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Sample records for species-specific quantitative analyses

  1. Total and species-specific quantitative analyses of trace elements in sediment by isotope dilution inductively coupled plasma mass spectrometry

    International Nuclear Information System (INIS)

    Inagaki, Kazumi; Takatsu, Akiko; Yarita, Takashi; Okamoto, Kensaku; Chiba, Koichi

    2009-01-01

    Isotope dilution inductively coupled plasma mass spectrometry (ID-ICP-MS) is one of the reliable methods for total and species-specific quantitative analysis of trace elements. However, several technical problems (e.g. spectral interference caused from sample constituents) should be overcome to obtain reliable analytical results when environmental samples are analyzed by ID-ICP-MS. In our laboratory, various methods based on ID-ICP-MS have been investigated for reliable quantitative analyses of trace elements in environmental samples. In this paper, coprecipitate separation/ID-ICP-MS for the determination of trace elements in sediment, cation exchange disk filtration/ID-ICP-MS for the determination of selenium in sediment, species-specific ID-ICP-MS using 118 Sn/labeled organotin compounds for the determination of butyltins and phenyltins, and the application of the ID-ICP-MS methods to the certification of sediment reference materials are described. (author)

  2. Species-specific detection and quantification of common barnacle larvae from the Japanese coast using quantitative real-time PCR.

    Science.gov (United States)

    Endo, Noriyuki; Sato, Kana; Matsumura, Kiyotaka; Yoshimura, Erina; Odaka, Yukiko; Nogata, Yasuyuki

    2010-11-01

    Species-specific detection and quantification methods for barnacle larvae using quantitative real-time polymerase chain reaction (qPCR) were developed. Species-specific primers for qPCR were designed for 13 barnacle species in the mitochondrial 12S ribosomal RNA gene region. Primer specificity was examined by PCR using template DNA extracted from each of the 13 barnacle species, other unidentified barnacle species, and field collected zooplankton samples. The resulting PCR products comprised single bands following agarose gel electrophoresis when the templates corresponded to primers. The amplifications were highly species-specific even for the field plankton samples. The field plankton samples were subjected to qPCR assay. The calculated DNA contents for each barnacle species were closely correlated with the number of larvae measured by microscopic examination. The method could be applied to quantify barnacle larvae in natural plankton samples.

  3. Using niche-modelling and species-specific cost analyses to determine a multispecies corridor in a fragmented landscape

    Science.gov (United States)

    Zurano, Juan Pablo; Selleski, Nicole; Schneider, Rosio G.

    2017-01-01

    Misiones, Argentina, contains the largest remaining tract of Upper Paraná Atlantic Forest ecoregion; however, ~50% of native forest is unprotected and located in a mosaic of plantations, agriculture, and pastures. Existing protected areas are becoming increasingly isolated due to ongoing habitat modification. These factors, combined with lower than expected regional carnivore densities, emphasize the need to understand the effect of fragmentation on animal movement and connectivity between protected areas. Using detection dogs and genetic analyses of scat, we collected data on jaguars (Panthera onca), pumas (Puma concolor), ocelots (Leopardus pardalis), oncillas (Leopardus tigrinus), and bush dogs (Speothos venaticus) across habitats that varied in vegetation, disturbance, human proximity, and protective status. With MaxEnt we evaluated habitat use, habitat suitability, and potential species richness for the five carnivores across northern-central Misiones, Argentina. Through a multifaceted cost analysis that included unique requirements of each carnivore and varying degrees of overlap among them, we determined the optimal location for primary/secondary corridors that would link the northern-central zones of the Green Corridor in Misiones and identified areas within these corridors needing priority management. A secondary analysis, comparing these multispecies corridors with the jaguar’s unique requirements, demonstrated that this multispecies approach balanced the preferences of all five species and effectively captured areas required by this highly restricted and endangered carnivore. We emphasize the potential importance of expanding beyond a single umbrella or focal species when developing biological corridors that aim to capture the varied ecological requirements of coexisting species and ecological processes across the landscape. Detection dogs and genetic analyses of scat allow data on multiple species to be collected efficiently across multiple habitat

  4. Quantitative iTRAQ-based secretome analysis reveals species-specific and temporal shifts in carbon utilization strategies among manganese(II)-oxidizing Ascomycete fungi

    Energy Technology Data Exchange (ETDEWEB)

    Zeiner, Carolyn A.; Purvine, Samuel O.; Zink, Erika M.; Paša-Tolić, Ljiljana; Chaput, Dominique L.; Wu, Si; Santelli, Cara M.; Hansel, Colleen M.

    2017-09-01

    Fungi generate a wide range of extracellular hydrolytic and oxidative enzymes and reactive metabolites, collectively known as the secretome, that synergistically drive plant litter decomposition in the environment. While secretome studies of model organisms have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or directly compared temporal patterns of enzyme utilization among diverse species. Thus, the mechanisms of carbon (C) degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of iTRAQ proteomics and custom bioinformatic analyses to compare the protein composition of the secretomes of four manganese(II)-oxidizing Ascomycete fungi over a three-week time course. We demonstrate that although the fungi produce a similar suite of extracellular enzymes, they exhibit striking differences in the regulation of these enzymes among species and over time, revealing species-specific and temporal shifts in C utilization strategies as they degrade the same substrate. Specifically, our findings suggest that Paraconiothyrium sporulosum AP3s5-JAC2a and Alternaria alternata SRC1lrK2f employ sequential enzyme secretion patterns concomitant with decreasing resource availability, Stagonospora sp. SRC1lsM3a preferentially degrades proteinaceous substrate before switching to carbohydrates, and Pyrenochaeta sp. DS3sAY3a utilizes primarily peptidases to aggressively attack carbon sources in a concentrated burst. This work highlights the diversity of operative metabolic strategies among cellulose-degrading Ascomycetes and enhances our understanding of their role in C turnover in the environment.

  5. Quantitative analyses of shrinkage characteristics of neem ...

    African Journals Online (AJOL)

    Quantitative analyses of shrinkage characteristics of neem (Azadirachta indica A. Juss.) wood were carried out. Forty five wood specimens were prepared from the three ecological zones of north eastern Nigeria, viz: sahel savanna, sudan savanna and guinea savanna for the research. The results indicated that the wood ...

  6. Quantitative Analyse und Visualisierung der Herzfunktionen

    Science.gov (United States)

    Sauer, Anne; Schwarz, Tobias; Engel, Nicole; Seitel, Mathias; Kenngott, Hannes; Mohrhardt, Carsten; Loßnitzer, Dirk; Giannitsis, Evangelos; Katus, Hugo A.; Meinzer, Hans-Peter

    Die computergestützte bildbasierte Analyse der Herzfunktionen ist mittlerweile Standard in der Kardiologie. Die verfügbaren Produkte erfordern meist ein hohes Maß an Benutzerinteraktion und somit einen erhöhten Zeitaufwand. In dieser Arbeit wird ein Ansatz vorgestellt, der dem Kardiologen eine größtenteils automatische Analyse der Herzfunktionen mittels MRT-Bilddaten ermöglicht und damit Zeitersparnis schafft. Hierbei werden alle relevanten herzphysiologsichen Parameter berechnet und mithilfe von Diagrammen und Graphen visualisiert. Diese Berechnungen werden evaluiert, indem die ermittelten Werte mit manuell vermessenen verglichen werden. Der hierbei berechnete mittlere Fehler liegt mit 2,85 mm für die Wanddicke und 1,61 mm für die Wanddickenzunahme immer noch im Bereich einer Pixelgrösse der verwendeten Bilder.

  7. Book Review: Qualitative-Quantitative Analyses of Dutch and ...

    African Journals Online (AJOL)

    Abstract. Book Title: Qualitative-Quantitative Analyses of Dutch and Afrikaans Grammar and Lexicon. Book Author: Robert S. Kirsner. 2014. John Benjamins Publishing Company ISBN 9789027215772, price ZAR481.00. 239 pages ...

  8. Quantitative metagenomic analyses based on average genome size normalization

    DEFF Research Database (Denmark)

    Frank, Jeremy Alexander; Sørensen, Søren Johannes

    2011-01-01

    provide not just a census of the community members but direct information on metabolic capabilities and potential interactions among community members. Here we introduce a method for the quantitative characterization and comparison of microbial communities based on the normalization of metagenomic data...... marine sources using both conventional small-subunit (SSU) rRNA gene analyses and our quantitative method to calculate the proportion of genomes in each sample that are capable of a particular metabolic trait. With both environments, to determine what proportion of each community they make up and how......). These analyses demonstrate how genome proportionality compares to SSU rRNA gene relative abundance and how factors such as average genome size and SSU rRNA gene copy number affect sampling probability and therefore both types of community analysis....

  9. Qualitative and Quantitative Analyses of Glycogen in Human Milk.

    Science.gov (United States)

    Matsui-Yatsuhashi, Hiroko; Furuyashiki, Takashi; Takata, Hiroki; Ishida, Miyuki; Takumi, Hiroko; Kakutani, Ryo; Kamasaka, Hiroshi; Nagao, Saeko; Hirose, Junko; Kuriki, Takashi

    2017-02-22

    Identification as well as a detailed analysis of glycogen in human milk has not been shown yet. The present study confirmed that glycogen is contained in human milk by qualitative and quantitative analyses. High-performance anion exchange chromatography (HPAEC) and high-performance size exclusion chromatography with a multiangle laser light scattering detector (HPSEC-MALLS) were used for qualitative analysis of glycogen in human milk. Quantitative analysis was carried out by using samples obtained from the individual milks. The result revealed that the concentration of human milk glycogen varied depending on the mother's condition-such as the period postpartum and inflammation. The amounts of glycogen in human milk collected at 0 and 1-2 months postpartum were higher than in milk collected at 3-14 months postpartum. In the milk from mothers with severe mastitis, the concentration of glycogen was about 40 times higher than that in normal milk.

  10. Quantitative numerical method for analysing slip traces observed by AFM

    International Nuclear Information System (INIS)

    Veselý, J; Cieslar, M; Coupeau, C; Bonneville, J

    2013-01-01

    Atomic force microscopy (AFM) is used more and more routinely to study, at the nanometre scale, the slip traces produced on the surface of deformed crystalline materials. Taking full advantage of the quantitative height data of the slip traces, which can be extracted from these observations, requires however an adequate and robust processing of the images. In this paper an original method is presented, which allows the fitting of AFM scan-lines with a specific parameterized step function without any averaging treatment of the original data. This yields a quantitative and full description of the changes in step shape along the slip trace. The strength of the proposed method is established on several typical examples met in plasticity by analysing nano-scale structures formed on the sample surface by emerging dislocations. (paper)

  11. Species specificity in major urinary proteins by parallel evolution.

    Directory of Open Access Journals (Sweden)

    Darren W Logan

    Full Text Available Species-specific chemosignals, pheromones, regulate social behaviors such as aggression, mating, pup-suckling, territory establishment, and dominance. The identity of these cues remains mostly undetermined and few mammalian pheromones have been identified. Genetically-encoded pheromones are expected to exhibit several different mechanisms for coding 1 diversity, to enable the signaling of multiple behaviors, 2 dynamic regulation, to indicate age and dominance, and 3 species-specificity. Recently, the major urinary proteins (Mups have been shown to function themselves as genetically-encoded pheromones to regulate species-specific behavior. Mups are multiple highly related proteins expressed in combinatorial patterns that differ between individuals, gender, and age; which are sufficient to fulfill the first two criteria. We have now characterized and fully annotated the mouse Mup gene content in detail. This has enabled us to further analyze the extent of Mup coding diversity and determine their potential to encode species-specific cues.Our results show that the mouse Mup gene cluster is composed of two subgroups: an older, more divergent class of genes and pseudogenes, and a second class with high sequence identity formed by recent sequential duplications of a single gene/pseudogene pair. Previous work suggests that truncated Mup pseudogenes may encode a family of functional hexapeptides with the potential for pheromone activity. Sequence comparison, however, reveals that they have limited coding potential. Similar analyses of nine other completed genomes find Mup gene expansions in divergent lineages, including those of rat, horse and grey mouse lemur, occurring independently from a single ancestral Mup present in other placental mammals. Our findings illustrate that increasing genomic complexity of the Mup gene family is not evolutionarily isolated, but is instead a recurring mechanism of generating coding diversity consistent with a species-specific

  12. Comparison of simplified quantitative analyses of FDG uptake

    International Nuclear Information System (INIS)

    Graham, M.M.; Peterson, L.M.; Hayward, R.M.

    2000-01-01

    Quantitative analysis of [ 18 F]-fluoro-deoxyglucose (FDG) uptake is important in oncologic positron emission tomography (PET) studies to be able to set an objective threshold in determining if a tissue is malignant or benign, in assessing response to therapy, and in attempting to predict the aggressiveness of an individual tumor. The most common method used today for simple, clinical quantitation is standardized uptake value (SUV). SUV is normalized for body weight. Other potential normalization factors are lean body mass (LBM) or body surface area (BSA). More complex quantitation schemes include simplified kinetic analysis (SKA), Patlak graphical analysis (PGA), and parameter optimization of the complete kinetic model to determine FDG metabolic rate (FDGMR). These various methods were compared in a group of 40 patients with colon cancer metastatic to the liver. The methods were assessed by (1) correlation with FDGMR, (2) ability to predict survival using Kaplan-Meier plots, and (3) area under receiver operating characteristic (ROC) curves for distinguishing between tumor and normal liver. The best normalization scheme appears to be BSA with minor differences depending on the specific formula used to calculate BSA. Overall, PGA is the best predictor of outcome and best discriminator between normal tissue and tumor. SKA is almost as good. In conventional PET imaging it is worthwhile to normalize SUV using BSA. If a single blood sample is available, it is possible to use the SKA method, which is distinctly better. If more than one image is available, along with at least one blood sample, PGA is feasible and should produce the most accurate results

  13. Quantitative analysis with energy dispersive X-ray fluorescence analyser

    International Nuclear Information System (INIS)

    Kataria, S.K.; Kapoor, S.S.; Lal, M.; Rao, B.V.N.

    1977-01-01

    Quantitative analysis of samples using radioisotope excited energy dispersive x-ray fluorescence system is described. The complete set-up is built around a locally made Si(Li) detector x-ray spectrometer with an energy resolution of 220 eV at 5.94 KeV. The photopeaks observed in the x-ray fluorescence spectra are fitted with a Gaussian function and the intensities of the characteristic x-ray lines are extracted, which in turn are used for calculating the elemental concentrations. The results for a few typical cases are presented. (author)

  14. The Gutenberg English Poetry Corpus: Exemplary Quantitative Narrative Analyses

    Directory of Open Access Journals (Sweden)

    Arthur M. Jacobs

    2018-04-01

    Full Text Available This paper describes a corpus of about 3,000 English literary texts with about 250 million words extracted from the Gutenberg project that span a range of genres from both fiction and non-fiction written by more than 130 authors (e.g., Darwin, Dickens, Shakespeare. Quantitative narrative analysis (QNA is used to explore a cleaned subcorpus, the Gutenberg English Poetry Corpus (GEPC, which comprises over 100 poetic texts with around two million words from about 50 authors (e.g., Keats, Joyce, Wordsworth. Some exemplary QNA studies show author similarities based on latent semantic analysis, significant topics for each author or various text-analytic metrics for George Eliot’s poem “How Lisa Loved the King” and James Joyce’s “Chamber Music,” concerning, e.g., lexical diversity or sentiment analysis. The GEPC is particularly suited for research in Digital Humanities, Computational Stylistics, or Neurocognitive Poetics, e.g., as training and test corpus for stimulus development and control in empirical studies.

  15. Species-specific separation of lake plankton reveals divergent food assimilation patterns in rotifers.

    Science.gov (United States)

    Burian, Alfred; Kainz, Martin J; Schagerl, Michael; Yasindi, Andrew

    2014-06-01

    1. The analysis of functional groups with a resolution to the individual species level is a basic requirement to better understand complex interactions in aquatic food webs. Species-specific stable isotope analyses are currently applied to analyse the trophic role of large zooplankton or fish species, but technical constraints complicate their application to smaller-sized plankton. 2. We investigated rotifer food assimilation during a short-term microzooplankton bloom in the East African soda lake Nakuru by developing a method for species-specific sampling of rotifers. 3. The two dominant rotifers, Brachionus plicatilis and Brachionus dimidiatus , were separated to single-species samples (purity >95%) and significantly differed in their isotopic values (4.1‰ in δ 13 C and 1.5‰ in δ 15 N). Bayesian mixing models indicated that isotopic differences were caused by different assimilation of filamentous cyanobacteria and particles plicatilis (48%), whereas it was hardly ingested by B. dimidiatus . Overall, A . fusiformis was, relative to its biomass, assimilated to small extents, demonstrating a high grazing resistance of this species. 5. In combination with high population densities, these results demonstrate a strong potential of rotifer blooms to shape phytoplankton communities and are the first in situ demonstration of a quantitatively important direct trophic link between rotifers and filamentous cyanobacteria.

  16. A quantitative method to analyse an open answer questionnaire: A case study about the Boltzmann Factor

    International Nuclear Information System (INIS)

    Battaglia, Onofrio Rosario; Di Paola, Benedetto

    2015-01-01

    This paper describes a quantitative method to analyse an openended questionnaire. Student responses to a specially designed written questionnaire are quantitatively analysed by not hierarchical clustering called k-means method. Through this we can characterise behaviour students with respect their expertise to formulate explanations for phenomena or processes and/or use a given model in the different context. The physics topic is about the Boltzmann Factor, which allows the students to have a unifying view of different phenomena in different contexts.

  17. Grundlegende quantitative Analysen medizinischer Prüfungen [Basic quantitative analyses of medical examinations

    Directory of Open Access Journals (Sweden)

    Möltner, Andreas

    2006-08-01

    Full Text Available [english] The evaluation steps are described which are necessary for an elementary test-theoretic analysis of an exam and sufficient as a basis of item-revisions, improvements of the composition of tests and feedback to teaching coordinators and curriculum developers. These steps include the evaluation of the results, the analysis of item difficulty and discrimination and - where appropriate - the corresponding evaluation of single answers. To complete the procedure, the internal consistency is determined, which makes an estimate of the reliability and significance of the examination. [german] Es werden die Auswertungsschritte beschrieben, die für eine einfache testtheoretische Analyse einer Prüfung notwendig sowie als Grundlage von Aufgabenrevisionen, Verbesserungen von Prüfungszusammenstellungen und Rückmeldung an Lehrbeauftragte und Curriculumsentwickler ausreichend sind. Diese Schritte umfassen die Ergebnisauswertung, die Analyse der Aufgabenschwierigkeiten und der Trennschärfen, sowie - wo angebracht - die entsprechenden Auswertungen der Einzelantworten. Vervollständigt wird das Vorgehen durch die Bestimmung der internen Konsistenz, durch die die Zuverlässigkeit und Aussagekraft (Reliabilität der Prüfung abgeschätzt wird.

  18. Quantitative micro x-ray fluorescence analyses without reference standard material; Referenzprobenfreie quantitative Mikro-Roentgenfluoreszenzanalyse

    Energy Technology Data Exchange (ETDEWEB)

    Wolff, Timo

    2009-07-15

    X-ray fluorescence analysis (XRF) is a standard method for non-destructive investigations. Due to the development of polycapillary optics and SDDdetectors requiring no cooling with liquid nitrogen, XRF becomes a suitable method for a large number of applications, e. g. for the analysis of objects in arts and archaeology. Spectrometers developed for those purposes allow investigations outside of laboratories und provide excitation areas with diameters of 10-70 {mu}m. In most applications, quantification of XRF data is realized by the usage of standard reference materials. Due to absorption processes in the samples the accuracy of the results depends strongly on the similarity of the sample and the reference standard. In cases where no suitable references are available, quantification can be done based on the ''fundamental parameter (fp) method''. This quantification procedure is based on a set of equations describing the fluorescence production and detection mathematical. The cross sections for the interaction of x-rays with matter can be taken from different databases. During an iteration process the element concentrations can be determined. Quantitative XRF based on fundamental parameters requires an accurate knowledge of the excitation spectrum. In case of a conventional setup this spectrum is given by the X-ray tube spectrum and can be calculated. The use of polycapillary optics in micro-XRF spectrometers changes the spectral distribution of the excitation radiation. For this reason it is necessary to access the transmission function of the used optic. The aim of this work is to find a procedure to describe this function for routine quantification based on fundamental parameters. Most of the measurements have been carried out using a commercial spectrometer developed for applications in arts and archaeology. On the one hand the parameters of the lens, used in the spectrometer, have been investigated by different experimental characterization

  19. Quantitative Model for Economic Analyses of Information Security Investment in an Enterprise Information System

    Directory of Open Access Journals (Sweden)

    Bojanc Rok

    2012-11-01

    Full Text Available The paper presents a mathematical model for the optimal security-technology investment evaluation and decision-making processes based on the quantitative analysis of security risks and digital asset assessments in an enterprise. The model makes use of the quantitative analysis of different security measures that counteract individual risks by identifying the information system processes in an enterprise and the potential threats. The model comprises the target security levels for all identified business processes and the probability of a security accident together with the possible loss the enterprise may suffer. The selection of security technology is based on the efficiency of selected security measures. Economic metrics are applied for the efficiency assessment and comparative analysis of different protection technologies. Unlike the existing models for evaluation of the security investment, the proposed model allows direct comparison and quantitative assessment of different security measures. The model allows deep analyses and computations providing quantitative assessments of different options for investments, which translate into recommendations facilitating the selection of the best solution and the decision-making thereof. The model was tested using empirical examples with data from real business environment.

  20. Quantitative analysis of fission products by {gamma} spectrography; Analyse quantitative des produits de fission par spectrographie {gamma}

    Energy Technology Data Exchange (ETDEWEB)

    Malet, G

    1962-07-01

    The activity of the fission products present in treated solutions of irradiated fuels is given as a function of the time of cooling and of the irradiation time. The variation of the ratio ({sup 144}Ce + {sup 144}Pr activity/{sup 137}Cs activity) as a function of these same parameters is also given. From these results a method is deduced giving the 'age' of the solution analyzed. By {gamma}-scintillation spectrography it was possible to estimate the following elements individually: {sup 141}Ce, {sup 144}Ce + {sup 144}Pr, {sup 103}Ru, {sup 106}Ru + {sup 106}Rh, {sup 137}Cs, {sup 95}Zr + {sup 95}Nb. Yield curves are given for the case of a single emitter. Of the various existing methods, that of the least squares was used for the quantitative analysis of the afore-mentioned fission products. The accuracy attained varies from 3 to 10%. (author) [French] L'activite des produits de fission presents dans les solutions de traitement de combustibles irradies est donnee en fonction du temps de refroidissement et du temps d'irradiation. On etudie de plus la variation du rapport Activite du {sup 144}Ce + {sup 144}Pr /Activite du {sup 137}Cs en fonction de ces memes parametres. De ces resultats, on deduit une methode donnant l'age de la solution analysee. La spectrographie {gamma} a scintillation a permis le dosage individuel des produits suivants: {sup 141}Ce, {sup 144}Ce + {sup 144}Pr, {sup 103}Ru, {sup 106}Ru + {sup 106}Rh, {sup 137}Cs, {sup 95}Zr + {sup 95}Nb. Des courbes de rendement sont donnees dans le cas d'un emetteur unique. Des differentes methodes existantes, la methode des moindres carres a ete employee pour l'analyse quantitative des produits de fission precites. La precision obtenue varie entre 3 et 10 pour cent. (auteur)

  1. Quantitative methods for analysing cumulative effects on fish migration success: a review.

    Science.gov (United States)

    Johnson, J E; Patterson, D A; Martins, E G; Cooke, S J; Hinch, S G

    2012-07-01

    It is often recognized, but seldom addressed, that a quantitative assessment of the cumulative effects, both additive and non-additive, of multiple stressors on fish survival would provide a more realistic representation of the factors that influence fish migration. This review presents a compilation of analytical methods applied to a well-studied fish migration, a more general review of quantitative multivariable methods, and a synthesis on how to apply new analytical techniques in fish migration studies. A compilation of adult migration papers from Fraser River sockeye salmon Oncorhynchus nerka revealed a limited number of multivariable methods being applied and the sub-optimal reliance on univariable methods for multivariable problems. The literature review of fisheries science, general biology and medicine identified a large number of alternative methods for dealing with cumulative effects, with a limited number of techniques being used in fish migration studies. An evaluation of the different methods revealed that certain classes of multivariable analyses will probably prove useful in future assessments of cumulative effects on fish migration. This overview and evaluation of quantitative methods gathered from the disparate fields should serve as a primer for anyone seeking to quantify cumulative effects on fish migration survival. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

  2. Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.

    Science.gov (United States)

    Schmid, Volker J; Cremer, Marion; Cremer, Thomas

    2017-07-01

    Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools for (semi-) automated, quantitative 3D analyses of the spatial nuclear organization. These tools allow the quantitative assessment of highly resolved different chromatin compaction levels in individual cell nuclei, which reflect functionally different regions or sub-compartments of the 3D nuclear landscape, and measurements of absolute distances between sites of different chromatin compaction. In addition, these tools allow 3D mapping of specific DNA/RNA sequences and nuclear proteins relative to the 3D chromatin compaction maps and comparisons of multiple cell nuclei. The tools are available in the free and open source R packages nucim and bioimagetools. We discuss the use of masks for the segmentation of nuclei and the use of DNA stains, such as DAPI, as a proxy for local differences in chromatin compaction. We further discuss the limitations of 3D maps of the nuclear landscape as well as problems of the biological interpretation of such data. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. 75 FR 29537 - Draft Transportation Conformity Guidance for Quantitative Hot-spot Analyses in PM2.5

    Science.gov (United States)

    2010-05-26

    ... Quantitative Hot- spot Analyses in PM 2.5 and PM 10 Nonattainment and Maintenance Areas AGENCY: Environmental... finalized, this guidance would help state and local agencies complete quantitative PM 2.5 and PM 10 hot-spot... projects. A hot-spot analysis includes an estimation of project-level emissions, air quality modeling, and...

  4. OXA-258 from Achromobacter ruhlandii: a Species Specific Marker

    OpenAIRE

    Papalia, Mariana Andrea; Almuzara, Marisa; Cejas, Daniela; Traglia, German Matias; Ramirez, Maria Soledad; Galanternik, Laura; Vay, Carlos Alberto; Gutkind, Gabriel Osvaldo; Radice, Marcela Alejandra

    2015-01-01

    A new blaOXA-258 gene is described as species specific taxonomic marker for Achromobacter ruhlandii isolates (all recovered from cystic fibrosis patients). Even if the OXA-258 differs from OXA-114 variants, isolates could be misidentified as A. xiloxosidans by the amplification of an inner fragment from the OXA coding gene. A robust Identification of A. ruhlandii can be achieved by sequencing this single OXA gene as well as a more laborious recently proposed MLST scheme Fil: Papalia, Maria...

  5. QTL for the species-specific male and female genital morphologies in Ohomopterus ground beetles.

    Science.gov (United States)

    Sasabe, Masataka; Takami, Yasuoki; Sota, Teiji

    2010-12-01

    Animals with internal fertilization often exhibit marked diversification in genital morphology among closely related species. However, our knowledge of the genetic architecture underlying genital evolution is still limited. We constructed genetic linkage maps and analysed quantitative trait loci (QTL) for F(2) hybrids of two closely related species of the carabid beetles Carabus (Ohomopterus) iwawakianus and C. (O.) maiyasanus, which show matching male and female genital shapes within species, but marked differences in genital morphologies between species. The linkage maps comprised both amplified fragment length polymorphism and microsatellite markers. Composite interval mapping to detect QTL for three traits of male copulatory piece (length, width, weight) and two traits for female vaginal appendix (length, width) resulted in the detection of one to five significant QTL for each trait. The QTL explained large proportions of phenotypic variance. Thus, the interspecific difference in the genital morphologies appeared to be determined by relatively small numbers of genes with large genetic effects. QTL of different traits for the same or different sexes co-occurred on five of eight linkage groups with significant QTL; in particular, three QTL for different male and female genital traits occurred almost at the same position. Each of the male genital traits showed uniform signs of additive genetic effects, suggesting that directional selection has led to species-specific morphologies. However, the signs of additive genetic effects in each female genital trait were not uniform, suggesting that coevolution between sexes is not necessarily concerted. This result requires further assessment because the sample size of F(2) females was small. © 2010 Blackwell Publishing Ltd.

  6. Practicable methods for histological section thickness measurement in quantitative stereological analyses.

    Science.gov (United States)

    Matenaers, Cyrill; Popper, Bastian; Rieger, Alexandra; Wanke, Rüdiger; Blutke, Andreas

    2018-01-01

    The accuracy of quantitative stereological analysis tools such as the (physical) disector method substantially depends on the precise determination of the thickness of the analyzed histological sections. One conventional method for measurement of histological section thickness is to re-embed the section of interest vertically to its original section plane. The section thickness is then measured in a subsequently prepared histological section of this orthogonally re-embedded sample. However, the orthogonal re-embedding (ORE) technique is quite work- and time-intensive and may produce inaccurate section thickness measurement values due to unintentional slightly oblique (non-orthogonal) positioning of the re-embedded sample-section. Here, an improved ORE method is presented, allowing for determination of the factual section plane angle of the re-embedded section, and correction of measured section thickness values for oblique (non-orthogonal) sectioning. For this, the analyzed section is mounted flat on a foil of known thickness (calibration foil) and both the section and the calibration foil are then vertically (re-)embedded. The section angle of the re-embedded section is then calculated from the deviation of the measured section thickness of the calibration foil and its factual thickness, using basic geometry. To find a practicable, fast, and accurate alternative to ORE, the suitability of spectral reflectance (SR) measurement for determination of plastic section thicknesses was evaluated. Using a commercially available optical reflectometer (F20, Filmetrics®, USA), the thicknesses of 0.5 μm thick semi-thin Epon (glycid ether)-sections and of 1-3 μm thick plastic sections (glycolmethacrylate/ methylmethacrylate, GMA/MMA), as regularly used in physical disector analyses, could precisely be measured within few seconds. Compared to the measured section thicknesses determined by ORE, SR measures displayed less than 1% deviation. Our results prove the applicability

  7. A high seroprevalence of antibodies to pertussis toxin among Japanese adults: Qualitative and quantitative analyses.

    Directory of Open Access Journals (Sweden)

    Takumi Moriuchi

    Full Text Available In 2013, national serosurveillance detected a high seroprevalence of antibodies to pertussis toxin (PT from Bordetella pertussis among Japanese adults. Thus, we aimed to determine the cause(s of this high seroprevalence, and analyzed the titers of antibodies to PT and filamentous hemagglutinin (FHA among adults (35-44 years old, young children (4-7 years old, and older children (10-14 years old. Our quantitative analyses revealed that adults had higher seroprevalences of anti-PT IgG and PT-neutralizing antibodies, and similar titers of anti-FHA IgG, compared to the young and older children. Positive correlations were observed between the titers of PT-neutralizing antibodies and anti-PT IgG in all age groups (rs values of 0.326-0.522, although the correlation tended to decrease with age. The ratio of PT-neutralizing antibodies to anti-PT IgG was significantly different when we compared the serum and purified IgG fractions among adults (p = 0.016, although this result was not observed among young and older children. Thus, it appears that some adults had non-IgG immunoglobulins to PT. Our analyses also revealed that adults had high-avidity anti-PT IgG (avidity index: 63.5%, similar results were observed among the children; however, the adults had lower-avidity anti-FHA IgG (37.9%, p < 0.05. It is possible that low-avidity anti-FHA IgG is related to infection with other respiratory pathogens (e.g., Bordetella parapertussis, Haemophilus influenzae, or Mycoplasma pneumoniae, which produces antibodies to FHA-like proteins. Our observations suggest that these adults had been infected with B. pertussis and other pathogen(s during their adulthood.

  8. Quantitative Prediction of Coalbed Gas Content Based on Seismic Multiple-Attribute Analyses

    Directory of Open Access Journals (Sweden)

    Renfang Pan

    2015-09-01

    Full Text Available Accurate prediction of gas planar distribution is crucial to selection and development of new CBM exploration areas. Based on seismic attributes, well logging and testing data we found that seismic absorption attenuation, after eliminating the effects of burial depth, shows an evident correlation with CBM gas content; (positive structure curvature has a negative correlation with gas content; and density has a negative correlation with gas content. It is feasible to use the hydrocarbon index (P*G and pseudo-Poisson ratio attributes for detection of gas enrichment zones. Based on seismic multiple-attribute analyses, a multiple linear regression equation was established between the seismic attributes and gas content at the drilling wells. Application of this equation to the seismic attributes at locations other than the drilling wells yielded a quantitative prediction of planar gas distribution. Prediction calculations were performed for two different models, one using pre-stack inversion and the other one disregarding pre-stack inversion. A comparison of the results indicates that both models predicted a similar trend for gas content distribution, except that the model using pre-stack inversion yielded a prediction result with considerably higher precision than the other model.

  9. Microsegregation in multicomponent alloy analysed by quantitative phase-field model

    International Nuclear Information System (INIS)

    Ohno, M; Takaki, T; Shibuta, Y

    2015-01-01

    Microsegregation behaviour in a ternary alloy system has been analysed by means of quantitative phase-field (Q-PF) simulations with a particular attention directed at an influence of tie-line shift stemming from different liquid diffusivities of the solute elements. The Q-PF model developed for non-isothermal solidification in multicomponent alloys with non-zero solid diffusivities was applied to analysis of microsegregation in a ternary alloy consisting of fast and slow diffusing solute elements. The accuracy of the Q-PF simulation was first verified by performing the convergence test of segregation ratio with respect to the interface thickness. From one-dimensional analysis, it was found that the microsegregation of slow diffusing element is reduced due to the tie-line shift. In two-dimensional simulations, the refinement of microstructure, viz., the decrease of secondary arms spacing occurs at low cooling rates due to the formation of diffusion layer of slow diffusing element. It yields the reductions of degrees of microsegregation for both the fast and slow diffusing elements. Importantly, in a wide range of cooling rates, the degree of microsegregation of the slow diffusing element is always lower than that of the fast diffusing element, which is entirely ascribable to the influence of tie-line shift. (paper)

  10. Quantitative proteomic analyses of the microbial degradation of estrone under various background nitrogen and carbon conditions.

    Science.gov (United States)

    Du, Zhe; Chen, Yinguang; Li, Xu

    2017-10-15

    Microbial degradation of estrogenic compounds can be affected by the nitrogen source and background carbon in the environment. However, the underlying mechanisms are not well understood. The objective of this study was to elucidate the molecular mechanisms of estrone (E1) biodegradation at the protein level under various background nitrogen (nitrate or ammonium) and carbon conditions (no background carbon, acetic acid, or humic acid as background carbon) by a newly isolated bacterial strain. The E1 degrading bacterial strain, Hydrogenophaga atypica ZD1, was isolated from river sediments and its proteome was characterized under various experimental conditions using quantitative proteomics. Results show that the E1 degradation rate was faster when ammonium was used as the nitrogen source than with nitrate. The degradation rate was also faster when either acetic acid or humic acid was present in the background. Proteomics analyses suggested that the E1 biodegradation products enter the tyrosine metabolism pathway. Compared to nitrate, ammonium likely promoted E1 degradation by increasing the activities of the branched-chain-amino-acid aminotransferase (IlvE) and enzymes involved in the glutamine synthetase-glutamine oxoglutarate aminotransferase (GS-GOGAT) pathway. The increased E1 degradation rate with acetic acid or humic acid in the background can also be attributed to the up-regulation of IlvE. Results from this study can help predict and explain E1 biodegradation kinetics under various environmental conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Pulmonary nodule characterization: A comparison of conventional with quantitative and visual semi-quantitative analyses using contrast enhancement maps

    International Nuclear Information System (INIS)

    Petkovska, Iva; Shah, Sumit K.; McNitt-Gray, Michael F.; Goldin, Jonathan G.; Brown, Matthew S.; Kim, Hyun J.; Brown, Kathleen; Aberle, Denise R.

    2006-01-01

    Purpose: To determine whether conventional nodule densitometry or analysis based on contrast enhancement maps of indeterminate lung nodules imaged with contrast-enhanced CT can distinguish benign from malignant lung nodules. Materials and method: Thin section, contrast-enhanced CT (baseline, and post-contrast series acquired at 45, 90,180, and 360 s) was performed on 29 patients with indeterminate lung nodules (14 benign, 15 malignant). A thoracic radiologist identified the boundary of each nodule using semi-automated contouring to form a 3D region-of-interest (ROI) on each image series. The post-contrast series having the maximum mean enhancement was then volumetrically registered to the baseline series. The two series were subtracted volumetrically and the subtracted voxels were quantized into seven color-coded bins, forming a contrast enhancement map (CEM). Conventional nodule densitometry was performed to obtain the maximum difference in mean enhancement values for each nodule from a circular ROI. Three thoracic radiologists performed visual semi-quantitative analysis of each nodule, scoring each map for: (a) magnitude and (b) heterogeneity of enhancement throughout the entire volume of the nodule on a five-point scale. Receiver operator characteristic (ROC) analysis was conducted on these features to evaluate their diagnostic efficacy. Finally, 14 quantitative texture features were calculated for each map. A statistical analysis was performed to combine the 14 texture features to a single factor. ROC analysis of the derived aggregate factor was done as an indicator of malignancy. All features were analyzed for differences between benign and malignant nodules. Results: Using 15 HU as a threshold, 93% (14/15) of malignant and 79% (11/14) of benign nodules demonstrated enhancement. The ROC curve when higher values of enhancement indicate malignancy was generated and area under the curve (AUC) was 0.76. The visually scored magnitude of enhancement was found to be

  12. Halal authenticity of gelatin using species-specific PCR.

    Science.gov (United States)

    Shabani, Hessam; Mehdizadeh, Mehrangiz; Mousavi, Seyed Mohammad; Dezfouli, Ehsan Ansari; Solgi, Tara; Khodaverdi, Mahdi; Rabiei, Maryam; Rastegar, Hossein; Alebouyeh, Mahmoud

    2015-10-01

    Consumption of food products derived from porcine sources is strictly prohibited in Islam. Gelatin, mostly derived from bovine and porcine sources, has many applications in the food and pharmaceutical industries. To ensure that food products comply with halal regulations, development of valid and reliable analytical methods is very much required. In this study, a species-specific polymerase chain reaction (PCR) assay using conserved regions of mitochondrial DNA (cytochrome b gene) was performed to evaluate the halal authenticity of gelatin. After isolation of DNA from gelatin powders with known origin, conventional PCR using species-specific primers was carried out on the extracted DNA. The amplified expected PCR products of 212 and 271 bp were observed for porcine and bovine gelatin, respectively. The sensitivity of the method was tested on binary gelatin mixtures containing 0.1%, 1%, 10%, and 100% (w/w) of porcine gelatin within bovine gelatin and vice versa. Although most of the DNA is degraded due to the severe processing steps of gelatin production, the minimum level of 0.1% w/w of both porcine and bovine gelatin was detected. Moreover, eight food products labeled as containing bovine gelatin and eight capsule shells were subjected to PCR examination. The results showed that all samples contained bovine gelatin, and the absence of porcine gelatin was verified. This method of species authenticity is very useful to verify whether gelatin and gelatin-containing food products are derived from halal ingredients. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Are temperate canopy spiders tree-species specific?

