph A M

    2012-09-01

    This study demonstrates unequivocally the presence of crassulacean acid metabolism (CAM) in a species of the Rubiaceae, the fourth largest angiosperm plant family. The tropical Australian endemic epiphytic ant-plant, Myrmecodia beccarii Hook.f., exhibits net CO(2) uptake in the dark and a concomitant accumulation of titratable acidity in plants in the field and in cultivation. Plants growing near Cardwell, in a north Queensland coastal seasonally dry forest of Melaleuca viridiflora Sol. ex Gaertn., accumulated ~50 % of their 24 h carbon gain in the dark during the warm wet season. During the transition from the wet season to the dry season, 24 h carbon gain was reduced whilst the proportion of carbon accumulated during the dark increased. By mid dry season many plants exhibited zero net carbon uptake over 24 h, but CO(2) uptake in the dark was observed in some plants following localised rainfall. In a shade-house experiment, droughted plants in which CO(2) uptake in the light was absent and dark CO(2) uptake was reduced, were able to return to relatively high rates of CO(2) uptake in the light and dark within 12 h of rewatering.

  18. The botanical origin of kratom (Mitragyna speciosa; Rubiaceae) available as abused drugs in the Japanese markets.

    PubMed

    Maruyama, Takuro; Kawamura, Maiko; Kikura-Hanajiri, Ruri; Takayama, Hiromitsu; Goda, Yukihiro

    2009-07-01

    Kratom is the leaves of Mitragyna speciosa (Rubiaceae). Recently, kratom has been sold in street shops or on the Internet in Japan for the purpose of abuse due to its opium-like effects. In this study, we investigated the botanical origin of the commercial kratom products using the internal transcribed spacer (ITS) sequence analysis of rDNA in preparation for future regulation of this product. In addition, a previously reported method to authenticate the plant, utilizing polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was applied to the same products in order to estimate the method's accuracy and utility. The ITS sequence analysis of the commercial kratoms revealed that most of them were derived from M. speciosa or closely related plants, while the others were made from the same tribe plant as M. speciosa. The reported PCR-RFLP method could clearly distinguish kratoms from the other psychoactive plants available in the Japanese markets and also from related plants. The authentication method is considered to be useful for the practical regulation of the plant due to its wide range of application, high accuracy and simplicity.

  19. Screening of α-Glucosidase Inhibitory Activity from Some Plants of Apocynaceae, Clusiaceae, Euphorbiaceae, and Rubiaceae

    PubMed Central

    Elya, Berna; Basah, Katrin; Mun'im, Abdul; Yuliastuti, Wulan; Bangun, Anastasia; Septiana, Eva Kurnia

    2012-01-01

    Diabetes mellitus (DM) is recognized as a serious global health problem that is characterized by high blood sugar levels. Type 2 DM is more common in diabetic populations. In this type of DM, inhibition of α-glucosidase is a useful treatment to delay the absorption of glucose after meals. As a megabiodiversity country, Indonesia still has a lot of potential unexploited forests to be developed as a medicine source, including as the α-glucosidase inhibitor. In this study, we determine the α-glucosidase inhibitory activity of 80% ethanol extracts of leaves and twigs of some plants from the Apocynaceae, Clusiaceae, Euphorbiaceae, and Rubiaceae. Inhibitory activity test of the α-glucosidase was performed in vitro using spectrophotometric methods. Compared with the control acarbose (IC50 117.20 μg/mL), thirty-seven samples of forty-five were shown to be more potent α-glucosidase inhibitors with IC50 values in the range 2.33–112.02 μg/mL. PMID:22187534

  20. New and resurrected Hawaiian species of pilo (Coprosma, Rubiaceae) from the island of Maui

    PubMed Central

    Cantley, Jason T.; Sporck-Koehler, Margaret J.; Chau, Marian M.

    2016-01-01

    Abstract Two species of Coprosma (Rubiaceae) J.R.Forst. & G.Forst. are described from the island of Maui of the Hawaiian Archipelago. A newly described taxon, Coprosma cordicarpa J.Cantley, Sporck-Koehler, & M.Chau, sp. nov. is locally common in medium to high elevation dry forests and shrublands of leeward East Maui. The second taxon is resurrected from the synonymy of Coprosma foliosa A.Gray as Coprosma stephanocarpa Hillebr. and occurs in mesic to wet rainforests of both East and West Maui. Both taxa are segregated from Coprosma foliosa, with which they share similar morphological characters. A conspicuous and persistent calyx of the fruit and various floral characters most easily differentiate both taxa from other Hawaiian taxa. The newly described Coprosma cordicarpa is further distinguished from Coprosma stephanocarpa by a central constriction of the fruit with a depressed apex, which gives it a characteristic heart shape. Furthermore, the taxa are largely separated phenologically, ecologically, and geographically. Descriptions, conservation status, and specimens examined for the new species are included. PMID:27081343

  1. Projected shifts in Coffea arabica suitability among major global producing regions due to climate change.

    PubMed

    Ovalle-Rivera, Oriana; Läderach, Peter; Bunn, Christian; Obersteiner, Michael; Schroth, Götz

    2015-01-01

    Regional studies have shown that climate change will affect climatic suitability for Arabica coffee (Coffea arabica) within current regions of production. Increases in temperature and changes in precipitation patterns will decrease yield, reduce quality and increase pest and disease pressure. This is the first global study on the impact of climate change on suitability to grow Arabica coffee. We modeled the global distribution of Arabica coffee under changes in climatic suitability by 2050s as projected by 21 global circulation models. The results suggest decreased areas suitable for Arabica coffee in Mesoamerica at lower altitudes. In South America close to the equator higher elevations could benefit, but higher latitudes lose suitability. Coffee regions in Ethiopia and Kenya are projected to become more suitable but those in India and Vietnam to become less suitable. Globally, we predict decreases in climatic suitability at lower altitudes and high latitudes, which may shift production among the major regions that produce Arabica coffee. PMID:25875230

  2. Soluble and bound hydroxycinnamates in coffee pulp (Coffea arabica) from seven cultivars at three ripening stages.

    PubMed

    Rodríguez-Durán, Luis V; Ramírez-Coronel, Ma Ascención; Aranda-Delgado, Eduardo; Nampoothiri, K Madhavan; Favela-Torres, Ernesto; Aguilar, Cristóbal N; Saucedo-Castañeda, Gerardo

    2014-08-01

    The contents of soluble and bound hydroxycinnamates (HCAs) were analyzed in coffee pulp (CP) of seven cultivars of Coffea arabica at three different ripening stages. Methodologies for the extraction and analysis of HCAs were evaluated and improved. HCAs were present mainly in the soluble fraction (68-97%). Chlorogenic acid was the main phenolic acid (94-98%) in the soluble fraction, whereas caffeic acid was the most abundant HCA found in the bound fraction (72-88%). Small amounts of free and bound ferulic and p-coumaric acids were also detected. The content of total HCAs in CP reached the maximum concentration at the semiripe stage (7.4-25.5 mg/g CP, dw) but decreased at the ripe stage for six of the seven cultivars. These findings suggest that unripe or semiripe coffee cherries, considered as defective cherries, are a potential inexpensive source of phenolic compounds, such as chlorogenic and caffeic acids.

  3. Projected Shifts in Coffea arabica Suitability among Major Global Producing Regions Due to Climate Change

    PubMed Central

    Ovalle-Rivera, Oriana; Läderach, Peter; Bunn, Christian; Obersteiner, Michael; Schroth, Götz

    2015-01-01

    Regional studies have shown that climate change will affect climatic suitability for Arabica coffee (Coffea arabica) within current regions of production. Increases in temperature and changes in precipitation patterns will decrease yield, reduce quality and increase pest and disease pressure. This is the first global study on the impact of climate change on suitability to grow Arabica coffee. We modeled the global distribution of Arabica coffee under changes in climatic suitability by 2050s as projected by 21 global circulation models. The results suggest decreased areas suitable for Arabica coffee in Mesoamerica at lower altitudes. In South America close to the equator higher elevations could benefit, but higher latitudes lose suitability. Coffee regions in Ethiopia and Kenya are projected to become more suitable but those in India and Vietnam to become less suitable. Globally, we predict decreases in climatic suitability at lower altitudes and high latitudes, which may shift production among the major regions that produce Arabica coffee. PMID:25875230

  4. Projected shifts in Coffea arabica suitability among major global producing regions due to climate change.

    PubMed

    Ovalle-Rivera, Oriana; Läderach, Peter; Bunn, Christian; Obersteiner, Michael; Schroth, Götz

    2015-01-01

    Regional studies have shown that climate change will affect climatic suitability for Arabica coffee (Coffea arabica) within current regions of production. Increases in temperature and changes in precipitation patterns will decrease yield, reduce quality and increase pest and disease pressure. This is the first global study on the impact of climate change on suitability to grow Arabica coffee. We modeled the global distribution of Arabica coffee under changes in climatic suitability by 2050s as projected by 21 global circulation models. The results suggest decreased areas suitable for Arabica coffee in Mesoamerica at lower altitudes. In South America close to the equator higher elevations could benefit, but higher latitudes lose suitability. Coffee regions in Ethiopia and Kenya are projected to become more suitable but those in India and Vietnam to become less suitable. Globally, we predict decreases in climatic suitability at lower altitudes and high latitudes, which may shift production among the major regions that produce Arabica coffee.

  5. Molecular and biochemical characterization of endo-beta-mannanases from germinating coffee (Coffea arabica) grains.

    PubMed

    Marraccini, P; Rogers, W J; Allard, C; André, M L; Caillet, V; Lacoste, N; Lausanne, F; Michaux, S

    2001-06-01

    The activity of endo-beta-mannanase ([1-->4]-beta-mannan endohydrolase EC 3.2.1.78) is likely to be central to the metabolism of cell wall mannans during the germination of grains of coffee (Coffea spp.). In the present paper, we report the cloning and sequencing of two endo-beta-mannanase cDNAs (manA and manB) by different strategies from Coffea arabica L.. The manA cDNA was obtained by the use of oligonucleotides homologous to published sequences of other endo-beta-mannanases and manB by the use of oligonucleotides deduced from a purified enzyme from coffee. ManA and B proteins share about 56% sequence homology and include highly conserved regions found in other mannan endohydrolases. Purification of the activity by chromatography followed by separation by two-dimensional electrophoresis and amino acid sequencing demonstrated the existence of at least seven isomers of the ManB form. The existence of multiple manB genes was also indicated by Southern analysis, whereas only one or two gene copies were detected for manA. Northern hybridizations with manA- and manB-specific probes showed that mRNA transcripts for both cDNAs were present at the same periods of bean germination with transcript peaks at 20 days after imbibition of water (DAI). Transcripts were not detected during grain maturation or in the other tissues such as roots, stems, flowers and leaves. The peak endo-beta-mannanase activity occurred at approximately 28 DAI and was not detected in grains prior to imbibition. Activity and mRNA levels appeared to be tightly co-ordinated. Tests of substrate specificity with the purified ManB enzyme showed that activity required a minimum of five mannose units to function efficiently.

  6. Xanthine degradation and related enzyme activities in leaves and fruits of two coffea species differing in caffeine catabolism.

    PubMed

    Vitória, A P; Mazzafera, P

    1999-05-01

    The degradation of xanthine was studied in young and aged leaves and in immature and mature fruits of Coffea arabica and Coffea dewevrei, which differ with respect to caffeine catabolism. Radioisotope feeding experiments showed that leaves degraded xanthine more readily than fruits but that mature fruits and aged leaves were less efficient than younger tissues. In all cases, a significant part of the recovered radioactivity was in the ureides. Xanthine dehydrogenase was characterized as the enzyme responsible for xanthine degradation, and its activity and that of uricase were consistent with the results obtained in the radioisotope feeding experiments. Activities of allantoinase and allantoate amidohydrolase could not be detected. Considerable levels of endogenous allantoin and allantoic acid were found in fruits and leaves. Therefore, ureide accumulation might be a consequence of low enzyme activity. There was no positive correlation between urease activity and the data from the radioisotope feeding experiments.

  7. Effect of Coffea canephora aqueous extract on microbial counts in ex vivo oral biofilms: a case study.

    PubMed

    Antonio, Andréa Gonçalves; Iorio, Natália Lopes Pontes; Farah, Adriana; Netto dos Santos, Kátia Regina; Maia, Lucianne Cople

    2012-05-01

    In the present study, the ex vivo antimicrobial effect of brewed coffee was tested on oral biofilms. For this, unsweetened and sweetened (10 % sucrose) brewed light-roasted Coffea canephora at 20 % was used in biofilms formed by non-stimulated saliva from three volunteers. After 30 min contact with unsweetened and sweetened brews, the average microorganism count in the biofilms reduced by 15.2 % and 12.4 %, respectively, with no statistical difference among them. We also observed a drop of microorganisms in the biofilms after treatment with sucrose solution at 5 % compared to control (saline) and to sucrose at 1 % and 3 %. In conclusion, Coffea canephora extract reduces the microbial count in oral biofilm, and our data suggest that sucrose concentration in coffee brew can influence its antimicrobial property against the referred biofilm.

  8. A survey of mangiferin and hydroxycinnamic acid ester accumulation in coffee (Coffea) leaves: biological implications and uses

    PubMed Central

    Campa, Claudine; Mondolot, Laurence; Rakotondravao, Arsene; Bidel, Luc P. R.; Gargadennec, Annick; Couturon, Emmanuel; La Fisca, Philippe; Rakotomalala, Jean-Jacques; Jay-Allemand, Christian; Davis, Aaron P.

    2012-01-01

    Background and Aims The phenolic composition of Coffea leaves has barely been studied, and therefore this study conducts the first detailed survey, focusing on mangiferin and hydroxycinnamic acid esters (HCEs). Methods Using HPLC, including a new technique allowing quantification of feruloylquinic acid together with mangiferin, and histochemical methods, mangiferin content and tissue localization were compared in leaves and fruits of C. pseudozanguebariae, C. arabica and C. canephora. The HCE and mangiferin content of leaves was evaluated for 23 species native to Africa or Madagascar. Using various statistical methods, data were assessed in relation to distribution, ecology, phylogeny and use. Key Results Seven of the 23 species accumulated mangiferin in their leaves. Mangiferin leaf-accumulating species also contain mangiferin in the fruits, but only in the outer (sporophytic) parts. In both leaves and fruit, mangiferin accumulation decreases with ageing. A relationship between mangiferin accumulation and UV levels is posited, owing to localization with photosynthetic tissues, and systematic distribution in high altitude clades and species with high altitude representatives. Analyses of mangiferin and HCE content showed that there are significant differences between species, and that samples can be grouped into species, with few exceptions. These data also provide independent support for various Coffea lineages, as proposed by molecular phylogenetic analyses. Sampling of the hybrids C. arabica and C. heterocalyx cf. indicates that mangiferin and HCE accumulation may be under independent parental influence. Conclusions This survey of the phenolic composition in Coffea leaves shows that mangiferin and HCE accumulation corresponds to lineage recognition and species delimitation, respectively. Knowledge of the spectrum of phenolic accumulation within species and populations could be of considerable significance for adaptation to specific environments. The potential

  9. Homostachydrine (pipecolic acid betaine) as authentication marker of roasted blends of Coffea arabica and Coffea canephora (Robusta) beans.

    PubMed

    Servillo, Luigi; Giovane, Alfonso; Casale, Rosario; Cautela, Domenico; D'Onofrio, Nunzia; Balestrieri, Maria Luisa; Castaldo, Domenico

    2016-08-15

    The occurrence of pipecolic acid betaine (homostachydrine) and its biosynthetic precursor N-methylpipecolic acid was detected for the first time in green coffee beans of Robusta and Arabica species. The analyses were conducted by HPLC-ESI tandem mass spectrometry and the metabolites identified by product ion spectra and comparison with authentic standards. N-methylpipecolic acid was found at similar levels in green coffee beans of Robusta and Arabica, whereas a noticeable difference of homostachydrine content was observed between the two green coffee bean species. Interestingly, homostachydrine content was found to be unaffected by coffee bean roasting treatment because of a noticeable heat stability, a feature that makes this compound a candidate marker to determine the content of Robusta and Arabica species in roasted coffee blends. To this end, a number of certified pure Arabica and Robusta green beans were analyzed for their homostachydrine content. Results showed that homostachydrine content was 1.5±0.5mg/kg in Arabica beans and 31.0±10.0mg/kg in Robusta beans. Finally, to further support the suitability of homostachydrine as quality marker of roasted blends of Arabica and Robusta coffee beans, commercial samples of roasted ground coffee blends were analyzed and the correspondence between the derived percentages of Arabica and Robusta beans with those declared on packages by manufacturers was verified. PMID:27006213

  10. Homostachydrine (pipecolic acid betaine) as authentication marker of roasted blends of Coffea arabica and Coffea canephora (Robusta) beans.

    PubMed

    Servillo, Luigi; Giovane, Alfonso; Casale, Rosario; Cautela, Domenico; D'Onofrio, Nunzia; Balestrieri, Maria Luisa; Castaldo, Domenico

    2016-08-15

    The occurrence of pipecolic acid betaine (homostachydrine) and its biosynthetic precursor N-methylpipecolic acid was detected for the first time in green coffee beans of Robusta and Arabica species. The analyses were conducted by HPLC-ESI tandem mass spectrometry and the metabolites identified by product ion spectra and comparison with authentic standards. N-methylpipecolic acid was found at similar levels in green coffee beans of Robusta and Arabica, whereas a noticeable difference of homostachydrine content was observed between the two green coffee bean species. Interestingly, homostachydrine content was found to be unaffected by coffee bean roasting treatment because of a noticeable heat stability, a feature that makes this compound a candidate marker to determine the content of Robusta and Arabica species in roasted coffee blends. To this end, a number of certified pure Arabica and Robusta green beans were analyzed for their homostachydrine content. Results showed that homostachydrine content was 1.5±0.5mg/kg in Arabica beans and 31.0±10.0mg/kg in Robusta beans. Finally, to further support the suitability of homostachydrine as quality marker of roasted blends of Arabica and Robusta coffee beans, commercial samples of roasted ground coffee blends were analyzed and the correspondence between the derived percentages of Arabica and Robusta beans with those declared on packages by manufacturers was verified.

  11. Efecto de la dieta artificial MP sobre la emergencia y relacion de sexos de Phymastichus coffea (Hymenoptera:Eulophidae) mantenido sobre su hueped, Hypothenemus hampei (Coleoptera: Scloytidae)a traves de generaciones contin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phymastichus coffea La Salle (Hymenoptera: Eulophidae) is an endoparasitoid that attacks the adult coffee berry borer, Hypothenemus hampei Ferrari (Coleoptera: Scolytidae). The MP diet developed by Portilla and Streett is the only reported diet that allows cultures of P. coffea to develop and repr...

  12. Cyclotide Discovery in Gentianales Revisited—Identification and Characterization of Cyclic Cystine-Knot Peptides and Their Phylogenetic Distribution in Rubiaceae Plants

    PubMed Central

    Koehbach, Johannes; Attah, Alfred F.; Berger, Andreas; Hellinger, Roland; Kutchan, Toni M.; Carpenter, Eric J.; Rolf, Megan; Sonibare, Mubo A.; Moody, Jones O.; Ka-Shu Wong, Gane; Dessein, Steven; Greger, Harald; Gruber, Christian W.

    2013-01-01

    Cyclotides are a unique class of ribosomally synthesized cysteine-rich miniproteins characterized by a head-to-tail cyclized backbone and three conserved disulfide-bonds in a knotted arrangement. Originally they were discovered in the coffee-family plant Oldenlandia affinis (Rubiaceae) and have since been identified in several species of the violet, cucurbit, pea, potato, and grass families. However, the identification of novel cyclotide-containing plant species still is a major challenge due to the lack of a rapid and accurate analytical workflow in particular for large sampling numbers. As a consequence, their phylogeny in the plant kingdom remains unclear. To gain further insight into the distribution and evolution of plant cyclotides, we analyzed ~300 species of >40 different families, with special emphasis on plants from the order Gentianales. For this purpose, we have developed a refined screening methodology combining chemical analysis of plant extracts and bioinformatic analysis of transcript databases. Using mass spectrometry and transcriptome-mining, we identified nine novel cyclotide-containing species and their related cyclotide precursor genes in the tribe Palicoureeae. The characterization of novel peptide sequences underlines the high variability and plasticity of the cyclotide framework, and a comparison of novel precursor proteins from Carapichea ipecacuanha illustrated their typical cyclotide gene architectures. Phylogenetic analysis of their distribution within the Psychotria alliance revealed cyclotides to be restricted to Palicourea, Margaritopsis, Notopleura, Carapichea, Chassalia, and Geophila. In line with previous reports, our findings confirm cyclotides to be one of the largest peptide families within the plant kingdom and suggest that their total number may exceed tens of thousands. PMID:23897543

  13. Post-Boreotropical dispersals explain the pantropical disjunction in Paederia (Rubiaceae)

    PubMed Central

    Nie, Ze-Long; Deng, Tao; Meng, Ying; Sun, Hang; Wen, Jun

    2013-01-01

    Background and Aims Pantropical intercontinental disjunction is a common biogeographical pattern in flowering plants exhibiting a discontinuous distribution primarily in tropical Asia, Africa and the Americas. Only a few plant groups with this pattern have been investigated at the generic level with molecular phylogenetic and biogeographical methods. Paederia (Rubiaceae) is a pantropical genus of 31 species of woody lianas, with the greatest species diversity in continental Asia and Madagascar and only two species from tropical America. The aim of this study was to reconstruct the biogeographical history of Paederia based on phylogenetic analyses to explore how the genus attained its pantropical distribution. Methods Maximum parsimony and Bayesian inference were used for phylogenetic analyses using sequences of five plastid markers (the rbcL gene, rps16 intron, trnT-F region, atpB-rbcL spacer and psbA-trnH spacer). Biogeographical inferences were based on a Bayesian uncorrelated lognormal relaxed molecular clock together with both Bayesian and likelihood ancestral area reconstructions. Key Results The data suggest an early diverged Asian lineage sister to the clade of the remaining species consisting of a predominantly Asian sub-clade and a primarily Malagasy sub-clade. Paederia is inferred to have originated in the Oligocene in tropical continental Asia. It then reached Africa in the early to middle Miocene, most probably via long-distance dispersal across the Indian Ocean. The two Neotropical species are inferred to have derived independently in the late Miocene from ancestors of Asia and East Africa, respectively. Conclusions The results demonstrate the importance of post-Boreotropical long-distance dispersals (across three major oceans) in shaping the global pantropical disjunction in some plants, such as Paederia, with small, winged diaspores adapted to long-distance dispersal by various agents including wind, ocean currents or birds. Overland migration is

  14. Structural Evidence in Plectroniella armata (Rubiaceae) for Possible Material Exchange between Domatia and Mites

    PubMed Central

    Tilney, Patricia M.; van Wyk, Abraham E.; van der Merwe, Chris F.

    2012-01-01

    Domatia are small structures on the lower surface of a leaf, usually taking the form of cavities, pouches, domes with an opening, or hairs (or a combination of these), and located in the axils between the main veins. They are found in many dicotyledons including certain members of the Rubiaceae. As part of an ongoing study of selected southern African members of the tribe Vanguerieae of this family, their structure in transverse section was investigated. In some taxa, such as Plectroniella armata, light microscopic (LM) observations revealed large numbers of stomata in the domatia as well as a number of channel-like structures extending across the cuticle toward the cavity of the domatia. The cuticle of the epidermis lining the domatia also appeared thicker than in other parts of the leaves. The epidermis in P. armata was also examined using transmission electron microscopy (TEM). Domatia have been shown to house mainly mites, many of which are predatory or fungivorous, in a symbiotic (mutualistic) relationship with the plant. To date, much research has focussed on the role of domatia in providing shelter for various organisms, their eggs and their young. However, the TEM study revealed the apparent “channels” and thick cuticle seen under LM to be electron dense non-cellulosic branching fibrils within pronounced, often closely spaced cuticular folds. The functional significance of these fibrils and folds requires further investigation. Folding of cell walls and membranes at ultrastructural level is usually functionally associated with an increased surface area to facilitate active exchange of compounds/metabolites. This may indicate that translocation of substances and/or other forms of communication is possible between the domatium and its inhabitants. This therefore suggests a far more active role for the leaf in the symbiotic relationship than was previously thought. More work is required to test such a possibility. PMID:22792206

  15. Morphology, ecophysiology and germination of seeds of the neotropical tree Alibertia patinoi (Rubiaceae).

    PubMed

    Escobar Escobar, Diego Fernando; Torres, Alba Marina

    2013-06-01

    Alibertia patinoi (Rubiaceae) is of economic and cultural importance for communities in the Colombian Pacific and Amazon regions, where it is cultivated and mature fruits are highly appreciated and consumed. Since there is a lack of knowledge of the seed physiology of this species, we describe here the germination behavior and morphometry of seeds of Alibertia patinoi, and relate them to its habitat. Fruits were collected from a mixed food crop and a commercial plantation in Guaimía village, Buenaventura, Colombia, a tropical rain forest area. We measured length, width, thickness, mass (n = 1 400), and moisture content of seeds (n = 252). Primary dormancy tests were conducted (n = 200), followed by imbibition (n=252) and germination dynamics, under different conditions of light and temperature specific to understory and forest clearings (n = 300 seeds). Finally, seed storage behavior was established (n = 100 seeds). We observed that size and mass of seeds had a narrow range of values that did not differ within or among fruits and that the species did not exhibit primary dormancy. The seeds are recalcitrant, and recently harvested seeds exhibited higher seed moisture content (ca. 44%) and continuous metabolism. The seed germination percentage was observed to be higher under the specific dense canopy forest light and temperature conditions; furthermore, neither enriched far-red light nor darkness conditions inhibited germination. We concluded that rapid germination could be the establishment strategy of this species. Also, the physiological traits (i.e., rapid germination rate, low germination requirements, absence of primary dormancy, and recalcitrant behavior) and seed size and mass, suggest that A. patinoi is adapted to conditions of mature tropical rain forests.

  16. Some South African Rubiaceae Tree Leaf Extracts Have Antimycobacterial Activity Against Pathogenic and Non-pathogenic Mycobacterium Species.

    PubMed

    Aro, Abimbola O; Dzoyem, Jean P; Hlokwe, Tiny M; Madoroba, Evelyn; Eloff, Jacobus N; McGaw, Lyndy J

    2015-07-01

    Tuberculosis (TB) caused by Mycobacterium tuberculosis remains an ongoing threat to human health. Many plant species contain antimycobacterial compounds, which may serve as template molecules for new anti-TB drugs. The Rubiaceae family is the largest family of trees in southern Africa, and preliminary evidence revealed antimycobacterial activity in several species of the genus, motivating further studies. Leaf extracts of 15 tree species from the Rubiaceae family were screened for antimycobacterial activity against pathogenic M. tuberculosis and non-pathogenic Mycobacterium smegmatis, Mycobacterium aurum and Mycobacterium bovis BCG (Bacillus Calmette-Guérin) using a twofold serial microdilution assay. Cytotoxicity was determined using a tetrazolium-based colorimetric assay against C3A liver cells and Vero kidney cells. Minimum inhibitory concentration values as low as 0.04 mg/mL against M. smegmatis and M. tuberculosis were recorded. Activity against M. aurum was the best predictor of activity against pathogenic M. tuberculosis (correlation coefficient = 0.9). Bioautography indicated at least 40 different antimycobacterial compounds in the extracts. Cytotoxicity of the extracts varied, and Oxyanthus speciosus had the most promising selectivity index values. PMID:25857273

  17. 454-pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta-expressed pathogen-secreted proteins and plant functions in a late compatible plant-rust interaction.

    PubMed

    Fernandez, Diana; Tisserant, Emilie; Talhinhas, Pedro; Azinheira, Helena; Vieira, Ana; Petitot, Anne-Sophie; Loureiro, Andreia; Poulain, Julie; Da Silva, Corinne; Silva, Maria Do Céu; Duplessis, Sébastien

    2012-01-01

    Coffee (Coffea arabica L.), one of the key export and cash crops in tropical and subtropical countries, suffers severe losses from the rust fungus Hemileia vastatrix. The transcriptome of H. vastatrix was analysed during a compatible interaction with coffee to obtain an exhaustive repertoire of the genes expressed during infection and to identify potential effector genes. Large-scale sequencing (454-GS-FLEX Titanium) of mixed coffee and rust cDNAs obtained from 21-day rust-infected leaves generated 352 146 sequences which assembled into 22 774 contigs. In the absence of any reference genomic sequences for Coffea or Hemileia, specific trinucleotide frequencies within expressed sequence tags (ESTs) and blast homology against a set of dicots and basidiomycete genomes were used to distinguish pathogen from plant sequences. About 30% (6763) of the contigs were assigned to H. vastatrix and 61% (13 951) to C. arabica. The majority (60%) of the rust sequences did not show homology to any genomic database, indicating that they were potential novel fungal genes. In silico analyses of the 6763 H. vastatrix contigs predicted 382 secreted proteins and identified homologues of the flax rust haustorially expressed secreted proteins (HESPs) and bean rust transferred protein 1 (RTP1). These rust candidate effectors showed conserved amino-acid domains and conserved patterns of cysteine positions suggestive of conserved functions during infection of host plants. Quantitative reverse transcription-polymerase chain reaction profiling of selected rust genes revealed dynamic expression patterns during the time course of infection of coffee leaves. This study provides the first valuable genomic resource for the agriculturally important plant pathogen H. vastatrix and the first comprehensive C. arabica EST dataset.

  18. Sustained Photosynthetic Performance of Coffea spp. under Long-Term Enhanced [CO2

    PubMed Central

    Ramalho, José C.; Rodrigues, Ana P.; Semedo, José N.; Pais, Isabel P.; Martins, Lima D.; Simões-Costa, Maria C.; Leitão, António E.; Fortunato, Ana S.; Batista-Santos, Paula; Palos, Isabel M.; Tomaz, Marcelo A.; Scotti-Campos, Paula; Lidon, Fernando C.; DaMatta, Fábio M.

    2013-01-01

    Coffee is one of the world’s most traded agricultural products. Modeling studies have predicted that climate change will have a strong impact on the suitability of current cultivation areas, but these studies have not anticipated possible mitigating effects of the elevated atmospheric [CO2] because no information exists for the coffee plant. Potted plants from two genotypes of Coffea arabica and one of C. canephora were grown under controlled conditions of irradiance (800 μmol m-2 s-1), RH (75%) and 380 or 700 μL CO2 L-1 for 1 year, without water, nutrient or root development restrictions. In all genotypes, the high [CO2] treatment promoted opposite trends for stomatal density and size, which decreased and increased, respectively. Regardless of the genotype or the growth [CO2], the net rate of CO2 assimilation increased (34-49%) when measured at 700 than at 380 μL CO2 L-1. This result, together with the almost unchanged stomatal conductance, led to an instantaneous water use efficiency increase. The results also showed a reinforcement of photosynthetic (and respiratory) components, namely thylakoid electron transport and the activities of RuBisCo, ribulose 5-phosphate kinase, malate dehydrogenase and pyruvate kinase, what may have contributed to the enhancements in the maximum rates of electron transport, carboxylation and photosynthetic capacity under elevated [CO2], although these responses were genotype dependent. The photosystem II efficiency, energy driven to photochemical events, non-structural carbohydrates, photosynthetic pigment and membrane permeability did not respond to [CO2] supply. Some alterations in total fatty acid content and the unsaturation level of the chloroplast membranes were noted but, apparently, did not affect photosynthetic functioning. Despite some differences among the genotypes, no clear species-dependent responses to elevated [CO2] were observed. Overall, as no apparent sign of photosynthetic down-regulation was found, our data

  19. Sustained photosynthetic performance of Coffea spp. under long-term enhanced [CO2].

    PubMed

    Ramalho, José C; Rodrigues, Ana P; Semedo, José N; Pais, Isabel P; Martins, Lima D; Simões-Costa, Maria C; Leitão, António E; Fortunato, Ana S; Batista-Santos, Paula; Palos, Isabel M; Tomaz, Marcelo A; Scotti-Campos, Paula; Lidon, Fernando C; DaMatta, Fábio M

    2013-01-01

    Coffee is one of the world's most traded agricultural products. Modeling studies have predicted that climate change will have a strong impact on the suitability of current cultivation areas, but these studies have not anticipated possible mitigating effects of the elevated atmospheric [CO2] because no information exists for the coffee plant. Potted plants from two genotypes of Coffea arabica and one of C. canephora were grown under controlled conditions of irradiance (800 μmol m(-2) s(-1)), RH (75%) and 380 or 700 μL CO2 L(-1) for 1 year, without water, nutrient or root development restrictions. In all genotypes, the high [CO2] treatment promoted opposite trends for stomatal density and size, which decreased and increased, respectively. Regardless of the genotype or the growth [CO2], the net rate of CO2 assimilation increased (34-49%) when measured at 700 than at 380 μL CO2 L(-1). This result, together with the almost unchanged stomatal conductance, led to an instantaneous water use efficiency increase. The results also showed a reinforcement of photosynthetic (and respiratory) components, namely thylakoid electron transport and the activities of RuBisCo, ribulose 5-phosphate kinase, malate dehydrogenase and pyruvate kinase, what may have contributed to the enhancements in the maximum rates of electron transport, carboxylation and photosynthetic capacity under elevated [CO2], although these responses were genotype dependent. The photosystem II efficiency, energy driven to photochemical events, non-structural carbohydrates, photosynthetic pigment and membrane permeability did not respond to [CO2] supply. Some alterations in total fatty acid content and the unsaturation level of the chloroplast membranes were noted but, apparently, did not affect photosynthetic functioning. Despite some differences among the genotypes, no clear species-dependent responses to elevated [CO2] were observed. Overall, as no apparent sign of photosynthetic down-regulation was found, our

  20. Host-range Characterization of Two Pratylenchus coffeae Isolates from Brazil

    PubMed Central

    Silva, R. A.; Inomoto, M. M.

    2002-01-01

    Two isolates of Pratylenchus coffeae were collected from coffee roots (in Marília, São Paulo State, Brazil) and Aglaonema (in Rio de Janeiro City, Rio de Janeiro State, Brazil) and maintained in the laboratory on alfalfa callus. Twenty-four plants were tested in the greenhouse to characterize the host preference of these isolates. The host ranges of the isolates differed from each other and, interestingly, coffee, banana, and citrus were not among the better hosts of either isolate. Rather, sorghum, maize, rice, millet, okra, melon, eggplant, and lettuce were the best hosts of the Marília isolate. Poor hosts included French marigold, Rangpur lime, banana, sesame, peanut, sunflower, cotton, French bean, onion, and small onion. The best hosts of the Rio de Janeiro isolate were sesame, soybean, sorghum, castor oil plant, watermelon, squash, eggplant, and melon; the poorest hosts were French marigold, coffee, Rangpur lime, banana, sunflower, peanut, maize, millet, French bean, cotton, onion, sweet pepper, lettuce, okra, and small onion. These isolates have important molecular and morphological differences, suggesting host preference is linked to these characteristics. PMID:19265921

  1. Host-range characterization of two Pratylenchus coffeae isolates from Brazil.

    PubMed

    Silva, R A; Inomoto, M M

    2002-06-01

    Two isolates of Pratylenchus coffeae were collected from coffee roots (in Marília, São Paulo State, Brazil) and Aglaonema (in Rio de Janeiro City, Rio de Janeiro State, Brazil) and maintained in the laboratory on alfalfa callus. Twenty-four plants were tested in the greenhouse to characterize the host preference of these isolates. The host ranges of the isolates differed from each other and, interestingly, coffee, banana, and citrus were not among the better hosts of either isolate. Rather, sorghum, maize, rice, millet, okra, melon, eggplant, and lettuce were the best hosts of the Marília isolate. Poor hosts included French marigold, Rangpur lime, banana, sesame, peanut, sunflower, cotton, French bean, onion, and small onion. The best hosts of the Rio de Janeiro isolate were sesame, soybean, sorghum, castor oil plant, watermelon, squash, eggplant, and melon; the poorest hosts were French marigold, coffee, Rangpur lime, banana, sunflower, peanut, maize, millet, French bean, cotton, onion, sweet pepper, lettuce, okra, and small onion. These isolates have important molecular and morphological differences, suggesting host preference is linked to these characteristics.

  2. Modeling the Agroecological Land Suitability for Coffea arabica L. in Central America

    NASA Astrophysics Data System (ADS)

    Lara, Leonel; Rasche, Livia; Schneider, Uwe

    2016-04-01

    Coffee production is an important income source for small farms in Central America, but climate change threatens the production. In order to develop efficient adaptation strategies, an assessment of local conditions and opportunities is essential. Lack or uncertainty of information are common challenges for such assessments. A tool to resolve these challenges is Bayesian network analysis. In this study, we developed ALECA, the first Bayesian network model to evaluate the agroecological land suitability for Coffea arabica L. A new set of suitability functions was created and subsequently used to populate the conditional probability tables of the variables. The variables include temperature, precipitation and dry season length for the climate, slope and aspect for the landform, and soil pH, cation exchange capacity and texture for the soil component. We validated ALECA by comparing a map of current coffee areas, and specific coffee areas with known suitability for coffee production in Central America to the suitability evaluations of the model; and proceeded to explore 1) the capabilities of the model to manage data uncertainty, and 2) the changes to suitability scores under climate change. The results showed that the area suitable for coffee production will decline in Central America under climate change, underlining the need for models like ALECA, which can be used to produce reliable land evaluations at local, national and regional scales under uncertainty.

  3. Galactinol synthase transcriptional profile in two genotypes of Coffea canephora with contrasting tolerance to drought

    PubMed Central

    Santos, Tiago Benedito Dos; de Lima, Rogério Barbosa; Nagashima, Getúlio Takashi; Petkowicz, Carmen Lucia de Oliveira; Carpentieri-Pípolo, Valéria; Pereira, Luiz Filipe Protasio; Domingues, Douglas Silva; Vieira, Luiz Gonzaga Esteves

    2015-01-01

    Increased synthesis of galactinol and raffinose family oligosaccharides (RFOs) has been reported in vegetative tissues in response to a range of abiotic stresses. In this work, we evaluated the transcriptional profile of a Coffea canephora galactinol synthase gene (CcGolS1) in two clones that differed in tolerance to water deficit in order to assess the contribution of this gene to drought tolerance. The expression of CcGolS1 in leaves was differentially regulated by water deficit, depending on the intensity of stress and the genotype. In clone 109A (drought-susceptible), the abundance of CcGolS1 transcripts decreased upon exposure to drought, reaching minimum values during recovery from severe water deficit and stress. In contrast, CcGolS1 gene expression in clone 14 (drought-tolerant) was stimulated by water deficit. Changes in galactinol and RFO content did not correlate with variation in the steady-state transcript level. However, the magnitude of increase in RFO accumulation was higher in the tolerant cultivar, mainly under severe water deficit. The finding that the drought-tolerant coffee clone showed enhanced accumulation of CcGolS1 transcripts and RFOs under water deficit suggests the possibility of using this gene to improve drought tolerance in this important crop. PMID:26273221

  4. Green synthesis of silver nanoparticles using Coffea arabica seed extract and its antibacterial activity.

    PubMed

    Dhand, Vivek; Soumya, L; Bharadwaj, S; Chakra, Shilpa; Bhatt, Deepika; Sreedhar, B

    2016-01-01

    A novel green source was opted to synthesize silver nanoparticles using dried roasted Coffea arabica seed extract. Bio-reduction of silver was complete when the mixture (AgNO3+extract) changed its color from light to dark brown. UV-vis spectroscopy result showed maximum adsorption at 459 nm, which represents the characteristic surface plasmon resonance of nanosilver. X-ray crystal analysis showed that the silver nanoparticles are highly crystalline and exhibit a cubic, face centered lattice with characteristic (111), (200), (220) and (311) orientations. Particles exhibit spherical and ellipsoidal shaped structures as observed from TEM. Composition analysis obtained from SEM-EDXA confirmed the presence of elemental signature of silver. FTIR results recorded a downward shift of absorption bands between 800-1500 cm(-1) indicting the formation of silver nanoparticles. The mean particle size investigated using DLS was found to be in between 20-30 nm respectively. Anti-bacterial activity of silver nanoparticles on E. coli and S. aureus demonstrated diminished bacterial growth with the development of well-defined inhibition zones.

  5. Characterization of Coffea arabica monofloral honey from Espírito Santo, Brazil.

    PubMed

    Kadri, Samir Moura; Zaluski, Rodrigo; Pereira Lima, Giuseppina Pace; Mazzafera, Paulo; de Oliveira Orsi, Ricardo

    2016-07-15

    In this study, samples of coffee honey produced in Espírito Santo State, Brazil, were characterized based on their melissopalynology, physicochemical and nutritional properties, and mineral and caffeine contents. The caffeine content in the nectar from coffee flowers was measured by high performance liquid chromatography (HPLC). Blends of honey were obtained from three Coffea arabica crops, each with 10 colonies of Africanized Apis mellifera. All honey samples contained monofloral (75-78%) pollen belonging to C. arabica. Physicochemical parameters (total acidity, pH, moisture, dry matter, ash, and qualitative hydroxymethylfurfural) were within the approved limits established by EU legislation. Coffee honey contains high levels of ascorbic acid (294.68 mg kg(-1)) and low amounts of total flavonoids (3.51 ± 0.18 mg QE kg(-1)). The most abundant minerals were potassium and calcium (962.59 ± 154.3 and 343.75 ± 25.56 mg kg(-1), respectively). The caffeine content in coffee nectar (1.64 mg kg(-1)) was approximately 8-fold lower than that in honey (12.02 ± 0.81 mg kg(-1)). PMID:26948612

  6. Homeologous gene expression in response to growing temperature in a recent Allopolyploid (Coffea arabica L.).

    PubMed

    Combes, Marie-Christine; Cenci, Alberto; Baraille, Hélène; Bertrand, Benoît; Lashermes, Philippe

    2012-01-01

    Allopolyploidy is considered as a major factor contributing to speciation, diversification, and plant ecological adaptation. In particular, the expression of duplicate genes (homeologs) can be altered leading to functional plasticity and to phenotypic novelty. This study investigated the influence of growing temperatures on homeologous gene expression in Coffea arabica L., a recent allopolyploid involving 2 closely related diploid parental species. The relative expression of homeologs of 13 genes all located in the same genomic region was analyzed using an SNP ratio quantification method based on dideoxy-terminated sequences of cDNA amplicons. The relative expression of homeologous genes varied depending on the gene, the organ, and the growing condition. Nevertheless, expression of both homeologs was always detected (i.e., no silencing). Although the growing conditions were suitable for one or other of the parental species, neither subgenome appeared preferentially expressed. Furthermore, relative homeologous expression showed moderate variations across organs and conditions and appeared uncorrelated between adjacent genes. These results indicate the absence of signs of subfunctionalization suggesting C. arabica has not undergone noticeable diploidization. Furthermore, these results suggest that the expression of homeologous genes in C. arabica is regulated by a shared trans-regulation mechanism acting similarly on the 2 subgenomes and that the observed biases in the relative homeolog expression may result from cis fine-scale factors. PMID:22039298

  7. Characterization of Coffea arabica monofloral honey from Espírito Santo, Brazil.

    PubMed

    Kadri, Samir Moura; Zaluski, Rodrigo; Pereira Lima, Giuseppina Pace; Mazzafera, Paulo; de Oliveira Orsi, Ricardo

    2016-07-15

    In this study, samples of coffee honey produced in Espírito Santo State, Brazil, were characterized based on their melissopalynology, physicochemical and nutritional properties, and mineral and caffeine contents. The caffeine content in the nectar from coffee flowers was measured by high performance liquid chromatography (HPLC). Blends of honey were obtained from three Coffea arabica crops, each with 10 colonies of Africanized Apis mellifera. All honey samples contained monofloral (75-78%) pollen belonging to C. arabica. Physicochemical parameters (total acidity, pH, moisture, dry matter, ash, and qualitative hydroxymethylfurfural) were within the approved limits established by EU legislation. Coffee honey contains high levels of ascorbic acid (294.68 mg kg(-1)) and low amounts of total flavonoids (3.51 ± 0.18 mg QE kg(-1)). The most abundant minerals were potassium and calcium (962.59 ± 154.3 and 343.75 ± 25.56 mg kg(-1), respectively). The caffeine content in coffee nectar (1.64 mg kg(-1)) was approximately 8-fold lower than that in honey (12.02 ± 0.81 mg kg(-1)).

  8. Green synthesis of silver nanoparticles using Coffea arabica seed extract and its antibacterial activity.

    PubMed

    Dhand, Vivek; Soumya, L; Bharadwaj, S; Chakra, Shilpa; Bhatt, Deepika; Sreedhar, B

    2016-01-01

    A novel green source was opted to synthesize silver nanoparticles using dried roasted Coffea arabica seed extract. Bio-reduction of silver was complete when the mixture (AgNO3+extract) changed its color from light to dark brown. UV-vis spectroscopy result showed maximum adsorption at 459 nm, which represents the characteristic surface plasmon resonance of nanosilver. X-ray crystal analysis showed that the silver nanoparticles are highly crystalline and exhibit a cubic, face centered lattice with characteristic (111), (200), (220) and (311) orientations. Particles exhibit spherical and ellipsoidal shaped structures as observed from TEM. Composition analysis obtained from SEM-EDXA confirmed the presence of elemental signature of silver. FTIR results recorded a downward shift of absorption bands between 800-1500 cm(-1) indicting the formation of silver nanoparticles. The mean particle size investigated using DLS was found to be in between 20-30 nm respectively. Anti-bacterial activity of silver nanoparticles on E. coli and S. aureus demonstrated diminished bacterial growth with the development of well-defined inhibition zones. PMID:26478284

  9. The Greater Phenotypic Homeostasis of the Allopolyploid Coffea arabica Improved the Transcriptional Homeostasis Over that of Both Diploid Parents.

    PubMed

    Bertrand, Benoît; Bardil, Amélie; Baraille, Hélène; Dussert, Stéphane; Doulbeau, Sylvie; Dubois, Emeric; Severac, Dany; Dereeper, Alexis; Etienne, Hervé

    2015-10-01

    Polyploidy impacts the diversity of plant species, giving rise to novel phenotypes and leading to ecological diversification. In order to observe adaptive and evolutionary capacities of polyploids, we compared the growth, primary metabolism and transcriptomic expression level in the leaves of the newly formed allotetraploid Coffea arabica species compared with its two diploid parental species (Coffea eugenioides and Coffea canephora), exposed to four thermal regimes (TRs; 18-14, 23-19, 28-24 and 33-29°C). The growth rate of the allopolyploid C. arabica was similar to that of C. canephora under the hottest TR and that of C. eugenioides under the coldest TR. For metabolite contents measured at the hottest TR, the allopolyploid showed similar behavior to C. canephora, the parent which tolerates higher growth temperatures in the natural environment. However, at the coldest TR, the allopolyploid displayed higher sucrose, raffinose and ABA contents than those of its two parents and similar linolenic acid leaf composition and Chl content to those of C. eugenioides. At the gene expression level, few differences between the allopolyploid and its parents were observed for studied genes linked to photosynthesis, respiration and the circadian clock, whereas genes linked to redox activity showed a greater capacity of the allopolyploid for homeostasis. Finally, we found that the overall transcriptional response to TRs of the allopolyploid was more homeostatic compared with its parents. This better transcriptional homeostasis of the allopolyploid C. arabica afforded a greater phenotypic homeostasis when faced with environments that are unsuited to the diploid parental species.

  10. The Greater Phenotypic Homeostasis of the Allopolyploid Coffea arabica Improved the Transcriptional Homeostasis Over that of Both Diploid Parents

    PubMed Central

    Bertrand, Benoît; Bardil, Amélie; Baraille, Hélène; Dussert, Stéphane; Doulbeau, Sylvie; Dubois, Emeric; Severac, Dany; Dereeper, Alexis; Etienne, Hervé

    2015-01-01

    Polyploidy impacts the diversity of plant species, giving rise to novel phenotypes and leading to ecological diversification. In order to observe adaptive and evolutionary capacities of polyploids, we compared the growth, primary metabolism and transcriptomic expression level in the leaves of the newly formed allotetraploid Coffea arabica species compared with its two diploid parental species (Coffea eugenioides and Coffea canephora), exposed to four thermal regimes (TRs; 18–14, 23–19, 28–24 and 33–29°C). The growth rate of the allopolyploid C. arabica was similar to that of C. canephora under the hottest TR and that of C. eugenioides under the coldest TR. For metabolite contents measured at the hottest TR, the allopolyploid showed similar behavior to C. canephora, the parent which tolerates higher growth temperatures in the natural environment. However, at the coldest TR, the allopolyploid displayed higher sucrose, raffinose and ABA contents than those of its two parents and similar linolenic acid leaf composition and Chl content to those of C. eugenioides. At the gene expression level, few differences between the allopolyploid and its parents were observed for studied genes linked to photosynthesis, respiration and the circadian clock, whereas genes linked to redox activity showed a greater capacity of the allopolyploid for homeostasis. Finally, we found that the overall transcriptional response to TRs of the allopolyploid was more homeostatic compared with its parents. This better transcriptional homeostasis of the allopolyploid C. arabica afforded a greater phenotypic homeostasis when faced with environments that are unsuited to the diploid parental species. PMID:26355011

  11. Revision of Kadua (Rubiaceae) in the Marquesas Islands, French Polynesia, with description of the new species K. lichtlei

    PubMed Central

    Wagner, Warren L.; Lorence, David H.

    2011-01-01

    Abstract During the preparation of the Vascular Flora of the Marquesas Islands three new species of Coprosma (Rubiaceae, tribe Anthospermeae) have come to light and are described herein: Coprosma fatuhivaensis W. L. Wagner & Lorence, Coprosma meyeri W. L. Wagner & Lorence, and Coprosma temetiuensis W. L. Wagner & Lorence. Descriptions, illustrations, conservation status, and specimen citations are provided. Amended descriptions of three previously described Marquesan Coprosma species are also provided as well as a key to the species, four of which fall into the Critically Endangered (CR) and two into the Endangered (EN) category. With the description of these the new species, Coprosma becomes the sixth largest lineage in the Marquesas Islands with six species after Psychotria (one lineage which has 9 spp.), Cyrtandra (8 spp.), Bidens (8 spp.), Melicope (7 spp.), and Ixora (7 spp.). PMID:22171185

  12. Development of SSR markers for Psychotria homalosperma (Rubiaceae) and cross-amplification in four other species1

    PubMed Central

    Sugai, Kyoko; Watanabe, Kenta; Kato, Hidetoshi; Sugawara, Takashi

    2016-01-01

    Premise of the study: Twenty-six microsatellite (simple sequence repeat [SSR]) markers were characterized in Psychotria homalosperma (Rubiaceae), an endemic evergreen tree in the Bonin Islands, Japan, to investigate the genetic structure and gene flow of the species. Methods and Results: Using next-generation sequencing, we developed 26 SSR markers for P. homalosperma with perfect motifs from di- to pentanucleotide repeats. Of these, the Chichijima and Hahajima island populations of P. homalosperma had mean allele numbers of 6.50 and 6.81, respectively. The mean expected heterozygosities were 0.578 and 0.606, respectively. In addition, 10 and eight of these markers were successfully amplified for P. boninensis and P. serpens, respectively, occurring in the same or adjacent areas. Conclusions: The SSR markers developed in this study will be useful for future studies concerning the population genetics of P. homalosperma and will facilitate the development of a conservation strategy. PMID:27213122

  13. Field-cage evaluation of the parasitoid Phymastichus coffea LaSalle (Hymenoptera: Eulophidae) as a natural enemy of the coffee berry borer

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phymastichus coffea (Hymenoptera: Eulophidae) is an African parasitoid that has been imported to Mexico and other Latin American countries for the biological control of the coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae: Scolytinae). As a part of the evaluation of this ...

  14. Evolution in Caffeoylquinic Acid Content and Histolocalization During Coffea canephora Leaf Development

    PubMed Central

    MONDOLOT, LAURENCE; LA FISCA, PHILIPPE; BUATOIS, BRUNO; TALANSIER, EMELINE; DE KOCHKO, ALEXANDRE; CAMPA, CLAUDINE

    2006-01-01

    • Background and Aims Caffeoylquinic acids are cinnamate conjugates derived from the phenylpropanoid pathway. They are generally involved in plant responses to biotic and abiotic stress and one of them, chlorogenic acid (5-O-caffeoylquinic acid, 5-CQA), is an intermediate in the lignin biosynthesis pathway. Caffeoylquinic acids, and particularly 5-CQA, are accumulated in coffee beans, where they can form vacuolar complexes with caffeine. Coffea canephora beans are known to have high caffeoylquinic acid content, but little is known about the content and diversity of these compounds in other plant parts. To gain new insights into the caffeoylquinic acid metabolism of C. canephora, caffeoylquinic acid content and in situ localization were assessed in leaves at different growth stages. • Methods HPLC analyses of caffeoylquinic acid content of leaves was conducted in conjunction with detailed histochemical and microspectrofluorometrical analysis. • Key Results and Conclusions HPLC analyses revealed that caffeoylquinic acid content was 10-fold lower in adult than in juvenile leaves. The most abundant cinnamate conjugate was 5-CQA, but dicaffeoylquinic acids (particularly in juvenile leaves) and feruloylquinic acids were also present. Using specific reagents, histochemical and microspectrofluorometrical analysis showed that caffeoylquinic acids (mono- and di-esters) were closely associated with chloroplasts in very young leaves. During leaf ageing, they were found to first accumulate intensively in specific chlorenchymatous bundle sheath cells and then in phloem sclerenchyma cells. The association with chloroplasts suggests that caffeoylquinic acids have a protective role against light damage. In older tissues, their presence in the leaf vascular system indicates that they are transported via phloem and confirms their involvement in lignification processes. In accordance with the hypothesis of a complex formation with caffeine, similar tissue distribution was

  15. [Growth and photosynthetic characteristics of field-grown Coffea arabica under different watering and fertilization managements].

    PubMed

    Cai, Chuantao; Cai, Zhiquan; Xie, Jiwu; Zhou, Qinghui; Cao, Kunfang; Yao, Tianquan; Wang, Hua

    2004-07-01

    Straw mulching and drip irrigation have been widely used for coffee production. In order to know if these techniques are suitable in Yunnan, five-year-old coffee plants were separated into 8 groups to grow in the field under 2 fertilization rates (low and high) and 4 watering regimes: dry straw mulching (M), drip irrigation (I), drip irrigation + straw mulching (MI) and control treatment (CK), and the effects of various watering and fertilization treatments on the growth and photosynthetic characteristics of Coffea arabica with the density of 4500 individuals per hectare were measured. The results showed that during one year's growth period, the coffee plants had two growth peaks, one was in May when the rainy season just begun, and the another was in August to September, the middle of rainy season. Higher fertilization promoted the relative height and length growth rates of the branches, but watering treatments hadn't significant effects on them. In dry season, watering significantly promoted the Pn, gs, Tr and WUE, while water status had no significant influence on the internal fluorescence features of PSII. In wet season, high-fertilized plants had a higher leaf nitrogen content and Pn than low-fertilized plants, and Pn was positively correlated with leaf nitrogen content. In both seasons, higher fertilization increased the WUE regardless of the watering treatments. At the same time, the high-fertilization treatment significantly alleviated diurnal photoinhibition, companying with a higher energy utilization through photochemistry and a higher energy dissipation through xanthophyll cycle, which appears that high-fertilized coffee plants have the mechanism to acclimate to strong light environment. All the results indicated that wet season is the optimum time for the photosynthesis and growth of C. arabica, and C. arabica needs a high fertilization investment and fine watering managements during its whole growth period. Among the three man-made watering treatments

  16. Dynamics of the concentration of IAA and some of its conjugates during the induction of somatic embryogenesis in Coffea canephora

    PubMed Central

    Ayil-Gutiérrez, Benajmín; Galaz-Ávalos, Rosa María; Peña-Cabrera, Eduardo; Loyola-Vargas, Victor Manuel

    2013-01-01

    Most of the somatic embryogenesis (SE) process requires the presence, either before or during the embryogenic process, of at least one exogenous auxin. This exogenous auxin induces the presence of endogenous auxins, which appears to be essential for SE induction. We found that during the preincubation period of SE in Coffea canephora, there is an important increase in both free and conjugated indole-3-acetic acid (IAA), as well as indole-3-butyric acid. This increase is accompanied by an increase in the expression of YUCCA (CcYUC), TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (CcTAA1), and GRETCHEN HAGEN 3 (GH3) genes. On the other hand, most of the IAA compounds decreased during the induction of SE. The results presented in this research suggest that a balance between free IAA and its amide conjugates is necessary to allow the expression of SE-related genes. PMID:24299659

  17. Homeologous genes involved in mannitol synthesis reveal unequal contributions in response to abiotic stress in Coffea arabica.

    PubMed

    de Carvalho, Kenia; Petkowicz, Carmen L O; Nagashima, Getulio T; Bespalhok Filho, João C; Vieira, Luiz G E; Pereira, Luiz F P; Domingues, Douglas S

    2014-10-01

    Polyploid plants can exhibit transcriptional modulation in homeologous genes in response to abiotic stresses. Coffea arabica, an allotetraploid, accounts for 75% of the world's coffee production. Extreme temperatures, salinity and drought limit crop productivity, which includes coffee plants. Mannitol is known to be involved in abiotic stress tolerance in higher plants. This study aimed to investigate the transcriptional responses of genes involved in mannitol biosynthesis and catabolism in C. arabica leaves under water deficit, salt stress and high temperature. Mannitol concentration was significantly increased in leaves of plants under drought and salinity, but reduced by heat stress. Fructose content followed the level of mannitol only in heat-stressed plants, suggesting the partitioning of the former into other metabolites during drought and salt stress conditions. Transcripts of the key enzymes involved in mannitol biosynthesis, CaM6PR, CaPMI and CaMTD, were modulated in distinct ways depending on the abiotic stress. Our data suggest that changes in mannitol accumulation during drought and salt stress in leaves of C. arabica are due, at least in part, to the increased expression of the key genes involved in mannitol biosynthesis. In addition, the homeologs of the Coffea canephora subgenome did not present the same pattern of overall transcriptional response, indicating differential regulation of these genes by the same stimulus. In this way, this study adds new information on the differential expression of C. arabica homeologous genes under adverse environmental conditions showing that abiotic stresses can influence the homeologous gene regulation pattern, in this case, mainly on those involved in mannitol pathway. PMID:24861101

  18. Molecular phylogenetics and generic assessment in the tribe Morindeae (Rubiaceae-Rubioideae): how to circumscribe Morinda L. to be monophyletic?

    PubMed

    Razafimandimbison, Sylvain G; McDowell, Timothy D; Halford, David A; Bremer, Birgitta

    2009-09-01

    Most of the species of the family Rubiaceae with flowers arranged in head inflorescences are currently classified in three distantly related tribes, Naucleeae (subfamily Cinchonoideae) and Morindeae and Schradereae (subfamily Rubioideae). Within Morindeae the type genus Morinda is traditionally and currently circumscribed based on its head inflorescences and syncarpous fruits (syncarps). These characters are also present in some members of its allied genera, raising doubts about the monophyly of Morinda. We perform Bayesian phylogenetic analyses using combined nrETS/nrITS/trnT-F data for 67 Morindeae taxa and five outgroups from the closely related tribes Mitchelleae and Gaertnereae to rigorously test the monophyly of Morinda as currently delimited and assess the phylogenetic value of head inflorescences and syncarps in Morinda and Morindeae and to evaluate generic relationships and limits in Morindeae. Our analyses demonstrate that head inflorescences and syncarps in Morinda and Morindeae are evolutionarily labile. Morinda is highly paraphyletic, unless the genera Coelospermum, Gynochthodes, Pogonolobus, and Sarcopygme are also included. Morindeae comprises four well-supported and morphologically distinct major lineages: Appunia clade, Morinda clade (including Sarcopygme and the lectotype M. royoc), Coelospermum clade (containing Pogonolobus and Morinda reticulata), and Gynochthodes-Morinda clade. Four possible alternatives for revising generic boundaries are presented to establish monophyletic units. We favor the recognition of the four major lineages of Morindeae as separate genera, because this classification reflects the occurrence of a considerable morphological diversity in the tribe and the phylogenetic and taxonomic distinctness of its newly delimited genera. PMID:19394432

  19. Morphology, secretion composition, and ecological aspects of stipular colleters in Rubiaceae species from tropical forest and savanna

    NASA Astrophysics Data System (ADS)

    Tresmondi, Fernanda; Nogueira, Anselmo; Guimarães, Elza; Machado, Silvia Rodrigues

    2015-12-01

    Colleters are secretory structures that produce and release mucilage or a mucilage-resin mixture protecting meristems and young structures against desiccation, herbivores, and pathogens. The secretions may vary in colleters of same or different types, indicating that the functionality of colleters may be more specific than previously thought. In this study, we compared 17 Rubiaceae species from savanna and forest environment focusing on colleter secretions and its ecological role. First, we evaluated the morphology, distribution, and histochemistry of stipular colleters using light and scanning electron microscopy. Additionally, we investigated the phenology, microclimate, and the proportion of damaged apices in the savanna and forest species. We recorded standard-type colleters, variable in distribution and size, in 14 of the 17 studied species. The secretion varied from predominantly hydrophilic, mixed to predominantly lipophilic. During the budding period, secretion covered the vegetative apices. Savanna species had a prevalence of lipid secretion in habitats with higher luminosity, which had a lower proportion of damaged apices. In contrast, forest species occurred in habitats with lower luminosity and had a higher proportion of damaged apices, in general with the absence of lipids in the colleters. These results highlight that colleters with similar morphology clearly differed in secretions among species, especially between species from savanna and forest, in which the colleters appear potentially associated with protection against irradiation in savanna, but not in the forest environment.

  20. Evolutionary Relationships and Biogeography of the Ant-Epiphytic Genus Squamellaria (Rubiaceae: Psychotrieae) and Their Taxonomic Implications

    PubMed Central

    Chomicki, Guillaume; Renner, Susanne S.

    2016-01-01

    Ecological research on ant/plant symbioses in Fiji, combined with molecular phylogenetics, has brought to light four new species of Squamellaria in the subtribe Hydnophytinae of the Rubiaceae tribe Psychotrieae and revealed that four other species, previously in Hydnophytum, need to be transferred to Squamellaria. The diagnoses of the new species are based on morphological and DNA traits, with further insights from microCT scanning of flowers and leaf δ13C ratios (associated with Crassulacean acid metabolism). Our field and phylogenetic work results in a new circumscription of the genus Squamellaria, which now contains 12 species (to which we also provide a taxonomic key), not 3 as in the last revision. A clock-dated phylogeny and a model-testing biogeographic framework were used to infer the broader geographic history of rubiaceous ant plants in the Pacific, specifically the successive expansion of Squamellaria to Vanuatu, the Solomon Islands, and Fiji. The colonization of Vanuatu may have occurred from Fiji, when these islands were still in the same insular arc, while the colonization of the Solomon islands may have occurred after the separation of this island from the Fiji/Vanuatu arc. Some of these ant-housing epiphytes must have dispersed with their specialized ants, for instance attached to floating timber. Others acquired new ant symbionts on different islands. PMID:27028599

  1. Evolutionary Relationships and Biogeography of the Ant-Epiphytic Genus Squamellaria (Rubiaceae: Psychotrieae) and Their Taxonomic Implications.

    PubMed

    Chomicki, Guillaume; Renner, Susanne S

    2016-01-01

    Ecological research on ant/plant symbioses in Fiji, combined with molecular phylogenetics, has brought to light four new species of Squamellaria in the subtribe Hydnophytinae of the Rubiaceae tribe Psychotrieae and revealed that four other species, previously in Hydnophytum, need to be transferred to Squamellaria. The diagnoses of the new species are based on morphological and DNA traits, with further insights from microCT scanning of flowers and leaf δ(13)C ratios (associated with Crassulacean acid metabolism). Our field and phylogenetic work results in a new circumscription of the genus Squamellaria, which now contains 12 species (to which we also provide a taxonomic key), not 3 as in the last revision. A clock-dated phylogeny and a model-testing biogeographic framework were used to infer the broader geographic history of rubiaceous ant plants in the Pacific, specifically the successive expansion of Squamellaria to Vanuatu, the Solomon Islands, and Fiji. The colonization of Vanuatu may have occurred from Fiji, when these islands were still in the same insular arc, while the colonization of the Solomon islands may have occurred after the separation of this island from the Fiji/Vanuatu arc. Some of these ant-housing epiphytes must have dispersed with their specialized ants, for instance attached to floating timber. Others acquired new ant symbionts on different islands. PMID:27028599

  2. Morphology, secretion composition, and ecological aspects of stipular colleters in Rubiaceae species from tropical forest and savanna.

    PubMed

    Tresmondi, Fernanda; Nogueira, Anselmo; Guimarães, Elza; Machado, Silvia Rodrigues

    2015-12-01

    Colleters are secretory structures that produce and release mucilage or a mucilage-resin mixture protecting meristems and young structures against desiccation, herbivores, and pathogens. The secretions may vary in colleters of same or different types, indicating that the functionality of colleters may be more specific than previously thought. In this study, we compared 17 Rubiaceae species from savanna and forest environment focusing on colleter secretions and its ecological role. First, we evaluated the morphology, distribution, and histochemistry of stipular colleters using light and scanning electron microscopy. Additionally, we investigated the phenology, microclimate, and the proportion of damaged apices in the savanna and forest species. We recorded standard-type colleters, variable in distribution and size, in 14 of the 17 studied species. The secretion varied from predominantly hydrophilic, mixed to predominantly lipophilic. During the budding period, secretion covered the vegetative apices. Savanna species had a prevalence of lipid secretion in habitats with higher luminosity, which had a lower proportion of damaged apices. In contrast, forest species occurred in habitats with lower luminosity and had a higher proportion of damaged apices, in general with the absence of lipids in the colleters. These results highlight that colleters with similar morphology clearly differed in secretions among species, especially between species from savanna and forest, in which the colleters appear potentially associated with protection against irradiation in savanna, but not in the forest environment.

  3. Morphology, secretion composition, and ecological aspects of stipular colleters in Rubiaceae species from tropical forest and savanna.

    PubMed

    Tresmondi, Fernanda; Nogueira, Anselmo; Guimarães, Elza; Machado, Silvia Rodrigues

    2015-12-01

    Colleters are secretory structures that produce and release mucilage or a mucilage-resin mixture protecting meristems and young structures against desiccation, herbivores, and pathogens. The secretions may vary in colleters of same or different types, indicating that the functionality of colleters may be more specific than previously thought. In this study, we compared 17 Rubiaceae species from savanna and forest environment focusing on colleter secretions and its ecological role. First, we evaluated the morphology, distribution, and histochemistry of stipular colleters using light and scanning electron microscopy. Additionally, we investigated the phenology, microclimate, and the proportion of damaged apices in the savanna and forest species. We recorded standard-type colleters, variable in distribution and size, in 14 of the 17 studied species. The secretion varied from predominantly hydrophilic, mixed to predominantly lipophilic. During the budding period, secretion covered the vegetative apices. Savanna species had a prevalence of lipid secretion in habitats with higher luminosity, which had a lower proportion of damaged apices. In contrast, forest species occurred in habitats with lower luminosity and had a higher proportion of damaged apices, in general with the absence of lipids in the colleters. These results highlight that colleters with similar morphology clearly differed in secretions among species, especially between species from savanna and forest, in which the colleters appear potentially associated with protection against irradiation in savanna, but not in the forest environment. PMID:26585374

  4. Anti-methicillin-resistant Staphylococcus aureus (MRSA) activity of Rubiaceae, Fabaceae and Poaceae plants: A search for new sources of useful alternative antibacterials against MRSA infections.

    PubMed

    Sharifi-Rad, M; Iriti, M; Sharifi-Rad, M; Gibbons, S; Sharifi-Rad, J

    2016-01-01

    In this study, we evaluated the effects of the extracts of the leaves of species from the Rubiaceae (Galium aparine L. and Asperula arvensis L.), Fabaceae (Lathyrus aphaca L. and Vicia narbonensis L.) and Poaceae (Digitaria sanguinalis (L.) Scop. and Hordeum murinum L.) plant families on a wide and extensive panel of isolated methicillin-resistant Staphylococcus aureus strains (MRSA). The effects of the methanolic leaf extracts of Rubiaceae, Fabaceae and Poaceae plants on MRSA were evaluated by the disc diffusion assay and the broth dilution method. Among a total of 177 S. aureus isolates, 92 (51.97%) were found to be methicillin-resistant in an antibiogram and this was confirmed by the presence of the mecA gene in polymerase chain reaction method. All MRSA isolates were sensitive to all extracts. There were dose-dependent inhibitions on tested microorganisms for all plant extracts which showed maximum inhibition zones at a concentration of 300 mg/L. L. aphaca, G. aparine and H. murinum exhibited the highest antibacterial activity on the MRSA strains compared to the positive control (P < 0.05), as well as higher total polyphenol and flavonoid contents than other plant extracts. Minimum inhibitory concentrations on MRSA isolates ranged from 388.4 ± 0.2 mg/L, in D. sanguinalis, to 5.5 ± 0.1 mg/L, in L. aphaca. The methanolic extracts of L. aphaca (Fabaceae), G. aparine (Rubiaceae), and H. murinum (Poaceae) proved to have high antibacterial activity on MRSA isolates, thus representing promising antimicrobial agents in clinical settings. PMID:27585260

  5. Anti-methicillin-resistant Staphylococcus aureus (MRSA) activity of Rubiaceae, Fabaceae and Poaceae plants: A search for new sources of useful alternative antibacterials against MRSA infections.

    PubMed

    Sharifi-Rad, M; Iriti, M; Sharifi-Rad, M; Gibbons, S; Sharifi-Rad, J

    2016-01-01

    In this study, we evaluated the effects of the extracts of the leaves of species from the Rubiaceae (Galium aparine L. and Asperula arvensis L.), Fabaceae (Lathyrus aphaca L. and Vicia narbonensis L.) and Poaceae (Digitaria sanguinalis (L.) Scop. and Hordeum murinum L.) plant families on a wide and extensive panel of isolated methicillin-resistant Staphylococcus aureus strains (MRSA). The effects of the methanolic leaf extracts of Rubiaceae, Fabaceae and Poaceae plants on MRSA were evaluated by the disc diffusion assay and the broth dilution method. Among a total of 177 S. aureus isolates, 92 (51.97%) were found to be methicillin-resistant in an antibiogram and this was confirmed by the presence of the mecA gene in polymerase chain reaction method. All MRSA isolates were sensitive to all extracts. There were dose-dependent inhibitions on tested microorganisms for all plant extracts which showed maximum inhibition zones at a concentration of 300 mg/L. L. aphaca, G. aparine and H. murinum exhibited the highest antibacterial activity on the MRSA strains compared to the positive control (P < 0.05), as well as higher total polyphenol and flavonoid contents than other plant extracts. Minimum inhibitory concentrations on MRSA isolates ranged from 388.4 ± 0.2 mg/L, in D. sanguinalis, to 5.5 ± 0.1 mg/L, in L. aphaca. The methanolic extracts of L. aphaca (Fabaceae), G. aparine (Rubiaceae), and H. murinum (Poaceae) proved to have high antibacterial activity on MRSA isolates, thus representing promising antimicrobial agents in clinical settings.

  6. Cloning, expression, crystallization and preliminary X-ray analysis of the XMT and DXMT N-methyltransferases from Coffea canephora (robusta)

    SciTech Connect

    McCarthy, Andrew A.; Biget, Laurent; Lin, Chenwei; Petiard, Vincent; Tanksley, Steve D.; McCarthy, James G.

    2007-04-01

    The genes encoding XMT and DXMT, the enzymes from Coffea canephora (robusta) that catalyse the three independent N-methyl transfer reactions in the caffeine-biosynthesis pathway, have been cloned and the proteins have been expressed in Escherichia coli. Both proteins have been crystallized in the presence of the demethylated cofactor S-adenosyl-l-cysteine (SAH) and substrate (xanthosine for XMT and theobromine for DXMT). Caffeine is a secondary metabolite produced by a variety of plants including Coffea canephora (robusta) and there is growing evidence that caffeine is part of a chemical defence strategy protecting young leaves and seeds from potential predators. The genes encoding XMT and DXMT, the enzymes from Coffea canephora (robusta) that catalyse the three independent N-methyl transfer reactions in the caffeine-biosynthesis pathway, have been cloned and the proteins have been expressed in Escherichia coli. Both proteins have been crystallized in the presence of the demethylated cofactor S-adenosyl-l-cysteine (SAH) and substrate (xanthosine for XMT and theobromine for DXMT). The crystals are orthorhombic, with space group P2{sub 1}2{sub 1}2{sub 1} for XMT and C222{sub 1} for DXMT. X-ray diffraction to 2.8 Å for XMT and to 2.5 Å for DXMT have been collected on beamline ID23-1 at the ESRF.

  7. Identification and mapping of a major gene (Ft1) involved in fructification time in the interspecific cross Coffea pseudozanguebariae x C. liberica var. Dewevrei: impact on caffeine content and seed weight.

    PubMed

    Akaffou, D S; Ky, C L; Barre, P; Hamon, S; Louarn, J; Noirot, M

    2003-05-01

    Fructification time was studied in the interspecific cross Coffea pseudozanguebariae x C. liberica var. Dewevrei (PSE x DEW). Parental species, F(1) hybrids and offspring of the first backcross generation (BC(1)), consisting of F(1) x PSE (BCPSE) and F(1) x DEW (BCDEW) plants, were observed. Fructification time can be split into two independent visual phases: the full-growth period, from blooming up to the end of fruit growth, and the maturation phase, defined by the green to red color change. Fructification time was found to be an additive trait. The full-growth period showed a bimodal distribution in the BCDEW hybrid, suggesting the involvement of Ft1, a major gene that was mapped on linkage group E. The main effects of Ft1 were to lower caffeine content and 100-seed weight, without any impact on chlorogenic acid, trigonelline and sucrose contents. Two molecular markers were identified that bracket Ft1 and which could be used for early marker-assisted selection.

  8. Analgesic effect of iridoid glycosides from Paederia scandens (LOUR.) MERRILL (Rubiaceae) on spared nerve injury rat model of neuropathic pain.

    PubMed

    Liu, Mei; Zhou, Lanlan; Chen, Zhiwu; Hu, Caibiao

    2012-09-01

    Iridoid glycosides of Paederia scandens (IGPS) is a major active component isolated from traditional Chinese herb P. scandens (LOUR.) MERRILL (Rubiaceae). The aim of the present study was to investigate the analgesic effect of IGPS on spared nerve injury (SNI) model of neuropathic pain. The SNI model in rats was established by complete transection of the common peroneal and tibial distal branches of the sciatic nerve, leaving the sural branch intact. The mechanical withdrawal threshold (MWT) in response to mechanical stimulation was measured by electronic von Frey filaments on day 1 before operation and on days 1, 3, 5, 7, 10, and 14 after operation, respectively. Nitric oxide synthase (NOS) activity and nitric oxide (NO) production of spinal cord were measured by spectrophotometry and its cyclic guanosine monophosphate (cGMP) content by radioimmunoassay, mRNA expression of inducible NOS (iNOS) and protein kinase G type I (PKG-I, including PKG Ια and PKG Iβ) of spinal cord were analyzed by RT-PCR. There was a marked mechanical hypersensitivity response observed on day 1 after operation in SNI model, which accompanied with decreased MWT. Treatment with IGPS (70, 140, 280 mg/kg) significantly alleviated SNI-induced mechanical hypersensitivity response evidenced by increased MWT; as well as markedly decreased NOS activity, NO and cGMP levels. At the same time, IGPS (70, 140, 280 mg/kg) could also inhibit mRNA expression of iNOS, PKG Ια and PKG Iβ in the spinal cord. The results suggested that IGPS possesses antinociceptive effect, which may be partly related to the inhibition of NO/cGMP/PKG signaling pathway in the rat SNI model of neuropathic pain. PMID:22698486

  9. Evolution of growth habit, inflorescence architecture, flower size, and fruit type in Rubiaceae: its ecological and evolutionary implications.

    PubMed

    Razafimandimbison, Sylvain G; Ekman, Stefan; McDowell, Timothy D; Bremer, Birgitta

    2012-01-01

    During angiosperm evolution, innovations in vegetative and reproductive organs have resulted in tremendous morphological diversity, which has played a crucial role in the ecological success of flowering plants. Morindeae (Rubiaceae) display considerable diversity in growth form, inflorescence architecture, flower size, and fruit type. Lianescent habit, head inflorescence, small flower, and multiple fruit are the predominant states, but arborescent habit, non-headed inflorescence, large flower, and simple fruit states occur in various genera. This makes Morindeae an ideal model for exploring the evolutionary appearances and transitions between the states of these characters. We reconstructed ancestral states for these four traits using a bayesian approach and combined nuclear/chloroplast data for 61 Morindeae species. The aim was to test three hypotheses: 1) self-supporting habit is generally ancestral in clades comprising both lianescent and arborescent species; 2) changes from lianescent to arborescent habit are uncommon due to "a high degree of specialization and developmental burden"; 3) head inflorescences and multiple fruits in Morindeae evolved from non-headed inflorescences and simple fruits, respectively. Lianescent habit, head inflorescence, large flower, and multiple fruit are inferred for Morindeae, making arborescent habit, non-headed inflorescence, small flower, and simple fruit derived within the tribe. The rate of change from lianescent to arborescent habit is much higher than the reverse change. Therefore, evolutionary changes between lianescent and arborescent forms can be reversible, and their frequency and trends vary between groups. Moreover, these changes are partly attributed to a scarcity of host trees for climbing plants in more open habitats. Changes from large to small flowers might have been driven by shifts to pollinators with progressively shorter proboscis, which are associated with shifts in breeding systems towards dioecy. A single

  10. Life history traits and host specificity of Japanese Trachyaphthona species (Coleoptera:Chrysomelidae), candidates as biological control agents against skunk vine, Paederia foetida (Rubiaceae),in Southeastern U.S. & Hawaii.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Skunk vine, Paederia foetida (Rubiaceae), is native to Asia and has been recognized as an invasive weedy vine of natural areas in Florida and Hawaii. It has overgrown on native vegetation and caused serious damage. The USDA Agricultural Research Service has been considering use of Trachyaphthona sor...

  11. Inter-genomic DNA Exchanges and Homeologous Gene Silencing Shaped the Nascent Allopolyploid Coffee Genome (Coffea arabica L.)

    PubMed Central

    Lashermes, Philippe; Hueber, Yann; Combes, Marie-Christine; Severac, Dany; Dereeper, Alexis

    2016-01-01

    Allopolyploidization is a biological process that has played a major role in plant speciation and evolution. Genomic changes are common consequences of polyploidization, but their dynamics over time are still poorly understood. Coffea arabica, a recently formed allotetraploid, was chosen to study genetic changes that accompany allopolyploid formation. Both RNA-seq and DNA-seq data were generated from two genetically distant C. arabica accessions. Genomic structural variation was investigated using C. canephora, one of its diploid progenitors, as reference genome. The fate of 9047 duplicate homeologous genes was inferred and compared between the accessions. The pattern of SNP density along the reference genome was consistent with the allopolyploid structure. Large genomic duplications or deletions were not detected. Two homeologous copies were retained and expressed in 96% of the genes analyzed. Nevertheless, duplicated genes were found to be affected by various genomic changes leading to homeolog loss or silencing. Genetic and epigenetic changes were evidenced that could have played a major role in the stabilization of the unique ancestral allotetraploid and its subsequent diversification. While the early evolution of C. arabica mainly involved homeologous crossover exchanges, the later stage appears to have relied on more gradual evolution involving gene conversion and homeolog silencing. PMID:27440920

  12. Construction and characterization of a BAC library from the Coffea arabica genotype Timor Hybrid CIFC 832/2.

    PubMed

    Cação, S M B; Silva, N V; Domingues, D S; Vieira, L G E; Diniz, L E C; Vinecky, F; Alves, G S C; Andrade, A C; Carpentieri-Pipolo, V; Pereira, L F P

    2013-06-01

    Most of the world's coffee production originates from Coffea arabica, an allotetraploid species with low genetic diversity and for which few genomic resources are available. Genomic libraries with large DNA fragment inserts are useful tools for the study of plant genomes, including the production of physical maps, integration studies of physical and genetic maps, genome structure analysis and gene isolation by positional cloning. Here, we report the construction and characterization of a Bacterial Artificial Chromosome (BAC) library from C. arabica Timor Hybrid CIFC 832/2, a parental genotype for several modern coffee cultivars. The BAC library consists of 56,832 clones with an average insert size of 118 kb, which represents a dihaploid genome coverage of five to sixfold. The content of organellar DNA was estimated at 1.04 and 0.5 % for chloroplast and mitochondrial DNA, respectively. The BAC library was screened for the NADPH-dependent mannose-6-phosphate reductase gene (CaM6PR) with markers positioned on four linkage groups of a partial C. arabica genetic map. A mixed approach using PCR and membrane hybridization of BAC pools allowed for the discovery of nine BAC clones with the CaM6PR gene and 53 BAC clones that were anchored to the genetic map with simple sequence repeat markers. This library will be a useful tool for future studies on comparative genomics and the identification of genes and regulatory elements controlling major traits in this economically important crop species.

  13. Aluminum induces changes in oxidative burst scavenging enzymes in Coffea arabica L. suspension cells with differential Al tolerance.

    PubMed

    Ramírez-Benítez, José Efraín; Muñoz-Sánchez, J Armando; Becerril-Chi, Karen M; Miranda-Ham, María de Lourdes; Castro-Concha, Lizbeth A; Hernández-Sotomayor, S M Teresa

    2011-11-01

    The accumulation of reactive oxygen species (ROS) and concomitant oxidative stress have been considered deleterious consequences of aluminum toxicity. However, several lines of evidence suggest that ROS can function as important signaling molecules in the plant defense system for protection from abiotic stress and the acquisition of tolerance. The role of ROS-scavenging enzymes was assayed in two different coffee cell suspension lines. We treated L2 (Al-sensitive) and LAMt (Al-tolerant) Coffea arabica suspension cells with 100 μM AlCl(3) and observed significant differences in catalase activity between the two cell lines. However, we did not observe any differences in superoxide dismutase or glutathione reductase activity in either cell line following Al treatment. ROS production was diminished in the LAMt cell line. Taken together, these results indicate that aluminum treatment may impair the oxidative stress response in L2 cells but not in LAMt cells. We suggest a possible role for Al-induced oxidative bursts in the signaling pathways that lead to Al resistance and protection from Al toxicity.

  14. The effect of irrigation on synchronization of coffee ( Coffea arabica L.) flowering and berry ripening at Chipinge, Zimbabwe

    NASA Astrophysics Data System (ADS)

    Masarirambi, M. T.; Chingwara, V.; Shongwe, V. D.

    Coffee ( Coffea arabica L.) is a short day plant that flowers and ripens irregularly in many subtropical and tropical production areas. This results in a prolonged, laborious and tiresome hand harvesting period which can potentially compromise coffee quality. Synchronising or scheduling the ripening of coffee berries can help in reducing harvesting costs through reduction of the number of cycles and harvest trips. This study was carried out to assess the quantity and frequency of irrigation, on stimulation of early, uniform flowering and berry ripening of coffee in order to reduce harvesting trips. High soil moisture depletion (25 cb or 30 cb) followed with increased irrigation levels resulted in increased number of flowers and subsequent number of berries per bunch at given assessment dates. Moisture depletion levels of 25 cb or 30 cb followed by application of 20 l or 25 l of water per tree advanced coffee flowering and subsequent berry ripening in this experiment when compared to other moisture depletion levels followed by application of 15 l of water per tree.

  15. Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures.

    PubMed

    Combes, Marie-Christine; Dereeper, Alexis; Severac, Dany; Bertrand, Benoît; Lashermes, Philippe

    2013-10-01

    Polyploidy has occurred throughout the evolutionary history of plants and led to diversification and plant ecological adaptation. Functional plasticity of duplicate genes is believed to play a major role in the environmental adaptation of polyploids. In this context, we characterized genome-wide homoeologous gene expression in Coffea arabica, a recent allopolyploid combining two subgenomes that derive from two closely related diploid species, and investigated its variation in response to changing environment. The transcriptome of leaves of C. arabica cultivated at different growing temperatures suitable for one or the other parental species was examined using RNA-sequencing. The relative contribution of homoeologs to gene expression was estimated for 9959 and 10,628 genes in warm and cold conditions, respectively. Whatever the growing conditions, 65% of the genes showed equivalent levels of homoeologous gene expression. In 92% of the genes, relative homoeologous gene expression varied < 10% between growing temperatures. The subgenome contributions to the transcriptome appeared to be only marginally altered by the different conditions (involving intertwined regulations of homeologs) suggesting that C. arabica's ability to tolerate a broader range of growing temperatures than its diploid parents does not result from differential use of homoeologs. PMID:23790161

  16. Trueness-to-type and agronomic characteristics of Coffea arabica trees micropropagated by the embryogenic cell suspension technique.

    PubMed

    Etienne, H; Bertrand, B

    2001-09-01

    Trueness-to-type and agronomic characteristics of trees of four coffee (Coffea arabica L.) F(1) hybrid clones derived from embryogenic cell suspensions were compared with those of trees produced from in vitro microcuttings. Three types of variants were observed among the 644 trees derived from embryogenic suspensions. Total frequency of the variants was 2.1% for trees originating from embryogenic cell suspensions, whereas no variant was found among the trees produced from microcuttings. The variant known as "thick leaf" had thick leaves, many abnormally starry flowers and low yields of large fruit. The "dwarf" variant was characterized by slow growth and small fruit. The "dwarf peaberry" variant had abnormal seeds in a single cavity, in addition to the "thick leaf" and "dwarf" characteristics. Compared with normal trees, the variants differed in leaf density and number of chloroplasts per guard cell. The variants aside, there were no differences in the main agronomic characteristics between trees produced from embryogenic suspensions and those produced from microcuttings. For all four clones, the trees had vegetative characteristics, productivity, fertility, and bean biochemical, mineral and organoleptic characteristics that were identical to those of the controls. We conclude that it is possible to generate coffee trees commercially with normal agronomic performance from embryogenic suspensions, because the frequency with which somaclonal variants occur is limited.

  17. The location of aluminium in protoplasts and suspension cells taken from Coffea arabica L. with different tolerance of Al.

    PubMed

    Ramírez-Benítez, J Efraín; Hernández-Sotomayor, S M Teresa; Muñoz-Sánchez, J Armando

    2009-11-01

    Biotechnological advances in coffee research (in vitro manipulation, multiplication, generation and development of transgenic coffee plants with specific traits like high yield and good quality) have contributed to description of the metabolic pathways involved in the response mechanisms to environmental factors like abiotic stress. Coffea arabica L. plants grow in acidic soils, and therefore aluminium (Al) toxicity is a major negative impact on crop productivity. To understand Al toxicity mechanisms in cells via the Al absorption kinetic, we isolated protoplasts from two C. arabica L. suspension cell lines: Al-sensitive (L2) and Al-tolerant (LAMt). Protoplasts of LAMt line exhibited lower Al absorption levels than protoplasts of the L2 line. Use of two fluorescent tracers (morin and calcofluor white) indicated that Al interacts with internal cell structures, such as the plasma membrane and nucleus, with differences in both cell lines. Al-tolerance in the LAMt is probably associated with the cell wall as well as intracellular structures. These data will help to better understand Al toxicity in C. arabica, and Al toxicity mechanisms in plant cells.

  18. Coprosma kawaikiniensis (Rubiaceae) a new species from the Dubautia-Sadleria shrubland-fernland community on Kaua'i, Hawaiian Islands.

    PubMed

    Wood, Kenneth R; Lorence, David H; Kiehn, Michael

    2016-01-01

    Coprosma kawaikiniensis K.R. Wood, Lorence & Kiehn (Rubiaceae), a rare endemic tree from Kaua'i, Hawaiian Islands, is described and illustrated along with a previously undescribed endemic plant community, the Dubautia-Sadleria shrubland-fernland (DSSF). The new species differs from Hawai'i congeners by its combination of opposite, long, elliptic to narrowly elliptic or ovate-elliptic leaves with revolute margins; caducous stipules 7-10 mm long, externally glabrous, densely hirtellous-pilose near the margins of the inner surface; unbranched inflorescences with peduncles 20-28 mm long; flowers 6-8 per cluster; and persistent calyx tube with 4-8 irregular dentate lobes. Known only from the windward slopes and ridges of southeastern Kaua'i below the Kawaikini summit, Coprosma kawaikiniensis falls into the IUCN Critically Endangered (CR) Red List category. PMID:27081342

  19. Coprosma kawaikiniensis (Rubiaceae) a new species from the Dubautia-Sadleria shrubland-fernland community on Kaua‘i, Hawaiian Islands

    PubMed Central

    Wood, Kenneth R.; Lorence, David H.; Kiehn, Michael

    2016-01-01

    Abstract Coprosma kawaikiniensis K.R. Wood, Lorence & Kiehn (Rubiaceae), a rare endemic tree from Kaua‘i, Hawaiian Islands, is described and illustrated along with a previously undescribed endemic plant community, the Dubautia-Sadleria shrubland-fernland (DSSF). The new species differs from Hawai‘i congeners by its combination of opposite, long, elliptic to narrowly elliptic or ovate-elliptic leaves with revolute margins; caducous stipules 7–10 mm long, externally glabrous, densely hirtellous-pilose near the margins of the inner surface; unbranched inflorescences with peduncles 20–28 mm long; flowers 6–8 per cluster; and persistent calyx tube with 4–8 irregular dentate lobes. Known only from the windward slopes and ridges of southeastern Kaua‘i below the Kawaikini summit, Coprosma kawaikiniensis falls into the IUCN Critically Endangered (CR) Red List category. PMID:27081342

  20. Pollinators of Richardia grandiflora (Rubiaceae): an Important Ruderal Species for Bees.

    PubMed

    Cruz, R M; Martins, C F

    2015-02-01

    Ruderal species may provide pollen and nectar to maintain the pollinators of crops in periods of floral resource shortage. The knowledge about the floral biology of these plant species and their interaction with insects is important for management strategies of agricultural systems. The study was carried out at an experimental research station in two different periods (August 2010-April 2011 and August 2012-January 2013). Floral biology was studied, and the reproductive system and reproductive efficacy (RE) were analyzed using controlled pollination experiments. Furthermore, floral visitors and pollination were identified and quantified. Reproductive success obtained in the open pollination and cross-pollination experiments was higher than those obtained in spontaneous self, hand self, and wind pollination. Richardia grandiflora bloomed throughout the experimental period, and flowers were visited by Coleoptera, Diptera, Hymenoptera, and Lepidoptera, which were observed foraging for pollen and/or nectar. Among the floral visitors, bees were the richest and most frequent group and often contacted anthers and stigmas during visits. Africanized honeybees touched the floral reproductive structures in all visits, and their frequency may be related to changes in the reproductive efficacy between the study periods. Pollinator species of crops cultivated at the experimental research station were frequent bee visitors of R. grandiflora. We demonstrated that R. grandiflora requires cross-pollination and biotic pollen vectors. Among floral visitors, bees are the main pollinators, especially the Africanized honeybees. R. grandiflora can be considered an important ruderal species for maintaining bee pollinator populations at the study site, providing resources during the period that crops are not blooming.

  1. Nueva dieta artificial para la producción masiva de Phymastichus Coffea (Himenóptera: Eulophidae) parasitoide de la broca del café, Hypothenemus hampei (Coleoptera: Scolytidae).

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phymastichus coffea (La Salle), (Hymenoptera: Eulophydae) is a parasitic wasp that attacks the adult coffee berry borer, Hypothenemus hampei (Ferrari) when it is tunnel into the berry. In 2001 a small colony of this parasitoid was introduced from CENICAFE, Colombia into United States to develop an i...

  2. The effects of nutrients and secondary compounds of Coffea arabica on the behavior and development of Coccus viridis.

    PubMed

    Fernandes, F L; Picanço, M C; Fernandes, M E S; Queiroz, R B; Xavier, V M; Martinez, H E P

    2012-04-01

    Phytochemicals may modify the food quality, reduce a plant's palatability to insects, or defend against pests. This work aimed to study 1) relationships between the nitrogen and potassium levels given to plants in nutritive solutions and the foliar phytochemical concentrations, 2) the effect of nutrients and secondary compounds of Coffea arabica on the behavior of Coccus viridis, and 3) tolerance of C. arabica to losses. Deficient, normal, and excessive nitrogen and potassium fertilization treatments were used. Each treatment had two plants (one infested and one noninfested plant). The contents of phytochemicals in the infested plants' leaves and their dry matter of roots, stems, and leaves as well as the total contents in noninfested plants, were determined. The adults and nymphs of C. viridis were counted for 60 d in all treatments. It was verified that elevated nitrogen and potassium levels in the nutritional solutions led to increased of nymphs and adults of C. viridis to the coffee plants over time. Potassium and nitrogen had both direct and indirect effects on C. viridis. The direct effect was because of the increase of the nitrogen content in the leaves. The indirect effect instead was because of reductions in the caffeine and chlorogenic acid contents in the leaves. This is the first study to show relationship nutrient levels of coffee phytochemicals in response to herbivory by scale insects. Caffeine and chlorogenic acid applied on coffee leaves stimulated the locomotory activity of the green scale, thus reducing their feeding compared with untreated leaves. The elevation of caffeine and chlorogenic acid levels in coffee leaves affect this generalist insect by stimulating the locomotion of crawlers.

  3. The effects of nutrients and secondary compounds of Coffea arabica on the behavior and development of Coccus viridis.

    PubMed

    Fernandes, F L; Picanço, M C; Fernandes, M E S; Queiroz, R B; Xavier, V M; Martinez, H E P

    2012-04-01

    Phytochemicals may modify the food quality, reduce a plant's palatability to insects, or defend against pests. This work aimed to study 1) relationships between the nitrogen and potassium levels given to plants in nutritive solutions and the foliar phytochemical concentrations, 2) the effect of nutrients and secondary compounds of Coffea arabica on the behavior of Coccus viridis, and 3) tolerance of C. arabica to losses. Deficient, normal, and excessive nitrogen and potassium fertilization treatments were used. Each treatment had two plants (one infested and one noninfested plant). The contents of phytochemicals in the infested plants' leaves and their dry matter of roots, stems, and leaves as well as the total contents in noninfested plants, were determined. The adults and nymphs of C. viridis were counted for 60 d in all treatments. It was verified that elevated nitrogen and potassium levels in the nutritional solutions led to increased of nymphs and adults of C. viridis to the coffee plants over time. Potassium and nitrogen had both direct and indirect effects on C. viridis. The direct effect was because of the increase of the nitrogen content in the leaves. The indirect effect instead was because of reductions in the caffeine and chlorogenic acid contents in the leaves. This is the first study to show relationship nutrient levels of coffee phytochemicals in response to herbivory by scale insects. Caffeine and chlorogenic acid applied on coffee leaves stimulated the locomotory activity of the green scale, thus reducing their feeding compared with untreated leaves. The elevation of caffeine and chlorogenic acid levels in coffee leaves affect this generalist insect by stimulating the locomotion of crawlers. PMID:22507006

  4. Functional characterization of three Coffea arabica L. monoterpene synthases: insights into the enzymatic machinery of coffee aroma.

    PubMed

    Del Terra, Lorenzo; Lonzarich, Valentina; Asquini, Elisa; Navarini, Luciano; Graziosi, Giorgio; Suggi Liverani, Furio; Pallavicini, Alberto

    2013-05-01

    The chemical composition of the coffee beverage is extremely complex, being made up of hundreds of volatile and non-volatile compounds, many of which are generated in the thermal reactions that occur during the roasting process. However, in the raw coffee bean there are also compounds that survive roasting and are therefore extracted into the beverage. Monoterpenes are an example of this category, as their presence has been reported in the coffee flower, fruit, seed, roasted bean and in the beverage aroma. The present work describes the isolation, heterologous expression and functional characterization of three Coffea arabica cDNAs coding for monoterpene synthases. RNA was purified from C. arabica (cv. Catuai Red) flowers, seeds and fruits at 4 successive ripening stages. Degenerate primers were designed on the most conserved regions of the monoterpene synthase gene family, and then used to isolate monoterpene synthase-like sequences from the cDNA libraries. After 5'- and 3'-RACE, the complete transcripts of 4 putative C. arabica monoterpene synthases (CofarTPS) were obtained. Gene expression in different tissues and developmental stages was analysed. After heterologous expression in Escherichia coli, enzyme activity and substrate specificity were evaluated in vitro by incubation of the recombinant proteins with geranyl pyrophosphate (GPP), geranylgeranyl pyrophosphate (GGPP) and farnesyl pyrophosphate (FPP), precursors respectively of mono-, di- and sesquiterpenes. The reaction products were characterized by HS-SPME GC-MS. CofarTPS1 was classified as a limonene synthase gene, while CofarTPS2 and 3 showed lower activity with the production of linalool and β-myrcene.

  5. Deciphering transcriptional networks that govern Coffea arabica seed development using combined cDNA array and real-time RT-PCR approaches.

    PubMed

    Salmona, Jordi; Dussert, Stéphane; Descroix, Frédéric; de Kochko, Alexandre; Bertrand, Benoît; Joët, Thierry

    2008-01-01

    Due to its economic importance, Coffea arabica is becoming the subject of increasing genomic research and, in particular, the genes involved in the final chemical composition of the bean and the sensorial quality of the coffee beverage. The aim of the present study was to decipher the transcriptional networks that govern the development of the C. arabica seed, a model for non-orthodox albuminous seeds of tropical origin. For this purpose, we developed a transcriptomic approach combining two techniques: targeted cDNA arrays, containing 266 selected candidate gene sequences, and real-time RT-PCR on a large subset of 111 genes. The combination of the two techniques allowed us to limit detection of false positives and to reveal the advantages of using large real-time RT-PCR screening. Multivariate analysis was conducted on both datasets and results were broadly convergent. First, principle component analysis (PCA) revealed a dramatic re-programming of the transcriptional machinery between early cell division and elongation, storage and maturation phases. Second, hierarchical clustering analysis (HCA) led to the identification of 11 distinct patterns of gene expression during seed development as well as to the detection of genes expressed at specific developmental stages that can be used as functional markers of phenological changes. In addition, this study led to the description of gene expression profiles for quality-related genes, most of them formerly uncharacterised in Coffea. Their involvement in storage compound synthesis and accumulation during endosperm development and final metabolic re-adjustments during maturation is discussed. PMID:18026845

  6. Inoculation of starter cultures in a semi-dry coffee (Coffea arabica) fermentation process.

    PubMed

    Evangelista, Suzana Reis; Miguel, Maria Gabriela da Cruz Pedrozo; Cordeiro, Cecília de Souza; Silva, Cristina Ferreira; Pinheiro, Ana Carla Marques; Schwan, Rosane Freitas

    2014-12-01

    The aim of this study was to evaluate the use of yeasts as starter cultures in coffee semi-dry processing. Arabica coffee was inoculated with one of the following starter cultures: Saccharomyces cerevisiae UFLA YCN727, S. cerevisiae UFLA YCN724, Candida parapsilosis UFLA YCN448 and Pichia guilliermondii UFLA YCN731. The control was not inoculated with a starter culture. Denaturing gradient gel electrophoresis (DGGE) was used to assess the microbial population, and organic acids and volatile compounds were quantified by HPLC and HS-SPME/GC, respectively. Sensory analyses were evaluated using the Temporal Dominance of Sensations (TDS). DGGE analysis showed that the inoculated yeasts were present throughout the fermentation. Other yeast species were also detected, including Debaryomyces hansenii, Cystofilobasidium ferigula and Trichosporon cavernicola. The bacterial population was diverse and was composed of the following genera: Weissella, Leuconostoc, Gluconobacter, Pseudomonas, Pantoea, Erwinia and Klebsiella. Butyric and propionic acids, were not detected in any treatment A total of 47 different volatiles compounds have been identified. The coffee inoculated with yeast had a caramel flavor that was not detected in the control, as assessed by TDS. The use of starter cultures during coffee fermentation is an interesting alternative for obtaining a beverage quality with distinctive flavor. PMID:25084650

  7. Protective effect of iridoid glycosides from Paederia scandens (LOUR.) MERRILL (Rubiaceae) on uric acid nephropathy rats induced by yeast and potassium oxonate.

    PubMed

    Hou, Shi-xiang; Zhu, Wen-jing; Pang, Ming-qun; Jeffry, Joseph; Zhou, Lan-lan

    2014-02-01

    Iridoid glycosides of Paederia scandens (IGPS) are an active component isolated from Chinese herb P. scandens (LOUR.) MERRILL (Rubiaceae). Uric acid nephropathy (UAN) is caused by excessive uric acid, which results in damage of kidney tissue via urate crystals deposition in the kidneys. This study aimed to investigate the protective effects of IGPS on UAN in rats induced by yeast and potassium oxonate. Treatment groups received different doses of IGPS and allopurinol (AP) daily for 35 days respectively. The results showed that treatment with IGPS significantly prevented the increases of uric acid in serum and the elevation of systolic blood pressure (SBP), attenuated renal tissue injury, improved renal function and reserved the biological activity of NOS-1. IGPS also inhibited the biological activity of TNF-α and TGF-β1, and suppressed the mRNA expressions of TNF-α and TGF-β1 in renal tissue. Taken together, the present and our previous findings suggest that IGPS exerts protective effects against kidney damage in UAN rats through its uric acid-lowering, anti-inflammatory and immunomodulatory properties. Furthermore, decreasing SBP by up regulation of NOS-1 expression and down regulation of TNF-α and TGF-β1 expression are involved in the effect of IGPS on high uric acid-induced nephropathy. PMID:24287205

  8. Genetic Variability of the Narrow Endemic Tree Antirhea aromatica Castillo‐Campos & Lorence, (Rubiaceae, Guettardeae) in a Tropical Forest of Mexico

    PubMed Central

    GONZÁLEZ‐ASTORGA, JORGE; CASTILLO‐CAMPOS, GONZALO

    2004-01-01

    • Background and Aims Genetic structure and variability were examined in the only three extant populations of the narrow‐endemic tree Antirhea aromatica (Rubiaceae, Guettardeae), an endangered species of the tropical forest of eastern Mexico. Patterns of genetic diversity within and among populations for adult plants and seedlings were obtained. • Methods Allozyme electrophoresis of 15 loci was conducted and the data analysed with statistical approximation for obtaining genetic diversity, structure and gene flow. • Key Results The mean expected heterozygosity (He) in the adult and seedling populations was 0·18 ± 0·08 and 0·20 ± 0·09, respectively. The genetic variation explained by differences among populations was 51 and 35 %, for adult and seedling populations, respectively. On average, gene flow between paired adult populations was low (Nm = 0·26 ± 0·09), compared with other trees from the tropical forest. • Conclusions The results indicated that the populations evaluated have high genetic variability, compared with other endemic and geographically narrowly distributed plant species, in areas with high levels of environmental heterogeneity (e.g. tropical forests). The conservation implications of the results are discussed, and in this regard it is proposed that A. aromatica should be considered as an indicator species with economic potential. It is suggested that sustainable management practices should be implemented and that the areas where the species is distributed should be declared a natural reserve to ensure the species conservation. PMID:15056561

  9. Photochemical efficiency of adult and young leaves of the neotropical understory shrub Psychotria limonensis (Rubiaceae) in response to changes in the light environment.