    Science.gov (United States)

    Mupepele, Anne-Christine; Müller, Tobias; Dittrich, Marcus; Floren, Andreas

    2014-01-01

    Arboreal spiders in deciduous and coniferous trees were investigated on their distribution and diversity. Insecticidal knock-down was used to comprehensively sample spiders from 175 trees from 2001 to 2003 in the Białowieża forest and three remote forests in Poland. We identified 140 species from 9273 adult spiders. Spider communities were distinguished between deciduous and coniferous trees. The richest fauna was collected from Quercus where beta diversity was also highest. A tree-species-specific pattern was clearly observed for Alnus, Carpinus, Picea and Pinus trees and also for those tree species that were fogged in only four or three replicates, namely Betula and Populus. This hitherto unrecognised association was mainly due to the community composition of common species identified in a Dufrene-Legendre indicator species analysis. It was not caused by spatial or temporal autocorrelation. Explaining tree-species specificity for generalist predators like spiders is difficult and has to involve physical and ecological tree parameters like linkage with the abundance of prey species. However, neither did we find a consistent correlation of prey group abundances with spiders nor could differences in spider guild composition explain the observed pattern. Our results hint towards the importance of deterministic mechanisms structuring communities of generalist canopy spiders although the casual relationship is not yet understood.

  14. Quantitative and qualitative analyses of subacromial impingement by kinematic open MRI.

    Science.gov (United States)

    Tasaki, Atsushi; Nimura, Akimoto; Nozaki, Taiki; Yamakawa, Akira; Niitsu, Mamoru; Morita, Wataru; Hoshikawa, Yoshimitsu; Akita, Keiichi

    2015-05-01

    Quantitative and qualitative kinematic analyses of subacromial impingement by 1.2T open MRI were performed to determine the location of impingement and the involvement of the acromioclavicular joint. In 20 healthy shoulders, 10 sequential images in the scapular plane were taken in a 10-s pause at equal intervals from 30° to maximum abduction in neutral and internal rotation. The distances between the rotator cuff (RC) and the acromion and the acromioclavicular joint were measured. To comprehend the positional relationships, cadaveric specimens were also observed. Although asymptomatic, the RC came into contact with the acromion and the acromioclavicular joint in six and five cases, respectively. The superior RC acted as a depressor for the humeral head against the acromion as the shoulder elevated. The mean elevation angle and distance at the closest position between the RC and the acromion in neutral rotation were 93.5° and 1.6 mm, respectively, while those between the RC and the acromioclavicular joint were 86.7° and 2.0 mm. When comparing this distance and angle, there was no significant difference between the RC to the acromion and to the acromioclavicular joint. The minimum distance between the RC and the acromion was significantly shorter than that between the greater tuberosity and the acromion. The location of RC closest to the acromion and the acromioclavicular joint differed significantly. Although asymptomatic, contact was found between the RC and the acromion and the acromioclavicular joint. The important role of the RC to prevent impingement was observed, and hence, dysfunction of the RC could lead to impingement that could result in a RC lesion. The RC lesions may differ when they are caused by impingement from either the acromion or the acromioclavicular joint.

  15. Forest Transpiration: Resolving Species-Specific Root Water Uptake Patterns

    Science.gov (United States)

    Blume, T.; Heidbuechel, I.; Simard, S.; Guntner, A.; Weiler, M.; Stewart, R. D.

    2016-12-01

    Transpiration and its spatio-temporal variability are still not fully understood, despite their importance for the global water cycle. This is in part due to our inability to measure transpiration comprehensively. Transpiration is usually either estimated with empirical equations based on climatic variables and crop factors, by measuring sap velocities, estimating sap wood area and scaling up to the forest stand based on a number of assumptions or by measuring the integral signal across a footprint with eddy flux towers. All these methods are focused on the cumulated loss of water to the atmosphere and do not provide information on where this water is coming from. In this study, spatio-temporal variability of root water uptake was investigated in a forest in the northeastern German lowlands. The soils are sandy and the depth of the unsaturated zone ranges from 1 to 30 m. We estimated root water uptake from different soil depths, from 0.1 m down to 2 m, based on diurnal fluctuations in soil moisture content during rain-free days. The 15 field sites cover different topographic positions and forest stands: 4 pure stands of both mature and young beech and pine and 9 mixed stands. The resulting daily data set of root water uptake shows that the forest stands differ in total amounts as well as in uptake depth distributions. Temporal dynamics of signal strength within the profile suggest a locally shifting spatial distribution of uptake that changes with water availability. The relationship of these depth-resolved uptake rates to overall soil water availability varies considerably between tree species. Using the physically-based soil hydrological model HYDRUS we investigated to what extent the observed patterns in uptake can be related to soil physical relationships alone and where tree species-specific aspects come into play. We furthermore used the model to test assumptions and estimate uncertainties of this soil moisture based estimation of plant water uptake. The

  16. Quantitative Research Methods in Chaos and Complexity: From Probability to Post Hoc Regression Analyses

    Science.gov (United States)

    Gilstrap, Donald L.

    2013-01-01

    In addition to qualitative methods presented in chaos and complexity theories in educational research, this article addresses quantitative methods that may show potential for future research studies. Although much in the social and behavioral sciences literature has focused on computer simulations, this article explores current chaos and…

  17. Species specific anaesthetics for fish anaesthesia and euthanasia.

    Science.gov (United States)

    Readman, Gareth D; Owen, Stewart F; Knowles, Toby G; Murrell, Joanna C

    2017-08-02

    There is a need to ensure that the care and welfare for fish maintained in the laboratory are to the highest standards. This extends to the use of anaesthetics for both scientific study, humane killing and euthanasia at end of life. An anaesthetic should not induce negative behaviours and fish should not seek to avoid the anaesthetic. Surprisingly little information is available to facilitate a humane choice of anaesthetic agent for fish despite over 100 years of use and the millions of fish currently held in thousands of laboratories worldwide. Using a chemotaxic choice chamber we found different species specific behavioural responses among four closely related fish species commonly held in the laboratory, exposed to three widely used anaesthetic agents. As previously found for zebrafish (Danio rerio), the use of MS-222 and benzocaine also appears to induce avoidance behaviours in medaka (Oryzias latipes); but etomidate could provide an alternative choice. Carp (Cyprinus carpio), although closely related to zebrafish showed avoidance behaviours to etomidate, but not benzocaine or MS-222; and rainbow trout (Oncorhynchus mykiss) showed no avoidance to the three agents tested. We were unable to ascertain avoidance responses in fathead minnows (Pimephales promelas) and suggest different test paradigms are required for that species.

  18. Biooxidation of Ciguatoxins Leads to Species-Specific Toxin Profiles.

    Science.gov (United States)

    Ikehara, Tsuyoshi; Kuniyoshi, Kyoko; Oshiro, Naomasa; Yasumoto, Takeshi

    2017-06-29

    Ciguatoxins (CTXs) contaminate fish worldwide and cause the foodborne illness ciguatera. In the Pacific, these toxins are produced by the dinoflagellate Gambierdiscus toxicus , which accumulates in fish through the food chain and undergoes oxidative modification, giving rise to numerous analogs. In this study, we examined the oxidation of CTXs in vitro with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis using reference toxins, and found that CTX4A, CTX4B, and CTX3C, which are produced by the alga, are oxidized to the analogs found in fish, namely CTX1B, 52- epi -54-deoxyCTX1B, 54-deoxyCTX1B, 2-hydroxyCTX3C, and 2,3-dihydroxyCTX3C. This oxidation was catalyzed by human CYP3A4, fish liver S9 fractions, and microsomal fractions prepared from representative ciguateric fishes ( Lutjanus bohar , L. monostigumus , and Oplegnathus punctatus ). In addition, fish liver S9 fractions prepared from non-ciguateric fishes ( L. gibbus and L. fulviflamma ) in Okinawa also converted CTX4A and CTX4B to CTX1B, 54-deoxyCTX1B, and 52- epi -54-deoxyCTX1B in vitro. This is the first study to demonstrate the enzymatic oxidation of these toxins, and provides insight into the mechanism underlying the development of species-specific toxin profiles and the fate of these toxins in humans and fish.

  19. Influenza virus and endothelial cells: a species specific relationship

    Directory of Open Access Journals (Sweden)

    Kirsty Renfree Short

    2014-12-01

    Full Text Available Influenza A virus infection is an important cause of respiratory disease in humans. The original reservoirs of influenza A virus are wild waterfowl and shorebirds, where virus infection causes limited, if any, disease. Both in humans and in wild waterbirds, epithelial cells are the main target of infection. However, influenza virus can spread from wild bird species to terrestrial poultry. Here, the virus can evolve into highly pathogenic avian influenza (HPAI. Part of this evolution involves increased viral tropism for endothelial cells. HPAI virus infections not only cause severe disease in chickens and other terrestrial poultry species but can also spread to humans and back to wild bird populations. Here, we review the role of the endothelium in the pathogenesis of influenza virus infection in wild birds, terrestrial poultry and humans with a particular focus on HPAI viruses. We demonstrate that whilst the endothelium is an important target of virus infection in terrestrial poultry and some wild bird species, in humans the endothelium is more important in controlling the local inflammatory milieu. Thus, the endothelium plays an important, but species-specific, role in the pathogenesis of influenza virus infection.

  20. Fine-scale genetic analysis of species-specific female preference in Drosophila simulans.

    Science.gov (United States)

    Laturney, M; Moehring, A J

    2012-09-01

    Behavioural differences are thought to be the first components to contribute to species isolation, yet the precise genetic basis of behavioural isolation remains poorly understood. Here, we used a combination of behaviour assays and genetic mapping to provide the first refined map locating candidate genes for interspecific female preference isolating Drosophila simulans from D. melanogaster. First, we tested whether two genes identified as affecting D. melanogaster female intraspecific mate choice also affect interspecific mate choice; neither of these genes was found to contribute to species-specific female preference. Next, we used deficiency mapping to locate genes on the right arm of the third chromosome for species-specific female preference and identified five small significant regions that contain candidate genes contributing to behavioural isolation. All five regions were located in areas that would have low interspecific recombination, which mirrors the results of other behavioural isolation studies that used quantitative trait locus (QTL) mapping, but without the potential concern of bias towards regions of low recombination that QTL mapping may have. As this model system may be refined to the individual gene level using the same methodology, this initial map we provide may potentially serve as a ready template for the identification and characterization of the first behavioural isolation genes. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

  1. Qualitative and Quantitative Security Analyses for ZigBee Wireless Sensor Networks

    DEFF Research Database (Denmark)

    Yuksel, Ender

    methods and techniques in different areas and brings them together to create an efficient verification system. The overall ambition is to provide a wide range of powerful techniques for analyzing models with quantitative and qualitative security information. We stated a new approach that first verifies...... applications, home automation, and traffic control. The challenges for research in this area are due to the unique features of wireless sensor devices such as low processing power and associated low energy. On top of this, wireless sensor networks need secure communication as they operate in open fields...... low level security protocol s in a qualitative manner and guarantees absolute security, and then takes these verified protocols as actions of scenarios to be verified in a quantitative manner. Working on the emerging ZigBee wireless sensor networks, we used probabilistic verification that can return...

  2. Quantitative analyses of the behavior of exogenously added bacteria during an acidulocomposting process.

    Science.gov (United States)

    Suematsu, Takatoshi; Yamashita, Satoshi; Hemmi, Hisashi; Yoshinari, Ayaka; Shimoyama, Takefumi; Nakayama, Toru; Nishino, Tokuzo

    2012-07-01

    The behavior of adventitious bacteria during an acidulocomposting process was quantitatively analyzed in garbage-free trials. The numbers of the added Bacillus subtilis and Pseudomonas putida cells diminished in a first-order manner with t(1/2) values of 0.45d and 0.79d, respectively, consistent with the observed stability of the acidulocomposting function. Copyright © 2012 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  3. Greek PDO saffron authentication studies using species specific molecular markers.

    Science.gov (United States)

    Bosmali, I; Ordoudi, S A; Tsimidou, M Z; Madesis, P

    2017-10-01

    Saffron, the spice produced from the red stigmas of the flower of Crocus sativus L. is a frequent target of fraud and mislabeling practices that cannot be fully traced using the ISO 3632 trade standard specifications and test methods. A molecular approach is proposed herein as a promising branding strategy for the authentication of highly esteemed saffron brands such as the Greek Protected Designation of Origin (PDO) "Krokos Kozanis". Specific ISSR (inter-simple sequence repeat) markers were used to assess for the first time, the within species variability of several populations of C. sativus L. from the cultivation area of "Krokos Kozanis" as well as the potential differences with the band pattern produced by other Crocus species. Then, species-specific markers were developed taking advantage of an advanced molecular technique such as the HRM analysis coupled with universal DNA barcoding regions (trnL) (Bar-HRM) and applied to saffron admixtures with some of the most common plant adulterants (Calendula officinalis, Carthamus tinctorius, Gardenia jasminoides, Zea mays and Curcuma longa). The sensitivity of the procedure was tested for turmeric as a case study whereas HPLC-fluorescence determination of secondary metabolites was also employed for comparison. The overall results indicated that the Bar-HRM approach is quite effective in terms of specificity and sensitivity. Its effectiveness regarding the detection of turmeric was comparable to that of a conventional HPLC method (0.5% vs 1.0%, w/w). Yet, the proposed DNA-based method is much faster, cost-effective and can be used even by non-geneticists, in any laboratory having access to an HRM-capable real-time PCR instrumentation. It can be, thus, regarded as a strong analytical tool in saffron authentication studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Comparative analyses identified species-specific functional roles in oral microbial genomes

    Science.gov (United States)

    Chen, Tsute; Gajare, Prasad; Olsen, Ingar; Dewhirst, Floyd E.

    2017-01-01

    ABSTRACT The advent of next generation sequencing is producing more genomic sequences for various strains of many human oral microbial species and allows for insightful functional comparisons at both intra- and inter-species levels. This study performed in-silico functional comparisons for currently available genomic sequences of major species associated with periodontitis including Aggregatibacter actinomycetemcomitans (AA), Porphyromonas gingivalis (PG), Treponema denticola (TD), and Tannerella forsythia (TF), as well as several cariogenic and commensal streptococcal species. Complete or draft sequences were annotated with the RAST to infer structured functional subsystems for each genome. The subsystems profiles were clustered to groups of functions with similar patterns. Functional enrichment and depletion were evaluated based on hypergeometric distribution to identify subsystems that are unique or missing between two groups of genomes. Unique or missing metabolic pathways and biological functions were identified in different species. For example, components involved in flagellar motility were found only in the motile species TD, as expected, with few exceptions scattered in several streptococcal species, likely associated with chemotaxis. Transposable elements were only found in the two Bacteroidales species PG and TF, and half of the AA genomes. Genes involved in CRISPR were prevalent in most oral species. Furthermore, prophage related subsystems were also commonly found in most species except for PG and Streptococcus mutans, in which very few genomes contain prophage components. Comparisons between pathogenic (P) and nonpathogenic (NP) genomes also identified genes potentially important for virulence. Two such comparisons were performed between AA (P) and several A. aphrophilus (NP) strains, and between S. mutans + S. sobrinus (P) and other oral streptococcal species (NP). This comparative genomics approach can be readily used to identify functions unique to or prevalent in a group of genomes. It can work with annotation systems using structured functional terms, such as RAST, KEGG and Gene Ontology, and obtain comprehensive functional insights into microbial genomics.

  5. Fluvial drainage networks: the fractal approach as an improvement of quantitative geomorphic analyses

    Science.gov (United States)

    Melelli, Laura; Liucci, Luisa; Vergari, Francesca; Ciccacci, Sirio; Del Monte, Maurizio

    2014-05-01

    Drainage basins are primary landscape units for geomorphological investigations. Both hillslopes and river drainage system are fundamental components in drainage basins analysis. As other geomorphological systems, also the drainage basins aim to an equilibrium condition where the sequence of erosion, transport and sedimentation approach to a condition of minimum energy effort. This state is revealed by a typical geometry of landforms and of drainage net. Several morphometric indexes can measure how much a drainage basin is far from the theoretical equilibrium configuration, revealing possible external disarray. In active tectonic areas, the drainage basins have a primary importance in order to highlight style, amount and rate of tectonic impulses, and morphometric indexes allow to estimate the tectonic activity classes of different sectors in a study area. Moreover, drainage rivers are characterized by a self-similarity structure; this promotes the use of fractals theory to investigate the system. In this study, fractals techniques are employed together with quantitative geomorphological analysis to study the Upper Tiber Valley (UTV), a tectonic intermontane basin located in northern Apennines (Umbria, central Italy). The area is the result of different tectonic phases. From Late Pliocene until present time the UTV is strongly controlled by a regional uplift and by an extensional phase with different sets of normal faults playing a fundamental role in basin morphology. Thirty-four basins are taken into account for the quantitative analysis, twenty on the left side of the basin, the others on the right side. Using fractals dimension of drainage networks, Horton's laws results, concavity and steepness indexes, and hypsometric curves, this study aims to obtain an evolutionary model of the UTV, where the uplift is compared to local subsidence induced by normal fault activity. The results highlight a well defined difference between western and eastern tributary basins

  6. Morphological and quantitative analyses on features of asymmetric mandible with X-ray CT images

    Energy Technology Data Exchange (ETDEWEB)

    Hayashi, Masaki; Isshiki, Yasushige; Nishikawa, Keiichi [Tokyo Dental Coll., Chiba (Japan)

    2001-09-01

    Biomechanical disproportion of the mandible causes morphological and quantitative changes in the bone and induces jaw deformities. The purpose of this study was to clarify the influence of the biomechanical disproportion on the structure and quality of the mandible, using spiral X-ray CT images. Subjects were 11 patients with mandibular asymmetry requiring orthognathic surgery. Lateral and vertical shift angles of the mandible against the maxilla were determined mathematically from the coordinates of structural reference points in 3-dimensional orthogonal coordinate systems as indices of the deformity degree. Several properties concerning thickness and CT value of mandibular cortical bone were measured as indices of the morphological and quantitative changes in mandibular cortical bone. Occlusal force was also measured using a pressure sensitive film as an index of biomechanical disproportion. Asymmetric indices of them were calculated from data of the left and right sides. The Pearson's correlation coefficients were obtained for these data. As a result, the mandible tended to shift laterally toward the side where the occlusal force at the second molar region was stronger and also to shift upward on that side. At the central incisor region of the laterally shifted side, CT values were relatively decreased. At the lateral incisor region, cortical bone density was relatively increased. At the first bicuspid region and the posterior tooth regions, cortical bone thickness was relatively decreased. (author)

  7. Morphological and quantitative analyses on features of asymmetric mandible with X-ray CT images

    International Nuclear Information System (INIS)

    Hayashi, Masaki; Isshiki, Yasushige; Nishikawa, Keiichi

    2001-01-01

    Biomechanical disproportion of the mandible causes morphological and quantitative changes in the bone and induces jaw deformities. The purpose of this study was to clarify the influence of the biomechanical disproportion on the structure and quality of the mandible, using spiral X-ray CT images. Subjects were 11 patients with mandibular asymmetry requiring orthognathic surgery. Lateral and vertical shift angles of the mandible against the maxilla were determined mathematically from the coordinates of structural reference points in 3-dimensional orthogonal coordinate systems as indices of the deformity degree. Several properties concerning thickness and CT value of mandibular cortical bone were measured as indices of the morphological and quantitative changes in mandibular cortical bone. Occlusal force was also measured using a pressure sensitive film as an index of biomechanical disproportion. Asymmetric indices of them were calculated from data of the left and right sides. The Pearson's correlation coefficients were obtained for these data. As a result, the mandible tended to shift laterally toward the side where the occlusal force at the second molar region was stronger and also to shift upward on that side. At the central incisor region of the laterally shifted side, CT values were relatively decreased. At the lateral incisor region, cortical bone density was relatively increased. At the first bicuspid region and the posterior tooth regions, cortical bone thickness was relatively decreased. (author)

  8. Vibrational algorithms for quantitative crystallographic analyses of hydroxyapatite-based biomaterials: I, theoretical foundations.

    Science.gov (United States)

    Pezzotti, Giuseppe; Zhu, Wenliang; Boffelli, Marco; Adachi, Tetsuya; Ichioka, Hiroaki; Yamamoto, Toshiro; Marunaka, Yoshinori; Kanamura, Narisato

    2015-05-01

    The Raman spectroscopic method has quantitatively been applied to the analysis of local crystallographic orientation in both single-crystal hydroxyapatite and human teeth. Raman selection rules for all the vibrational modes of the hexagonal structure were expanded into explicit functions of Euler angles in space and six Raman tensor elements (RTE). A theoretical treatment has also been put forward according to the orientation distribution function (ODF) formalism, which allows one to resolve the statistical orientation patterns of the nm-sized hydroxyapatite crystallite comprised in the Raman microprobe. Close-form solutions could be obtained for the Euler angles and their statistical distributions resolved with respect to the direction of the average texture axis. Polarized Raman spectra from single-crystalline hydroxyapatite and textured polycrystalline (teeth enamel) samples were compared, and a validation of the proposed Raman method could be obtained through confirming the agreement between RTE values obtained from different samples.

  9. [Quantitative and qualitative analyses for characteristics of the clock drawing in Alzheimer's disease].

    Science.gov (United States)

    Konagaya, Yoko; Konagaya, Masaaki; Watanabe, Tomoyuki; Washimi, Yukihiko

    2014-01-01

    We analyzed the results of the clock drawing test (CDT) in patients with Alzheimer's disease (AD) by quantitative and qualitative methods to evaluate its significance for cognitive function screening. We administered the CDT and mini-mental state examination (MMSE) to a total of 156 AD patients, and CDT performance was scored quantitatively in accordance with the method by Freedman, while the CDT error types were qualitatively classified by Rouleau's method. We divided AD patients into three groups by their MMSE total score (A: 23 ≤, B: 18~22, C: ≤ 17). The mean total scores of CDT and MMSE in AD were 11.5 ± 3.4 and 19.8 ± 4.7, respectively, and the total CDT scores showed significant positive correlation with the total MMSE scores (r = 0.450). Fewer than 80% of subjects drew the clock correctly for 8 out of 15 sub-items, and fewer were able to correctly draw clock hands than could correctly draw numbers, contour or a center. In analysis of CDT qualitative error types, the most common error types were spatial and/or planning deficit (SPD) (28.2%), and conceptual deficit (CD) (23.7%), which suggested visuospatial impairments and semantic impairments play essential roles in AD patients' poor clock drawings. The frequency of CD and SPD error types significantly increased as severity of cognitive function worsened (p < 0.001, p < 0.05, respectively), and those of stimulus-bound response and perseveration had tendency to increase as severity of cognitive function. The present study suggests that CDT is a useful screening method not only for the impairment of cognitive function and the severity of cognitive dysfunction, but also for identification of specific cognitive function impairments in AD patients.

  10. Quantitative Analyses of Core Promoters Enable Precise Engineering of Regulated Gene Expression in Mammalian Cells

    Science.gov (United States)

    Ede, Christopher; Chen, Ximin; Lin, Meng-Yin; Chen, Yvonne Y.

    2016-01-01

    Inducible transcription systems play a crucial role in a wide array of synthetic biology circuits. However, the majority of inducible promoters are constructed from a limited set of tried-and-true promoter parts, which are susceptible to common shortcomings such as high basal expression levels (i.e., leakiness). To expand the toolbox for regulated mammalian gene expression and facilitate the construction of mammalian genetic circuits with precise functionality, we quantitatively characterized a panel of eight core promoters, including sequences with mammalian, viral, and synthetic origins. We demonstrate that this selection of core promoters can provide a wide range of basal gene expression levels and achieve a gradient of fold-inductions spanning two orders of magnitude. Furthermore, commonly used parts such as minimal CMV and minimal SV40 promoters were shown to achieve robust gene expression upon induction, but also suffer from high levels of leakiness. In contrast, a synthetic promoter, YB_TATA, was shown to combine low basal expression with high transcription rate in the induced state to achieve significantly higher fold-induction ratios compared to all other promoters tested. These behaviors remain consistent when the promoters are coupled to different genetic outputs and different response elements, as well as across different host-cell types and DNA copy numbers. We apply this quantitative understanding of core promoter properties to the successful engineering of human T cells that respond to antigen stimulation via chimeric antigen receptor signaling specifically under hypoxic environments. Results presented in this study can facilitate the design and calibration of future mammalian synthetic biology systems capable of precisely programmed functionality. PMID:26883397

  11. Qualitative and quantitative analyses of flavonoids in Spirodela polyrrhiza by high-performance liquid chromatography coupled with mass spectrometry.

    Science.gov (United States)

    Qiao, Xue; He, Wen-ni; Xiang, Cheng; Han, Jian; Wu, Li-jun; Guo, De-an; Ye, Min

    2011-01-01

    Spirodela polyrrhiza (L.) Schleid. is a traditional Chinese herbal medicine for the treatment of influenza. Despite its wide use in Chinese medicine, no report on quality control of this herb is available so far. To establish qualitative and quantitative analytical methods by high-performance liquid chromatography (HPLC) coupled with mass spectrometry (MS) for the quality control of S. polyrrhiza. The methanol extract of S. polyrrhiza was analysed by HPLC/ESI-MS(n). Flavonoids were identified by comparing with reference standards or according to their MS(n) (n = 2-4) fragmentation behaviours. Based on LC/MS data, a standardised HPLC fingerprint was established by analysing 15 batches of commercial herbal samples. Furthermore, quantitative analysis was conducted by determining five major flavonoids, namely luteolin 8-C-glucoside, apigenin 8-C-glucoside, luteolin 7-O-glucoside, apigenin 7-O-glucoside and luteolin. A total of 18 flavonoids were identified by LC/MS, and 14 of them were reported from this herb for the first time. The HPLC fingerprints contained 10 common peaks, and could differentiate good quality batches from counterfeits. The total contents of five major flavonoids in S. polyrrhiza varied significantly from 4.28 to 19.87 mg/g. Qualitative LC/MS and quantitative HPLC analytical methods were established for the comprehensive quality control of S. polyrrhiza. Copyright © 2011 John Wiley & Sons, Ltd.

  12. Are anti-fouling effects in coralline algae species specific?

    Directory of Open Access Journals (Sweden)

    Alexandre Bigio Villas Bôas

    2004-03-01

    Full Text Available The crustose coralline algae are susceptible to be covered by other algae, which in turn can be affected by anti-fouling effects. In this study the hypothesis tested was that these algae can inhibit the growth of epiphytes in a species specific way. In the laboratory, propagules of Sargassum furcatum and Ulva fasciata were liberated and cultivated on pieces of coralline algae and slide covers (controls and their survival and growth were compared. Spongites and Hydrolithon significantly inhibited the growth of U. fasciata but not Sargassum. In the field, pieces of three species of live and dead coralline algae and their copies in epoxy putty discs were fixed on the rock. After one month epiphytic algae were identified and their dry mass quantified. Lithophyllum did not affect the epiphyte growth. In contrast Spongites and an unidentified coralline significantly inhibited the growth of Enteromorpha spp., Ulva fasciata and Hincksia mitchelliae. Colpomenia sinuosa was absent on all living crusts, but present on controls. Results show that the epiphyte-host relation depends on the species that are interacting. The sloughing of superficial cells of coralline crusts points to the possible action of physical anti-fouling effect, though a chemical one is not rejected.As algas calcárias crostosas são susceptíveis ao recobrimento por outras algas, entretanto, estas podem ser afetadas por efeitos anti-incrustantes. Neste estudo foi testada a hipótese de que estas algas possam inibir o crescimento somente de algumas espécies de epífitas. No laboratório, propágulos de Sargassum furcatum e Ulva fasciata foram liberados e cultivados sobre pedaços de algas calcárias e lamínulas de microscopia (controle e as suas sobrevivência e crescimento comparadas. Spongites e Hydrolithon inibiram significativamente o crescimento de U. fasciata, mas não de Sargassum. No campo, pedaços de três espécies de algas calcárias vivas, mortas e cópias destas em

  13. Age determination by teeth examination: a comparison between different morphologic and quantitative analyses.

    Science.gov (United States)

    Amariti, M L; Restori, M; De Ferrari, F; Paganelli, C; Faglia, R; Legnani, G

    1999-06-01

    Age determination by teeth examination is one of the main means of determining personal identification. Current studies have suggested different techniques for determining the age of a subject by means of the analysis of microscopic and macroscopic structural modifications of the tooth with ageing. The histological approach is useful among the various methodologies utilized for this purpose. It is still unclear as to what is the best technique, as almost all the authors suggest the use of the approach they themselves have tested. In the present study, age determination by means of microscopic techniques has been based on the quantitative analysis of three parameters, all well recognized in specialized literature: 1. dentinal tubules density/sclerosis 2. tooth translucency 3. analysis of the cementum thickness. After a description of the three methodologies (with automatic image processing of the dentinal sclerosis utilizing an appropriate computer program developed by the authors) the results obtained on cases using the three different approaches are presented, and the merits and failings of each technique are identified with the intention of identifying the one offering the least degree of error in age determination.

  14. Quantitative analyses of Streptococcus mutans biofilms with quartz crystal microbalance, microjet impingement and confocal microscopy.

    Science.gov (United States)

    Kreth, J; Hagerman, E; Tam, K; Merritt, J; Wong, D T W; Wu, B M; Myung, N V; Shi, W; Qi, F

    2004-10-01

    Microbial biofilm formation can be influenced by many physiological and genetic factors. The conventional microtiter plate assay provides useful but limited information about biofilm formation. With the fast expansion of the biofilm research field, there are urgent needs for more informative techniques to quantify the major parameters of a biofilm, such as adhesive strength and total biomass. It would be even more ideal if these measurements could be conducted in a real-time, non-invasive manner. In this study, we used quartz crystal microbalance (QCM) and microjet impingement (MJI) to measure total biomass and adhesive strength, respectively, of S. mutans biofilms formed under different sucrose concentrations. In conjunction with confocal laser scanning microscopy (CLSM) and the COMSTAT software, we show that sucrose concentration affects the biofilm strength, total biomass, and architecture in both qualitative and quantitative manners. Our data correlate well with previous observations about the effect of sucrose on the adherence of S. mutans to the tooth surface, and demonstrate that QCM is a useful tool for studying the kinetics of biofilm formation in real time and that MJI is a sensitive, easy-to-use device to measure the adhesive strength of a biofilm.

  15. Global earthquake casualties due to secondary effects: A quantitative analysis for improving rapid loss analyses

    Science.gov (United States)

    Marano, K.D.; Wald, D.J.; Allen, T.I.

    2010-01-01

    This study presents a quantitative and geospatial description of global losses due to earthquake-induced secondary effects, including landslide, liquefaction, tsunami, and fire for events during the past 40 years. These processes are of great importance to the US Geological Survey's (USGS) Prompt Assessment of Global Earthquakes for Response (PAGER) system, which is currently being developed to deliver rapid earthquake impact and loss assessments following large/significant global earthquakes. An important question is how dominant are losses due to secondary effects (and under what conditions, and in which regions)? Thus, which of these effects should receive higher priority research efforts in order to enhance PAGER's overall assessment of earthquakes losses and alerting for the likelihood of secondary impacts? We find that while 21.5% of fatal earthquakes have deaths due to secondary (non-shaking) causes, only rarely are secondary effects the main cause of fatalities. The recent 2004 Great Sumatra-Andaman Islands earthquake is a notable exception, with extraordinary losses due to tsunami. The potential for secondary hazards varies greatly, and systematically, due to regional geologic and geomorphic conditions. Based on our findings, we have built country-specific disclaimers for PAGER that address potential for each hazard (Earle et al., Proceedings of the 14th World Conference of the Earthquake Engineering, Beijing, China, 2008). We will now focus on ways to model casualties from secondary effects based on their relative importance as well as their general predictability. ?? Springer Science+Business Media B.V. 2009.

  16. Furthering the investigation of eruption styles through quantitative shape analyses of volcanic ash particles

    Science.gov (United States)

    Nurfiani, D.; Bouvet de Maisonneuve, C.

    2018-04-01

    Volcanic ash morphology has been quantitatively investigated for various aims such as studying the settling velocity of ash for modelling purposes and understanding the fragmentation processes at the origin of explosive eruptions. In an attempt to investigate the usefulness of ash morphometry for monitoring purposes, we analyzed the shape of volcanic ash particles through a combination of (1) traditional shape descriptors such as solidity, convexity, axial ratio and form factor and (2) fractal analysis using the Euclidean Distance transform (EDT) method. We compare ash samples from the hydrothermal eruptions of Iwodake (Japan) in 2013, Tangkuban Perahu (Indonesia) in 2013 and Marapi (Sumatra, Indonesia) in 2015, the dome explosions of Merapi (Java, Indonesia) in 2013, the Vulcanian eruptions of Merapi in 2010 and Tavurvur (Rabaul, Papaua New Guinea) in 2014, and the Plinian eruption of Kelud (Indonesia) in 2014. Particle size and shape measurements were acquired from a Particle Size Analyzer with a microscope camera attached to the instrument. Clear differences between dense/blocky particles from hydrothermal or dome explosions and vesicular particles produced by the fragmentation of gas-bearing molten magma are well highlighted by conventional shape descriptors and the fractal method. In addition, subtle differences between dense/blocky particles produced by hydrothermal explosions, dome explosions, or quench granulation during phreatomagmatic eruptions can be evidenced with the fractal method. The combination of shape descriptors and fractal analysis is therefore potentially able to distinguish between juvenile and non-juvenile magma, which is of importance for eruption monitoring.

  17. On the road to quantitative genetic/genomic analyses of root growth and development components underlying root architecture

    International Nuclear Information System (INIS)

    Draye, X.; Dorlodot, S. de; Lavigne, T.

    2006-01-01

    The quantitative genetic and functional genomic analyses of root development, growth and plasticity will be instrumental in revealing the major regulatory pathways of root architecture. Such knowledge, combined with in-depth consideration of root physiology (e.g. uptake, exsudation), form (space-time dynamics of soil exploration) and ecology (including root environment), will settle the bases for designing root ideotypes for specific environments, for low-input agriculture or for successful agricultural production with minimal impact on the environment. This report summarizes root research initiated in our lab between 2000 and 2004 in the following areas: quantitative analysis of root branching in bananas, high throughput characterisation of root morphology, image analysis, QTL mapping of detailed features of root architecture in rice, and attempts to settle a Crop Root Research Consortium. (author)

  18. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

    Directory of Open Access Journals (Sweden)

    Fagen Li

    Full Text Available Dense genetic maps, along with quantitative trait loci (QTLs detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR, expressed sequence tag (EST derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS, and diversity arrays technology (DArT markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age and wood density (56 months were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

  19. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus

    Science.gov (United States)

    Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

    2015-01-01

    Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10–56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa. PMID:26695430

  20. Analyses of musculoskeletal interactions in humans by quantitative computed tomography (QCT)

    International Nuclear Information System (INIS)

    Capiglioni, Ricardo; Cointry, Gustavo; Capozza, Ricardo; Gimenez, Carlos; Ferretti, Jose L.

    2001-01-01

    Bone and muscle cross-sectional properties were assessed by QCT at the L3 spinal level in normal women and men (n=93/5) aged 32-74 years and compared with the kyphosis angle (Ka) determined between T4 and T12 in lateral Rx's. The volumetric mineral density (vBMD) of trabecular bone, the bone mineral content (BMC) of the vertebral bodies and the fat-free areas of the peri spinal muscle (FFMA) varied in line and correlated negatively with the Ka. Multiple regression analyses showed that the trabecular vBMD and total BMC were the most significant independent determinants of the Ka, and that the FFMA and time since menopause were the only independent determinants of the bone properties, with no influence of the gender, age or anthropometric factors. (author)

  1. Stability Test and Quantitative and Qualitative Analyses of the Amino Acids in Pharmacopuncture Extracted from Scolopendra subspinipes mutilans

    Science.gov (United States)

    Cho, GyeYoon; Han, KyuChul; Yoon, JinYoung

    2015-01-01

    Objectives: Scolopendra subspinipes mutilans (S. subspinipes mutilans) is known as a traditional medicine and includes various amino acids, peptides and proteins. The amino acids in the pharmacopuncture extracted from S. subspinipes mutilans by using derivatization methods were analyzed quantitatively and qualitatively by using high performance liquid chromatography (HPLC) over a 12 month period to confirm its stability. Methods: Amino acids of pharmacopuncture extracted from S. subspinipes mutilans were derived by using O-phthaldialdehyde (OPA) & 9-fluorenyl methoxy carbonyl chloride (FMOC) reagent and were analyzed using HPLC. The amino acids were detected by using a diode array detector (DAD) and a fluorescence detector (FLD) to compare a mixed amino acid standard (STD) to the pharmacopuncture from centipedes. The stability tests on the pharmacopuncture from centipedes were done using HPLC for three conditions: a room temperature test chamber, an acceleration test chamber, and a cold test chamber. Results: The pharmacopuncture from centipedes was prepared by using the method of the Korean Pharmacopuncture Institute (KPI) and through quantitative analyses was shown to contain 9 amino acids of the 16 amino acids in the mixed amino acid STD. The amounts of the amino acids in the pharmacopuncture from centipedes were 34.37 ppm of aspartate, 123.72 ppm of arginine, 170.63 ppm of alanine, 59.55 ppm of leucine and 57 ppm of lysine. The relative standard deviation (RSD %) results for the pharmacopuncture from centipedes had a maximum value of 14.95% and minimum value of 1.795% on the room temperature test chamber, the acceleration test chamber and the cold test chamber stability tests. Conclusion: Stability tests on and quantitative and qualitative analyses of the amino acids in the pharmacopuncture extracted from centipedes by using derivatization methods were performed by using HPLC. Through research, we hope to determine the relationship between time and the

  2. Subcellular location and species specificity of pipecolate degradation

    International Nuclear Information System (INIS)

    Mihalik, S.J.; Rhead, W.J.

    1986-01-01

    Defects in pipecolic acid (PA) catabolism are characteristic of several inherited metabolic diseases including hyperpipecolic acidemia, Zellweger's Syndrome, neonatal-onset adrenoleukodystrophy, and infantile Refsum's disease. In the latter three diseases, peroxisomes are abnormal. The authors have studied the subcelluar distribution of the PA degradation to determine a mammalian model for the normal pathway. Crude light and heavy mitochondrial fractions (including lysosomes and peroxisomes) from kidney cortex or liver were separated on Percoll gradients. Individual fractions were then incubated at 37 0 C with 3H-2,3,4,5,6 L-PA. Using ion exchange chromatography, the production of 3H α-aminoadipic acid (AAA) and 3H-H2O were quantitated. AAA production paralleled the activity of the mitochondrial marker enzyme, glutamate dehydrogenase, in the rabbit, guinea pig, dog, pig, and sheep. 3H-AAA production ranged from 382 to 13,900 pmol/mg prot/h. Guinea pig kidney cortex exhibited highest specific activity. The mitochondrial enzyme was absent from human liver (n=3) and liver and kidney cortex from rat, mouse, and monkey. In these tissues, the activity followed the pattern of the peroxisomal core enzyme, urate oxidase

  3. Species-specific escape of Plasmodium sporozoites from oocysts of avian, rodent, and human malarial parasites.

    Science.gov (United States)

    Orfano, Alessandra S; Nacif-Pimenta, Rafael; Duarte, Ana P M; Villegas, Luis M; Rodrigues, Nilton B; Pinto, Luciana C; Campos, Keillen M M; Pinilla, Yudi T; Chaves, Bárbara; Barbosa Guerra, Maria G V; Monteiro, Wuelton M; Smith, Ryan C; Molina-Cruz, Alvaro; Lacerda, Marcus V G; Secundino, Nágila F C; Jacobs-Lorena, Marcelo; Barillas-Mury, Carolina; Pimenta, Paulo F P

    2016-08-02

    Malaria is transmitted when an infected mosquito delivers Plasmodium sporozoites into a vertebrate host. There are many species of Plasmodium and, in general, the infection is host-specific. For example, Plasmodium gallinaceum is an avian parasite, while Plasmodium berghei infects mice. These two parasites have been extensively used as experimental models of malaria transmission. Plasmodium falciparum and Plasmodium vivax are the most important agents of human malaria, a life-threatening disease of global importance. To complete their life cycle, Plasmodium parasites must traverse the mosquito midgut and form an oocyst that will divide continuously. Mature oocysts release thousands of sporozoites into the mosquito haemolymph that must reach the salivary gland to infect a new vertebrate host. The current understanding of the biology of oocyst formation and sporozoite release is mostly based on experimental infections with P. berghei, and the conclusions are generalized to other Plasmodium species that infect humans without further morphological analyses. Here, it is described the microanatomy of sporozoite escape from oocysts of four Plasmodium species: the two laboratory models, P. gallinaceum and P. berghei, and the two main species that cause malaria in humans, P. vivax and P. falciparum. It was found that sporozoites have species-specific mechanisms of escape from the oocyst. The two model species of Plasmodium had a common mechanism, in which the oocyst wall breaks down before sporozoites emerge. In contrast, P. vivax and P. falciparum sporozoites show a dynamic escape mechanism from the oocyst via polarized propulsion. This study demonstrated that Plasmodium species do not share a common mechanism of sporozoite escape, as previously thought, but show complex and species-specific mechanisms. In addition, the knowledge of this phenomenon in human Plasmodium can facilitate transmission-blocking studies and not those ones only based on the murine and avian models.

  4. Analyse quantitative des effluents de pyrolyse en milieu ouvert et fermé Quantitative Analysis of Pyrolysis Effluents in an Open and Closed System

    Directory of Open Access Journals (Sweden)

    Behar F.

    2006-11-01

    Full Text Available Dans la première partie de l'article, nous décrivons une technique de pyrolyse en milieu ouvert qui permet de caractériser les matières organiques complexes comme le kérogène, le charbon, les asphaltènes de roche et d'huiles, les substances humiques et fulviques etc. Les effluents de pyrolyse sont récupérés et fractionnés quantitativement puis analysés par des techniques spécifiques comme la chromatographie en phase gazeuse et le couplage chromatographie/spectrométrie de masse. Dans la deuxième partie, est présentée une technique de pyrolyse en milieu fermé pour simuler au laboratoire l'évolution thermique des kérogènes, asphaltènes ou huiles. Nous nous sommes surtout attachés à dresser des bilans massiques et des bilans de l'hydrogène sur l'ensemble des produits de pyrolyse. Pour cela, nous avons distingué cinq classes de poids moléculaire croissant : C1, C2-C5, C6-C13, C14+ et coke. La récupération quantitative et la séparation de chacune des cinq fractions permet une analyse moléculaire détaillée de chacune d'elles. The first part of this article describes an open pyrolysis system in order to characterize complex organic matter such as kerogen, coal, rock and oil asphaltenes and humic substances, etc. Pyrolysis effluents are recovered, fractionated quantitatively by liquid chromatography, and then they are analyzed by specific techniques such as gas chromatography and chromatography/mass-spectrometry coupling. The second part describes a pyrolysis technique in a closed system, used for the laboratory simulation of the thermal evolution of kerogens, asphaltenes or oils. A special effort has been made to give the mass and hydrogen balances for all pyrolysis products. For this, five classes have been distinguised with increasing molecular weight: C1, C2-C5, C6-C13, C14+ and coke. The quantitative recovery and the separation of each of the five fractions is used to make a detailed molecular analysis of each of

  5. Cloning, characterisation, and comparative quantitative expression analyses of receptor for advanced glycation end products (RAGE) transcript forms.

    Science.gov (United States)

    Sterenczak, Katharina A; Willenbrock, Saskia; Barann, Matthias; Klemke, Markus; Soller, Jan T; Eberle, Nina; Nolte, Ingo; Bullerdiek, Jörn; Murua Escobar, Hugo

    2009-04-01

    RAGE is a member of the immunoglobulin superfamily of cell surface molecules playing key roles in pathophysiological processes, e.g. immune/inflammatory disorders, Alzheimer's disease, diabetic arteriosclerosis and tumourigenesis. In humans 19 naturally occurring RAGE splicing variants resulting in either N-terminally or C-terminally truncated proteins were identified and are lately discussed as mechanisms for receptor regulation. Accordingly, deregulation of sRAGE levels has been associated with several diseases e.g. Alzheimer's disease, Type 1 diabetes, and rheumatoid arthritis. Administration of recombinant sRAGE to animal models of cancer blocked tumour growth successfully. In spite of its obvious relationship to cancer and metastasis data focusing sRAGE deregulation and tumours is rare. In this study we screened a set of tumours, healthy tissues and various cancer cell lines for RAGE splicing variants and analysed their structure. Additionally, we analysed the ratio of the mainly found transcript variants using quantitative Real-Time PCR. In total we characterised 24 previously not described canine and 4 human RAGE splicing variants, analysed their structure, classified their characteristics, and derived their respective protein forms. Interestingly, the healthy and the neoplastic tissue samples showed in majority RAGE transcripts coding for the complete receptor and transcripts showing insertions of intron 1.

  6. Quantitative characterization of colloidal assembly of graphene oxide-silver nanoparticle hybrids using aerosol differential mobility-coupled mass analyses.

    Science.gov (United States)

    Nguyen, Thai Phuong; Chang, Wei-Chang; Lai, Yen-Chih; Hsiao, Ta-Chih; Tsai, De-Hao

    2017-10-01

    In this work, we develop an aerosol-based, time-resolved ion mobility-coupled mass characterization method to investigate colloidal assembly of graphene oxide (GO)-silver nanoparticle (AgNP) hybrid nanostructure on a quantitative basis. Transmission electron microscopy (TEM) and zeta potential (ZP) analysis were used to provide visual information and elemental-based particle size distributions, respectively. Results clearly show a successful controlled assembly of GO-AgNP by electrostatic-directed heterogeneous aggregation between GO and bovine serum albumin (BSA)-functionalized AgNP under an acidic environment. Additionally, physical size, mass, and conformation (i.e., number of AgNP per nanohybrid) of GO-AgNP were shown to be proportional to the number concentration ratio of AgNP to GO (R) and the selected electrical mobility diameter. An analysis of colloidal stability of GO-AgNP indicates that the stability increased with its absolute ZP, which was dependent on R and environmental pH. The work presented here provides a proof of concept for systematically synthesizing hybrid colloidal nanomaterials through the tuning of surface chemistry in aqueous phase with the ability in quantitative characterization. Graphical Abstract Colloidal assembly of graphene oxide-silver nanoparticle hybrids characterized by aerosol differential mobility-coupled mass analyses.

  7. Gene Set Analyses of Genome-Wide Association Studies on 49 Quantitative Traits Measured in a Single Genetic Epidemiology Dataset

    Directory of Open Access Journals (Sweden)

    Jihye Kim

    2013-09-01

    Full Text Available Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait (pcorr < 0.05. Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.

  8. Quantitative X-ray Map Analyser (Q-XRMA): A new GIS-based statistical approach to Mineral Image Analysis

    Science.gov (United States)

    Ortolano, Gaetano; Visalli, Roberto; Godard, Gaston; Cirrincione, Rosolino

    2018-06-01

    We present a new ArcGIS®-based tool developed in the Python programming language for calibrating EDS/WDS X-ray element maps, with the aim of acquiring quantitative information of petrological interest. The calibration procedure is based on a multiple linear regression technique that takes into account interdependence among elements and is constrained by the stoichiometry of minerals. The procedure requires an appropriate number of spot analyses for use as internal standards and provides several test indexes for a rapid check of calibration accuracy. The code is based on an earlier image-processing tool designed primarily for classifying minerals in X-ray element maps; the original Python code has now been enhanced to yield calibrated maps of mineral end-members or the chemical parameters of each classified mineral. The semi-automated procedure can be used to extract a dataset that is automatically stored within queryable tables. As a case study, the software was applied to an amphibolite-facies garnet-bearing micaschist. The calibrated images obtained for both anhydrous (i.e., garnet and plagioclase) and hydrous (i.e., biotite) phases show a good fit with corresponding electron microprobe analyses. This new GIS-based tool package can thus find useful application in petrology and materials science research. Moreover, the huge quantity of data extracted opens new opportunities for the development of a thin-section microchemical database that, using a GIS platform, can be linked with other major global geoscience databases.

  9. Joint analyses of open comments and quantitative data: Added value in a job satisfaction survey of hospital professionals.

    Directory of Open Access Journals (Sweden)

    Ingrid Gilles

    Full Text Available To obtain a comprehensive understanding of the job opinions of hospital professionals by conducting qualitative analyses of the open comments included in a job satisfaction survey and combining these results with the quantitative results.A cross-sectional survey targeting all Lausanne University Hospital professionals was performed in the fall of 2013.The survey considered ten job satisfaction dimensions (e.g. self-fulfilment, workload, management, work-related burnout, organisational commitment, intent to stay and included an open comment section. Computer-assisted qualitative analyses were conducted on these comments. Satisfaction rates on the included dimensions and professional groups were entered as predictive variables in the qualitative analyses.Of 10 838 hospital professionals, 4978 participated in the survey and 1067 provided open comments. Data from 1045 respondents with usable comments constituted the analytic sample (133 physicians, 393 nurses, 135 laboratory technicians, 247 administrative staff, including researchers, 67 logistic staff, 44 psycho-social workers, and 26 unspecified.Almost a third of the comments addressed scheduling issues, mostly related to problems and exhaustion linked to shifts, work-life balance, and difficulties with colleagues' absences and the consequences for quality of care and patient safety. The other two-thirds related to classic themes included in job satisfaction surveys. Although some comments were provided equally by all professional groups, others were group specific: work and hierarchy pressures for physicians, healthcare quality and patient safety for nurses, skill recognition for administrative staff. Overall, respondents' comments were consistent with their job satisfaction ratings.Open comment analysis provides a comprehensive understanding of hospital professionals' job experiences, allowing better consideration of quality initiatives that match the needs of professionals with reality.

  10. Joint analyses of open comments and quantitative data: Added value in a job satisfaction survey of hospital professionals.

    Science.gov (United States)

    Gilles, Ingrid; Mayer, Mauro; Courvoisier, Nelly; Peytremann-Bridevaux, Isabelle

    2017-01-01

    To obtain a comprehensive understanding of the job opinions of hospital professionals by conducting qualitative analyses of the open comments included in a job satisfaction survey and combining these results with the quantitative results. A cross-sectional survey targeting all Lausanne University Hospital professionals was performed in the fall of 2013. The survey considered ten job satisfaction dimensions (e.g. self-fulfilment, workload, management, work-related burnout, organisational commitment, intent to stay) and included an open comment section. Computer-assisted qualitative analyses were conducted on these comments. Satisfaction rates on the included dimensions and professional groups were entered as predictive variables in the qualitative analyses. Of 10 838 hospital professionals, 4978 participated in the survey and 1067 provided open comments. Data from 1045 respondents with usable comments constituted the analytic sample (133 physicians, 393 nurses, 135 laboratory technicians, 247 administrative staff, including researchers, 67 logistic staff, 44 psycho-social workers, and 26 unspecified). Almost a third of the comments addressed scheduling issues, mostly related to problems and exhaustion linked to shifts, work-life balance, and difficulties with colleagues' absences and the consequences for quality of care and patient safety. The other two-thirds related to classic themes included in job satisfaction surveys. Although some comments were provided equally by all professional groups, others were group specific: work and hierarchy pressures for physicians, healthcare quality and patient safety for nurses, skill recognition for administrative staff. Overall, respondents' comments were consistent with their job satisfaction ratings. Open comment analysis provides a comprehensive understanding of hospital professionals' job experiences, allowing better consideration of quality initiatives that match the needs of professionals with reality.

  11. Species-specific nested PCR as a diagnostic tool for Brucella ovis infection in rams

    Directory of Open Access Journals (Sweden)

    L.F. Costa

    2013-02-01

    Full Text Available The aim of the present study was to evaluate a species-specific nested PCR based on a previously described species-specific PCR for detection of B. ovis in semen and urine samples of experimentally infected rams. The performance of the species-specific nested PCR was compared with the results of a genus-specific PCR. Fourteen rams were experimentally infected with the Brucella ovis REO 198 strain and samples of semen and urine were collected every week up to 180 days post infection. Out of 83 semen samples collected, 42 (50.6% were positive for the species-specific nested PCR, and 23 (27.7% were positive for the genus-specific PCR. Out of 75 urine samples, 49 (65.3% were positive for the species-specific nested PCR, whereas 11 (14.6% were genus-specific PCR positive. Species-specific nested PCR was significantly more sensitive (P<0.001 than the genus-specific PCR in semen and urine from experimentally infected rams. In conclusion, the species-specific nested PCR developed in this study may be used as a diagnostic tool for the detection of B. ovis in semen and urine samples from suspected rams.

  12. Underutilisation of routinely collected data in the HIV programme in Zambia: a review of quantitatively analysed peer-reviewed articles.

    Science.gov (United States)

    Munthali, Tendai; Musonda, Patrick; Mee, Paul; Gumede, Sehlulekile; Schaap, Ab; Mwinga, Alwyn; Phiri, Caroline; Kapata, Nathan; Michelo, Charles; Todd, Jim

    2017-06-13

    The extent to which routinely collected HIV data from Zambia has been used in peer-reviewed published articles remains unexplored. This paper is an analysis of peer-reviewed articles that utilised routinely collected HIV data from Zambia within six programme areas from 2004 to 2014. Articles on HIV, published in English, listed in the Directory of open access journals, African Journals Online, Google scholar, and PubMed were reviewed. Only articles from peer-reviewed journals, that utilised routinely collected data and included quantitative data analysis methods were included. Multi-country studies involving Zambia and another country, where the specific results for Zambia were not reported, as well as clinical trials and intervention studies that did not take place under routine care conditions were excluded, although community trials which referred patients to the routine clinics were included. Independent extraction was conducted using a predesigned data collection form. Pooled analysis was not possible due to diversity in topics reviewed. A total of 69 articles were extracted for review. Of these, 7 were excluded. From the 62 articles reviewed, 39 focused on HIV treatment and retention in care, 15 addressed prevention of mother-to-child transmission, 4 assessed social behavioural change, and 4 reported on voluntary counselling and testing. In our search, no articles were found on condom programming or voluntary male medical circumcision. The most common outcome measures reported were CD4+ count, clinical failure or mortality. The population analysed was children in 13 articles, women in 16 articles, and both adult men and women in 33 articles. During the 10 year period of review, only 62 articles were published analysing routinely collected HIV data in Zambia. Serious consideration needs to be made to maximise the utility of routinely collected data, and to benefit from the funds and efforts to collect these data. This could be achieved with government support

  13. Quantitative analyses at baseline and interim PET evaluation for response assessment and outcome definition in patients with malignant pleural mesothelioma

    Energy Technology Data Exchange (ETDEWEB)

    Lopci, Egesta; Chiti, Arturo [Humanitas Research Hospital, Nuclear Medicine Department, Rozzano, Milan (Italy); Zucali, Paolo Andrea; Perrino, Matteo; Gianoncelli, Letizia; Lorenzi, Elena; Gemelli, Maria; Santoro, Armando [Humanitas Research Hospital, Oncology, Rozzano (Italy); Ceresoli, Giovanni Luca [Humanitas Gavazzeni, Oncology, Bergamo (Italy); Giordano, Laura [Humanitas Research Hospital, Biostatistics, Rozzano (Italy)

    2015-04-01

    Quantitative analyses on FDG PET for response assessment are increasingly used in clinical studies, particularly with respect to tumours in which radiological assessment is challenging and complete metabolic response is rarely achieved after treatment. A typical example is malignant pleural mesothelioma (MPM), an aggressive tumour originating from mesothelial cells of the pleura. We present our results concerning the use of semiquantitative and quantitative parameters, evaluated at the baseline and interim PET examinations, for the prediction of treatment response and disease outcome in patients with MPM. We retrospectively analysed data derived from 131 patients (88 men, 43 women; mean age 66 years) with MPM who were referred to our institution for treatment between May 2004 and July 2013. Patients were investigated using FDG PET at baseline and after two cycles of pemetrexed-based chemotherapy. Responses were determined using modified RECIST criteria based on the best CT response after treatment. Disease control rate, progression-free survival (PFS) and overall survival (OS) were calculated for the whole population and were correlated with semiquantitative and quantitative parameters evaluated at the baseline and interim PET examinations; these included SUV{sub max}, total lesion glycolysis (TLG), percentage change in SUV{sub max} (ΔSUV{sub max}) and percentage change in TLG (ΔTLG). Disease control was achieved in 84.7 % of the patients, and median PFS and OS for the entire cohort were 7.2 and 14.3 months, respectively. The log-rank test showed a statistically significant difference in PFS between patients with radiological progression and those with partial response (PR) or stable disease (SD) (1.8 vs. 8.6 months, p < 0.001). Baseline SUV{sub max} and TLG showed a statistically significant correlation with PFS and OS (p < 0.001). In the entire population, both ΔSUV{sub max} and ΔTLG were correlated with disease control based on best CT response (p < 0

  14. Combined Metabonomic and Quantitative RT-PCR Analyses Revealed Metabolic Reprogramming Associated with Fusarium graminearum Resistance in Transgenic Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Fangfang Chen

    2018-01-01

    Full Text Available Fusarium head blight disease resulting from Fusarium graminearum (FG infection causes huge losses in global production of cereals and development of FG-resistant plants is urgently needed. To understand biochemistry mechanisms for FG resistance, here, we have systematically investigated the plant metabolomic phenotypes associated with FG resistance for transgenic Arabidopsis thaliana expressing a class-I chitinase (Chi, a Fusarium-specific recombinant antibody gene (CWP2 and fused Chi-CWP2. Plant disease indices, mycotoxin levels, metabonomic characteristics, and expression levels of several key genes were measured together with their correlations. We found that A. thaliana expressing Chi-CWP2 showed higher FG resistance with much lower disease indices and mycotoxin levels than the wild-type and the plants expressing Chi or CWP2 alone. The combined metabonomic and quantitative RT-PCR analyses revealed that such FG-resistance was closely associated with the promoted biosynthesis of secondary metabolites (phenylpropanoids, alkanoids and organic osmolytes (proline, betaine, glucose, myo-inositol together with enhanced TCA cycle and GABA shunt. These suggest that the concurrently enhanced biosyntheses of the shikimate-mediated secondary metabolites and organic osmolytes be an important strategy for A. thaliana to develop and improve FG resistance. These findings provide essential biochemical information related to FG resistance which is important for developing FG-resistant cereals.

  15. How do trees grow? Response from the graphical and quantitative analyses of computed tomography scanning data collected on stem sections.

    Science.gov (United States)

    Dutilleul, Pierre; Han, Li Wen; Beaulieu, Jean

    2014-06-01

    Tree growth, as measured via the width of annual rings, is used for environmental impact assessment and climate back-forecasting. This fascinating natural process has been studied at various scales in the stem (from cell and fiber within a growth ring, to ring and entire stem) in one, two, and three dimensions. A new approach is presented to study tree growth in 3D from stem sections, at a scale sufficiently small to allow the delineation of reliable limits for annual rings and large enough to capture directional variation in growth rates. The technology applied is computed tomography scanning, which provides - for one stem section - millions of data (indirect measures of wood density) that can be mapped, together with a companion measure of dispersion and growth ring limits in filigree. Graphical and quantitative analyses are reported for white spruce trees with circular vs non-circular growth. Implications for dendroclimatological research are discussed. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  16. Impact of vaccine herd-protection effects in cost-effectiveness analyses of childhood vaccinations. A quantitative comparative analysis.

    Science.gov (United States)

    Holubar, Marisa; Stavroulakis, Maria Christina; Maldonado, Yvonne; Ioannidis, John P A; Contopoulos-Ioannidis, Despina

    2017-01-01

    Inclusion of vaccine herd-protection effects in cost-effectiveness analyses (CEAs) can impact the CEAs-conclusions. However, empirical epidemiologic data on the size of herd-protection effects from original studies are limited. We performed a quantitative comparative analysis of the impact of herd-protection effects in CEAs for four childhood vaccinations (pneumococcal, meningococcal, rotavirus and influenza). We considered CEAs reporting incremental-cost-effectiveness-ratios (ICERs) (per quality-adjusted-life-years [QALY] gained; per life-years [LY] gained or per disability-adjusted-life-years [DALY] avoided), both with and without herd protection, while keeping all other model parameters stable. We calculated the size of the ICER-differences without vs with-herd-protection and estimated how often inclusion of herd-protection led to crossing of the cost-effectiveness threshold (of an assumed societal-willingness-to-pay) of $50,000 for more-developed countries or X3GDP/capita (WHO-threshold) for less-developed countries. We identified 35 CEA studies (20 pneumococcal, 4 meningococcal, 8 rotavirus and 3 influenza vaccines) with 99 ICER-analyses (55 per-QALY, 27 per-LY and 17 per-DALY). The median ICER-absolute differences per QALY, LY and DALY (without minus with herd-protection) were $15,620 (IQR: $877 to $48,376); $54,871 (IQR: $787 to $115,026) and $49 (IQR: $15 to $1,636) respectively. When the target-vaccination strategy was not cost-saving without herd-protection, inclusion of herd-protection always resulted in more favorable results. In CEAs that had ICERs above the cost-effectiveness threshold without herd-protection, inclusion of herd-protection led to crossing of that threshold in 45% of the cases. This impacted only CEAs for more developed countries, as all but one CEAs for less developed countries had ICERs below the WHO-cost-effectiveness threshold even without herd-protection. In several analyses, recommendation for the adoption of the target

  17. Diagnostic Performance and Utility of Quantitative EEG Analyses in Delirium: Confirmatory Results From a Large Retrospective Case-Control Study.

    Science.gov (United States)

    Fleischmann, Robert; Tränkner, Steffi; Bathe-Peters, Rouven; Rönnefarth, Maria; Schmidt, Sein; Schreiber, Stephan J; Brandt, Stephan A

    2018-03-01

    The lack of objective disease markers is a major cause of misdiagnosis and nonstandardized approaches in delirium. Recent studies conducted in well-selected patients and confined study environments suggest that quantitative electroencephalography (qEEG) can provide such markers. We hypothesize that qEEG helps remedy diagnostic uncertainty not only in well-defined study cohorts but also in a heterogeneous hospital population. In this retrospective case-control study, EEG power spectra of delirious patients and age-/gender-matched controls (n = 31 and n = 345, respectively) were fitted in a linear model to test their performance as binary classifiers. We subsequently evaluated the diagnostic performance of the best classifiers in control samples with normal EEGs (n = 534) and real-world samples including pathologic findings (n = 4294). Test reliability was estimated through split-half analyses. We found that the combination of spectral power at F3-P4 at 2 Hz (area under the curve [AUC] = .994) and C3-O1 at 19 Hz (AUC = .993) provided a sensitivity of 100% and a specificity of 99% to identify delirious patients among normal controls. These classifiers also yielded a false positive rate as low as 5% and increased the pretest probability of being delirious by 57% in an unselected real-world sample. Split-half reliabilities were .98 and .99, respectively. This retrospective study yielded preliminary evidence that qEEG provides excellent diagnostic performance to identify delirious patients even outside confined study environments. It furthermore revealed reduced beta power as a novel specific finding in delirium and that a normal EEG excludes delirium. Prospective studies including parameters of pretest probability and delirium severity are required to elaborate on these promising findings.

  18. A QUANTITATIVE METHOD FOR ANALYSING 3-D BRANCHING IN EMBRYONIC KIDNEYS: DEVELOPMENT OF A TECHNIQUE AND PRELIMINARY DATA

    Directory of Open Access Journals (Sweden)

    Gabriel Fricout

    2011-05-01

    Full Text Available The normal human adult kidney contains between 300,000 and 1 million nephrons (the functional units of the kidney. Nephrons develop at the tips of the branching ureteric duct, and therefore ureteric duct branching morphogenesis is critical for normal kidney development. Current methods for analysing ureteric branching are mostly qualitative and those quantitative methods that do exist do not account for the 3- dimensional (3D shape of the ureteric "tree". We have developed a method for measuring the total length of the ureteric tree in 3D. This method is described and preliminary data are presented. The algorithm allows for performing a semi-automatic segmentation of a set of grey level confocal images and an automatic skeletonisation of the resulting binary object. Measurements of length are automatically obtained, and numbers of branch points are manually counted. The final representation can be reconstructed by means of 3D volume rendering software, providing a fully rotating 3D perspective of the skeletonised tree, making it possible to identify and accurately measure branch lengths. Preliminary data shows the total length estimates obtained with the technique to be highly reproducible. Repeat estimates of total tree length vary by just 1-2%. We will now use this technique to further define the growth of the ureteric tree in vitro, under both normal culture conditions, and in the presence of various levels of specific molecules suspected of regulating ureteric growth. The data obtained will provide fundamental information on the development of renal architecture, as well as the regulation of nephron number.

  19. Molecular detection and species-specific identification of medically important Aspergillus species by real-time PCR in experimental invasive pulmonary aspergillosis.

    Science.gov (United States)

    Walsh, Thomas J; Wissel, Mark C; Grantham, Kevin J; Petraitiene, Ruta; Petraitis, Vidmantas; Kasai, Miki; Francesconi, Andrea; Cotton, Margaret P; Hughes, Johanna E; Greene, Lora; Bacher, John D; Manna, Pradip; Salomoni, Martin; Kleiboeker, Steven B; Reddy, Sushruth K

    2011-12-01

    Diagnosis of invasive pulmonary aspergillosis (IPA) remains a major challenge to clinical microbiology laboratories. We developed rapid and sensitive quantitative PCR (qPCR) assays for genus- and species-specific identification of Aspergillus infections by use of TaqMan technology. In order to validate these assays and understand their potential diagnostic utility, we then performed a blinded study of bronchoalveolar lavage (BAL) fluid specimens from well-characterized models of IPA with the four medically important species. A set of real-time qPCR primers and probes was developed by utilizing unique ITS1 regions for genus- and species-specific detection of the four most common medically important Aspergillus species (Aspergillus fumigatus, A. flavus, A. niger, and A. terreus). Pan-Aspergillus and species-specific qPCRs with BAL fluid were more sensitive than culture for detection of IPA caused by A. fumigatus in untreated (P < 0.0007) and treated (P ≤ 0.008) animals, respectively. For infections caused by A. terreus and A. niger, culture and PCR amplification from BAL fluid yielded similar sensitivities for untreated and treated animals. Pan-Aspergillus PCR was more sensitive than culture for detection of A. flavus in treated animals (P = 0.002). BAL fluid pan-Aspergillus and species-specific PCRs were comparable in sensitivity to BAL fluid galactomannan (GM) assay. The copy numbers from the qPCR assays correlated with quantitative cultures to determine the pulmonary residual fungal burdens in lung tissue. Pan-Aspergillus and species-specific qPCR assays may improve the rapid and accurate identification of IPA in immunocompromised patients.

  20. Quantitative DNA methylation analyses reveal stage dependent DNA methylation and association to clinico-pathological factors in breast tumors

    International Nuclear Information System (INIS)

    Klajic, Jovana; Tost, Jörg; Kristensen, Vessela N; Fleischer, Thomas; Dejeux, Emelyne; Edvardsen, Hege; Warnberg, Fredrik; Bukholm, Ida; Lønning, Per Eystein; Solvang, Hiroko; Børresen-Dale, Anne-Lise

    2013-01-01

    Aberrant DNA methylation of regulatory genes has frequently been found in human breast cancers and correlated to clinical outcome. In the present study we investigate stage specific changes in the DNA methylation patterns in order to identify valuable markers to understand how these changes affect breast cancer progression. Quantitative DNA methylation analyses of 12 candidate genes ABCB1, BRCCA1, CDKN2A, ESR1, GSTP1, IGF2, MGMT, HMLH1, PPP2R2B, PTEN, RASSF1A and FOXC1 was performed by pyrosequencing a series of 238 breast cancer tissue samples from DCIS to invasive tumors stage I to IV. Significant differences in methylation levels between the DCIS and invasive stage II tumors were observed for six genes RASSF1A, CDKN2A, MGMT, ABCB1, GSTP1 and FOXC1. RASSF1A, ABCB1 and GSTP1 showed significantly higher methylation levels in late stage compared to the early stage breast carcinoma. Z-score analysis revealed significantly lower methylation levels in DCIS and stage I tumors compared with stage II, III and IV tumors. Methylation levels of PTEN, PPP2R2B, FOXC1, ABCB1 and BRCA1 were lower in tumors harboring TP53 mutations then in tumors with wild type TP53. Z-score analysis showed that TP53 mutated tumors had significantly lower overall methylation levels compared to tumors with wild type TP53. Methylation levels of RASSF1A, PPP2R2B, GSTP1 and FOXC1 were higher in ER positive vs. ER negative tumors and methylation levels of PTEN and CDKN2A were higher in HER2 positive vs. HER2 negative tumors. Z-score analysis also showed that HER2 positive tumors had significantly higher z-scores of methylation compared to the HER2 negative tumors. Univariate survival analysis identifies methylation status of PPP2R2B as significant predictor of overall survival and breast cancer specific survival. In the present study we report that the level of aberrant DNA methylation is higher in late stage compared with early stage of invasive breast cancers and DCIS for genes mentioned above

  1. Use of species-specific PCR for the identification of 10 sea cucumber species

    Science.gov (United States)

    Wen, Jing; Zeng, Ling

    2014-11-01

    We developed a species-specific PCR method to identify species among dehydrated products of 10 sea cucumber species. Ten reverse species-specific primers designed from the 16S rRNA gene, in combination with one forward universal primer, generated PCR fragments of ca. 270 bp length for each species. The specificity of the PCR assay was tested with DNA of samples of 21 sea cucumber species. Amplification was observed in specific species only. The species-specific PCR method we developed was successfully applied to authenticate species of commercial products of dehydrated sea cucumber, and was proven to be a useful, rapid, and low-cost technique to identify the origin of the sea cucumber product.

  2. Species-Specific Thiol-Disulfide Equilibrium Constant: A Tool To Characterize Redox Transitions of Biological Importance.

    Science.gov (United States)

    Mirzahosseini, Arash; Somlyay, Máté; Noszál, Béla

    2015-08-13

    Microscopic redox equilibrium constants, a new species-specific type of physicochemical parameters, were introduced and determined to quantify thiol-disulfide equilibria of biological significance. The thiol-disulfide redox equilibria of glutathione with cysteamine, cysteine, and homocysteine were approached from both sides, and the equilibrium mixtures were analyzed by quantitative NMR methods to characterize the highly composite, co-dependent acid-base and redox equilibria. The directly obtained, pH-dependent, conditional constants were then decomposed by a new evaluation method, resulting in pH-independent, microscopic redox equilibrium constants for the first time. The 80 different, microscopic redox equilibrium constant values show close correlation with the respective thiolate basicities and provide sound means for the development of potent agents against oxidative stress.

  3. Scrambled eggs: A highly sensitive molecular diagnostic workflow for Fasciola species specific detection from faecal samples

    Science.gov (United States)

    Calvani, Nichola Eliza Davies; Windsor, Peter Andrew; Bush, Russell David

    2017-01-01

    transport of samples from endemic to non-endemic countries without the requirement of a complete cold chain. The commercially-available ELISA displayed poorer sensitivity, even after adjustment of the positive threshold (65–88%), compared to the sensitivity (91–100%) of the new molecular diagnostic workflow. Conclusions/Significance Species-specific assays for sensitive detection of Fasciola spp. enable ante-mortem diagnosis in both human and animal settings. This includes Southeast Asia where there are potentially many undocumented human cases and where post-mortem examination of production animals can be difficult. The new molecular workflow provides a sensitive and quantitative diagnostic approach for the rapid testing of medium to large sample sizes, potentially superseding the traditional sedimentation and FEC technique and enabling surveillance programs in locations where animal and human health funding is limited. PMID:28915255

  4. Scrambled eggs: A highly sensitive molecular diagnostic workflow for Fasciola species specific detection from faecal samples.

    Directory of Open Access Journals (Sweden)

    Nichola Eliza Davies Calvani

    2017-09-01

    to non-endemic countries without the requirement of a complete cold chain. The commercially-available ELISA displayed poorer sensitivity, even after adjustment of the positive threshold (65-88%, compared to the sensitivity (91-100% of the new molecular diagnostic workflow.Species-specific assays for sensitive detection of Fasciola spp. enable ante-mortem diagnosis in both human and animal settings. This includes Southeast Asia where there are potentially many undocumented human cases and where post-mortem examination of production animals can be difficult. The new molecular workflow provides a sensitive and quantitative diagnostic approach for the rapid testing of medium to large sample sizes, potentially superseding the traditional sedimentation and FEC technique and enabling surveillance programs in locations where animal and human health funding is limited.

  5. Scrambled eggs: A highly sensitive molecular diagnostic workflow for Fasciola species specific detection from faecal samples.

    Science.gov (United States)

    Calvani, Nichola Eliza Davies; Windsor, Peter Andrew; Bush, Russell David; Šlapeta, Jan

    2017-09-01

    -endemic countries without the requirement of a complete cold chain. The commercially-available ELISA displayed poorer sensitivity, even after adjustment of the positive threshold (65-88%), compared to the sensitivity (91-100%) of the new molecular diagnostic workflow. Species-specific assays for sensitive detection of Fasciola spp. enable ante-mortem diagnosis in both human and animal settings. This includes Southeast Asia where there are potentially many undocumented human cases and where post-mortem examination of production animals can be difficult. The new molecular workflow provides a sensitive and quantitative diagnostic approach for the rapid testing of medium to large sample sizes, potentially superseding the traditional sedimentation and FEC technique and enabling surveillance programs in locations where animal and human health funding is limited.