    PubMed

    Avalos, Gerardo; Mulkey, Stephen S

    2004-12-01

    We explored the short-term adjustment in photochemical efficiency (Fv/Fm) in adult and young leaves of the understory neotropical shrub Psychotria limonensis Krause (Rubiaceae) in response to rapid changes in the light environment. Leaves were collected from 20 individual plants growing under sun and shade conditions on Gigante Peninsula, Barro Colorado Natural Monument (Republic of Panama), during the wet season of 1996. Leaves were distributed in four sequences of light treatments (AB leaves were expanded under sun and were transferred to shade, BA leaves experienced the opposite transfer, and the controls AA and BB leaves that were expanded and maintained under sun or shade conditions). Adult and young leaves did not differ in overall photochemical efficiency. Instead, differences were found among light environments, for which leaves transferred from shade to sun showed the lowest Fv/Fm ratios. There was no relationship between photochemical efficiency and leaf temperature. In P. limonensis, understory plants are susceptible of photoinhibition independently of the leaf ontogenetic stage. The approach utilized in this experiment allowed the rapid exploration of this capacity, and could be applied to poorly studied understory species.

  10. Isolation and Characterization of cDNA Encoding Three Dehydrins Expressed During Coffea canephora (Robusta) Grain Development

    PubMed Central

    HINNIGER, CÉCILE; CAILLET, VICTORIA; MICHOUX, FRANCK; BEN AMOR, MOHAMED; TANKSLEY, STEVE; LIN, CHENWEI; MCCARTHY, JAMES

    2006-01-01

    • Background and Aims Dehydrins, or group 2 late embryogenic abundant proteins (LEA), are hydrophilic Gly-rich proteins that are induced in vegetative tissues in response to dehydration, elevated salt, and low temperature, in addition to being expressed during the late stages of seed maturation. With the aim of characterizing and studying genes involved in osmotic stress tolerance in coffee, several full-length cDNA-encoding dehydrins (CcDH1, CcDH2 and CcDH3) and an LEA protein (CcLEA1) from Coffea canephora (robusta) were isolated and characterized. • Methods The protein sequences deduced from the full-length cDNA were analysed to classify each dehydrin/LEA gene product and RT–PCR was used to determine the expression pattern of all four genes during pericarp and grain development, and in several other tissues of C. arabica and C. canephora. Primer-assisted genome walking was used to isolate the promoter region of the grain specific dehydrin gene (CcDH2). • Key Results The CcDH1 and CcDH2 genes encode Y3SK2 dehydrins and the CcDH3 gene encodes an SK3 dehydrin. CcDH1 and CcDH2 are expressed during the final stages of arabica and robusta grain development, but only the CcDH1 transcripts are clearly detected in other tissues such as pericarp, leaves and flowers. CcDH3 transcripts are also found in developing arabica and robusta grain, in addition to being detected in pericarp, stem, leaves and flowers. CcLEA1 transcripts were only detected during a brief period of grain development. Finally, over 1 kb of genomic sequence potentially encoding the entire grain-specific promoter region of the CcDH2 gene was isolated and characterized. • Conclusions cDNA sequences for three dehydrins and one LEA protein have been obtained and the expression of the associated genes has been determined in various tissues of arabica and robusta coffees. Because induction of dehydrin gene expression is associated with osmotic stress in other plants, the dehydrin sequences

  11. The epidermal cell structure of the secondary pollen presenter in Vangueria infausta (Rubiaceae: Vanguerieae) suggests a functional association with protruding onci in pollen grains.

    PubMed

    Tilney, Patricia M; van Wyk, Abraham E; van der Merwe, Chris F

    2014-01-01

    Secondary pollen presentation is a well-known phenomenon in the Rubiaceae with particularly conspicuous pollen presenters occurring in the tribe Vanguerieae. These knob-like structures are formed by a modification of the upper portion of the style and stigma, together known as the stylar head complex. In the flower bud and shortly before anthesis, the anthers surrounding the stylar head complex dehisce and release pollen grains which adhere to the pollen presenter. The epidermal cells of the pollen presenter facing the anthers are radially elongated with a characteristic wall thickening encircling the anticlinal walls of each cell towards the distal end. These cells were studied in the pollen presenter of Vangueria infausta using electron and light microscopy in conjunction with histochemical tests and immunohistochemical methods. Other prominent thickenings of the cell wall were also observed on the distal and proximal walls. All these thickenings were found to be rich in pectin and possibly xyloglucan. The terms "thickenings of Igersheim" and "bands of Igersheim" are proposed to refer, respectively, to these wall structures in general and those encircling the anticlinal walls of each cell near the distal end. The epidermal cells have an intricate ultrastructure with an abundance of organelles, including smooth and rough endoplasmic reticulum, Golgi apparatus, mitochondria and secretory vesicles. This indicates that these cells are likely to have an active physiological role. The pollen grains possess prominent protruding onci and observations were made on their structure and development. Walls of the protruding onci are also rich in pectin. Pectins are hydrophilic and known to be involved in the dehydration and rehydration of pollen grains. We hypothesise that the thickenings of Igersheim, as well as the protruding onci of the pollen grains, are functionally associated and part of the adaptive syndrome of secondary pollen presentation, at least in the Vanguerieae.

  12. Effects of a lyophilized aqueous extract of Feretia apodanthera Del. (Rubiaceae) on pentylenetetrazole-induced kindling, oxidative stress, and cognitive impairment in mice.

    PubMed

    Taiwe, G S; Moto, F C O; Ayissi, E R M; Ngoupaye, G T; Njapdounke, J S K; Nkantchoua, G C N; Kouemou, N; Omam, J P O; Kandeda, A K; Pale, S; Pahaye, D; Ngo Bum, E

    2015-02-01

    Feretia apodanthera Del. (Rubiaceae) is extensively used in ethnomedicine in Cameroon and Nigeria for epilepsy, febrile convulsions, and rheumatic pains and for enhancing cognitive performance. The aim of the present study was to examine the effects of a lyophilized aqueous extract of F. apodanthera on the course of kindling development, kindling-induced learning deficit, oxidative stress markers, and cholinesterase activity in pentylenetetrazole (PTZ)-kindled mice. Pentylenetetrazole, 30mg/kg, induced kindling in mice after 30.00±1.67days. The aqueous extract of F. apodanthera showed dose-dependent antiseizure effects. Feretia apodanthera (150-200mg/kg) significantly increased the latency to myoclonic jerks, clonic seizures, and generalized tonic-clonic seizures. The extract also improved the seizure score and decreased the number of myoclonic jerks. Pentylenetetrazole kindling induced significant oxidative stress and cognitive impairment which were reversed by pretreatment with F. apodanthera in a dose-dependent manner. The significant decrease in cholinesterase activity observed in the PTZ-kindled mice was reversed by pretreatment with the F. apodanthera extract. The results indicated that pretreatment with the aqueous extract of F. apodanthera antagonizes seizures, oxidative stress, and cognitive impairment in PTZ-kindled mice. The aqueous extract of F. apodanthera also showed anxiolytic activities, but the inhibition of memory impairment was not attributed to the anxiolytic activities of the plant. These results thus suggest the potential of F. apodanthera as an adjuvant in epilepsy both to prevent seizures as well as to protect against seizure-induced oxidative stress and memory impairment.

  13. Diversity and endemism in deglaciated areas: ploidy, relative genome size and niche differentiation in the Galium pusillum complex (Rubiaceae) in Northern and Central Europe

    PubMed Central

    Kolář, Filip; Lučanová, Magdalena; Vít, Petr; Urfus, Tomáš; Chrtek, Jindřich; Fér, Tomáš; Ehrendorfer, Friedrich; Suda, Jan

    2013-01-01

    Background and Aims Plants endemic to areas covered by ice sheets during the last glaciation represent paradigmatic examples of rapid speciation in changing environments, yet very few systems outside the harsh arctic zone have been comprehensively investigated so far. The Galium pusillum aggregate (Rubiaceae) is a challenging species complex that exhibits a marked differentiation in boreal parts of Northern Europe. As a first step towards understanding its evolutionary history in deglaciated regions, this study assesses cytological variation and ecological preferences of the northern endemics and compares the results with corresponding data for species occurring in neighbouring unglaciated parts of Central and Western Europe. Methods DNA flow cytometry was used together with confirmatory chromosome counts to determine ploidy levels and relative genome sizes in 1158 individuals from 181 populations. A formalized analysis of habitat preferences was applied to explore niche differentiation among species and ploidy levels. Key Results The G. pusillum complex evolved at diploid and tetraploid levels in Northern Europe, in contrast to the high-polyploid evolution of most other northern endemics. A high level of eco-geographic segregation was observed between different species (particularly along gradients of soil pH and competition) which is unusual for plants in deglaciated areas and most probably contributes to maintaining species integrity. Relative monoploid DNA contents of the species from previously glaciated regions were significantly lower than those of their counterparts from mostly unglaciated Central Europe, suggesting independent evolutionary histories. Conclusions The aggregate of G. pusillum in Northern Europe represents an exceptional case with a geographically vicariant and ecologically distinct diploid/tetraploid species endemic to formerly glaciated areas. The high level of interspecific differentiation substantially widens our perception of the

  14. The toxicity of a lipid transfer protein (Cc-LTP1) from Coffea canephora Seeds on the larval development of Callosobruchus maculatus (Coleoptera: Bruchidae).

    PubMed

    Zottich, Umberto; Da Cunha, Maura; Dias, Germana B; Rabelo, Guilherme R; Oliveira, Antonia Elenir A; Carvalho, André O; Fernandes, Kátia Valevski S; do Nascimento, Viviane V; Gomes, Valdirene M

    2014-10-01

    In this work, we analyzed the effects of coffee seed proteins, especially Cc-LTP1 on the larval development of Callosobruchus maculatus (F.) (Coleoptera: Bruchidae), a bruchid pest of beans and the most important insect pest of Vigna unguiculata (L.) Walp. Artificial seed assay, which incorporated the F/0-90 fraction from Coffea canephora seeds, resulted in the reduction of oviposition and caused an inhibition of C. maculatus larval development in a dose-dependent manner. The F/0-90 fraction used at a 4 % concentration resulted in the survival of no larvae. The purified Cc-LTP1, at a concentration of 0.5 %, also demonstrated effective inhibition of larval development, reducing both females oviposition and the weight and number of larvae. Cc-LTP1 was also able to inhibit the C. maculatus gut α-amylase activity, and immunolabeling by an anti-LTP serum was observed in the midgut tissues of the C. maculatus larvae. Cc-LTP1 has shown binding affinity towards microvillar cells, endoplasmic reticulum and mitochondria, as demonstrated by micrographic images taken by a transmission electron microscope. The results from this study indicate that Cc-LTP1 has insecticidal actions toward C. maculatus and exerts anti-nutritional effects with direct actions on intestinal tissues.

  15. Abiotic stresses affect differently the intron splicing and expression of chloroplast genes in coffee plants (Coffea arabica) and rice (Oryza sativa).

    PubMed

    Nguyen Dinh, Sy; Sai, Than Zaw Tun; Nawaz, Ghazala; Lee, Kwanuk; Kang, Hunseung

    2016-08-20

    Despite the increasing understanding of the regulation of chloroplast gene expression in plants, the importance of intron splicing and processing of chloroplast RNA transcripts under stress conditions is largely unknown. Here, to understand how abiotic stresses affect the intron splicing and expression patterns of chloroplast genes in dicots and monocots, we carried out a comprehensive analysis of the intron splicing and expression patterns of chloroplast genes in the coffee plant (Coffea arabica) as a dicot and rice (Oryza sativa) as a monocot under abiotic stresses, including drought, cold, or combined drought and heat stresses. The photosynthetic activity of both coffee plants and rice seedlings was significantly reduced under all stress conditions tested. Analysis of the transcript levels of chloroplast genes revealed that the splicing of tRNAs and mRNAs in coffee plants and rice seedlings were significantly affected by abiotic stresses. Notably, abiotic stresses affected differently the splicing of chloroplast tRNAs and mRNAs in coffee plants and rice seedlings. The transcript levels of most chloroplast genes were markedly downregulated in both coffee plants and rice seedlings upon stress treatment. Taken together, these results suggest that coffee and rice plants respond to abiotic stresses via regulating the intron splicing and expression of different sets of chloroplast genes. PMID:27448724

  16. Characterization and expression of two cDNA encoding 3-Hydroxy-3-methylglutaryl coenzyme A reductase isoforms in coffee (Coffea arabica L.).

    PubMed

    Tiski, Iris; Marraccini, Pierre; Pot, David; Vieira, Luiz Gonzaga Esteves; Pereira, Luiz Filipe Protasio

    2011-10-01

    In higher plants there are two independent pathways for isoprenoid biosynthesis, located in the cytosol (mevalonic acid or MVA pathway) or in the plastids [methylerythritol phosphate (MEP) pathway]. The 3-hydroxy-3-methyglutaryl-CoA reductase (HMGR) is the first committed step in the MVA pathway. Using the information available from the Brazilian Coffee Genome Project, we found 13 ESTs that originated two isoforms, CaHMGR1 and CaHMGR2, for the enzyme HMGR of Coffea arabica. A complementary DNA encoding the isoform CaHMGR1 was cloned, and its complete nucleotide sequence determined. The full-length cDNA of CaHMGR1 was 2,242 bp containing a 1,812-bp ORF encoding 604 amino acids. Bioinformatic analyses revealed that the deduced CaHMGR1 had extensive homology with other plant HMGRs and contained two transmembrane domains and two putative HMGR binding sites and two NADP(H)-binding sites. Under normal growth conditions, transcripts of isoform CaHMRG1 were detected in fruit tissues (pulp, perisperm, and endosperm) only at the initial stages of development, flower buds and leaves. CaHMRG2 was expressed in all tissues and during all fruit development stages examined. These results suggest a constitutive expression of isoform CaHMGR2, while the isoform CaHMGR1 shows temporal and tissue-specific transcriptional activation.

  17. Phenylpropanoid enzymes, phenolic polymers and metabolites as chemical defenses to infection of Pratylenchus coffeae in roots of resistant and susceptible bananas (Musa spp.).

    PubMed

    Vaganan, M Mayil; Ravi, I; Nandakumar, A; Sarumathi, S; Sundararaju, P; Mustaffa, M M

    2014-03-01

    Activity differences of the first (phenylalanine ammonia lyase, PAL) and the last (cinnamyl alcohol dehydrogenase, CAD) enzymes of phenylpropanoid pathway in the roots of resistant (Yangambi Km5 and Anaikomban) and susceptible (Nendran and Robusta) banana cultivars caused by root lesion nematode, Pratylenchus coffeae, were investigated. Also, the accumulation of phenolics and deposition of lignin polymers in cell walls in relation to resistance of the banana cultivars to the nematode were analyzed. Compared to the susceptible cultivars, the resistant cultivars had constitutively significantly higher PAL activity and total soluble and cell wall-bound phenolics than in susceptible cultivars. The resistant cultivars responded strongly to the infection of the nematode by induction of several-time higher PAL and CAD enzymes activities, soluble and wall-bound phenolics and enrichment of lignin polymers in cell wall and these biochemical parameters reached maximum at 7th day postinoculation. In addition, profiles of phenolic acid metabolites in roots of Yangambi Km5 and Nendran were analyzed by HPLC to ascertain the underlying biochemical mechanism of bananas resistance to the nematode. Identification and quantification of soluble and cell wall-bound phenolic acids showed six metabolites and only quantitative, no qualitative, differences occurred between the resistant and susceptible cvs. and between constitutive and induced contents. A very prominent increase of p-coumaric, ferulic and sinapic acids, which are precursors of monolignols of lignin, in resistant cv. was found. These constitutive and induced biochemical alterations are definitely the chemical defenses of resistant cvs. to the nematode infection.

  18. The toxicity of a lipid transfer protein (Cc-LTP1) from Coffea canephora Seeds on the larval development of Callosobruchus maculatus (Coleoptera: Bruchidae).

    PubMed

    Zottich, Umberto; Da Cunha, Maura; Dias, Germana B; Rabelo, Guilherme R; Oliveira, Antonia Elenir A; Carvalho, André O; Fernandes, Kátia Valevski S; do Nascimento, Viviane V; Gomes, Valdirene M

    2014-10-01

    In this work, we analyzed the effects of coffee seed proteins, especially Cc-LTP1 on the larval development of Callosobruchus maculatus (F.) (Coleoptera: Bruchidae), a bruchid pest of beans and the most important insect pest of Vigna unguiculata (L.) Walp. Artificial seed assay, which incorporated the F/0-90 fraction from Coffea canephora seeds, resulted in the reduction of oviposition and caused an inhibition of C. maculatus larval development in a dose-dependent manner. The F/0-90 fraction used at a 4 % concentration resulted in the survival of no larvae. The purified Cc-LTP1, at a concentration of 0.5 %, also demonstrated effective inhibition of larval development, reducing both females oviposition and the weight and number of larvae. Cc-LTP1 was also able to inhibit the C. maculatus gut α-amylase activity, and immunolabeling by an anti-LTP serum was observed in the midgut tissues of the C. maculatus larvae. Cc-LTP1 has shown binding affinity towards microvillar cells, endoplasmic reticulum and mitochondria, as demonstrated by micrographic images taken by a transmission electron microscope. The results from this study indicate that Cc-LTP1 has insecticidal actions toward C. maculatus and exerts anti-nutritional effects with direct actions on intestinal tissues. PMID:25097041

  19. New insights into somatic embryogenesis: leafy cotyledon1, baby boom1 and WUSCHEL-related homeobox4 are epigenetically regulated in Coffea canephora.

    PubMed

    Nic-Can, Geovanny I; López-Torres, Adolfo; Barredo-Pool, Felipe; Wrobel, Kazimierz; Loyola-Vargas, Víctor M; Rojas-Herrera, Rafael; De-la-Peña, Clelia

    2013-01-01

    Plant cells have the capacity to generate a new plant without egg fertilization by a process known as somatic embryogenesis (SE), in which differentiated somatic cells can form somatic embryos able to generate a functional plant. Although there have been advances in understanding the genetic basis of SE, the epigenetic mechanism that regulates this process is still unknown. Here, we show that the embryogenic development of Coffea canephora proceeds through a crosstalk between DNA methylation and histone modifications during the earliest embryogenic stages of SE. We found that low levels of DNA methylation, histone H3 lysine 9 dimethylation (H3K9me2) and H3K27me3 change according to embryo development. Moreover, the expression of LEAFY cotyledon1 (LEC1) and BABY BOOM1 (BBM1) are only observed after SE induction, whereas WUSCHEL-related homeobox4 (WOX4) decreases its expression during embryo maturation. Using a pharmacological approach, it was found that 5-Azacytidine strongly inhibits the embryogenic response by decreasing both DNA methylation and gene expression of LEC1 and BBM1. Therefore, in order to know whether these genes were epigenetically regulated, we used Chromatin Immunoprecipitation (ChIP) assays. It was found that WOX4 is regulated by the repressive mark H3K9me2, while LEC1 and BBM1 are epigenetically regulated by H3K27me3. We conclude that epigenetic regulation plays an important role during somatic embryogenic development, and a molecular mechanism for SE is proposed.

  20. Involvement of a novel intronic microRNA in cross regulation of N-methyltransferase genes involved in caffeine biosynthesis in Coffea canephora.

    PubMed

    Mohanan, Shibin; Gowda, Kalpashree; Kandukuri, Satyanarayana V; Chandrashekar, Arun

    2013-04-25

    There are numerous reports on intronic miRNAs from plants, most of which are involved in the regulation of unrelated genes. Some of the target genes are antagonistic to the host genes. Intronic miRNAs in animal systems, however, are known to have synergistic effects. This article is the first to report a similar regulatory effect of a miRNA originating from an intron in plants. NMT genes involved in caffeine biosynthesis were silenced to obtain transformants with reduced caffeine. Transcript analysis revealed the accumulation of transcripts for a related NMT gene (CaMTL1) in transformants bearing either antisense or RNAi constructs. The altered expression was assumed to relate to the silencing of the NMT genes. Bioinformatics analysis of the genes involved in biosynthesis revealed the presence of an intronic miRNA originating from the intron of the theobromine synthase gene targeting CaMTL1. The putative miRNA was cloned and sequenced. Modified 5'-RLM-RACE mapping of the cleavage site and subsequent Northern blotting experimentally demonstrated the presence and activity of such a miRNA in Coffea canephora. This novel regulatory mechanism previously unreported in plants will shed more light onto the evolution of multigene families and the role of introns in this process.

  1. In vitro nematicidal activity of extracts of Canthium mannii (Rubiaceae), on different life-cycle stages of Heligmosomoides polygyrus (Nematoda, Heligmosomatidae).

    PubMed

    Wabo Poné, J; Bilong Bilong, C F; Mpoame, M

    2010-06-01

    The increasing prevalence of anthelmintic-resistant strains of helminths, drug residues in animal products and high cost of conventional anthelmintics has created an interest in studying medicinal plants as an alternative source of anthelmintic. The potential nematicidal activities of four extracts from the bark of Canthium mannii (Rubiaceae) stem were investigated in vitro. Extracts were diluted in distilled water (DW) to obtain five different concentrations (1.5, 2.0, 2.5, 3.0 and 3.5 mg/ml) and put in contact with eggs and larvae of Heligmosomoides polygyrus. The different stages of the life cycle were also put in contact with the same concentration of mebendazole (MBZ, positive control). One millilitre of each extract at different concentrations and control were added to 1 ml solution containing 30-40 eggs or 10-15 larvae (L1, L2 and L3) and distributed in different Petri dishes. The eggs and larvae were incubated at 24 degrees C and exposure times were: 48 h for un-embryonated eggs, 6 h for embryonated eggs; 2, 4, 6 and 24 h for L1 and L2 larvae, 24-48 h for infective larvae (L3), and 5 days for the larval development test (from L1 to L3). DW and 1% dimethyl sulphoxide (DMSO) were used as placebo and DMSO control, respectively. Significant effects were obtained with three of the four extracts, and differences were observed depending on the parasite stage. Cold water extract (CWE), hot water extract (HWE) and ethanol extract (ETE) inhibited embryonic development (40, 45 and 10%) and hatching of embryonated eggs (40, 85 and 80%), respectively, at 3.5 mg/ml. Only ETE killed L1 (97.18%) and L2 (92.68%) larvae of H. polygyrus after 24 h at 3.5 mg/ml and drastically reduced the production rate (6% at 3.0 and 3.5 mg/ml) of infective larvae (L3) after 5 days of incubation compared to other extracts (P < 0.05). However, the infective larvae of H. polygyrus were resistant to the effect of each of the tested products (extracts and mebendazole). These in vitro results

  2. The Multi-Resistant Reaction of Drought-Tolerant Coffee 'Conilon Clone 14' to Meloidogyne spp. and Late Hypersensitive-Like Response in Coffea canephora.

    PubMed

    Lima, Edriana A; Furlanetto, Cleber; Nicole, Michel; Gomes, Ana C M M; Almeida, Maria R A; Jorge-Júnior, Aldemiro; Correa, Valdir R; Salgado, Sônia Maria; Ferrão, Maria A G; Carneiro, Regina M D G

    2015-06-01

    Root-knot nematodes (RKN), Meloidogyne spp., have major economic impact on coffee production in Central and South America. Genetic control of RKN constitutes an essential part for integrated pest management strategy. The objective of this study was to evaluate the resistance of Coffea canephora genotypes (clones) to Meloidogyne spp. Sensitive and drought-tolerant coffee genotypes were used to infer their resistance using nematode reproduction factor and histopathology. Eight clonal genotypes were highly resistant to M. paranaensis. 'Clone 14' (drought-tolerant) and 'ESN2010-04' were the only genotypes highly resistant and moderately resistant, respectively, to both M. incognita races 3 and 1. Several clones were highly resistant to both avirulent and virulent M. exigua. Clone 14 and ESN2010-04 showed multiple resistance to major RKNs tested. Roots of 'clone 14' (resistant) and 'clone 22' (susceptible) were histologically studied against infection by M. incognita race 3 and M. paranaensis. Reduction of juvenile (J2) penetration in clone 14 was first seen at 2 to 6 days after inoculation (DAI). Apparent early hypersensitive reaction (HR) was seen in root cortex between 4 and 6 DAI, which led to cell death and prevention of some nematode development. At 12 to 20 DAI, giant cells formed in the vascular cylinder, besides normal development into J3/J4. From 32 to 45 DAI, giant cells were completely degenerated. Late, intense HR and cell death were frequently observed around young females and giant cells reported for the first time in coffee pathosystem. These results provide rational bases for future studies, including prospection, characterization, and expression profiling of genomic loci involved in both drought tolerance and resistance to multiple RKN species. PMID:25738554

  3. New Insights into Somatic Embryogenesis: LEAFY COTYLEDON1, BABY BOOM1 and WUSCHEL-RELATED HOMEOBOX4 Are Epigenetically Regulated in Coffea canephora

    PubMed Central

    Nic-Can, Geovanny I.; López-Torres, Adolfo; Barredo-Pool, Felipe; Wrobel, Kazimierz; Loyola-Vargas, Víctor M.; Rojas-Herrera, Rafael; De-la-Peña, Clelia

    2013-01-01

    Plant cells have the capacity to generate a new plant without egg fertilization by a process known as somatic embryogenesis (SE), in which differentiated somatic cells can form somatic embryos able to generate a functional plant. Although there have been advances in understanding the genetic basis of SE, the epigenetic mechanism that regulates this process is still unknown. Here, we show that the embryogenic development of Coffea canephora proceeds through a crosstalk between DNA methylation and histone modifications during the earliest embryogenic stages of SE. We found that low levels of DNA methylation, histone H3 lysine 9 dimethylation (H3K9me2) and H3K27me3 change according to embryo development. Moreover, the expression of LEAFY COTYLEDON1 (LEC1) and BABY BOOM1 (BBM1) are only observed after SE induction, whereas WUSCHEL-RELATED HOMEOBOX4 (WOX4) decreases its expression during embryo maturation. Using a pharmacological approach, it was found that 5-Azacytidine strongly inhibits the embryogenic response by decreasing both DNA methylation and gene expression of LEC1 and BBM1. Therefore, in order to know whether these genes were epigenetically regulated, we used Chromatin Immunoprecipitation (ChIP) assays. It was found that WOX4 is regulated by the repressive mark H3K9me2, while LEC1 and BBM1 are epigenetically regulated by H3K27me3. We conclude that epigenetic regulation plays an important role during somatic embryogenic development, and a molecular mechanism for SE is proposed. PMID:23977240

  4. The Multi-Resistant Reaction of Drought-Tolerant Coffee 'Conilon Clone 14' to Meloidogyne spp. and Late Hypersensitive-Like Response in Coffea canephora.

    PubMed

    Lima, Edriana A; Furlanetto, Cleber; Nicole, Michel; Gomes, Ana C M M; Almeida, Maria R A; Jorge-Júnior, Aldemiro; Correa, Valdir R; Salgado, Sônia Maria; Ferrão, Maria A G; Carneiro, Regina M D G

    2015-06-01

    Root-knot nematodes (RKN), Meloidogyne spp., have major economic impact on coffee production in Central and South America. Genetic control of RKN constitutes an essential part for integrated pest management strategy. The objective of this study was to evaluate the resistance of Coffea canephora genotypes (clones) to Meloidogyne spp. Sensitive and drought-tolerant coffee genotypes were used to infer their resistance using nematode reproduction factor and histopathology. Eight clonal genotypes were highly resistant to M. paranaensis. 'Clone 14' (drought-tolerant) and 'ESN2010-04' were the only genotypes highly resistant and moderately resistant, respectively, to both M. incognita races 3 and 1. Several clones were highly resistant to both avirulent and virulent M. exigua. Clone 14 and ESN2010-04 showed multiple resistance to major RKNs tested. Roots of 'clone 14' (resistant) and 'clone 22' (susceptible) were histologically studied against infection by M. incognita race 3 and M. paranaensis. Reduction of juvenile (J2) penetration in clone 14 was first seen at 2 to 6 days after inoculation (DAI). Apparent early hypersensitive reaction (HR) was seen in root cortex between 4 and 6 DAI, which led to cell death and prevention of some nematode development. At 12 to 20 DAI, giant cells formed in the vascular cylinder, besides normal development into J3/J4. From 32 to 45 DAI, giant cells were completely degenerated. Late, intense HR and cell death were frequently observed around young females and giant cells reported for the first time in coffee pathosystem. These results provide rational bases for future studies, including prospection, characterization, and expression profiling of genomic loci involved in both drought tolerance and resistance to multiple RKN species.

  5. Three new genera and three new species of Lasiopteridi (Diptera: Cecidomyiidae) on Rubiaceae from Guadeloupe, French West Indies, and a key to genera of Neotropical Lasiopteridi unplaced to tribe.

    PubMed

    Gagné, Raymond J; Etienne, Jean

    2015-10-12

    Three new genera of Lasiopteridi (Diptera: Cecidomyiidae), Faramitella Gagné, new genus, Anapeza Gagné, new genus, and Pellacara Gagné, new genus, each with one new species, are described. The new species are from leaf galls on Rubiaceae collected in Guadeloupe, F.W.I.: Faramitella planicauda Gagné, new species, was reared from Faramea occidentalis (L.) A. Rich.; Anapeza tumida Gagné, new species, and Pellacara postica, new species, were both reared from Psychotria mapourioides DC. The three new genera belong to Lasiopteridi but are unassigned to tribe. A key to the adult stage of these and 23 other Neotropical genera of unplaced Lasiopteridi whose adults are known is provided.

  6. Three new genera and three new species of Lasiopteridi (Diptera: Cecidomyiidae) on Rubiaceae from Guadeloupe, French West Indies, and a key to genera of Neotropical Lasiopteridi unplaced to tribe.

    PubMed

    Gagné, Raymond J; Etienne, Jean

    2015-01-01

    Three new genera of Lasiopteridi (Diptera: Cecidomyiidae), Faramitella Gagné, new genus, Anapeza Gagné, new genus, and Pellacara Gagné, new genus, each with one new species, are described. The new species are from leaf galls on Rubiaceae collected in Guadeloupe, F.W.I.: Faramitella planicauda Gagné, new species, was reared from Faramea occidentalis (L.) A. Rich.; Anapeza tumida Gagné, new species, and Pellacara postica, new species, were both reared from Psychotria mapourioides DC. The three new genera belong to Lasiopteridi but are unassigned to tribe. A key to the adult stage of these and 23 other Neotropical genera of unplaced Lasiopteridi whose adults are known is provided. PMID:26624324

  7. Characterizing plasma membrane H+-ATPase in two varieties of coffee leaf (Coffea arabica L.) and its interaction with an elicitor fraction from the orange rust fungus (H. vastatrix Berk and Br.) race II.

    PubMed

    Osses, Luis R; Godoy, César A

    2006-04-01

    Early intercellular signaling in Coffea arabica L.-Hemileia vastatrix host-pathogen interaction was studied, using inside-out plasma membrane from two varieties of coffee leaf and a fungal fraction to determine the plant's biochemical responses. Microsomal pellets (100,000 x g) from the susceptible (Caturra) and resistant (Colombia) coffee leaf varieties were purified by partitioning in two-polymer DEX (6.3% w/w) and PEG (6.3% w/w) system aqueous phase. Fungal material was obtained from orange rust Hemileia vastatrix Berk and Br. race II urediospore germ tubes. Plasma membrane vesicles were preferentially localized to PEG phase, as indicated by its enzyme marker distribution. Both H(+)-ATPase activities displayed similar kinetic and biochemical characteristics, comparable to those described for P-type ATPases. Several enzymes may play pivotal roles in plants regarding early interaction with fungal elicitors. Studies of fungal fractions' effects on H(+)-ATPase and both varieties' proton pumping activities were thus carried out. Concentration as low as 0.1 Gluc eq. ml(-1) fungal fraction induced specific inhibition of H(+)-ATPase and the resistant variety's proton pumping activities. The present work describes characterizing the H(+)-ATPase plasma membrane from two Coffea arabica L. varieties (Caturra and Colombia) for the first time and the race specific inhibitory effect of a crude fungal fraction on both H(+)-ATPase and the resistant variety's proton pumping activities.

  8. Conversion of nicotinic acid to trigonelline is catalyzed by N-methyltransferase belonged to motif B′ methyltransferase family in Coffea arabica

    SciTech Connect

    Mizuno, Kouichi; Matsuzaki, Masahiro; Kanazawa, Shiho; Tokiwano, Tetsuo; Yoshizawa, Yuko; Kato, Misako

    2014-10-03

    Graphical abstract: Trigonelline synthase catalyzes the conversion of nicotinic acid to trigonelline. We isolated and characterized trigonelline synthase gene(s) from Coffea arabica. - Highlights: • Trigonelline is a major compound in coffee been same as caffeine is. • We isolated and characterized trigonelline synthase gene. • Coffee trigonelline synthases are highly homologous with coffee caffeine synthases. • This study contributes the fully understanding of pyridine alkaloid metabolism. - Abstract: Trigonelline (N-methylnicotinate), a member of the pyridine alkaloids, accumulates in coffee beans along with caffeine. The biosynthetic pathway of trigonelline is not fully elucidated. While it is quite likely that the production of trigonelline from nicotinate is catalyzed by N-methyltransferase, as is caffeine synthase (CS), the enzyme(s) and gene(s) involved in N-methylation have not yet been characterized. It should be noted that, similar to caffeine, trigonelline accumulation is initiated during the development of coffee fruits. Interestingly, the expression profiles for two genes homologous to caffeine synthases were similar to the accumulation profile of trigonelline. We presumed that these two CS-homologous genes encoded trigonelline synthases. These genes were then expressed in Escherichiacoli, and the resulting recombinant enzymes that were obtained were characterized. Consequently, using the N-methyltransferase assay with S-adenosyl[methyl-{sup 14}C]methionine, it was confirmed that these recombinant enzymes catalyzed the conversion of nicotinate to trigonelline, coffee trigonelline synthases (termed CTgS1 and CTgS2) were highly identical (over 95% identity) to each other. The sequence homology between the CTgSs and coffee CCS1 was 82%. The pH-dependent activity curve of CTgS1 and CTgS2 revealed optimum activity at pH 7.5. Nicotinate was the specific methyl acceptor for CTgSs, and no activity was detected with any other nicotinate derivatives, or

  9. Fruit load and branch ring-barking affect carbon allocation and photosynthesis of leaf and fruit of Coffea arabica in the field.

    PubMed

    Vaast, Philippe; Angrand, Jobert; Franck, Nicolas; Dauzat, Jean; Génard, Michel

    2005-06-01

    Increasing fruit load (from no berries present to 25, 50 and 100% of the initial fruit load) significantly decreased branch growth on 5-year-old coffee (Coffea arabica L.) trees of the dwarf cultivar 'Costa Rica 95', during their third production cycle. Ring-barking the branches further reduced their growth. Berry dry mass at harvest was significantly reduced by increasing fruit load. Dry matter allocation to berries was four times that allocated to branch growth during the cycle. Branch dieback and berry drop were significantly higher at greater fruit loads. This illustrates the importance of berry sink strength and indicates that there is competition for carbohydrates between berries and shoots and also among berries. Leaf net photosynthesis (P(n)) increased with increasing fruit load. Furthermore, leaves of non-isolated branches bearing full fruit load achieved three times higher P(n) than leaves of isolated (ring-barked) branches without berries, indicating strong relief of leaf P(n) inhibition by carbohydrate demand from berries and other parts of the coffee tree when excess photoassimilates could be exported. Leaf P(n) was significantly higher in the morning than later during the day. This reduction in leaf P(n) is generally attributed to stomatal closure in response to high irradiance, temperature and vapor pressure deficit in the middle of the day; however, it could also be a feedback effect of reserves accumulating during the morning when climatic conditions for leaf P(n) were optimal, because increased leaf mass ratio was observed in leaves of ring-barked branches with low or no fruit loads. Rates of CO(2) emission by berries decreased and calculated photosynthetic rates of berries increased with increasing photosynthetic photon flux (PPF) especially at low PPFs (0 to 100 micromol m(-2) s(-1)). The photosynthetic contribution of berries at the bean-filling stage was estimated to be about 30% of their daily respiration costs and 12% of their total carbon

  10. Differentially Accumulated Proteins in Coffea arabica Seeds during Perisperm Tissue Development and Their Relationship to Coffee Grain Size.

    PubMed

    Alves, Leonardo Cardoso; Magalhães, Diogo Maciel De; Labate, Mônica Teresa Veneziano; Guidetti-Gonzalez, Simone; Labate, Carlos Alberto; Domingues, Douglas Silva; Sera, Tumoru; Vieira, Luiz Gonzaga Esteves; Pereira, Luiz Filipe Protasio

    2016-02-24

    Coffee is one of the most important crops for developing countries. Coffee classification for trading is related to several factors, including grain size. Larger grains have higher market value then smaller ones. Coffee grain size is determined by the development of the perisperm, a transient tissue with a highly active metabolism, which is replaced by the endosperm during seed development. In this study, a proteomics approach was used to identify differentially accumulated proteins during perisperm development in two genotypes with regular (IPR59) and large grain sizes (IPR59-Graudo) in three developmental stages. Twenty-four spots were identified by MALDI-TOF/TOF-MS, corresponding to 15 proteins. We grouped them into categories as follows: storage (11S), methionine metabolism, cell division and elongation, metabolic processes (mainly redox), and energy. Our data enabled us to show that perisperm metabolism in IPR59 occurs at a higher rate than in IPR59-Graudo, which is supported by the accumulation of energy and detoxification-related proteins. We hypothesized that grain and fruit size divergences between the two coffee genotypes may be due to the comparatively earlier triggering of seed development processes in IPR59. We also demonstrated for the first time that the 11S protein is accumulated in the coffee perisperm.

  11. Differentially Accumulated Proteins in Coffea arabica Seeds during Perisperm Tissue Development and Their Relationship to Coffee Grain Size.

    PubMed

    Alves, Leonardo Cardoso; Magalhães, Diogo Maciel De; Labate, Mônica Teresa Veneziano; Guidetti-Gonzalez, Simone; Labate, Carlos Alberto; Domingues, Douglas Silva; Sera, Tumoru; Vieira, Luiz Gonzaga Esteves; Pereira, Luiz Filipe Protasio

    2016-02-24

    Coffee is one of the most important crops for developing countries. Coffee classification for trading is related to several factors, including grain size. Larger grains have higher market value then smaller ones. Coffee grain size is determined by the development of the perisperm, a transient tissue with a highly active metabolism, which is replaced by the endosperm during seed development. In this study, a proteomics approach was used to identify differentially accumulated proteins during perisperm development in two genotypes with regular (IPR59) and large grain sizes (IPR59-Graudo) in three developmental stages. Twenty-four spots were identified by MALDI-TOF/TOF-MS, corresponding to 15 proteins. We grouped them into categories as follows: storage (11S), methionine metabolism, cell division and elongation, metabolic processes (mainly redox), and energy. Our data enabled us to show that perisperm metabolism in IPR59 occurs at a higher rate than in IPR59-Graudo, which is supported by the accumulation of energy and detoxification-related proteins. We hypothesized that grain and fruit size divergences between the two coffee genotypes may be due to the comparatively earlier triggering of seed development processes in IPR59. We also demonstrated for the first time that the 11S protein is accumulated in the coffee perisperm. PMID:26809209

  12. Tea, coffee, and cocoa as ultraviolet radiation protectants for beet armyworm nucleopolyhedrovirus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The addition of 1% (wt/v) aqueous extracts of cocoa (Theobroma cacao L.) (Malvales: Malvaceae), coffee (Coffea arabica L.) (Gentianales: Rubiaceae), green, and black tea (Camellia sinensis L.) (Ericales: Theaceae) provided excellent ultraviolet (UV) radiation protection for the beet armyworm, Spodo...

  13. Evaluating bee (Hymenoptera: Apoidea) diversity using malaise traps in coffee landscapes of Costa Rica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Even though Arabica coffee (Coffea arabica Linnaeus, Rubiaceae) can self-pollinate, bees are important pollinators, without which there is lower fruit quality and yield. We studied bee diversity in coffee agroecosystems in Costa Rica during two coffee flowering seasons (2005 and 2006). Malaise traps...

  14. Study of composition of espresso coffee prepared from various roast degrees of Coffea arabica L. coffee beans.

    PubMed

    Kučera, Lukáš; Papoušek, Roman; Kurka, Ondřej; Barták, Petr; Bednář, Petr

    2016-05-15

    Espresso coffee samples prepared at various roasting degrees defined according to its basic conventional classification (light, medium, medium-dark and dark roasted) were analyzed by ultra-performance liquid chromatography/tandem mass spectrometry. Obtained raw data were processed using multivariate statistical analysis (Principal Component Analysis, PCA) to evaluate chemical differences between each roasting degrees (untargeted part of study). All four roasting degrees were resolved in appropriate Score plot. Orthogonal Projections to Latent Structures provided signals of significant markers describing the differences among particular roasting degrees. Detailed interpretation of those signals by targeted LC/MS(2) analysis revealed four groups of compounds. The first two groups involve chlorogenic acids and related lactones. The signals of other two sets of markers were ascribed to some specific atractylosides and particular melanoidins. Ratios of contents of selected representatives of each group to the sum of all identified markers were proposed as definite parameters for determination of roasting degree of Brazilian coffee Arabica. PMID:26776030

  15. Study of composition of espresso coffee prepared from various roast degrees of Coffea arabica L. coffee beans.

    PubMed

    Kučera, Lukáš; Papoušek, Roman; Kurka, Ondřej; Barták, Petr; Bednář, Petr

    2016-05-15

    Espresso coffee samples prepared at various roasting degrees defined according to its basic conventional classification (light, medium, medium-dark and dark roasted) were analyzed by ultra-performance liquid chromatography/tandem mass spectrometry. Obtained raw data were processed using multivariate statistical analysis (Principal Component Analysis, PCA) to evaluate chemical differences between each roasting degrees (untargeted part of study). All four roasting degrees were resolved in appropriate Score plot. Orthogonal Projections to Latent Structures provided signals of significant markers describing the differences among particular roasting degrees. Detailed interpretation of those signals by targeted LC/MS(2) analysis revealed four groups of compounds. The first two groups involve chlorogenic acids and related lactones. The signals of other two sets of markers were ascribed to some specific atractylosides and particular melanoidins. Ratios of contents of selected representatives of each group to the sum of all identified markers were proposed as definite parameters for determination of roasting degree of Brazilian coffee Arabica.

  16. Incidence and distribution of filamentous fungi during fermentation, drying and storage of coffee (Coffea arabica L.) beans

    PubMed Central

    Silva, Cristina Ferreira; Batista, Luis Roberto; Schwan, Rosane Freitas

    2008-01-01

    The objective of this work was to isolate and characterize filamentous fungi present in different stages of harvest, fermentation, drying and storage of coffee beans processed by natural method. The cherries were hand-picked and then placed on a cement drying platform where they remained until reached 11% of humidity. Microbial counts were found in all samples during fermentation and drying of the coffee beans. Counts of fungi in the coffee cherries collected from the tree (time 0) were around 1.5 x 103 CFU/g. This number increased slowly during the fermentation and drying reaching values of 2 x 105 CFU/g within 22 days of processing. Two hundred and sixty three isolates of filamentous fungi were identified. The distribution of species during fermentation and drying was very varied while there was a predominance of Aspergillus species during storage period. The genera found were Pestalotia (4), Paecelomyces (4), Cladosporium (26), Fusarium (34), Penicillium (81) and Aspergillus (112) and comprised 38 different species. PMID:24031259

  17. Evidence of genetic tolerance to low availability of phosphorus in the soil among genotypes of Coffea canephora.

    PubMed

    Martins, L D; Rodrigues, W N; Machado, L S; Brinate, S V B; Colodetti, T V; Amaral, J F T; Tomaz, M A

    2015-01-01

    The expansion of agriculture to new areas in order to increase the competitiveness of coffee producing countries has resulted in cultivation expanding into regions with lower natural fertility. This scenario has created the need to differentiate genotypes of Conilon coffee based on their tolerance to low levels of nutrients in the soil, especially phosphorus, which imposes high limitations on crop yield in tropical regions. In this context, the objective of this study was to identify differential tolerance among genotypes of Conilon coffee cultivated in environments with different levels of phosphorus availability in the soil. The experiment was conducted in a controlled environment, following a completely randomized design, with three replications in a factorial scheme 13 x 3, the factors were as follows: 13 genotypes of Conilon coffee from groups of different ripening cycles and three environments with different levels of phosphorus availability in the soil (fertilization without phosphorus supply, and phosphorus supply at 50 and 100% of recommendations). Discrimination of tolerance was based on 14 variables, including vegetative growth, accumulation of dry matter, nutrient content, and nutritional efficiencies. Estimates of genetic parameters indicated high genotypic variability for genotypes cultivated in environments with low phosphorus availability in the soil. It was possible to classify genotypes 22, 23, 24, 67, 76, 77, and 83 as tolerant of a low availability of phosphorus in the soil during early development. There was no clear relationship between ripening cycles and the tolerance of the genotypes to low phosphorus availability in the soil. PMID:26400289

  18. Characterization and estimation of proanthocyanidins and other phenolics in coffee pulp (Coffea arabica) by thiolysis-high-performance liquid chromatography.

    PubMed

    Ramirez-Coronel, Maria Ascencion; Marnet, Nathalie; Kolli, V S Kumar; Roussos, Sevastianos; Guyot, Sylvain; Augur, Christopher

    2004-03-10

    Fresh and 3-day-old coffee pulp of the Arabica variety were analyzed for polyphenol composition followed by characterization by two different methods. The first method consisted in subjecting coffee pulp powder to direct thiolysis. For the second method, coffee pulp was subjected to successive solvent extractions, followed by thiolysis. Quantification of phenolic compounds was then achieved by high-performance liquid chromatography (HPLC) analysis of thiolysis products. Four major classes of polyphenols were identified: flavan-3-ols (monomers and procyanidins), hydroxycinnamic acids, flavonols, and anthocyanidins. Differences in concentration of procyanidins were observed between fresh and 3-day-old coffee pulp. Constitutive units were mainly epicatechin, representing more than 90% of the proanthocyanidin units, with average degrees of polymerization in the range of 3.8-9.1. Monomer to hexamer units of flavan-3-ols from fresh coffee pulp were separated by normal-phase HPLC. Molecular size of oligomeric proanthocyanidins was obtained by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Results obtained confirm the presence of oligomers of the flavan-3-ol (-)-epicatechin.

  19. Long-term elevated air [CO2 ] strengthens photosynthetic functioning and mitigates the impact of supra-optimal temperatures in tropical Coffea arabica and C. canephora species.

    PubMed

    Rodrigues, Weverton P; Martins, Madlles Q; Fortunato, Ana S; Rodrigues, Ana P; Semedo, José N; Simões-Costa, Maria C; Pais, Isabel P; Leitão, António E; Colwell, Filipe; Goulao, Luis; Máguas, Cristina; Maia, Rodrigo; Partelli, Fábio L; Campostrini, Eliemar; Scotti-Campos, Paula; Ribeiro-Barros, Ana I; Lidon, Fernando C; DaMatta, Fábio M; Ramalho, José C

    2016-01-01

    The tropical coffee crop has been predicted to be threatened by future climate changes and global warming. However, the real biological effects of such changes remain unknown. Therefore, this work aims to link the physiological and biochemical responses of photosynthesis to elevated air [CO2 ] and temperature in cultivated genotypes of Coffea arabica L. (cv. Icatu and IPR108) and Coffea canephora cv. Conilon CL153. Plants were grown for ca. 10 months at 25/20°C (day/night) and 380 or 700 μl CO2 l(-1) and then subjected to temperature increase (0.5°C day(-1) ) to 42/34°C. Leaf impacts related to stomatal traits, gas exchanges, C isotope composition, fluorescence parameters, thylakoid electron transport and enzyme activities were assessed at 25/20, 31/25, 37/30 and 42/34°C. The results showed that (1) both species were remarkably heat tolerant up to 37/30°C, but at 42/34°C a threshold for irreversible nonstomatal deleterious effects was reached. Impairments were greater in C. arabica (especially in Icatu) and under normal [CO2 ]. Photosystems and thylakoid electron transport were shown to be quite heat tolerant, contrasting to the enzymes related to energy metabolism, including RuBisCO, which were the most sensitive components. (2) Significant stomatal trait modifications were promoted almost exclusively by temperature and were species dependent. Elevated [CO2 ], (3) strongly mitigated the impact of temperature on both species, particularly at 42/34°C, modifying the response to supra-optimal temperatures, (4) promoted higher water-use efficiency under moderately higher temperature (31/25°C) and (5) did not provoke photosynthetic downregulation. Instead, enhancements in [CO2 ] strengthened photosynthetic photochemical efficiency, energy use and biochemical functioning at all temperatures. Our novel findings demonstrate a relevant heat resilience of coffee species and that elevated [CO2 ] remarkably mitigated the impact of heat on coffee physiology, therefore

  20. The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae

    PubMed Central

    Sabir, Jamal S. M.; Jansen, Robert K.; Arasappan, Dhivya; Calderon, Virginie; Noutahi, Emmanuel; Zheng, Chunfang; Park, Seongjun; Sabir, Meshaal J.; Baeshen, Mohammed N.; Hajrah, Nahid H.; Khiyami, Mohammad A.; Baeshen, Nabih A.; Obaid, Abdullah Y.; Al-Malki, Abdulrahman L.; Sankoff, David; El-Mabrouk, Nadia; Ruhlman, Tracey A.

    2016-01-01

    Alkaloid accumulation in plants is activated in response to stress, is limited in distribution and specific alkaloid repertoires are variable across taxa. Rauvolfioideae (Apocynaceae, Gentianales) represents a major center of structural expansion in the monoterpenoid indole alkaloids (MIAs) yielding thousands of unique molecules including highly valuable chemotherapeutics. The paucity of genome-level data for Apocynaceae precludes a deeper understanding of MIA pathway evolution hindering the elucidation of remaining pathway enzymes and the improvement of MIA availability in planta or in vitro. We sequenced the nuclear genome of Rhazya stricta (Apocynaceae, Rauvolfioideae) and present this high quality assembly in comparison with that of coffee (Rubiaceae, Coffea canephora, Gentianales) and others to investigate the evolution of genome-scale features. The annotated Rhazya genome was used to develop the community resource, RhaCyc, a metabolic pathway database. Gene family trees were constructed to identify homologs of MIA pathway genes and to examine their evolutionary history. We found that, unlike Coffea, the Rhazya lineage has experienced many structural rearrangements. Gene tree analyses suggest recent, lineage-specific expansion and diversification among homologs encoding MIA pathway genes in Gentianales and provide candidate sequences with the potential to close gaps in characterized pathways and support prospecting for new MIA production avenues. PMID:27653669

  1. Gang Identifiers and Terminology.

    ERIC Educational Resources Information Center

    Cantrell, Mary Lynn

    1992-01-01

    Provides lists of gang identifiers and terminology. Suggests that, to find out names and associated identifiers of local gangs, readers should talk to their local police. Included in listing are descriptions of gang-related symbols, physical signals, graffiti, slogans, right-left rules, colors, clothing, jewelry, hair styles, and fingernails. Also…

  2. Functional analysis of the relative growth rate, chemical composition, construction and maintenance costs, and the payback time of Coffea arabica L. leaves in response to light and water availability

    PubMed Central

    Cavatte, Paulo C.; Rodríguez-López, Nélson F.; Martins, Samuel C. V.; Mattos, Mariela S.; Sanglard, Lílian M. V. P.; DaMatta, Fábio M.

    2012-01-01

    In this study, the combined effects of light and water availability on the functional relationships of the relative growth rate (RGR), leaf chemical composition, construction and maintenance costs, and benefits in terms of payback time for Coffea arabica are presented. Coffee plants were grown for 8 months in 100% or 15% full sunlight and then a four-month water shortage was implemented. Plants grown under full sunlight were also transferred to shade and vice versa. Overall, most of the traits assessed were much more responsive to the availability of light than to the water supply. Larger construction costs (12%), primarily associated with elevated phenol and alkaloid pools, were found under full sunlight. There was a positive correlation between these compounds and the RGR, the mass-based net carbon assimilation rate and the carbon isotope composition ratio, which, in turn, correlated negatively with the specific leaf area. The payback time was remarkably lower in the sun than in shade leaves and increased greatly in water-deprived plants. The differences in maintenance costs among the treatments were narrow, with no significant impact on the RGR, and there was no apparent trade-off in resource allocation between growth and defence. The current irradiance during leaf bud formation affected both the specific leaf area and leaf physiology upon transferring the plants from low to high light and vice versa. In summary, sun-grown plants fixed more carbon for growth and secondary metabolism, with the net effect of an increased RGR. PMID:22378951

  3. Metal alloy identifier

    DOEpatents

    Riley, William D.; Brown, Jr., Robert D.

    1987-01-01

    To identify the composition of a metal alloy, sparks generated from the alloy are optically observed and spectrographically analyzed. The spectrographic data, in the form of a full-spectrum plot of intensity versus wavelength, provide the "signature" of the metal alloy. This signature can be compared with similar plots for alloys of known composition to establish the unknown composition by a positive match with a known alloy. An alternative method is to form intensity ratios for pairs of predetermined wavelengths within the observed spectrum and to then compare the values of such ratios with similar values for known alloy compositions, thereby to positively identify the unknown alloy composition.

  4. Identifying and Managing Risk.

    ERIC Educational Resources Information Center

    Abraham, Janice M.

    1999-01-01

    The role of the college or university chief financial officer in institutional risk management is (1) to identify risk (physical, casualty, fiscal, business, reputational, workplace safety, legal liability, employment practices, general liability), (2) to develop a campus plan to reduce and control risk, (3) to transfer risk, and (4) to track and…

  5. Identifying Marine Phytoplankton

    NASA Astrophysics Data System (ADS)

    Hargraves, Paul E.

    Until recently, anyone who needed to accurately identify marine phytoplankton had one of four choices: use the outdated Englishlanguage volumes by E. E. Cupp and N. I. Hendey plus the more recent book by J. Dodge, acquire a working knowledge of German and use the old volumes by Schiller and Hustedt, spend huge amounts of time in an exceedingly well-equipped marine science library trying in vain to keep up with the rapidly evolving field of phytoplankton systematics and taxonomy, or track down one of the rarest of endangered species—a phytoplankton taxonomist—and beg for help.To these unfortunate choices is added one considerably more hopeful: Identifying Marine Phytoplankton. This volume, which has seven contributing authors, contains most of the taxonomic groups that make up the planktonic autotrophs and some heterotrophs of the seas, coasts, and estuaries of the world (missing are cyanobacteria and some of the picoplankton groups).

  6. On identified predictive control

    NASA Technical Reports Server (NTRS)

    Bialasiewicz, Jan T.

    1993-01-01

    Self-tuning control algorithms are potential successors to manually tuned PID controllers traditionally used in process control applications. A very attractive design method for self-tuning controllers, which has been developed over recent years, is the long-range predictive control (LRPC). The success of LRPC is due to its effectiveness with plants of unknown order and dead-time which may be simultaneously nonminimum phase and unstable or have multiple lightly damped poles (as in the case of flexible structures or flexible robot arms). LRPC is a receding horizon strategy and can be, in general terms, summarized as follows. Using assumed long-range (or multi-step) cost function the optimal control law is found in terms of unknown parameters of the predictor model of the process, current input-output sequence, and future reference signal sequence. The common approach is to assume that the input-output process model is known or separately identified and then to find the parameters of the predictor model. Once these are known, the optimal control law determines control signal at the current time t which is applied at the process input and the whole procedure is repeated at the next time instant. Most of the recent research in this field is apparently centered around the LRPC formulation developed by Clarke et al., known as generalized predictive control (GPC). GPC uses ARIMAX/CARIMA model of the process in its input-output formulation. In this paper, the GPC formulation is used but the process predictor model is derived from the state space formulation of the ARIMAX model and is directly identified over the receding horizon, i.e., using current input-output sequence. The underlying technique in the design of identified predictive control (IPC) algorithm is the identification algorithm of observer/Kalman filter Markov parameters developed by Juang et al. at NASA Langley Research Center and successfully applied to identification of flexible structures.

  7. Identifying conical singularities

    SciTech Connect

    Oliveira-Neto, G. |

    1996-09-01

    A method based upon the concept of holonomy of a metric space{endash}time ({ital M},{ital g}), in order to identify the presence of conical singularities in {ital M} is proposed. The validity and usefulness of this so-called holonomy method is proven by applying it to a set of four-dimensional space{endash}times and one three-dimensional space{endash}time. The holonomy method predictions are confirmed by the comparison with the predictions obtained after coordinate transformations which take the metrics {ital g}, to a new basis where the global properties of conical singularities are explicitly seen. {copyright} {ital 1996 American Institute of Physics.}

  8. List identifies threatened ecosystems

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2012-09-01

    The International Union for Conservation of Nature (IUCN) announced on 9 September that it will develop a new Red List of Ecosystems that will identify which ecosystems are vulnerable or endangered. The list, which is modeled on the group's Red List of Threatened Species™, could help to guide conservation activities and influence policy processes such as the Convention on Biological Diversity, according to the group. “We will assess the status of marine, terrestrial, freshwater, and subterranean ecosystems at local, regional, and global levels,” stated Jon Paul Rodriguez, leader of IUCN's Ecosystems Red List Thematic Group. “The assessment can then form the basis for concerted implementation action so that we can manage them sustainably if their risk of collapse is low or restore them if they are threatened and then monitor their recovery.”

  9. Identifying potential academic leaders

    PubMed Central

    White, David; Krueger, Paul; Meaney, Christopher; Antao, Viola; Kim, Florence; Kwong, Jeffrey C.

    2016-01-01

    Objective To identify variables associated with willingness to undertake leadership roles among academic family medicine faculty. Design Web-based survey. Bivariate and multivariable analyses (logistic regression) were used to identify variables associated with willingness to undertake leadership roles. Setting Department of Family and Community Medicine at the University of Toronto in Ontario. Participants A total of 687 faculty members. Main outcome measures Variables related to respondents’ willingness to take on various academic leadership roles. Results Of all 1029 faculty members invited to participate in the survey, 687 (66.8%) members responded. Of the respondents, 596 (86.8%) indicated their level of willingness to take on various academic leadership roles. Multivariable analysis revealed that the predictors associated with willingness to take on leadership roles were as follows: pursuit of professional development opportunities (odds ratio [OR] 3.79, 95% CI 2.29 to 6.27); currently holding at least 1 leadership role (OR 5.37, 95% CI 3.38 to 8.53); a history of leadership training (OR 1.86, 95% CI 1.25 to 2.78); the perception that mentorship is important for one’s current role (OR 2.25, 95% CI 1.40 to 3.60); and younger age (OR 0.97, 95% CI 0.95 to 0.99). Conclusion Willingness to undertake new or additional leadership roles was associated with 2 variables related to leadership experiences, 2 variables related to perceptions of mentorship and professional development, and 1 demographic variable (younger age). Interventions that support opportunities in these areas might expand the pool and strengthen the academic leadership potential of faculty members. PMID:27331226

  10. Identifying Adolescent Sleep Problems

    PubMed Central

    Short, Michelle A.; Gradisar, Michael; Gill, Jason; Camfferman, Danny

    2013-01-01

    Objectives To examine the efficacy of self-report and parental report of adolescent sleep problems and compare these findings to the incidence of adolescents who fulfill clinical criteria for a sleep problem. Sleep and daytime functioning factors that predict adolescents’ self-identification of a sleep problem will also be examined. Method 308 adolescents (aged 13–17 years) from eight socioeconomically diverse South Australian high schools participated in this study. Participants completed a survey battery during class time, followed by a 7-day Sleep Diary and the Flinders Fatigue Scale completed on the final day of the study. Parents completed a Sleep, Medical, Education and Family History Survey. Results The percentage of adolescents fulfilling one or more of the criteria for a sleep problem was inordinately high at 66%. Adolescent self-reporting a sleep problem was significantly lower than the adolescents who had one or more of the clinical criteria for a sleep problem (23.1% vs. 66.6%; χ2 = 17.46, p<.001). Parental report of their adolescent having a sleep problem was significantly lower than adolescent self-report (14.3% vs. 21.1%, p<.001). Adolescents who reported unrefreshing sleep were 4.81 times more likely to report a sleep problem. For every hour that bedtime was delayed, the odds of self-reporting a sleep problem increased by 1.91 times, while each additional 10 minutes taken to fall asleep increased the odds 1.40 times. Conclusion While many adolescents were found to have sleep patterns indicative of a sleep problem, only a third of this number self-identify having a sleep problem, while only a sixth of this number are indicated by parental report. This study highlights important features to target in future sleep education and intervention strategies for both adolescents and parents. PMID:24086501

  11. Stochastic control system parameter identifiability

    NASA Technical Reports Server (NTRS)

    Lee, C. H.; Herget, C. J.

    1975-01-01

    The parameter identification problem of general discrete time, nonlinear, multiple input/multiple output dynamic systems with Gaussian white distributed measurement errors is considered. The knowledge of the system parameterization was assumed to be known. Concepts of local parameter identifiability and local constrained maximum likelihood parameter identifiability were established. A set of sufficient conditions for the existence of a region of parameter identifiability was derived. A computation procedure employing interval arithmetic was provided for finding the regions of parameter identifiability. If the vector of the true parameters is locally constrained maximum likelihood (CML) identifiable, then with probability one, the vector of true parameters is a unique maximal point of the maximum likelihood function in the region of parameter identifiability and the constrained maximum likelihood estimation sequence will converge to the vector of true parameters.

  12. Near Identifiability of Dynamical Systems

    NASA Technical Reports Server (NTRS)

    Hadaegh, F. Y.; Bekey, G. A.

    1987-01-01

    Concepts regarding approximate mathematical models treated rigorously. Paper presents new results in analysis of structural identifiability, equivalence, and near equivalence between mathematical models and physical processes they represent. Helps establish rigorous mathematical basis for concepts related to structural identifiability and equivalence revealing fundamental requirements, tacit assumptions, and sources of error. "Structural identifiability," as used by workers in this field, loosely translates as meaning ability to specify unique mathematical model and set of model parameters that accurately predict behavior of corresponding physical system.

  13. Identifying Occupationally Specific Affective Behaviors.

    ERIC Educational Resources Information Center

    Pucel, David J.

    1993-01-01

    Data from two groups of cosmetology instructors (n=15) and two groups of machinist instructors (n=17) validated the Occupational Affective Behavior Analysis instrument as capable of identifying affective behaviors viewed as important to success in a given occupation. (SK)

  14. Identifying Clients Predisposed To Failure

    ERIC Educational Resources Information Center

    Carnes, G. D.

    1973-01-01

    Studies are reviewed that report the prediction of rehabilitation failure from personality measures. Related research is discussed that suggest the dynamics underlying a key concept, the "hypochondriacally organized personality" which is identifiable from the Rorschach anatomy response percentage. (Author)

  15. Endophytic bacteria in Coffea arabica L.

    PubMed

    Vega, Fernando E; Pava-Ripoll, Monica; Posada, Francisco; Buyer, Jeffrey S

    2005-01-01

    Eighty-seven culturable endophytic bacterial isolates in 19 genera were obtained from coffee plants collected in Colombia (n = 67), Hawaii (n = 17), and Mexico (n = 3). Both Gram positive and Gram negative bacteria were isolated, with a greater percentage (68%) being Gram negative. Tissues yielding bacterial endophytes included adult plant leaves, various parts of the berry (e.g., crown, pulp, peduncle and seed), and leaves, stems, and roots of seedlings. Some of the bacteria also occurred as epiphytes. The highest number of bacteria among the berry tissues sampled was isolated from the seed, and includes Bacillus , Burkholderia , Clavibacter , Curtobacterium , Escherichia , Micrococcus , Pantoea , Pseudomonas , Serratia , and Stenotrophomonas . This is the first survey of the endophytic bacteria diversity in various coffee tissues, and the first study reporting endophytic bacteria in coffee seeds. The possible role for these bacteria in the biology of the coffee plant remains unknown.

  16. Individual Identifiability Predicts Population Identifiability in Forensic Microsatellite Markers.

    PubMed

    Algee-Hewitt, Bridget F B; Edge, Michael D; Kim, Jaehee; Li, Jun Z; Rosenberg, Noah A

    2016-04-01

    Highly polymorphic genetic markers with significant potential for distinguishing individual identity are used as a standard tool in forensic testing [1, 2]. At the same time, population-genetic studies have suggested that genetically diverse markers with high individual identifiability also confer information about genetic ancestry [3-6]. The dual influence of polymorphism levels on ancestry inference and forensic desirability suggests that forensically useful marker sets with high levels of individual identifiability might also possess substantial ancestry information. We study a standard forensic marker set-the 13 CODIS loci used in the United States and elsewhere [2, 7-9]-together with 779 additional microsatellites [10], using direct population structure inference to test whether markers with substantial individual identifiability also produce considerable information about ancestry. Despite having been selected for individual identification and not for ancestry inference [11], the CODIS markers generate nontrivial model-based clustering patterns similar to those of other sets of 13 tetranucleotide microsatellites. Although the CODIS markers have relatively low values of the F(ST) divergence statistic, their high heterozygosities produce greater ancestry inference potential than is possessed by less heterozygous marker sets. More generally, we observe that marker sets with greater individual identifiability also tend toward greater population identifiability. We conclude that population identifiability regularly follows as a byproduct of the use of highly polymorphic forensic markers. Our findings have implications for the design of new forensic marker sets and for evaluations of the extent to which individual characteristics beyond identification might be predicted from current and future forensic data.

  17. Identifying tier one key suppliers.

    PubMed

    Wicks, Steve

    2013-01-01

    In today's global marketplace, businesses are becoming increasingly reliant on suppliers for the provision of key processes, activities, products and services in support of their strategic business goals. The result is that now, more than ever, the failure of a key supplier has potential to damage reputation, productivity, compliance and financial performance seriously. Yet despite this, there is no recognised standard or guidance for identifying a tier one key supplier base and, up to now, there has been little or no research on how to do so effectively. This paper outlines the key findings of a BCI-sponsored research project to investigate good practice in identifying tier one key suppliers, and suggests a scalable framework process model and risk matrix tool to help businesses effectively identify their tier one key supplier base. PMID:23615061

  18. Identifying tier one key suppliers.

    PubMed

    Wicks, Steve

    2013-01-01

    In today's global marketplace, businesses are becoming increasingly reliant on suppliers for the provision of key processes, activities, products and services in support of their strategic business goals. The result is that now, more than ever, the failure of a key supplier has potential to damage reputation, productivity, compliance and financial performance seriously. Yet despite this, there is no recognised standard or guidance for identifying a tier one key supplier base and, up to now, there has been little or no research on how to do so effectively. This paper outlines the key findings of a BCI-sponsored research project to investigate good practice in identifying tier one key suppliers, and suggests a scalable framework process model and risk matrix tool to help businesses effectively identify their tier one key supplier base.

  19. "Geriatricizing" Hospitalists: Identifying Educational Opportunities

    ERIC Educational Resources Information Center

    Friedman, Susan M.; Gillespie, Suzanne M.; Medina-Walpole, Annette M.; Caprio, Thomas V.; Karuza, Jurgis; McCann, Robert M.

    2013-01-01

    The objective of this study was to identify differences between geriatricians and hospitalists in caring for hospitalized older adults, so as to inform faculty development programs that have the goal of improving older patient care. Eleven hospitalists and 13 geriatricians were surveyed regarding knowledge, confidence, and practice patterns in…

  20. Identifiability, exchangeability and confounding revisited

    PubMed Central

    Greenland, Sander; Robins, James M

    2009-01-01

    In 1986 the International Journal of Epidemiology published "Identifiability, Exchangeability and Epidemiological Confounding". We review the article from the perspective of a quarter century after it was first drafted and relate it to subsequent developments on confounding, ignorability, and collapsibility. PMID:19732410

  1. Identifying Intellectually Superior Black Children.

    ERIC Educational Resources Information Center

    Ryan, Judith S.

    1983-01-01

    The effectiveness of several methods used to identify intellectually superior black children was evaluated. Findings suggest that less commonly used identification methods, such as parents' opinion and the Leiter International Performance Scale, may point out these children more accurately than do traditional measures. (Author/PP)

  2. Identifying the Gifted Child Humorist.

    ERIC Educational Resources Information Center

    Fern, Tami L.

    1991-01-01

    This study attempted to identify gifted child humorists among 1,204 children in grades 3-6. Final identification of 13 gifted child humorists was determined through application of such criteria as funniness, originality, and exemplary performance or product. The influence of intelligence, development, social factors, sex differences, family…

  3. Identifying Innovative Agricultural Education Programs

    ERIC Educational Resources Information Center

    Rayfield, John; Murphy, Tim; Briers, Gary; Lewis, Lauren

    2012-01-01

    Researchers identified innovative agricultural education programs across the United States. A Delphi study was conducted with the teachers in innovative programs. According to the teachers, innovative programs in 2020 will use hands-on activities and will be run by highly motivated teachers. The purpose of innovative programs in the future will be…

  4. [Identifying victims of a disaster].

    PubMed

    de Boer, Hans H; Kloosterman, Ate D; de Bruijn, Arie G; Maat, George J R

    2014-01-01

    Identifying the victims of a disaster is important for the next of kin, to issue a death certificate and, if necessary, for forensic investigations. In the Netherlands victims are identified by the Dutch disaster victim identification team, which is part of the national forensic investigation team ('Landelijk Team Forensische Opsporing'). Ante-mortem data are collected during the identification process; these include the victim's specific medical characteristics and the DNA profile of the victim and their family members. The victim's own doctor can play an important role in the ante-mortem investigation because of his or her knowledge of their personal medical details, and of the possible availability of samples for establishing a DNA profile. The ante-mortem data are then compared with post-mortem data. For a definitive identification at least 1 primary identification characteristic has to be established from the physical remains - dermatoglyphics, the DNA profile or the dental status.

  5. Identifying and managing problem drinkers.

    PubMed Central

    Kahan, M.

    1996-01-01

    Problem drinking is far more common than severe alcohol dependence and is associated with considerable morbidity and health care costs. Whereas patients with alcohol dependence respond best to intensive treatment, one or more brief sessions of physician advice and counseling reduces alcohol consumption among problem drinkers. The two most useful tools to identify problem drinkers are the CAGE and the drinking problem question. PMID:8653034

  6. Identifying Network Perturbation in Cancer

    PubMed Central

    Logsdon, Benjamin A.; Gentles, Andrew J.; Lee, Su-In

    2016-01-01

    We present a computational framework, called DISCERN (DIfferential SparsE Regulatory Network), to identify informative topological changes in gene-regulator dependence networks inferred on the basis of mRNA expression datasets within distinct biological states. DISCERN takes two expression datasets as input: an expression dataset of diseased tissues from patients with a disease of interest and another expression dataset from matching normal tissues. DISCERN estimates the extent to which each gene is perturbed—having distinct regulator connectivity in the inferred gene-regulator dependencies between the disease and normal conditions. This approach has distinct advantages over existing methods. First, DISCERN infers conditional dependencies between candidate regulators and genes, where conditional dependence relationships discriminate the evidence for direct interactions from indirect interactions more precisely than pairwise correlation. Second, DISCERN uses a new likelihood-based scoring function to alleviate concerns about accuracy of the specific edges inferred in a particular network. DISCERN identifies perturbed genes more accurately in synthetic data than existing methods to identify perturbed genes between distinct states. In expression datasets from patients with acute myeloid leukemia (AML), breast cancer and lung cancer, genes with high DISCERN scores in each cancer are enriched for known tumor drivers, genes associated with the biological processes known to be important in the disease, and genes associated with patient prognosis, in the respective cancer. Finally, we show that DISCERN can uncover potential mechanisms underlying network perturbation by explaining observed epigenomic activity patterns in cancer and normal tissue types more accurately than alternative methods, based on the available epigenomic data from the ENCODE project. PMID:27145341

  7. Identifying teaching in wild animals.

    PubMed

    Thornton, Alex; Raihani, Nichola J

    2010-08-01

    After a long period of neglect, the study of teaching in nonhuman animals is beginning to take a more prominent role in research on social learning. Unlike other forms of social learning, teaching requires knowledgeable individuals to play an active role in facilitating learning by the naive. Casting aside anthropocentric requirements for cognitive mechanisms assumed to underpin teaching in our own species, researchers are now beginning to discover evidence for teaching across a wide range of taxa. Nevertheless, unequivocal evidence for teaching remains scarce, with convincing experimental data limited to meerkats, pied babblers, and tandem-running ants. In this review, our aim is to stimulate further research in different species and contexts by providing conceptual and methodological guidelines for identifying teaching, with a focus on natural populations. We begin by highlighting the fact that teaching is a form of cooperative behavior that functions to promote learning in others and show that consideration of these key characteristics is critical in helping to identify suitable targets for future research. We then go on to discuss potential observational, experimental, and statistical techniques that may assist researchers in providing evidence that the criteria that make up the accepted operational definition of teaching have been met. Supplemental materials for this article may be downloaded from http://lb.psychonomic-journals.org/content/supplemental.

  8. Identifying teaching in wild animals.

    PubMed

    Thornton, Alex; Raihani, Nichola J

    2010-08-01

    After a long period of neglect, the study of teaching in nonhuman animals is beginning to take a more prominent role in research on social learning. Unlike other forms of social learning, teaching requires knowledgeable individuals to play an active role in facilitating learning by the naive. Casting aside anthropocentric requirements for cognitive mechanisms assumed to underpin teaching in our own species, researchers are now beginning to discover evidence for teaching across a wide range of taxa. Nevertheless, unequivocal evidence for teaching remains scarce, with convincing experimental data limited to meerkats, pied babblers, and tandem-running ants. In this review, our aim is to stimulate further research in different species and contexts by providing conceptual and methodological guidelines for identifying teaching, with a focus on natural populations. We begin by highlighting the fact that teaching is a form of cooperative behavior that functions to promote learning in others and show that consideration of these key characteristics is critical in helping to identify suitable targets for future research. We then go on to discuss potential observational, experimental, and statistical techniques that may assist researchers in providing evidence that the criteria that make up the accepted operational definition of teaching have been met. Supplemental materials for this article may be downloaded from http://lb.psychonomic-journals.org/content/supplemental. PMID:20628167

  9. "Geriatricizing" hospitalists: identifying educational opportunities.

    PubMed

    Friedman, Susan M; Gillespie, Suzanne M; Medina-Walpole, Annette M; Caprio, Thomas V; Karuza, Jurgis; McCann, Robert M

    2013-01-01

    The objective of this study was to identify differences between geriatricians and hospitalists in caring for hospitalized older adults, so as to inform faculty development programs that have the goal of improving older patient care. Eleven hospitalists and 13 geriatricians were surveyed regarding knowledge, confidence, and practice patterns in caring for hospitalized older adults, targeting areas previously defined as central to taking care of older hospitalized patients. Overall, geriatricians had more confidence and more knowledge in caring for older hospitalized adults. The areas in which hospitalists expressed the least confidence were in caring for patients with dementia, self-care issues, and care planning. Geriatricians reported more routine medication reviews, functional and cognitive assessments, and fall evaluations. Geriatricians and hospitalists differ in their approach to older adults. Where these differences reflect lack of knowledge or experience, they set the stage for developing curricula to help narrow these gaps. PMID:23971409

  10. Important caves to be identified

    NASA Astrophysics Data System (ADS)

    Criteria to identify significant caves on federal land are being developed by the Interior Department's Bureau of Land Management and the Agriculture Department's Forest Service under requirements of the Federal Cave Resources Protection Act of 1988. The departments gave advance notice of proposed rulemaking March 3 and invited suggestions and comments from the public for 30 days.The law requires protection, to the extent practical, of significant caves on lands administered by the Secretaries of Agriculture and Interior and includes authority to issue and revoke permits for collection and removal of cave resources and special provisions for regulation of cave resources on Indian lands. Final regulations must be published by August 18, 1989.

  11. Identifying vulnerable surface water utilities

    SciTech Connect

    Clark, R.M.; Grayman, W.M.; Males, R.M.; Kilgore, R.

    1989-01-01

    Although industrial discharges from point sources are regulated by the Federal Water Pollution Control Acts, National Pollutant Discharge Elimination System (NPDES), some toxic pollutants continue to be discharged into surface waters. Frequently these same surface waters are major sources of drinking water. The Safe Drinking Water Act Amendments have specified a large number of new contaminant levels, (MCLs) at the microgram per liter level. It is possible that many water utilities finding that these new MCLs are violated will seek to identify upstream dischargers and request that regulatory agencies force them to install discharge controls rather than pay for expensive water treatment processes. The study reported in the paper documents the development of a data base management system and a water quality modeling approach that allows drinking water utilities to assess the impact of these upstream discharges on raw water quality. The report makes recommendations to USEPA for modifying its NPDES procedures.

  12. Identifying methamphetamine exposure in children

    PubMed Central

    Castaneto, Marisol S.; Barnes, Allan J.; Scheidweiler, Karl B.; Schaffer, Michael; Rogers, Kristen K.; Stewart, Deborah; Huestis, Marilyn A.

    2013-01-01

    Introduction Methamphetamine (MAMP) use, distribution and manufacture remain a serious public health and safety problem in the United States, and children environmentally exposed to MAMP face a myriad of developmental, social and health risks, including severe abuse and neglect necessitating child protection involvement. It is recommended that drug-endangered children receive medical evaluation and care with documentation of overall physical and mental conditions and have urine drug testing.1 The primary aim of this study was to determine the best biological matrix to detect MAMP, amphetamine (AMP), methylenedioxymethamphetamine (MDMA), methylenedioxyamphetamine (MDA) and methylenedioxyethylamphetamine (MDEA) in environmentally exposed children. Method 91 children, environmentally exposed to household MAMP intake, were medically evaluated at the Child and Adolescent Abuse Resource and Evaluation (CAARE) Diagnostic and Treatment Center at the University of California, Davis (UCD) Children's Hospital. MAMP, AMP, MDMA, MDA and MDEA were quantified in urine and oral fluid (OF) by gas chromatography mass spectrometry (GCMS) and in hair by liquid chromatography tandem mass spectrometry (LCMSMS). Results Overall drug detection rates in OF, urine and hair were 6.9%, 22.1% and 77.8%, respectively. Seventy children (79%) tested positive for 1 or more drugs in 1 or more matrices. MAMP was the primary analyte detected in all 3 biological matrices. All positive OF (n=5) and 18 of 19 positive urine specimens also had a positive hair test. Conclusion Hair analysis offered a more sensitive tool for identifying MAMP, AMP and MDMA environmental exposure in children than urine or OF testing. A negative urine, or hair test does not exclude the possibility of drug exposure, but hair testing provided the greatest sensitivity for identifying drug-exposed children. PMID:24263642

  13. Identifying and Inactivating Bacterial Spores

    NASA Technical Reports Server (NTRS)

    Newcombe, David; Dekas, Anne; Venkateswaran, Kasthuri

    2009-01-01

    Problems associated with, and new strategies for, inactivating resistant organisms like Bacillus canaveralius (found at Kennedy Space Center during a survey of three NASA cleanrooms) have been defined. Identifying the particular component of the spore that allows its heightened resistance can guide the development of sterilization procedures that are targeted to the specific molecules responsible for resistance, while avoiding using unduly harsh methods that jeopardize equipment. The key element of spore resistance is a multilayered protein shell that encases the spore called the spore coat. The coat of the best-studied spore-forming microbe, B. subtilis, consists of at least 45 proteins, most of which are poorly characterized. Several protective roles for the coat are well characterized including resistance to desiccation, large toxic molecules, ortho-phthalaldehyde, and ultraviolet (UV) radiation. One important long-term specific goal is an improved sterilization procedure that will enable NASA to meet planetary protection requirements without a terminal heat sterilization step. This would support the implementation of planetary protection policies for life-detection missions. Typically, hospitals and government agencies use biological indicators to ensure the quality control of sterilization processes. The spores of B. canaveralius that are more resistant to osmotic stress would serve as a better biological indicator for potential survival than those in use currently.

  14. Priority Planetary Science Missions Identified

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2011-03-01

    The U.S. National Research Council's (NRC) planetary science decadal survey report, released on 7 March, lays out a grand vision for priority planetary science missions for 2013-2022 within a tightly constrained fiscal environment. The cost-conscious report, issued by NRC's Committee on the Planetary Science Decadal Survey, identifies high-priority flagship missions, recommends a number of potential midsized missions, and indicates support for some smaller missions. The report states that the highest-priority flagship mission for the decade is the Mars Astrobiology Explorer-Cacher (MAX-C)—the first of three components of a NASA/European Space Agency Mars sample return campaign—provided that the mission scope can be reduced so that MAX-C costs no more than $2.5 billion. The currently estimated mission cost of $3.5 billion “would take up a disproportionate near-term share of the overall budget for NASA's Planetary Science Division,” the report notes.

  15. Identifying representative trees from ensembles.

    PubMed

    Banerjee, Mousumi; Ding, Ying; Noone, Anne-Michelle

    2012-07-10

    Tree-based methods have become popular for analyzing complex data structures where the primary goal is risk stratification of patients. Ensemble techniques improve the accuracy in prediction and address the instability in a single tree by growing an ensemble of trees and aggregating. However, in the process, individual trees get lost. In this paper, we propose a methodology for identifying the most representative trees in an ensemble on the basis of several tree distance metrics. Although our focus is on binary outcomes, the methods are applicable to censored data as well. For any two trees, the distance metrics are chosen to (1) measure similarity of the covariates used to split the trees; (2) reflect similar clustering of patients in the terminal nodes of the trees; and (3) measure similarity in predictions from the two trees. Whereas the latter focuses on prediction, the first two metrics focus on the architectural similarity between two trees. The most representative trees in the ensemble are chosen on the basis of the average distance between a tree and all other trees in the ensemble. Out-of-bag estimate of error rate is obtained using neighborhoods of representative trees. Simulations and data examples show gains in predictive accuracy when averaging over such neighborhoods. We illustrate our methods using a dataset of kidney cancer treatment receipt (binary outcome) and a second dataset of breast cancer survival (censored outcome).

  16. Identifying problem and compulsive gamblers.

    PubMed Central

    van Es, R.

    2000-01-01

    OBJECTIVE: To present a meta-analysis of current research on the prevalence, identification, and treatment of problem and compulsive gamblers. QUALITY OF EVIDENCE: Problem and compulsive gambling was not a socio-scientific concern until the last two decades. Hence research on this topic is limited. The summary and analysis for this paper relied on computer searches of journal and news abstracts in addition to direct contact with organizations addressing the identification and treatment of compulsive gamblers. MAIN MESSAGE: An estimated 5% of those who gamble run into problems. About 1% of those who gamble are predicted to experience serious problems. Successful treatment of problem and compulsive gambling continues to be a challenge. Although cognitive therapy has been the favoured approach, a combination of several therapeutic approaches is advocated. CONCLUSIONS: Problem and compulsive gambling can present a real health threat. As with other addictions, treatment strategies continue to be a baffling social problem. Aware and informed physicians can have a pivotal role in the difficult process of identifying, acknowledging, and remediating problem and compulsive gambling. PMID:10907572

  17. Can tests identify creative people?

    NASA Astrophysics Data System (ADS)

    Bell, Peter M.

    It is always a popular pursuit by academic administrators to assess the creativity or innovative qualities of scientists in order to evaluate their research capabilities. Of course, traditionally such evaluations have been fraught with subjectivity (i.e., innovative scientists are commonly thought to be weird, under 40 years old, independent, risk-taking, etc.), and thus such evaluations have not been highly valued. In recent years, through testing, the American Chemical Society (ACS) has attempted to give respectability to the art of predicting the creativity of a scientist. ACS, which draws its members from both industrial and academic laboratories, held a symposium on the subject of evaluating the creativity of scientists. The proceedings were published by ACS as ‘Innovation and U.S. Research: Problems and Recommendations’ (W. N. Smith and C.F. Larson, eds., 1980). In the proceedings, as reported in the July 1982 Chemtec (all quotes here are from the Chemtec article), A. Nisson was able to identify only the following two-part characteristic of an innovative person: (1) a low threshold to ‘a state of discomfort with some aspect of the order of things, the status quo,’ and (2) ‘an extraordinarily high level of mental stamina enabling him or her to persist until the state of discomfort is removed.’

  18. Identifying barriers to billing compliance.

    PubMed

    Lorence, Daniel P; Ibrahim, Ibrahim Awad

    2003-01-01

    Programs designed toward the control of health care fraud are leading to increasingly aggressive enforcement and prosecutorial efforts by federal regulators, related to over-reimbursement for service providers. Greater penalties for fraudulent practices have been touted as an effective deterrent to practices that encourage, or fail to prevent, incorrect claims for reimbursement. In such a context, this study sought to examine the extent of compliance management barriers through a national survey of all accredited US health information managers, examining likely barriers to payment of health care claims. Using data from a series of surveys on the stated compliance actions of more than 16,000 health care managers, we find that the publication and dissemination of compliance enforcement regulations had a significant effect on the reduction of fraud. Results further suggest that significant non-adoption of proper billing compliance measures continues to occur, despite the existence of counter-fraud prosecution risk designed to enforce proper compliance. Finally, we identify benchmarks of compliance management and show how they vary across demographic, practice setting, and market characteristics. We find significant variation in influence across practice settings and managed care markets. While greater publicity related to proper billing procedures generally leads to greater compliance awareness, this trend may have created pockets of "institutional non-compliance," which result in an increase in the prevalence of non-compliant management actions. As a more general proposition, we find that it is not sufficient to consider compliance actions independent of institutional or industry-wide influences. PMID:12967244

  19. RECOVIR Software for Identifying Viruses

    NASA Technical Reports Server (NTRS)

    Chakravarty, Sugoto; Fox, George E.; Zhu, Dianhui

    2013-01-01

    Most single-stranded RNA (ssRNA) viruses mutate rapidly to generate a large number of strains with highly divergent capsid sequences. Determining the capsid residues or nucleotides that uniquely characterize these strains is critical in understanding the strain diversity of these viruses. RECOVIR (an acronym for "recognize viruses") software predicts the strains of some ssRNA viruses from their limited sequence data. Novel phylogenetic-tree-based databases of protein or nucleic acid residues that uniquely characterize these virus strains are created. Strains of input virus sequences (partial or complete) are predicted through residue-wise comparisons with the databases. RECOVIR uses unique characterizing residues to identify automatically strains of partial or complete capsid sequences of picorna and caliciviruses, two of the most highly diverse ssRNA virus families. Partition-wise comparisons of the database residues with the corresponding residues of more than 300 complete and partial sequences of these viruses resulted in correct strain identification for all of these sequences. This study shows the feasibility of creating databases of hitherto unknown residues uniquely characterizing the capsid sequences of two of the most highly divergent ssRNA virus families. These databases enable automated strain identification from partial or complete capsid sequences of these human and animal pathogens.

  20. DNA Microarrays for Identifying Fishes

    PubMed Central

    Nölte, M.; Weber, H.; Silkenbeumer, N.; Hjörleifsdottir, S.; Hreggvidsson, G. O.; Marteinsson, V.; Kappel, K.; Planes, S.; Tinti, F.; Magoulas, A.; Garcia Vazquez, E.; Turan, C.; Hervet, C.; Campo Falgueras, D.; Antoniou, A.; Landi, M.; Blohm, D.

    2008-01-01

    In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a “Fish Chip” for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products. PMID:18270778

  1. Identifying ELIXIR Core Data Resources

    PubMed Central

    Durinx, Christine; McEntyre, Jo; Appel, Ron; Apweiler, Rolf; Barlow, Mary; Blomberg, Niklas; Cook, Chuck; Gasteiger, Elisabeth; Kim, Jee-Hyub; Lopez, Rodrigo; Redaschi, Nicole; Stockinger, Heinz; Teixeira, Daniel; Valencia, Alfonso

    2016-01-01

    The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR’s sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure. PMID:27803796

  2. Experimental methods for identifying failure mechanisms

    NASA Technical Reports Server (NTRS)

    Daniel, I. M.

    1983-01-01

    Experimental methods for identifying failure mechanisms in fibrous composites are studied. Methods to identify failure in composite materials includes interferometry, holography, fractography and ultrasonics.

  3. NIH Researchers Identify OCD Risk Gene

    MedlinePlus

    ... News From NIH NIH Researchers Identify OCD Risk Gene Past Issues / Summer 2006 Table of Contents For ... and Alcoholism (NIAAA) have identified a previously unknown gene variant that doubles an individual's risk for obsessive- ...

  4. 29 CFR 4010.7 - Identifying information.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 9 2010-07-01 2010-07-01 false Identifying information. 4010.7 Section 4010.7 Labor... DISCLOSURE REQUIREMENTS ANNUAL FINANCIAL AND ACTUARIAL INFORMATION REPORTING § 4010.7 Identifying information..., http://www.pbgc.gov, the following identifying information with respect to each member of the...

  5. 29 CFR 4010.7 - Identifying information.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 29 Labor 9 2013-07-01 2013-07-01 false Identifying information. 4010.7 Section 4010.7 Labor... DISCLOSURE REQUIREMENTS ANNUAL FINANCIAL AND ACTUARIAL INFORMATION REPORTING § 4010.7 Identifying information..., http://www.pbgc.gov, the following identifying information with respect to each member of the...

  6. Method of identifying plant pathogen tolerance

    DOEpatents

    Ecker, J.R.; Staskawicz, B.J.; Bent, A.F.; Innes, R.W.

    1997-10-07

    A process for identifying a plant having disease tolerance comprising administering to a plant an inhibitory amount of ethylene and screening for ethylene insensitivity, thereby identifying a disease tolerant plant, is described. Plants identified by the foregoing process are also described. 7 figs.

  7. 47 CFR 2.926 - FCC identifier.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false FCC identifier. 2.926 Section 2.926... Authorizations § 2.926 FCC identifier. (a) A grant of equipment authorization issued by the Commission will list the validated FCC Identifier consisting of the grantee code assigned by the FCC pursuant to...

  8. Method of identifying plant pathogen tolerance

    DOEpatents

    Ecker, Joseph R.; Staskawicz, Brian J.; Bent, Andrew F.; Innes, Roger W.

    1997-10-07

    A process for identifying a plant having disease tolerance comprising administering to a plant an inhibitory amount of ethylene and screening for ethylene insensitivity, thereby identifying a disease tolerant plant, is described. Plants identified by the foregoing process are also described.

  9. Ability of Slovakian Pupils to Identify Birds

    ERIC Educational Resources Information Center

    Prokop, Pavol; Rodak, Rastislav

    2009-01-01

    A pupil's ability to identify common organisms is necessary for acquiring further knowledge of biology. We investigated how pupils were able to identify 25 bird species following their song, growth habits, or both features presented simultaneously. Just about 19% of birds were successfully identified by song, about 39% by growth habit, and 45% of…

  10. A Priori Identifiability Analysis of Cardiovascular Models

    PubMed Central

    Kirk, Jonathan A.; Saccomani, Maria P.; Shroff, Sanjeev G.

    2013-01-01

    Model parameters, estimated from experimentally measured data, can provide insight into biological processes that are not experimentally measurable. Whether this optimized parameter set is a physiologically relevant complement to the experimentally measured data, however, depends on the optimized parameter set being unique, a model property known as a priori global identifiability. However, a priori identifiability analysis is not common practice in the biological world, due to the lack of easy-to-use tools. Here we present a program, Differential Algebra for Identifiability of Systems (DAISY), that facilitates identifiability analysis. We applied DAISY to several cardiovascular models: systemic arterial circulation (Windkessel, T-Tube) and cardiac muscle contraction (complex stiffness, crossbridge cycling-based). All models were globally identifiable except the T-Tube model. In this instance, DAISY was able to provide insight into making the model identifiable. We applied numerical parameter optimization techniques to estimate unknown parameters in a model DAISY found globally identifiable. While all the parameters could be accurately estimated, a sensitivity analysis was first necessary to identify the required experimental data. Global identifiability is a prerequisite for numerical parameter optimization, and in a variety of cardiovascular models, DAISY provided a reliable, fast, and simple platform to provide this identifiability analysis. PMID:26726299

  11. Helping You Identify Quality Laboratory Services

    MedlinePlus

    Helping You Identify Quality Laboratory Services Selecting quality health care services for yourself, a relative or friend requires special thought and attention. The Joint Commission has prepared ...

  12. Identifying Bilingual Semantic Neural Representations across Languages

    ERIC Educational Resources Information Center

    Buchweitz, Augusto; Shinkareva, Svetlana V.; Mason, Robert A.; Mitchell, Tom M.; Just, Marcel Adam

    2012-01-01

    The goal of the study was to identify the neural representation of a noun's meaning in one language based on the neural representation of that same noun in another language. Machine learning methods were used to train classifiers to identify which individual noun bilingual participants were thinking about in one language based solely on their…

  13. Identifying Opinion Leaders to Promote Behavior Change

    ERIC Educational Resources Information Center

    Valente, Thomas W.; Pumpuang, Patchareeya

    2007-01-01

    This article reviews 10 techniques used to identify opinion leaders to promote behavior change. Opinion leaders can act as gatekeepers for interventions, help change social norms, and accelerate behavior change. Few studies document the manner in which opinion leaders are identified, recruited, and trained to promote health. The authors categorize…

  14. Self-Identifying Emergency Radio Beacons

    NASA Technical Reports Server (NTRS)

    Friedman, Morton L.

    1987-01-01

    Rescue teams aided by knowledge of vehicle in distress. Similar to conventional emergency transmitters except contains additional timing and modulating circuits. Additions to standard emergency transmitter enable transmitter to send rescuers identifying signal in addition to conventional distress signal created by sweep generator. Data generator contains identifying code.

  15. Healthcare Identifiers legislation: a whiff of fourberie.

    PubMed

    Mendelson, Danuta

    2010-05-01

    The Healthcare Identifiers Bill 2010 (Cth), which will establish "the national e-health Healthcare Identifiers Service to provide that patients, healthcare providers and provider organisations can be consistently identified", is in the process of being enacted by the Australian Federal Parliament. The legislation will enable the government to assign to each "healthcare recipient" a 26-digit electronic "Healthcare Identifier", which will be accessible, with or without the recipient's consent, to a broad range of health care service providers as well as other entities. The individual Healthcare Identifier file will initially contain such identifying information as, where applicable, the Medicare number and/or the Veterans' Affairs number; name; address; gender; date of birth; and "the date of birth accuracy indicator" presumably birth certificate. However, since each "service" provided by a health care provider to a health care recipient will be automatically recorded on each individual's Healthcare Identifier file, in time these electronic files should contain a full record of such services or contacts. Moreover, the Healthcare Identifiers are considered a "key" to, or a "foundation stone" for, the implementation of the shared electronic health records scheme, because they will enable linkage with and retrieval of each patient's clinical records throughout the health care service system. However, there has been virtually no discussion about the legal, ethical and social implications of this legislation. PMID:20552931

  16. Identifying Information Focuses in Listening Comprehension

    ERIC Educational Resources Information Center

    Zhang, Hong-yan

    2011-01-01

    The study explains the process of learners' listening comprehension within Halliday's information theory in functional grammar, including the skills of identifying focuses while listening in college English teaching. Identifying information focuses in listening is proved to improve the students' communicative listening ability by the means of a…

  17. Portable Radiometer Identifies Minerals in the Field

    NASA Technical Reports Server (NTRS)

    Goetz, A. F. H.; Machida, R. A.

    1982-01-01

    Hand-held optical instrument aids in identifying minerals in field. Can be used in exploration for minerals on foot or by aircraft. The radiometer is especially suitable for identifying clay and carbonate minerals. Radiometer measures reflectances of mineral at two wavelengths, computes ratio of reflectances, and displays ratio to user.

  18. EZID: Long term identifiers made easy (Invited)

    NASA Astrophysics Data System (ADS)

    Starr, J.

    2013-12-01

    Scholarly research is producing ever increasing amounts of digital research data, and this data should be managed throughout the research life cycle both as part of good scientific practice, but also to comply with funder mandates, such as the 2013 OSTP Public Access Memo (http://www.whitehouse.gov/sites/default/files/microsites/ostp/ostp_public_access_memo_2013.pdf). By assigning unique and persistent identifiers to data objects, data managers can gain control and flexibility over what can be a daunting task. This is due to the fact that the objects can be moved to new locations without disruption to links, as long as the identifier target is maintained. EZID is a tool that makes assigning and maintaining unique, persistent identifiers easy. It was designed and built by California Digital Library (CDL) and has both a user interface and a RESTful API. EZID currently offers services for two globally unique, persistent identifier schemes: Digital Object Identifiers (DOIs) and Archival Resource Keys (ARKs). DOIs are identifiers originating from the publishing world and are in widespread use for journal articles. CDL is able to offer DOIs because of being a founding member of DataCite (http://www.datacite.org/), an international consortium established to provide easier access to scientific research data on the Internet. ARKs are identifiers originating from the library, archive and museum community. Like DOIs, they become persistent when the objects and identifier forwarding information is maintained. DOIs and ARKs have a key role in data management and, therefore, in data management plans. DOIs are the recommended identifier for use in data citation, and ARKs provide the maximum flexibility needed for data documentation and management throughout the early phases of a project. The two identifier schemes are able to be used together, and EZID is made to work with both. EZID clients, coming from education, research, government, and the private sector, are utilizing the

  19. Structural Identifiability of Dynamic Systems Biology Models

    PubMed Central

    Villaverde, Alejandro F.

    2016-01-01

    A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas. PMID:27792726

  20. Discrimination of SM-identified individuals.

    PubMed

    Wright, Susan

    2006-01-01

    The belief that sadomasochism (SM) is violence or abusive behavior has resulted in harassment, physical attacks, and discrimination against SM-identified individuals. Historically, they were often opposed by self-identified feminists. One reason the women who practiced SM were targeted was the official opposition to sadomasochistic practices promulgated by the National Organization for Women (NOW). Current statistics of incidents of discrimination, harassment and physical attacks against SM-identified individuals and SM groups are compiled by the National Coalition for Sexual Freedom (NCSF). PMID:16803765

  1. Researchers Identify Genes Linked to Hot Flashes

    MedlinePlus

    ... fullstory_161579.html Researchers Identify Genes Linked to Hot Flashes Mutations found in women of all races, ... Some women may be genetically predisposed to suffer hot flashes before or during menopause, a new study ...

  2. Identifying Pornographic Materials with Judgment Analysis

    ERIC Educational Resources Information Center

    Houston, Judith A.; Houston, Samuel R.

    1974-01-01

    The primary purpose of this study was to determine if a policy-capturing methodology (JAN) which has been successfully utilized in military and educational research could be adapted for use as a procedure in identifying pornographic material. (Author)

  3. Study Identifies Genetic Subtypes of Crohn's Disease

    MedlinePlus

    ... medlineplus.gov/news/fullstory_161499.html Study Identifies Genetic Subtypes of Crohn's Disease Findings may help explain ... disease appears to have at least two distinct genetic subtypes, which could explain why the condition is ...

  4. Study Identifies New Lymphoma Treatment Target

    Cancer.gov

    NCI researchers have identified new therapeutic targets for diffuse large B-cell lymphoma. Drugs that hit these targets are under clinical development and the researchers hope to begin testing them in clinical trials of patients with DLBCL.

  5. Identifying signs of intimate partner violence.

    PubMed

    Ali, Parveen; McGarry, Julie; Dhingra, Katie

    2016-02-01

    Intimate partner violence is a major public health and social problem that affects people everywhere. Nurses can play an important role in identifying victims who present to healthcare settings with domestic abuse-related health issues. Evidence suggests that most women who present to emergency departments have experienced domestic abuse at some point in their lives, but that only 5% are identified by healthcare professionals. To identify and respond to victims effectively, emergency nurses must understand domestic abuse and its associated complexities. This article provides an overview of these issues, including the different types of abuse, and their prevalence, causes and effects on health. The article also explores how emergency nurses can identify and manage the effects of violence at work. PMID:26853673

  6. Asteroid Redirect Mission: Identify, Redirect, Explore

    NASA Video Gallery

    NASA is developing a first-ever mission to identify, capture and redirect a near-Earth asteroid to a stable orbit around the moon, where astronauts will explore it in the 2020s, returning with samp...

  7. Newly identified YSO candidates towards LDN 1188

    NASA Astrophysics Data System (ADS)

    Marton , G.; Verebélyi, E.; Kiss, Cs.; Smidla, J.

    2013-11-01

    We present an analysis of young stellar object (YSO) candidates towards the LDN 1188 molecular cloud. The YSO candidates were selected from the WISE all-sky catalogue, based on a statistical method. We found 601 candidates in the region, and classified them as Class I, Flat, and Class II YSOs. Groups were identified and described with the Minimal Spanning Tree (MST) method. Previously identified molecular cores show evidence of ongoing star formation at different stages throughout the cloud complex.

  8. ORCID Author Identifiers: A Primer for Librarians.

    PubMed

    Akers, Katherine G; Sarkozy, Alexandra; Wu, Wendy; Slyman, Alison

    2016-01-01

    The ORCID (Open Researcher and Contributor ID) registry helps disambiguate authors and streamline research workflows by assigning unique 16-digit author identifiers that enable automatic linkages between researchers and their scholarly activities. This article describes how ORCID works, the benefits of using ORCID, and how librarians can promote ORCID at their institutions by raising awareness of ORCID, helping researchers create and populate ORCID profiles, and integrating ORCID identifiers into institutional repositories and other university research information systems.

  9. ORCID Author Identifiers: A Primer for Librarians.

    PubMed

    Akers, Katherine G; Sarkozy, Alexandra; Wu, Wendy; Slyman, Alison

    2016-01-01

    The ORCID (Open Researcher and Contributor ID) registry helps disambiguate authors and streamline research workflows by assigning unique 16-digit author identifiers that enable automatic linkages between researchers and their scholarly activities. This article describes how ORCID works, the benefits of using ORCID, and how librarians can promote ORCID at their institutions by raising awareness of ORCID, helping researchers create and populate ORCID profiles, and integrating ORCID identifiers into institutional repositories and other university research information systems. PMID:27054531

  10. Connecting Research and Researchers: ORCID Identifiers (Invited)

    NASA Astrophysics Data System (ADS)

    Haak, L.; Bryant, R.

    2013-12-01

    Lack of standards for identification of researchers is a major challenge for the research community. It is difficult not only to unambiguously associate researchers with their own work, but also to track use and re-use of those works. The goal of ORCID (orcid.org) is to connect research with researchers, ultimately saving researchers time in entering data, improving discoverability, and facilitating the flow of research information and data re-use. ORCID is a community-driven non-profit organization that provides an open registry of unique persistent identifiers for researchers. We work collaboratively with the research community to embed these identifiers in research workflows, including manuscript submission, grant application, and data set deposit. In this presentation, we will provide an overview of ORCID, an in particular how it is being used as a switchboard to connect existing but fragmented researcher identifiers. ORCID also provides researchers search and link tools to link their ORCID identifier to their existing datasets, grants, other research works, and an automated method to link new works to their identifier. ORCID is fundamental to solving the name ambiguity problem for researchers and scholars. Together with unique and persistent identifiers for publications, data sets, and research samples, ORCID is an essential underpinning needed to support interoperability between research systems.

  11. IDENTIFYING COLLISIONAL FAMILIES IN THE KUIPER BELT

    SciTech Connect

    Marcus, Robert A.; Ragozzine, Darin; Murray-Clay, Ruth A.; Holman, Matthew J.