  6. Interdiffusion of the aluminum magnesium system. Quantitative analysis and numerical model; Interdiffusion des Aluminium-Magnesium-Systems. Quantitative Analyse und numerische Modellierung

    Energy Technology Data Exchange (ETDEWEB)

    Seperant, Florian

    2012-03-21

    Aluminum coatings are a promising approach to protect magnesium alloys against corrosion and thereby making them accessible to a variety of technical applications. Thermal treatment enhances the adhesion of the aluminium coating on magnesium by interdiffusion. For a deeper understanding of the diffusion process at the interface, a quantitative description of the Al-Mg system is necessary. On the basis of diffusion experiments with infinite reservoirs of aluminum and magnesium, the interdiffusion coefficients of the intermetallic phases of the Al-Mg-system are calculated with the Sauer-Freise method for the first time. To solve contradictions in the literature concerning the intrinsic diffusion coefficients, the possibility of a bifurcation of the Kirkendall plane is considered. Furthermore, a physico-chemical description of interdiffusion is provided to interpret the observed phase transitions. The developed numerical model is based on a temporally varied discretization of the space coordinate. It exhibits excellent quantitative agreement with the experimentally measured concentration profile. This confirms the validity of the obtained diffusion coefficients. Moreover, the Kirkendall shift in the Al-Mg system is simulated for the first time. Systems with thin aluminum coatings on magnesium also exhibit a good correlation between simulated and experimental concentration profiles. Thus, the diffusion coefficients are also valid for Al-coated systems. Hence, it is possible to derive parameters for a thermal treatment by simulation, resulting in an optimized modification of the magnesium surface for technical applications.

  7. Nonstructural Protein L* Species Specificity Supports a Mouse Origin for Vilyuisk Human Encephalitis Virus.

    Science.gov (United States)

    Drappier, Melissa; Opperdoes, Fred R; Michiels, Thomas

    2017-07-15

    Vilyuisk human encephalitis virus (VHEV) is a picornavirus related to Theiler's murine encephalomyelitis virus (TMEV). VHEV was isolated from human material passaged in mice. Whether this VHEV is of human or mouse origin is therefore unclear. We took advantage of the species-specific activity of the nonstructural L* protein of theiloviruses to track the origin of TMEV isolates. TMEV L* inhibits RNase L, the effector enzyme of the interferon pathway. By using coimmunoprecipitation and functional RNase L assays, the species specificity of RNase L antagonism was tested for L* from mouse (DA) and rat (RTV-1) TMEV strains as well as for VHEV. Coimmunoprecipitation and functional assay data confirmed the species specificity of L* activity and showed that L* from rat strain RTV-1 inhibited rat but not mouse or human RNase L. Next, we showed that the VHEV L* protein was phylogenetically related to L* of mouse viruses and that it failed to inhibit human RNase L but readily antagonized mouse RNase L, unambiguously showing the mouse origin of VHEV. IMPORTANCE Defining the natural host of a virus can be a thorny issue, especially when the virus was isolated only once or when the isolation story is complex. The species Theilovirus includes Theiler's murine encephalomyelitis virus (TMEV), infecting mice and rats, and Saffold virus (SAFV), infecting humans. One TMEV strain, Vilyuisk human encephalitis virus (VHEV), however, was isolated from mice that were inoculated with cerebrospinal fluid of a patient presenting with chronic encephalitis. It is therefore unclear whether VHEV was derived from the human sample or from the inoculated mouse. The L* protein encoded by TMEV inhibits RNase L, a cellular enzyme involved in innate immunity, in a species-specific manner. Using binding and functional assays, we show that this species specificity even allows discrimination between TMEV strains of mouse and of rat origins. The VHEV L* protein clearly inhibited mouse but not human RNase L

  8. Elucidating Microbial Species-Specific Effects on Organic Matter Transformation in Marine Sediments

    Science.gov (United States)

    Mahmoudi, N.; Enke, T. N.; Beaupre, S. R.; Teske, A.; Cordero, O. X.; Pearson, A.

    2017-12-01

    Microbial transformation and decomposition of organic matter in sediments constitutes one of the largest fluxes of carbon in marine environments. Mineralization of sedimentary organic matter by microorganisms results in selective degradation such that bioavailable or accessible compounds are rapidly metabolized while more recalcitrant, complex compounds are preserved and buried in sediment. Recent studies have found that the ability to use different carbon sources appears to vary among microorganisms, suggesting that the availability of certain pools of carbon can be specific to the taxa that utilize the pool. This implies that organic matter mineralization in marine environments may depend on the metabolic potential of the microbial populations that are present and active. The goal of our study was to investigate the extent to which organic matter availability and transformation may be species-specific using sediment from Guaymas Basin (Gulf of California). We carried out time-series incubations using bacterial isolates and sterilized sediment in the IsoCaRB system which allowed us to measure the production rates and natural isotopic signatures (δ13C and Δ14C) of microbially-respired CO2. Separate incubations using two different marine bacterial isolates (Vibrio sp. and Pseudoalteromonas sp.) and sterilized Guaymas Basin sediment under oxic conditions showed that the rate and total quantity of organic matter metabolized by these two species differs. Approximately twice as much CO2 was collected during the Vibrio sp. incubation compared to the Pseudoalteromonas sp. incubation. Moreover, the rate at which organic matter was metabolized by the Vibrio sp. was much higher than the Pseudoalteromonas sp. indicating the intrinsic availability of organic matter in sediments may depend on the species that is present and active. Isotopic analyses of microbially respired CO2 will be used to constrain the type and age of organic matter that is accessible to each species

  9. Studies of CTNNBL1 and FDFT1 variants and measures of obesity: analyses of quantitative traits and case-control studies in 18,014 Danes

    DEFF Research Database (Denmark)

    Andreasen, Camilla Helene; Mogensen, Mette Sloth; Borch-Johnsen, Knut

    2009-01-01

    of obesity-related quantitative traits, and case-control studies in large study samples of Danes. METHODS: The FDFT1 rs7001819, CTNNBL1 rs6013029 and rs6020846 were genotyped, using TaqMan allelic discrimination, in a combined study sample comprising 18,014 participants ascertained from; the population...... and a previous study. FDFT1 rs7001819 showed no association with obesity, neither when analysing quantitative traits nor when performing case-control studies of obesity.......). The most significantly associating variants within CTNNBL1 including rs6013029 and rs6020846 were additionally confirmed to associate with morbid obesity in a French Caucasian case-control sample. The aim of this study was to investigate the impact of these three variants on obesity, through analyses...

  10. Comparison of multipoint linkage analyses for quantitative traits in the CEPH data: parametric LOD scores, variance components LOD scores, and Bayes factors.

    Science.gov (United States)

    Sung, Yun Ju; Di, Yanming; Fu, Audrey Q; Rothstein, Joseph H; Sieh, Weiva; Tong, Liping; Thompson, Elizabeth A; Wijsman, Ellen M

    2007-01-01

    We performed multipoint linkage analyses with multiple programs and models for several gene expression traits in the Centre d'Etude du Polymorphisme Humain families. All analyses provided consistent results for both peak location and shape. Variance-components (VC) analysis gave wider peaks and Bayes factors gave fewer peaks. Among programs from the MORGAN package, lm_multiple performed better than lm_markers, resulting in less Markov-chain Monte Carlo (MCMC) variability between runs, and the program lm_twoqtl provided higher LOD scores by also including either a polygenic component or an additional quantitative trait locus.

  11. Reduced Number of Pigmented Neurons in the Substantia Nigra of Dystonia Patients? Findings from Extensive Neuropathologic, Immunohistochemistry, and Quantitative Analyses

    Directory of Open Access Journals (Sweden)

    Diego Iacono

    2015-05-01

    Full Text Available Background: Dystonias (Dys represent the third most common movement disorder after essential tremor (ET and Parkinson's disease (PD. While some pathogenetic mechanisms and genetic causes of Dys have been identified, little is known about their neuropathologic features. Previous neuropathologic studies have reported generically defined neuronal loss in various cerebral regions of Dys brains, mostly in the basal ganglia (BG, and specifically in the substantia nigra (SN. Enlarged pigmented neurons in the SN of Dys patients with and without specific genetic mutations (e.g., GAG deletions in DYT1 dystonia have also been described. Whether or not Dys brains are associated with decreased numbers or other morphometric changes of specific neuronal types is unknown and has never been addressed with quantitative methodologies. Methods: Quantitative immunohistochemistry protocols were used to estimate neuronal counts and volumes of nigral pigmented neurons in 13 SN of Dys patients and 13 SN of age‐matched control subjects (C. Results: We observed a significant reduction (∼20% of pigmented neurons in the SN of Dys compared to C (p<0.01. Neither significant volumetric changes nor evident neurodegenerative signs were observed in the remaining pool of nigral pigmented neurons in Dys brains. These novel quantitative findings were confirmed after exclusion of possible co‐occurring SN pathologies including Lewy pathology, tau‐neurofibrillary tangles, β‐amyloid deposits, ubiquitin (ubiq, and phosphorylated‐TAR DNA‐binding protein 43 (pTDP43‐positive inclusions. Discussion: A reduced number of nigral pigmented neurons in the absence of evident neurodegenerative signs in Dys brains could indicate previously unconsidered pathogenetic mechanisms of Dys such as neurodevelopmental defects in the SN.

  12. Quantitation and Identification of Intact Major Milk Proteins for High-Throughput LC-ESI-Q-TOF MS Analyses.

    Directory of Open Access Journals (Sweden)

    Delphine Vincent

    Full Text Available Cow's milk is an important source of proteins in human nutrition. On average, cow's milk contains 3.5% protein. The most abundant proteins in bovine milk are caseins and some of the whey proteins, namely beta-lactoglobulin, alpha-lactalbumin, and serum albumin. A number of allelic variants and post-translationally modified forms of these proteins have been identified. Their occurrence varies with breed, individuality, stage of lactation, and health and nutritional status of the animal. It is therefore essential to have reliable methods of detection and quantitation of these proteins. Traditionally, major milk proteins are quantified using liquid chromatography (LC and ultra violet detection method. However, as these protein variants co-elute to some degree, another dimension of separation is beneficial to accurately measure their amounts. Mass spectrometry (MS offers such a tool. In this study, we tested several RP-HPLC and MS parameters to optimise the analysis of intact bovine proteins from milk. From our tests, we developed an optimum method that includes a 20-28-40% phase B gradient with 0.02% TFA in both mobile phases, at 0.2 mL/min flow rate, using 75°C for the C8 column temperature, scanning every 3 sec over a 600-3000 m/z window. The optimisations were performed using external standards commercially purchased for which ionisation efficiency, linearity of calibration, LOD, LOQ, sensitivity, selectivity, precision, reproducibility, and mass accuracy were demonstrated. From the MS analysis, we can use extracted ion chromatograms (EICs of specific ion series of known proteins and integrate peaks at defined retention time (RT window for quantitation purposes. This optimum quantitative method was successfully applied to two bulk milk samples from different breeds, Holstein-Friesian and Jersey, to assess differences in protein variant levels.

  13. Radiation effects on the species-specific cell sorting-out of the cellular slime molds

    International Nuclear Information System (INIS)

    Satow, Takashi

    1976-01-01

    The effects of gamma-rays irradiation on the development and the species-specific cell sorting-out of the cellular slime mold, Dictyostelium discoideum, were investigated. The interphase amoebae of the organism showed extremely resistant to 60 Co gamma-rays. The percentage of non-stained cells estimated by dye staining method was more than 90% at the dose of 270 kR. The amoebae irradiated at 270 kR performed the development similar in the most respects to that of the un-irradiated amoebae except that a little portion of the fruiting bodies were abnormal and that the appearance of aggregates and slugs delayed 3 hrs. The ability of the species-specific cell sorting-out was not affected by gamma-rays irradiation at 270 kR. (auth.)

  14. Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts

    Directory of Open Access Journals (Sweden)

    Ouyang Shu

    2005-09-01

    Full Text Available Abstract Background The Solanaceae is a family of closely related species with diverse phenotypes that have been exploited for agronomic purposes. Previous studies involving a small number of genes suggested sequence conservation across the Solanaceae. The availability of large collections of Expressed Sequence Tags (ESTs for the Solanaceae now provides the opportunity to assess sequence conservation and divergence on a genomic scale. Results All available ESTs and Expressed Transcripts (ETs, 449,224 sequences for six Solanaceae species (potato, tomato, pepper, petunia, tobacco and Nicotiana benthamiana, were clustered and assembled into gene indices. Examination of gene ontologies revealed that the transcripts within the gene indices encode a similar suite of biological processes. Although the ESTs and ETs were derived from a variety of tissues, 55–81% of the sequences had significant similarity at the nucleotide level with sequences among the six species. Putative orthologs could be identified for 28–58% of the sequences. This high degree of sequence conservation was supported by expression profiling using heterologous hybridizations to potato cDNA arrays that showed similar expression patterns in mature leaves for all six solanaceous species. 16–19% of the transcripts within the six Solanaceae gene indices did not have matches among Solanaceae, Arabidopsis, rice or 21 other plant gene indices. Conclusion Results from this genome scale analysis confirmed a high level of sequence conservation at the nucleotide level of the coding sequence among Solanaceae. Additionally, the results indicated that part of the Solanaceae transcriptome is likely to be unique for each species.

  15. A systematic identification of species-specific protein succinylation sites using joint element features information

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    Hasan MM

    2017-08-01

    Full Text Available Md Mehedi Hasan,1 Mst Shamima Khatun,2 Md Nurul Haque Mollah,2 Cao Yong,3 Dianjing Guo1 1School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong, People’s Republic of China; 2Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh; 3Department of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen Graduate School, Shenzhen, People’s Republic of China Abstract: Lysine succinylation, an important type of protein posttranslational modification, plays significant roles in many cellular processes. Accurate identification of succinylation sites can facilitate our understanding about the molecular mechanism and potential roles of lysine succinylation. However, even in well-studied systems, a majority of the succinylation sites remain undetected because the traditional experimental approaches to succinylation site identification are often costly, time-consuming, and laborious. In silico approach, on the other hand, is potentially an alternative strategy to predict succinylation substrates. In this paper, a novel computational predictor SuccinSite2.0 was developed for predicting generic and species-specific protein succinylation sites. This predictor takes the composition of profile-based amino acid and orthogonal binary features, which were used to train a random forest classifier. We demonstrated that the proposed SuccinSite2.0 predictor outperformed other currently existing implementations on a complementarily independent dataset. Furthermore, the important features that make visible contributions to species-specific and cross-species-specific prediction of protein succinylation site were analyzed. The proposed predictor is anticipated to be a useful computational resource for lysine succinylation site prediction. The integrated species-specific online tool of SuccinSite2.0 is publicly

  16. Genus and species-specific IgG and IgM antibodies pulmonary tuberculosis

    International Nuclear Information System (INIS)

    Butt, T.; Abbassi, S.A.; Ahmad, R.N.; Mahmood, A.; Karamat, K.A; Malik, H.S.; Anwar, M.

    2004-01-01

    Objective: To evaluate three different enzyme immunoassays for serological diagnosis of pulmonary tuberculosis and to compare their diagnostic accuracy in different combinations. Subjects and Methods: Sera from patients suffering from pulmonary tuberculosis (n=94) with sputum positive for acid fast bacilli (AFB) and sera from control group of healthy individuals (n=90) with sputum negative for AFB were tested by Pathozyme-Myco G EIA, Pathozyme-TB Complex Plus EIA and Pathozyme Myco M EIA kits for the genus-specific IgG and IgM, and the species-specific IgG antibodies against antigens of Mycobacterium tuberculosis. Results: The detection of IgG against genus-specific antigens by Pathozyme-Myco G had a sensitivity of 46% and a specificity of 93%, of IgG against species-specific antigens by Pathozyme- TB Complex Plus had a sensitivity of 64% and specificity of 97% and of IgM against genus-specific antigens by Pathozyme Myco M had a sensitivity of 67% and specificity of 98%. When the results of these immunoassays were evaluated in combination, their sensitivity improved. Combination of genus-specific IgM and species-specific IgG yielded best results with a sensitivity of 87% and specificity of 93%. Conclusion: The sensitivity of serological diagnosis of tuberculosis is low, but it can be increased by utilizing a combination of several antigens. (author)

  17. Development of a species-specific coproantigen ELISA for human Taenia solium taeniasis.

    Science.gov (United States)

    Guezala, Maria-Claudia; Rodriguez, Silvia; Zamora, Humberto; Garcia, Hector H; Gonzalez, Armando E; Tembo, Alice; Allan, James C; Craig, Philip S

    2009-09-01

    Taenia solium causes human neurocysticercosis and is endemic in underdeveloped countries where backyard pig keeping is common. Microscopic fecal diagnostic methods for human T. solium taeniasis are not very sensitive, and Taenia saginata and Taenia solium eggs are indistinguishable under the light microscope. Coproantigen (CoAg) ELISA methods are very sensitive, but currently only genus (Taenia) specific. This paper describes the development of a highly species-specific coproantigen ELISA test to detect T. solium intestinal taeniasis. Sensitivity was maintained using a capture antibody of rabbit IgG against T. solium adult whole worm somatic extract, whereas species specificity was achieved by utilization of an enzyme-conjugated rabbit IgG against T. solium adult excretory-secretory (ES) antigen. A known panel of positive and negative human fecal samples was tested with this hybrid sandwich ELISA. The ELISA test gave 100% specificity and 96.4% sensitivity for T. solium tapeworm carriers (N = 28), with a J index of 0.96. This simple ELISA incorporating anti-adult somatic and anti-adult ES antibodies provides the first potentially species-specific coproantigen test for human T. solium taeniasis.

  18. Quantitative proteome and phosphoproteome analyses of Streptomyces coelicolor reveal proteins and phosphoproteins modulating differentiation and secondary metabolism

    DEFF Research Database (Denmark)

    Rioseras, Beatriz; Sliaha, Pavel V; Gorshkov, Vladimir

    2018-01-01

    identified and quantified 3461 proteins corresponding to 44.3% of the S. coelicolor proteome across three developmental stages: vegetative hypha (MI); secondary metabolite producing hyphae (MII); and sporulating hyphae. A total of 1350 proteins exhibited more than 2-fold expression changes during....../Thr/Tyr kinases, making this genus an outstanding model for the study of bacterial protein phosphorylation events. We used mass spectrometry based quantitative proteomics and phosphoproteomics to characterize bacterial differentiation and activation of secondary metabolism of Streptomyces coelicolor. We...... the bacterial differentiation process. These proteins include 136 regulators (transcriptional regulators, transducers, Ser/Thr/Tyr kinases, signalling proteins), as well as 542 putative proteins with no clear homology to known proteins which are likely to play a role in differentiation and secondary metabolism...

  19. [Development of quantitative analyse method for determination of alkaloid cytisin in Spartium junceum L., growing in Georgia].

    Science.gov (United States)

    Iavich, P A; Churadze, L I; Suladze, T Sh; Rukhadze, T A

    2011-12-01

    The aim of the research was to develop a method for quantitative determination of cytisine in Spartium junceum L. We used the above-ground parts of plants. In developing a method of analysis we used the method of 3-phase extraction. In this case the best results were obtained in the system: chopped raw material - water solution of ammonia - chloroform. In this case, the amount of alkaloids extracted almost entirely from the plant and goes into the chloroform phase. Evaluation of the results was carried out by the validation. The method for determination of cytisine in raw product was proposed. The method comprises the following steps-extraction of raw materials extracting chloroform phase and its evaporation, the translation of solids in methanol, the chromatographic separation cytisine and its fixation of the spectrophotometer method. The method is reproducible, has the required accuracy, is easy to analysis (less than 9 hours).

  20. Process Review for Development of Quantitative Risk Analyses for Transboundary Animal Disease to Pathogen-Free Territories

    Directory of Open Access Journals (Sweden)

    Jonathan Miller

    2017-10-01

    Full Text Available Outbreaks of transboundary animal diseases (TADs have the potential to cause significant detriment to animal, human, and environmental health; severe economic implications; and national security. Challenges concerning data sharing, model development, decision support, and disease emergence science have recently been promoted. These challenges and recommendations have been recognized and advocated in the disciplines intersecting with outbreak prediction and forecast modeling regarding infectious diseases. To advance the effective application of computation and risk communication, analytical products ought to follow a collaboratively agreed common plan for implementation. Research articles should seek to inform and assist prioritization of national and international strategies in developing established criteria to identify and follow best practice standards to assess risk model attributes and performance. A well-defined framework to help eliminate gaps in policy, process, and planning knowledge areas would help alleviate the intense need for the formation of a comprehensive strategy for countering TAD outbreak risks. A quantitative assessment that accurately captures the risk of introduction of a TAD through various pathways can be a powerful tool in guiding where government, academic, and industry resources ought to be allocated, whether implementation of additional risk management solutions is merited, and where research efforts should be directed to minimize risk. This review outlines a part of a process for the development of quantitative risk analysis to collect, analyze, and communicate this knowledge. A more comprehensive and unabridged manual was also developed. The framework used in supporting the application of aligning computational tools for readiness continues our approach to apply a preparedness mindset to challenges concerning threats to global biosecurity, secure food systems, and risk-mitigated agricultural economies.

  1. Quantitative analysis of textures produced in a hot-extruded zirconium plate; Analyse quantitative des textures developpees dans une plaque de zirconium filee a chaud

    Energy Technology Data Exchange (ETDEWEB)

    Couterne, J [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires. Institut national des sciences et techniques nucleaires, laboratoire de metallurgie

    1967-01-01

    etudiees par la methode de Schulz en se referant a un etalon isotrope. Ces textures ont. ete determinees soit parallelement au plan de la plaque, soit parallelement au plan des rives. Tous les resultats sont analyses dans une discussion finale qui permet, en particulier au voisinage des aretes de la plaque, de montrer que certaines composantes des textures observees clans les deux series d'enregistrements, sont en fait l'expression de la meme texture vue sous deux angles differents. D'autre part. it est montre que le zirconium ainsi mis en forme comporte des textures d'ecrouissage et de recristallisation posterieure a l'ecrouissage precedent. En schematisant l'ensemble des textures determinees, on observe trois textures dont deux deja signalees dans la bibliographie et comparable a celles des produits lamines: ces textures sont telles que les plans. (0001 presentent des inclinaisons respectives de 36 deg C et 60 deg C par rapport a un plan tangent a la courbe (enveloppe des vitesses d'ecoulement transverse) resulant de la geometrie du filage considere; la troisieme texture est definie par le fait que le plan (0001) est orthogonal aux surfaces exterieures de la plaque. La direction de filage associee a ces plans et commune aux trois textures est du type <1010>. Des essais dilatometriques ont ete effectues sur des echantillons preleves dans le sens du filage et clans le sens transverse. Ces essais mettent en evidence l'anisotropie dilatometrique du zirconium ainsi qu'un changement de pente de la courbe ({alpha}{sub v}){sub a} en fonction de la temperature a partir de 400 drg C, pouvant etre explique par la variation de la configuration electronique du metal a partir de cette temperature. (auteur)

  2. Quantitative analysis of textures produced in a hot-extruded zirconium plate; Analyse quantitative des textures developpees dans une plaque de zirconium filee a chaud

    Energy Technology Data Exchange (ETDEWEB)

    Couterne, J. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires. Institut national des sciences et techniques nucleaires, laboratoire de metallurgie

    1967-01-01

    ete etudiees par la methode de Schulz en se referant a un etalon isotrope. Ces textures ont. ete determinees soit parallelement au plan de la plaque, soit parallelement au plan des rives. Tous les resultats sont analyses dans une discussion finale qui permet, en particulier au voisinage des aretes de la plaque, de montrer que certaines composantes des textures observees clans les deux series d'enregistrements, sont en fait l'expression de la meme texture vue sous deux angles differents. D'autre part. it est montre que le zirconium ainsi mis en forme comporte des textures d'ecrouissage et de recristallisation posterieure a l'ecrouissage precedent. En schematisant l'ensemble des textures determinees, on observe trois textures dont deux deja signalees dans la bibliographie et comparable a celles des produits lamines: ces textures sont telles que les plans. (0001 presentent des inclinaisons respectives de 36 deg C et 60 deg C par rapport a un plan tangent a la courbe (enveloppe des vitesses d'ecoulement transverse) resulant de la geometrie du filage considere; la troisieme texture est definie par le fait que le plan (0001) est orthogonal aux surfaces exterieures de la plaque. La direction de filage associee a ces plans et commune aux trois textures est du type <1010>. Des essais dilatometriques ont ete effectues sur des echantillons preleves dans le sens du filage et clans le sens transverse. Ces essais mettent en evidence l'anisotropie dilatometrique du zirconium ainsi qu'un changement de pente de la courbe ({alpha}{sub v}){sub a} en fonction de la temperature a partir de 400 drg C, pouvant etre explique par la variation de la configuration electronique du metal a partir de cette temperature. (auteur)

  3. Detection and Characterization of Reactive Oxygen and Nitrogen Species in Biological Systems by Monitoring Species-Specific Products.

    Science.gov (United States)

    Hardy, Micael; Zielonka, Jacek; Karoui, Hakim; Sikora, Adam; Michalski, Radosław; Podsiadły, Radosław; Lopez, Marcos; Vasquez-Vivar, Jeannette; Kalyanaraman, Balaraman; Ouari, Olivier

    2018-05-20

    Since the discovery of the superoxide dismutase enzyme, the generation and fate of short-lived oxidizing, nitrosating, nitrating, and halogenating species in biological systems has been of great interest. Despite the significance of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in numerous diseases and intracellular signaling, the rigorous detection of ROS and RNS has remained a challenge. Recent Advances: Chemical characterization of the reactions of selected ROS and RNS with electron paramagnetic resonance (EPR) spin traps and fluorescent probes led to the establishment of species-specific products, which can be used for specific detection of several forms of ROS and RNS in cell-free systems and in cultured cells in vitro and in animals in vivo. Profiling oxidation products from the ROS and RNS probes provides a rigorous method for detection of those species in biological systems. Formation and detection of species-specific products from the probes enables accurate characterization of the oxidative environment in cells. Measurement of the total signal (fluorescence, chemiluminescence, etc.) intensity does not allow for identification of the ROS/RNS formed. It is critical to identify the products formed by using chromatographic or other rigorous techniques. Product analyses should be accompanied by monitoring of the intracellular probe level, another factor controlling the yield of the product(s) formed. More work is required to characterize the chemical reactivity of the ROS/RNS probes, and to develop new probes/detection approaches enabling real-time, selective monitoring of the specific products formed from the probes. Antioxid. Redox Signal. 28, 1416-1432.

  4. Bacterial communities of two ubiquitous Great Barrier Reef corals reveals both site- and species-specificity of common bacterial associates.

    Directory of Open Access Journals (Sweden)

    E Charlotte E Kvennefors

    Full Text Available BACKGROUND: Coral-associated bacteria are increasingly considered to be important in coral health, and altered bacterial community structures have been linked to both coral disease and bleaching. Despite this, assessments of bacterial communities on corals rarely apply sufficient replication to adequately describe the natural variability. Replicated data such as these are crucial in determining potential roles of bacteria on coral. METHODOLOGY/PRINCIPAL FINDINGS: Denaturing Gradient Gel Electrophoresis (DGGE of the V3 region of the 16S ribosomal DNA was used in a highly replicated approach to analyse bacterial communities on both healthy and diseased corals. Although site-specific variations in the bacterial communities of healthy corals were present, host species-specific bacterial associates within a distinct cluster of gamma-proteobacteria could be identified, which are potentially linked to coral health. Corals affected by "White Syndrome" (WS underwent pronounced changes in their bacterial communities in comparison to healthy colonies. However, the community structure and bacterial ribotypes identified in diseased corals did not support the previously suggested theory of a bacterial pathogen as the causative agent of the syndrome. CONCLUSIONS/SIGNIFICANCE: This is the first study to employ large numbers of replicated samples to assess the bacterial communities of healthy and diseased corals, and the first culture-independent assessment of bacterial communities on WS affected Acroporid corals on the GBR. Results indicate that a minimum of 6 replicate samples are required in order to draw inferences on species, spatial or health-related changes in community composition, as a set of clearly distinct bacterial community profiles exist in healthy corals. Coral bacterial communities may be both site and species specific. Furthermore, a cluster of gamma-proteobacterial ribotypes may represent a group of specific common coral and marine

  5. Quantitative anatomical and behavioral analyses of regeneration and collateral sprouting following spinal cord transection in the nurse shark (ginglymostoma cirratum).

    Science.gov (United States)

    Gelderd, J B

    1979-01-01

    The spinal cord was transected at the mid-thoracic level in 32 nurse sharks. Four animals per group were sacrificed at intervals of 10, 20, 30, 40, 60 and 90 days postoperative. Two groups of fish underwent a subsequent spinla1 cord retransection at the same site at 90 days and were sacrificed 10 and 20 days later. Three sections of spinal cord were removed from each shark for histological analysis. Behaviorally, timed trials for swimming speed and a strength test for axial musculature contraction caudal to the lesion site were performed at 5 day postoperative intervals. Histological analysis showed little regeneration (9-13 percent) of two descending tracts 90 days following the lesion and no return of rostrally controlled movements caudal to the lesion. However, synaptic readjustment did occur caudal to the lesion. This phenomenon was attributed to local segmental sprouting of adjacent, intact nerve fibers. A close correlation was shown between this synaptic readjustment and the strength of uncontrollable undulatory movements seen caudal to the lesion site following spinal cord transection. The relationship of regeneration and collateral sprouting to quantitative behavioral changes is discussed.

  6. Quantitative Analyses of Force-Induced Amyloid Formation in Candida albicans Als5p: Activation by Standard Laboratory Procedures.

    Directory of Open Access Journals (Sweden)

    Cho X J Chan

    Full Text Available Candida albicans adhesins have amyloid-forming sequences. In Als5p, these amyloid sequences cluster cell surface adhesins to create high avidity surface adhesion nanodomains. Such nanodomains form after force is applied to the cell surface by atomic force microscopy or laminar flow. Here we report centrifuging and resuspending S. cerevisiae cells expressing Als5p led to 1.7-fold increase in initial rate of adhesion to ligand coated beads. Furthermore, mechanical stress from vortex-mixing of Als5p cells or C. albicans cells also induced additional formation of amyloid nanodomains and consequent activation of adhesion. Vortex-mixing for 60 seconds increased the initial rate of adhesion 1.6-fold. The effects of vortex-mixing were replicated in heat-killed cells as well. Activation was accompanied by increases in thioflavin T cell surface fluorescence measured by flow cytometry or by confocal microscopy. There was no adhesion activation in cells expressing amyloid-impaired Als5pV326N or in cells incubated with inhibitory concentrations of anti-amyloid dyes. Together these results demonstrated the activation of cell surface amyloid nanodomains in yeast expressing Als adhesins, and further delineate the forces that can activate adhesion in vivo. Consequently there is quantitative support for the hypothesis that amyloid forming adhesins act as both force sensors and effectors.

  7. Quantitative analyses reveal distinct sensitivities of the capture of HIV-1 primary viruses and pseudoviruses to broadly neutralizing antibodies.

    Science.gov (United States)

    Kim, Jiae; Jobe, Ousman; Peachman, Kristina K; Michael, Nelson L; Robb, Merlin L; Rao, Mangala; Rao, Venigalla B

    2017-08-01

    Development of vaccines capable of eliciting broadly neutralizing antibodies (bNAbs) is a key goal to controlling the global AIDS epidemic. To be effective, bNAbs must block the capture of HIV-1 to prevent viral acquisition and establishment of reservoirs. However, the role of bNAbs, particularly during initial exposure of primary viruses to host cells, has not been fully examined. Using a sensitive, quantitative, and high-throughput qRT-PCR assay, we found that primary viruses were captured by host cells and converted into a trypsin-resistant form in less than five minutes. We discovered, unexpectedly, that bNAbs did not block primary virus capture, although they inhibited the capture of pseudoviruses/IMCs and production of progeny viruses at 48h. Further, viruses escaped bNAb inhibition unless the bNAbs were present in the initial minutes of exposure of virus to host cells. These findings will have important implications for HIV-1 vaccine design and determination of vaccine efficacy. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  8. Combining emission inventory and isotope ratio analyses for quantitative source apportionment of heavy metals in agricultural soil.

    Science.gov (United States)

    Chen, Lian; Zhou, Shenglu; Wu, Shaohua; Wang, Chunhui; Li, Baojie; Li, Yan; Wang, Junxiao

    2018-08-01

    Two quantitative methods (emission inventory and isotope ratio analysis) were combined to apportion source contributions of heavy metals entering agricultural soils in the Lihe River watershed (Taihu region, east China). Source apportionment based on the emission inventory method indicated that for Cd, Cr, Cu, Pb, and Zn, the mean percentage input from atmospheric deposition was highest (62-85%), followed by irrigation (12-27%) and fertilization (1-14%). Thus, the heavy metals were derived mainly from industrial activities and traffic emissions. For Ni the combined percentage input from irrigation and fertilization was approximately 20% higher than that from atmospheric deposition, indicating that Ni was mainly derived from agricultural activities. Based on isotope ratio analysis, atmospheric deposition accounted for 57-93% of Pb entering soil, with the mean value of 69.3%, which indicates that this was the major source of Pb entering soil in the study area. The mean contributions of irrigation and fertilization to Pb pollution of soil ranged from 0% to 10%, indicating that they played only a marginally important role. Overall, the results obtained using the two methods were similar. This study provides a reliable approach for source apportionment of heavy metals entering agricultural soils in the study area, and clearly have potential application for future studies in other regions. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Vibrational algorithms for quantitative crystallographic analyses of hydroxyapatite-based biomaterials: II, application to decayed human teeth.

    Science.gov (United States)

    Adachi, Tetsuya; Pezzotti, Giuseppe; Yamamoto, Toshiro; Ichioka, Hiroaki; Boffelli, Marco; Zhu, Wenliang; Kanamura, Narisato

    2015-05-01

    A systematic investigation, based on highly spectrally resolved Raman spectroscopy, was undertaken to research the efficacy of vibrational assessments in locating chemical and crystallographic fingerprints for the characterization of dental caries and the early detection of non-cavitated carious lesions. Raman results published by other authors have indicated possible approaches for this method. However, they conspicuously lacked physical insight at the molecular scale and, thus, the rigor necessary to prove the efficacy of this spectroscopy method. After solving basic physical challenges in a companion paper, we apply them here in the form of newly developed Raman algorithms for practical dental research. Relevant differences in mineral crystallite (average) orientation and texture distribution were revealed for diseased enamel at different stages compared with healthy mineralized enamel. Clear spectroscopy features could be directly translated in terms of a rigorous and quantitative classification of crystallography and chemical characteristics of diseased enamel structures. The Raman procedure enabled us to trace back otherwise invisible characteristics in early caries, in the translucent zone (i.e., the advancing front of the disease) and in the body of lesion of cavitated caries.

  10. Quantitative and molecular analyses of mutation in a pSV2gpt transformed CHO cell line

    International Nuclear Information System (INIS)

    Stankowski, L.F. Jr.; Tindall, K.R.; Hsie, A.W.

    1983-01-01

    Following NDA-mediated gene transfer we have isolated a cell line useful for studying gene mutation at the molecular level. This line, AS52, derived from a hypoxanthine-guanine phosphoribosyl transferase (HGPRT) deficient Chinese hamster ovary (CHO) cell line, carries a single copy of the E. coli xanthine-guanine phosphoribosyl transferase (XGPRT) gene (gpt) and exhibits a spontaneous mutant frequency of 20 TG/sup r/ mutants/10 6 clonable cells. As with HGPRT - mutants, XGPRT - mutants can be selected in 6-thioguanine. AS52 (XGPRT + ) and wild type CHO (HGPRT + ) cell exhibit almost identical cytotoxic responses to various agents. We observed significant differences in mutation induction by UV light and ethyl methanesulfonate (EMS). Ratios of XGPRT - to HGPRT - mutants induced per unit dose (J/m 2 for UV light and μg/ml for EMS) are 1.4 and 0.70, respectively. Preliminary Southern blot hybridization analyses has been performed on 30 XGPRT - AS52 mutants. A majority of spontaneous mutants have deletions ranging in size from 1 to 4 kilobases (9/19) to complete loss of gpt sequences (4/19); the remainder have no detectable (5/19) or only minor (1/19) alterations. 5/5 UV-induced and 5/6 EMS-induced mutants do not show a detectable change. Similar analyses are underway for mutations induced by x-irradiation and ICR 191 treatment

  11. The influence of the design matrix on treatment effect estimates in the quantitative analyses of single-subject experimental design research.

    Science.gov (United States)

    Moeyaert, Mariola; Ugille, Maaike; Ferron, John M; Beretvas, S Natasha; Van den Noortgate, Wim

    2014-09-01

    The quantitative methods for analyzing single-subject experimental data have expanded during the last decade, including the use of regression models to statistically analyze the data, but still a lot of questions remain. One question is how to specify predictors in a regression model to account for the specifics of the design and estimate the effect size of interest. These quantitative effect sizes are used in retrospective analyses and allow synthesis of single-subject experimental study results which is informative for evidence-based decision making, research and theory building, and policy discussions. We discuss different design matrices that can be used for the most common single-subject experimental designs (SSEDs), namely, the multiple-baseline designs, reversal designs, and alternating treatment designs, and provide empirical illustrations. The purpose of this article is to guide single-subject experimental data analysts interested in analyzing and meta-analyzing SSED data. © The Author(s) 2014.

  12. Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure.