    2011-05-20

    The identification and characterization of numerous collisional families-clusters of bodies with a common collisional origin-in the asteroid belt has added greatly to the understanding of asteroid belt formation and evolution. More recent study has also led to an appreciation of physical processes that had previously been neglected (e.g., the Yarkovsky effect). Collisions have certainly played an important role in the evolution of the Kuiper Belt as well, though only one collisional family has been identified in that region to date, around the dwarf planet Haumea. In this paper, we combine insights into collisional families from numerical simulations with the current observational constraints on the dynamical structure of the Kuiper Belt to investigate the ideal sizes and locations for identifying collisional families. We find that larger progenitors (r {approx} 500 km) result in more easily identifiable families, given the difficulty in identifying fragments of smaller progenitors in magnitude-limited surveys, despite their larger spread and less frequent occurrence. However, even these families do not stand out well from the background. Identifying families as statistical overdensities is much easier than characterizing families by distinguishing individual members from interlopers. Such identification seems promising, provided the background population is well known. In either case, families will also be much easier to study where the background population is small, i.e., at high inclinations. Overall, our results indicate that entirely different techniques for identifying families will be needed for the Kuiper Belt, and we provide some suggestions.

  12. Identifying glass compositions in fly ash

    NASA Astrophysics Data System (ADS)

    Aughenbaugh, Katherine; Stutzman, Paul; Juenger, Maria

    2016-01-01

    In this study, four Class F fly ashes were studied with a scanning electron microscope; the glassy phases were identified and their compositions quantified using point compositional analysis with k-means clustering and multispectral image analysis. The results showed that while the bulk oxide contents of the fly ashes were different, the four fly ashes had somewhat similar glassy phase compositions. Aluminosilicate glasses (AS), calcium aluminosilicate glasses (CAS), a mixed glass, and, in one case, a high iron glass were identified in the fly ashes. Quartz and iron crystalline phases were identified in each fly ash as well. The compositions of the three main glasses identified, AS, CAS, and mixed glass, were relatively similar in each ash. The amounts of each glass were varied by fly ash, with the highest calcium fly ash containing the most of calcium-containing glass. Some of the glasses were identified as intermixed in individual particles, particularly the calcium-containing glasses. Finally, the smallest particles in the fly ashes, with the most surface area available to react in alkaline solution, such as when mixed with portland cement or in alkali-activated fly ash, were not different in composition than the large particles, with each of the glasses represented. The method used in the study may be applied to a fly ash of interest for use as a cementing material in order to understand its potential for reactivity.

  13. Scientometric methods for identifying emerging technologies

    DOEpatents

    Abercrombie, Robert K; Schlicher, Bob G; Sheldon, Frederick T

    2015-11-03

    Provided is a method of generating a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial application. During the period of innovation and technology transfer, the impact of scholarly works, patents and on-line web news sources are identified. As trends develop, currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e., scholarly publications and citation, worldwide patents, news archives, and on-line mapping networks) are assembled to become one collective network (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the example subject domain.

  14. Identifying Adverse Drug Events by Relational Learning.

    PubMed

    Page, David; Costa, Vítor Santos; Natarajan, Sriraam; Barnard, Aubrey; Peissig, Peggy; Caldwell, Michael

    2012-07-01

    The pharmaceutical industry, consumer protection groups, users of medications and government oversight agencies are all strongly interested in identifying adverse reactions to drugs. While a clinical trial of a drug may use only a thousand patients, once a drug is released on the market it may be taken by millions of patients. As a result, in many cases adverse drug events (ADEs) are observed in the broader population that were not identified during clinical trials. Therefore, there is a need for continued, post-marketing surveillance of drugs to identify previously-unanticipated ADEs. This paper casts this problem as a reverse machine learning task, related to relational subgroup discovery and provides an initial evaluation of this approach based on experiments with an actual EMR/EHR and known adverse drug events. PMID:24955289

  15. Photoacoustic tomography to identify inflammatory arthritis

    NASA Astrophysics Data System (ADS)

    Rajian, Justin Rajesh; Girish, Gandikota; Wang, Xueding

    2012-09-01

    Identifying neovascularity (angiogenesis) as an early feature of inflammatory arthritis can help in early accurate diagnosis and treatment monitoring of this disease. Photoacoustic tomography (PAT) is a hybrid imaging modality which relies on intrinsic differences in the optical absorption among the tissues being imaged. Since blood has highly absorbing chromophores including both oxygenated and deoxygenated hemoglobin, PAT holds potential in identifying early angiogenesis associated with inflammatory joint diseases. PAT is used to identify changes in the development of inflammatory arthritis in a rat model. Imaging at two different wavelengths, 1064 nm and 532 nm, on rats revealed that there is a significant signal enhancement in the ankle joints of the arthritis affected rats when compared to the normal control group. Histology images obtained from both the normal and the arthritis affected rats correlated well with the PAT findings. Results support the fact that the emerging PAT could become a new tool for clinical management of inflammatory arthritis.

  16. Identifying Turbulent Structures through Topological Segmentation

    SciTech Connect

    Bremer, Peer-Timo; Gruber, Andrea; Bennett, Janine C.; Gyulassy, Attila; Kolla, Hemanth; Chen, Jacqueline H.; Grout, Ray W.

    2016-01-01

    A new method of extracting vortical structures from a turbulent flow is proposed whereby topological segmentation of an indicator function scalar field is used to identify the regions of influence of the individual vortices. This addresses a long-standing challenge in vector field topological analysis: indicator functions commonly used produce a scalar field based on the local velocity vector field; reconstructing regions of influence for a particular structure requires selecting a threshold to define vortex extent. In practice, the same threshold is rarely meaningful throughout a given flow. By also considering the topology of the indicator field function, the characteristics of vortex strength and extent can be separated and the ambiguity in the choice of the threshold reduced. The proposed approach is able to identify several types of vortices observed in a jet in cross-flow configuration simultaneously where no single threshold value for a selection of common indicator functions appears able to identify all of these vortex types.

  17. Identifying gaps in international food safety regulation.

    PubMed

    McGrady, Benn; Ho, Christina S

    2011-01-01

    The rise in food importation in countries such as the United States, coupled with food safety incidents, has led to increased concern with the safety of imported food. This concern has prompted discussion of how international law and governance mechanisms might enhance food safety. This paper identifies the objectives underlying multilateral approaches to food safety such as raising food safety standards abroad, information sharing and ensuring market access. The paper then explores how these objectives are integrated into the international system and identifies how the current state of the law creates imbalances in the pursuit of these objectives.

  18. On identifiability of flexible structure parameters

    NASA Technical Reports Server (NTRS)

    Joshi, S. M.; Goglia, G. L.

    1983-01-01

    This report investigates the identifiability of modal parameters of flexible structures. Expressions are derived for Cramer-Rao lower bounds for the modal parameters, that is, frequencies, damping ratios and mode shapes or slopes. The optimal initial state, which maximizes the trace of the Fisher information matrix in the absence of persistent input, is obtained. The concepts discussed are applied to a finite-element model of the 122 meter hoop/column antenna. The numerical results show that the identifiability of the structural frequencies is excellent, followed by that of the damping ratios and the mode-slopes.

  19. Identifying node importance in complex networks

    NASA Astrophysics Data System (ADS)

    Hu, Ping; Fan, Wenli; Mei, Shengwei

    2015-07-01

    In this paper, we propose a novel node importance evaluation method from the perspective of the existence of mutual dependence among nodes. The node importance comprises its initial importance and the importance contributions from both the adjacent and non-adjacent nodes according to the dependence strength between them. From the simulation analyses on an example network and the ARPA network, we observe that our method can well identify the node importance. Then, the cascading failures on the Netscience and E-mail networks demonstrate that the networks are more vulnerable when continuously removing the important nodes identified by our method, which further proves the accuracy of our method.

  20. Identifying, analysing and solving problems in practice.

    PubMed

    Hewitt-Taylor, Jaqui

    When a problem is identified in practice, it is important to clarify exactly what it is and establish the cause before seeking a solution. This solution-seeking process should include input from those directly involved in the problematic situation, to enable individuals to contribute their perspective, appreciate why any change in practice is necessary and what will be achieved by the change. This article describes some approaches to identifying and analysing problems in practice so that effective solutions can be devised. It includes a case study and examples of how the Five Whys analysis, fishbone diagram, problem tree analysis, and Seven-S Model can be used to analyse a problem.

  1. Inverted File Compression through Document Identifier Reassignment.

    ERIC Educational Resources Information Center

    Shieh, Wann-Yun; Chen, Tien-Fu; Shann, Jean Jyh-Jiun; Chung, Chung-Ping

    2003-01-01

    Discusses the use of inverted files in information retrieval systems and proposes a document identifier reassignment method to reduce the average gap values in an inverted file. Highlights include the d-gap technique; document similarity; heuristic algorithms; file compression; and performance evaluation from a simulation environment. (LRW)

  2. 34 CFR 300.32 - Personally identifiable.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 2 2010-07-01 2010-07-01 false Personally identifiable. 300.32 Section 300.32 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF SPECIAL EDUCATION AND REHABILITATIVE SERVICES, DEPARTMENT OF EDUCATION ASSISTANCE TO STATES FOR THE EDUCATION...

  3. Student Success Factors: Identifying Key Predictors

    ERIC Educational Resources Information Center

    Sulaiman, Ainin; Mohezar, Suhana

    2006-01-01

    The authors' main aim in this study was to identify key predictors of Master of Business Administration (MBA) students' academic performance. The authors measured performance by the students' cumulative grade point average achieved, using data from the Students Information Systems and Application database. The authors found that a student's…

  4. National Board Certification Identifies Strong Teachers

    ERIC Educational Resources Information Center

    Education Digest: Essential Readings Condensed for Quick Review, 2009

    2009-01-01

    Advanced certification through the National Board for Professional Teaching Standards (NBPTS) is an effective way to identify highly skilled teachers, according to a congressionally mandated report from the National Research Council. Students taught by NBPTS-certified teachers make greater gains on achievement tests than students taught by…

  5. A screening cascade to identify ERβ ligands

    PubMed Central

    Filgueira, Carly S.; Benod, Cindy; Lou, Xiaohua; Gunamalai, Prem S.; Villagomez, Rosa A.; Strom, Anders; Gustafsson, Jan-Åke; Berkenstam, Anders L.; Webb, Paul

    2014-01-01

    The establishment of effective high throughput screening cascades to identify nuclear receptor (NR) ligands that will trigger defined, therapeutically useful sets of NR activities is of considerable importance. Repositioning of existing approved drugs with known side effect profiles can provide advantages because de novo drug design suffers from high developmental failure rates and undesirable side effects which have dramatically increased costs. Ligands that target estrogen receptor β (ERβ) could be useful in a variety of diseases ranging from cancer to neurological to cardiovascular disorders. In this context, it is important to minimize cross-reactivity with ERα, which has been shown to trigger increased rates of several types of cancer. Because of high sequence similarities between the ligand binding domains of ERα and ERβ, preferentially targeting one subtype can prove challenging. Here, we describe a sequential ligand screening approach comprised of complementary in-house assays to identify small molecules that are selective for ERβ. Methods include differential scanning fluorimetry, fluorescence polarization and a GAL4 transactivation assay. We used this strategy to screen several commercially-available chemical libraries, identifying thirty ERβ binders that were examined for their selectivity for ERβ versus ERα, and tested the effects of selected ligands in a prostate cancer cell proliferation assay. We suggest that this approach could be used to rapidly identify candidates for drug repurposing. PMID:25422593

  6. Identifying the Culturally Different Gifted Student.

    ERIC Educational Resources Information Center

    Chambers, Jack A.; Barron, Frank

    The study was designed to provide a relatively simple method of identifying gifted Mexican-American elementary school children, using as Ss approximately 298 Mexican-Americans (in grades 3-6) from both urban and rural schools. Ss were rated by present and former teachers on traits found to be characteristic of highly creative and talented…

  7. Problems Identifying Independent and Dependent Variables

    ERIC Educational Resources Information Center

    Leatham, Keith R.

    2012-01-01

    This paper discusses one step from the scientific method--that of identifying independent and dependent variables--from both scientific and mathematical perspectives. It begins by analyzing an episode from a middle school mathematics classroom that illustrates the need for students and teachers alike to develop a robust understanding of…

  8. How to Identify High-Growth Schools

    ERIC Educational Resources Information Center

    Pfeiffer, Linda E.

    2015-01-01

    When researching school options, parents may want to look for schools with high-growth scores which, according to research, may be indicators of other characteristics such as programming, leadership, culture, and size. This quick guide offers parents tips on how to identify high-growth schools and what to ask when evaluating school options. An…

  9. Using lice to identify cowbird hosts

    USGS Publications Warehouse

    Hahn, D.C.; Osenton, P.C.; Price, R.W.

    1995-01-01

    Avian lice may link fledgling Brown-headed Cowbirds to the host species that raised them. Lice, if host-specific and transferred to nestling cowbirds, could serve to identify the principal host species raising cowbirds in a local area. This approach of trapping cowbird fledglings in a feeding flock, then collecting and identifying the lice they carry is economical. The alternative requires a team of people to locate large numbers of parasitized host nests. We trapped 250 cowbird fledglings during June-August 1994 on Patuxent Research Center, and from them we collected 426 lice identified as representing 6 genera and 12 species. We. also collected and identified 347 lice from 30 known host species that were mist-netted on our Center. The lice found on cowbird fledglings in this population can be linked to Wood Thrush, Red-eyed Vireo, Common Yellowthroat, Rufous-sided Towhee, Red-winged Blackbird, Common Grackle, Song Sparrow, Field Sparrow, and Tree sparrow, based on this study and also on published reports.

  10. Methods for Identifying Versioned and Plagiarized Documents.

    ERIC Educational Resources Information Center

    Hoad, Timothy C.; Zobel, Justin

    2003-01-01

    Describes research that was conducted to develop and evaluate techniques for identifying plagiarism, revisions, and different versions of online documents. Highlights include ranking; parsing; similarity measures; identity measures; fingerprinting documents; measuring effectiveness via recall and precision; and experiments on two document…

  11. Identifying the Multiple Intelligences of Your Students

    ERIC Educational Resources Information Center

    McClellan, Joyce A.; Conti, Gary J.

    2008-01-01

    One way of addressing individual differences among adult learners is to identify the Multiple Intelligences of the learner. Multiple Intelligences refers to the concept developed by Howard Gardner that challenges the traditional view of intelligence and explains the presence of nine different Multiple Intelligences. The purpose of this study was…

  12. Identifying Mentors for Student Employees on Campus

    ERIC Educational Resources Information Center

    Frock, David

    2015-01-01

    Purpose: This exploratory research project aims to seek an effective process for identifying supervisors of part-time student employees who also serve in a mentoring capacity. Design/methodology/approach: This paper is based on a review of literature and an evaluation process focused on established traits and functions of mentoring as applied to…

  13. DOI: A New Identifier for Digital Content.

    ERIC Educational Resources Information Center

    Berinstein, Paula

    1998-01-01

    Previews Digital Object Identifiers (DOIs), a potential unifying classification system for the Web and the Internet developed by the Association of American Publishers and the Corporation for National Research Initiatives. Discusses issues and problems surrounding DOI implementation and usage and how DOI would affect publishers, users,…

  14. The SAT Gender Gap: Identifying the Causes.

    ERIC Educational Resources Information Center

    Rosser, Phyllis

    Questions on the Scholastic Aptitude Test (SAT) with the largest score differences between women and men of all racial and ethnic groups were identified. Patterns of difficulty that would explain the SAT's continuing underprediction of female first-year college performance were studied. An item analysis of one form of the June 1986 SAT for 1,112…

  15. Identifying Protein-Calorie Malnutrition Workshop.

    ERIC Educational Resources Information Center

    Walker, Susan S.; Barker, Ellen M.

    Instructional materials are provided for a workshop to enable participants to assist in identifying patients at risk with protein-calorie malnutrition and in corrrecting this nutritional deficiency. Representative topics are nutrients; protein, mineral, and vitamin sources, functions, and deficiency symptoms; malnutrition; nutritional deficiency…

  16. Can Effective Teacher Behavior Be Identified?

    ERIC Educational Resources Information Center

    Bonesronning, Hans

    2004-01-01

    The present paper departs from the hypothesis that successful teachers are characterized by being able to manipulate student effort. Grading is identified as a potential teachers' tool, and its quantitative importance is investigated by estimation of an education production function. The main econometric problems are omitted variables biases due…

  17. Identify Your Brand, Before You Market.

    ERIC Educational Resources Information Center

    Claggett, Laura

    2002-01-01

    Discusses marketing in special libraries and suggests that librarians need to identify library services that set them apart from others. Highlights include the competitive environment and alternatives for the consumer; value that the library offers; targeting consumers; return on investment; and determining why consumers choose your services. (LRW)

  18. Embedded sensor having an identifiable orientation

    DOEpatents

    Bennett, Thomas E.; Nelson, Drew V.

    2002-01-01

    An apparatus and method is described wherein a sensor, such as a mechanical strain sensor, embedded in a fiber core, is "flagged" to identify a preferred orientation of the sensor. The identifying "flag" is a composite material, comprising a plurality of non-woven filaments distributed in a resin matrix, forming a small planar tab. The fiber is first subjected to a stimulus to identify the orientation providing the desired signal response, and then sandwiched between first and second layers of the composite material. The fiber, and therefore, the sensor orientation is thereby captured and fixed in place. The process for achieving the oriented fiber includes, after identifying the fiber orientation, carefully laying the oriented fiber onto the first layer of composite, moderately heating the assembled layer for a short period in order to bring the composite resin to a "tacky" state, heating the second composite layer as the first, and assembling the two layers together such that they merge to form a single consolidated block. The consolidated block achieving a roughly uniform distribution of composite filaments near the embedded fiber such that excess resin is prevented from "pooling" around the periphery of the fiber.

  19. Identifying Effectiveness Criteria for Internet Payment Systems.

    ERIC Educational Resources Information Center

    Shon, Tae-Hwan; Swatman, Paula M. C.

    1998-01-01

    Examines Internet payment systems (IPS): third-party, card, secure Web server, electronic token, financial electronic data interchange (EDI), and micropayment based. Reports the results of a Delphi survey of experts identifying and classifying IPS effectiveness criteria and classifying types of IPS providers. Includes the survey invitation letter…

  20. Identifying Determinants of Commitment and Turnover Behavior.

    ERIC Educational Resources Information Center

    Grady, Thomas L.

    A study tested the precursors to vocational teachers' commitment to teaching as suggested by the commitment model proposed by Pierce and Dunham. Important consequences of commitment were examined by identifying relationships between commitment, behavioral intentions, and resulting turnover. The study examined the entire population of teachers…

  1. Identifying Benefit Segments among College Students.

    ERIC Educational Resources Information Center

    Brown, Joseph D.

    1991-01-01

    Using concept of market segmentation (dividing market into distinct groups requiring different product benefits), surveyed 398 college students to determine benefit segments among students selecting a college to attend and factors describing each benefit segment. Identified one major segment of students (classroomers) plus three minor segments…

  2. Identifying Specific Comprehension Deficits in Children

    ERIC Educational Resources Information Center

    Gifford, Diane Baty

    2013-01-01

    Research has shown that educators may be missing an under-identified population of approximately 10 percent of typically developing children, who have fluent, age-appropriate decoding and word recognition skills, yet have specific difficulties with other higher-level text processing factors. These children are said to have specific comprehension…

  3. Identifying Teaching Methods that Engage Entrepreneurship Students

    ERIC Educational Resources Information Center

    Balan, Peter; Metcalfe, Mike

    2012-01-01

    Purpose: Entrepreneurship education particularly requires student engagement because of the complexity of the entrepreneurship process. The purpose of this paper is to describe how an established measure of engagement can be used to identify relevant teaching methods that could be used to engage any group of entrepreneurship students.…

  4. Neoplasms identified in free-flying birds

    USGS Publications Warehouse

    Siegfried, L.M.

    1983-01-01

    Nine neoplasms were identified in carcasses of free-flying wild birds received at the National Wildlife Health Laboratory; gross and microscopic descriptions are reported herein. The prevalence of neoplasia in captive and free-flying birds is discussed, and lesions in the present cases are compared with those previously described in mammals and birds.

  5. Identifying Ethical Hypernorms for Accounting Educators

    ERIC Educational Resources Information Center

    Siegel, Philip H.; Mintz, Steven; Naser-Tavakolian, Mohsen; O'Shaughnessy, John

    2012-01-01

    Accounting educators have a unique role in academe because students learn about codes of ethics that will guide their actions as professionals. We identify hypernorms related to internal auditing educators that reflect unethical behaviors believed to be universally unacceptable by that community. We then compare the results to a prior survey of…

  6. Identify, Organize, and Retrieve Items Using Zotero

    ERIC Educational Resources Information Center

    Clark, Brian; Stierman, John

    2009-01-01

    Librarians build collections. To do this they use tools that help them identify, organize, and retrieve items for the collection. Zotero (zoh-TAIR-oh) is such a tool that helps the user build a library of useful books, articles, web sites, blogs, etc., discovered while surfing online. A visit to Zotero's homepage, www.zotero.org, shows a number of…

  7. Diagnostics Tools Identify Faults Prior to Failure

    NASA Technical Reports Server (NTRS)

    2013-01-01

    Through the SBIR program, Rochester, New York-based Impact Technologies LLC collaborated with Ames Research Center to commercialize the Center s Hybrid Diagnostic Engine, or HyDE, software. The fault detecting program is now incorporated into a software suite that identifies potential faults early in the design phase of systems ranging from printers to vehicles and robots, saving time and money.

  8. Identifying Concrete and Formal Operational Children.

    ERIC Educational Resources Information Center

    Docherty, Edward M.

    This paper presents a study designed to determine if groups of concrete and formal operational children can be identified through the technique of cluster analysis, using a battery of Piagetian tasks. A Total of 64 subjects, 8 boys and 8 girls from each of the second, fourth, sixth, and eighth grade levels, were selected from a public elementary…

  9. Techniques for identifying predators of goose nests

    USGS Publications Warehouse

    Anthony, R.M.; Grand, J.B.; Fondell, T.F.; Miller, David A.

    2006-01-01

    We used cameras and artificial eggs to identify nest predators of dusky Canada goose Branta canadensis occidentalis nests during 1997-2000. Cameras were set up at 195 occupied goose nests and 60 artificial nests. We placed wooden eggs and domestic goose eggs that were emptied and then filled with wax or foam in an additional 263 natural goose nests to identify predators from marks in the artificial eggs. All techniques had limitations, but each correctly identified predators and estimated their relative importance. Nests with cameras had higher rates of abandonment than natural nests, especially during laying. Abandonment rates were reduced by deploying artificial eggs late in laying and reducing time at nests. Predation rates for nests with cameras were slightly lower than for nests without cameras. Wax-filled artificial eggs caused mortality of embryos in natural nests, but were better for identifying predator marks at artificial nests. Use of foam-filled artificial eggs in natural nests was the most cost effective means of monitoring nest predation. ?? Wildlife Biology (2006).

  10. Odor recognition: familiarity, identifiability, and encoding consistency.

    PubMed

    Rabin, M D; Cain, W S

    1984-04-01

    The investigation examined the association between the perceived identity of odorous stimuli and the ability to recognize the previous occurrence of them. The stimuli comprised 20 relatively familiar odorous objects such as chocolate, leather, popcorn, and soy sauce. Participants rated the familiarity of the odors and sought to identify them. At various intervals up to 7 days after initial inspection, the participants sought to recognize the odors among sets of distractor odors that included such items as soap, cloves, pipe tobacco, and so on. The recognition response entailed a confidence rating as to whether or not an item had appeared in the original set. At the time of testing, the participants also sought to identify the stimuli again. The results upheld previous findings of excellent initial recognition memory for environmentally relevant odors and slow forgetting. The results also uncovered, for the first time, a strong association between recognition memory and identifiability, rated familiarity, and the ability to use an odor label consistently at inspection and subsequent testing. Encodability seems to enhance rather than to permit recognizability. Even items identified incorrectly or inconsistently were recognized at levels above chance.

  11. Identifying Advanced Technologies for Education's Future.

    ERIC Educational Resources Information Center

    Moore, Gwendolyn B.; Yin, Robert K.

    A study to determine how three advanced technologies might be applied to the needs of special education students helped inspire the development of a new method for identifying such applications. This new method, named the "Hybrid Approach," combines features of the two traditional methods: technology-push and demand-pull. Technology-push involves…

  12. Identifying marker typing incompatibilities in linkage analysis

    SciTech Connect

    Stringham, H.M.; Boehnke, M.

    1996-10-01

    A common problem encountered in linkage analyses is that execution of the computer program is halted because of genotypes in the data that are inconsistent with Mendelian inheritance. Such inconsistencies may arise because of pedigree errors or errors in typing. In some cases, the source of the inconsistencies is easily identified by examining the pedigree. In others, the error is not obvious, and substantial time and effort are required to identify the responsible genotypes. We have developed two methods for automatically identifying those individuals whose genotypes are most likely the cause of the inconsistencies. First, we calculate the posterior probability of genotyping error for each member of the pedigree, given the marker data on all pedigree members and allowing anyone in the pedigree to have an error. Second, we identify those individuals whose genotypes could be solely responsible for the inconsistency in the pedigree. We illustrate these methods with two examples: one a pedigree error, the second a genotyping error. These methods have been implemented as a module of the pedigree analysis program package MENDEL. 9 refs., 2 figs., 2 tabs.

  13. Automated igneous rock identifiers for Mars Exploration

    NASA Astrophysics Data System (ADS)

    Gulick, V. C.; Morris, R. L.; Gazis, P.; Bishop, J. L.; Alena, R.; Hart, S. D.; Horton, A.

    2003-04-01

    A key task for human or robotic explorers on the surface of Mars is choosing which particular rock or mineral samples should be selected for more intensive study. The usual challenges of such a task are compounded by the lack of sensory input available to a suited astronaut or the limited downlink bandwidth available to a rover. Additional challenges facing a human mission include limited surface time and the similarities in appearance of important minerals (e.g. carbonates, silicates, salts). Yet the choice of which sample to collect is critical. To address this challenge we are developing science analysis algorithms to interface with a Geologist's Field Assistant (GFA) device that will allow robotic or human remote explorers to better sense and explore their surroundings during limited surface excursions [1]. We aim for our algorithms to interpret spectral and imaging data obtained by various sensors. Our algorithms, for example, will identify key minerals, rocks, and sediments from mid-IR, Raman, and visible/near-IR spectra as well as from high-resolution and microscopic images to help interpret data and to provide high-level advice to the remote explorer. A top-level system will consider multiple inputs from raw sensor data output by imagers and spectrometers (visible/near-IR, mid-IR, and Raman) as well as human opinion to identify rock and mineral samples. Our prototype image analysis system identifies some igneous rocks from texture and color information. Spectral analysis algorithms have also been developed that successfully identify quartz, silica polymorphs, calcite, pyroxene, and jarosite from both visible/near-IR and mid-IR spectra. We have also developed spectral recognizers that identify high-iron pyroxenes and iron-bearing minerals using visible/near-IR spectra only. We are building a combined image and spectral database of rocks and minerals with which to continue development of our algorithms. Future plans include developing algorithms to identify

  14. Data Identifiers and Citations Enable Reproducible Science

    NASA Astrophysics Data System (ADS)

    Tilmes, C.

    2011-12-01

    Modern science often involves data processing with tremendous volumes of data. Keeping track of that data has been a growing challenge for data center. Researchers who access and use that data don't always reference and cite their data sources adequately for consumers of their research to follow their methodology or reproduce their analyses or experiments. Recent research has led to recommendations for good identifiers and citations that can help address this problem. This paper will describe some of the best practices in data identifiers, reference and citation. Using a simplified example scenario based on a long term remote sensing satellite mission, it will explore issues in identifying dynamic data sets and the importance of good data citations for reproducibility. It will describe the difference between granule and collection level identifiers, using UUIDs and DOIs to illustrate some recommendations for developing identifiers and assigning them during data processing. As data processors create data products, the provenance of the input products and precise steps that led to their creation are recorded and published for users of the data to see. As researchers access the data from an archive, they can use the provenance to help understand the genesis of the data, which could have effects on their usage of the data. By citing the data on publishing their research, others can retrieve the precise data used in their research and reproduce the analyses and experiments to confirm the results. Describing the experiment to a sufficient extent to reproduce the research enforces a formal approach that lends credibility to the results, and ultimately, to the policies of decision makers depending on that research.

  15. Identifying bilingual semantic neural representations across languages

    PubMed Central

    Buchweitz, Augusto; Shinkareva, Svetlana V.; Mason, Robert A.; Mitchell, Tom M.; Just, Marcel Adam

    2015-01-01

    The goal of the study was to identify the neural representation of a noun's meaning in one language based on the neural representation of that same noun in another language. Machine learning methods were used to train classifiers to identify which individual noun bilingual participants were thinking about in one language based solely on their brain activation in the other language. The study shows reliable (p < .05) pattern-based classification accuracies for the classification of brain activity for nouns across languages. It also shows that the stable voxels used to classify the brain activation were located in areas associated with encoding information about semantic dimensions of the words in the study. The identification of the semantic trace of individual nouns from the pattern of cortical activity demonstrates the existence of a multi-voxel pattern of activation across the cortex for a single noun common to both languages in bilinguals. PMID:21978845

  16. Wham: Identifying Structural Variants of Biological Consequence.

    PubMed

    Kronenberg, Zev N; Osborne, Edward J; Cone, Kelsey R; Kennedy, Brett J; Domyan, Eric T; Shapiro, Michael D; Elde, Nels C; Yandell, Mark

    2015-12-01

    Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools-Lumpy, Delly and SoftSearch-and demonstrate Wham's ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/.

  17. Identifying Potential Noise Sources within Acoustic Signals

    NASA Astrophysics Data System (ADS)

    Holcomb, Victoria; Lewalle, Jacques

    2013-11-01

    We test a new algorithm for its ability to detect sources of noise within random background. The goal of these tests is to better understand how to identify sources within acoustic signals while simultaneously determining the strengths and weaknesses of the algorithm in question. Unlike previously published algorithms, the antenna method does not pinpoint events by looking for the most energetic portions of a signal. The algorithm searches for the ideal lag combinations between three signals by taking excerpts of possible events. The excerpt with the lowest calculated minimum distance between possible events is how the algorithm identifies sources. At the minimum distance, the events are close in time and frequency. This method can be compared to the cross correlation and denoising methods to better understand its effectiveness. This work is supported in part by Spectral Energies LLC, under an SBIR grant from AFRL, as well as the Syracuse University MAE department.

  18. Guidelines for identifying suspect/counterfeit material

    SciTech Connect

    1995-09-01

    These guidelines are intended to assist users of products in identifying: substandard, misrepresented, or fraudulently marked items. The guidelines provide information about such topics as: precautions, inspection and testing, dispositioning identified items, installed inspection and reporting suspect/counterfeit materials. These guidelines apply to users who are developing procurement documents, product acceptance/verification methods, company procedures, work instructions, etc. The intent of these SM guidelines in relation to the Quality Assurance Program Description (QAPD) and implementing company Management Control Procedures is not to substitute or replace existing requirements, as defined in either the QAPD or company implementing instructions (Management Control Procedures). Instead, the guidelines are intended to provide a consolidated source of information addressing the issue of Suspect/Counterfeit materials. These guidelines provide an extensive suspect component listing and suspect indications listing. Users can quickly check their suspect items against the list of manufacturers products (i.e., type, LD. number, and nameplate information) by consulting either of these listings.

  19. Identifying, analysing and solving problems in practice.

    PubMed

    Hewitt-Taylor, Jaqui

    When a problem is identified in practice, it is important to clarify exactly what it is and establish the cause before seeking a solution. This solution-seeking process should include input from those directly involved in the problematic situation, to enable individuals to contribute their perspective, appreciate why any change in practice is necessary and what will be achieved by the change. This article describes some approaches to identifying and analysing problems in practice so that effective solutions can be devised. It includes a case study and examples of how the Five Whys analysis, fishbone diagram, problem tree analysis, and Seven-S Model can be used to analyse a problem. PMID:22848969

  20. Persistent Identifiers for Dutch cultural heritage institutions

    NASA Astrophysics Data System (ADS)

    Ras, Marcel; Kruithof, Gijsbert

    2016-04-01

    Over the past years, more and more collections belonging to archives, libraries, media, museums, and knowledge institutes are being digitised and made available online. These are exciting times for ALM institutions. They are realising that, in the information society, their collections are goldmines. Unfortunately most heritage institutions in the Netherlands do not yet meet the basic preconditions for long-term availability of their collections. The digital objects often have no long lasting fixed reference yet. URL's and web addresses change. Some digital objects that were referenced in Europeana and other portals can no longer be found. References in scientific articles have a very short life span, which is damaging for scholarly research. In 2015, the Dutch Digital Heritage Network (NDE) has started a two-year work program to co-ordinate existing initiatives in order to improve the (long-term) accessibility of the Dutch digital heritage for a wide range of users, anytime, anyplace. The Digital Heritage Network is a partnership established on the initiative of the Ministry of Education, Culture and Science. The members of the NDE are large, national institutions that strive to professionally preserve and manage digital data, e.g. the National Library, The Netherlands Institute for Sound and Vision, the Netherlands Cultural Heritage Agency, the Royal Netherlands Academy of Arts and Sciences, the National Archive of the Netherlands and the DEN Foundation, and a growing number of associations and individuals both within and outside the heritage sector. By means of three work programmes the goals of the Network should be accomplished and improve the visibility, the usability and the sustainability of digital heritage. Each programme contains of a set of projects. Within the sustainability program a project on creating a model for persistent identifiers is taking place. The main goals of the project are (1) raise awareness among cultural heritage institutions on the

  1. Trustworthy persistent identifier systems of the future

    NASA Astrophysics Data System (ADS)

    Golodoniuc, Pavel; Klump, Jens; Car, Nicholas

    2016-04-01

    Over the last two decades, persistent identifier (PID) systems have seen some significant changes in their governance policies, system capabilities, and technology. The development of most systems was driven by two main application areas, namely archives and libraries. Guidelines and criteria for trustworthy PID systems have been clearly devised (Bütikofer, 2009) and many PID system implementations for the identification of static digital objects have been built (e.g., PURL). However systems delivering persistent identifiers for dynamic datasets are not yet mature. There has been a rapid proliferation of different PID systems caused by the specific technical or organisational requirements of various communities that could not be met by existing systems such as DOI, ISBN, and EAN. Many of these different systems were limited by their inability to provide native means of persistent identifier resolution. This has prompted a decoupling of PID-associated data from the resolution service and this is where the Handle system has played a significant role. The Handle allowed to build a distributed system of independently managed resolver services. A trustworthy PID system must be designed to outlive the objects it provides persistent identifiers for, which may cease to exist or otherwise be deprecated, and the technology used to implement it, which will certainly need to change with time. We propose that such a system should rest on four pillars of agreements - (i) definitions, (ii) policies, (iii) services, and (iv) data services, to ensure longevity. While we believe all four pillars are equally important, we intentionally leave regulating aspects of issuing of identifiers and their registration out of the scope of this paper and focus on the agreements that have to be established between PID resolver services and the data sources indicated by the persistent identifiers. We propose an approach to development of PID systems that combines the use of (a) the Handle system

  2. Chemical Proteomic Platform To Identify Citrullinated Proteins

    PubMed Central

    2015-01-01

    Anti-citrullinated protein antibodies (ACPAs) are a hallmark of rheumatoid arthritis (RA) and are routinely used for disease diagnosis. Protein citrullination is also increased in cancer and other autoimmune disorders, suggesting that citrullinated proteins may serve as biomarkers for diseases beyond RA. To identify these citrullinated proteins, we developed biotin-conjugated phenylglyoxal (biotin-PG). Using this probe and our platform technology, we identified >50 intracellular citrullinated proteins. More than 20 of these are involved in RNA splicing, suggesting, for the first time, that citrullination modulates RNA biology. Overall, this chemical proteomic platform will play a key role in furthering our understanding of protein citrullination in rheumatoid arthritis and potentially a wider spectrum of inflammatory diseases. PMID:26360112

  3. Using filtering effects to identify objects.

    PubMed

    Carroll, T L; Rachford, Frederic J

    2012-06-01

    Reflecting signals off of targets is a method widely used to locate objects, but the reflected signal also contains information that can be used to identify the object. In radar or sonar, the signal amplitudes used are small enough that only linear effects are present, so we can consider the effect of the target on the signal as a linear filter. Using the known effects of linear filters on chaotic signals, we can create a reference that allows us to match a particular target to a particular reflected signal. Furthermore, if some parts of this "filter" vary only slowly as the aspect angle of the object changes, we can produce a reference that averages out the parts that are highly angle dependent so that one reference can be used to identify the target over a range of angles.

  4. Identifying bilingual semantic neural representations across languages.

    PubMed

    Buchweitz, Augusto; Shinkareva, Svetlana V; Mason, Robert A; Mitchell, Tom M; Just, Marcel Adam

    2012-03-01

    The goal of the study was to identify the neural representation of a noun's meaning in one language based on the neural representation of that same noun in another language. Machine learning methods were used to train classifiers to identify which individual noun bilingual participants were thinking about in one language based solely on their brain activation in the other language. The study shows reliable (p<.05) pattern-based classification accuracies for the classification of brain activity for nouns across languages. It also shows that the stable voxels used to classify the brain activation were located in areas associated with encoding information about semantic dimensions of the words in the study. The identification of the semantic trace of individual nouns from the pattern of cortical activity demonstrates the existence of a multi-voxel pattern of activation across the cortex for a single noun common to both languages in bilinguals.

  5. Identifying sex and age of akiapolaau

    USGS Publications Warehouse

    Pratt, T.K.; Fancy, S.G.; Harada, C.K.; Lindsey, G.D.; Jacobi, J.D.

    1994-01-01

    Methods for identifying the sex and age of the Akiapolaau (Hemignathus munroi), an endangered honeycreeper found only on the island of Hawaii, were developed by examination and measurement of 73 museum specimens and 24 live birds captured in mist nests. Akiapolaau probably undergo a single annual molt, with most birds molting between February and July. The mottled juvenal plumage is replaced by a first basic plumage characterized by yellowish-gray or yellowish-green underparts and often by retained wingbars. Male Akiapolaau may not attain adult plumage until their third molt. In adult females, only the throat and upper breast become yellow, whereas in adult males the superciliaries, cheeks, and entire underparts are yellow. Adult males have greater exposed culmen, gonys, wing chord, tail, and tarsus lengths than do females. Akiapolaau in first prebasic molt or older can be identified as to sex by culmen length, that of males being >23.4 mm.

  6. Identifying a novel locus for psoriatic arthritis

    PubMed Central

    Budu-Aggrey, Ashley; Bowes, John

    2016-01-01

    A number of studies have identified genetic risk loci for PsA, the majority of which also confer risk for psoriasis. The stronger heritability of PsA in comparison with psoriasis suggests that there should be risk loci that are specific for PsA. Identifying such loci could potentially inform therapy development to provide more effective treatments for PsA patients, especially with a considerable proportion being non-responsive to current therapies. Evidence of a PsA-specific locus has been previously found at HLA-B27 within the MHC region. A recent study has provided evidence of non-HLA risk loci that are specific for PsA at IL23R, PTPN22 and on chromosome 5q31. Functional characterization of these loci will provide further understanding of the pathways underlying PsA, and enable us to apply genetic findings for patient benefit. PMID:26255310

  7. Identifying spatial priorities for protecting ecosystem services

    PubMed Central

    Luck, Gary W

    2012-01-01

    Priorities for protecting ecosystem services must be identified to ensure future human well-being. Approaches to broad-scale spatial prioritization of ecosystem services are becoming increasingly popular and are a vital precursor to identifying locations where further detailed analyses of the management of ecosystem services is required (e.g., examining trade-offs among management actions). Prioritization approaches often examine the spatial congruence between priorities for protecting ecosystem services and priorities for protecting biodiversity; therefore, the spatial prioritization method used is crucial because it will influence the alignment of service protection and conservation goals. While spatial prioritization of ecosystem services and prioritization for conservation share similarities, such as the need to document threats and costs, the former differs substantially from the latter owing to the requirement to measure the following components: supply of services; availability of human-derived alternatives to service provision; capacity to meet beneficiary demand; and site dependency in and scale of service delivery. We review studies that identify broad-scale spatial priorities for managing ecosystem services and demonstrate that researchers have used different approaches and included various measures for identifying priorities, and most studies do not consider all of the components listed above. We describe a conceptual framework for integrating each of these components into spatial prioritization of ecosystem services and illustrate our approach using a worked example for water provision. A fuller characterization of the biophysical and social context for ecosystem services that we call for should improve future prioritization and the identification of locations where ecosystem-service management is especially important or cost effective. PMID:24555017

  8. Identifying the learning needs of senior nurses.

    PubMed

    Cerinus, Marie

    There has been a drive to encourage nurses into positions of leadership but, despite the importance of considering how the senior nurse role should be developed and the needs of senior nurses, little literature exists on the subject. To explore senior nurse development, one health. board in Scotland invited senior nurses to participate in a "development conversation". Key points were noted during each conversation and themed. This article outlines the needs identified and explores how they could be addressed. PMID:27386709

  9. Identifying Topics in Microblogs Using Wikipedia.

    PubMed

    Yıldırım, Ahmet; Üsküdarlı, Suzan; Özgür, Arzucan

    2016-01-01

    Twitter is an extremely high volume platform for user generated contributions regarding any topic. The wealth of content created at real-time in massive quantities calls for automated approaches to identify the topics of the contributions. Such topics can be utilized in numerous ways, such as public opinion mining, marketing, entertainment, and disaster management. Towards this end, approaches to relate single or partial posts to knowledge base items have been proposed. However, in microblogging systems like Twitter, topics emerge from the culmination of a large number of contributions. Therefore, identifying topics based on collections of posts, where individual posts contribute to some aspect of the greater topic is necessary. Models, such as Latent Dirichlet Allocation (LDA), propose algorithms for relating collections of posts to sets of keywords that represent underlying topics. In these approaches, figuring out what the specific topic(s) the keyword sets represent remains as a separate task. Another issue in topic detection is the scope, which is often limited to specific domain, such as health. This work proposes an approach for identifying domain-independent specific topics related to sets of posts. In this approach, individual posts are processed and then aggregated to identify key tokens, which are then mapped to specific topics. Wikipedia article titles are selected to represent topics, since they are up to date, user-generated, sophisticated articles that span topics of human interest. This paper describes the proposed approach, a prototype implementation, and a case study based on data gathered during the heavily contributed periods corresponding to the four US election debates in 2012. The manually evaluated results (0.96 precision) and other observations from the study are discussed in detail. PMID:26991442

  10. Identifying Fossil Bacteria in Martian Materials

    NASA Technical Reports Server (NTRS)

    Westall, F.; McKay, D. S.; Gibson, E. K., Jr.

    1999-01-01

    Within the next decade, robotic missions are going to Mars with the search for evidence for extant and extinct life as at least one of the mission objectives. Moreover, the first Martian samples will be returned to Earth in 2008. It is therefore imperative that we can be certain that we can identify life in Martian rocks. In this paper we will not be discussing extant life but will concentrate on fossil life.

  11. Identifying Topics in Microblogs Using Wikipedia

    PubMed Central

    Yıldırım, Ahmet; Üsküdarlı, Suzan; Özgür, Arzucan

    2016-01-01

    Twitter is an extremely high volume platform for user generated contributions regarding any topic. The wealth of content created at real-time in massive quantities calls for automated approaches to identify the topics of the contributions. Such topics can be utilized in numerous ways, such as public opinion mining, marketing, entertainment, and disaster management. Towards this end, approaches to relate single or partial posts to knowledge base items have been proposed. However, in microblogging systems like Twitter, topics emerge from the culmination of a large number of contributions. Therefore, identifying topics based on collections of posts, where individual posts contribute to some aspect of the greater topic is necessary. Models, such as Latent Dirichlet Allocation (LDA), propose algorithms for relating collections of posts to sets of keywords that represent underlying topics. In these approaches, figuring out what the specific topic(s) the keyword sets represent remains as a separate task. Another issue in topic detection is the scope, which is often limited to specific domain, such as health. This work proposes an approach for identifying domain-independent specific topics related to sets of posts. In this approach, individual posts are processed and then aggregated to identify key tokens, which are then mapped to specific topics. Wikipedia article titles are selected to represent topics, since they are up to date, user-generated, sophisticated articles that span topics of human interest. This paper describes the proposed approach, a prototype implementation, and a case study based on data gathered during the heavily contributed periods corresponding to the four US election debates in 2012. The manually evaluated results (0.96 precision) and other observations from the study are discussed in detail. PMID:26991442

  12. Diffraction gratings used as identifying markers

    DOEpatents

    Deason, V.A.; Ward, M.B.

    1991-03-26

    A finely detailed diffraction grating is applied to an object as an identifier or tag which is unambiguous, difficult to duplicate, or remove and transfer to another item, and can be read and compared with prior readings with relative ease. The exact pattern of the diffraction grating is mapped by diffraction moire techniques and recorded for comparison with future readings of the same grating. 7 figures.

  13. Identifying the Universal Part of TMDs

    NASA Astrophysics Data System (ADS)

    Van der Veken, F. F.; Stefanis, N. G.

    2016-08-01

    We attempt to identify a path layout in the definition of transverse-momentum-dependent T-odd parton distribution functions (TMD)s which combines features of both, initial- and final-state interactions, so that it remains universal despite the fact that the Wilson lines entering such TMDs change their orientation. The generic structure of the quark correlator for this path layout is calculated.

  14. Identifying spatial priorities for protecting ecosystem services.

    PubMed

    Luck, Gary W; Chan, Kai Ma; Klien, Carissa J

    2012-01-01

    Priorities for protecting ecosystem services must be identified to ensure future human well-being. Approaches to broad-scale spatial prioritization of ecosystem services are becoming increasingly popular and are a vital precursor to identifying locations where further detailed analyses of the management of ecosystem services is required (e.g., examining trade-offs among management actions). Prioritization approaches often examine the spatial congruence between priorities for protecting ecosystem services and priorities for protecting biodiversity; therefore, the spatial prioritization method used is crucial because it will influence the alignment of service protection and conservation goals. While spatial prioritization of ecosystem services and prioritization for conservation share similarities, such as the need to document threats and costs, the former differs substantially from the latter owing to the requirement to measure the following components: supply of services; availability of human-derived alternatives to service provision; capacity to meet beneficiary demand; and site dependency in and scale of service delivery. We review studies that identify broad-scale spatial priorities for managing ecosystem services and demonstrate that researchers have used different approaches and included various measures for identifying priorities, and most studies do not consider all of the components listed above. We describe a conceptual framework for integrating each of these components into spatial prioritization of ecosystem services and illustrate our approach using a worked example for water provision. A fuller characterization of the biophysical and social context for ecosystem services that we call for should improve future prioritization and the identification of locations where ecosystem-service management is especially important or cost effective. PMID:24555017

  15. Identifying Topics in Microblogs Using Wikipedia.

    PubMed

    Yıldırım, Ahmet; Üsküdarlı, Suzan; Özgür, Arzucan

    2016-01-01

    Twitter is an extremely high volume platform for user generated contributions regarding any topic. The wealth of content created at real-time in massive quantities calls for automated approaches to identify the topics of the contributions. Such topics can be utilized in numerous ways, such as public opinion mining, marketing, entertainment, and disaster management. Towards this end, approaches to relate single or partial posts to knowledge base items have been proposed. However, in microblogging systems like Twitter, topics emerge from the culmination of a large number of contributions. Therefore, identifying topics based on collections of posts, where individual posts contribute to some aspect of the greater topic is necessary. Models, such as Latent Dirichlet Allocation (LDA), propose algorithms for relating collections of posts to sets of keywords that represent underlying topics. In these approaches, figuring out what the specific topic(s) the keyword sets represent remains as a separate task. Another issue in topic detection is the scope, which is often limited to specific domain, such as health. This work proposes an approach for identifying domain-independent specific topics related to sets of posts. In this approach, individual posts are processed and then aggregated to identify key tokens, which are then mapped to specific topics. Wikipedia article titles are selected to represent topics, since they are up to date, user-generated, sophisticated articles that span topics of human interest. This paper describes the proposed approach, a prototype implementation, and a case study based on data gathered during the heavily contributed periods corresponding to the four US election debates in 2012. The manually evaluated results (0.96 precision) and other observations from the study are discussed in detail.

  16. Identifying duplicate content using statistically improbable phrases

    PubMed Central

    Errami, Mounir; Sun, Zhaohui; George, Angela C.; Long, Tara C.; Skinner, Michael A.; Wren, Jonathan D.; Garner, Harold R.

    2010-01-01

    Motivation: Document similarity metrics such as PubMed's ‘Find related articles’ feature, which have been primarily used to identify studies with similar topics, can now also be used to detect duplicated or potentially plagiarized papers within literature reference databases. However, the CPU-intensive nature of document comparison has limited MEDLINE text similarity studies to the comparison of abstracts, which constitute only a small fraction of a publication's total text. Extending searches to include text archived by online search engines would drastically increase comparison ability. For large-scale studies, submitting short phrases encased in direct quotes to search engines for exact matches would be optimal for both individual queries and programmatic interfaces. We have derived a method of analyzing statistically improbable phrases (SIPs) for assistance in identifying duplicate content. Results: When applied to MEDLINE citations, this method substantially improves upon previous algorithms in the detection of duplication citations, yielding a precision and recall of 78.9% (versus 50.3% for eTBLAST) and 99.6% (versus 99.8% for eTBLAST), respectively. Availability: Similar citations identified by this work are freely accessible in the Déjà vu database, under the SIP discovery method category at http://dejavu.vbi.vt.edu/dejavu/ Contact: merrami@collin.edu PMID:20472545

  17. DBSI: DNA-binding site identifier

    PubMed Central

    Zhu, Xiaolei; Ericksen, Spencer S.; Mitchell, Julie C.

    2013-01-01

    In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding. DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound (APO-29) and 30 bound (HOLO-30) protein structures distinct from the training data. We computed 480 candidate features for identifying protein residues that bind DNA, including new features that capture the electrostatic microenvironment within shells near the protein surface. Our iterative feature selection process identified features important in other models, as well as features unique to the DBSI model, such as a banded electrostatic feature with spatial separation comparable with the canonical width of the DNA minor groove. Validations and comparisons with established methods using a range of performance metrics clearly demonstrate the predictive advantage of DBSI, and its comparable performance on unbound (APO-29) and bound (HOLO-30) conformations demonstrates robustness to binding-induced protein conformational changes. Finally, we offer our feature data table to others for integration into their own models or for testing improved feature selection and model training strategies based on DBSI. PMID:23873960

  18. Identifying personal microbiomes using metagenomic codes

    PubMed Central

    Franzosa, Eric A.; Huang, Katherine; Meadow, James F.; Gevers, Dirk; Lemon, Katherine P.; Bohannan, Brendan J. M.; Huttenhower, Curtis

    2015-01-01

    Community composition within the human microbiome varies across individuals, but it remains unknown if this variation is sufficient to uniquely identify individuals within large populations or stable enough to identify them over time. We investigated this by developing a hitting set-based coding algorithm and applying it to the Human Microbiome Project population. Our approach defined body site-specific metagenomic codes: sets of microbial taxa or genes prioritized to uniquely and stably identify individuals. Codes capturing strain variation in clade-specific marker genes were able to distinguish among 100s of individuals at an initial sampling time point. In comparisons with follow-up samples collected 30–300 d later, ∼30% of individuals could still be uniquely pinpointed using metagenomic codes from a typical body site; coincidental (false positive) matches were rare. Codes based on the gut microbiome were exceptionally stable and pinpointed >80% of individuals. The failure of a code to match its owner at a later time point was largely explained by the loss of specific microbial strains (at current limits of detection) and was only weakly associated with the length of the sampling interval. In addition to highlighting patterns of temporal variation in the ecology of the human microbiome, this work demonstrates the feasibility of microbiome-based identifiability—a result with important ethical implications for microbiome study design. The datasets and code used in this work are available for download from huttenhower.sph.harvard.edu/idability. PMID:25964341

  19. Dynamic Method for Identifying Collected Sample Mass

    NASA Technical Reports Server (NTRS)

    Carson, John

    2008-01-01

    G-Sample is designed for sample collection missions to identify the presence and quantity of sample material gathered by spacecraft equipped with end effectors. The software method uses a maximum-likelihood estimator to identify the collected sample's mass based on onboard force-sensor measurements, thruster firings, and a dynamics model of the spacecraft. This makes sample mass identification a computation rather than a process requiring additional hardware. Simulation examples of G-Sample are provided for spacecraft model configurations with a sample collection device mounted on the end of an extended boom. In the absence of thrust knowledge errors, the results indicate that G-Sample can identify the amount of collected sample mass to within 10 grams (with 95-percent confidence) by using a force sensor with a noise and quantization floor of 50 micrometers. These results hold even in the presence of realistic parametric uncertainty in actual spacecraft inertia, center-of-mass offset, and first flexibility modes. Thrust profile knowledge is shown to be a dominant sensitivity for G-Sample, entering in a nearly one-to-one relationship with the final mass estimation error. This means thrust profiles should be well characterized with onboard accelerometers prior to sample collection. An overall sample-mass estimation error budget has been developed to approximate the effect of model uncertainty, sensor noise, data rate, and thrust profile error on the expected estimate of collected sample mass.

  20. Identifying web usage behavior of bank customers

    NASA Astrophysics Data System (ADS)

    Araya, Sandro; Silva, Mariano; Weber, Richard

    2002-03-01

    The bank Banco Credito e Inversiones (BCI) started its virtual bank in 1996 and its registered customers perform currently more than 10,000 Internet transactions daily, which typically cause les than 10% of traditional transaction costs. Since most of the customers are still not registered for online banking, one of the goals of the virtual bank is to increase then umber of registered customers. Objective of the presented work was to identify customers who are likely to perform online banking but still do not use this medium for their transactions. This objective has been reached by determining profiles of registered customers who perform many transactions online. Based on these profiles the bank's Data Warehouse is explored for twins of these heavy users that are still not registered for online banking. We applied clustering in order to group the registered customers into five classes. One of these classes contained almost 30% of all registered customers and could clearly be identified as class of heavy users. Next a neural network assigned online customers to the previously found five classes. Applying the network trained on online customers to all the bank customers identified twins of heavy users that, however had not performed online transactions so far. A mailing to these candidates informing about the advantages of online banking doubled the number of registrations compared to previous campaigns.

  1. Interrogator system for identifying electrical circuits

    DOEpatents

    Jatko, W.B.; McNeilly, D.R.

    1988-04-12

    A system for interrogating electrical leads to correctly ascertain the identity of equipment attached to remote ends of the leads is disclosed. The system includes a source of a carrier signal generated in a controller/receiver to be sent over the leads and an identifier unit at the equipment. The identifier is activated by command of the carrier and uses a portion of the carrier to produce a supply voltage. Each identifier is uniquely programmed for a specific piece of equipment, and causes the impedance of the circuit to be modified whereby the carrier signal is modulated according to that program. The modulation can be amplitude, frequency or phase modulation. A demodulator in the controller/receiver analyzes the modulated carrier signal, and if a verified signal is recognized displays and/or records the information. This information can be utilized in a computer system to prepare a wiring diagram of the electrical equipment attached to specific leads. Specific circuit values are given for amplitude modulation, and the system is particularly described for use with thermocouples. 6 figs.

  2. Interrogator system for identifying electrical circuits

    DOEpatents

    Jatko, William B.; McNeilly, David R.

    1988-01-01

    A system for interrogating electrical leads to correctly ascertain the identity of equipment attached to remote ends of the leads. The system includes a source of a carrier signal generated in a controller/receiver to be sent over the leads and an identifier unit at the equipment. The identifier is activated by command of the carrier and uses a portion of the carrier to produce a supply voltage. Each identifier is uniquely programmed for a specific piece of equipment, and causes the impedance of the circuit to be modified whereby the carrier signal is modulated according to that program. The modulation can be amplitude, frequency or phase modulation. A demodulator in the controller/receiver analyzes the modulated carrier signal, and if a verified signal is recognized displays and/or records the information. This information can be utilized in a computer system to prepare a wiring diagram of the electrical equipment attached to specific leads. Specific circuit values are given for amplitude modulation, and the system is particularly described for use with thermocouples.

  3. Identifiability of large phylogenetic mixture models.

    PubMed

    Rhodes, John A; Sullivant, Seth

    2012-01-01

    Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. Such models are of increasing interest for data analysis, as they can capture the variety of evolutionary processes that may be occurring across long sequences of DNA or proteins. The fundamental question of whether parameters of such a model are identifiable is difficult to address, due to the complexity of the parameterization. Identifiability is, however, essential to their use for statistical inference.We analyze mixture models on large trees, with many mixture components, showing that both numerical and tree parameters are indeed identifiable in these models when all trees are the same. This provides a theoretical justification for some current empirical studies, and indicates that extensions to even more mixture components should be theoretically well behaved. We also extend our results to certain mixtures on different trees, using the same algebraic techniques.

  4. Identifying chemicals that are planetary boundary threats.

    PubMed

    MacLeod, Matthew; Breitholtz, Magnus; Cousins, Ian T; de Wit, Cynthia A; Persson, Linn M; Rudén, Christina; McLachlan, Michael S

    2014-10-01

    Rockström et al. proposed a set of planetary boundaries that delimit a "safe operating space for humanity". Many of the planetary boundaries that have so far been identified are determined by chemical agents. Other chemical pollution-related planetary boundaries likely exist, but are currently unknown. A chemical poses an unknown planetary boundary threat if it simultaneously fulfills three conditions: (1) it has an unknown disruptive effect on a vital Earth system process; (2) the disruptive effect is not discovered until it is a problem at the global scale, and (3) the effect is not readily reversible. In this paper, we outline scenarios in which chemicals could fulfill each of the three conditions, then use the scenarios as the basis to define chemical profiles that fit each scenario. The chemical profiles are defined in terms of the nature of the effect of the chemical and the nature of exposure of the environment to the chemical. Prioritization of chemicals in commerce against some of the profiles appears feasible, but there are considerable uncertainties and scientific challenges that must be addressed. Most challenging is prioritizing chemicals for their potential to have a currently unknown effect on a vital Earth system process. We conclude that the most effective strategy currently available to identify chemicals that are planetary boundary threats is prioritization against profiles defined in terms of environmental exposure combined with monitoring and study of the biogeochemical processes that underlie vital Earth system processes to identify currently unknown disruptive effects.

  5. Persistent Identifiers, Discoverability and Open Science (Communication)

    NASA Astrophysics Data System (ADS)

    Murphy, Fiona; Lehnert, Kerstin; Hanson, Brooks

    2016-04-01

    Early in 2016, the American Geophysical Union announced it was incorporating ORCIDs into its submission workflows. This was accompanied by a strong statement supporting the use of other persistent identifiers - such as IGSNs, and the CrossRef open registry 'funding data'. This was partly in response to funders' desire to track and manage their outputs. However the more compelling argument, and the reason why the AGU has also signed up to the Center for Open Science's Transparency and Openness Promotion (TOP) Guidelines (http://cos.io/top), is that ultimately science and scientists will be the richer for these initiatives due to increased opportunities for interoperability, reproduceability and accreditation. The AGU has appealed to the wider community to engage with these initiatives, recognising that - unlike the introduction of Digital Object Identifiers (DOIs) for articles by CrossRef - full, enriched use of persistent identifiers throughout the scientific process requires buy-in from a range of scholarly communications stakeholders. At the same time, across the general research landscape, initiatives such as Project CRediT (contributor roles taxonomy), Publons (reviewer acknowledgements) and the forthcoming CrossRef DOI Event Tracker are contributing to our understanding and accreditation of contributions and impact. More specifically for earth science and scientists, the cross-functional Coalition for Publishing Data in the Earth and Space Sciences (COPDESS) was formed in October 2014 and is working to 'provide an organizational framework for Earth and space science publishers and data facilities to jointly implement and promote common policies and procedures for the publication and citation of data across Earth Science journals'. Clearly, the judicious integration of standards, registries and persistent identifiers such as ORCIDs and International Geo Sample Numbers (IGSNs) to the research and research output processes is key to the success of this venture

  6. Identifying predictive factors in melanoma progression.

    PubMed

    Dabrowska, D M; Elashoff, R M; Ho, W; Morton, D L

    1998-01-01

    Identification of risk factors is a fundamental goal of melanoma studies. The current understanding of melanoma progression is based primarily on two-stage modeling. A multistate Markov chain process combined with Cox proportional hazard regression is used to model the melanoma progression. The model is applied to 3,434 patients initially diagnosed as AJCC stage I or stage II. Parameter estimates are obtained using Cox regression and supplemented by plots of survival probabilities. Age is associated with increased risk of progression from stage I, II to stage III and from stage III to stage IV. Males experienced an increased risk of stage I, II to stage III progression. Primary tumor located on extremities decreased the risk of all transitions. Clark's level of invasion >III and Breslow's depth >1 mm increased the risk of progression from stage I, II to stage III and stage IV. The following interactions among the prognostic factors were identified for the first time in this research: interaction of age and gender in progression from stage I, II to stage III; interactions of level and depth and site by gender were found in the progression from stage I, II to stage III; interaction of site and gender in progression from stage III to stage IV and stage IV to death. Also we identified primary site as a new prognostic factor for the progression from stage IV to death. The study employed a multistate model in order to identify prognostic factors relevant for disease progression. The unique feature is the modeling of interactions among the prognostic factors and their identification. PMID:9538154

  7. Identifying suitable sites for Florida panther reintroduction

    USGS Publications Warehouse

    Thatcher, Cindy; van Manen, Frank T.; Clark, Joseph D.

    2006-01-01

    A major objective of the 1995 Florida Panther (Puma concolor cory) Recovery Plan is the establishment of 2 additional panther populations within the historic range. Our goal was to identify prospective sites for Florida panther reintroduction within the historic range based on quantitative landscape assessments. First, we delineated 86 panther home ranges using telemetry data collected from 1981 to 2001 in south Florida to develop a Mahalanobis distance (D2) habitat model, using 4 anthropogenic variables and 3 landscape variables mapped at a 500-m resolution. From that analysis, we identified 9 potential reintroduction sites of sufficient size to support a panther population. We then developed a similar D2 model at a higher spatial resolution to quantify the area of favorable panther habitat at each site. To address potential for the population to expand, we calculated the amount of favorable habitat adjacent to each prospective reintroduction site within a range of dispersal distances of female panthers. We then added those totals to the contiguous patches to estimate the total amount of effective panther habitat at each site. Finally, we developed an expert-assisted model to rank and incorporate potentially important habitat variables that were not appropriate for our empirical analysis (e.g., area of public lands, livestock density). Anthropogenic factors heavily influenced both the landscape and the expert-assisted models. Of the 9 areas we identified, the Okefenokee National Wildlife Refuge, Ozark National Forest, and Felsenthal National Wildlife Refuge regions had the highest combination of effective habitat area and expert opinion scores. Sensitivity analyses indicated that variability among key model parameters did not affect the high ranking of those sites. Those sites should be considered as starting points for the field evaluation of potential reintroduction sites.

  8. Identifying Airborne Pathogens in Time to Respond

    SciTech Connect

    Hazi, A

    2006-01-25

    Among the possible terrorist activities that might threaten national security is the release of an airborne pathogen such as anthrax. Because the potential damage to human health could be severe, experts consider 1 minute to be an operationally useful time limit for identifying the pathogen and taking action. Many commercial systems can identify airborne pathogenic microbes, but they take days or, at best, hours to produce results. The Department of Homeland Security (DHS) and other U.S. government agencies are interested in finding a faster approach. To answer this national need, a Livermore team, led by scientist Eric Gard, has developed the bioaerosol mass spectrometry (BAMS) system--the only instrument that can detect and identify spores at low concentrations in less than 1 minute. BAMS can successfully distinguish between two related but different spore species. It can also sort out a single spore from thousands of other particles--biological and nonbiological--with no false positives. The BAMS team won a 2005 R&D 100 Award for developing the system. Livermore's Laboratory Directed Research and Development (LDRD) Program funded the biomedical aspects of the BAMS project, and the Department of Defense's Technical Support Working Group and Defense Advanced Research Project Agency funded the biodefense efforts. Developing a detection system that can analyze small samples so quickly has been challenging. Livermore engineer Vincent Riot, who worked on the BAMS project, explains, ''A typical spore weighs approximately one-trillionth of a gram and is dispersed in the atmosphere, which contains naturally occurring particles that could be present at concentrations thousands of times higher. Previous systems also had difficulty separating benign organisms from those that are pathogenic but very similar, which has resulted in false alarms''.

  9. Identifying Data in the Earth Sciences (Invited)

    NASA Astrophysics Data System (ADS)

    Duerr, R. E.

    2010-12-01

    The problem of identity has vexed humanity throughout all of recorded history. A wide variety of methods; from assigned identifiers to taxonomic techniques and beyond; have historically been used to resolve the issue of whether this thing, whatever or whomever it may be, is what it purports to be. Yet none have ultimately proved to be flawless. Not surprisingly then, the issue of identity is just as much an issue in this digital era as it has ever been. Given the mutability of digital objects it would be surprising indeed if it were not more of an issue. This presents a quandary for science given its foundations in the concept of repeatability. How can one repeat what cannot be identified? In the Earth sciences the problem is even more acute. Unlike other fields of research, the majority of observations in the Earth sciences are not repeatable, they occur at a distinct place and time and are therefore unique and irreplaceable. One would think that this uniqueness would make identification easier; yet the realities of current scientific practice and technology means that it just isn't so. Not surprisingly then, a number of identification schemes have been implemented by various communities - academic, commercial, and non-profit. Many of these schemes purport to be the answer to the question of identification, at least for that community. But is this so for the Earth Sciences? That is the question that was posed to the data lifecycle focus group of the Earth Science Data Systems Technology Infusion Working Group (ESDSWG TIWG) and the Preservation Cluster of the Federation of Earth Science Information Partners (ESIP). In this talk, an assessment of the applicability of these technologies and identification schemes to the Earth Sciences is summarized, and ongoing identifier test-bed activities within the ESIP Federation are described.

  10. [MRSA clones identified in outpatient dermatology clinics].

    PubMed

    Hosoya, Shino; Ito, Teruyo; Misawa, Shigeki; Yoshiike, Takashi; Oguri, Toyoko; Hiramatsu, Keiichi

    2014-11-01

    To know the characteristics of methicillin-resistant Staphylococcus aureus (MRSA) strains disseminating through the Japanese community, we have determined types of Staphylococcal cassette chromosome mec (SCCmec) elements, Multi-Locus Sequence Typing (MLST), and carriages of four exotoxin genes (toxic-shock syndrome toxin, Panton-Valentine Leukocidine, and exfoliative toxins a and b) using 54 MRSA strains isolated from outpatients attending dermatology clinics at the four university hospitals of Juntendo University. Ten clonal complexes and 12 SCCmec types have been identified. As a result, more than 15 MRSA clones that were defined by the combination of genotype and SCCmec type, were identified. Among them, Clonal Complex (CC) 5-type IIa SCCmec strains were the most major (16 strains). In contrast to the fact that CC5- type IIa SCCmec strains known as a hospital-associated MRSA clone in Japan carried toxic-shock syndrome toxin gene (tst), only 2 of 16 strains have been shown to carry tst. Thirty-eight (70.4%) of isolates belonged to the clones distinct from the CC5-type IIa SCCmec strains. Among them, CC8 strains were major (12 strains), which contained 9 tst-positive CC8-type IVl SCCmec clones and a CC8-type IVa SCCmec strain carrying the Panton Valentine Leukocidin gene (lukS, F-PV). Clones related to impetigo were also identified: 7 exfoliative toxin b (etb) -positive clones, CC89-type IIa SCCmec and CC89-type V SCCmec strains; and 2 exfoliative toxin a (eta) -positive CC121-type V SCCmec strains. Other clones were as follows: CC1-type IVa SCCmec, CC8-type I SCCmec, CC81-type IVg SCCmec, CC97-type IVc SCCmec, CC91-type IVa SCCmec, CC59-type IVg SCCmec, CC45-type IIn SCCmec, CC89-SCCmec nontypeable, and CC8-type IVm, novel subtype of type IV SCCmec were identified in this study. Our data showed that many novel MRSA clones have emerged in the community. PMID:25764806

  11. Identifying and managing malnutrition in the community.

    PubMed

    McEvilly, Aimee

    2016-01-01

    Malnutrition affects more than 3 million people in the UK, most of whom live in the community. Malnutrition is both a cause and consequence of disease and can lead to increased mortality and morbidity, delayed recovery from illness and impaired body function which can make carrying out activities of daily living difficult. Managing malnutrition in the community involves identifying malnutrition using a universally validated screening tool and implementing appropriate care plans according to the degree of malnutrition. Regional and local guidance can be used to assist healthcare professionals to prescribe appropriate oral nutritional supplements and monitor nutritional aims and goals. PMID:27396860

  12. Identifying related journals through log analysis

    PubMed Central

    Lu, Zhiyong; Xie, Natalie; Wilbur, W. John

    2009-01-01

    Motivation: With the explosion of biomedical literature and the evolution of online and open access, scientists are reading more articles from a wider variety of journals. Thus, the list of core journals relevant to their research may be less obvious and may often change over time. To help researchers quickly identify appropriate journals to read and publish in, we developed a web application for finding related journals based on the analysis of PubMed log data. Availability: http://www.ncbi.nlm.nih.gov/IRET/Journals Contact: luzh@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19734155

  13. Identifying PHM market and network opportunities.

    PubMed

    Grube, Mark E; Krishnaswamy, Anand; Poziemski, John; York, Robert W

    2015-11-01

    Two key processes for healthcare organizations seeking to assume a financially sustainable role in population health management (PHM), after laying the groundwork for the effort, are to identify potential PHM market opportunities and determine the scope of the PHM network. Key variables organizations should consider with respect to market opportunities include the patient population, the overall insurance/employer market, and available types of insurance products. Regarding the network's scope, organizations should consider both traditional strategic criteria for a viable network and at least five additional criteria: network essentiality and PHM care continuum, network adequacy, service distribution right-sizing, network growth strategy, and organizational agility.

  14. IDENTIFYING PERFORMANCE ASSURANCE CHALLENGES FOR SMART MANUFACTURING

    PubMed Central

    Helu, Moneer; Morris, Katherine; Jung, Kiwook; Lyons, Kevin; Leong, Swee

    2015-01-01

    Smart manufacturing has the potential to address many of the challenges faced by industry. However, the manufacturing community often needs assistance to leverage available technologies to improve their systems. To assure the performance of these technologies, this paper proposes a shared knowledge base that collects problem areas, solutions, and best practices for manufacturing technology. An Implementation Risk Assessment Framework (IRAF) is also described to identify the primary weaknesses of technologies in specific manufacturing contexts. Such approaches have the potential to stimulate new ideas and drive standardization activities critical to scale up and deploy smart manufacturing technologies successfully and quickly. PMID:26783512

  15. Identifying insanity acquittals: is it any easier?

    PubMed

    Cirincione, C; Jacobs, C

    1999-08-01

    Following the highly publicized insanity acquittal of John Hinckley in 1982, legislators throughout the country attempted to reform the insanity defense. At the time, policy makers had virtually no empirical evidence with which to guide their reforms. The focus of this research is to determine if more informed policy-making would be possible today? Results show that more states are able to identify cases involving an insanity acquittal than during the 1980's and provide annual data on the number of rate of insanity acquittals. The data collected by many of the states have significant limitation.

  16. Anti-Rga: identifying serologic characteristics.

    PubMed

    Strohm, P L; Molthan, L

    1982-12-01

    Anti-Rga is a rare alloantibody that is difficult to recognize and identify. Although posing no apparent transfusion risk itself, it can mask the presence of underlying alloantibodies which could be transfusion risks. The five patients reported here demonstrate the serologic findings characteristic of anti-Rga. Known Rg(a-) test cells and multiple "target cells" in neutralization studies are needed to demonstrate partial neutralization findings and to detect underlying alloantibody. Other observations were that clotted samples of red cells retained Rga reactivity for 49 days, whereas EDTA-anticoagulated red cell samples lost such reactivity after 13 days. Frozen red cells tested within hours of deglycerolization showed excellent Rga reactivity.

  17. Defining the criteria for identifying constitutional epimutations.

    PubMed

    Sloane, Mathew A; Ward, Robyn L; Hesson, Luke B

    2016-01-01

    In the January 2016 issue of Clinical Epigenetics, Quiñonez-Silva et al. (Clin Epigenetics 8:1, 2016) described a possible constitutional epimutation of the RB1 gene as a cause of hereditary predisposition to retinoblastoma. The term constitutional epimutation describes an epigenetic aberration in normal tissues that predisposes to disease. The data presented by Quiñonez-Silva et al. are interesting, but further analysis is required to demonstrate a constitutional epimutation in this family. Here, we define the criteria and describe the experimental approach necessary to identify an epigenetic aberration as a constitutional epimutation. PMID:27096027

  18. Identifying inference attacks against healthcare data repositories

    PubMed Central

    Vaidya, Jaideep; Shafiq, Basit; Jiang, Xiaoqian; Ohno-Machado, Lucila

    Health care data repositories play an important role in driving progress in medical research. Finding new pathways to discovery requires having adequate data and relevant analysis. However, it is critical to ensure the privacy and security of the stored data. In this paper, we identify a dangerous inference attack against naive suppression based approaches that are used to protect sensitive information. We base our attack on the querying system provided by the Healthcare Cost and Utilization Project, though it applies in general to any medical database providing a query capability. We also discuss potential solutions to this problem. PMID:24303279

  19. Method of identifying defective particle coatings

    DOEpatents

    Cohen, Mark E.; Whiting, Carlton D.

    1986-01-01

    A method for identifying coated particles having defective coatings desig to retain therewithin a build-up of gaseous materials including: (a) Pulling a vacuum on the particles; (b) Backfilling the particles at atmospheric pressure with a liquid capable of wetting the exterior surface of the coated particles, said liquid being a compound which includes an element having an atomic number higher than the highest atomic number of any element in the composition which forms the exterior surface of the particle coating; (c) Drying the particles; and (d) Radiographing the particles. By television monitoring, examination of the radiographs is substantially enhanced.

  20. Identifying Synonymous Regulatory Elements in Vertebrate Genomes

    SciTech Connect

    Ovcharenko, I; Nobrega, M A

    2005-02-07

    Synonymous gene regulation, defined as driving shared temporal and/or spatial expression of groups of genes, is likely predicated on genomic elements that contain similar modules of certain transcription factor binding sites (TFBS). We have developed a method to scan vertebrate genomes for evolutionary conserved modules of TFBS in a predefined configuration, and created a tool, named SynoR that identify synonymous regulatory elements (SREs) in vertebrate genomes. SynoR performs de novo identification of SREs utilizing known patterns of TFBS in active regulatory elements (REs) as seeds for genome scans. Layers of multiple-species conservation allow the use of differential phylogenetic sequence conservation filters in the search of SREs and the results are displayed as to provide an extensive annotation of genes containing detected REs. Gene Ontology categories are utilized to further functionally classify the identified genes, and integrated GNF Expression Atlas 2 data allow the cataloging of tissue-specificities of the predicted SREs. We illustrate how this new tool can be used to establish a linkage between human diseases and noncoding genomic content. SynoR is publicly available at http://synor.dcode.org.

  1. Identifying nonlinear biomechanical models by multicriteria analysis

    NASA Astrophysics Data System (ADS)

    Srdjevic, Zorica; Cveticanin, Livija

    2012-02-01

    In this study, the methodology developed by Srdjevic and Cveticanin (International Journal of Industrial Ergonomics 34 (2004) 307-318) for the nonbiased (objective) parameter identification of the linear biomechanical model exposed to vertical vibrations is extended to the identification of n-degree of freedom (DOF) nonlinear biomechanical models. The dynamic performance of the n-DOF nonlinear model is described in terms of response functions in the frequency domain, such as the driving-point mechanical impedance and seat-to-head transmissibility function. For randomly generated parameters of the model, nonlinear equations of motion are solved using the Runge-Kutta method. The appropriate data transformation from the time-to-frequency domain is performed by a discrete Fourier transformation. Squared deviations of the response functions from the target values are used as the model performance evaluation criteria, thus shifting the problem into the multicriteria framework. The objective weights of criteria are obtained by applying the Shannon entropy concept. The suggested methodology is programmed in Pascal and tested on a 4-DOF nonlinear lumped parameter biomechanical model. The identification process over the 2000 generated sets of parameters lasts less than 20 s. The model response obtained with the imbedded identified parameters correlates well with the target values, therefore, justifying the use of the underlying concept and the mathematical instruments and numerical tools applied. It should be noted that the identified nonlinear model has an improved accuracy of the biomechanical response compared to the accuracy of a linear model.

  2. Identifying emotional intelligence in professional nursing practice.

    PubMed

    Kooker, Barbara Molina; Shoultz, Jan; Codier, Estelle E

    2007-01-01

    The National Center for Health Workforce Analysis projects that the shortage of registered nurses in the United States will double by 2010 and will nearly quadruple to 20% by 2015 (Bureau of Health Professionals Health Resources and Services Administration. [2002]. Projected supply, demand, and shortages of registered nurses, 2000-2020 [On-line]. Available: http:bhpr.hrsa.gov/healthworkforce/reports/rnprojects/report.htm). The purpose of this study was to use the conceptual framework of emotional intelligence to analyze nurses' stories about their practice to identify factors that could be related to improved nurse retention and patient/client outcomes. The stories reflected evidence of the competencies and domains of emotional intelligence and were related to nurse retention and improved outcomes. Nurses recognized their own strengths and limitations, displayed empathy and recognized client needs, nurtured relationships, used personal influence, and acted as change agents. Nurses were frustrated when organizational barriers conflicted with their knowledge/intuition about nursing practice, their communications were disregarded, or their attempts to create a shared vision and teamwork were ignored. Elements of professional nursing practice, such as autonomy, nurse satisfaction, respect, and the professional practice environment, were identified in the excerpts of the stories. The shortage of practicing nurses continues to be a national issue. The use of emotional intelligence concepts may provide fresh insights into ways to keep nurses engaged in practice and to improve nurse retention and patient/client outcomes. PMID:17292131

  3. White dwarfs identified in LAMOST DR 2

    NASA Astrophysics Data System (ADS)

    Guo, Jincheng; Zhao, Jingkun; Tziamtzis, Anestis; Liu, Jifeng; Li, Lifang; Zhang, Yong; Hou, Yonghui; Wang, Yuefei

    2015-12-01

    Here we present a catalogue of 1056 spectroscopically identified hydrogen-dominated white dwarfs (DAWDs), 34 helium-dominated white dwarfs (DBWDs) and 276 white dwarf main sequence (WDMS) binaries from the Large sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) survey data release 2 (DR2). 383 DAWDs, 4 DBWDs and 138 WDMSs are new identifications after cross-match with literature. There are ˜4100 k spectra in total from DR 2. The low ratio of white dwarfs found in LAMOST is attributed to biased selection of LAMOST input catalogue and much brighter targets relative to stars observed in Sloan Digital Sky Survey. In this paper, a new DAWD selection method is adopted as a new attempt and supplement to the traditional methods. The effective temperature, surface gravity, mass, cooling age and distance of high signal-to-noise DAWDs are estimated. The peak of the mass distribution is found to be ˜0.6 M⊙, which is consistent with previous work. The parameters of WDMS binaries are also provided in this paper. As the foundation of our future work, which is to identify more WDs with debris disc, WDs found in LAMOST showed a lot of potential. Interesting infrared-excess WDs will be reported in our forthcoming paper.

  4. Using Dissimilarity Metrics to Identify Interesting Designs

    NASA Technical Reports Server (NTRS)

    Feather, Martin; Kiper, James

    2006-01-01

    A computer program helps to blend the power of automated-search software, which is able to generate large numbers of design solutions, with the insight of expert designers, who are able to identify preferred designs but do not have time to examine all the solutions. From among the many automated solutions to a given design problem, the program selects a smaller number of solutions that are worthy of scrutiny by the experts in the sense that they are sufficiently dissimilar from each other. The program makes the selection in an interactive process that involves a sequence of data-mining steps interspersed with visual displays of results of these steps to the experts. At crucial points between steps, the experts provide directives to guide the process. The program uses heuristic search techniques to identify nearly optimal design solutions and uses dissimilarity metrics defined by the experts to characterize the degree to which solutions are interestingly different. The search, data-mining, and visualization features of the program were derived from previously developed risk-management software used to support a risk-centric design methodology

  5. Identifying Novel Transcriptional Regulators with Circadian Expression

    PubMed Central

    Schick, Sandra; Thakurela, Sudhir; Fournier, David; Hampel, Mareike Hildegard

    2015-01-01

    Organisms adapt their physiology and behavior to the 24-h day-night cycle to which they are exposed. On a cellular level, this is regulated by intrinsic transcriptional-translational feedback loops that are important for maintaining the circadian rhythm. These loops are organized by members of the core clock network, which further regulate transcription of downstream genes, resulting in their circadian expression. Despite progress in understanding circadian gene expression, only a few players involved in circadian transcriptional regulation, including transcription factors, epigenetic regulators, and long noncoding RNAs, are known. Aiming to discover such genes, we performed a high-coverage transcriptome analysis of a circadian time course in murine fibroblast cells. In combination with a newly developed algorithm, we identified many transcription factors, epigenetic regulators, and long intergenic noncoding RNAs that are cyclically expressed. In addition, a number of these genes also showed circadian expression in mouse tissues. Furthermore, the knockdown of one such factor, Zfp28, influenced the core clock network. Mathematical modeling was able to predict putative regulator-effector interactions between the identified circadian genes and may help for investigations into the gene regulatory networks underlying circadian rhythms. PMID:26644408

  6. Identifying separate components of surround suppression.

    PubMed

    Schallmo, Michael-Paul; Murray, Scott O

    2016-01-01

    Surround suppression is a well-known phenomenon in which the response to a visual stimulus is diminished by the presence of neighboring stimuli. This effect is observed in neural responses in areas such as primary visual cortex, and also manifests in visual contrast perception. Studies in animal models have identified at least two separate mechanisms that may contribute to surround suppression: one that is monocular and resistant to contrast adaptation, and another that is binocular and strongly diminished by adaptation. The current study was designed to investigate whether these two mechanisms exist in humans and if they can be identified psychophysically using eye-of-origin and contrast adaptation manipulations. In addition, we examined the prediction that the monocular suppression component is broadly tuned for orientation, while suppression between eyes is narrowly tuned. Our results confirmed that when center and surrounding stimuli were presented dichoptically (in opposite eyes), suppression was orientation-tuned. Following adaptation in the surrounding region, no dichoptic suppression was observed, and monoptic suppression no longer showed orientation selectivity. These results are consistent with a model of surround suppression that depends on both low-level and higher level components. This work provides a method to assess the separate contributions of these components during spatial context processing in human vision.

  7. DNA Barcoding Identifies Illegal Parrot Trade.

    PubMed

    Gonçalves, Priscila F M; Oliveira-Marques, Adriana R; Matsumoto, Tania E; Miyaki, Cristina Y

    2015-01-01

    Illegal trade threatens the survival of many wild species, and molecular forensics can shed light on various questions raised during the investigation of cases of illegal trade. Among these questions is the identity of the species involved. Here we report a case of a man who was caught in a Brazilian airport trying to travel with 58 avian eggs. He claimed they were quail eggs, but authorities suspected they were from parrots. The embryos never hatched and it was not possible to identify them based on morphology. As 29% of parrot species are endangered, the identity of the species involved was important to establish a stronger criminal case. Thus, we identified the embryos' species based on the analyses of mitochondrial DNA sequences (cytochrome c oxidase subunit I gene [COI] and 16S ribosomal DNA). Embryonic COI sequences were compared with those deposited in BOLD (The Barcode of Life Data System) while their 16S sequences were compared with GenBank sequences. Clustering analysis based on neighbor-joining was also performed using parrot COI and 16S sequences deposited in BOLD and GenBank. The results, based on both genes, indicated that 57 embryos were parrots (Alipiopsitta xanthops, Ara ararauna, and the [Amazona aestiva/A. ochrocephala] complex), and 1 was an owl. This kind of data can help criminal investigations and to design species-specific anti-poaching strategies, and demonstrate how DNA sequence analysis in the identification of bird species is a powerful conservation tool.

  8. Identifying MMORPG Bots: A Traffic Analysis Approach

    NASA Astrophysics Data System (ADS)

    Chen, Kuan-Ta; Jiang, Jhih-Wei; Huang, Polly; Chu, Hao-Hua; Lei, Chin-Laung; Chen, Wen-Chin

    2008-12-01

    Massively multiplayer online role playing games (MMORPGs) have become extremely popular among network gamers. Despite their success, one of MMORPG's greatest challenges is the increasing use of game bots, that is, autoplaying game clients. The use of game bots is considered unsportsmanlike and is therefore forbidden. To keep games in order, game police, played by actual human players, often patrol game zones and question suspicious players. This practice, however, is labor-intensive and ineffective. To address this problem, we analyze the traffic generated by human players versus game bots and propose general solutions to identify game bots. Taking Ragnarok Online as our subject, we study the traffic generated by human players and game bots. We find that their traffic is distinguishable by 1) the regularity in the release time of client commands, 2) the trend and magnitude of traffic burstiness in multiple time scales, and 3) the sensitivity to different network conditions. Based on these findings, we propose four strategies and two ensemble schemes to identify bots. Finally, we discuss the robustness of the proposed methods against countermeasures of bot developers, and consider a number of possible ways to manage the increasingly serious bot problem.

  9. DNA Barcoding Identifies Illegal Parrot Trade.

    PubMed

    Gonçalves, Priscila F M; Oliveira-Marques, Adriana R; Matsumoto, Tania E; Miyaki, Cristina Y

    2015-01-01

    Illegal trade threatens the survival of many wild species, and molecular forensics can shed light on various questions raised during the investigation of cases of illegal trade. Among these questions is the identity of the species involved. Here we report a case of a man who was caught in a Brazilian airport trying to travel with 58 avian eggs. He claimed they were quail eggs, but authorities suspected they were from parrots. The embryos never hatched and it was not possible to identify them based on morphology. As 29% of parrot species are endangered, the identity of the species involved was important to establish a stronger criminal case. Thus, we identified the embryos' species based on the analyses of mitochondrial DNA sequences (cytochrome c oxidase subunit I gene [COI] and 16S ribosomal DNA). Embryonic COI sequences were compared with those deposited in BOLD (The Barcode of Life Data System) while their 16S sequences were compared with GenBank sequences. Clustering analysis based on neighbor-joining was also performed using parrot COI and 16S sequences deposited in BOLD and GenBank. The results, based on both genes, indicated that 57 embryos were parrots (Alipiopsitta xanthops, Ara ararauna, and the [Amazona aestiva/A. ochrocephala] complex), and 1 was an owl. This kind of data can help criminal investigations and to design species-specific anti-poaching strategies, and demonstrate how DNA sequence analysis in the identification of bird species is a powerful conservation tool. PMID:26245790

  10. A novel method for identifying shahtoosh.

    PubMed

    Fei, Jing; Yang, Juan; Zhou, Hui; Tang, Minfeng; Lu, Weiming; Yan, An; Hou, Yin; Zhang, Shuyu

    2014-05-01

    Shahtoosh, the down hair of the Tibetan antelope (Pantholops hodgsonii), is the noblest and most expensive wool in the world. The population of the animal has declined dramatically due to commercial poaching for the fiber. Traditional inspection for detection of shahtoosh has been performed by microscopic analysis. We developed a TaqMan real-time PCR-based DNA analysis method for identifying shahtoosh fibers. A set of probe and primers for the mitochondrial 12S ribosomal RNA gene that binds specifically to Tibetan antelope DNA was designed. A signal was detected with sensitivity to the 1:10,000 dilution of shahtoosh DNA. A fiber mixture of 1% of shahtoosh mixed with cashmere and even a single fiber can be detected with this method. The method is faster, more cost-effective and more sensitive than other traditional sequencing methods and can be directly applied to identify shahtoosh and its processed products, which will be of value in illegal trade investigations. PMID:24502476

  11. Identifying Bitcoin users by transaction behavior

    NASA Astrophysics Data System (ADS)

    Monaco, John V.

    2015-05-01

    Digital currencies, such as Bitcoin, offer convenience and security to criminals operating in the black marketplace. Some Bitcoin marketplaces, such as Silk Road, even claim anonymity. This claim contradicts the findings in this work, where long term transactional behavior is used to identify and verify account holders. Transaction timestamps and network properties observed over time contribute to this finding. The timestamp of each transaction is the result of many factors: the desire purchase an item, daily schedule and activities, as well as hardware and network latency. Dynamic network properties of the transaction, such as coin flow and the number of edge outputs and inputs, contribute further to reveal account identity. In this paper, we propose a novel methodology for identifying and verifying Bitcoin users based on the observation of Bitcoin transactions over time. The behavior we attempt to quantify roughly occurs in the social band of Newell's time scale. A subset of the Blockchain 230686 is taken, selecting users that initiated between 100 and 1000 unique transactions per month for at least 6 different months. This dataset shows evidence of being nonrandom and nonlinear, thus a dynamical systems approach is taken. Classification and authentication accuracies are obtained under various representations of the monthly Bitcoin samples: outgoing transactions, as well as both outgoing and incoming transactions are considered, along with the timing and dynamic network properties of transaction sequences. The most appropriate representations of monthly Bitcoin samples are proposed. Results show an inherent lack of anonymity by exploiting patterns in long-term transactional behavior.

  12. Identifying barriers to Muslim integration in France

    PubMed Central

    Adida, Claire L.; Laitin, David D.; Valfort, Marie-Anne

    2010-01-01

    Is there a Muslim disadvantage in economic integration for second-generation immigrants to Europe? Previous research has failed to isolate the effect that religion may have on an immigrant family's labor market opportunities because other factors, such as country of origin or race, confound the result. This paper uses a correspondence test in the French labor market to identify and measure this religious effect. The results confirm that in the French labor market, anti-Muslim discrimination exists: a Muslim candidate is 2.5 times less likely to receive a job interview callback than is his or her Christian counterpart. A high-n survey reveals, consistent with expectations from the correspondence test, that second-generation Muslim households in France have lower income compared with matched Christian households. The paper thereby contributes to both substantive debates on the Muslim experience in Europe and methodological debates on how to measure discrimination. Following the National Academy of Sciences’ 2001 recommendations on combining a variety of methodologies and applying them to real-world situations, this research identifies, measures, and infers consequences of discrimination based on religious affiliation, controlling for potentially confounding factors, such as race and country of origin. PMID:21098283

  13. Authentication of Coffea arabica according to Triacylglycerol Stereospecific Composition

    PubMed Central

    Cossignani, L.; Simonetti, M. S.; Blasi, F.

    2016-01-01

    Stereospecific analysis is an important tool for the characterization of lipid fraction of food products. In the present research, an approach to characterize arabica and robusta varieties by structural analysis of the triacylglycerol (TAG) fraction is reported. The lipids were Soxhlet extracted from ground roasted coffee beans with petroleum ether, and the fatty acids (FA) were determined as their corresponding methyl esters. The results of a chemical-enzymatic-chromatographic method were elaborated by a chemometric procedure, Linear Discriminant Analysis (LDA). According to the total and intrapositional FA composition of TAG fraction, the obtained results were able to characterize roasted pure coffee samples and coffee mixtures with 10% robusta coffee added to arabica coffee. Totally correct classified samples were obtained when the TAG stereospecific results of the considered coffee mixture (90 : 10 arabica/robusta) were elaborated by LDA procedure. PMID:27547482

  14. Authentication of Coffea arabica according to Triacylglycerol Stereospecific Composition.

    PubMed

    Cossignani, L; Montesano, D; Simonetti, M S; Blasi, F

    2016-01-01

    Stereospecific analysis is an important tool for the characterization of lipid fraction of food products. In the present research, an approach to characterize arabica and robusta varieties by structural analysis of the triacylglycerol (TAG) fraction is reported. The lipids were Soxhlet extracted from ground roasted coffee beans with petroleum ether, and the fatty acids (FA) were determined as their corresponding methyl esters. The results of a chemical-enzymatic-chromatographic method were elaborated by a chemometric procedure, Linear Discriminant Analysis (LDA). According to the total and intrapositional FA composition of TAG fraction, the obtained results were able to characterize roasted pure coffee samples and coffee mixtures with 10% robusta coffee added to arabica coffee. Totally correct classified samples were obtained when the TAG stereospecific results of the considered coffee mixture (90 : 10 arabica/robusta) were elaborated by LDA procedure. PMID:27547482

  15. Lipoxygenase distribution in coffee (Coffea arabica L.) berries.

    PubMed

    Patui, Sonia; Peresson, Carlo; Braidot, Enrico; Tubaro, Franco; Colussi, Alessio; Bonnländer, Bernd; Macrì, Francesco; Vianello, Angelo

    2007-10-01

    In this paper lipoxygenase (LOX) presence was investigated in coffee berries to determine its involvement in lipid degradative metabolism of plants grown in organic and conventional cultivations. An immunochemical analysis has evidenced a ca. 80 kDa protein, cross-reacting with an anti-LOX antibody, only in the pulp fraction of berries obtained from plants of both cultivations. LOX activity in this fraction could be monitored either as conjugated diene formation or reaction products (determined by HPLC) and was mainly associated with a heavy membrane fraction (HMF, enriched in tonoplast, endoplasmic reticulum, plasma membrane, and mitochondria) and a light membrane fraction (LMF, enriched in plasma membrane and endoplasmic reticulum, with low levels of tonoplast and mitochondria). The LOX activity of LMF from berries of both cultivations showed an optimum at pH 8.0. The HMF exhibited a different activity peak in samples from conventional (pH 8.0) and organic (pH 5.5) cultures, suggesting the presence of different isoenzymes. These findings were also confirmed by variation of the ratio of 9- and 13-hydroperoxides in organic (1:1) and conventional cultivations (1:10), indicating that the organic one was subjected to an oxidative stress in the coffee pulp fraction leading to the expression of an acidic LOX. Such de novo synthesized LOX activity could be responsible for the production of secondary metabolites, which may interfere with the organoleptic profile of coffee.

  16. Somatic Embryogenesis: Identified Factors that Lead to Embryogenic Repression. A Case of Species of the Same Genus

    PubMed Central

    Nic-Can, Geovanny I.; Galaz-Ávalos, Rosa M.; De-la-Peña, Clelia; Alcazar-Magaña, Armando; Wrobel, Kazimierz; Loyola-Vargas, Víctor M.

    2015-01-01

    Somatic embryogenesis is a powerful biotechnological tool for the mass production of economically important cultivars. Due to the cellular totipotency of plants, somatic cells under appropriate conditions are able to develop a complete functional embryo. During the induction of somatic embryogenesis, there are different factors involved in the success or failure of the somatic embryogenesis response. Among these factors, the origin of the explant, the culture medium and the in vitro environmental conditions have been the most studied. However, the secretion of molecules into the media has not been fully addressed. We found that the somatic embryogenesis of Coffea canephora, a highly direct embryogenic species, is disrupted by the metabolites secreted from C. arabica, a poorly direct embryogenic species. These metabolites also affect DNA methylation. Our results show that the abundance of two major phenolic compounds, caffeine and chlorogenic acid, are responsible for inhibiting somatic embryogenesis in C. canephora. PMID:26038822

  17. Process Architecture for Managing Digital Object Identifiers

    NASA Astrophysics Data System (ADS)

    Wanchoo, L.; James, N.; Stolte, E.

    2014-12-01

    In 2010, NASA's Earth Science Data and Information System (ESDIS) Project implemented a process for registering Digital Object Identifiers (DOIs) for data products distributed by Earth Observing System Data and Information System (EOSDIS). For the first 3 years, ESDIS evolved the process involving the data provider community in the development of processes for creating and assigning DOIs, and guidelines for the landing page. To accomplish this, ESDIS established two DOI User Working Groups: one for reviewing the DOI process whose recommendations were submitted to ESDIS in February 2014; and the other recently tasked to review and further develop DOI landing page guidelines for ESDIS approval by end of 2014. ESDIS has recently upgraded the DOI system from a manually-driven system to one that largely automates the DOI process. The new automated feature include: a) reviewing the DOI metadata, b) assigning of opaque DOI name if data provider chooses, and c) reserving, registering, and updating the DOIs. The flexibility of reserving the DOI allows data providers to embed and test the DOI in the data product metadata before formally registering with EZID. The DOI update process allows the changing of any DOI metadata except the DOI name unless the name has not been registered. Currently, ESDIS has processed a total of 557 DOIs of which 379 DOIs are registered with EZID and 178 are reserved with ESDIS. The DOI incorporates several metadata elements that effectively identify the data product and the source of availability. Of these elements, the Uniform Resource Locator (URL) attribute has the very important function of identifying the landing page which describes the data product. ESDIS in consultation with data providers in the Earth Science community is currently developing landing page guidelines that specify the key data product descriptive elements to be included on each data product's landing page. This poster will describe in detail the unique automated process and

  18. Identifying the seasonal origins of human campylobacteriosis.

    PubMed

    Strachan, N J C; Rotariu, O; Smith-Palmer, A; Cowden, J; Sheppard, S K; O'Brien, S J; Maiden, M C J; Macrae, M; Bessell, P R; Matthews, L; Reid, S W J; Innocent, G T; Ogden, I D; Forbes, K J

    2013-06-01

    Human campylobacteriosis exhibits a distinctive seasonality in temperate regions. This paper aims to identify the origins of this seasonality. Clinical isolates [typed by multi-locus sequence typing (MLST)] and epidemiological data were collected from Scotland. Young rural children were found to have an increased burden of disease in the late spring due to strains of non-chicken origin (e.g. ruminant and wild bird strains from environmental sources). In contrast the adult population had an extended summer peak associated with chicken strains. Travel abroad and UK mainland travel were associated with up to 17% and 18% of cases, respectively. International strains were associated with chicken, had a higher diversity than indigenous strains and a different spectrum of MLST types representative of these countries. Integrating empirical epidemiology and molecular subtyping can successfully elucidate the seasonal components of human campylobacteriosis. The findings will enable public health officials to focus strategies to reduce the disease burden.

  19. Identifying States of a Financial Market

    NASA Astrophysics Data System (ADS)

    Münnix, Michael C.; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H.; Guhr, Thomas; Stanley, H. Eugene

    2012-09-01

    The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992-2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical ``market states''. Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen.

  20. Identifying States of a Financial Market

    PubMed Central

    Münnix, Michael C.; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H.; Guhr, Thomas; Stanley, H. Eugene

    2012-01-01

    The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992–2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical “market states”. Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen. PMID:22966419

  1. Identifying Multiquark Hadrons from Heavy Ion Collisions

    SciTech Connect

    Cho, Sungtae; Furumoto, Takenori; Yazaki, Koichi; Hyodo, Tetsuo; Jido, Daisuke; Ohnishi, Akira; Ko, Che Ming; Lee, Su Houng; Nielsen, Marina; Sekihara, Takayasu; Yasui, Shigehiro

    2011-05-27

    Identifying hadronic molecular states and/or hadrons with multiquark components either with or without exotic quantum numbers is a long-standing challenge in hadronic physics. We suggest that studying the production of these hadrons in relativistic heavy ion collisions offers a promising resolution to this problem as yields of exotic hadrons are expected to be strongly affected by their structures. Using the coalescence model for hadron production, we find that, compared to the case of a nonexotic hadron with normal quark numbers, the yield of an exotic hadron is typically an order of magnitude smaller when it is a compact multiquark state and a factor of 2 or more larger when it is a loosely bound hadronic molecule. We further find that some of the newly proposed heavy exotic states could be produced and realistically measured in these experiments.

  2. Identifying seasonal stars in Kaurna astronomical traditions

    NASA Astrophysics Data System (ADS)

    Hamacher, Duane W.

    2015-03-01

    Early ethnographers and missionaries recorded Aboriginal languages and oral traditions across Australia. Their general lack of astronomical training resulted in misidentifications, transcription errors and omissions in these records. In western Victoria and southeast South Australia many astronomical traditions were recorded but, cur- iously, some of the brightest stars in the sky were omitted. Scholars claimed these stars did not feature in Aboriginal traditions. This continues to be repeated in the literature, but current research shows that these stars may in fact feature in Aboriginal traditions and could be seasonal calendar markers. This paper uses established techniques to identify seasonal stars in the traditions of the Kaurna Aboriginal people of the Adelaide Plains, South Australia.

  3. Automatic Prosodic Analysis to Identify Mild Dementia.

    PubMed

    Gonzalez-Moreira, Eduardo; Torres-Boza, Diana; Kairuz, Héctor Arturo; Ferrer, Carlos; Garcia-Zamora, Marlene; Espinoza-Cuadros, Fernando; Hernandez-Gómez, Luis Alfonso

    2015-01-01

    This paper describes an exploratory technique to identify mild dementia by assessing the degree of speech deficits. A total of twenty participants were used for this experiment, ten patients with a diagnosis of mild dementia and ten participants like healthy control. The audio session for each subject was recorded following a methodology developed for the present study. Prosodic features in patients with mild dementia and healthy elderly controls were measured using automatic prosodic analysis on a reading task. A novel method was carried out to gather twelve prosodic features over speech samples. The best classification rate achieved was of 85% accuracy using four prosodic features. The results attained show that the proposed computational speech analysis offers a viable alternative for automatic identification of dementia features in elderly adults. PMID:26558287

  4. Identifying the seasonal origins of human campylobacteriosis

    PubMed Central

    STRACHAN, N. J. C.; ROTARIU, O.; SMITH-PALMER, A.; COWDEN, J.; SHEPPARD, S. K.; O’BRIEN, S. J.; MAIDEN, M. C. J.; MACRAE, M.; BESSELL, P. R.; MATTHEWS, L.; REID, S. W. J.; INNOCENT, G. T.; OGDEN, I. D.; FORBES, K. J.

    2014-01-01

    SUMMARY Human campylobacteriosis exhibits a distinctive seasonality in temperate regions. This paper aims to identify the origins of this seasonality. Clinical isolates [typed by multi-locus sequence typing (MLST)] and epidemiological data were collected from Scotland. Young rural children were found to have an increased burden of disease in the late spring due to strains of non-chicken origin (e.g. ruminant and wild bird strains from environmental sources). In contrast the adult population had an extended summer peak associated with chicken strains. Travel abroad and UK mainland travel were associated with up to 17% and 18% of cases, respectively. International strains were associated with chicken, had a higher diversity than indigenous strains and a different spectrum of MLST types representative of these countries. Integrating empirical epidemiology and molecular subtyping can successfully elucidate the seasonal components of human campylobacteriosis. The findings will enable public health officials to focus strategies to reduce the disease burden. PMID:22989449

  5. Identifying Dyads and their conservation in Drosphila.

    NASA Astrophysics Data System (ADS)

    Dan, Debasis

    2007-03-01

    Core promoter regions in Drosophila are enriched with binding sites like TATA, Inr, DPE, MTE, etc. They have very strict spacing between each other in promoters where they occur together. For example, in Drosophila melanogaster TATA-Inr has a spacing of 25-30 bp. Our aim in this work is to identify all such pair of motifs having strict positional constraint in the core promoters of all Drosophila species. We discover how these motifs and the spacing between them evolve within Drosophila species. For this we analyze 700 bp upstream and 300 bp downstream of TSS in D. melanogaster and the corresponding orthologous region in other Drosophila species. For each species, this 1000 bp region is searched for statistically over-represented compound words of the form W1NLW2, where L is the spacing between words W1 and W2. These compound words are systematically clustered for further analysis.