    Science.gov (United States)

    Heuer, Sigrid; Lu, Xiaochun; Chin, Joong Hyoun; Tanaka, Juan Pariasca; Kanamori, Hiroyuki; Matsumoto, Takashi; De Leon, Teresa; Ulat, Victor Jun; Ismail, Abdelbagi M; Yano, Masahiro; Wissuwa, Matthias

    2009-06-01

    The phosphorus uptake 1 (Pup1) locus was identified as a major quantitative trait locus (QTL) for tolerance of phosphorus deficiency in rice. Near-isogenic lines with the Pup1 region from tolerant donor parent Kasalath typically show threefold higher phosphorus uptake and grain yield in phosphorus-deficient field trials than the intolerant parent Nipponbare. In this study, we report the fine mapping of the Pup1 locus to the long arm of chromosome 12 (15.31-15.47 Mb). Genes in the region were initially identified on the basis of the Nipponbare reference genome, but did not reveal any obvious candidate genes related to phosphorus uptake. Kasalath BAC clones were therefore sequenced and revealed a 278-kbp sequence significantly different from the syntenic regions in Nipponbare (145 kb) and in the indica reference genome of 93-11 (742 kbp). Size differences are caused by large insertions or deletions (INDELs), and an exceptionally large number of retrotransposon and transposon-related elements (TEs) present in all three sequences (45%-54%). About 46 kb of the Kasalath sequence did not align with the entire Nipponbare genome, and only three Nipponbare genes (fatty acid alpha-dioxygenase, dirigent protein and aspartic proteinase) are highly conserved in Kasalath. Two Nipponbare genes (expressed proteins) might have evolved by at least three TE integrations in an ancestor gene that is still present in Kasalath. Several predicted Kasalath genes are novel or unknown genes that are mainly located within INDEL regions. Our results highlight the importance of sequencing QTL regions in the respective donor parent, as important genes might not be present in the current reference genomes.

  13. Observation and quantitative analyses of the skeletal and central nervous systems of human embryos and fetuses using microimaging techniques

    International Nuclear Information System (INIS)

    Shiota, Kohei; Yamada, Shigehito; Tsuchiya, Maiko; Nakajima, Takashi; Takakuwa, Tetsuya; Morimoto, Naoki; Ogihara, Naomichi; Katayama, Kazumichi; Kose, Katsumi

    2011-01-01

    High resolution images have been available to trace the organogenesis of the central nervous system (CNS) and crania of human embryo and fetus with microimaging techniques of CT, novel MR microscopy and episcopic fluorescence image capture (EFIC). The helical CT was conducted for Kyoto University's stock specimens of 31 fetuses at gestational stages 8-24 weeks to observe the skeletal development of neuro- and viscero-cranium in 2D and 3D view. Sixty seven landmarks were defined on the images at outer surface and lumen of the skull to analyze the morphological development. Increase of cranial length was found significant relative to width and height in fetus, confirming the faster development of neurocranium than viscero-region. Next, 1.5/2.34 T MR microscopic imaging was conducted for fixed specimens of >1000 embryos at 4-8 weeks after fertilization. For this, a newly developed contrast optimization by mapping the specimen with the relaxation time had been performed to acquire the highest resolution in the world of 80-120 micrometer, which enabled to image primordia of the inner embryonic structures like brain, spinal cord, choroid plexus, skeletons of skull and spinal column. The finding was thought helpful for analysis and diagnosis of their early development. EFIC of embryos was conducted firstly in the world, where spontaneous fluorescence of their cross section was captured by the fluorescent microscope with the resolution as high as <10 micrometer to reconstruct 2D/3D images. EFIC was found to give images of embryonic CNS, ventricular system, layering structures of brain and spinal cord without staining, and to give sequential changes of their volumes quantitated during the development. The reported microimaging techniques were concluded useful for analysis of normal and abnormal early development of CNS and skull in humans. (T.T.)

  14. Quantitative PCR and immunohistochemical analyses of HMGB1 and RAGE expression in canine disseminated histiocytic sarcoma (malignant histiocytosis).

    Science.gov (United States)

    Sterenczak, Katharina A; Kleinschmidt, Sven; Wefstaedt, Patrick; Eberle, Nina; Hewicker-Trautwein, Marion; Bullerdiek, Jörn; Nolte, Ingo; Murua Escobar, Hugo

    2011-05-01

    Disorders of histiocytic origin affecting humans and dogs share various similarities. Canine disseminated histiocytic sarcoma (DHS) (formerly known as malignant histiocytosis) is an aggressive neoplasm of interstitial dendritic cells (DCs). The receptor for glycation end products (RAGE) and the high mobility group box1 protein (HMGB1) have been shown to be required for the maturation and migration of DCs. Thus, deregulation of the expression of these genes could have a major effect on the progression of histiocytic disorders. Neoplastic canine DHS samples and non-neoplastic control samples were analysed immunohistochemically and via real-time PCR. Significant down-regulation of RAGE in the lung tumour samples and down-regulation of HMGB1 in the lung, lymph node and spleen tumour samples were detected compared to their non-neoplastic counterparts. RAGE and HMGB1 expression down-regulation in canine DHS points to a role in the progression of histiocytic disorders.

  15. Species-specific ant brain manipulation by a specialized fungal parasite.

    Science.gov (United States)

    de Bekker, Charissa; Quevillon, Lauren E; Smith, Philip B; Fleming, Kimberly R; Ghosh, Debashis; Patterson, Andrew D; Hughes, David P

    2014-08-29

    A compelling demonstration of adaptation by natural selection is the ability of parasites to manipulate host behavior. One dramatic example involves fungal species from the genus Ophiocordyceps that control their ant hosts by inducing a biting behavior. Intensive sampling across the globe of ants that died after being manipulated by Ophiocordyceps suggests that this phenomenon is highly species-specific. We advance our understanding of this system by reconstructing host manipulation by Ophiocordyceps parasites under controlled laboratory conditions and combining this with field observations of infection rates and a metabolomics survey. We report on a newly discovered species of Ophiocordyceps unilateralis sensu lato from North America that we use to address the species-specificity of Ophiocordyceps-induced manipulation of ant behavior. We show that the fungus can kill all ant species tested, but only manipulates the behavior of those it infects in nature. To investigate if this could be explained at the molecular level, we used ex vivo culturing assays to measure the metabolites that are secreted by the fungus to mediate fungus-ant tissue interactions. We show the fungus reacts heterogeneously to brains of different ant species by secreting a different array of metabolites. By determining which ion peaks are significantly enriched when the fungus is grown alongside brains of its naturally occurring host, we discovered candidate compounds that could be involved in behavioral manipulation by O. unilateralis s.l.. Two of these candidates are known to be involved in neurological diseases and cancer. The integrative work presented here shows that ant brain manipulation by O. unilateralis s.l. is species-specific seemingly because the fungus produces a specific array of compounds as a reaction to the presence of the host brain it has evolved to manipulate. These studies have resulted in the discovery of candidate compounds involved in establishing behavioral manipulation

  16. Species-specific isotopic fractionation of mercury during methylation by bacteria

    International Nuclear Information System (INIS)

    Rodriguez-Gonzalez, P.; Epov, V.N.; Bridou, R.; Tessier, E.; Monperrus, M.; Guyoneaud, R.; Amouroux, D.

    2009-01-01

    Full text: The environmental reactivity of Hg is extremely dependent on its chemical form. In fact, Hg bioaccumulation is due to the greater trophic transfer efficiency of methylmercury which is formed as a result of biotic or abiotic transformations caused by specific redox gradients and bacterial activity. The study of stable isotope biogeochemistry of Hg may provide a powerful tool to track and understand its cycle and pathways in the environment. This work presents the measurement of species-specific Hg isotopic composition by GC-MCICPMS during Hg methylation experiments using cultures of pure bacterial strains incubated with Hg (II) standard NIST 3133. (author)

  17. Statistical properties of interval mapping methods on quantitative trait loci location: impact on QTL/eQTL analyses

    Directory of Open Access Journals (Sweden)

    Wang Xiaoqiang

    2012-04-01

    Full Text Available Abstract Background Quantitative trait loci (QTL detection on a huge amount of phenotypes, like eQTL detection on transcriptomic data, can be dramatically impaired by the statistical properties of interval mapping methods. One of these major outcomes is the high number of QTL detected at marker locations. The present study aims at identifying and specifying the sources of this bias, in particular in the case of analysis of data issued from outbred populations. Analytical developments were carried out in a backcross situation in order to specify the bias and to propose an algorithm to control it. The outbred population context was studied through simulated data sets in a wide range of situations. The likelihood ratio test was firstly analyzed under the "one QTL" hypothesis in a backcross population. Designs of sib families were then simulated and analyzed using the QTL Map software. On the basis of the theoretical results in backcross, parameters such as the population size, the density of the genetic map, the QTL effect and the true location of the QTL, were taken into account under the "no QTL" and the "one QTL" hypotheses. A combination of two non parametric tests - the Kolmogorov-Smirnov test and the Mann-Whitney-Wilcoxon test - was used in order to identify the parameters that affected the bias and to specify how much they influenced the estimation of QTL location. Results A theoretical expression of the bias of the estimated QTL location was obtained for a backcross type population. We demonstrated a common source of bias under the "no QTL" and the "one QTL" hypotheses and qualified the possible influence of several parameters. Simulation studies confirmed that the bias exists in outbred populations under both the hypotheses of "no QTL" and "one QTL" on a linkage group. The QTL location was systematically closer to marker locations than expected, particularly in the case of low QTL effect, small population size or low density of markers, i

  18. Uncovering iron regulation with species-specific transcriptome patterns in Atlantic and coho salmon during a Caligus rogercresseyi infestation.

    Science.gov (United States)

    Valenzuela-Muñoz, V; Boltaña, S; Gallardo-Escárate, C

    2017-09-01

    Salmon species cultured in Chile evidence different levels of susceptibility to the sea louse Caligus rogercresseyi. These differences have mainly been associated with specific immune responses. Moreover, iron regulation seems to be an important mechanism to confer immunity during the host infestation. This response called nutritional immunity has been described in bacterial infections, despite that no comprehensive studies involving in marine ectoparasites infestation have been reported. With this aim, we analysed the transcriptome profiles of Atlantic and coho salmon infected with C. rogercresseyi to evidence modulation of the iron metabolism as a proxy of nutritional immune responses. Whole transcriptome sequencing was performed in samples of skin and head kidney from Atlantic and coho salmon infected with sea lice. RNA-seq analyses revealed significant upregulation of transcripts in both salmon species at 7 and 14 dpi in skin and head kidney, respectively. However, iron regulation transcripts were differentially modulated, evidencing species-specific expression profiles. Genes related to heme degradation and iron transport such as hepcidin, transferrin and haptoglobin were primary upregulated in Atlantic salmon; meanwhile, in coho salmon, genes associated with heme biosynthesis were strongly transcribed. In summary, Atlantic salmon, which are more susceptible to infestation, presented molecular mechanisms to deplete cellular iron availability, suggesting putative mechanisms of nutritional immunity. In contrast, resistant coho salmon were less affected by sea lice, mainly activating pro-inflammatory mechanisms to cope with infestation. © 2017 John Wiley & Sons Ltd.

  19. Species-specific response-topography of chickens' and pigeons' water-induced autoshaped responding.

    Science.gov (United States)

    Ploog, Bertram O

    2014-07-01

    Four pigeons and eight chickens received autoshaping training where a keylight (conditioned stimulus) signaled response-independent deliveries of water (unconditioned stimulus). Pigeons drink while keeping their beaks submerged in water and moving their beaks to create suction ("mumbling"), whereas chickens drink by trapping a small amount of water in their mouths and then lifting their heads so the water trickles down. This experiment tested whether these and other species-specific differences in drinking and related behaviors of pigeons and chickens would be reflected in the form of conditioned (autoshaped) responding. Touchscreens and videotapes were used for data recording. Results showed that chickens moved their heads more than pigeons when drinking (unconditioned response). The birds also differed in conditioned responding in the presence of the keylight: Pigeons produced more keyswitch closures and mumbled at the keylight more than chickens whereas chickens scratched more than pigeons. In conclusion, with this unique comparative method that employed identical contingencies and comparable deprivation levels, species-specific differences in unconditioned responses and, more importantly, differences in their corresponding conditioned responses were observed. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Endogenous retroviruses function as species-specific enhancer elements in the placenta.

    Science.gov (United States)

    Chuong, Edward B; Rumi, M A Karim; Soares, Michael J; Baker, Julie C

    2013-03-01

    The mammalian placenta is remarkably distinct between species, suggesting a history of rapid evolutionary diversification. To gain insight into the molecular drivers of placental evolution, we compared biochemically predicted enhancers in mouse and rat trophoblast stem cells (TSCs) and found that species-specific enhancers are highly enriched for endogenous retroviruses (ERVs) on a genome-wide level. One of these ERV families, RLTR13D5, contributes hundreds of mouse-specific histone H3 lysine 4 monomethylation (H3K4me1)- and histone H3 lysine 27 acetylation (H3K27ac)-defined enhancers that functionally bind Cdx2, Eomes and Elf5-core factors that define the TSC regulatory network. Furthermore, we show that RLTR13D5 is capable of driving gene expression in rat placental cells. Analysis in other tissues shows that species-specific ERV enhancer activity is generally restricted to hypomethylated tissues, suggesting that tissues permissive for ERV activity gain access to an otherwise silenced source of regulatory variation. Overall, our results implicate ERV enhancer co-option as a mechanism underlying the extensive evolutionary diversification of placental development.

  1. Identification of hare meat by a species-specific marker of mitochondrial origin.

    Science.gov (United States)

    Santos, Cristina G; Melo, Vitor S; Amaral, Joana S; Estevinho, Letícia; Oliveira, M Beatriz P P; Mafra, Isabel

    2012-03-01

    Meat species identification in food has gained increasing interest in recent years due to public health, economic and legal concerns. Following the consumer trend towards high quality products, game meat has earned much attention. The aim of the present work was to develop a DNA-based technique able to identify hare meat. Mitochondrial cytochrome b gene was used to design species-specific primers for hare detection. The new primers proved to be highly specific to Lepus species, allowing the detection of 0.01% of hare meat in pork meat by polymerase chain reaction (PCR). A real-time PCR assay with the new intercalating EvaGreen dye was further proposed as a specific and fast tool for hare identification with increased sensitivity (1pg) compared to end-point PCR (10pg). It can be concluded that the proposed new primers can be used by both species-specific end-point PCR or real-time PCR to accurately authenticate hare meat. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. Evidence for simvastatin anti-inflammatory actions based on quantitative analyses of NETosis and other inflammation/oxidation markers

    Science.gov (United States)

    Al-Ghoul, Walid M.; Kim, Margarita S.; Fazal, Nadeem; Azim, Anser C.; Ali, Ashraf

    2014-01-01

    Simvastatin (SMV) has been shown to exhibit promising anti-inflammatory properties alongside its classic cholesterol lowering action. We tested these emerging effects in a major thermal injury mouse model (3rd degree scald, ~20% TBSA) with previously documented, inflammation-mediated intestinal defects. Neutrophil extracellular traps (NETs) inflammation measurement methods were used alongside classic gut mucosa inflammation and leakiness measurements with exogenous melatonin treatment as a positive control. Our hypothesis is that simvastatin has protective therapeutic effects against early postburn gut mucosa inflammation and leakiness. To test this hypothesis, we compared untreated thermal injury (TI) adult male mice with TI littermates treated with simvastatin (0.2 mg/kg i.p., TI + SMV) immediately following burn injury and two hours before being sacrificed the day after; melatonin-treated (Mel) (1.86 mg/kg i.p., TI + Mel) mice were compared as a positive control. Mice were assessed for the following: (1) tissue oxidation and neutrophil infiltration in terminal ileum mucosa using classic carbonyl, Gr-1, and myeloperoxidase immunohistochemical or biochemical assays, (2) NETosis in terminal ileum and colon mucosa homogenates and peritoneal and fluid blood samples utilizing flow cytometric analyses of the surrogate NETosis biomarkers, picogreen and Gr-1, and (3) transepithelial gut leakiness as measured in terminal ileum and colon with FITC-dextran and transepithelial electrical resistance (TEER). Our results reveal that simvastatin and melatonin exhibit consistently comparable therapeutic protective effects against the following: (1) gut mucosa oxidative stress as revealed in the terminal ileum by markers of protein carbonylation as well as myeloperoxidase (MPO) and Gr-1 infiltration, (2) NETosis as revealed in the gut milieu, peritoneal lavage and plasma utilizing picogreen and Gr-1 flow cytometry and microscopy, and (3) transepithelial gut leakiness as

  3. Dry-air drying at room temperature - a practical pre-treatment method of tree leaves for quantitative analyses of phenolics?

    Science.gov (United States)

    Tegelberg, Riitta; Virjamo, Virpi; Julkunen-Tiitto, Riitta

    2018-03-09

    In ecological experiments, storage of plant material is often needed between harvesting and laboratory analyses when the number of samples is too large for immediate, fresh analyses. Thus, accuracy and comparability of the results call for pre-treatment methods where the chemical composition remains unaltered and large number of samples can be treated efficiently. To study if a fast dry-air drying provides an efficient pre-treatment method for quantitative analyses of phenolics. Dry-air drying of mature leaves was done in a drying room equipped with dehumifier (10% relative humidity, room temperature) and results were compared to freeze-drying or freeze-drying after pre-freezing in liquid nitrogen. The quantities of methanol-soluble phenolics of Betula pendula Roth, Betula pubescens Ehrh., Salix myrsinifolia Salisb., Picea abies L. Karsten and Pinus sylvestris L. were analysed with HPLC and condensed tannins were analysed using the acid-butanol test. In deciduous tree leaves (Betula, Salix), the yield of most of the phenolic compounds was equal or higher in samples dried in dry-air room than the yield from freeze-dried samples. In Picea abies needles, however, dry-air drying caused severe reductions in picein, stilbenes, condensed tannin and (+)-catechin concentrations compared to freeze-drying. In Pinus sylvestris highest yields of neolignans but lowest yields of acetylated flavonoids were obtained from samples freeze-dried after pre-freezing. Results show that dry-air drying provides effective pre-treatment method for quantifying the soluble phenolics for deciduous tree leaves, but when analysing coniferous species, the different responses between structural classes of phenolics should be taken into account. Copyright © 2018 John Wiley & Sons, Ltd.

  4. HIV-1 Vif's Capacity To Manipulate the Cell Cycle Is Species Specific.

    Science.gov (United States)

    Evans, Edward L; Becker, Jordan T; Fricke, Stephanie L; Patel, Kishan; Sherer, Nathan M

    2018-04-01

    Cells derived from mice and other rodents exhibit profound blocks to HIV-1 virion production, reflecting species-specific incompatibilities between viral Tat and Rev proteins and essential host factors cyclin T1 (CCNT1) and exportin-1 (XPO1, also known as CRM1), respectively. To determine if mouse cell blocks other than CCNT1 and XPO1 affect HIV's postintegration stages, we studied HIV-1 NL4-3 gene expression in mouse NIH 3T3 cells modified to constitutively express HIV-1-compatible versions of CCNT1 and XPO1 (3T3.CX cells). 3T3.CX cells supported both Rev-independent and Rev-dependent viral gene expression and produced relatively robust levels of virus particles, confirming that CCNT1 and XPO1 represent the predominant blocks to these stages. Unexpectedly, however, 3T3.CX cells were remarkably resistant to virus-induced cytopathic effects observed in human cell lines, which we mapped to the viral protein Vif and its apparent species-specific capacity to induce G 2 /M cell cycle arrest. Vif was able to mediate rapid degradation of human APOBEC3G and the PPP2R5D regulatory B56 subunit of the PP2A phosphatase holoenzyme in mouse cells, thus demonstrating that Vif NL4-3 's modulation of the cell cycle can be functionally uncoupled from some of its other defined roles in CUL5-dependent protein degradation. Vif was also unable to induce G 2 /M cell cycle arrest in other nonhuman cell types, including cells derived from nonhuman primates, leading us to propose that one or more human-specific cofactors underpin Vif's ability to modulate the cell cycle. IMPORTANCE Cells derived from mice and other rodents exhibit profound blocks to HIV-1 replication, thus hindering the development of a low-cost small-animal model for studying HIV/AIDS. Here, we engineered otherwise-nonpermissive mouse cells to express HIV-1-compatible versions of two species-specific host dependency factors, cyclin T1 (CCNT1) and exportin-1 (XPO1) (3T3.CX cells). We show that 3T3.CX cells rescue HIV-1

  5. A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins.

    Science.gov (United States)

    Quintales, Luis; Soriano, Ignacio; Vázquez, Enrique; Segurado, Mónica; Antequera, Francisco

    2015-04-01

    Nucleosomes are the basic structural units of chromatin. Most of the yeast genome is organized in a pattern of positioned nucleosomes that is stably maintained under a wide range of physiological conditions. In this work, we have searched for sequence determinants associated with positioned nucleosomes in four species of fission and budding yeasts. We show that mononucleosomal DNA follows a highly structured base composition pattern, which differs among species despite the high degree of histone conservation. These nucleosomal signatures are present in transcribed and non-transcribed regions across the genome. In the case of open reading frames, they correctly predict the relative distribution of codons on mononucleosomal DNA, and they also determine a periodicity in the average distribution of amino acids along the proteins. These results establish a direct and species-specific connection between the position of each codon around the histone octamer and protein composition.

  6. Species-specific associations between soil-transmitted helminths and micronutrients in Vietnamese schoolchildren

    DEFF Research Database (Denmark)

    de Gier, Brechje; Nga, Tran Thuy; Winichagoon, Pattanee

    2016-01-01

    6-9 years were recruited from two primary schools. STH infections were determined in stool samples. Hemoglobin, ferritin, retinol, and zinc were measured in blood samples, as well as C-reactive protein to control for inflammation. Iodine excretion was measured in urine. Associations of single...... and multiple infections with Ascaris lumbricoides, Trichuris trichiura, and hookworm with micronutrient status (hemoglobin, plasma ferritin, retinol, zinc, and urinary iodine) were estimated by multiple regression analysis. Ascaris infections showed a specific and intensity-dependent negative association...... with vitamin A. Trichuris and hookworm infections were associated with lower hemoglobin concentration, but not with plasma ferritin. Trichuris-infected children had zinc deficiency less often than uninfected children. In conclusion, our study shows species-specific associations between STH infections...

  7. LC-MS/MS Identification of Species-Specific Muscle Peptides in Processed Animal Proteins.

    Science.gov (United States)

    Marchis, Daniela; Altomare, Alessandra; Gili, Marilena; Ostorero, Federica; Khadjavi, Amina; Corona, Cristiano; Ru, Giuseppe; Cappelletti, Benedetta; Gianelli, Silvia; Amadeo, Francesca; Rumio, Cristiano; Carini, Marina; Aldini, Giancarlo; Casalone, Cristina

    2017-12-06

    An innovative analytical strategy has been applied to identify signature peptides able to distinguish among processed animal proteins (PAPs) derived from bovine, pig, fish, and milk products. Proteomics was first used to elucidate the proteome of each source. Starting from the identified proteins and using a funnel based approach, a set of abundant and well characterized peptides with suitable physical-chemical properties (signature peptides) and specific for each source was selected. An on-target LC-ESI-MS/MS method (MRM mode) was set up using standard peptides and was then applied to selectively identify the PAP source and also to distinguish proteins from bovine carcass and milk proteins. We believe that the method described meets the request of the European Commission which has developed a strategy for gradually lifting the "total ban" toward "species to species ban", therefore requiring official methods for species-specific discrimination in feed.

  8. Use of Brucella abortus species specific polymerase chain reaction assay for the diagnosis of bovine brucellosis.

    Science.gov (United States)

    Chisi, Songelwayo L; Schmidt, Tracy; Akol, George W; Van Heerden, Henriette

    2017-09-27

    Serology is primarily used in the diagnosis of bovine brucellosis. Bacterial culture and isolation is the gold standard in diagnosing brucellosis but, like serology, it does not offer complete (100%) diagnostic sensitivity and specificity. Polymerase chain reaction (PCR) has been suggested to offer better specificity and sensitivity. In this study, we evaluated the performance of Brucella abortus species specific (BaSS) PCR directly from different samples in the diagnosis of bovine brucellosis in naturally infected cattle in KwaZulu-Natal province of South Africa with known infectious status from culture. The BaSS PCR had a low diagnostic sensitivity (DSe) of 70%, but was able to identify vaccine strains using abomasal fluid from aborted foetuses and detect Brucella DNA from decomposing samples. The best sample for the BaSS PCR was abomasal fluid.

  9. Development of an improved species specific PCR test for detection of Haemophilus parasuis

    DEFF Research Database (Denmark)

    Angen, Øystein; Oliveira, Simone; Ahrens, Peter

    2007-01-01

    , the present PCR test was found to be 100% species specific for H. parasuis, in contrast to the PCR test of Oliveira et al., which also tested positive for strains belonging to A. indolicus, A. porcinus, and A. minor, species commonly occurring in the upper respiratory tract. However, when the PCR test...... with representatives of H. parasuis. The test was further evaluated on 55 clinical samples from 16 Danish pigs suspected for being infected with H. parasuis, showing polyserositis or septicemia at autopsy as well as on 492 nasal swabs. The test was compared with the performance of a PCR test earlier published...... by Oliveira et al. [Oliveira, S., Galina, L., Pijoan, C., 2001. Development of a PCR test to diagnose Haemophilus parasuis infections. J. Vet. Diagn. Invest. 13, 495-501]. The sensitivity of the present PCR test was found to be slightly lower when applied on clinical samples from diseased pigs and 10-fold...

  10. In vivo synthesized 34S enriched amino acid standards for species specific isotope dilution of proteins

    DEFF Research Database (Denmark)

    Hermann, Gerrit; Moller, Laura Hyrup; Gammelgaard, Bente

    2016-01-01

    (ICP-MS) combined to anion exchange showed that very high concentrated spike material could be produced with [small mu ]mol amounts of proteinogenic sulfur containing amino acids per g cell dry weight. An enrichment of 34S to 96.3 +/- 0.4% (n = 3) and 98.5 +/- 0.4% (n = 3) for cysteic acid...... with the concept of species specific isotope dilution analysis (IDA). The method relies on the determination of the two sulfur containing amino acids, cysteine and methionine by sulfur speciation analysis and is hence applicable to any protein containing sulfur. In vivo synthesis using 34S as sulfur source...... and methionine sulfone, respectively, was assessed. The established IDA method was validated for the absolute quantification of commercially available lysozyme and ceruloplasmin standards including the calculation of a total combined uncertainty budget....

  11. Temporal Lobe Lesions and Perception of Species-Specific Vocalizations by Macaques

    Science.gov (United States)

    Heffner, Henry E.; Heffner, Rickye S.

    1984-10-01

    Japanese macaques were trained to discriminate two forms of their coo vocalization before and after unilateral and bilateral ablation of the temporal cortex. Unilateral ablation of the left superior temporal gyrus, including auditory cortex, resulted in an initial impairment in the discrimination, but similar unilateral ablation of the right superior temporal gyrus had no effect. Bilateral temporal lesions including auditory cortex completely abolished the ability of the animals to discriminate their coos. Neither unilateral nor bilateral ablation of cortex dorsal to and sparing the auditory cortex had any effect on the discrimination. The perception of species-specific vocalizations by Japanese macaques seems to be mediated by the temporal cortex, with the left hemisphere playing a predominant role.

  12. Identification of campylobacteria isolated from Danish broilers by phenotypic tests and species-specific PCR assays

    DEFF Research Database (Denmark)

    Wainø, M.; Bang, Dang Duong; Lund, Marianne

    2003-01-01

    campylobacterial cultures, 108 Campylobacter jejuni cultures and 351 campylobacterial cultures other than Camp. jejuni were subjected to various species-specific PCR assays. On the basis of the genotypic tests, it was demonstrated that Camp. jejuni and Camp. coli constituted approx. 99% of all cultures, while...... other species identified were Helicobacter pullorum, Camp. lari and Camp. upsaliensis. However, 29% of the 309 Camp. coli cultures identified by phenotypic tests were hippurate-variable or negative Camp. jejuni cultures, whereas some Camp. lari cultures and unspeciated campylobacter cultures belonged...... and Impact of the Study: Future phenotypic test schemes should be designed to allow a more accurate differentiation of Campylobacter and related species. Preferably, the phenotypic tests should be supplemented with a genotypic strategy to disclose the true campylobacterial species diversity in broilers....

  13. Conjugated action of two species-specific invasion proteins for fetoplacental listeriosis.

    Science.gov (United States)

    Disson, Olivier; Grayo, Solène; Huillet, Eugénie; Nikitas, Georgios; Langa-Vives, Francina; Dussurget, Olivier; Ragon, Marie; Le Monnier, Alban; Babinet, Charles; Cossart, Pascale; Lecuit, Marc

    2008-10-23

    The ability to cross host barriers is an essential virulence determinant of invasive microbial pathogens. Listeria monocytogenes is a model microorganism that crosses human intestinal and placental barriers, and causes severe maternofetal infections by an unknown mechanism. Several studies have helped to characterize the bacterial invasion proteins InlA and InlB. However, their respective species specificity has complicated investigations on their in vivo role. Here we describe two novel and complementary animal models for human listeriosis: the gerbil, a natural host for L. monocytogenes, and a knock-in mouse line ubiquitously expressing humanized E-cadherin. Using these two models, we uncover the essential and interdependent roles of InlA and InlB in fetoplacental listeriosis, and thereby decipher the molecular mechanism underlying the ability of a microbe to target and cross the placental barrier.

  14. Species-specific variation in the phosphorus nutritional sources by microphytoplankton in a Mediterranean estuary

    Directory of Open Access Journals (Sweden)

    MARLY CAROLINA MARTINEZ SOTO

    2015-08-01

    Full Text Available We investigated the species-specific phosphorus (P nutrition sources in the microphytoplankton community in the Mahon estuary (Minorca, Western Mediterranean in 2011, under two contrasting hydrographic scenarios. Estuarine flow, nutrient concentrations, phytoplankton community composition and enzyme-labeled fluorescence (ELF were measured in June and October, corresponding to the beginning and the end of summer. Dissolved inorganic nitrogen (DIN and inorganic phosphate (Pi exhibited enhanced concentrations in the inner estuary where N:P molar ratios suggested P-limitation in both surveys. Pi was low and variable (0.09±0.02 μmol•l-1 in June and 0.06±0.02 μmol•l-1 in October, whereas organic phosphorus remained a more reliable P source. Even though ambient Pi concentrations were slightly higher on June, when the microphytoplankton assemblage was dominated by dinoflagellates, the percentage of cells expressing ELF labeling was notably higher (65% of total cells than in October (12%, when the presence of diatoms characterized the microphytoplankton community. ELF was mainly expressed by dinoflagellate taxa, whereas diatoms only expressed significant AP in the inner estuary during the June survey. A P-addition bioassay in which response of AP to Pi enrichment was evaluated showed remarkable reduction in AP with increasing Pi. However, some dinoflagellate species maintained AP even when Pi was supplied in excess. We suggest that in the case of some dinoflagellate species AP is not as tightly controlled by ambient Pi as previously believed. AP activity in these species could indicate selective use of organic phosphorus, or slow metabolic response to changes in P forms, rather than physiological stress to low Pi availability. We emphasize the importance of identifying the links between the different P sources and the species-specific requirements, in order to understand the ecological response to anthropogenic biogeochemical perturbations.

  15. Species-specific optical genosensors for the detection of mycotoxigenic Fusarium fungi in food samples

    International Nuclear Information System (INIS)

    Peltomaa, Riikka; Vaghini, Silvia; Patiño, Belén; Benito-Peña, Elena; Moreno-Bondi, María C.

    2016-01-01

    Plant-pathogenic Fusarium species, Fusarium verticillioides and Fusarium proliferatum, are the major producers of fumonisins which are one of the most common mycotoxins found in maize. Herein, we report the development of specific and sensitive genosensors for detecting these two closely related Fusarium species in food samples. The sensors are based on species-specific capture and detection probes, which bind to the intergenic spacer region of rDNA (IGS). Oligonucleotide functionalized magnetic microbeads are used to capture the target DNA which is then detected using biotinylated detection probes and a streptavidin-coupled label. The developed genosensors had detection limits of 1.8 pM and 3.0 pM for F. proliferatum and F. verticillioides, respectively, using synthetic DNA targets. Furthermore, the biosensors were used to analyze natural fungal contamination of commercial maize samples. After amplification of the genomic DNA the sensors detected the presence of the fungi, in accordance with previous results obtained with PCR. No cross-reactivity between F. verticillioides and F. proliferatum, or other fungi species tested, was observed. The developed biosensors can provide a valuable tool to evaluate the potential for mycotoxin contamination in conditions where detection of mycotoxins directly is challenging. - Highlights: • Optical genosensors detect fumonisin producing Fusarium species in maize samples. • Oligonucleotide probes designed on the intergenic spacer region of rDNA can distinguish between closely related species. • Sandwich hybridization assay with magnetic microbeads allows species-specific detection of Fusarium spp. directly from PCR.

  16. Species-specific optical genosensors for the detection of mycotoxigenic Fusarium fungi in food samples

    Energy Technology Data Exchange (ETDEWEB)

    Peltomaa, Riikka; Vaghini, Silvia [Department of Analytical Chemistry, Faculty of Chemistry, Complutense University, Ciudad Universitaria s/n, Madrid 28040 (Spain); Patiño, Belén [Department of Microbiology III, Faculty of Biology, Complutense University, Ciudad Universitaria s/n, Madrid 28040 (Spain); Benito-Peña, Elena, E-mail: elenabp@ucm.es [Department of Analytical Chemistry, Faculty of Chemistry, Complutense University, Ciudad Universitaria s/n, Madrid 28040 (Spain); Moreno-Bondi, María C., E-mail: mcmbondi@ucm.es [Department of Analytical Chemistry, Faculty of Chemistry, Complutense University, Ciudad Universitaria s/n, Madrid 28040 (Spain)

    2016-09-07

    Plant-pathogenic Fusarium species, Fusarium verticillioides and Fusarium proliferatum, are the major producers of fumonisins which are one of the most common mycotoxins found in maize. Herein, we report the development of specific and sensitive genosensors for detecting these two closely related Fusarium species in food samples. The sensors are based on species-specific capture and detection probes, which bind to the intergenic spacer region of rDNA (IGS). Oligonucleotide functionalized magnetic microbeads are used to capture the target DNA which is then detected using biotinylated detection probes and a streptavidin-coupled label. The developed genosensors had detection limits of 1.8 pM and 3.0 pM for F. proliferatum and F. verticillioides, respectively, using synthetic DNA targets. Furthermore, the biosensors were used to analyze natural fungal contamination of commercial maize samples. After amplification of the genomic DNA the sensors detected the presence of the fungi, in accordance with previous results obtained with PCR. No cross-reactivity between F. verticillioides and F. proliferatum, or other fungi species tested, was observed. The developed biosensors can provide a valuable tool to evaluate the potential for mycotoxin contamination in conditions where detection of mycotoxins directly is challenging. - Highlights: • Optical genosensors detect fumonisin producing Fusarium species in maize samples. • Oligonucleotide probes designed on the intergenic spacer region of rDNA can distinguish between closely related species. • Sandwich hybridization assay with magnetic microbeads allows species-specific detection of Fusarium spp. directly from PCR.

  17. Species-specific variation in nesting and postfledging resource selection for two forest breeding migrant songbirds.

    Directory of Open Access Journals (Sweden)

    Julianna M A Jenkins

    Full Text Available Habitat selection is a fundamental component of community ecology, population ecology, and evolutionary biology and can be especially important to species with complex annual habitat requirements, such as migratory birds. Resource preferences on the breeding grounds may change during the postfledging period for migrant songbirds, however, the degree to which selection changes, timing of change, and whether all or only a few species alter their resource use is unclear. We compared resource selection for nest sites and resource selection by postfledging juvenile ovenbirds (Seiurus aurocapilla and Acadian flycatchers (Empidonax virescens followed with radio telemetry in Missouri mature forest fragments from 2012-2015. We used Bayesian discrete choice modeling to evaluate support for local vegetation characteristics on the probability of selection for nest sites and locations utilized by different ages of postfledging juveniles. Patterns of resource selection variation were species-specific. Resource selection models indicated that Acadian flycatcher habitat selection criteria were similar for nesting and dependent postfledging juveniles and selection criteria diverged when juveniles became independent from adults. After independence, flycatcher resource selection was more associated with understory foliage density. Ovenbirds differed in selection criteria between the nesting and postfledging periods. Fledgling ovenbirds selected areas with higher densities of understory structure compared to nest sites, and the effect of foliage density on selection increased as juveniles aged and gained independence. The differences observed between two sympatric forest nesting species, in both the timing and degree of change in resource selection criteria over the course of the breeding season, illustrates the importance of considering species-specific traits and postfledging requirements when developing conservation efforts, especially when foraging guilds or

  18. Species-specific flight styles of flies are reflected in the response dynamics of a homologue motion sensitive neuron

    Directory of Open Access Journals (Sweden)

    Bart eGeurten

    2012-03-01

    Full Text Available Hoverflies and blowflies have distinctly different flight styles. Yet, both species have been shown to structure their flight behaviour in a way that facilitates extraction of 3D information from the image flow on the retina (optic flow. Neuronal candidates to analyse the optic flow are the tangential cells in the third optical ganglion – the lobula complex. These neurons are directionally selective and integrate the optic flow over large parts of the visual field. Homologue tangential cells in hoverflies and blowflies have a similar morphology. Because blowflies and hoverflies have similar neuronal layout but distinctly different flight behaviours, they are an ideal substrate to pinpoint potential neuronal adaptations to the different flight styles.In this article we describe the relationship between locomotion behaviour and motion vision on three different levels:1.We compare the different flight styles based on the categorisation of flight behaviour into prototypical movements.2.We measure the species specific dynamics of the optic flow under naturalistic flight conditions. We found the translational optic flow of both species to be very different.3.We describe possible adaptations of a homologue motion sensitive neuron. We stimulate this cell in blowflies (Calliphora and hoverflies (Eristalis with naturalistic optic flow generated by both species during free flight. The characterized hoverfly tangential cell responds faster to transient changes in the optic flow than its blowfly homologue. It is discussed whether and how the different dynamical response properties aid optic flow analysis.