  6. Advances in identifying beryllium sensitization and disease.

    PubMed

    Middleton, Dan; Kowalski, Peter

    2010-01-01

    Beryllium is a lightweight metal with unique qualities related to stiffness, corrosion resistance, and conductivity. While there are many useful applications, researchers in the 1930s and 1940s linked beryllium exposure to a progressive occupational lung disease. Acute beryllium disease is a pulmonary irritant response to high exposure levels, whereas chronic beryllium disease (CBD) typically results from a hypersensitivity response to lower exposure levels. A blood test, the beryllium lymphocyte proliferation test (BeLPT), was an important advance in identifying individuals who are sensitized to beryllium (BeS) and thus at risk for developing CBD. While there is no true "gold standard" for BeS, basic epidemiologic concepts have been used to advance our understanding of the different screening algorithms.

  7. Automatic Prosodic Analysis to Identify Mild Dementia

    PubMed Central

    Gonzalez-Moreira, Eduardo; Torres-Boza, Diana; Kairuz, Héctor Arturo; Ferrer, Carlos; Garcia-Zamora, Marlene; Espinoza-Cuadros, Fernando; Hernandez-Gómez, Luis Alfonso

    2015-01-01

    This paper describes an exploratory technique to identify mild dementia by assessing the degree of speech deficits. A total of twenty participants were used for this experiment, ten patients with a diagnosis of mild dementia and ten participants like healthy control. The audio session for each subject was recorded following a methodology developed for the present study. Prosodic features in patients with mild dementia and healthy elderly controls were measured using automatic prosodic analysis on a reading task. A novel method was carried out to gather twelve prosodic features over speech samples. The best classification rate achieved was of 85% accuracy using four prosodic features. The results attained show that the proposed computational speech analysis offers a viable alternative for automatic identification of dementia features in elderly adults. PMID:26558287

  8. Identifying the immunomodulatory components of helminths.

    PubMed

    Shepherd, C; Navarro, S; Wangchuk, P; Wilson, D; Daly, N L; Loukas, A

    2015-06-01

    Immunomodulatory components of helminths offer great promise as an entirely new class of biologics for the treatment of inflammatory diseases. Here, we discuss the emerging themes in helminth-driven immunomodulation in the context of therapeutic drug discovery. We broadly define the approaches that are currently applied by researchers to identify these helminth molecules, highlighting key areas of potential exploitation that have been mostly neglected thus far, notably small molecules. Finally, we propose that the investigation of immunomodulatory compounds will enable the translation of current and future research efforts into potential treatments for autoimmune and allergic diseases, while at the same time yielding new insights into the molecular interface of host-parasite biology.

  9. Identifying miRNAs, targets and functions

    PubMed Central

    Liu, Bing; Li, Jiuyong

    2014-01-01

    microRNAs (miRNAs) are small endogenous non-coding RNAs that function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets and further inferring miRNA functions have been a critical strategy for understanding normal biological processes of miRNAs and their roles in the development of disease. In this review, we focus on computational methods of inferring miRNA functions, including miRNA functional annotation and inferring miRNA regulatory modules, by integrating heterogeneous data sources. We also briefly introduce the research in miRNA discovery and miRNA-target identification with an emphasis on the challenges to computational biology. PMID:23175680

  10. Identifying financial crises in real time

    NASA Astrophysics Data System (ADS)

    da Fonseca, Eder Lucio; Ferreira, Fernando F.; Muruganandam, Paulsamy; Cerdeira, Hilda A.

    2013-03-01

    Following the thermodynamic formulation of a multifractal measure that was shown to enable the detection of large fluctuations at an early stage, here we propose a new index which permits us to distinguish events like financial crises in real time. We calculate the partition function from which we can obtain thermodynamic quantities analogous to the free energy and specific heat. The index is defined as the normalized energy variation and it can be used to study the behavior of stochastic time series, such as financial market daily data. Famous financial market crashes-Black Thursday (1929), Black Monday (1987) and the subprime crisis (2008)-are identified with clear and robust results. The method is also applied to the market fluctuations of 2011. From these results it appears as if the apparent crisis of 2011 is of a different nature to the other three. We also show that the analysis has forecasting capabilities.

  11. Advances in Identifying Beryllium Sensitization and Disease

    PubMed Central

    Middleton, Dan; Kowalski, Peter

    2010-01-01

    Beryllium is a lightweight metal with unique qualities related to stiffness, corrosion resistance, and conductivity. While there are many useful applications, researchers in the 1930s and l940s linked beryllium exposure to a progressive occupational lung disease. Acute beryllium disease is a pulmonary irritant response to high exposure levels, whereas chronic beryllium disease (CBD) typically results from a hypersensitivity response to lower exposure levels. A blood test, the beryllium lymphocyte proliferation test (BeLPT), was an important advance in identifying individuals who are sensitized to beryllium (BeS) and thus at risk for developing CBD. While there is no true “gold standard” for BeS, basic epidemiologic concepts have been used to advance our understanding of the different screening algorithms. PMID:20195436

  12. Identifying states of a financial market.

    PubMed

    Münnix, Michael C; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H; Guhr, Thomas; Stanley, H Eugene

    2012-01-01

    The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992-2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical "market states". Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen. PMID:22966419

  13. Identifying states of a financial market.

    PubMed

    Münnix, Michael C; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H; Guhr, Thomas; Stanley, H Eugene

    2012-01-01

    The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992-2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical "market states". Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen.

  14. Identifying and Analyzing Web Server Attacks

    SciTech Connect

    Seifert, Christian; Endicott-Popovsky, Barbara E.; Frincke, Deborah A.; Komisarczuk, Peter; Muschevici, Radu; Welch, Ian D.

    2008-08-29

    Abstract: Client honeypots can be used to identify malicious web servers that attack web browsers and push malware to client machines. Merely recording network traffic is insufficient to perform comprehensive forensic analyses of such attacks. Custom tools are required to access and analyze network protocol data. Moreover, specialized methods are required to perform a behavioral analysis of an attack, which helps determine exactly what transpired on the attacked system. This paper proposes a record/replay mechanism that enables forensic investigators to extract application data from recorded network streams and allows applications to interact with this data in order to conduct behavioral analyses. Implementations for the HTTP and DNS protocols are presented and their utility in network forensic investigations is demonstrated.

  15. Identifying decohering paths in closed quantum systems

    NASA Technical Reports Server (NTRS)

    Albrecht, Andreas

    1990-01-01

    A specific proposal is discussed for how to identify decohering paths in a wavefunction of the universe. The emphasis is on determining the correlations among subsystems and then considering how these correlations evolve. The proposal is similar to earlier ideas of Schroedinger and of Zeh, but in other ways it is closer to the decoherence functional of Griffiths, Omnes, and Gell-Mann and Hartle. There are interesting differences with each of these which are discussed. Once a given coarse-graining is chosen, the candidate paths are fixed in this scheme, and a single well defined number measures the degree of decoherence for each path. The normal probability sum rules are exactly obeyed (instantaneously) by these paths regardless of the level of decoherence. Also briefly discussed is how one might quantify some other aspects of classicality. The important role that concrete calculations play in testing this and other proposals is stressed.

  16. Method of identifying features in indexed data

    DOEpatents

    Jarman, Kristin H [Richland, WA; Daly, Don Simone [Richland, WA; Anderson, Kevin K [Richland, WA; Wahl, Karen L [Richland, WA

    2001-06-26

    The present invention is a method of identifying features in indexed data, especially useful for distinguishing signal from noise in data provided as a plurality of ordered pairs. Each of the plurality of ordered pairs has an index and a response. The method has the steps of: (a) providing an index window having a first window end located on a first index and extending across a plurality of indices to a second window end; (b) selecting responses corresponding to the plurality of indices within the index window and computing a measure of dispersion of the responses; and (c) comparing the measure of dispersion to a dispersion critical value. Advantages of the present invention include minimizing signal to noise ratio, signal drift, varying baseline signal and combinations thereof.

  17. Photomaximization test for identifying photoallergic contact sensitizers.

    PubMed

    Kaidbey, K H; Kligman, A M

    1980-04-01

    The photomaximization procedure was designed to identify topical photocontact sensitizers following the format of the maximization test for contact sensitizers. The test agent is applied for 24 hours followed by exposure to three Minimal Erythema Doses (MED) of solar simulated radiation twice weekly for 3 weeks (six exposures) in a panel of 25 white Caucasoids. The subjects are challenged 2 weeks later with 4.0 J/cm2 of long-wave ultraviolet radiation (UV-A). Photocontact sensitization was induced to 3,3'4',5-tetrachlorosalicylanilide (TCSA); dibromosalicylanilide (DBS) but not to tribomosalicylanilide unless the latter was contaminated with DBS. Jadit and bithionol were weak photoallergens. The highest rate of sensitization was given by 6-methylcoumarin, a widely used synthetic fragrance. Hexachlorophene and trichlorocarbanilide were negative. PMID:7389322

  18. Photomaximization test for identifying photoallergic contact sensitizers.

    PubMed

    Kaidbey, K H; Kligman, A M

    1980-04-01

    The photomaximization procedure was designed to identify topical photocontact sensitizers following the format of the maximization test for contact sensitizers. The test agent is applied for 24 hours followed by exposure to three Minimal Erythema Doses (MED) of solar simulated radiation twice weekly for 3 weeks (six exposures) in a panel of 25 white Caucasoids. The subjects are challenged 2 weeks later with 4.0 J/cm2 of long-wave ultraviolet radiation (UV-A). Photocontact sensitization was induced to 3,3'4',5-tetrachlorosalicylanilide (TCSA); dibromosalicylanilide (DBS) but not to tribomosalicylanilide unless the latter was contaminated with DBS. Jadit and bithionol were weak photoallergens. The highest rate of sensitization was given by 6-methylcoumarin, a widely used synthetic fragrance. Hexachlorophene and trichlorocarbanilide were negative.

  19. Device for identifying a circumferential position

    DOEpatents

    Mikesell, Charles R.

    1985-01-01

    A device is described which accurately and reproducibly identifies points on the circumference of a non-vertical pipe for use as reference marks for pipe inspections. The device comprises a light-permeable disk-shaped chamber having a plurality of pockets spaced about its circumference, a light source transmitting a beam of light through the chamber, and a light-activated switch positioned to detect the light beam. The chamber contains a freely moving ball sized to be retained by the pockets. The device is mounted to revolve about the axis of the pipe. As it revolves the ball moves from one pocket of the chamber to another, interrupting the beam of light and triggering the light-activated switch, thereby indicating that the device has passed to a pre-selected circumferential position on the non-vertical pipe.

  20. Device for identifying a circumferential position

    DOEpatents

    Mikesell, C.R.

    1982-06-29

    A device is described which accurately and reproducibly identifies points on the circumference of a non-vertical pipe for use as reference marks for pipe inspections. The device comprises a light-permeable disk-shaped chamber having a plurality of pockets spaced about its circumference, a light source transmitting a beam of light through the chamber, and a light-activated switch positioned to detect the light beam. The chamber contains a freely moving ball sized to be retained by the pockets. The device is mounted to revolve about the axis of the pipe. As it revolves the ball moves from one pocket of the chamber to another, interrupting the beam of light and triggering the light-activated switch, thereby indicating that the device has passed to a pre-selected circumferential position on the non-vertical pipe.

  1. Identifying environmental correlates of intraspecific genetic variation.

    PubMed

    Harrisson, K A; Yen, J D L; Pavlova, A; Rourke, M L; Gilligan, D; Ingram, B A; Lyon, J; Tonkin, Z; Sunnucks, P

    2016-09-01

    Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution). PMID:27273322

  2. Vulnerability of critical infrastructures : identifying critical nodes.

    SciTech Connect

    Cox, Roger Gary; Robinson, David Gerald

    2004-06-01

    The objective of this research was the development of tools and techniques for the identification of critical nodes within critical infrastructures. These are nodes that, if disrupted through natural events or terrorist action, would cause the most widespread, immediate damage. This research focuses on one particular element of the national infrastructure: the bulk power system. Through the identification of critical elements and the quantification of the consequences of their failure, site-specific vulnerability analyses can be focused at those locations where additional security measures could be effectively implemented. In particular, with appropriate sizing and placement within the grid, distributed generation in the form of regional power parks may reduce or even prevent the impact of widespread network power outages. Even without additional security measures, increased awareness of sensitive power grid locations can provide a basis for more effective national, state and local emergency planning. A number of methods for identifying critical nodes were investigated: small-world (or network theory), polyhedral dynamics, and an artificial intelligence-based search method - particle swarm optimization. PSO was found to be the only viable approach and was applied to a variety of industry accepted test networks to validate the ability of the approach to identify sets of critical nodes. The approach was coded in a software package called Buzzard and integrated with a traditional power flow code. A number of industry accepted test networks were employed to validate the approach. The techniques (and software) are not unique to power grid network, but could be applied to a variety of complex, interacting infrastructures.

  3. Ultrasonic Detectors Safely Identify Dangerous, Costly Leaks

    NASA Technical Reports Server (NTRS)

    2013-01-01

    In 1990, NASA grounded its space shuttle fleet. The reason: leaks detected in the hydrogen fuel systems of the Space Shuttles Atlantis and Columbia. Unless the sources of the leaks could be identified and fixed, the shuttles would not be safe to fly. To help locate the existing leaks and check for others, Kennedy Space Center engineers used portable ultrasonic detectors to scan the fuel systems. As a gas or liquid escapes from a leak, the resulting turbulence creates ultrasonic noise, explains Gary Mohr, president of Elmsford, New York-based UE Systems Inc., a long-time leader in ultrasonic detector technologies. "In lay terms, the leak is like a dog whistle, and the detector is like the dog ear." Because the ultrasound emissions from a leak are highly localized, they can be used not only to identify the presence of a leak but also to help pinpoint a leak s location. The NASA engineers employed UE s detectors to examine the shuttle fuel tanks and solid rocket boosters, but encountered difficulty with the devices limited range-certain areas of the shuttle proved difficult or unsafe to scan up close. To remedy the problem, the engineers created a long-range attachment for the detectors, similar to "a zoom lens on a camera," Mohr says. "If you are on the ground, and the leak is 50 feet away, the detector would now give you the same impression as if you were only 25 feet away." The enhancement also had the effect of reducing background noise, allowing for a clearer, more precise detection of a leak s location.

  4. Identifying hidden voice and video streams

    NASA Astrophysics Data System (ADS)

    Fan, Jieyan; Wu, Dapeng; Nucci, Antonio; Keralapura, Ram; Gao, Lixin

    2009-04-01

    Given the rising popularity of voice and video services over the Internet, accurately identifying voice and video traffic that traverse their networks has become a critical task for Internet service providers (ISPs). As the number of proprietary applications that deliver voice and video services to end users increases over time, the search for the one methodology that can accurately detect such services while being application independent still remains open. This problem becomes even more complicated when voice and video service providers like Skype, Microsoft, and Google bundle their voice and video services with other services like file transfer and chat. For example, a bundled Skype session can contain both voice stream and file transfer stream in the same layer-3/layer-4 flow. In this context, traditional techniques to identify voice and video streams do not work. In this paper, we propose a novel self-learning classifier, called VVS-I , that detects the presence of voice and video streams in flows with minimum manual intervention. Our classifier works in two phases: training phase and detection phase. In the training phase, VVS-I first extracts the relevant features, and subsequently constructs a fingerprint of a flow using the power spectral density (PSD) analysis. In the detection phase, it compares the fingerprint of a flow to the existing fingerprints learned during the training phase, and subsequently classifies the flow. Our classifier is not only capable of detecting voice and video streams that are hidden in different flows, but is also capable of detecting different applications (like Skype, MSN, etc.) that generate these voice/video streams. We show that our classifier can achieve close to 100% detection rate while keeping the false positive rate to less that 1%.

  5. Identifying environmental correlates of intraspecific genetic variation.

    PubMed

    Harrisson, K A; Yen, J D L; Pavlova, A; Rourke, M L; Gilligan, D; Ingram, B A; Lyon, J; Tonkin, Z; Sunnucks, P

    2016-09-01

    Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).

  6. Identifying Crucial Parameter Correlations Maintaining Bursting Activity

    PubMed Central

    Doloc-Mihu, Anca; Calabrese, Ronald L.

    2014-01-01

    Recent experimental and computational studies suggest that linearly correlated sets of parameters (intrinsic and synaptic properties of neurons) allow central pattern-generating networks to produce and maintain their rhythmic activity regardless of changing internal and external conditions. To determine the role of correlated conductances in the robust maintenance of functional bursting activity, we used our existing database of half-center oscillator (HCO) model instances of the leech heartbeat CPG. From the database, we identified functional activity groups of burster (isolated neuron) and half-center oscillator model instances and realistic subgroups of each that showed burst characteristics (principally period and spike frequency) similar to the animal. To find linear correlations among the conductance parameters maintaining functional leech bursting activity, we applied Principal Component Analysis (PCA) to each of these four groups. PCA identified a set of three maximal conductances (leak current, Leak; a persistent K current, K2; and of a persistent Na+ current, P) that correlate linearly for the two groups of burster instances but not for the HCO groups. Visualizations of HCO instances in a reduced space suggested that there might be non-linear relationships between these parameters for these instances. Experimental studies have shown that period is a key attribute influenced by modulatory inputs and temperature variations in heart interneurons. Thus, we explored the sensitivity of period to changes in maximal conductances of Leak, K2, and P, and we found that for our realistic bursters the effect of these parameters on period could not be assessed because when varied individually bursting activity was not maintained. PMID:24945358

  7. Newly Identified Pathogens Associated with Periodontitis

    PubMed Central

    Pérez-Chaparro, P.J.; Gonçalves, C.; Figueiredo, L.C.; Faveri, M.; Lobão, E.; Tamashiro, N.; Duarte, P.; Feres, M.

    2014-01-01

    There is substantial evidence supporting the role of certain oral bacteria species in the onset and progression of periodontitis. Nevertheless, results of independent-culture diagnostic methods introduced about a decade ago have pointed to the existence of new periodontal pathogens. However, the data of these studies have not been evaluated together, which may generate some misunderstanding on the actual role of these microorganisms in the etiology of periodontitis. The aim of this systematic review was to determine the current weight of evidence for newly identified periodontal pathogens based on the results of “association” studies. This review was conducted and reported in accordance with the PRISMA statement. The MEDLINE, EMBASE, and Cochrane databases were searched up to September 2013 for studies (1) comparing microbial data of subgingival plaque samples collected from subjects with periodontitis and periodontal health and (2) evaluating at least 1 microorganism other than the already-known periodontal pathogens. From 1,450 papers identified, 41 studies were eligible. The data were extracted and registered in predefined piloted forms. The results suggested that there is moderate evidence in the literature to support the association of 17 species or phylotypes from the phyla Bacteroidetes, Candidatus Saccharibacteria, Firmicutes, Proteobacteria, Spirochaetes, and Synergistetes. The phylum Candidatus Saccharibacteria and the Archaea domain also seem to have an association with disease. These data point out the importance of previously unidentified species in the etiology of periodontitis and might guide future investigations on the actual role of these suspected new pathogens in the onset and progression of this infection. PMID:25074492

  8. RBCS1 expression in coffee: Coffea orthologs, Coffea arabica homeologs, and expression variability between genotypes and under drought stress

    PubMed Central

    2011-01-01

    Background In higher plants, the inhibition of photosynthetic capacity under drought is attributable to stomatal and non-stomatal (i.e., photochemical and biochemical) effects. In particular, a disruption of photosynthetic metabolism and Rubisco regulation can be observed. Several studies reported reduced expression of the RBCS genes, which encode the Rubisco small subunit, under water stress. Results Expression of the RBCS1 gene was analysed in the allopolyploid context of C. arabica, which originates from a natural cross between the C. canephora and C. eugenioides species. Our study revealed the existence of two homeologous RBCS1 genes in C. arabica: one carried by the C. canephora sub-genome (called CaCc) and the other carried by the C. eugenioides sub-genome (called CaCe). Using specific primer pairs for each homeolog, expression studies revealed that CaCe was expressed in C. eugenioides and C. arabica but was undetectable in C. canephora. On the other hand, CaCc was expressed in C. canephora but almost completely silenced in non-introgressed ("pure") genotypes of C. arabica. However, enhanced CaCc expression was observed in most C. arabica cultivars with introgressed C. canephora genome. In addition, total RBCS1 expression was higher for C. arabica cultivars that had recently introgressed C. canephora genome than for "pure" cultivars. For both species, water stress led to an important decrease in the abundance of RBCS1 transcripts. This was observed for plants grown in either greenhouse or field conditions under severe or moderate drought. However, this reduction of RBCS1 gene expression was not accompanied by a decrease in the corresponding protein in the leaves of C. canephora subjected to water withdrawal. In that case, the amount of RBCS1 was even higher under drought than under unstressed (irrigated) conditions, which suggests great stability of RBCS1 under adverse water conditions. On the other hand, for C. arabica, high nocturnal expression of RBCS1 could also explain the accumulation of the RBCS1 protein under water stress. Altogether, the results presented here suggest that the content of RBCS was not responsible for the loss of photosynthetic capacity that is commonly observed in water-stressed coffee plants. Conclusion We showed that the CaCe homeolog was expressed in C. eugenioides and non-introgressed ("pure") genotypes of C. arabica but that it was undetectable in C. canephora. On the other hand, the CaCc homeolog was expressed in C. canephora but highly repressed in C. arabica. Expression of the CaCc homeolog was enhanced in C. arabica cultivars that experienced recent introgression with C. canephora. For both C. canephora and C. arabica species, total RBCS1 gene expression was highly reduced with WS. Unexpectedly, the accumulation of RBCS1 protein was observed in the leaves of C. canephora under WS, possibly coming from nocturnal RBCS1 expression. These results suggest that the increase in the amount of RBCS1 protein could contribute to the antioxidative function of photorespiration in water-stressed coffee plants. PMID:21575242

  9. Identifying sites for elk restoration in Arkansas

    USGS Publications Warehouse

    Telesco, R.L.; Van Manen, F.T.; Clark, J.D.; Cartwright, Michael E.

    2007-01-01

    We used spatial data to identify potential areas for elk (Cervus elaphus) restoration in Arkansas. To assess habitat, we used locations of 239 elk groups collected from helicopter surveys in the Buffalo National River area of northwestern Arkansas, USA, from 1992 to 2002. We calculated the Mahalanobis distance (D2) statistic based on the relationship between those elk-group locations and a suite of 9 landscape variables to evaluate winter habitat in Arkansas. We tested model performance in the Buffalo National River area by comparing the D2 values of pixels representing areas with and without elk pellets along 19 fixed-width transects surveyed in March 2002. Pixels with elk scat had lower D2 values than pixels in which we found no pellets (logistic regression: Wald χ2 = 24.37, P < 0.001), indicating that habitat characteristics were similar to those selected by the aerially surveyed elk. Our D2 model indicated that the best elk habitat primarily occurred in northern and western Arkansas and was associated with areas of high landscape heterogeneity, heavy forest cover, gently sloping ridge tops and valleys, low human population density, and low road densities. To assess the potential for elk–human conflicts in Arkansas, we used the analytical hierarchy process to rank the importance of 8 criteria based on expert opinion from biologists involved in elk management. The biologists ranked availability of forage on public lands as having the strongest influence on the potential for elk–human conflict (33%), followed by human population growth rate (22%) and the amount of private land in row crops (18%). We then applied those rankings in a weighted linear summation to map the relative potential for elk–human conflict. Finally, we used white-tailed deer (Odocoileus virginianus) densities to identify areas where success of elk restoration may be hampered due to meningeal worm (Parelaphostrongylus tenuis) transmission. By combining results of the 3 spatial data layers

  10. Using Hyperspectral Imagery to Identify Turfgrass Stresses

    NASA Technical Reports Server (NTRS)

    Hutto, Kendall; Shaw, David

    2008-01-01

    The use of a form of remote sensing to aid in the management of large turfgrass fields (e.g. golf courses) has been proposed. A turfgrass field of interest would be surveyed in sunlight by use of an airborne hyperspectral imaging system, then the raw observational data would be preprocessed into hyperspectral reflectance image data. These data would be further processed to identify turfgrass stresses, to determine the spatial distributions of those stresses, and to generate maps showing the spatial distributions. Until now, chemicals and water have often been applied, variously, (1) indiscriminately to an entire turfgrass field without regard to localization of specific stresses or (2) to visible and possibly localized signs of stress for example, browning, damage from traffic, or conspicuous growth of weeds. Indiscriminate application is uneconomical and environmentally unsound; the amounts of water and chemicals consumed could be insufficient in some areas and excessive in most areas, and excess chemicals can leak into the environment. In cases in which developing stresses do not show visible signs at first, it could be more economical and effective to take corrective action before visible signs appear. By enabling early identification of specific stresses and their locations, the proposed method would provide guidance for planning more effective, more economical, and more environmentally sound turfgrass-management practices, including application of chemicals and water, aeration, and mowing. The underlying concept of using hyperspectral imagery to generate stress maps as guides to efficient management of vegetation in large fields is not new; it has been applied in the growth of crops to be harvested. What is new here is the effort to develop an algorithm that processes hyperspectral reflectance data into spectral indices specific to stresses in turfgrass. The development effort has included a study in which small turfgrass plots that were, variously, healthy or

  11. Use of lice to identify cowbird hosts

    USGS Publications Warehouse

    Hahn, D.C.; Price, R.D.; Osenton, P.C.

    2000-01-01

    The host specificity of avian lice (Phthiraptera) may be utilized by biologists to investigate the brood parasitism patterns of Brown-headed Cowbirds (Molothrus ater). As nestlings, brood parasites have a unique opportunity to encounter lice that are typically host specific. Lice are permanent hemimetabolic ectoparasites, a group found strictly on the body of the host, and they are transferred almost exclusively by bodily contact between hosts during care of young and at copulation. We investigated whether cowbird nestlings become infested with avian lice from their host parents and carry these lice away when they fledge, in effect bearing ectoparasite indicators of the species that raised them. The technique of examining the lice on cowbird fledglings to identify their foster parents would be much less costly than hiring a team of experts to determine parasitism patterns in the conventional way by finding hundreds of songbird nests. We examined 244 cowbird fledglings and found that they carried a rich fauna of lice representing 11 species and six genera, almost the entire spectrum of louse genera known to occur on passerines. We also examined 320 songbirds from 30 species, all known hosts of the Brown-headed Cowbird. As a group the host birds bore a diversity of louse species comparable to that on the fledgling cowbirds: 13 species of lice from seven genera. In contrast, most individual passerine host species yielded only 1 or 2 louse species, significantly fewer than the cowbird fledglings (p < 0.0001). Of 44 fledgling cowbirds carrying lice, 11 were linked to their probable avian foster parents via louse indicators, and these are the Wood Thrush and Red-winged Blackbird. Eighteen additional fledglings were linked to one of two possible foster parents. We concluded that cowbird fledglings do carry away host lice and this survey technique provides a partial assessment of local community parasitism patterns. The incomplete state of passerine louse taxonomy requires

  12. Pseudonymization of patient identifiers for translational research

    PubMed Central

    2013-01-01

    Background The usage of patient data for research poses risks concerning the patients’ privacy and informational self-determination. Next-generation-sequencing technologies and various other methods gain data from biospecimen, both for translational research and personalized medicine. If these biospecimen are anonymized, individual research results from genomic research, which should be offered to patients in a clinically relevant timeframe, cannot be associated back to the individual. This raises an ethical concern and challenges the legitimacy of anonymized patient samples. In this paper we present a new approach which supports both data privacy and the possibility to give feedback to patients about their individual research results. Methods We examined previously published privacy concepts regarding a streamlined de-pseudonymization process and a patient-based pseudonym as applicable to research with genomic data and warehousing approaches. All concepts identified in the literature review were compared to each other and analyzed for their applicability to translational research projects. We evaluated how these concepts cope with challenges implicated by personalized medicine. Therefore, both person-centricity issues and a separation of pseudonymization and de-pseudonymization stood out as a central theme in our examination. This motivated us to enhance an existing pseudonymization method regarding a separation of duties. Results The existing concepts rely on external trusted third parties, making de-pseudonymization a multistage process involving additional interpersonal communication, which might cause critical delays in patient care. Therefore we propose an enhanced method with an asymmetric encryption scheme separating the duties of pseudonymization and de-pseudonymization. The pseudonymization service provider is unable to conclude the patient identifier from the pseudonym, but assigns this ability to an authorized third party (ombudsman) instead. To solve

  13. Identifying image preferences based on demographic attributes

    NASA Astrophysics Data System (ADS)

    Fedorovskaya, Elena A.; Lawrence, Daniel R.

    2014-02-01

    The intent of this study is to determine what sorts of images are considered more interesting by which demographic groups. Specifically, we attempt to identify images whose interestingness ratings are influenced by the demographic attribute of the viewer's gender. To that end, we use the data from an experiment where 18 participants (9 women and 9 men) rated several hundred images based on "visual interest" or preferences in viewing images. The images were selected to represent the consumer "photo-space" - typical categories of subject matter found in consumer photo collections. They were annotated using perceptual and semantic descriptors. In analyzing the image interestingness ratings, we apply a multivariate procedure known as forced classification, a feature of dual scaling, a discrete analogue of principal components analysis (similar to correspondence analysis). This particular analysis of ratings (i.e., ordered-choice or Likert) data enables the investigator to emphasize the effect of a specific item or collection of items. We focus on the influence of the demographic item of gender on the analysis, so that the solutions are essentially confined to subspaces spanned by the emphasized item. Using this technique, we can know definitively which images' ratings have been influenced by the demographic item of choice. Subsequently, images can be evaluated and linked, on one hand, to their perceptual and semantic descriptors, and, on the other hand, to the preferences associated with viewers' demographic attributes.

  14. Identifying recycled ash in basaltic eruptions

    NASA Astrophysics Data System (ADS)

    D'Oriano, Claudia; Bertagnini, Antonella; Cioni, Raffaello; Pompilio, Massimo

    2014-07-01

    Deposits of mid-intensity basaltic explosive eruptions are characterized by the coexistence of different types of juvenile clasts, which show a large variability of external properties and texture, reflecting alternatively the effects of primary processes related to magma storage or ascent, or of syn-eruptive modifications occurred during or immediately after their ejection. If fragments fall back within the crater area before being re-ejected during the ensuing activity, they are subject to thermally- and chemically-induced alterations. These `recycled' clasts can be considered as cognate lithic for the eruption/explosion they derive. Their exact identification has consequences for a correct interpretation of eruption dynamics, with important implications for hazard assessment. On ash erupted during selected basaltic eruptions (at Stromboli, Etna, Vesuvius, Gaua-Vanuatu), we have identified a set of characteristics that can be associated with the occurrence of intra-crater recycling processes, based also on the comparison with results of reheating experiments performed on primary juvenile material, at variable temperature and under different redox conditions.

  15. Asteroid Secular Dynamics: Ceres’ Fingerprint Identified

    NASA Astrophysics Data System (ADS)

    Novaković, Bojan; Maurel, Clara; Tsirvoulis, Georgios; Knežević, Zoran

    2015-07-01

    Here we report on the significant role of a so far overlooked dynamical aspect, namely, a secular resonance between the dwarf planet Ceres and other asteroids. We demonstrate that this type of secular resonance can be the dominant dynamical factor in certain regions of the main asteroid belt. Specifically, we performed a dynamical analysis of the asteroids belonging to the (1726) Hoffmeister family. To identify which dynamical mechanisms are actually at work in this part of the main asteroid belt, i.e., to isolate the main perturber(s), we study the evolution of this family in time. The study is accomplished using numerical integrations of test particles performed within different dynamical models. The obtained results reveal that the post-impact evolution of the Hoffmeister asteroid family is a direct consequence of the nodal secular resonance with Ceres. This leads us to the conclusion that similar effects must exist in other parts of the asteroid belt. In this respect, the obtained results shed light on an important and entirely new aspect of the long-term dynamics of small bodies. Ceres’ fingerprint in asteroid dynamics, expressed through the discovered secular resonance effect, completely changes our understanding of the way in which perturbations by Ceres-like objects affect the orbits of nearby bodies.

  16. Identifying the sea level signal: Surf's up

    NASA Astrophysics Data System (ADS)

    Maggs, William Ward

    Of all the dire consequences of the greenhouse effect, global sea level rise is potentially the most destructive to human life and property. But the processes that increase the volume of the oceans are so poorly understood that theoreticians are taking their lead from scientists trying to actually measure current changes in sea level that might be caused by the greenhouse effect. As with surface temperature, precipitation, and other measures of climate change, identifying the greenhouse signal is a daunting problem.Climate models that predict mean temperature increases around the world of up to several degrees C in the next 50-100 years in response to human-induced global warming have given rise to a scientific consensus that mountain glaciers and ice sheets will begin to melt and the water in oceans will slightly expand, raising sea level. Such increases would inundate some of the most densely populated and highly cultivated areas on the planet, displacing and endangering many millions of people at a devastating economic and social cost.

  17. Identifying Wind and Solar Ramping Events: Preprint

    SciTech Connect

    Florita, A.; Hodge, B. M.; Orwig, K.

    2013-01-01

    Wind and solar power are playing an increasing role in the electrical grid, but their inherent power variability can augment uncertainties in power system operations. One solution to help mitigate the impacts and provide more flexibility is enhanced wind and solar power forecasting; however, its relative utility is also uncertain. Within the variability of solar and wind power, repercussions from large ramping events are of primary concern. At the same time, there is no clear definition of what constitutes a ramping event, with various criteria used in different operational areas. Here the Swinging Door Algorithm, originally used for data compression in trend logging, is applied to identify variable generation ramping events from historic operational data. The identification of ramps in a simple and automated fashion is a critical task that feeds into a larger work of 1) defining novel metrics for wind and solar power forecasting that attempt to capture the true impact of forecast errors on system operations and economics, and 2) informing various power system models in a data-driven manner for superior exploratory simulation research. Both allow inference on sensitivities and meaningful correlations, as well as the ability to quantify the value of probabilistic approaches for future use in practice.

  18. Identifying Lagrangian fronts with favourable fishery conditions

    NASA Astrophysics Data System (ADS)

    Prants, S. V.; Budyansky, M. V.; Uleysky, M. Yu.

    2014-08-01

    Lagrangian fronts (LFs) in the ocean are defined as boundaries between surface waters with strongly different Lagrangian properties. They can be accurately detected in a given velocity field by computing synoptic maps for displacements of synthetic tracers and other Lagrangian indicators. We use Pacific saury catch and location data for a number of commercial fishery seasons in the region of the northwest Pacific with one of the richest fishery in the world. It is shown statistically that the saury fishing grounds with maximal catches are not randomly distributed over the region but located mainly along the sharp LFs where productive cold waters of the Oyashio Current, warmer waters of the southern branch of the Soya Current, and waters of warm-core Kuroshio rings converge. Computation of those fronts in altimetric geostrophic velocity fields both in the years with the First and Second Oyashio Intrusions shows that in spite of different oceanographic conditions LF locations may serve as good indicators of potential fishing grounds. Possible biophysical reasons for saury aggregation near sharp LFs are discussed. We propose a mechanism for effective export of nutrient rich waters based on stretching of material lines in the vicinity of hyperbolic objects in the ocean. The developed method, based on identifying LFs in any velocity fields, is quite general and may be applied to find potential fishing grounds for the other pelagic fish.

  19. Identifying orthoimages in Web Map Services

    NASA Astrophysics Data System (ADS)

    Florczyk, A. J.; Nogueras-Iso, J.; Zarazaga-Soria, F. J.; Béjar, R.

    2012-10-01

    Orthoimages are essential in many Web applications to facilitate the background context that helps to understand other georeferenced information. Catalogues and service registries of Spatial Data Infrastructures do not necessarily register all the services providing access to imagery data on the Web, and it is not easy to automatically identify whether the data offered by a Web service are directly imagery data or not. This work presents a method for an automatic detection of the orthoimage layers offered by Web Map Services. The method combines two types of heuristics. The first one consists in analysing the text in the capabilities document. The second type is content-based heuristics, which analyse the content offered by the Web Map Service layers. These heuristics gather and analyse the colour features of a sample collection of image fragments that represent the offered content. An experiment has been performed over a set of Web Map Service layers, which have been fetched from a repository of capabilities documents gathered from the Web. This has proven the efficiency of the method (precision of 87% and recall of 60%). This functionality has been offered as a Web Processing Service, and it has been integrated within the Virtual Spain project to provide a catalogue of orthoimages and build realistic 3D views.

  20. Ebola virus infection modeling and identifiability problems

    PubMed Central

    Nguyen, Van Kinh; Binder, Sebastian C.; Boianelli, Alessandro; Meyer-Hermann, Michael; Hernandez-Vargas, Esteban A.

    2015-01-01

    The recent outbreaks of Ebola virus (EBOV) infections have underlined the impact of the virus as a major threat for human health. Due to the high biosafety classification of EBOV (level 4), basic research is very limited. Therefore, the development of new avenues of thinking to advance quantitative comprehension of the virus and its interaction with the host cells is urgently needed to tackle this lethal disease. Mathematical modeling of the EBOV dynamics can be instrumental to interpret Ebola infection kinetics on quantitative grounds. To the best of our knowledge, a mathematical modeling approach to unravel the interaction between EBOV and the host cells is still missing. In this paper, a mathematical model based on differential equations is used to represent the basic interactions between EBOV and wild-type Vero cells in vitro. Parameter sets that represent infectivity of pathogens are estimated for EBOV infection and compared with influenza virus infection kinetics. The average infecting time of wild-type Vero cells by EBOV is slower than in influenza infection. Simulation results suggest that the slow infecting time of EBOV could be compensated by its efficient replication. This study reveals several identifiability problems and what kind of experiments are necessary to advance the quantification of EBOV infection. A first mathematical approach of EBOV dynamics and the estimation of standard parameters in viral infections kinetics is the key contribution of this work, paving the way for future modeling works on EBOV infection. PMID:25914675

  1. Indexing molecules with chemical graph identifiers.

    PubMed

    Gregori-Puigjané, Elisabet; Garriga-Sust, Rut; Mestres, Jordi

    2011-09-01

    Fast and robust algorithms for indexing molecules have been historically considered strategic tools for the management and storage of large chemical libraries. This work introduces a modified and further extended version of the molecular equivalence number naming adaptation of the Morgan algorithm (J Chem Inf Comput Sci 2001, 41, 181-185) for the generation of a chemical graph identifier (CGI). This new version corrects for the collisions recognized in the original adaptation and includes the ability to deal with graph canonicalization, ensembles (salts), and isomerism (tautomerism, regioisomerism, optical isomerism, and geometrical isomerism) in a flexible manner. Validation of the current CGI implementation was performed on the open NCI database and the drug-like subset of the ZINC database containing 260,071 and 5,348,089 structures, respectively. The results were compared with those obtained with some of the most widely used indexing codes, such as the CACTVS hash code and the new InChIKey. The analyses emphasize the fact that compound management activities, like duplicate analysis of chemical libraries, are sensitive to the exact definition of compound uniqueness and thus still depend, to a minor extent, on the type and flexibility of the molecular index being used.

  2. Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.

    PubMed

    Edmunds, Richard C; Su, Baofeng; Balhoff, James P; Eames, B Frank; Dahdul, Wasila M; Lapp, Hilmar; Lundberg, John G; Vision, Todd J; Dunham, Rex A; Mabee, Paula M; Westerfield, Monte

    2016-01-01

    Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology. PMID:26500251

  3. GT-Scan: identifying unique genomic targets

    PubMed Central

    O’Brien, Aidan; Bailey, Timothy L.

    2014-01-01

    Summary: A number of technologies, including CRISPR/Cas, transcription activator-like effector nucleases and zinc-finger nucleases, allow the user to target a chosen locus for genome editing or regulatory interference. Specificity, however, is a major problem, and the targeted locus must be chosen with care to avoid inadvertently affecting other loci (‘off-targets’) in the genome. To address this we have created ‘Genome Target Scan’ (GT-Scan), a flexible web-based tool that ranks all potential targets in a user-selected region of a genome in terms of how many off-targets they have. GT-Scan gives the user flexibility to define the desired characteristics of targets and off-targets via a simple ‘target rule’, and its interactive output allows detailed inspection of each of the most promising candidate targets. GT-Scan can be used to identify optimal targets for CRISPR/Cas systems, but its flexibility gives it potential to be adapted to other genome-targeting technologies as well. Availability and implementation: GT-Scan can be run via the web at: http://gt-scan.braembl.org.au. Contact: t.bailey@uq.edu.au PMID:24860161

  4. Identifying materials limits of chemically amplified photoresists

    NASA Astrophysics Data System (ADS)

    Wu, Wen-li; Prabhu, Vivek M.; Lin, Eric K.

    2007-03-01

    Chemically amplified photoresists are likely to remain the primary imaging materials for the semiconductor industry. As feature sizes decrease to dimensions comparable to the characteristic size of the molecules in the photoresist, a significant challenge lies in identifying the ultimate resolution limit of these materials. To address this challenge, we investigated model photoresist materials with high resolution measurements to examine the effect of individual factors among interdependent process steps on line-edge roughness (LER). Using a bilayer film sample geometry, we measured the internal deprotection interface with nanometer resolution as a function of photoacid size, initial resist copolymer composition, and amine base quencher by neutron reflectivity and infrared spectroscopy. After development, we found that the resist chemistry and additives can play an important role in LER through its influence on acid diffusion. However, these model experiments suggest that there is a limit in LER even with an idealized exposure image contrast and decreases in the width of the reaction-diffusion front. However, there may be opportunities to further decrease LER during development by tuning the response of the photoresist to the developer solution.

  5. Experimental approaches for identifying schizophrenia risk genes.

    PubMed

    Mantripragada, Kiran K; Carroll, Liam S; Williams, Nigel M

    2010-01-01

    Schizophrenia is a severe, debilitating and common psychiatric disorder, which directly affects approximately 1% of the population worldwide. Although previous studies have unequivocally shown that schizophrenia has a strong genetic component, our understanding of its pathophysiology remains limited. The precise genetic architecture of schizophrenia remains elusive and is likely to be complex. It is believed that multiple genetic variants, with each contributing a modest effect on disease risk, interact with environmental factors resulting in the phenotype. In this chapter, we summarise the main molecular genetic approaches that have been utilised in identifying susceptibility genes for schizophrenia and discuss the advantages and disadvantages of each approach. First, we detail the findings of linkage mapping in pedigrees (affected families), which analyse the co-segregation of polymorphic genetic markers with disease phenotype. Second, the contribution of targeted and genome-wide association studies, which compare differential allelic frequencies in schizophrenia cases and matched controls, is presented. Third, we discuss about the identification of susceptibility genes through analysis of chromosomal structural variation (gains and losses of genetic material). Lastly, we introduce the concept of re-sequencing, where the entire genome/exome is sequenced both in affected and unaffected individuals. This approach has the potential to provide a clarified picture of the majority of the genetic variation underlying disease pathogenesis. PMID:21312414

  6. Identifying Cognitive States Using Regularity Partitions

    PubMed Central

    2015-01-01

    Functional Magnetic Resonance (fMRI) data can be used to depict functional connectivity of the brain. Standard techniques have been developed to construct brain networks from this data; typically nodes are considered as voxels or sets of voxels with weighted edges between them representing measures of correlation. Identifying cognitive states based on fMRI data is connected with recording voxel activity over a certain time interval. Using this information, network and machine learning techniques can be applied to discriminate the cognitive states of the subjects by exploring different features of data. In this work we wish to describe and understand the organization of brain connectivity networks under cognitive tasks. In particular, we use a regularity partitioning algorithm that finds clusters of vertices such that they all behave with each other almost like random bipartite graphs. Based on the random approximation of the graph, we calculate a lower bound on the number of triangles as well as the expectation of the distribution of the edges in each subject and state. We investigate the results by comparing them to the state of the art algorithms for exploring connectivity and we argue that during epochs that the subject is exposed to stimulus, the inspected part of the brain is organized in an efficient way that enables enhanced functionality. PMID:26317983

  7. Pharmaceutical identifier confirmation via DART-TOF.

    PubMed

    Easter, Jacob L; Steiner, Robert R

    2014-07-01

    Pharmaceutical analysis comprises a large amount of the casework in forensic controlled substances laboratories. In order to reduce the time of analysis for pharmaceuticals, a Direct Analysis in Real Time ion source coupled with an accurate mass time-of-flight (DART-TOF) mass spectrometer was used to confirm identity. DART-TOF spectral data for pharmaceutical samples were analyzed and evaluated by comparison to standard spectra. Identical mass pharmaceuticals were differentiated using collision induced dissociation fragmentation, present/absent ions, and abundance comparison box plots; principal component analysis (PCA) and linear discriminant analysis (LDA) were used for differentiation of identical mass mixed drug spectra. Mass assignment reproducibility and robustness tests were performed on the DART-TOF spectra. Impacts on the forensic science community include a decrease in analysis time over the traditional gas chromatograph/mass spectrometry (GC/MS) confirmations, better laboratory efficiency, and simpler sample preparation. Using physical identifiers and the DART-TOF to confirm pharmaceutical identity will eliminate the use of GC/MS and effectively reduce analysis time while still complying with accepted analysis protocols. This will prove helpful in laboratories with large backlogs and will simplify the confirmation process.

  8. Strategies for identifying new prions in yeast.

    PubMed

    MacLea, Kyle S; Ross, Eric D

    2011-01-01

    The unexpected discovery of two prions, [URE3] and [PSI+], in Saccharomyces cerevisiae led to questions about how many other proteins could undergo similar prion-based structural conversions. However, [URE3] and [PSI+] were discovered by serendipity in genetic screens. Cataloging the full range of prions in yeast or in other organisms will therefore require more systematic search methods. Taking advantage of some of the unique features of prions, various researchers have developed bioinformatic and experimental methods for identifying novel prion proteins. These methods have generated long lists of prion candidates. The systematic testing of some of these prion candidates has led to notable successes; however, even in yeast, where rapid growth rate and ease of genetic manipulation aid in testing for prion activity, such candidate testing is laborious. Development of better methods to winnow the field of prion candidates will greatly aid in the discovery of new prions, both in yeast and in other organisms, and help us to better understand the role of prions in biology.

  9. [Techniques for identifying the epidural space].

    PubMed

    Figueredo, E

    2005-01-01

    A large part of the success of epidural anesthesia rests on correct identification of the epidural space. The last hundred years have seen the description of numerous techniques for locating the space in the most straightforward, effective, safe, and reliable manner. To evaluate the advantages and disadvantages of these approaches and the complications associated with each, we carried out a MEDLINE search using the following key words: "epidural analgesia," "epidural anesthesia," "epidural space," "identification," and "loss of resistance" (LOR). Traditional, complementary, and instrument-guided techniques used to identify the epidural space were analyzed. The results of clinical trials comparing different LOR techniques were evaluated. LOR with air, with isotonic saline, or a combination of both were the techniques shown to be simplest and safest. With respect to safety, LOR with air led to the greatest number of complications (pneumocephalus, air embolism, insufficient analgesia, higher incidence of dural puncture, nerve root compression, subcutaneous emphysema). When a small air bubble is created inside the syringe, LOR with saline solution is reliable and teachable, as well as safe and effective.

  10. Identifying dark matter interactions in monojet searches

    SciTech Connect

    Agrawal, Prateek; Rentala, Vikram

    2014-05-22

    We study the discrimination of quark-initiated jets from gluon-initiated jets in monojet searches for dark matter using the technique of averaged jet energy profiles. We demonstrate our results in the context of effective field theories of dark matter interactions with quarks and gluons, but our methods apply more generally to a wide class of models. Different effective theories of dark matter and the standard model backgrounds each have a characteristic quark/gluon fraction for the leading jet. When used in conjunction with the traditional cut-and-count monojet search, the jet energy profile can be used to set stronger bounds on contact interactions of dark matter. In the event of a discovery of a monojet excess at the 14 TeV LHC, contact interactions between dark matter with quarks or with gluons can be differentiated at the 95% confidence level. For a given rate at the LHC, signal predictions at direct detection experiments for different dark matter interactions can span five orders of magnitude. Lastly, the ability to identify these interactions allows us to make a tighter connection between LHC searches and direct detection experiments.

  11. Identifying dark matter interactions in monojet searches

    DOE PAGES

    Agrawal, Prateek; Rentala, Vikram

    2014-05-22

    We study the discrimination of quark-initiated jets from gluon-initiated jets in monojet searches for dark matter using the technique of averaged jet energy profiles. We demonstrate our results in the context of effective field theories of dark matter interactions with quarks and gluons, but our methods apply more generally to a wide class of models. Different effective theories of dark matter and the standard model backgrounds each have a characteristic quark/gluon fraction for the leading jet. When used in conjunction with the traditional cut-and-count monojet search, the jet energy profile can be used to set stronger bounds on contact interactionsmore » of dark matter. In the event of a discovery of a monojet excess at the 14 TeV LHC, contact interactions between dark matter with quarks or with gluons can be differentiated at the 95% confidence level. For a given rate at the LHC, signal predictions at direct detection experiments for different dark matter interactions can span five orders of magnitude. Lastly, the ability to identify these interactions allows us to make a tighter connection between LHC searches and direct detection experiments.« less

  12. Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

    PubMed Central

    Edmunds, Richard C.; Su, Baofeng; Balhoff, James P.; Eames, B. Frank; Dahdul, Wasila M.; Lapp, Hilmar; Lundberg, John G.; Vision, Todd J.; Dunham, Rex A.; Mabee, Paula M.; Westerfield, Monte

    2016-01-01

    Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology. PMID:26500251

  13. Indexing molecules with chemical graph identifiers.

    PubMed

    Gregori-Puigjané, Elisabet; Garriga-Sust, Rut; Mestres, Jordi

    2011-09-01

    Fast and robust algorithms for indexing molecules have been historically considered strategic tools for the management and storage of large chemical libraries. This work introduces a modified and further extended version of the molecular equivalence number naming adaptation of the Morgan algorithm (J Chem Inf Comput Sci 2001, 41, 181-185) for the generation of a chemical graph identifier (CGI). This new version corrects for the collisions recognized in the original adaptation and includes the ability to deal with graph canonicalization, ensembles (salts), and isomerism (tautomerism, regioisomerism, optical isomerism, and geometrical isomerism) in a flexible manner. Validation of the current CGI implementation was performed on the open NCI database and the drug-like subset of the ZINC database containing 260,071 and 5,348,089 structures, respectively. The results were compared with those obtained with some of the most widely used indexing codes, such as the CACTVS hash code and the new InChIKey. The analyses emphasize the fact that compound management activities, like duplicate analysis of chemical libraries, are sensitive to the exact definition of compound uniqueness and thus still depend, to a minor extent, on the type and flexibility of the molecular index being used. PMID:21647928

  14. Identifying and helping battered pregnant women.

    PubMed

    Parker, B; McFarlane, J

    1991-01-01

    This article highlights strategies in identifying and helping battered pregnant women. Studies report that 40-60% of battered women were abused during pregnancy inflicted in the form of blows to the abdomen, injuries to the breasts and genitals, and sexual assault. Because battering during pregnancy has been a prevalent occurrence, assessment during prenatal visits is most critical. This paper outlines several assessment approaches in dealing with battered pregnant women in specific circumstances, giving important consideration to her safety due to the potential risk of homicide. A Danger Assessment tool is utilized in assessing for potential homicide. Intervening with victims of abuse is difficult. The role of the nurse is to assist in the development of problem-solving and decision-making skills while the woman is still in extreme confusion or feeling of conflicting loyalties. Routine assessment for physical and sexual abuse during the prenatal period is recommended in order to prevent further abuse thus promoting maternal-child well being. PMID:2056861

  15. Functional genomics identifies drivers of medulloblastoma dissemination.

    PubMed

    Mumert, Michael; Dubuc, Adrian; Wu, Xiaochong; Northcott, Paul A; Chin, Steven S; Pedone, Carolyn A; Taylor, Michael D; Fults, Daniel W

    2012-10-01

    Medulloblastomas are malignant brain tumors that arise in the cerebellum in children and disseminate via the cerebrospinal fluid to the leptomeningeal spaces of the brain and spinal cord. Challenged by the poor prognosis for patients with metastatic dissemination, pediatric oncologists have developed aggressive treatment protocols, combining surgery, craniospinal radiation, and high-dose chemotherapy, that often cause disabling neurotoxic effects in long-term survivors. Insights into the genetic control of medulloblastoma dissemination have come from transposon insertion mutagenesis studies. Mobilizing the Sleeping Beauty transposon in cerebellar neural progenitor cells caused widespread dissemination of typically nonmetastatic medulloblastomas in Patched(+/-) mice, in which Shh signaling is hyperactive. Candidate metastasis genes were identified by sequencing the insertion sites and then mapping these sequences back to the mouse genome. To determine whether genes located at transposon insertion sites directly caused medulloblastomas to disseminate, we overexpressed candidate genes in Nestin(+) neural progenitors in the cerebella of mice by retroviral transfer in combination with Shh. We show here that ectopic expression of Eras, Lhx1, Ccrk, and Akt shifted the in vivo growth characteristics of Shh-induced medulloblastomas from a localized pattern to a disseminated pattern in which tumor cells seeded the leptomeningeal spaces of the brain and spinal cord. PMID:22875024

  16. Can we identify source lithology of basalt?

    PubMed

    Yang, Zong-Feng; Zhou, Jun-Hong

    2013-01-01

    The nature of source rocks of basaltic magmas plays a fundamental role in understanding the composition, structure and evolution of the solid earth. However, identification of source lithology of basalts remains uncertainty. Using a parameterization of multi-decadal melting experiments on a variety of peridotite and pyroxenite, we show here that a parameter called FC3MS value (FeO/CaO-3*MgO/SiO2, all in wt%) can identify most pyroxenite-derived basalts. The continental oceanic island basalt-like volcanic rocks (MgO>7.5%) (C-OIB) in eastern China and Mongolia are too high in the FC3MS value to be derived from peridotite source. The majority of the C-OIB in phase diagrams are equilibrium with garnet and clinopyroxene, indicating that garnet pyroxenite is the dominant source lithology. Our results demonstrate that many reputed evolved low magnesian C-OIBs in fact represent primary pyroxenite melts, suggesting that many previous geological and petrological interpretations of basalts based on the single peridotite model need to be reconsidered.