  19. High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute

    Directory of Open Access Journals (Sweden)

    Md. Tariqul Islam

    2015-01-01

    Full Text Available MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops.

  20. Detection of all Chlamydophila and Chlamydia spp. of veterinary interest using species-specific real-time PCR assays.

    Science.gov (United States)

    Pantchev, Alexandra; Sting, Reinhard; Bauerfeind, Rolf; Tyczka, Judith; Sachse, Konrad

    2010-12-01

    The aim of the present study was to analyse the occurrence of chlamydiae in several mammalian host species. Clinical samples that previously tested positive in a Chlamydiaceae-specific real-time PCR were retested using six species-specific real-time PCR assays to identify the chlamydial species involved. Chlamydophila (Cp.) abortus was the agent most frequently found in cattle, sheep, horses, goats, and pigs. Detection in cattle of Cp. psittaci (11% of samples) and Chlamydia (C.) suis (9%), as well as Cp. psittaci in a goat sample was somewhat unexpected. DNA of two different chlamydiae was identified in 56 (12.7%) of 440 samples tested. Cp. felis was the predominant species found in cats, while in guinea pigs and rabbits only Cp. caviae was detected. Interestingly, the latter two pathogens were also identified in samples from dogs. The data show that mixed chlamydial infections are not rare and suggest an extended host range of individual species. Copyright © 2009 Elsevier Ltd. All rights reserved.

  1. Coagulase-negative Staphylococcus species in bulk milk: Prevalence, distribution, and associated subgroup- and species-specific risk factors.

    Science.gov (United States)

    De Visscher, A; Piepers, S; Haesebrouck, F; Supré, K; De Vliegher, S

    2017-01-01

    Coagulase-negative staphylococci (CNS) have become the main pathogens causing bovine mastitis in recent years. A huge variation in species distribution among herds has been observed in several studies, emphasizing the need to identify subgroup- and species-specific herd-level factors to improve our understanding of the differences in ecological and epidemiological nature between species. The use of bulk milk samples enables the inclusion of a large(r) number of herds needed to identify herd-level risk factors and increases the likelihood of recovering enough isolates per species needed for conducting subgroup- and, eventually, species-specific analyses at the same time. This study aimed to describe the prevalence and distribution of CNS species in bulk milk samples and to identify associated subgroup- and species-specific herd-level factors. Ninety percent of all bulk milk samples yielded CNS. Staphylococcus equorum was the predominant species, followed by Staphylococcus haemolyticus and Staphylococcus epidermidis. A seasonal effect was observed for several CNS species. Bulk milk samples from herds with a loose-pack or a tiestall housing system were more likely to yield CNS species compared with herds with a freestall barn, except for S. epidermidis, Staphylococcus simulans, and Staphylococcus cohnii. In September, herds in which udders were clipped had lower odds of yielding Staphylococcus chromogenes, S. simulans, and Staphylococcus xylosus, the CNS species assumed to be most relevant for udder health, in their bulk milk than herds in which udder clipping was not practiced. Bulk milk of herds participating in a monthly veterinary udder health-monitoring program was more likely to yield these 3 CNS species. Herds always receiving their milk quality premium or predisinfecting teats before attachment of the milking cluster had lower odds of having S. equorum in their bulk milk. Herds not using a single dry cotton or paper towel for each cow during premilking udder

  2. Everyday life and social relations in home-living patients with mild Alzheimer's disease and their caregivers: Quantitative and qualitative analyses

    DEFF Research Database (Denmark)

    Sørensen, Lisbeth Villemoes

    2007-01-01

    Everyday life and social relations in home-living patients with mild Alzheimer’s disease (AD) and their caregivers: quantitative and qualitative analyses. This PhD project was carried out between April 2004 and March 2007 during my employment as project coordinator in the Memory Disorder Research...... and the presence of neuropsychiatric symptoms. In the second study, data were collected using semi-structured research interviews with 11 patients before their participation in the DAISY intervention programme. Grounded theory analysis of the interview data revealed that the basic social psychological problem...... faced by the patients was: their awareness of decline in personal dignity and value. Coping strategies used to meet these problems were adaptations to the altered situation in order to maintain a feeling of well-being. In the third study, data were collected using individual semi-structured research...

  3. Elastic fibers in human skin: quantitation of elastic fibers by computerized digital image analyses and determination of elastin by radioimmunoassay of desmosine.

    Science.gov (United States)

    Uitto, J; Paul, J L; Brockley, K; Pearce, R H; Clark, J G

    1983-10-01

    The elastic fibers in the skin and other organs can be affected in several disease processes. In this study, we have developed morphometric techniques that allow accurate quantitation of the elastic fibers in punch biopsy specimens of skin. In this procedure, the elastic fibers, visualized by elastin-specific stains, are examined through a camera unit attached to the microscope. The black and white images sensing various gray levels are then converted to binary images after selecting a threshold with an analog threshold selection device. The binary images are digitized and the data analyzed by a computer program designed to express the properties of the image, thus allowing determination of the volume fraction occupied by the elastic fibers. As an independent measure of the elastic fibers, alternate tissue sections were used for assay of desmosine, an elastin-specific cross-link compound, by a radioimmunoassay. The clinical applicability of the computerized morphometric analyses was tested by examining the elastic fibers in the skin of five patients with pseudoxanthoma elasticum or Buschke-Ollendorff syndrome. In the skin of 10 healthy control subjects, the elastic fibers occupied 2.1 +/- 1.1% (mean +/- SD) of the dermis. The volume fractions occupied by the elastic fibers in the lesions of pseudoxanthoma elasticum or Buschke-Ollendorff syndrome were increased as much as 6-fold, whereas the values in the unaffected areas of the skin in the same patients were within normal limits. A significant correlation between the volume fraction of elastic fibers, determined by computerized morphometric analyses, and the concentration of desmosine, quantitated by radioimmunoassay, was noted in the total material. These results demonstrate that computerized morphometric techniques are helpful in characterizing disease processes affecting skin. This methodology should also be applicable to other tissues that contain elastic fibers and that are affected in various heritable and

  4. A bottom-up approach in estimating the measurement uncertainty and other important considerations for quantitative analyses in drug testing for horses.

    Science.gov (United States)

    Leung, Gary N W; Ho, Emmie N M; Kwok, W Him; Leung, David K K; Tang, Francis P W; Wan, Terence S M; Wong, April S Y; Wong, Colton H F; Wong, Jenny K Y; Yu, Nola H

    2007-09-07

    derive the combined standard uncertainty. Finally, an expanded uncertainty is calculated at 99% one-tailed confidence level by multiplying the standard uncertainty with an appropriate coverage factor (k). A sample is considered positive if the determined concentration of the threshold substance exceeds its threshold by the expanded uncertainty. In addition, other important considerations, which can have a significant impact on quantitative analyses, will be presented.

  5. Combined metabonomic and quantitative real-time PCR analyses reveal systems metabolic changes in Jurkat T-cells treated with HIV-1 Tat protein.

    Science.gov (United States)

    Liao, Wenting; Tan, Guangguo; Zhu, Zhenyu; Chen, Qiuli; Lou, Ziyang; Dong, Xin; Zhang, Wei; Pan, Wei; Chai, Yifeng

    2012-11-02

    HIV-1 Tat protein is released by infected cells and can affect bystander uninfected T cells and induce numerous biological responses which contribute to its pathogenesis. To elucidate the complex pathogenic mechanism, we conducted a comprehensive investigation on Tat protein-related extracellular and intracellular metabolic changes in Jurkat T-cells using combined gas chromatography-mass spectrometry (GC-MS), reversed-phase liquid chromatography-mass spectrometry (RPLC-MS) and a hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS)-based metabonomics approach. Quantitative real-time PCR (qRT-PCR) analyses were further employed to measure expressions of several relevant enzymes together with perturbed metabolic pathways. Combined metabonomic and qRT-PCR analyses revealed that HIV-1 Tat caused significant and comprehensive metabolic changes, as represented by significant changes of 37 metabolites and 10 relevant enzymes in HIV-1 Tat-treated cells. Using MetaboAnalyst 2.0, it was found that 11 pathways (Impact-value >0.10) among the regulated pathways were acutely perturbed, including sphingolipid metabolism, glycine, serine and threonine metabolism, pyruvate metabolism, inositol phosphate metabolism, arginine and proline metabolism, citrate cycle, phenylalanine metabolism, tryptophan metabolism, pentose phosphate pathway, glycerophospholipid metabolism, glycolysis or gluconeogenesis. These results provide metabolic evidence of the complex pathogenic mechanism of HIV-1 Tat protein as a "viral toxin", and would help obligate Tat protein as "an important target" for therapeutic intervention and vaccine development.

  6. Nesting behaviour influences species-specific gas exchange across avian eggshells.

    Science.gov (United States)

    Portugal, Steven J; Maurer, Golo; Thomas, Gavin H; Hauber, Mark E; Grim, Tomáš; Cassey, Phillip

    2014-09-15

    Carefully controlled gas exchange across the eggshell is essential for the development of the avian embryo. Water vapour conductance (G(H2O)) across the shell, typically measured as mass loss during incubation, has been demonstrated to optimally ensure the healthy development of the embryo while avoiding desiccation. Accordingly, eggs exposed to sub-optimal gas exchange have reduced hatching success. We tested the association between eggshell G(H2O) and putative life-history correlates of adult birds, ecological nest parameters and physical characteristics of the egg itself to investigate how variation in G(H2O) has evolved to maintain optimal water loss across a diverse set of nest environments. We measured gas exchange through eggshell fragments in 151 British breeding bird species and fitted phylogenetically controlled, general linear models to test the relationship between G(H2O) and potential predictor parameters of each species. Of our 17 life-history traits, only two were retained in the final model: wet-incubating parent and nest type. Eggs of species where the parent habitually returned to the nest with wet plumage had significantly higher G(H2O) than those of parents that returned to the nest with dry plumage. Eggs of species nesting in ground burrows, cliffs and arboreal cups had significantly higher G(H2O) than those of species nesting on the ground in open nests or cups, in tree cavities and in shallow arboreal nests. Phylogenetic signal (measured as Pagel's λ) was intermediate in magnitude, suggesting that differences observed in the G(H2O) are dependent upon a combination of shared ancestry and species-specific life history and ecological traits. Although these data are correlational by nature, they are consistent with the hypothesis that parents constrained to return to the nest with wet plumage will increase the humidity of the nest environment, and the eggs of these species have evolved a higher G(H2O) to overcome this constraint and still

  7. Species-specific intrinsic water use efficiency and its mediation of carbon assimilation during the drought

    Science.gov (United States)

    Yi, K.; Wenzel, M. K.; Maxwell, J. T.; Novick, K. A.; Gray, A.; Roman, D. T.

    2015-12-01

    Drought is expected to occur more frequently and intensely in the future, and many studies have suggested frequent and intense droughts can significantly alter carbon and water cycling in forest ecosystems, consequently decreasing the ability of forests to assimilate carbon. Predicting the impact of drought on forest ecosystem processes requires an understanding of species-specific responses to drought, especially in eastern US where species composition is highly dynamic. An emerging approach for describing species-specific drought response is to classify the plant water use strategy into isohydric and anisohydric behaviors. Trees utilizing isohydric behavior regulate water potential by closing stomata to reduce water loss during drought conditions, while anisohydric trees allow water potential to drop by sustaining stomatal conductance, but with the risk of hydraulic failure caused by cavitation of xylem tissues. Since catastrophic cavitation occurs infrequently in the relatively wet eastern U.S., we hypothesize that 1) tree growth of isohydric trees will be more limited during the drought than the anisohydric trees due to decreased stomatal conductance, but 2) variation in intrinsic water use efficient (iWUE) during drought in isohydric trees will mediate the effects of drought on carbon assimilation. We will test these hypotheses by 1) analyzing tree-ring chronologies and dendrometer data on productivity, and 2) estimating intrinsic water use efficiency (iWUE) at multiple scales by analyzing gas exchange data for the leaf-level, inter-annual variability of d13C in tree stem cores for the tree-level, and eddy covariance technique for the stand-level. Our study site is the Morgan-Monroe State Forest (Indiana, USA). A 46 m flux tower has been continuously recording the carbon, water and energy fluxes, and tree diameter has been measured every 2 weeks using dendrometers, since 1998. Additional research, including gas exchange measurements performed during the

  8. Link-N: The missing link towards intervertebral disc repair is species-specific.

    Directory of Open Access Journals (Sweden)

    Frances C Bach

    Full Text Available Degeneration of the intervertebral disc (IVD is a frequent cause for back pain in humans and dogs. Link-N stabilizes proteoglycan aggregates in cartilaginous tissues and exerts growth factor-like effects. The human variant of Link-N facilitates IVD regeneration in several species in vitro by inducing Smad1 signaling, but it is not clear whether this is species specific. Dogs with IVD disease could possibly benefit from Link-N treatment, but Link-N has not been tested on canine IVD cells. If Link-N appears to be effective in canines, this would facilitate translation of Link-N into the clinic using the dog as an in vivo large animal model for human IVD degeneration.This study's objective was to determine the effect of the human and canine variant of Link-N and short (s Link-N on canine chondrocyte-like cells (CLCs and compare this to those on already studied species, i.e. human and bovine CLCs. Extracellular matrix (ECM production was determined by measuring glycosaminoglycan (GAG content and histological evaluation. Additionally, the micro-aggregates' DNA content was measured. Phosphorylated (p Smad1 and -2 levels were determined using ELISA.Human (sLink-N induced GAG deposition in human and bovine CLCs, as expected. In contrast, canine (sLink-N did not affect ECM production in human CLCs, while it mainly induced collagen type I and II deposition in bovine CLCs. In canine CLCs, both canine and human (sLink-N induced negligible GAG deposition. Surprisingly, human and canine (sLink-N did not induce Smad signaling in human and bovine CLCs. Human and canine (sLink-N only mildly increased pSmad1 and Smad2 levels in canine CLCs.Human and canine (sLink-N exerted species-specific effects on CLCs from early degenerated IVDs. Both variants, however, lacked the potency as canine IVD regeneration agent. While these studies demonstrate the challenges of translational studies in large animal models, (sLink-N still holds a regenerative potential for humans.

  9. Species-specific AFLP markers for identification of Zingiber officinale, Z. montanum and Z. zerumbet (Zingiberaceae).

    Science.gov (United States)

    Ghosh, S; Majumder, P B; Sen Mandi, S

    2011-02-08

    The Zingiber genus, which includes the herbs known as gingers, commonly used in cooking, is well known for its medicinal properties, as described in the Indian pharmacopoeia. Different members of this genus, although somewhat similar in morphology, differ widely in their pharmacological and therapeutic properties. The most important species of this genus, with maximal therapeutic properties, is Zingiber officinale (garden ginger), which is often adulterated with other less-potent Zingiber sp. There is an existing demand in the herbal drug industry for an authentication system for the Zingiber sp in order to facilitate their commercial use as genuine phytoceuticals. To this end, we used amplified fragment length polymorphism (AFLP) to produce DNA fingerprints for three Zingiber species. Sixteen collections (six of Z. officinale, five of Z. montanum, and five of Z. zerumbet) were used in the study. Seven selective primer pairs were found to be useful for all the accessions. A total of 837 fragments were produced by these primer pairs. Species-specific markers were identified for all three Zingiber species (91 for Z. officinale, 82 for Z. montanum, and 55 for Z. zerumbet). The dendogram analysis generated from AFLP patterns showed that Z. montanum and Z. zerumbet are phylogenetically closer to each other than to Z. officinale. The AFLP fingerprints of the Zingiber species could be used to authenticate Zingiber sp-derived drugs and to resolve adulteration-related problems faced by the commercial users of these herbs.

  10. Species-specific associations between overstory and understory tree species in a semideciduous tropical forest

    Directory of Open Access Journals (Sweden)

    Flaviana Maluf Souza

    2015-03-01

    Full Text Available We investigated the occurrence of associations between overstory and understory tree species in a semideciduous tropical forest. We identified and measured all trees of nine canopy species with diameter at breast height ≥4.8 cm in a 10.24 ha plot and recorded all individuals beneath their canopies ("understory individuals" within the same diameter class. The total density of understory individuals did not significantly differ under different overstory species. One overstory species (Ceiba speciosa showed higher understory species richness compared with five other species. There was a strong positive association between three overstory species (Esenbeckia leiocarpa, Savia dictyocarpa, and C. speciosa and the density of seven understory species (Balfourodendron riedelianum, Chrysophyllum gonocarpum, E. leiocarpa, Holocalyx balansae, Machaerium stipitatum, Rhaminidium elaeocarpum, and S. dictyocarpa. These results probably reflect the outcome of a complex set of interactions including facilitation and competition, and further studies are necessary to better understand the magnitude and type of the effects of individual overstory species on understory species. The occurrence of species-specific associations shown here reinforces the importance of non-random processes in structuring plant communities and suggest that the influence of overstory species on understory species in high-diversity forests may be more significant than previously thought.

  11. Species-specific evolution of class I MHC genes in iguanas (order: Squamata; subfamily: Iguaninae).

    Science.gov (United States)

    Glaberman, Scott; Caccone, Adalgisa

    2008-07-01

    Over the last few decades, the major histocompatibility complex (MHC) has emerged as a model for understanding the influence of natural selection on genetic diversity in populations as well as for investigating the genetic basis of host resistance to pathogens. However, many vertebrate taxa remain underrepresented in the field of MHC research, preventing its application to studies of disease, evolution, and conservation genetics in these groups. This is particularly true for squamates, which are by far the most diversified order of non-avian reptiles but have not been the subject of any recent MHC studies. In this paper, we present MHC class I complementary DNA data from three squamate species in the subfamily Iguaninae (iguanas): the Galápagos marine iguana (Amblyrhynchus cristatus), the Galápagos land iguana (Conolophus subcristatus), and the green iguana (Iguana iguana). All sequences obtained are related to the few published class I genes from other squamates. There is evidence for multiple loci in each species, and the conserved alpha-3 domain appears to be evolving in a species-specific manner. Conversely, there is some indication of shared polymorphism between species in the peptide-binding alpha-1 and alpha-2 domains, suggesting that these two regions have different phylogenetic histories. The great similarity between alpha-3 sequences in marine iguanas in particular suggests that concerted evolution is acting to homogenize class I loci within species. However, while less likely, the data are also compatible with a birth and death model of evolution.

  12. Plants of the fynbos biome harbour host species-specific bacterial communities.

    Science.gov (United States)

    Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

    2016-08-01

    The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Species-specific effects of soil fauna on fungal foraging and decomposition.

    Science.gov (United States)

    Crowther, Thomas W; Boddy, Lynne; Jones, T Hefin

    2011-10-01

    Decomposer fungi are primary decomposing agents in terrestrial soils. Their mycelial networks play an important role in nutrient mineralisation and distribution, but are also nutritious resources for various soil invertebrates. Global climate change is predicted to alter the diversity and community composition of these soil fauna. To understand whether changes in invertebrate species diversity are likely to affect fungal-mediated decomposition, this study compared the grazing potentials of different invertebrate taxa and functional groups. Specifically, the grazing impacts of seven invertebrate taxa on the growth and spatial distribution of six basidiomycete fungi growing from beech wood blocks in soil microcosms were explored. Wood decay rates by fungi were also compared. The consequences of grazing were both taxon- and species-specific. Generally, macro-invertebrates caused the greatest damage, while meso- and micro-invertebrates often stimulated mycelial growth. Invertebrate size, preferences and population dynamics are likely to influence grazing potentials. Effects of grazing varied between fungi, with mycelial morphology and biochemistry possibly influencing susceptibility. Heavy grazing indirectly increased fungal-mediated wood decomposition. Changes in invertebrate community composition are predicted to have consequences for fungal growth, activity and community structure in woodland soils. Abiotic climate change factors including CO(2) and temperature affect mycelial productivity directly, but the indirect effects, mediated through changes in the soil invertebrate community, may be equally important in controlling ecosystem functioning.

  14. Diastereoisomer- and species-specific distribution of hexabromocyclododecane (HBCD) in fish and marine invertebrates.

    Science.gov (United States)

    Son, Min-Hui; Kim, Jongchul; Shin, Eun-Su; Seo, Sung-Hee; Chang, Yoon-Seok

    2015-12-30

    The levels and distributional characteristics of hexabromocyclododecane (HBCD) diastereoisomers have been largely reported for various fish and select shellfish. In this study, we reclassified a number and variety of marine invertebrates, including shellfish, to further contribute to the comprehensive understanding of the effects and assessment of human exposure to HBCD. Overall, 30 marine invertebrate species (n=188) were investigated and the following order of ∑2HBCD (α- and γ-HBCD) was observed: fish>chordata>cephalopoda>echinodermata>bivalve>crustacea. The marine invertebrates that were reclassified into nektonic and benthic organisms showed similar concentration of ∑2HBCD. The feeding habits and modes of the marine organisms were considered to compare the degree of bioaccumulation and diastereoisomer-specific distribution of HBCD due to the effects of the environment in and around pollution sources, as well as the organisms' metabolic capacities. To the best of our knowledge, this is the first study to examine the species-specific distribution patterns of HBCD for both fish and marine invertebrates. We expect to significantly expand the understanding of the environmental fate of HBCD for marine organisms. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Detection of Ophiocordyceps sinensis and Its Common Adulterates Using Species-Specific Primers

    Science.gov (United States)

    Liu, Yang; Wang, Xiao-yue; Gao, Zi-tong; Han, Jian-ping; Xiang, Li

    2017-01-01

    Ophiocordyceps sinensis is a fungus that infects Hepialidae caterpillars, mummifying the larvae and producing characteristic fruiting bodies (stromata) that are processed into one of the most valued traditional Chinese medicines (TCM). The product commands a very high price due to a high demand but a very limited supply. Adulteration with other fungi is a common problem and there is a need to test preparation for the presence of the correct fungus. In the current study, a PCR-based approach for the identification of O. sinensis based on a segment of the internal transcribed spacer (ITS) region was developed. The segments is 146-bp in size and is likely to be amplified even in materials where processing led to DNA fragmentation. Primer development was based on the alignment of sequence data generated from a total of 89 samples of O. sinensis and potential adulterants as well as sequences date from 41 Ophiocordyceps species and 26 Cordyceps species available in GenBank. Tests with primer pair, DCF4/DCR4, demonstrated generation of an amplicon from DNA extracted from O. sinensis stromata, but not from extracts derived from adulterants. Species-specific primer pairs were also developed and tested for detection of the common adulterants, Cordyceps gunnii, Cordyceps cicadae, Cordyceps militaris, Cordyceps liangshanensis and Ophiocordyceps nutans. The collection of primers developed in the present study will be useful for the authentication of preparation claiming to only contain O. sinensis and for the detection of fungi used as adulterants in these preparations. PMID:28680424

  16. Species-specific calls evoke asymmetric activity in the monkey's temporal poles.

    Science.gov (United States)

    Poremba, Amy; Malloy, Megan; Saunders, Richard C; Carson, Richard E; Herscovitch, Peter; Mishkin, Mortimer

    2004-01-29

    It has often been proposed that the vocal calls of monkeys are precursors of human speech, in part because they provide critical information to other members of the species who rely on them for survival and social interactions. Both behavioural and lesion studies suggest that monkeys, like humans, use the auditory system of the left hemisphere preferentially to process vocalizations. To investigate the pattern of neural activity that might underlie this particular form of functional asymmetry in monkeys, we measured local cerebral metabolic activity while the animals listened passively to species-specific calls compared with a variety of other classes of sound. Within the superior temporal gyrus, significantly greater metabolic activity occurred on the left side than on the right, only in the region of the temporal pole and only in response to monkey calls. This functional asymmetry was absent when these regions were separated by forebrain commissurotomy, suggesting that the perception of vocalizations elicits concurrent interhemispheric interactions that focus the auditory processing within a specialized area of one hemisphere.

  17. Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

    Science.gov (United States)

    Godec, Jernej; Tan, Yan; Liberzon, Arthur; Tamayo, Pablo; Bhattacharya, Sanchita; Butte, Atul J; Mesirov, Jill P; Haining, W Nicholas

    2016-01-19

    Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when comparing various datasets. For instance, conservation of the transcriptional response to sepsis in mouse models and human disease remains controversial. To improve transcriptional analysis in immunology, we created ImmuneSigDB: a manually annotated compendium of ∼5,000 gene-sets from diverse cell states, experimental manipulations, and genetic perturbations in immunology. Analysis using ImmuneSigDB identified signatures induced in activated myeloid cells and differentiating lymphocytes that were highly conserved between humans and mice. Sepsis triggered conserved patterns of gene expression in humans and mouse models. However, we also identified species-specific biological processes in the sepsis transcriptional response: although both species upregulated phagocytosis-related genes, a mitosis signature was specific to humans. ImmuneSigDB enables granular analysis of transcriptomic data to improve biological understanding of immune processes of the human and mouse immune systems. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Behavioral Relevance of Species-Specific Vasotocin Anatomy in Gregarious Finches

    Directory of Open Access Journals (Sweden)

    Aubrey M Kelly

    2013-12-01

    Full Text Available Despite substantial species differences in the vasotocin/vasopressin (VT/VP circuitry of the medial bed nucleus of the stria terminalis (BSTm and lateral septum (LS; a primary projection target of BSTm VT/VP cells, functional consequences of this variation are poorly known. Previous experiments in the highly gregarious zebra finch (Estrildidae: Taeniopygia guttata demonstrate that BSTm VT neurons promote gregariousness in a male-specific manner and reduce anxiety in both sexes. However, in contrast to the zebra finch, the less gregarious Angolan blue waxbill (Estrildidae: Uraeginthus angolensis exhibits fewer VT-immunoreactive cells in the BSTm as well as differences in receptor distribution across the LS subnuclei, suggesting that knockdown of VT production in the BSTm would produce behavioral effects in Angolan blue waxbills that are distinct from zebra finches. Thus, we here quantified social contact, gregariousness (i.e. preference for the larger of two groups, and anxiety-like behavior following bilateral antisense knockdown of VT production in the BSTm of male and female Angolan blue waxbills. We find that BSTm VT neurons promote social contact, but not gregariousness (as in male zebra finches, and that antisense effects on social contact are significantly stronger in male waxbills than in females. Knockdown of BSTm VT production has no effect on anxiety-like behavior. These data provide novel evidence that species differences in the VT/VP circuitry arising in the BSTm are accompanied by species-specific effects on affiliation behaviors.

  19. Species-Specific Mechanisms of Neuron Subtype Specification Reveal Evolutionary Plasticity of Amniote Brain Development

    Directory of Open Access Journals (Sweden)

    Tadashi Nomura

    2018-03-01

    Full Text Available Summary: Highly ordered brain architectures in vertebrates consist of multiple neuron subtypes with specific neuronal connections. However, the origin of and evolutionary changes in neuron specification mechanisms remain unclear. Here, we report that regulatory mechanisms of neuron subtype specification are divergent in developing amniote brains. In the mammalian neocortex, the transcription factors (TFs Ctip2 and Satb2 are differentially expressed in layer-specific neurons. In contrast, these TFs are co-localized in reptilian and avian dorsal pallial neurons. Multi-potential progenitors that produce distinct neuronal subtypes commonly exist in the reptilian and avian dorsal pallium, whereas a cis-regulatory element of avian Ctip2 exhibits attenuated transcription suppressive activity. Furthermore, the neuronal subtypes distinguished by these TFs are not tightly associated with conserved neuronal connections among amniotes. Our findings reveal the evolutionary plasticity of regulatory gene functions that contribute to species differences in neuronal heterogeneity and connectivity in developing amniote brains. : Neuronal heterogeneity is essential for assembling intricate neuronal circuits. Nomura et al. find that species-specific transcriptional mechanisms underlie diversities of excitatory neuron subtypes in mammalian and non-mammalian brains. Species differences in neuronal subtypes and connections suggest functional plasticity of regulatory genes for neuronal specification during amniote brain evolution. Keywords: Ctip2, Satb2, multi-potential progenitors, transcriptional regulation, neuronal connectivity

  20. Species-specific deletion of the viral attachment glycoprotein of avian metapneumovirus.

    Science.gov (United States)

    Kong, Byung-Whi; Foster, Linda K; Foster, Douglas N

    2008-03-01

    The avian metapneumovirus (AMPV) genome encodes the fusion (F), small hydrophobic (SH), and attachment glycoprotein (G) as envelope glycoproteins. The F and G proteins mainly function to allow viral entry into host cells during the early steps of the virus life cycle. The highly variable AMPV G protein is a major determinant for distinguishing virus subtypes. Sequence analysis was used to determine if any differences between avian or mammalian cell propagated subtype C AMPV could be detected for the 1.8kb G gene. As a result, the complete 1.8kb G gene was found to be present when AMPV was propagated in our immortal turkey turbinate (TT-1) cell line regardless of passage number. Surprisingly, AMPV propagated for 15 or more passages in mammalian Vero cells revealed an essentially deleted G gene in the viral genome, resulting in no G gene mRNA expression. Although the Vero cell propagated AMPV genome contained a small 122 nucleotide fragment of the G gene, no other mRNA variants were detected from either mammalian or avian propagated AMPV. The G gene truncation might be caused by cellular molecular mechanisms that are species-specific. The lack of viral gene deletions suggests that avian cell propagated AMPV will provide a better alternative host for live recombinant vaccine development based on a reverse genetics system.

  1. Rapid species specific identification and subtyping of Yersinia enterocolitica by MALDI-TOF mass spectrometry.

    Science.gov (United States)

    Stephan, Roger; Cernela, Nicole; Ziegler, Dominik; Pflüger, Valentin; Tonolla, Mauro; Ravasi, Damiana; Fredriksson-Ahomaa, Maria; Hächler, Herbert

    2011-11-01

    Yersinia enterocolitica are Gram-negative pathogens and known as important causes of foodborne infections. Rapid and reliable identification of strains of the species Y. enterocolitica within the genus Yersinia and the differentiation of the pathogenic from the non-pathogenic biotypes has become increasingly important. We evaluated here the application of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid species identification and subtyping of Y. enterocolitica. To this end, we developed a reference MS database library including 19 Y. enterocolitica (non-pathogenic biotype 1A and pathogenic biotypes 2 and 4) as well as 24 non-Y. enterocolitica strains, belonging to eleven different other Yersinia spp. The strains provided reproducible and unique mass spectra profiles covering a wide molecular mass range (2000 to 30,000 Da). Species-specific and biotype-specific biomarker protein mass patterns were determined for Y. enterocolitica. The defined biomarker mass patterns (SARAMIS SuperSpectrum™) were validated using 117 strains from various Y. enterocolitica bioserotypes in a blind-test. All strains were correctly identified and for all strains the mass spectrometry-based identification scheme yielded identical results compared to a characterization by a combination of biotyping and serotyping. Our study demonstrates that MALDI-TOF-MS is a reliable and powerful tool for the rapid identification of Y. enterocolitica strains to the species level and allows subtyping of strains to the biotype level. Copyright © 2011 Elsevier B.V. All rights reserved.

  2. Determination of correction coefficients for quantitative analysis by mass spectrometry. Application to uranium impurities analysis; Recherche des coefficients de correction permettant l'analyse quantitative par spectrometrie de masse. Application a l'analyse d'impuretes dans l'uranium

    Energy Technology Data Exchange (ETDEWEB)

    Billon, J P [Commissariat a l' Energie Atomique, Bruyeres-le-Chatel (France). Centre d' Etudes

    1970-07-01

    Some of basic principles in spark source mass spectrometry are recalled. It is shown how this method can lead to quantitative analysis when attention is paid to some theoretical aspects. A time constant relation being assumed between the analysed solid sample and the ionic beam it gives we determined experimental relative sensitivity factors for impurities in uranium matrix. Results being in fairly good agreement with: an unelaborate theory on ionization yield in spark-source use of theoretically obtained relative sensitivity factors in uranium matrix has been developed. (author) [French] Apres avoir rappele quelques principes fondamentaux regissant la spectrometrie de masse a etincelles, nous avons montre que moyennant un certain nombre de precautions, il etait possible d'utiliser cette methode en analyse quantitative. Ayant admis qu'il existait une relation constante dans le temps entre l'echantillon solide analyse et le faisceau ionique qui en est issu, nous avons d'abord entrepris de determiner des coefficients de correction experimentaux pour des matrices d'uranium. Les premiers resultats pratiques semblant en accord avec une theorie simple relative au rendement d'ionisation dans la source a etincelles, nous avons etudie la possibilite d'appliquer directement les coefficients theoriques ainsi definis, l'application etant toujours faite sur des matrices d'uranium. (auteur)

  3. Qualitative and Quantitative Drug residue analyses: Florfenicol in white-tailed deer (Odocoileus virginianus) and supermarket meat by liquid chromatography tandem-mass spectrometry.

    Science.gov (United States)

    Anderson, Shanoy C; Subbiah, Seenivasan; Gentles, Angella; Austin, Galen; Stonum, Paul; Brooks, Tiffanie A; Brooks, Chance; Smith, Ernest E

    2016-10-15

    A method for confirmation and detection of Florfenicol amine residues in white-tailed deer tissues was developed and validated in our laboratory. Tissue samples were extracted with ethyl acetate and cleaned up on sorbent (Chem-elut) cartridges. Liguid chromatography (LC) separation was achieved on a Zorbax Eclipse plus C18 column with gradient elution using a mobile phase composed of ammonium acetate in water and methanol at a flow rate of 300μL/min. Qualitative and quantitative analyses were carried out using liquid chromatography - heated electrospray ionization(HESI) and atmospheric pressure chemical ionization (APCI)-tandem mass spectrometry in the multiple reaction monitoring (MRM) interface. The limits of detection (LODs) for HESI and APCI probe were 1.8ng/g and 1.4ng/g respectively. Limits of quantitation (LOQs) for HESI and APCI probe were 5.8ng/g and 3.4ng/g respectively. Mean recovery values ranged from 79% to 111% for APCI and 30% to 60% for HESI. The validated method was used to determine white-tailed deer florfenicol tissue residue concentration 10-days after exposure. Florfenicol tissue residues concentration ranged from 0.4 to 0.6μg/g for liver and 0.02-0.05μg/g for muscle and a trace in blood samples. The concentration found in the tested edible tissues were lower than the maximum residual limit (MRL) values established by the federal drug administration (FDA) for bovine tissues. In summary, the resulting optimization procedures using the sensitivity of HESI and APCI probes in the determination of florfenicol in white-tailed deer tissue are the most compelling conclusions in this study, to the extent that we have applied this method in the evaluation of supermarket samples drug residue levels as a proof of principle. Copyright © 2016. Published by Elsevier B.V.

  4. Certification of methylmercury in cod fish tissue certified reference material by species-specific isotope dilution mass spectrometric analysis

    Energy Technology Data Exchange (ETDEWEB)

    Inagaki, Kazumi; Kuroiwa, Takayoshi; Narukawa, Tomohiro; Yarita, Takashi; Takatsu, Akiko; Okamoto, Kensaku; Chiba, Koichi [National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Environmental Standard Section, Tsukuba, Ibaraki (Japan)

    2008-07-15

    A new cod fish tissue certified reference material, NMIJ CRM 7402-a, for methylmercury analysis was certified by the National Metrological Institute of Japan in the National Institute of Advanced Industrial Science and Technology (NMIJ/AIST). Cod fish was collected from the sea close to Japan. The cod muscle was powdered by freeze-pulverization and was placed into 600 glass bottles (10 g each), which were sterilized with {gamma}-ray irradiation. The certification was carried out using species-specific isotope dilution gas chromatography inductively coupled plasma mass spectrometry (SSID-GC-ICPMS), where {sup 202}Hg-enriched methylmercury (MeHg) was used as the spike compound. In order to avoid any possible analytical biases caused by nonquantitative extraction, degradation and/or formation of MeHg in sample preparations, two different extraction methods (KOH/methanol and HCl/methanol extractions) were performed, and one of these extraction methods utilized two different derivatization methods (ethylation and phenylation). A double ID method was adopted to minimize the uncertainty arising from the analyses. In order to ensure not only the reliability of the analytical results but also traceability to SI units, the standard solution of MeHg used for the reverse-ID was prepared from high-purity MeHg chloride and was carefully assayed as follows: the total mercury was determined by ID-ICPMS following aqua regia digestion, and the ratio of Hg as MeHg to the total Hg content was estimated by GC-ICPMS. The certified value given for MeHg is 0.58 {+-} 0.02 mg kg{sup -1} as Hg. (orig.)

  5. Teat apex colonization with coagulase-negative Staphylococcus species before parturition: Distribution and species-specific risk factors.