  17. Identifying recycled ash in basaltic eruptions.

    PubMed

    D'Oriano, Claudia; Bertagnini, Antonella; Cioni, Raffaello; Pompilio, Massimo

    2014-07-28

    Deposits of mid-intensity basaltic explosive eruptions are characterized by the coexistence of different types of juvenile clasts, which show a large variability of external properties and texture, reflecting alternatively the effects of primary processes related to magma storage or ascent, or of syn-eruptive modifications occurred during or immediately after their ejection. If fragments fall back within the crater area before being re-ejected during the ensuing activity, they are subject to thermally- and chemically-induced alterations. These 'recycled' clasts can be considered as cognate lithic for the eruption/explosion they derive. Their exact identification has consequences for a correct interpretation of eruption dynamics, with important implications for hazard assessment. On ash erupted during selected basaltic eruptions (at Stromboli, Etna, Vesuvius, Gaua-Vanuatu), we have identified a set of characteristics that can be associated with the occurrence of intra-crater recycling processes, based also on the comparison with results of reheating experiments performed on primary juvenile material, at variable temperature and under different redox conditions.

  18. Can we identify source lithology of basalt?

    PubMed Central

    Yang, Zong-Feng; Zhou, Jun-Hong

    2013-01-01

    The nature of source rocks of basaltic magmas plays a fundamental role in understanding the composition, structure and evolution of the solid earth. However, identification of source lithology of basalts remains uncertainty. Using a parameterization of multi-decadal melting experiments on a variety of peridotite and pyroxenite, we show here that a parameter called FC3MS value (FeO/CaO-3*MgO/SiO2, all in wt%) can identify most pyroxenite-derived basalts. The continental oceanic island basalt-like volcanic rocks (MgO>7.5%) (C-OIB) in eastern China and Mongolia are too high in the FC3MS value to be derived from peridotite source. The majority of the C-OIB in phase diagrams are equilibrium with garnet and clinopyroxene, indicating that garnet pyroxenite is the dominant source lithology. Our results demonstrate that many reputed evolved low magnesian C-OIBs in fact represent primary pyroxenite melts, suggesting that many previous geological and petrological interpretations of basalts based on the single peridotite model need to be reconsidered. PMID:23676779

  19. Identifying the causes of contact dermatitis.

    PubMed

    Jones, Ruth; Horn, Helen M

    2014-06-01

    Contact dermatitis results from skin contact with an exogenous substance. It can be caused by direct contact, airborne particles, vapours or light. Individuals of any age can be affected. The two most common variants are irritant contact dermatitis (ICD) and allergic contact dermatitis (ACD). ICD is more common and has a worse prognosis. Other less common forms of contact dermatitis include photocontact allergy and, in food handlers, protein contact dermatitis. ICD is a form of eczema and is induced by direct inflammatory pathways without prior sensitisation. Classical ACD is mediated by type 4 cell-mediated immunity. Sensitisation occurs within 5 to 16 days of skin contact with a potential allergen but at this first exposure there is no inflammation. Frequent exposure and high concentrations of potential allergens increase the risk of sensitisation. If eczema is recurrent/persistent, or occurs in an individual with no previous history of eczema, contact dermatitis should be considered. Dorsal aspects of the hands are most often affected by ICD, usually with involvement of the finger webs. Cumulative effects of water, soaps and detergents are the most common cause of ICD which affects the hands more often than any other site. Nickel, fragrances, rubber accelerators and biocides are the most common sensitisers in ACD. Patients with leg ulcers and stasis eczema are at especially high risk of developing allergies to ingredients of their topical treatments, dressings and bandages. If ACD is suspected the patient should be referred to secondary care for patch testing. Age should not be a deterrent to patch testing. Accurate diagnosis, avoidance of identified allergens and protection from irritants are the key to successful treatment.

  20. A newly-identified lineage of Schistosoma.

    PubMed

    Morgan, Jess A T; DeJong, Randall J; Kazibwe, Francis; Mkoji, Gerald M; Loker, Eric S

    2003-08-01

    Because of their role in causing schistosomiasis, flukes of the genus Schistosoma are the best known of all digeneans. The genus has traditionally been divided into four familiar species groups. Here we report on three poorly known species of Schistosoma, one of which, Schistosoma hippopotami, is known from the hippopotamus, one of which is provisionally identified as Schistosoma edwardiense, another hippo parasite, and a third that has not previously been described. All were collected from freshwater snails obtained from Lake Edward, western Uganda, the type locality for both known hippo schistosomes. The three different kinds of schistosome cercariae differ from one another in size, and all are readily differentiated by their long tail stems from the cercariae of human-infecting species. Furthermore, each was recovered from a different genus of snail host, Biomphalaria sudanica, Bulinus truncatus or Ceratophallus natalensis. Molecular analysis, based on 8350 bases of combined nuclear and mitochondrial DNA, groups these three long tail-stem cercariae into a well supported clade that does not associate with any of the recognised species groups. The placement of this clade, basal to all African species plus several Asian species, suggests that there has been an ancient association between Schistosoma and hippos. This new African Schistosoma clade advocates the need for further modification of the traditional species group-based classification. Two of the four species groups are paraphyletic. It also suggests that Schistosoma has been remarkably plastic with respect to adapting to snail hosts-three distantly related genera of planorbid snails have been exploited by worms within a single clade. Finally, it adds a new layer of complexity to deciphering the origins of Schistosoma, often considered to be African but recently challenged as being Asian. In the late Cenozoic the distribution of hippo species straddled both Africa and Asia and they may have provided a means

  1. Identifying Fishes through DNA Barcodes and Microarrays

    PubMed Central

    Kochzius, Marc; Seidel, Christian; Antoniou, Aglaia; Botla, Sandeep Kumar; Campo, Daniel; Cariani, Alessia; Vazquez, Eva Garcia; Hauschild, Janet; Hervet, Caroline; Hjörleifsdottir, Sigridur; Hreggvidsson, Gudmundur; Kappel, Kristina; Landi, Monica; Magoulas, Antonios; Marteinsson, Viggo; Nölte, Manfred; Planes, Serge; Tinti, Fausto; Turan, Cemal; Venugopal, Moleyur N.; Weber, Hannes; Blohm, Dietmar

    2010-01-01

    Background International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of “DNA barcoding” and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the “position of label” effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products. PMID

  2. Identifying Groundwater Droughts using standardized Water Levels

    NASA Astrophysics Data System (ADS)

    Haas, J. C.; Birk, S.

    2015-12-01

    Drought indices are frequently used to compare the occurrence and characteristics of droughts at different sites as well as to characterize different hydrometeorological aspects of drought. The existing indices have been mostly focused on precipitation, soil moisture, and surface waters though. To enable a comparison of groundwater drought with other hydrometeorological aspects of drought, the Standardized Groundwater level Index SGI was proposed by Bloomfield and Marchant (2013). So far, the SGI has been applied only to consolidated aquifers in the UK. The purpose of this work is to assess the applicability and performance of the SGI in unconsolidated, porous aquifers situated in valleys, which represent the main sources of drinking water in many regions. For this purpose, long-term time series of groundwater levels both in wet and dry regions of Austria are analyzed and compared with time series of precipitation, evapotranspiration and river stages. It is shown that large drought events, such as 2003 with only 79% of the long-term average precipitation, but also less severe events are reflected by negative SGI anomalies. To identify and classify time periods with a groundwater deficit, such benchmark years are used to propose a threshold value of the SGI defining the onset of a drought. Time periods where a clear drop in SGI does not correspond to a significant anomaly in precipitation are also visible in the data. More detailed investigations into small valley fill aquifers in the south-east of Austria reveal that the SGI may closely correlate with river stage fluctuations. Also, effects of the geographic setting (mountainous area vs. lowland) and the impacts of human activities (hydropower, drinking water extraction) are shown. Bloomfield, J. P., Marchant, B. P., Analysis of groundwater drought building on the standardised precipitation index approach, Hydrology and Earth System Sciences, 17, 4769-4787, 2013.

  3. Identifying Hendra virus diversity in pteropid bats.

    PubMed

    Smith, Ina; Broos, Alice; de Jong, Carol; Zeddeman, Anne; Smith, Craig; Smith, Greg; Moore, Fred; Barr, Jennifer; Crameri, Gary; Marsh, Glenn; Tachedjian, Mary; Yu, Meng; Kung, Yu Hsin; Wang, Lin-Fa; Field, Hume

    2011-01-01

    Hendra virus (HeV) causes a zoonotic disease with high mortality that is transmitted to humans from bats of the genus Pteropus (flying foxes) via an intermediary equine host. Factors promoting spillover from bats to horses are uncertain at this time, but plausibly encompass host and/or agent and/or environmental factors. There is a lack of HeV sequence information derived from the natural bat host, as previously sequences have only been obtained from horses or humans following spillover events. In order to obtain an insight into possible variants of HeV circulating in flying foxes, collection of urine was undertaken in multiple flying fox roosts in Queensland, Australia. HeV was found to be geographically widespread in flying foxes with a number of HeV variants circulating at the one time at multiple locations, while at times the same variant was found circulating at disparate locations. Sequence diversity within variants allowed differentiation on the basis of nucleotide changes, and hypervariable regions in the genome were identified that could be used to differentiate circulating variants. Further, during the study, HeV was isolated from the urine of flying foxes on four occasions from three different locations. The data indicates that spillover events do not correlate with particular HeV isolates, suggesting that host and/or environmental factors are the primary determinants of bat-horse spillover. Thus future spillover events are likely to occur, and there is an on-going need for effective risk management strategies for both human and animal health.

  4. Identifying Periods of Drowsy Driving Using EEG

    PubMed Central

    Brown, Timothy; Johnson, Robin; Milavetz, Gary

    2013-01-01

    Drowsy driving is a significant contributor to death and injury crashes on our nation’s highways. Predictive neurophysiologic/physiologic solutions to reduce these incidences have been proposed and developed. EEG based metrics were found to be promising in initial studies, but remain controversial in their efficacy, primarily due to failures to develop replication studies within the simulation settings used for development, and real-world validation. This analysis sought to address these short comings by assessing the utility of the B-Alert algorithms, in a replication study of driving and drowsiness. Data were collected on the National Advanced Driving Simulator from 72 volunteer drivers exposed to three types of roadways at three times of day representing different levels of drowsiness. EEG metrics, collected using the B-Alert X10 Wireless Headset were evaluated to determine their utility in future predictive studies. The replication of the B-Alert algorithms was a secondary focus for this analysis, resulting in highly variable start times within each time of day segment, leading to EEG data being confounded by the diurnal variations that occur in the basal EEG signal. Regardless of this limitation, the analysis revealed promising outcomes. The EEG based algorithms for sleep onset, drowsiness, as well as fatigue related power spectral bandwidths (i.e. lateral central, and parietal alpha) varied with time of day of the drives. Interestingly, EEG metrics of cognitive workload were also sensative to the terrain of the drives. The replicaiton of the B-Alert algorithms were a secondary focuse in the study design, Taken together, these data indicate great potential of carefully designed studies to utilize neurophysiologic metrics to identify time of day and task and road conditions that may be at greatest risk during fatigued/drowsy periods. PMID:24406950

  5. Identifying natural flow regimes using fish communities

    NASA Astrophysics Data System (ADS)

    Chang, Fi-John; Tsai, Wen-Ping; Wu, Tzu-Ching; Chen, Hung-kwai; Herricks, Edwin E.

    2011-10-01

    SummaryModern water resources management has adopted natural flow regimes as reasonable targets for river restoration and conservation. The characterization of a natural flow regime begins with the development of hydrologic statistics from flow records. However, little guidance exists for defining the period of record needed for regime determination. In Taiwan, the Taiwan Eco-hydrological Indicator System (TEIS), a group of hydrologic statistics selected for fisheries relevance, is being used to evaluate ecological flows. The TEIS consists of a group of hydrologic statistics selected to characterize the relationships between flow and the life history of indigenous species. Using the TEIS and biosurvey data for Taiwan, this paper identifies the length of hydrologic record sufficient for natural flow regime characterization. To define the ecological hydrology of fish communities, this study connected hydrologic statistics to fish communities by using methods to define antecedent conditions that influence existing community composition. A moving average method was applied to TEIS statistics to reflect the effects of antecedent flow condition and a point-biserial correlation method was used to relate fisheries collections with TEIS statistics. The resulting fish species-TEIS (FISH-TEIS) hydrologic statistics matrix takes full advantage of historical flows and fisheries data. The analysis indicates that, in the watersheds analyzed, averaging TEIS statistics for the present year and 3 years prior to the sampling date, termed MA(4), is sufficient to develop a natural flow regime. This result suggests that flow regimes based on hydrologic statistics for the period of record can be replaced by regimes developed for sampled fish communities.

  6. Identifying periods of drowsy driving using EEG.

    PubMed

    Brown, Timothy; Johnson, Robin; Milavetz, Gary

    2013-01-01

    Drowsy driving is a significant contributor to death and injury crashes on our nation's highways. Predictive neurophysiologic/physiologic solutions to reduce these incidences have been proposed and developed. EEG based metrics were found to be promising in initial studies, but remain controversial in their efficacy, primarily due to failures to develop replication studies within the simulation settings used for development, and real-world validation. This analysis sought to address these short comings by assessing the utility of the B-Alert algorithms, in a replication study of driving and drowsiness. Data were collected on the National Advanced Driving Simulator from 72 volunteer drivers exposed to three types of roadways at three times of day representing different levels of drowsiness. EEG metrics, collected using the B-Alert X10 Wireless Headset were evaluated to determine their utility in future predictive studies. The replication of the B-Alert algorithms was a secondary focus for this analysis, resulting in highly variable start times within each time of day segment, leading to EEG data being confounded by the diurnal variations that occur in the basal EEG signal. Regardless of this limitation, the analysis revealed promising outcomes. The EEG based algorithms for sleep onset, drowsiness, as well as fatigue related power spectral bandwidths (i.e. lateral central, and parietal alpha) varied with time of day of the drives. Interestingly, EEG metrics of cognitive workload were also sensative to the terrain of the drives. The replicaiton of the B-Alert algorithms were a secondary focuse in the study design, Taken together, these data indicate great potential of carefully designed studies to utilize neurophysiologic metrics to identify time of day and task and road conditions that may be at greatest risk during fatigued/drowsy periods.

  7. Identifying Hendra virus diversity in pteropid bats.

    PubMed

    Smith, Ina; Broos, Alice; de Jong, Carol; Zeddeman, Anne; Smith, Craig; Smith, Greg; Moore, Fred; Barr, Jennifer; Crameri, Gary; Marsh, Glenn; Tachedjian, Mary; Yu, Meng; Kung, Yu Hsin; Wang, Lin-Fa; Field, Hume

    2011-01-01

    Hendra virus (HeV) causes a zoonotic disease with high mortality that is transmitted to humans from bats of the genus Pteropus (flying foxes) via an intermediary equine host. Factors promoting spillover from bats to horses are uncertain at this time, but plausibly encompass host and/or agent and/or environmental factors. There is a lack of HeV sequence information derived from the natural bat host, as previously sequences have only been obtained from horses or humans following spillover events. In order to obtain an insight into possible variants of HeV circulating in flying foxes, collection of urine was undertaken in multiple flying fox roosts in Queensland, Australia. HeV was found to be geographically widespread in flying foxes with a number of HeV variants circulating at the one time at multiple locations, while at times the same variant was found circulating at disparate locations. Sequence diversity within variants allowed differentiation on the basis of nucleotide changes, and hypervariable regions in the genome were identified that could be used to differentiate circulating variants. Further, during the study, HeV was isolated from the urine of flying foxes on four occasions from three different locations. The data indicates that spillover events do not correlate with particular HeV isolates, suggesting that host and/or environmental factors are the primary determinants of bat-horse spillover. Thus future spillover events are likely to occur, and there is an on-going need for effective risk management strategies for both human and animal health. PMID:21980413

  8. Understanding and identifying amino acid repeats.

    PubMed

    Luo, Hong; Nijveen, Harm

    2014-07-01

    Amino acid repeats (AARs) are abundant in protein sequences. They have particular roles in protein function and evolution. Simple repeat patterns generated by DNA slippage tend to introduce length variations and point mutations in repeat regions. Loss of normal and gain of abnormal function owing to their variable length are potential risks leading to diseases. Repeats with complex patterns mostly refer to the functional domain repeats, such as the well-known leucine-rich repeat and WD repeat, which are frequently involved in protein–protein interaction. They are mainly derived from internal gene duplication events and stabilized by ‘gate-keeper’ residues, which play crucial roles in preventing inter-domain aggregation. AARs are widely distributed in different proteomes across a variety of taxonomic ranges, and especially abundant in eukaryotic proteins. However, their specific evolutionary and functional scenarios are still poorly understood. Identifying AARs in protein sequences is the first step for the further investigation of their biological function and evolutionary mechanism. In principle, this is an NP-hard problem, as most of the repeat fragments are shaped by a series of sophisticated evolutionary events and become latent periodical patterns. It is not possible to define a uniform criterion for detecting and verifying various repeat patterns. Instead, different algorithms based on different strategies have been developed to cope with different repeat patterns. In this review, we attempt to describe the amino acid repeat-detection algorithms currently available and compare their strategies based on an in-depth analysis of the biological significance of protein repeats. PMID:23418055

  9. Quantitative proteomics for identifying biomarkers for Rabies

    PubMed Central

    2013-01-01

    Introduction Rabies is a fatal acute viral disease of the central nervous system, which is a serious public health problem in Asian and African countries. Based on the clinical presentation, rabies can be classified into encephalitic (furious) or paralytic (numb) rabies. Early diagnosis of this disease is particularly important as rabies is invariably fatal if adequate post exposure prophylaxis is not administered immediately following the bite. Methods In this study, we carried out a quantitative proteomic analysis of the human brain tissue from cases of encephalitic and paralytic rabies along with normal human brain tissues using an 8-plex isobaric tags for relative and absolute quantification (iTRAQ) strategy. Results and conclusion We identified 402 proteins, of which a number of proteins were differentially expressed between encephalitic and paralytic rabies, including several novel proteins. The differentially expressed molecules included karyopherin alpha 4 (KPNA4), which was overexpressed only in paralytic rabies, calcium calmodulin dependent kinase 2 alpha (CAMK2A), which was upregulated in paralytic rabies group and glutamate ammonia ligase (GLUL), which was overexpressed in paralytic as well as encephalitic rabies. We validated two of the upregulated molecules, GLUL and CAMK2A, by dot blot assays and further validated CAMK2A by immunohistochemistry. These molecules need to be further investigated in body fluids such as cerebrospinal fluid in a larger cohort of rabies cases to determine their potential use as antemortem diagnostic biomarkers in rabies. This is the first study to systematically profile clinical subtypes of human rabies using an iTRAQ quantitative proteomics approach. PMID:23521751

  10. Defining and identifying Sleeping Beauties in science

    PubMed Central

    Ke, Qing; Ferrara, Emilio; Radicchi, Filippo; Flammini, Alessandro

    2015-01-01

    A Sleeping Beauty (SB) in science refers to a paper whose importance is not recognized for several years after publication. Its citation history exhibits a long hibernation period followed by a sudden spike of popularity. Previous studies suggest a relative scarcity of SBs. The reliability of this conclusion is, however, heavily dependent on identification methods based on arbitrary threshold parameters for sleeping time and number of citations, applied to small or monodisciplinary bibliographic datasets. Here we present a systematic, large-scale, and multidisciplinary analysis of the SB phenomenon in science. We introduce a parameter-free measure that quantifies the extent to which a specific paper can be considered an SB. We apply our method to 22 million scientific papers published in all disciplines of natural and social sciences over a time span longer than a century. Our results reveal that the SB phenomenon is not exceptional. There is a continuous spectrum of delayed recognition where both the hibernation period and the awakening intensity are taken into account. Although many cases of SBs can be identified by looking at monodisciplinary bibliographic data, the SB phenomenon becomes much more apparent with the analysis of multidisciplinary datasets, where we can observe many examples of papers achieving delayed yet exceptional importance in disciplines different from those where they were originally published. Our analysis emphasizes a complex feature of citation dynamics that so far has received little attention, and also provides empirical evidence against the use of short-term citation metrics in the quantification of scientific impact. PMID:26015563

  11. Identifying human influences on atmospheric temperature.

    PubMed

    Santer, Benjamin D; Painter, Jeffrey F; Mears, Carl A; Doutriaux, Charles; Caldwell, Peter; Arblaster, Julie M; Cameron-Smith, Philip J; Gillett, Nathan P; Gleckler, Peter J; Lanzante, John; Perlwitz, Judith; Solomon, Susan; Stott, Peter A; Taylor, Karl E; Terray, Laurent; Thorne, Peter W; Wehner, Michael F; Wentz, Frank J; Wigley, Tom M L; Wilcox, Laura J; Zou, Cheng-Zhi

    2013-01-01

    We perform a multimodel detection and attribution study with climate model simulation output and satellite-based measurements of tropospheric and stratospheric temperature change. We use simulation output from 20 climate models participating in phase 5 of the Coupled Model Intercomparison Project. This multimodel archive provides estimates of the signal pattern in response to combined anthropogenic and natural external forcing (the fingerprint) and the noise of internally generated variability. Using these estimates, we calculate signal-to-noise (S/N) ratios to quantify the strength of the fingerprint in the observations relative to fingerprint strength in natural climate noise. For changes in lower stratospheric temperature between 1979 and 2011, S/N ratios vary from 26 to 36, depending on the choice of observational dataset. In the lower troposphere, the fingerprint strength in observations is smaller, but S/N ratios are still significant at the 1% level or better, and range from three to eight. We find no evidence that these ratios are spuriously inflated by model variability errors. After removing all global mean signals, model fingerprints remain identifiable in 70% of the tests involving tropospheric temperature changes. Despite such agreement in the large-scale features of model and observed geographical patterns of atmospheric temperature change, most models do not replicate the size of the observed changes. On average, the models analyzed underestimate the observed cooling of the lower stratosphere and overestimate the warming of the troposphere. Although the precise causes of such differences are unclear, model biases in lower stratospheric temperature trends are likely to be reduced by more realistic treatment of stratospheric ozone depletion and volcanic aerosol forcing.

  12. Identifying human influences on atmospheric temperature

    PubMed Central

    Santer, Benjamin D.; Painter, Jeffrey F.; Mears, Carl A.; Doutriaux, Charles; Caldwell, Peter; Arblaster, Julie M.; Cameron-Smith, Philip J.; Gillett, Nathan P.; Gleckler, Peter J.; Lanzante, John; Perlwitz, Judith; Solomon, Susan; Stott, Peter A.; Taylor, Karl E.; Terray, Laurent; Thorne, Peter W.; Wehner, Michael F.; Wentz, Frank J.; Wigley, Tom M. L.; Wilcox, Laura J.; Zou, Cheng-Zhi

    2013-01-01

    We perform a multimodel detection and attribution study with climate model simulation output and satellite-based measurements of tropospheric and stratospheric temperature change. We use simulation output from 20 climate models participating in phase 5 of the Coupled Model Intercomparison Project. This multimodel archive provides estimates of the signal pattern in response to combined anthropogenic and natural external forcing (the fingerprint) and the noise of internally generated variability. Using these estimates, we calculate signal-to-noise (S/N) ratios to quantify the strength of the fingerprint in the observations relative to fingerprint strength in natural climate noise. For changes in lower stratospheric temperature between 1979 and 2011, S/N ratios vary from 26 to 36, depending on the choice of observational dataset. In the lower troposphere, the fingerprint strength in observations is smaller, but S/N ratios are still significant at the 1% level or better, and range from three to eight. We find no evidence that these ratios are spuriously inflated by model variability errors. After removing all global mean signals, model fingerprints remain identifiable in 70% of the tests involving tropospheric temperature changes. Despite such agreement in the large-scale features of model and observed geographical patterns of atmospheric temperature change, most models do not replicate the size of the observed changes. On average, the models analyzed underestimate the observed cooling of the lower stratosphere and overestimate the warming of the troposphere. Although the precise causes of such differences are unclear, model biases in lower stratospheric temperature trends are likely to be reduced by more realistic treatment of stratospheric ozone depletion and volcanic aerosol forcing. PMID:23197824

  13. Identifying hidden sexual bridging communities in Chicago.

    PubMed

    Youm, Yoosik; Mackesy-Amiti, Mary Ellen; Williams, Chyvette T; Ouellet, Lawrence J

    2009-07-01

    Bridge populations can play a central role in the spread of human immunodeficiency virus (HIV) by providing transmission links between higher and lower prevalence populations. While social network methods are well suited to the study of bridge populations, analyses tend to focus on dyads (i.e., risk between drug and/or sex partners) and ignore bridges between distinct subpopulations. This study takes initial steps toward moving the analysis of sexual network linkages beyond individual and risk group levels to a community level in which Chicago's 77 community areas are examined as subpopulations for the purpose of identifying potential bridging communities. Of particular interest are "hidden" bridging communities; that is, areas with above-average levels of sexual ties with other areas but whose below-average AIDS prevalence may hide their potential importance for HIV prevention. Data for this analysis came from the first wave of recruiting at the Chicago Sexual Acquisition and Transmission of HIV Cooperative Agreement Program site. Between August 2005 through October 2006, respondent-driven sampling was used to recruit users of heroin, cocaine, or methamphetamine, men who have sex with men regardless of drug use, the sex partners of these two groups, and sex partners of the sex partners. In this cross-sectional study of the sexual transmission of HIV, participants completed a network-focused computer-assisted self-administered interview, which included questions about the geographic locations of sexual contacts with up to six recent partners. Bridging scores for each area were determined using a matrix representing Chicago's 77 community areas and were assessed using two measures: non-redundant ties and flow betweenness. Bridging measures and acquired immunodeficiency syndrome (AIDS) case prevalence rates were plotted for each community area on charts representing four conditions: below-average bridging and AIDS prevalence, below-average bridging and above

  14. Identifying Canadian Freshwater Fishes through DNA Barcodes

    PubMed Central

    Hubert, Nicolas; Hanner, Robert; Holm, Erling; Mandrak, Nicholas E.; Taylor, Eric; Burridge, Mary; Watkinson, Douglas; Dumont, Pierre; Curry, Allen; Bentzen, Paul; Zhang, Junbin; April, Julien; Bernatchez, Louis

    2008-01-01

    efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics. PMID:22423312

  15. Identifying Thoracic Malignancies Through Pleural Fluid Biomarkers

    PubMed Central

    Porcel, José M.; Esquerda, Aureli; Martínez-Alonso, Montserrat; Bielsa, Silvia; Salud, Antonieta

    2016-01-01

    Abstract The diagnosis of malignant pleural effusions may be challenging when cytological examination of aspirated pleural fluid is equivocal or noncontributory. The purpose of this study was to identify protein candidate biomarkers differentially expressed in the pleural fluid of patients with mesothelioma, lung adenocarcinoma, lymphoma, and tuberculosis (TB). A multiplex protein biochip comprising 120 biomarkers was used to determine the pleural fluid protein profile of 29 mesotheliomas, 29 lung adenocarcinomas, 12 lymphomas, and 35 tuberculosis. The relative abundance of these predetermined biomarkers among groups served to establish the differential diagnosis of: malignant versus benign (TB) effusions, lung adenocarcinoma versus mesothelioma, and lymphoma versus TB. The selected putative markers were validated using widely available commercial techniques in an independent sample of 102 patients. Significant differences were found in the protein expressions of metalloproteinase-9 (MMP-9), cathepsin-B, C-reactive protein, and chondroitin sulfate between malignant and TB effusions. When integrated into a scoring model, these proteins yielded 85% sensitivity, 100% specificity, and an area under the curve (AUC) of 0.98 for labeling malignancy in the verification sample. For lung adenocarcinoma–mesothelioma discrimination, combining CA19-9, CA15-3, and kallikrein-12 had maximal discriminatory capacity (65% sensitivity, 100% specificity, AUC 0.94); figures which also refer to the validation set. Last, cathepsin-B in isolation was only moderately useful (sensitivity 89%, specificity 62%, AUC 0.75) in separating lymphomatous and TB effusions. However, this last differentiation improved significantly when cathepsin-B was used with respect to the patient's age (sensitivity 72%, specificity 100%, AUC 0.94). In conclusion, panels of 4 (i.e., MMP-9, cathepsin-B, C-reactive protein, chondroitin sulfate), or 3 (i.e., CA19-9, CA15-3, kallikrein-12) different protein

  16. Identifying and Tracing Persistent Identifiers of Research Resources : Automation, Metrics and Analytics

    NASA Astrophysics Data System (ADS)

    Maull, K. E.; Hart, D.; Mayernik, M. S.

    2015-12-01

    Formal and informal citations and acknowledgements for research infrastructures, such as data collections, software packages, and facilities, are an increasingly important function of attribution in scholarly literature. While such citations provide the appropriate links, even if informally, to their origins, they are often done so inconsistently, making such citations hard to analyze. While significant progress has been made in the past few years in the development of recommendations, policies, and procedures for creating and promoting citable identifiers, progress has been mixed in tracking how data sets and other digital infrastructures have actually been identified and cited in the literature. Understanding the full extent and value of research infrastructures through the lens of scholarly literature requires significant resources, and thus, we argue must rely on automated approaches that mine and track persistent identifiers to scientific resources. Such automated approaches, however, face a number of unique challenges, from the inconsistent and informal referencing practices of authors, to unavailable, embargoed or hard-to-obtain full-text resources for text analytics, to inconsistent and capricious impact metrics. This presentation will discuss work to develop and evaluate tools for automating the tracing of research resource identification and referencing in the research literature via persistent citable identifiers. Despite the impediments, automated processes are of considerable importance in enabling these traceability efforts to scale, as the numbers of identifiers being created for unique scientific resources continues to grow rapidly. Such efforts, if successful, should improve the ability to answer meaningful questions about research resources as they continue to grow as a target of advanced analyses in research metrics.

  17. 7 CFR 56.41 - Check grading officially identified product.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... (CONTINUED) VOLUNTARY GRADING OF SHELL EGGS Grading of Shell Eggs Prerequisites to Packaging Shell Eggs Identified with Grademarks § 56.41 Check grading officially identified product. Officially identified...

  18. CFHT and VLT Identify Extremely Remote Galaxy

    NASA Astrophysics Data System (ADS)

    2003-05-01

    , the chances for detecting those distant objects are optimal. The astronomers talk about "maximizing the contrast" of objects showing emission lines at this wavelength. The CFHT Search Programme ESO PR Photo 13b/03 ESO PR Photo 13b/03 [Preview - JPEG: 494 x 400 pix - 83k [Normal - JPEG: 987 x 800 pix - 920k] Caption : PR Photo 13b/03 displays the image of a particular object (at the center), as seen at various wavelengths (colours) on CCD-frames obtained through different optical filters with the CFH12K camera at the CFHT. The object is only visible in the NB920 frame in which emission at the near-infrared wavelength 920 nm is registered (upper left). It is not seen in any of the others ( B lue [450 nm], V isual [550 nm], R ed [650 nm], I [800 nm]), nor in a combination of these (the "sum" of BVRI , the so-called "detection" image, here labeled as "Det"; it is used to detect closer objects from their optical colours for spectroscopic follow-up observations). The indicated object was later shown to be an extremely distant galaxy and has been designated z6VDF J022803-041618 . Each of the six photos covers 20 x 20 arcsec 2 ; North is up, East is right. Based on the above considerations, an international team of astronomers [2] installed a narrow-band optical filter centered at the near-infrared wavelength 920 nm on the CFH12K instrument at the Canada-France-Hawaii telescope on Mauna Kea (Hawaii, USA) to search for extremely distant galaxies. The CFH12K is a wide-field camera used at the prime focus of the CFHT, providing a field-of-view of approx. 30 x 40 arcmin 2 , somewhat larger than the full moon [5]. By comparing images of the same sky field taken through different filters, the astronomers were able to identify objects which appear comparatively "bright" in the NB920 image and "faint" (or are even not visible) in the corresponding images obtained through the other filters. A striking example is shown in PR Photo 13b/03 - the object at the center is well visible in

  19. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  20. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  1. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  2. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  3. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  4. 3 Drugs Identified to Potentially Fight Zika Virus

    MedlinePlus

    ... 160680.html 3 Drugs Identified to Potentially Fight Zika Virus But only one is already approved in ... developing fetuses protection against the damaging effects of Zika virus, a new multicenter study reports. Researchers identified ...

  5. Identifying Novice Student Programming Misconceptions and Errors from Summative Assessments

    ERIC Educational Resources Information Center

    Veerasamy, Ashok Kumar; D'Souza, Daryl; Laakso, Mikko-Jussi

    2016-01-01

    This article presents a study aimed at examining the novice student answers in an introductory programming final e-exam to identify misconceptions and types of errors. Our study used the Delphi concept inventory to identify student misconceptions and skill, rule, and knowledge-based errors approach to identify the types of errors made by novices…

  6. 28 CFR 22.21 - Use of identifiable data.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... STATISTICAL INFORMATION § 22.21 Use of identifiable data. Research or statistical information identifiable to a private person may be used only for research or statistical purposes. ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Use of identifiable data. 22.21...

  7. 75 FR 14539 - Furnishing Identifying Number of Tax Return Preparer

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-26

    ... Internal Revenue Service 26 CFR Part 1 RIN 1545-BI28 Furnishing Identifying Number of Tax Return Preparer... guidance to tax return preparers on furnishing an identifying number on tax returns and claims for refund of tax that they prepare. These proposed regulations provide guidance on the identifying number of...

  8. 26 CFR 41.6109-1 - Identifying numbers.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 26 Internal Revenue 16 2010-04-01 2010-04-01 true Identifying numbers. 41.6109-1 Section 41.6109-1... Application to Tax On Use of Certain Highway Motor Vehicles § 41.6109-1 Identifying numbers. Every person required under § 41.6011(a)-1 to make a return must provide the identifying number required by...

  9. 26 CFR 41.6109-1 - Identifying numbers.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 26 Internal Revenue 16 2011-04-01 2011-04-01 false Identifying numbers. 41.6109-1 Section 41.6109... Application to Tax On Use of Certain Highway Motor Vehicles § 41.6109-1 Identifying numbers. Every person required under § 41.6011(a)-1 to make a return must provide the identifying number required by...

  10. 12 CFR 210.27 - Reliance on identifying number.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 2 2011-01-01 2011-01-01 false Reliance on identifying number. 210.27 Section... J) Funds Transfers Through Fedwire § 210.27 Reliance on identifying number. (a) Reliance by a Federal Reserve Bank on number to identify an intermediary bank or beneficiary's bank. A Federal...

  11. 25 CFR 23.82 - Assistance in identifying language interpreters.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false Assistance in identifying language interpreters. 23.82... WELFARE ACT Assistance to State Courts § 23.82 Assistance in identifying language interpreters. Upon the... shall assist in identifying language interpreters. Such requests for assistance should be sent to...

  12. 25 CFR 23.82 - Assistance in identifying language interpreters.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Assistance in identifying language interpreters. 23.82... WELFARE ACT Assistance to State Courts § 23.82 Assistance in identifying language interpreters. Upon the... shall assist in identifying language interpreters. Such requests for assistance should be sent to...

  13. Which are the best identifiers for record linkage?

    PubMed

    Quantin, Catherine; Binquet, Christine; Bourquard, Karima; Pattisina, Ronny; Gouyon-Cornet, Béatrice; Ferdynus, Cyril; Gouyon, Jean-Bernard; François-André, Allaert

    2004-01-01

    As a linkage using less informative identifiers could lead to linkage errors, it is essential to quantify the information associated to each identifier. The aim of this study was to estimate the discriminating power of different identifiers susceptible to be used in a record linkage process. This work showed the interest of three identifiers when linking data concerning a same patient using an automatic procedure based on the method proposed by Jaro; the date of birth, the first and the last names seemed to be the more appropriate identifiers. Including a poorly discriminating identifier like gender did not improve the results. Moreover, adding a second christian name, often missing, increased linkage errors. On the contrary, it seemed that using a phonetic treatment adapted to the French language could improve the results of linkage in comparison to the Soundex. However, whatever, the method used it seems necessary to improve the quality of identifier collection as it could greatly influence linkage results.

  14. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  15. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  16. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  17. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  18. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  19. Identifying and integrating helpful and harmful religious beliefs into psychotherapy.

    PubMed

    Rosenfield, George W

    2010-12-01

    The 2 main roles of the psychotherapist involve identifying and understanding the client's problems/strengths and treating problems. Suggestions are offered to guide addressing or avoiding religious beliefs in both roles. Types of religious beliefs that contribute to distress, particularly for youth, are identified and treatment options are offered.

  20. 37 CFR 211.5 - Deposit of identifying material.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... material. 211.5 Section 211.5 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY OF CONGRESS COPYRIGHT OFFICE AND PROCEDURES MASK WORK PROTECTION § 211.5 Deposit of identifying material. (a) General. This section prescribes rules pertaining to the deposit of identifying material for registration of...

  1. 37 CFR 211.5 - Deposit of identifying material.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... material. 211.5 Section 211.5 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY OF CONGRESS COPYRIGHT OFFICE AND PROCEDURES MASK WORK PROTECTION § 211.5 Deposit of identifying material. (a) General. This section prescribes rules pertaining to the deposit of identifying material for registration of...

  2. 42 CFR 433.138 - Identifying liable third parties.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 4 2011-10-01 2011-10-01 false Identifying liable third parties. 433.138 Section... SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION Third Party Liability § 433.138 Identifying liable third parties. (a) Basic provisions. The agency must take reasonable...

  3. National variety trials identify clones with high potential

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quality potato varieties are the backbone of a strong potato industry. Variety trials have been used to identify promising new varieties for well over a century. Trials are repeated and information collected over many years in order to confidently identify lines that may be well suited for productio...

  4. 45 CFR 162.506 - Standard unique health plan identifier.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 1 2013-10-01 2013-10-01 false Standard unique health plan identifier. 162.506 Section 162.506 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES ADMINISTRATIVE DATA STANDARDS AND RELATED REQUIREMENTS ADMINISTRATIVE REQUIREMENTS Standard Unique Health Identifier for Health Plans §...

  5. Gasoline identifier based on SH0 plate acoustic waves.

    PubMed

    Kuznetsova, Iren E; Zaitsev, Boris D; Seleznev, Eugenii P; Verona, Enrico

    2016-08-01

    The present paper is devoted to the development of gasoline identifier based on zero order shear-horizontal (SH0) acoustic wave propagating in piezoelectric plate. It has been found that the permittivity of gasoline is increased when its octane number rises. The development of such identifier is experimentally demonstrated to be possible. PMID:27125559

  6. 48 CFR 2009.570-7 - Conflicts identified after award.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 6 2011-10-01 2011-10-01 false Conflicts identified after... COMMISSION COMPETITION AND ACQUISITION PLANNING CONTRACTOR QUALIFICATIONS Organizational Conflicts of Interest 2009.570-7 Conflicts identified after award. If potential organizational conflicts of interest...

  7. 48 CFR 2009.570-7 - Conflicts identified after award.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true Conflicts identified after... COMMISSION COMPETITION AND ACQUISITION PLANNING CONTRACTOR QUALIFICATIONS Organizational Conflicts of Interest 2009.570-7 Conflicts identified after award. If potential organizational conflicts of interest...

  8. Identifiability Results for Several Classes of Linear Compartment Models.

    PubMed

    Meshkat, Nicolette; Sullivant, Seth; Eisenberg, Marisa

    2015-08-01

    Identifiability concerns finding which unknown parameters of a model can be estimated, uniquely or otherwise, from given input-output data. If some subset of the parameters of a model cannot be determined given input-output data, then we say the model is unidentifiable. In this work, we study linear compartment models, which are a class of biological models commonly used in pharmacokinetics, physiology, and ecology. In past work, we used commutative algebra and graph theory to identify a class of linear compartment models that we call identifiable cycle models, which are unidentifiable but have the simplest possible identifiable functions (so-called monomial cycles). Here we show how to modify identifiable cycle models by adding inputs, adding outputs, or removing leaks, in such a way that we obtain an identifiable model. We also prove a constructive result on how to combine identifiable models, each corresponding to strongly connected graphs, into a larger identifiable model. We apply these theoretical results to several real-world biological models from physiology, cell biology, and ecology. PMID:26337290

  9. Identifying Evidence of Reflective Ability in Preservice Teacher Electronic Portfolios

    ERIC Educational Resources Information Center

    Sulzen, James

    2011-01-01

    Results of this study identified "evidence markers" that characterize reflection in preservice teacher electronic portfolios. Examples of such markers include openness to self-learning, willingness to self-critique, analytical detail of reflections, and taking responsibility for pupil learning challenges. To identify the markers, school of…

  10. Identifying causal effects of climate extremes on societies

    NASA Astrophysics Data System (ADS)

    Hsiang, S. M.

    2015-12-01

    We discuss recent advances in the application of quasi-experimental techniques to identify causal effects of climate extremes on human societies using historical data. Results identifying effects on economic productivity, violence, migration, and global trade will be discussed. We will discuss how these statistical findings can be applied to calibrate modeling exercises and areas for future research.

  11. Method of identifying hairpin DNA probes by partial fold analysis

    DOEpatents

    Miller, Benjamin L.; Strohsahl, Christopher M.

    2009-10-06

    Method of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

  12. Method of identifying hairpin DNA probes by partial fold analysis

    DOEpatents

    Miller, Benjamin L.; Strohsahl, Christopher M.

    2008-10-28

    Methods of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

  13. Identifying a K-10 Developmental Framework for Teaching Philosophy

    ERIC Educational Resources Information Center

    Poulton, Janette

    2014-01-01

    The intention of the study was to identify predictable opportunities for teachers to scaffold middle year students' philosophical learning. Such opportunities were identified in terms of students' readiness to learn certain behaviours in the context of a "community of inquiry". Thus it was hoped that the project would provide a…

  14. 25 CFR 23.81 - Assistance in identifying witnesses.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Assistance in identifying witnesses. 23.81 Section 23.81 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR HUMAN SERVICES INDIAN CHILD WELFARE ACT Assistance to State Courts § 23.81 Assistance in identifying witnesses. Upon the request of a party in...

  15. 33 CFR 23.12 - Coast Guard identifying insignia.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Coast Guard identifying insignia. 23.12 Section 23.12 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY GENERAL DISTINCTIVE MARKINGS FOR COAST GUARD VESSELS AND AIRCRAFT § 23.12 Coast Guard identifying...

  16. 33 CFR 23.12 - Coast Guard identifying insignia.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Coast Guard identifying insignia. 23.12 Section 23.12 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY GENERAL DISTINCTIVE MARKINGS FOR COAST GUARD VESSELS AND AIRCRAFT § 23.12 Coast Guard identifying...

  17. 33 CFR 23.12 - Coast Guard identifying insignia.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Coast Guard identifying insignia. 23.12 Section 23.12 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY GENERAL DISTINCTIVE MARKINGS FOR COAST GUARD VESSELS AND AIRCRAFT § 23.12 Coast Guard identifying...

  18. 33 CFR 23.12 - Coast Guard identifying insignia.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Coast Guard identifying insignia. 23.12 Section 23.12 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY GENERAL DISTINCTIVE MARKINGS FOR COAST GUARD VESSELS AND AIRCRAFT § 23.12 Coast Guard identifying...

  19. 33 CFR 23.12 - Coast Guard identifying insignia.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Coast Guard identifying insignia. 23.12 Section 23.12 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY GENERAL DISTINCTIVE MARKINGS FOR COAST GUARD VESSELS AND AIRCRAFT § 23.12 Coast Guard identifying...

  20. 25 CFR 304.5 - Dies to identify tribe.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 2 2013-04-01 2013-04-01 false Dies to identify tribe. 304.5 Section 304.5 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER, USE OF GOVERNMENT MARK § 304.5 Dies to identify tribe. Dies are marked with name of tribe. A Navajo stamp will...

  1. 25 CFR 304.5 - Dies to identify tribe.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 2 2011-04-01 2011-04-01 false Dies to identify tribe. 304.5 Section 304.5 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER, USE OF GOVERNMENT MARK § 304.5 Dies to identify tribe. Dies are marked with name of tribe. A Navajo stamp will...

  2. 25 CFR 304.5 - Dies to identify tribe.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 2 2010-04-01 2010-04-01 false Dies to identify tribe. 304.5 Section 304.5 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER, USE OF GOVERNMENT MARK § 304.5 Dies to identify tribe. Dies are marked with name of tribe. A Navajo stamp will...

  3. 25 CFR 304.5 - Dies to identify tribe.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 25 Indians 2 2014-04-01 2014-04-01 false Dies to identify tribe. 304.5 Section 304.5 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER, USE OF GOVERNMENT MARK § 304.5 Dies to identify tribe. Dies are marked with name of tribe. A Navajo stamp will...

  4. 25 CFR 304.5 - Dies to identify tribe.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 25 Indians 2 2012-04-01 2012-04-01 false Dies to identify tribe. 304.5 Section 304.5 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER, USE OF GOVERNMENT MARK § 304.5 Dies to identify tribe. Dies are marked with name of tribe. A Navajo stamp will...

  5. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... standards in 30 CFR chapter I. (3) Occupational Safety and Health Administration (OSHA), 29 CFR part 1910... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals....

  6. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... standards in 30 CFR chapter I. (3) Occupational Safety and Health Administration (OSHA), 29 CFR part 1910... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals....

  7. 42 CFR 401.118 - Deletion of identifying details.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 2 2010-10-01 2010-10-01 false Deletion of identifying details. 401.118 Section 401.118 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Deletion of identifying details. When CMS publishes or otherwise makes available an opinion or...

  8. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... standards in 30 CFR chapter I. (3) Occupational Safety and Health Administration (OSHA), 29 CFR part 1910... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals....

  9. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... standards in 30 CFR chapter I. (3) Occupational Safety and Health Administration (OSHA), 29 CFR part 1910... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals....

  10. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... standards in 30 CFR chapter I. (3) Occupational Safety and Health Administration (OSHA), 29 CFR part 1910... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals....

  11. Gasoline identifier based on SH0 plate acoustic waves.

    PubMed

    Kuznetsova, Iren E; Zaitsev, Boris D; Seleznev, Eugenii P; Verona, Enrico

    2016-08-01

    The present paper is devoted to the development of gasoline identifier based on zero order shear-horizontal (SH0) acoustic wave propagating in piezoelectric plate. It has been found that the permittivity of gasoline is increased when its octane number rises. The development of such identifier is experimentally demonstrated to be possible.

  12. Identifying, Measuring and Monitoring Value during Project Development

    ERIC Educational Resources Information Center

    Kliniotou, Maria

    2004-01-01

    This paper describes the findings of the research done by Loughborough University in conjunction with ten construction industry collaborators in an attempt to identify what construction professionals mean by value. The aim of the research is to establish a common approach to identify value in projects and to monitor its development throughout the…

  13. 36 CFR 1223.16 - How are vital records identified?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... ADMINISTRATION RECORDS MANAGEMENT MANAGING VITAL RECORDS § 1223.16 How are vital records identified? Agencies identify vital records in the context of the emergency management function. Vital records are those that are needed to perform the most critical functions of the agency and those needed to protect legal...

  14. 49 CFR 7.6 - Deletion of identifying detail.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false Deletion of identifying detail. 7.6 Section 7.6 Transportation Office of the Secretary of Transportation PUBLIC AVAILABILITY OF INFORMATION Information Required To Be Made Public by DOT § 7.6 Deletion of identifying detail. Whenever it is determined to...

  15. 75 FR 60309 - Furnishing Identifying Number of Tax Return Preparer

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-30

    ... Treasury Department and the IRS published in the Federal Register (75 FR 14539) a notice of proposed... Internal Revenue Service 26 CFR Parts 1 and 602 RIN 1545-BI28 Furnishing Identifying Number of Tax Return... how the IRS will define the identifying number of tax return preparers and set forth requirements...

  16. 44 CFR 5.27 - Deletion of identifying details.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Deletion of identifying details. 5.27 Section 5.27 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY..., FEMA may delete identifying details when making available or publishing an opinion, statement of...

  17. Identifying costs for capitation in psychiatric case management.

    PubMed

    Baker, J J; Chiverton, P; Hines, V

    1998-01-01

    This article presents an example of how one hospital identified costs for capitation in psychiatric case management. An 18-month postacute case management pilot project collected data on a nurse-specific and patient-specific basis. Costs were identified using activity-based costing methodology. PMID:9502055

  18. The Language Adviser's Role: Identifying and Responding to Needs

    ERIC Educational Resources Information Center

    Reinders, Hayo; Hacker, Penny; Lewis, Marilyn

    2004-01-01

    Tertiary institutions increasingly offer language advisory sessions for second language students and staff. Advisers help students to identify language and learning needs, they recommend resources and strategies and they provide feedback and encouragement. Especially in the first few sessions, identifying and prioritising needs are arguably among…

  19. 26 CFR 31.6109-1 - Supplying of identifying numbers.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 15, 1974. See 26 CFR § 31.6109-1 (revised as of April 1, 1973) for provisions with respect to... 26 Internal Revenue 15 2010-04-01 2010-04-01 false Supplying of identifying numbers. 31.6109-1... Subtitle F, Internal Revenue Code of 1954) § 31.6109-1 Supplying of identifying numbers. (a) In...

  20. 26 CFR 1.6109-1 - Identifying numbers.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ..., see 26 CFR § 1.6109-1 (revised as of April 1, 1973). ... 26 Internal Revenue 13 2011-04-01 2011-04-01 false Identifying numbers. 1.6109-1 Section 1.6109-1...) INCOME TAXES (CONTINUED) Miscellaneous Provisions § 1.6109-1 Identifying numbers. (a) Information to...