    Science.gov (United States)

    De Visscher, A; Piepers, S; Haesebrouck, F; De Vliegher, S

    2016-02-01

    Coagulase-negative staphylococci (CNS) are the main cause of bovine intramammary infections and are also abundantly present in extramammary habitats such as teat apices. Teat apex colonization (TAC) with CNS has already been explored in lactating dairy cows at the species level, whereas this is not true for dry cows and end-term heifers. Therefore, the aim of this observational study was to describe CNS TAC in nonlactating dairy cows and end-term heifers in Flemish dairy herds and to identify associated risk factors at the herd, cow, and quarter level. All CNS were molecularly identified to the species level using transfer RNA intergenic spacer PCR (tDNA-PCR) and sequencing of the 16S rRNA gene, allowing for species-specific statistical analyses using multivariable, multilevel logistic regression. Staphylococcus devriesei, Staphylococcus chromogenes, Staphylococcus haemolyticus, and Staphylococcus equorum were the most frequently isolated species. Staphylococcus chromogenes was the sole species colonizing teat apices of cows and heifers in all herds, whereas large between-herd differences were observed for the other species. Teat apices of red and white Holstein Friesians, of quarters dried off without an internal teat sealer, and swabbed in months with lower precipitation and higher ambient temperature were significantly more likely to be colonized by S. devriesei. Slightly dirty teat apices and teat apices swabbed in months with lower precipitation had higher odds of being colonized by S. chromogenes, whereas teat apices sampled in months with lower precipitation and higher ambient temperature were more likely to be colonized by S. haemolyticus. Dirty teat apices and teat apices swabbed in months with lower ambient temperature in combination with low precipitation had higher odds of being colonized by S. equorum. Diverse factors explaining CNS TAC, yet mostly related to humidity, ambient temperature, and hygiene, substantiate differences in epidemiological

  6. Sorted gene genealogies and species-specific nonsynonymous substitutions point to putative postmating prezygotic isolation genes in Allonemobius crickets

    Directory of Open Access Journals (Sweden)

    Suegene Noh

    2016-02-01

    Full Text Available In the Allonemobius socius complex of crickets, reproductive isolation is primarily accomplished via postmating prezygotic barriers. We tested seven protein-coding genes expressed in the male ejaculate for patterns of evolution consistent with a putative role as postmating prezygotic isolation genes. Our recently diverged species generally lacked sequence variation. As a result, ω-based tests were only mildly successful. Some of our genes showed evidence of elevated ω values on the internal branches of gene trees. In a couple of genes, these internal branches coincided with both species branching events of the species tree, between A. fasciatus and the other two species, and between A. socius and A. sp. nov. Tex. In comparison, more successful approaches were those that took advantage of the varying degrees of lineage sorting and allele sharing among our young species. These approaches were particularly powerful within the contact zone. Among the genes we tested we found genes with genealogies that indicated relatively advanced degrees of lineage sorting across both allopatric and contact zone alleles. Within a contact zone between two members of the species complex, only a subset of genes maintained allelic segregation despite evidence of ongoing gene flow in other genes. The overlap in these analyses was arginine kinase (AK and apolipoprotein A-1 binding protein (APBP. These genes represent two of the first examples of sperm maturation, capacitation, and motility proteins with fixed non-synonymous substitutions between species-specific alleles that may lead to postmating prezygotic isolation. Both genes express ejaculate proteins transferred to females during copulation and were previously identified through comparative proteomics. We discuss the potential function of these genes in the context of the specific postmating prezygotic isolation phenotype among our species, namely conspecific sperm precedence and the superior ability of

  7. Mercury speciation analysis in seafood by species-specific isotope dilution: method validation and occurrence data

    Energy Technology Data Exchange (ETDEWEB)

    Clemens, Stephanie; Guerin, Thierry [Agence Nationale de Securite Sanitaire de l' Alimentation, Laboratoire de Securite des Aliments de Maisons-Alfort, Unite des Contaminants Inorganiques et Mineraux de l' Environnement, ANSES, Maisons-Alfort (France); Monperrus, Mathilde; Donard, Olivier F.X.; Amouroux, David [IPREM UMR 5254 CNRS - Universite de Pau et des Pays de l' Adour, Laboratoire de Chimie Analytique Bio-Inorganique et Environnement, Institut des Sciences Analytiques et de Physico-chimie pour l' Environnement et les Materiaux, Pau Cedex (France)

    2011-11-15

    Methylmercury (MeHg) and total mercury (THg) in seafood were determined using species-specific isotope dilution analysis and gas chromatography combined with inductively coupled plasma mass spectrometry. Sample preparation methods (extraction and derivation step) were evaluated on certified reference materials using isotopically enriched Hg species. Solid-liquid extraction, derivation by propylation and automated agitation gave excellent accuracy and precision results. Satisfactory figures of merit for the selected method were obtained in terms of limit of quantification (1.2 {mu}g Hg kg{sup -1} for MeHg and 1.4 {mu}g Hg kg{sup -1} for THg), repeatability (1.3-1.7%), intermediate precision reproducibility (1.5% for MeHg and 2.2% for THg) and trueness (bias error less than 7%). By means of a recent strategy based on accuracy profiles ({beta}-expectation tolerance intervals), the selected method was successfully validated in the range of approximately 0.15-5.1 mg kg{sup -1} for MeHg and 0.27-5.2 mg kg{sup -1} for THg. Probability {beta} was set to 95% and the acceptability limits to {+-}15%. The method was then applied to 62 seafood samples representative of consumption in the French population. The MeHg concentrations were generally low (1.9-588 {mu}g kg{sup -1}), and the percentage of MeHg varied from 28% to 98% in shellfish and from 84% to 97% in fish. For all real samples tested, methylation and demethylation reactions were not significant, except in one oyster sample. The method presented here could be used for monitoring food contamination by MeHg and inorganic Hg in the future to more accurately assess human exposure. (orig.)

  8. Molecular diagnostic for boll weevil (Coleoptera: Curculionidae) based on amplification of three species-specific microsatellites.

    Science.gov (United States)

    Kim, Kyung Seok; Szendrei, Zsofia; Rodriguez-Saona, Cesar; Mulder, Phillip G; Sappington, Thomas W

    2009-04-01

    The boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), is a serious pest of cultivated cotton, Gossypium hirsutum L., in the Americas, and reinfestation of zones from which they have been eradicated is of perpetual concern. Extensive arrays of pheromone traps monitor for reintroductions, but occasionally the traps collect nontarget weevils that can be misidentified by scouts. For example, the congeneric pepper weevil, Anthonomus eugenii Cano, and other superficially similar weevils are attracted to components of the boll weevil lure or trap color. Although morphologically distinguishable by trained personnel, the potential for misidentification is compounded when captured weevils are dismembered or partially consumed by ants or ground beetles that sometimes feed on them in the traps. Because misidentification can have expensive consequences, a molecular diagnostic tool would be of great value to eradication managers. We demonstrate that a cocktail of three primer pairs in a single polymerase chain reaction (PCR) amplify species-specific microsatellites that unambiguously distinguish the boll weevil from three other weevil species tested, including pepper weevil; cranberry weevil, Anthonomus eugenii musculus Say; and pecan weevil, Curculio caryae Horn. However, it does not distinguish the boll weevil from the subspecific "thurberia" weevil. A universal internal transcribed spacer primer pair included in the cocktail cross-amplifies DNA from all species, serving as a positive control. Furthermore, the diagnostic primers amplified the target microsatellites from various boll weevil adult body parts, indicating that the PCR technology using the primer cocktail is sensitive enough to positively identify a boll weevil even when the body is partly degraded.

  9. Species-Specific Effects on Ecosystem Functioning Can Be Altered by Interspecific Interactions.

    Science.gov (United States)

    Clare, David S; Spencer, Matthew; Robinson, Leonie A; Frid, Christopher L J

    2016-01-01

    Biological assemblages are constantly undergoing change, with species being introduced, extirpated and experiencing shifts in their densities. Theory and experimentation suggest that the impacts of such change on ecosystem functioning should be predictable based on the biological traits of the species involved. However, interspecific interactions could alter how species affect functioning, with the strength and sign of interactions potentially depending on environmental context (e.g. homogenous vs. heterogeneous conditions) and the function considered. Here, we assessed how concurrent changes to the densities of two common marine benthic invertebrates, Corophium volutator and Hediste diversicolor, affected the ecological functions of organic matter consumption and benthic-pelagic nutrient flux. Complementary experiments were conducted within homogenous laboratory microcosms and naturally heterogeneous field plots. When the densities of the species were increased within microcosms, interspecific interactions enhanced effects on organic matter consumption and reduced effects on nutrient flux. Trait-based predictions of how each species would affect functioning were only consistently supported when the density of the other species was low. In field plots, increasing the density of either species had a positive effect on organic matter consumption (with no significant interspecific interactions) but no effect on nutrient flux. Our results indicate that species-specific effects on ecosystem functioning can be altered by interspecific interactions, which can be either facilitative (positive) or antagonistic (negative) depending on the function considered. The impacts of biodiversity change may therefore not be predictable based solely on the biological traits of the species involved. Possible explanations for why interactions were detected in microcosms but not in the field are discussed.

  10. Species-Specific Effects on Ecosystem Functioning Can Be Altered by Interspecific Interactions.

    Directory of Open Access Journals (Sweden)

    David S Clare

    Full Text Available Biological assemblages are constantly undergoing change, with species being introduced, extirpated and experiencing shifts in their densities. Theory and experimentation suggest that the impacts of such change on ecosystem functioning should be predictable based on the biological traits of the species involved. However, interspecific interactions could alter how species affect functioning, with the strength and sign of interactions potentially depending on environmental context (e.g. homogenous vs. heterogeneous conditions and the function considered. Here, we assessed how concurrent changes to the densities of two common marine benthic invertebrates, Corophium volutator and Hediste diversicolor, affected the ecological functions of organic matter consumption and benthic-pelagic nutrient flux. Complementary experiments were conducted within homogenous laboratory microcosms and naturally heterogeneous field plots. When the densities of the species were increased within microcosms, interspecific interactions enhanced effects on organic matter consumption and reduced effects on nutrient flux. Trait-based predictions of how each species would affect functioning were only consistently supported when the density of the other species was low. In field plots, increasing the density of either species had a positive effect on organic matter consumption (with no significant interspecific interactions but no effect on nutrient flux. Our results indicate that species-specific effects on ecosystem functioning can be altered by interspecific interactions, which can be either facilitative (positive or antagonistic (negative depending on the function considered. The impacts of biodiversity change may therefore not be predictable based solely on the biological traits of the species involved. Possible explanations for why interactions were detected in microcosms but not in the field are discussed.

  11. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

    KAUST Repository

    Lee, Onon

    2010-11-18

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. © 2011 International Society for Microbial Ecology All rights reserved.

  12. Lichens biomonitoring as feasible methodology to assess air pollution in natural ecosystems: combined study of quantitative PAHs analyses and lichen biodiversity in the Pyrenees Mountains.

    Science.gov (United States)

    Blasco, María; Domeño, Celia; Nerín, Cristina

    2008-06-01

    The air quality in the Aragón valley, in the central Pyrenees, has been assessed by evaluation of lichen biodiversity and mapped by elaboration of the Index of Air Purity (IAP) based on observations of the presence and abundance of eight kinds of lichen with different sensitivity to air pollution. The IAP values obtained have been compared with quantitative analytical measures of 16 PAHs in the lichen Evernia prunastri, because this species was associated with a wide range of traffic exposure and levels of urbanization. Analyses of PAHs were carried out by the DSASE method followed by an SPE clean-up step and GC-MS analysis. The concentration of total PAHs found in lichen samples from the Aragón valley ranged from 692 to 6420 ng g(-1) and the PAHs profile showed predominance of compounds with three aromatic rings. The influence of the road traffic in the area has been shown because values over the median concentration of PAHs (>1092 ng g(-1)), percentage of combustion PAHs (>50%), and equivalent toxicity (>169) were found in lichens collected at places exposed to the influence of traffic. The combination of both methods suggests IAP as a general method for evaluating the air pollution referenced to PAHs because it can be correlated with the content of combustion PAHs and poor lichen biodiversity can be partly explained by the air pollution caused by specific PAHs.

  13. Quantitative analyses of postmortem heat shock protein mRNA profiles in the occipital lobes of human cerebral cortices: implications in cause of death.

    Science.gov (United States)

    Chung, Ukhee; Seo, Joong-Seok; Kim, Yu-Hoon; Son, Gi Hoon; Hwang, Juck-Joon

    2012-11-01

    Quantitative RNA analyses of autopsy materials to diagnose the cause and mechanism of death are challenging tasks in the field of forensic molecular pathology. Alterations in mRNA profiles can be induced by cellular stress responses during supravital reactions as well as by lethal insults at the time of death. Here, we demonstrate that several gene transcripts encoding heat shock proteins (HSPs), a gene family primarily responsible for cellular stress responses, can be differentially expressed in the occipital region of postmortem human cerebral cortices with regard to the cause of death. HSPA2 mRNA levels were higher in subjects who died due to mechanical asphyxiation (ASP), compared with those who died by traumatic injury (TI). By contrast, HSPA7 and A13 gene transcripts were much higher in the TI group than in the ASP and sudden cardiac death (SCD) groups. More importantly, relative abundances between such HSP mRNA species exhibit a stronger correlation to, and thus provide more discriminative information on, the death process than does routine normalization to a housekeeping gene. Therefore, the present study proposes alterations in HSP mRNA composition in the occipital lobe as potential forensic biological markers, which may implicate the cause and process of death.

  14. Re-evaluation of a novel approach for quantitative myocardial oedema detection by analysing tissue inhomogeneity in acute myocarditis using T2-mapping.

    Science.gov (United States)

    Baeßler, Bettina; Schaarschmidt, Frank; Treutlein, Melanie; Stehning, Christian; Schnackenburg, Bernhard; Michels, Guido; Maintz, David; Bunck, Alexander C

    2017-12-01

    To re-evaluate a recently suggested approach of quantifying myocardial oedema and increased tissue inhomogeneity in myocarditis by T2-mapping. Cardiac magnetic resonance data of 99 patients with myocarditis were retrospectively analysed. Thirthy healthy volunteers served as controls. T2-mapping data were acquired at 1.5 T using a gradient-spin-echo T2-mapping sequence. T2-maps were segmented according to the 16-segments AHA-model. Segmental T2-values, segmental pixel-standard deviation (SD) and the derived parameters maxT2, maxSD and madSD were analysed and compared to the established Lake Louise criteria (LLC). A re-estimation of logistic regression models revealed that all models containing an SD-parameter were superior to any model containing global myocardial T2. Using a combined cut-off of 1.8 ms for madSD + 68 ms for maxT2 resulted in a diagnostic sensitivity of 75% and specificity of 80% and showed a similar diagnostic performance compared to LLC in receiver-operating-curve analyses. Combining madSD, maxT2 and late gadolinium enhancement (LGE) in a model resulted in a superior diagnostic performance compared to LLC (sensitivity 93%, specificity 83%). The results show that the novel T2-mapping-derived parameters exhibit an additional diagnostic value over LGE with the inherent potential to overcome the current limitations of T2-mapping. • A novel quantitative approach to myocardial oedema imaging in myocarditis was re-evaluated. • The T2-mapping-derived parameters maxT2 and madSD were compared to traditional Lake-Louise criteria. • Using maxT2 and madSD with dedicated cut-offs performs similarly to Lake-Louise criteria. • Adding maxT2 and madSD to LGE results in further increased diagnostic performance. • This novel approach has the potential to overcome the limitations of T2-mapping.

  15. Organ- and species-specific accumulation of metals in two land snail species (Gastropoda, Pulmonata)

    Energy Technology Data Exchange (ETDEWEB)

    Boshoff, Magdalena, E-mail: magdalena.boshoff@ua.ac.be [University of Antwerp, Systemic Physiological and Ecotoxicological Research, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Jordaens, Kurt [Royal Museum for Central Africa (JEMU), Leuvensesteenweg 13, B-3080 Tervuren (Belgium); University of Antwerp, Evolutionary Ecology Group, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Backeljau, Thierry [University of Antwerp, Evolutionary Ecology Group, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Royal Belgian Institute of Natural Sciences (JEMU), Vautierstraat 29, B-1000 Brussels (Belgium); Lettens, Suzanna [Research Institute for Nature and Forest (INBO), Kliniekstraat 25, B-1070 Brussels (Belgium); Tack, Filip [Ghent University, Laboratory of Analytical Chemistry and Applied Ecochemistry, Coupure Links 265, B-9000 Ghent (Belgium); Vandecasteele, Bart [Institute for Agricultural and Fisheries Research (ILVO), Burg van Gansberghelaan 109, B-9820 Merelbeke (Belgium); De Jonge, Maarten; Bervoets, Lieven [University of Antwerp, Systemic Physiological and Ecotoxicological Research, Groenenborgerlaan 171, B-2020 Antwerp (Belgium)

    2013-04-01

    In order to evaluate the usefulness of terrestrial gastropods as bioindicators there is a need for studies that simultaneously compare (1) concentrations of metals in reference and polluted plots, (2) species within the same polluted habitat, (3) metal accumulation patterns in different organs and (4) metal accumulation patterns in relation to soil physicochemical properties. This study aims to assess metal accumulation patterns in two land snail species. Instead of analyzing an organism as a whole, investigating the partitioning of metals in different organs can provide information on the actual toxicological relevant fractions. Therefore, concentrations of Ag, Cd, Cr, Cu, Ni and Zn were examined in five different organs of Cepaea nemoralis, as well as in the foot and the body of Succinea putris. Snails were sampled at four polluted dredged sediment disposal localities and three adjacent less polluted reference plots situated along waterways in Flanders, Belgium. Due to the small size and problematic dissection of S. putris only the concentrations in the foot of both species could be compared. For this reason only, C. nemoralis can be described as a better bioindicator species that allows a far more detailed analysis of organ metal accumulation. This study showed that organs other than the digestive gland may be involved in the immobilization and detoxification of metals. Furthermore, pH, soil fractionation (clay %, silt %, sand %) and organic matter, correlate with metal accumulation in organs. However, most often the soil metal concentrations did not correlate with the concentrations found in snail organs. Metal concentrations in organs of both species (1) differed among polluted plots but rarely between polluted and reference plots within a locality, (2) were organ-specific (digestive gland > foot > albumen gland = spermoviduct = ovotestis), (3) were species-specific and (4) depended on the metal type (high Cd and Cu concentrations were observed in the

  16. The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes.

    Science.gov (United States)

    Shmakov, Sergey A; Sitnik, Vassilii; Makarova, Kira S; Wolf, Yuri I; Severinov, Konstantin V; Koonin, Eugene V

    2017-09-19

    Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR- cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average). Among the detected protospacers, the majority, typically 80 to 90%, originated from viral genomes, including proviruses, and among the rest, the most common source was genes that are integrated into microbial chromosomes but are involved in plasmid conjugation or replication. Thus, almost all spacers with identifiable protospacers target mobile genetic elements (MGE). The GC content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes showed a nearly perfect correlation and were almost identical. Given the near absence of self-targeting spacers, these findings are most compatible with the possibility that the spacers, including the dark matter, are derived almost completely from the species-specific microbial mobilomes. IMPORTANCE The principal function of CRISPR-Cas systems is thought to be protection of bacteria and archaea against viruses and other parasitic genetic elements. The CRISPR defense function is mediated by sequences from parasitic elements, known as spacers, that are inserted into CRISPR arrays and then transcribed and employed as guides to identify and inactivate the cognate parasitic genomes. However, only a small fraction of the CRISPR spacers

  17. Systematic development of Phytophthora species-specific mitochondrial diagnostic markers for economically important members of the genus

    Science.gov (United States)

    The genus Phytophthora contains many invasive species to the USA that have the potential to cause significant damage to agriculture and native ecosystems. A genus and species-specific diagnostic assay was previously reported based on mitochondrial gene order differences that allowed for the systemat...

  18. Putative and unique gene sequence utilization for the design of species specific probes as modeled by Lactobacillus plantarum

    Science.gov (United States)

    The concept of utilizing putative and unique gene sequences for the design of species specific probes was tested. The abundance profile of assigned functions within the Lactobacillus plantarum genome was used for the identification of the putative and unique gene sequence, csh. The targeted gene (cs...

  19. Quantitative in vivo analyses reveal calcium-dependent phosphorylation sites and identifies a novel component of the Toxoplasma invasion motor complex.

    Directory of Open Access Journals (Sweden)

    Thomas Nebl

    2011-09-01

    Full Text Available Apicomplexan parasites depend on the invasion of host cells for survival and proliferation. Calcium-dependent signaling pathways appear to be essential for micronemal release and gliding motility, yet the target of activated kinases remains largely unknown. We have characterized calcium-dependent phosphorylation events during Toxoplasma host cell invasion. Stimulation of live tachyzoites with Ca²⁺-mobilizing drugs leads to phosphorylation of numerous parasite proteins, as shown by differential 2-DE display of ³²[P]-labeled protein extracts. Multi-dimensional Protein Identification Technology (MudPIT identified ∼546 phosphorylation sites on over 300 Toxoplasma proteins, including 10 sites on the actomyosin invasion motor. Using a Stable Isotope of Amino Acids in Culture (SILAC-based quantitative LC-MS/MS analyses we monitored changes in the abundance and phosphorylation of the invasion motor complex and defined Ca²⁺-dependent phosphorylation patterns on three of its components--GAP45, MLC1 and MyoA. Furthermore, calcium-dependent phosphorylation of six residues across GAP45, MLC1 and MyoA is correlated with invasion motor activity. By analyzing proteins that appear to associate more strongly with the invasion motor upon calcium stimulation we have also identified a novel 15-kDa Calmodulin-like protein that likely represents the MyoA Essential Light Chain of the Toxoplasma invasion motor. This suggests that invasion motor activity could be regulated not only by phosphorylation but also by the direct binding of calcium ions to this new component.

  20. Quantitative analyses of regional [{sup 11}C]PE2I binding to the dopamine transporter in the human brain: a PET study

    Energy Technology Data Exchange (ETDEWEB)

    Jucaite, Aurelija [Karolinska Institutet, Department of Woman and Child Health, Stockholm (Sweden); Odano, Ikuo [Niigata University, Department of Sensory and Integrative Medicine, Asahimachi-dori Niigata (Japan); Olsson, Hans; Pauli, Stefan; Halldin, Christer; Farde, Lars [Karolinska Institutet, Psychiatry Section, Department of Clinical Neuroscience, Stockholm (Sweden)

    2006-06-15

    The dopamine transporter (DAT) is a plasma membrane protein of central interest in the pathophysiology of neuropsychiatric disorders and is known to be a target for psychostimulant drugs. [{sup 11}C]PE2I is a new radioligand which binds selectively and with moderate affinity to central DAT, as has been demonstrated in vitro by autoradiography and in vivo by positron emission tomography (PET). The aims of the present PET study were to quantify regional [{sup 11}C]PE2I binding to DAT in the human brain and to compare quantitative methods with regard to suitability for applied clinical studies. One PET measurement was performed in each of eight healthy male subjects. The binding potential (BP) values were obtained by applying kinetic compartment analysis, which uses the metabolite-corrected arterial plasma curve as an input function. They were compared with the BP values quantified by two reference tissue approaches, using cerebellum as a reference region representing free and non-specific radioligand binding. The radioactivity concentration was highest in the striatum, lower in the midbrain and very low in the cerebellum. The regional [{sup 11}C]PE2I binding could be interpreted by kinetic compartment models. However, the BP values in the striatum obtained by the compartment analyses were about 30% higher than the BP values obtained using reference tissue methods. We suggest that the difference may be explained by the inaccurate metabolite correction, small amounts of radioactive metabolites that could account for the presence of non-specific binding in the cerebellum and insufficient data acquisition time. (orig.)

  1. Species specific isotope dilution for the accurate and SI traceable determination of arsenobetaine and methylmercury in cuttlefish and prawn

    Energy Technology Data Exchange (ETDEWEB)

    Kumkrong, Paramee [National Research Council Canada, 1200 Montreal Rd, Ottawa, Ontario, K1A 0R6 (Canada); Thailand Institute of Scientific and Technological Research, 35 Mu 3 Tambon Khlong Ha, Amphoe Khlong Luang, Pathum Thani, 12120 (Thailand); Thiensong, Benjaporn [Thailand Institute of Scientific and Technological Research, 35 Mu 3 Tambon Khlong Ha, Amphoe Khlong Luang, Pathum Thani, 12120 (Thailand); Le, Phuong Mai; McRae, Garnet; Windust, Anthony [National Research Council Canada, 1200 Montreal Rd, Ottawa, Ontario, K1A 0R6 (Canada); Deawtong, Suladda [Thailand Institute of Scientific and Technological Research, 35 Mu 3 Tambon Khlong Ha, Amphoe Khlong Luang, Pathum Thani, 12120 (Thailand); Meija, Juris; Maxwell, Paulette [National Research Council Canada, 1200 Montreal Rd, Ottawa, Ontario, K1A 0R6 (Canada); Yang, Lu, E-mail: Lu.yang@nrc-cnrc.gc.ca [National Research Council Canada, 1200 Montreal Rd, Ottawa, Ontario, K1A 0R6 (Canada); Mester, Zoltán [National Research Council Canada, 1200 Montreal Rd, Ottawa, Ontario, K1A 0R6 (Canada)

    2016-11-02

    Methods based on species specific isotope dilution were developed for the accurate and SI traceable determination of arsenobetaine (AsBet) and methylmercury (MeHg) in prawn and cuttlefish tissues by LC-MS/MS and SPME GC-ICPMS. Quantitation of AsBet and MeHg were achieved by using a {sup 13}C-enriched AsBet spike (NRC CRM CBET-1) and an enriched spike of Me{sup 198}Hg (NRC CRM EMMS-1), respectively, wherein analyte mass fractions in enriched spikes were determined by reverse isotope dilution using natural abundance AsBet and MeHg primary standards. Purity of these primary standards were characterized by quantitative {sup 1}H-NMR with the use of NIST SRM 350b benzoic acid as a primary calibrator, ensuring the final measurement results traceable to SI. Validation of employed methods of ID LC-MS/MS and ID SPME GC-ICPMS was demonstrated by analysis of several biological CRMs (DORM-4, TORT-3, DOLT-5, BCR-627 and BCR-463) with satisfying results. The developed methods were applied for the determination of AsBet and MeHg in two new certified reference materials (CRMs) prawn (PRON-1) and cuttlefish (SQID-1) produced jointly by Thailand Institute of Scientific and Technological Research (TISTR) and National Research Council Canada (NRC). With additional measurements of AsBet using LC-ICPMS with standard additions calibration and external calibration at NRC and TISTR, respectively, certified values of 1.206 ± 0.058 and 13.96 ± 0.54 mg kg{sup −1} for AsBet as As (expanded uncertainty, k = 2) were obtained for the new CRMs PRON-1 and SQID-1, respectively. The reference value of 0.324 ± 0.028 mg kg{sup −1} as Hg (expanded uncertainty, k = 2) for MeHg was obtained for the SQID-1 based on the results obtained by ID SPME GC-ICPMS method only, whereas MeHg in PRON-1 was found to be < 0.015 mg kg{sup −1}. It was found that AsBet comprised 69.7% and 99.0% of total As in the prawn and cuttlefish, respectively, whereas MeHg comprised 94.5% of total Hg in

  2. Species specific isotope dilution for the accurate and SI traceable determination of arsenobetaine and methylmercury in cuttlefish and prawn

    International Nuclear Information System (INIS)

    Kumkrong, Paramee; Thiensong, Benjaporn; Le, Phuong Mai; McRae, Garnet; Windust, Anthony; Deawtong, Suladda; Meija, Juris; Maxwell, Paulette; Yang, Lu; Mester, Zoltán

    2016-01-01

    Methods based on species specific isotope dilution were developed for the accurate and SI traceable determination of arsenobetaine (AsBet) and methylmercury (MeHg) in prawn and cuttlefish tissues by LC-MS/MS and SPME GC-ICPMS. Quantitation of AsBet and MeHg were achieved by using a "1"3C-enriched AsBet spike (NRC CRM CBET-1) and an enriched spike of Me"1"9"8Hg (NRC CRM EMMS-1), respectively, wherein analyte mass fractions in enriched spikes were determined by reverse isotope dilution using natural abundance AsBet and MeHg primary standards. Purity of these primary standards were characterized by quantitative "1H-NMR with the use of NIST SRM 350b benzoic acid as a primary calibrator, ensuring the final measurement results traceable to SI. Validation of employed methods of ID LC-MS/MS and ID SPME GC-ICPMS was demonstrated by analysis of several biological CRMs (DORM-4, TORT-3, DOLT-5, BCR-627 and BCR-463) with satisfying results. The developed methods were applied for the determination of AsBet and MeHg in two new certified reference materials (CRMs) prawn (PRON-1) and cuttlefish (SQID-1) produced jointly by Thailand Institute of Scientific and Technological Research (TISTR) and National Research Council Canada (NRC). With additional measurements of AsBet using LC-ICPMS with standard additions calibration and external calibration at NRC and TISTR, respectively, certified values of 1.206 ± 0.058 and 13.96 ± 0.54 mg kg"−"1 for AsBet as As (expanded uncertainty, k = 2) were obtained for the new CRMs PRON-1 and SQID-1, respectively. The reference value of 0.324 ± 0.028 mg kg"−"1 as Hg (expanded uncertainty, k = 2) for MeHg was obtained for the SQID-1 based on the results obtained by ID SPME GC-ICPMS method only, whereas MeHg in PRON-1 was found to be < 0.015 mg kg"−"1. It was found that AsBet comprised 69.7% and 99.0% of total As in the prawn and cuttlefish, respectively, whereas MeHg comprised 94.5% of total Hg in cuttlefish. - Highlights:

  3. Simultaneous speciation of mercury and butyltin compounds in natural waters and snow by propylation and species-specific isotope dilution mass spectrometry analysis

    Energy Technology Data Exchange (ETDEWEB)

    Monperrus, M.; Tessier, E.; Veschambre, S.; Amouroux, D.; Donard, O. [Universite de Pau et des Pays de L' Adour, Laboratoire de Chimie Analytique Bio-inorganique et Environnement, CNRS UMR 5034, Helioparc, Pau (France)

    2005-02-01

    A robust method has been developed for simultaneous determination of mercury and butyltin compounds in aqueous samples. This method is capable of providing accurate results for analyte concentrations in the picogram per liter to nanogram per liter range. The simultaneous determination of the mercury and tin compounds is achieved by species-specific isotope dilution, derivatization, and gas chromatography-inductively coupled plasma mass spectrometer (GC-ICP-MS). In derivatization by ethylation and propylation, reaction conditions such as pH and the effect of chloride were carefully studied. Ethylation was found to be more sensitive to matrix effects, especially for mercury compounds. Propylation was thus the preferred derivatization method for simultaneous determination of organomercury and organotin compounds in environmental samples. The analytical method is highly accurate and precise, with RSD values of 1 and 3% for analyte concentrations in the picogram per liter to nanogram per liter range. By use of cleaning procedures and SIDMS blank measurements, detection limits in the range 10-60 pg L{sup -1} were achieved; these are suitable for determination of background levels of these contaminants in environmental samples. This was demonstrated by using the method for analysis of real snow and seawater samples. This work illustrates the great advantage of species-specific isotope dilution for the validation of an analytical speciation method - the possibility of overcoming species transformations and non-quantitative recovery. Analysis time is saved by use of the simultaneous method, because of the use of a single sample-preparation procedure and one analysis. (orig.)

  4. Dimensionality Analyses of the "GRE"® revised General Test Verbal and Quantitative Measures. ETS GRE® Board Research Report. ETS GRE®-16-02. ETS Research Report. RR-16-20

    Science.gov (United States)

    Robin, Frédéric; Bejar, Isaac; Liang, Longjuan; Rijmen, Frank

    2016-01-01

    Exploratory and confirmatory factor analyses of domestic data from the" GRE"® revised General Test, introduced in 2011, were conducted separately for the verbal (VBL) and quantitative (QNT) reasoning measures to evaluate the unidimensionality and local independence assumptions required by item response theory (IRT). Results based on data…

  5. Zur Analyse internationaler Migrationsprozesse. Makro-quantitative Perspektiven und eine vergleichende Fallstudie über die Lage der türkischen Community in Österreich.

    OpenAIRE

    Tausch, Arno

    2010-01-01

    The present article presents at first a German language summary about recent quantitative studies by the author and his associates about global development since the end of Communism in up to 175 nations of the world, using 26 predictor variables to evaluate the determinants of 30 processes of development on a global scale. As correctly predicted by quantitative dependency and world system research of the 1980s and 1990s, core capital penetration (MNC penetration) has very signifi...

  6. Quantitative Analyses about Market- and Prevalence-Based Needs for Adapted Physical Education Teachers in the Public Schools in the United States

    Science.gov (United States)

    Zhang, Jiabei

    2011-01-01

    The purpose of this study was to analyze quantitative needs for more adapted physical education (APE) teachers based on both market- and prevalence-based models. The market-based need for more APE teachers was examined based on APE teacher positions funded, while the prevalence-based need for additional APE teachers was analyzed based on students…

  7. Malazy, a degenerate, species-specific transposable element in Cercospora zeae-maydis.

    Science.gov (United States)

    Shim, Won-Bo; Dunkle, Larry D

    2005-01-01

    Two fungal pathogens, Cercospora zeae-maydis Groups I and II, cause gray leaf spot of maize. During the sequencing of a cosmid library from C. zeae-maydis Group I, we discovered a sequence with high similarity to Maggy, a transposable element from Magnaporthe grisea. The element from C. zeae-maydis, named Malazy, contained 194-base-pair terminal repeats and sequences with high similarity to reverse transcriptase and integrase, components of the POL gene in the gypsy-like retrotransposons in fungi. Sequences with similarity to other POL gene components, protease and ribonuclease, were not detected in Malazy. A single copy of the element was detected by PCR and Southern analyses in all six North American isolates of C. zeae-maydis Group I but was not detected in the four isolates of C. zeae-maydis Group II from three continents or in phylogenetically related species. Fragments of the core domains of reverse transcriptase and integrase contained a high frequency of stop codons that were conserved in all six isolates of Group I. Additional C:G to T:A transitions in occasional isolates usually were silent mutations, while two resulted in isolate-specific stop codons. The absence of Malazy from related species suggests that it was acquired after the divergence of C. zeae-maydis Groups I and II. The high frequency of stop codons and the presence of a single copy of the element suggest that it was inactivated soon after it was acquired. Because the element is inactive and because reading frames for other genes were not found in sequences flanking the element, Malazy does not appear to be the cause of differences leading to speciation or genetic diversity between C. zeae-maydis Groups I and II.

  8. Species-specific chitin-binding module 18 expansion in the amphibian pathogen Batrachochytrium dendrobatidis.

    Science.gov (United States)

    Abramyan, John; Stajich, Jason E

    2012-01-01

    spread and associated decline in amphibian populations, it is imperative to incorporate novel genomic and genetic techniques into the study of this species. In this study, we present the first reported potential pathogenicity factors in B. dendrobatidis. In silico studies such as this allow us to identify putative targets for more specific molecular analyses, furthering our hope for the control of this pathogen.

  9. Semi-quantitative and simulation analyses of effects of {gamma} rays on determination of calibration factors of PET scanners with point-like {sup 22}Na sources

    Energy Technology Data Exchange (ETDEWEB)

    Hasegawa, Tomoyuki [School of Allied Health Sciences, Kitasato University, 1-15-1, Kitasato, Minamiku, Sagamihara, Kanagawa, 252-0373 (Japan); Sato, Yasushi [National Institute of Advanced Industrial Science and Technology, 1-1-1, Umezono, Tsukuba, Ibaraki, 305-8568 (Japan); Oda, Keiichi [Tokyo Metropolitan Institute of Gerontology, 1-1, Nakamachi, Itabashi, Tokyo, 173-0022 (Japan); Wada, Yasuhiro [RIKEN Center for Molecular Imaging Science, 6-7-3, Minamimachi, Minatoshima, Chuo, Kobe, Hyogo, 650-0047 (Japan); Murayama, Hideo [National Institute of Radiological Sciences, 4-9-1, Anagawa, Inage, Chiba, 263-8555 (Japan); Yamada, Takahiro, E-mail: hasegawa@kitasato-u.ac.jp [Japan Radioisotope Association, 2-28-45, Komagome, Bunkyo-ku, Tokyo, 113-8941 (Japan)

    2011-09-21

    The uncertainty of radioactivity concentrations measured with positron emission tomography (PET) scanners ultimately depends on the uncertainty of the calibration factors. A new practical calibration scheme using point-like {sup 22}Na radioactive sources has been developed. The purpose of this study is to theoretically investigate the effects of the associated 1.275 MeV {gamma} rays on the calibration factors. The physical processes affecting the coincidence data were categorized in order to derive approximate semi-quantitative formulae. Assuming the design parameters of some typical commercial PET scanners, the effects of the {gamma} rays as relative deviations in the calibration factors were evaluated by semi-quantitative formulae and a Monte Carlo simulation. The relative deviations in the calibration factors were less than 4%, depending on the details of the PET scanners. The event losses due to rejecting multiple coincidence events of scattered {gamma} rays had the strongest effect. The results from the semi-quantitative formulae and the Monte Carlo simulation were consistent and were useful in understanding the underlying mechanisms. The deviations are considered small enough to correct on the basis of precise Monte Carlo simulation. This study thus offers an important theoretical basis for the validity of the calibration method using point-like {sup 22}Na radioactive sources.

  10. Radiation applications in art and archaeometry X-ray fluorescence applications to archaeometry. Possibility of obtaining non-destructive quantitative analyses

    International Nuclear Information System (INIS)

    Milazzo, Mario

    2004-01-01

    The possibility of obtaining quantitative XRF analysis in archaeometric applications is considered in the following cases: - Examinations of metallic objects with irregular surface: coins, for instance. - Metallic objects with a natural or artificial patina on the surface. - Glass or ceramic samples for which the problems for quantitative analysis rise from the non-detectability of matrix low Z elements. The fundamental parameter method for quantitative XRF analysis is based on a numerical procedure involving he relative values of XRF lines intensity. As a consequence it can be applied also to the experimental XRF spectra obtained for metallic objects if the correction for the irregular shape consists only in introducing a constant factor which does not affect the XRF intensity relative value. This is in fact possible in non-very-restrictive conditions for the experimental set up. The finenesses of coins with a superficial patina can be evaluated by resorting to the measurements of Rayleigh to Compton scattering intensity ratio at an incident energy higher than the one of characteristic X-ray. For glasses and ceramics the measurements of the Compton scattered intensity of the exciting radiation and the use of a proper scaling law make possible to evaluate the matrix absorption coefficients for all characteristic X-ray line energies

  11. The induction of species-specific immunity against Schistosoma japonicum by exposure of rats to ultra-violet attenuated cercariae

    International Nuclear Information System (INIS)

    Moloney, N.A.; Webbe, G.; Hinchcliffe, P.

    1987-01-01

    Single percutaneous immunizations of Fischer rats with 1000 ultra-violet attenuated Schistosoma japonicum cercariae induced 52-88% resistance to challenge 4 weeks later. Increasing this to 3 immunizations induced 90% resistance to challenge, and this level of protection remained undiminished for up to 40 weeks after vaccination. Rats vaccinated with gamma-irradiated S. mansoni cercariae were resistant to challenge with S. mansoni but not S. japonicum. Similarly rats vaccinated with u.v.-attenuated S. japonicum cercariae were not resistant to heterologous challenge. Thus irradiated vaccines are species-specific in both permissive and non-permissive hosts. (author)

  12. Qualitative and quantitative analyses of the bifidobacterial microbiota in the colonic mucosa of patients with colorectal cancer, diverticulitis and inflammatory bowel disease

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    AIM: To characterize the bifidobacterial microbiota of the colonic mucosa in patients with colon cancer,inflammatory bowel disease or diverticulitis.METHODS: A sample of the distal colonic mucosa was taken during surgery from a total of 34 patients,twenty-one with diagnosed colorectal cancer, nine with diverticulitis and four with inflammatory bowel disease, requiring surgery for their condition. Bacterial DNA was extracted from the resected mucosal samples and bifidobacterial mucosa-associated microbiota was qualitatively and quantitatively determined by means of qualitative and quantitative PCR.RESULTS: Bifidobacteria were found in 100% of the samples from patients with diverticulitis or IBD and a 76% of those suffering colon cancer. The species B. longum and B. bifidum were the most widely found, followed by B. animalis, B. catenulatum and B.adolescentis. B. breve, B. dentium and B. angulatum were not detected in any sample. A significantly higher occurrence of B. longum was observed in patients with diverticulitis than in those with colon cancer or IBD (100%, 62% and 75%, respectively, P < 0.05).Similar results were obtained for B. animalis (56%, 0%and 25%, P < 0.05), while B. adolescentis was only found in the mucosa from patients with colon cancer (5 out of 21, 24%). At the quantitative level, patients with colon cancer or IBD showed lower counts of total Bifidobacterium (4.94 and 5.91 vs 6.96 log Cells/sample,respectively, P < 0.05) and of the species B.longum (4.05 and 4.79 vs 6.76, P < 0.05) than those with diverticulitis.CONCLUSION: Aberrancies in mucosa associated microbiota are present in different intestinal diseases.This may indicate a role of the microbiota in the pathogenesis of these diseases.

  13. Species-specific control of external superoxide levels by the coral holobiont during a natural bleaching event

    Science.gov (United States)

    Diaz, Julia M.; Hansel, Colleen M.; Apprill, Amy; Brighi, Caterina; Zhang, Tong; Weber, Laura; McNally, Sean; Xun, Liping

    2016-12-01

    The reactive oxygen species superoxide (O2.-) is both beneficial and detrimental to life. Within corals, superoxide may contribute to pathogen resistance but also bleaching, the loss of essential algal symbionts. Yet, the role of superoxide in coral health and physiology is not completely understood owing to a lack of direct in situ observations. By conducting field measurements of superoxide produced by corals during a bleaching event, we show substantial species-specific variation in external superoxide levels, which reflect the balance of production and degradation processes. Extracellular superoxide concentrations are independent of light, algal symbiont abundance and bleaching status, but depend on coral species and bacterial community composition. Furthermore, coral-derived superoxide concentrations ranged from levels below bulk seawater up to ~120 nM, some of the highest superoxide concentrations observed in marine systems. Overall, these results unveil the ability of corals and/or their microbiomes to regulate superoxide in their immediate surroundings, which suggests species-specific roles of superoxide in coral health and physiology.

  14. Loop-mediated isothermal amplification (LAMP) assays for the species-specific detection of Eimeria that infect chickens.

    Science.gov (United States)

    Barkway, Christopher P; Pocock, Rebecca L; Vrba, Vladimir; Blake, Damer P

    2015-02-20

    Eimeria species parasites, protozoa which cause the enteric disease coccidiosis, pose a serious threat to the production and welfare of chickens. In the absence of effective control clinical coccidiosis can be devastating. Resistance to the chemoprophylactics frequently used to control Eimeria is common and sub-clinical infection is widespread, influencing feed conversion ratios and susceptibility to other pathogens such as Clostridium perfringens. Despite the availability of polymerase chain reaction (PCR)-based tools, diagnosis of Eimeria infection still relies almost entirely on traditional approaches such as lesion scoring and oocyst morphology, but neither is straightforward. Limitations of the existing molecular tools include the requirement for specialist equipment and difficulties accessing DNA as template. In response a simple field DNA preparation protocol and a panel of species-specific loop-mediated isothermal amplification (LAMP) assays have been developed for the seven Eimeria recognised to infect the chicken. We now provide a detailed protocol describing the preparation of genomic DNA from intestinal tissue collected post-mortem, followed by setup and readout of the LAMP assays. Eimeria species-specific LAMP can be used to monitor parasite occurrence, assessing the efficacy of a farm's anticoccidial strategy, and to diagnose sub-clinical infection or clinical disease with particular value when expert surveillance is unavailable.

  15. Species-specific patterns of diel migration into the Oxygen Minimum Zone by euphausiids in the Humboldt Current Ecosystem

    Science.gov (United States)

    Antezana, Tarsicio

    2009-12-01

    A series of stratified bongo net samples taken over a 2 day period at ca. 18°S, about 20 nm off the coast of Peru, South America, suggest species-specific patterns of diel vertical migration into the Oxygen Minimum Zone (OMZ) of the Humboldt Current Ecosystem (HCE). The OMZ was the most dramatic feature of the water column and seemed to determine the extent of migration: Stylocheiron affine migrated only to the shallow oxycline; whereas Euphausia mucronata, Euphausia eximia, Euphausia distinguenda and Euphausia tenera migrated to the core of the OMZ; and Nematoscelis gracilis to beneath the core of the OMZ. Some differences were also found in the timing and duration of the ascent and descent, and residence times in shallow and deep layers. E. mucronata, N. gracilis and E. distinguenda displayed a normal descent during sunrise, and ascent during sunset. E. eximia and E. tenera also descended during sunrise but seemed to begin their ascent earlier in the afternoon and consequently shortened their deep residence times. S. affine showed the most extended residence times at the shallow layer and the shortest vertical displacement. Day and night vertical stratification and differences in the timing of migration into and out of the OMZ of the HCE suggest a community structure based on habitat partitioning whereby species avoided co-occurrence in time and space. Species-specific patterns of vertical stratification and migratory chronology are examined with regard to body and gill sizes, feeding adaptations of euphausiids, and potential food resources at the OMZ.

  16. Species-specific markers for the differential diagnosis of Trypanosoma cruzi and Trypanosoma rangeli and polymorphisms detection in Trypanosoma rangeli.

    Science.gov (United States)

    Ferreira, Keila Adriana Magalhães; Fajardo, Emanuella Francisco; Baptista, Rodrigo P; Macedo, Andrea Mara; Lages-Silva, Eliane; Ramírez, Luis Eduardo; Pedrosa, André Luiz

    2014-06-01

    Trypanosoma cruzi and Trypanosoma rangeli are kinetoplastid parasites which are able to infect humans in Central and South America. Misdiagnosis between these trypanosomes can be avoided by targeting barcoding sequences or genes of each organism. This work aims to analyze the feasibility of using species-specific markers for identification of intraspecific polymorphisms and as target for diagnostic methods by PCR. Accordingly, primers which are able to specifically detect T. cruzi or T. rangeli genomic DNA were characterized. The use of intergenic regions, generally divergent in the trypanosomatids, and the serine carboxypeptidase gene were successful. Using T. rangeli genomic sequences for the identification of group-specific polymorphisms and a polymorphic AT(n) dinucleotide repeat permitted the classification of the strains into two groups, which are entirely coincident with T. rangeli main lineages, KP1 (+) and KP1 (-), previously determined by kinetoplast DNA (kDNA) characterization. The sequences analyzed totalize 622 bp (382 bp represent a hypothetical protein sequence, and 240 bp represent an anonymous sequence), and of these, 581 (93.3%) are conserved sites and 41 bp (6.7%) are polymorphic, with 9 transitions (21.9%), 2 transversions (4.9%), and 30 (73.2%) insertion/deletion events. Taken together, the species-specific markers analyzed may be useful for the development of new strategies for the accurate diagnosis of infections. Furthermore, the identification of T. rangeli polymorphisms has a direct impact in the understanding of the population structure of this parasite.

  17. Species-Specific Variations in the Nutritional Quality of Southern Ocean Phytoplankton in Response to Elevated pCO2

    Directory of Open Access Journals (Sweden)

    Cathryn Wynn-Edwards

    2014-06-01

    Full Text Available Increased seawater pCO2 has the potential to alter phytoplankton biochemistry, which in turn may negatively affect the nutritional quality of phytoplankton as food for grazers. Our aim was to identify how Antarctic phytoplankton, Pyramimonas gelidicola, Phaeocystis antarctica, and Gymnodinium sp., respond to increased pCO2. Cultures were maintained in a continuous culture setup to ensure stable CO2 concentrations. Cells were subjected to a range of pCO2 from ambient to 993 µatm. We measured phytoplankton response in terms of cell size, cellular carbohydrate content, and elemental, pigment and fatty acid composition and content. We observed few changes in phytoplankton biochemistry with increasing CO2 concentration which were species-specific and predominantly included differences in the fatty acid composition. The C:N ratio was unaffected by CO2 concentration in the three species, while carbohydrate content decreased in Pyramimonas gelidicola, but increased in Phaeocystis antarctica. We found a significant reduction in the content of nutritionally important polyunsaturated fatty acids in Pyramimonas gelidicola cultures under high CO2 treatment, while cellular levels of the polyunsaturated fatty acid 20:5ω3, EPA, in Gymnodinium sp. increased. These changes in fatty acid profile could affect the nutritional quality of phytoplankton as food for grazers, however, further research is needed to identify the mechanisms for the observed species-specific changes and to improve our ability to extrapolate laboratory-based experiments on individual species to natural communities.

  18. A qualitative and quantitative evaluation of the peptide characteristics of microwave- and ultrasound-assisted digestion in discovery and targeted proteomic analyses.

    Science.gov (United States)

    Guo, Zhengguang; Cheng, Jie; Sun, Haidan; Sun, Wei

    2017-08-30

    Fast digestion methods can dramatically accelerate enzyme digestion and increase the throughput of proteomic analysis. However, the peptide characteristics of fast digestion methods and their performance in discovery and targeted proteomic analysis must be systematically evaluated. Three digestion methods, including overnight digestion, microwave-assisted protein enzymatic digestion (MAPED), and high-intensity focused ultrasonic-assisted enzymatic digestion (HIFUSAED), in trypsin or in trypsin/Lys-C were comprehensively compared in both discovery and targeted proteomics analysis using the HeLa cell proteome. In discovery proteomic analysis, the highest numbers of peptides and proteins were identified when the sample was digested via the MAPED method with trypsin/Lys-C. The fast digestion methods showed a higher mis-cleavage rate and a lower semi-tryptic rate than the overnight digestion method. In both label-free quantitative analysis and targeted proteomic analysis, both fully cleaved peptides (FCPs) and mis-cleaved peptides (MCPs) from the fast digestion methods and the overnight digestion method showed good reproducibility if they showed good abundance. When both the FCPs and MCPs were included in the analysis, the MAPED with trypsin/Lys-C method showed the best results for both discovery proteomic analysis and relative quantitative targeted proteomic analysis. These results will be beneficial for the application of fast digestion methods to proteomics. Copyright © 2017 John Wiley & Sons, Ltd.

  19. Quantitative risk trends deriving from PSA-based event analyses. Analysis of results from U.S.NRC's accident sequence precursor program

    International Nuclear Information System (INIS)

    Watanabe, Norio

    2004-01-01

    The United States Nuclear Regulatory Commission (U.S.NRC) has been carrying out the Accident Sequence Precursor (ASP) Program to identify and categorize precursors to potential severe core damage accident sequences using the probabilistic safety assessment (PSA) technique. The ASP Program has identified a lot of risk significant events as precursors that occurred at U.S. nuclear power plants. Although the results from the ASP Program include valuable information that could be useful for obtaining and characterizing risk significant insights and for monitoring risk trends in nuclear power industry, there are only a few attempts to determine and develop the trends using the ASP results. The present study examines and discusses quantitative risk trends for the industry level, using two indicators, that is, the occurrence frequency of precursors and the annual core damage probability, deriving from the results of the ASP analysis. It is shown that the core damage risk at U.S. nuclear power plants has been lowered and the likelihood of risk significant events has been remarkably decreasing. As well, the present study demonstrates that two risk indicators used here can provide quantitative information useful for examining and monitoring the risk trends and/or risk characteristics in nuclear power industry. (author)

  20. Post-event reviews: Using a quantitative approach for analysing incident response to demonstrate the value of business continuity programmes and increase planning efficiency.

    Science.gov (United States)

    Vaidyanathan, Karthik

    2017-01-01

    Business continuity management is often thought of as a proactive planning process for minimising impact from large-scale incidents and disasters. While this is true, and it is critical to plan for the worst, consistently validating plan effectiveness against smaller disruptions can enable an organisation to gain key insights about its business continuity readiness, drive programme improvements, reduce costs and provide an opportunity to quantitatively demonstrate the value of the programme to management. This paper describes a post mortem framework which is used as a continuous improvement mechanism for tracking, reviewing and learning from real-world events at Microsoft Customer Service & Support. This approach was developed and adopted because conducting regular business continuity exercises proved difficult and expensive in a complex and distributed operations environment with high availability requirements. Using a quantitative approach to measure response to incidents, and categorising outcomes based on such responses, enables business continuity teams to provide data-driven insights to leadership, change perceptions of incident root cause, and instil a higher level of confidence towards disaster response readiness and incident management. The scope of the framework discussed here is specific to reviewing and driving improvements from operational incidents. However, the concept can be extended to learning and evolving readiness plans for other types of incidents.

  1. A mass spectrographic investigation of the methods for obtaining quantitative analyses for the mass balance of P and B through a submerged arc silicon smelter

    International Nuclear Information System (INIS)

    Rogers, D.E.C.; Jones, D.S.; Wegman, J.W.; Brain, L.; Van Wamelen, J.

    1983-11-01

    Mass spectrographic analyses of silica, silicon and silica reducing agents have been made using an arc discharge mass spectrograph. Analyses of certified standards and standard mixtures are given. An evaluation of doping techniques shows that the solid doping technique is satisfactory and that the liquid doping technique leads to significant errors. The amount of liquid dopant absorbed onto the substrate matrix varied from one compound to another and from one matrix to another. Comparison of analyses of solid-doped and undoped certified standards shows that all of the solid dopant is taken up by the sample. Analysis of silica reducing agents used in the arc reduction furnace shows that the major source of contamination by B and P is likely to be the coal and wood. Silica contains 0.4 ppm of B and 4 ppm of P and is a minor source of contamination. The levels in silicon are about 10 ppm for B and 20 ppm for P. A mass balance on P cannot be made and the missing amount is larger than the inaccuracy of the analysis. For analyses of feedstocks where the smelter outlet fumes are not sampled an accuracy of analysis to a factor of two is sufficient for the analysis of the coal and wood chips

  2. Study on radiation degradation of hydroxylamine derivatives. Pt.3: Qualitative and quantitative analyses of hydrogen and carbon monoxide produced by radiation degradation of N,N-diethyl hydroxylamine

    International Nuclear Information System (INIS)

    Wang Jinhua; Bao Borong; Wu Minghong; Sun Xilian

    2004-01-01

    The qualitative and quantitative analysis of hydrogen and carbon monoxide produced by radiation degradation of N,N-diethyl hydroxylamine is performed on a 2 m column packed with 5 Angstrom molecular sieve and equipped with a thermal conductivity detector. The analysis of hydrogen employs argon as a carrier gas, the column temperature is 85 degree C and the detector temperature is 110 degree C; the analysis of carbon monoxide employs hydrogen as a carrier gas, the column temperature is 50 degree C and the detector temperature is 80 degree C. The results show that the volume fraction of hydrogen is increased with the increase of dose, but has little relationship with the concentration of N,N-diethyl hydroxylamine. Carbon monoxide is only produced when the absorption dose is very high and the volume fraction is very low

  3. Quantitative and mixed analyses to identify factors that affect cervical cancer screening uptake among lesbian and bisexual women and transgender men.

    Science.gov (United States)

    Johnson, Michael J; Mueller, Martina; Eliason, Michele J; Stuart, Gail; Nemeth, Lynne S

    2016-12-01

    The purposes of this study were to measure the prevalence of, and identify factors associated with, cervical cancer screening among a sample of lesbian, bisexual and queer women, and transgender men. Past research has found that lesbian, bisexual and queer women underuse cervical screening service. Because deficient screening remains the most significant risk factor for cervical cancer, it is essential to understand the differences between routine and nonroutine screeners. A convergent-parallel mixed methods design. A convenience sample of 21- to 65-year-old lesbian and bisexual women and transgender men were recruited in the USA from August-December 2014. Quantitative data were collected via a 48-item Internet questionnaire (N = 226), and qualitative data were collected through in-depth telephone interviews (N = 20) and open-ended questions on the Internet questionnaire. Seventy-three per cent of the sample was routine cervical screeners. The results showed that a constellation of factors influence the use of cervical cancer screening among lesbian, bisexual and queer women. Some of those factors overlap with the general female population, whereas others are specific to the lesbian, bisexual or queer identity. Routine screeners reported feeling more welcome in the health care setting, while nonroutine screeners reported more discrimination related to their sexual orientation and gender expression. Routine screeners were also more likely to 'out' to their provider. The quantitative and qualitative factors were also compared and contrasted. Many of the factors identified in this study to influence cervical cancer screening relate to the health care environment and to interactions between the patient and provider. Nurses should be involved with creating welcoming environments for lesbian, bisexual and queer women and their partners. Moreover, nurses play a large role in patient education and should promote self-care behaviours among lesbian women and transgender

  4. Re-evaluation of a novel approach for quantitative myocardial oedema detection by analysing tissue inhomogeneity in acute myocarditis using T2-mapping

    International Nuclear Information System (INIS)

    Baessler, Bettina; Treutlein, Melanie; Maintz, David; Bunck, Alexander C.; Schaarschmidt, Frank; Stehning, Christian; Schnackenburg, Bernhard; Michels, Guido

    2017-01-01

    To re-evaluate a recently suggested approach of quantifying myocardial oedema and increased tissue inhomogeneity in myocarditis by T2-mapping. Cardiac magnetic resonance data of 99 patients with myocarditis were retrospectively analysed. Thirthy healthy volunteers served as controls. T2-mapping data were acquired at 1.5 T using a gradient-spin-echo T2-mapping sequence. T2-maps were segmented according to the 16-segments AHA-model. Segmental T2-values, segmental pixel-standard deviation (SD) and the derived parameters maxT2, maxSD and madSD were analysed and compared to the established Lake Louise criteria (LLC). A re-estimation of logistic regression models revealed that all models containing an SD-parameter were superior to any model containing global myocardial T2. Using a combined cut-off of 1.8 ms for madSD + 68 ms for maxT2 resulted in a diagnostic sensitivity of 75% and specificity of 80% and showed a similar diagnostic performance compared to LLC in receiver-operating-curve analyses. Combining madSD, maxT2 and late gadolinium enhancement (LGE) in a model resulted in a superior diagnostic performance compared to LLC (sensitivity 93%, specificity 83%). The results show that the novel T2-mapping-derived parameters exhibit an additional diagnostic value over LGE with the inherent potential to overcome the current limitations of T2-mapping. (orig.)

  5. Re-evaluation of a novel approach for quantitative myocardial oedema detection by analysing tissue inhomogeneity in acute myocarditis using T2-mapping

    Energy Technology Data Exchange (ETDEWEB)

    Baessler, Bettina; Treutlein, Melanie; Maintz, David; Bunck, Alexander C. [University Hospital of Cologne, Department of Radiology, Cologne (Germany); Schaarschmidt, Frank [Leibniz Universitaet Hannover, Institute of Biostatistics, Faculty of Natural Sciences, Hannover (Germany); Stehning, Christian [Philips Research, Hamburg (Germany); Schnackenburg, Bernhard [Philips, Healthcare Germany, Hamburg (Germany); Michels, Guido [University Hospital of Cologne, Department III of Internal Medicine, Heart Centre, Cologne (Germany)

    2017-12-15

    To re-evaluate a recently suggested approach of quantifying myocardial oedema and increased tissue inhomogeneity in myocarditis by T2-mapping. Cardiac magnetic resonance data of 99 patients with myocarditis were retrospectively analysed. Thirthy healthy volunteers served as controls. T2-mapping data were acquired at 1.5 T using a gradient-spin-echo T2-mapping sequence. T2-maps were segmented according to the 16-segments AHA-model. Segmental T2-values, segmental pixel-standard deviation (SD) and the derived parameters maxT2, maxSD and madSD were analysed and compared to the established Lake Louise criteria (LLC). A re-estimation of logistic regression models revealed that all models containing an SD-parameter were superior to any model containing global myocardial T2. Using a combined cut-off of 1.8 ms for madSD + 68 ms for maxT2 resulted in a diagnostic sensitivity of 75% and specificity of 80% and showed a similar diagnostic performance compared to LLC in receiver-operating-curve analyses. Combining madSD, maxT2 and late gadolinium enhancement (LGE) in a model resulted in a superior diagnostic performance compared to LLC (sensitivity 93%, specificity 83%). The results show that the novel T2-mapping-derived parameters exhibit an additional diagnostic value over LGE with the inherent potential to overcome the current limitations of T2-mapping. (orig.)

  6. The relationships between termite mound CH4/CO2 emissions and internal concentration ratios are species specific

    Directory of Open Access Journals (Sweden)

    H. Jamali

    2013-04-01

    Full Text Available We investigated the relative importance of CH4 and CO2 fluxes from soil and termite mounds at four different sites in the tropical savannas of northern Australia near Darwin and assessed different methods to indirectly predict CH4 fluxes based on CO2 fluxes and internal gas concentrations. The annual flux from termite mounds and surrounding soil was dominated by CO2 with large variations among sites. On a carbon dioxide equivalent (CO2-e basis, annual CH4 flux estimates from termite mounds were 5- to 46-fold smaller than the concurrent annual CO2 flux estimates. Differences between annual soil CO2 and soil CH4 (CO2-e fluxes were even greater, soil CO2 fluxes being almost three orders of magnitude greater than soil CH4 (CO2-e fluxes at site. The contribution of CH4 and CO2 emissions from termite mounds to the total CH4 and CO2 emissions from termite mounds and soil in CO2-e was less than 1%. There were significant relationships between mound CH4 flux and mound CO2 flux, enabling the prediction of CH4 flux from measured CO2 flux; however, these relationships were clearly termite species specific. We also observed significant relationships between mound flux and gas concentration inside mound, for both CH4 and CO2, and for all termite species, thereby enabling the prediction of flux from measured mound internal gas concentration. However, these relationships were also termite species specific. Using the relationship between mound internal gas concentration and flux from one species to predict mound fluxes from other termite species (as has been done in the past would result in errors of more than 5-fold for mound CH4 flux and 3-fold for mound CO2 flux. This study highlights that CO2 fluxes from termite mounds are generally more than one order of magnitude greater than CH4 fluxes. There are species-specific relationships between CH4 and CO2 fluxes from a mound, and between the inside mound concentration of a gas and the mound flux emission of the

  7. The relationship between termite mound CH4/CO2 emissions and internal concentration ratios are species specific

    Science.gov (United States)

    Jamali, H.; Livesley, S. J.; Hutley, L. B.; Fest, B.; Arndt, S. K.

    2012-12-01

    1. We investigated the relative importance of CH4 and CO2 fluxes from soil and termite mounds at four different sites in the tropical savannas of Northern Australia near Darwin and assessed different methods to indirectly predict CH4 fluxes based on CO2 fluxes and internal gas concentrations. 2. The annual flux from termite mounds and surrounding soil was dominated by CO2 with large variations among sites. On a CO2-e basis, annual CH4 flux estimates from termite mounds were 5- to 46-fold smaller than the concurrent annual CO2 flux estimates. Differences between annual soil CO2 and soil CH4 (CO2-e) fluxes were even greater, soil CO2 fluxes being almost three orders of magnitude greater than soil CH4 (CO2-e) fluxes at site. 3. There were significant relationships between mound CH4 flux and mound CO2 flux, enabling the prediction of CH4 flux from measured CO2 flux, however, these relationships were clearly termite species specific. 4. We also observed significant relationships between mound flux and gas concentration inside mound, for both CH4 and CO2, and for all termite species, thereby enabling the prediction of flux from measured mound internal gas concentration. However, these relationships were also termite species specific. Using the relationship between mound internal gas concentration and flux from one species to predict mound fluxes from other termite species (as has been done in past) would result in errors of more than 5-fold for CH4 and 3-fold for CO2. 5. This study highlights that CO2 fluxes from termite mounds are generally more than one order of magnitude greater than CH4 fluxes. There are species-specific relationships between CH4 and CO2 fluxes from a~mound, and between the inside mound concentration of a gas and the mound flux emission of the same gas, but these relationships vary greatly among termite species. Consequently, there is no generic relationship that will allow for the prediction of CH4 fluxes from termite mounds of all species.

  8. The relationships between termite mound CH4/CO2 emissions and internal concentration ratios are species specific

    Science.gov (United States)

    Jamali, H.; Livesley, S. J.; Hutley, L. B.; Fest, B.; Arndt, S. K.

    2013-04-01

    We investigated the relative importance of CH4 and CO2 fluxes from soil and termite mounds at four different sites in the tropical savannas of northern Australia near Darwin and assessed different methods to indirectly predict CH4 fluxes based on CO2 fluxes and internal gas concentrations. The annual flux from termite mounds and surrounding soil was dominated by CO2 with large variations among sites. On a carbon dioxide equivalent (CO2-e) basis, annual CH4 flux estimates from termite mounds were 5- to 46-fold smaller than the concurrent annual CO2 flux estimates. Differences between annual soil CO2 and soil CH4 (CO2-e) fluxes were even greater, soil CO2 fluxes being almost three orders of magnitude greater than soil CH4 (CO2-e) fluxes at site. The contribution of CH4 and CO2 emissions from termite mounds to the total CH4 and CO2 emissions from termite mounds and soil in CO2-e was less than 1%. There were significant relationships between mound CH4 flux and mound CO2 flux, enabling the prediction of CH4 flux from measured CO2 flux; however, these relationships were clearly termite species specific. We also observed significant relationships between mound flux and gas concentration inside mound, for both CH4 and CO2, and for all termite species, thereby enabling the prediction of flux from measured mound internal gas concentration. However, these relationships were also termite species specific. Using the relationship between mound internal gas concentration and flux from one species to predict mound fluxes from other termite species (as has been done in the past) would result in errors of more than 5-fold for mound CH4 flux and 3-fold for mound CO2 flux. This study highlights that CO2 fluxes from termite mounds are generally more than one order of magnitude greater than CH4 fluxes. There are species-specific relationships between CH4 and CO2 fluxes from a mound, and between the inside mound concentration of a gas and the mound flux emission of the same gas, but

  9. Is the C-terminal insertional signal in Gram-negative bacterial outer membrane proteins species-specific or not?

    Directory of Open Access Journals (Sweden)

    Paramasivam Nagarajan

    2012-09-01

    Full Text Available Abstract Background In Gram-negative bacteria, the outer membrane is composed of an asymmetric lipid bilayer of phopspholipids and lipopolysaccharides, and the transmembrane proteins that reside in this membrane are almost exclusively β-barrel proteins. These proteins are inserted into the membrane by a highly conserved and essential machinery, the BAM complex. It recognizes its substrates, unfolded outer membrane proteins (OMPs, through a C-terminal motif that has been speculated to be species-specific, based on theoretical and experimental results from only two species, Escherichia coli and Neisseria meningitidis, where it was shown on the basis of individual sequences and motifs that OMPs from the one cannot easily be over expressed in the other, unless the C-terminal motif was adapted. In order to determine whether this species specificity is a general phenomenon, we undertook a large-scale bioinformatics study on all predicted OMPs from 437 fully sequenced proteobacterial strains. Results We were able to verify the incompatibility reported between Escherichia coli and Neisseria meningitidis, using clustering techniques based on the pairwise Hellinger distance between sequence spaces for the C-terminal motifs of individual organisms. We noticed that the amino acid position reported to be responsible for this incompatibility between Escherichia coli and Neisseria meningitidis does not play a major role for determining species specificity of OMP recognition by the BAM complex. Instead, we found that the signal is more diffuse, and that for most organism pairs, the difference between the signals is hard to detect. Notable exceptions are the Neisseriales, and Helicobacter spp. For both of these organism groups, we describe the specific sequence requirements that are at the basis of the observed difference. Conclusions Based on the finding that the differences between the recognition motifs of almost all organisms are small, we assume that

  10. Quantitative analyses of impurity silicon-carbide (SiC) and high-purity-titanium by neutron activation analyses based on k0-standardization method. Development of irradiation silicon technology in productivity using research reactor (Joint research)

    International Nuclear Information System (INIS)

    Motohashi, Jun; Takahashi, Hiroyuki; Magome, Hirokatsu; Sasajima, Fumio; Tokunaga, Okihiro; Kawasaki, Kozo; Onizawa, Koji; Isshiki, Masahiko

    2009-07-01

    JRR-3 and JRR-4 have been providing neutron-transmutation-doped silicon (NTD-Si) by using the silicon NTD process, which is a method to produce a high quality semiconductor. The domestic supply of NTD-Si is insufficient for the demand, and the market of NTD-Si is significantly growing at present. It is very important to increase achieve the production. To fulfill the requirement, we have been investigating a neutron filter, which is made of high-purity-titanium, for uniform doping. Silicon-carbide (SiC) semiconductor doped with NTD technology is considered suitable for high power devices with superior performances to conventional Si-based devices. We are very interested in the SiC as well. This report presents the results obtained after the impurity contents in the high-purity-titanium and SiC were analyzed by neutron activation analyses (NAA) using k 0 -standardization method. There were 6 and 9 impurity elements detected from the high-purity-titanium and SiC, respectively. Among those Sc from the high-purity-titanium and Fe from SiC were comparatively long half life nuclides. From the viewpoint of exposure in handling them, we need to examine the impurity control of materials. (author)

  11. Everyday life and social relations in home-living patients with mild Alzheimer's disease and their caregivers: Quantitative and qualitative analyses

    DEFF Research Database (Denmark)

    Sørensen, Lisbeth Villemoes

    2007-01-01

    and the presence of neuropsychiatric symptoms. In the second study, data were collected using semi-structured research interviews with 11 patients before their participation in the DAISY intervention programme. Grounded theory analysis of the interview data revealed that the basic social psychological problem...... with the changes they face in relation to everyday life and social relations; and 3) to identify and analyse the experience of patients and their spousal caregivers concerning the impact of an intensive psychosocial intervention programme with tailored counselling, education courses and support groups, conducted...

  12. Species-specific activity of SIV Nef and HIV-1 Vpu in overcoming restriction by tetherin/BST2.

    Directory of Open Access Journals (Sweden)

    Bin Jia

    2009-05-01

    Full Text Available Tetherin, also known as BST2, CD317 or HM1.24, was recently identified as an interferon-inducible host-cell factor that interferes with the detachment of virus particles from infected cells. HIV-1 overcomes this restriction by expressing an accessory protein, Vpu, which counteracts tetherin. Since lentiviruses of the SIV(smm/mac/HIV-2 lineage do not have a vpu gene, this activity has likely been assumed by other viral gene products. We found that deletion of the SIV(mac239 nef gene significantly impaired virus release in cells expressing rhesus macaque tetherin. Virus release could be restored by expressing Nef in trans. However, Nef was unable to facilitate virus release in the presence of human tetherin. Conversely, Vpu enhanced virus release in the presence of human tetherin, but not in the presence of rhesus tetherin. In accordance with the species-specificity of Nef in mediating virus release, SIV Nef downregulated cell-surface expression of rhesus tetherin, but did not downregulate human tetherin. The specificity of SIV Nef for rhesus tetherin mapped to four amino acids in the cytoplasmic domain of the molecule that are missing from human tetherin, whereas the specificity of Vpu for human tetherin mapped to amino acid differences in the transmembrane domain. Nef alleles of SIV(smm, HIV-2 and HIV-1 were also able to rescue virus release in the presence of both rhesus macaque and sooty mangabey tetherin, but were generally ineffective against human tetherin. Thus, the ability of Nef to antagonize tetherin from these Old World primates appears to be conserved among the primate lentiviruses. These results identify Nef as the viral gene product of SIV that opposes restriction by tetherin in rhesus macaques and sooty mangabeys, and reveal species-specificity in the activities of both Nef and Vpu in overcoming tetherin in their respective hosts.

  13. Is Drosophila-microbe association species-specific or region specific? A study undertaken involving six Indian Drosophila species.

    Science.gov (United States)

    Singhal, Kopal; Khanna, Radhika; Mohanty, Sujata

    2017-06-01

    The present work aims to identify the microbial diversity associated with six Indian Drosophila species using next generation sequencing (NGS) technology and to discover the nature of their distribution across species and eco-geographic regions. Whole fly gDNA of six Drosophila species were used to generate sequences in an Illumina platform using NGS technology. De novo based assembled raw reads were blasted against the NR database of NCBI using BLASTn for identification of their bacterial loads. We have tried to include Drosophila species from different taxonomical groups and subgroups and from three different eco-climatic regions India; four species belong to Central India, while the rest two, D. melanogaster and D. ananassae, belong to West and South India to determine both their species-wise and region-wide distribution. We detected the presence of 33 bacterial genera across all six study species, predominated by the class Proteobacteria. Amongst all, D. melanogaster was found to be the most diverse by carrying around 85% of the bacterial diversity. Our findings infer both species-specific and environment-specific nature of the bacterial species inhabiting the Drosophila host. Though the present results are consistent with most of the earlier studies, they also remain incoherent with some. The present study outcome on the host-bacteria association and their species specific adaptation may provide some insight to understand the host-microbial interactions and the phenotypic implications of microbes on the host physiology. The knowledge gained may be importantly applied into the recent insect and pest population control strategy going to implement through gut microflora in India and abroad.

  14. Characterization of Foodborne Strains of Staphylococcus aureus by Shotgun Proteomics: Functional Networks, Virulence Factors and Species-Specific Peptide Biomarkers

    Science.gov (United States)

    Carrera, Mónica; Böhme, Karola; Gallardo, José M.; Barros-Velázquez, Jorge; Cañas, Benito; Calo-Mata, Pilar

    2017-01-01

    In the present work, we applied a shotgun proteomics approach for the fast and easy characterization of 20 different foodborne strains of Staphylococcus aureus (S. aureus), one of the most recognized foodborne pathogenic bacteria. A total of 644 non-redundant proteins were identified and analyzed via an easy and rapid protein sample preparation procedure. The results allowed the differentiation of several proteome datasets from the different strains (common, accessory, and unique datasets), which were used to determine relevant functional pathways and differentiate the strains into different Euclidean hierarchical clusters. Moreover, a predicted protein-protein interaction network of the foodborne S. aureus strains was created. The whole confidence network contains 77 nodes and 769 interactions. Most of the identified proteins were surface-associated proteins that were related to pathways and networks of energy, lipid metabolism and virulence. Twenty-seven virulence factors were identified, and most of them corresponded to autolysins, N-acetylmuramoyl-L-alanine amidases, phenol-soluble modulins, extracellular fibrinogen-binding proteins and virulence factor EsxA. Potential species-specific peptide biomarkers were screened. Twenty-one species-specific peptide biomarkers, belonging to eight different proteins (nickel-ABC transporter, N-acetylmuramoyl-L-alanine amidase, autolysin, clumping factor A, gram-positive signal peptide YSIRK, cysteine protease/staphopain, transcriptional regulator MarR, and transcriptional regulator Sar-A), were proposed to identify S. aureus. These results constitute the first major dataset of peptides and proteins of foodborne S. aureus strains. This repository may be useful for further studies, for the development of new therapeutic treatments for S. aureus food intoxications and for microbial source-tracking in foodstuffs. PMID:29312172

  15. Species specific and environment induced variation of δ13C and δ15N in alpine plants

    Directory of Open Access Journals (Sweden)

    Yang eYang

    2015-06-01

    Full Text Available Stable carbon and nitrogen isotope signals in plant tissues integrate plant-environment interactions over long periods. In this study, we hypothesized that humid alpine life conditions are narrowing the scope for significant deviations from common carbon, water and nitrogen relations as captured by stable isotope signals. We explored the variation in δ13C and δ15N in 32 plant species from tissue type to ecosystem scale across a suite of locations at c. 2500 m elevation in the Swiss Alps. Foliar δ13C and δ15N varied among species by about 3-4 ‰ and 7-8 ‰ respectively. However, there was no overall difference in means of δ13C and δ15N for species sampled in different plant communities or when bulk plant dry matter harvests of different plant communities were compared. δ13C was found to be highly species specific, so that the ranking among species was mostly maintained across 11 habitats. However, δ15N varied significantly from place to place in all species (a range of 2.7 ‰ except in Fabaceae (Trifolium alpinum and Juncaceae (Luzula lutea. There was also a substantial variation among individuals of the same species collected next to each other. No difference was found in foliar δ15N of non-legumes, which were either collected next to or away from the most common legume, T. alpinum. δ15N data place Cyperaceae and Juncaceae, just like Fabaceae, in a low discrimination category, well separated from other families. Soil δ15N was higher than in plants and increased with soil depth. The results indicate a high functional diversity in alpine plants that is similar to that reported for low elevation plants. We conclude that the surprisingly high variation in δ13C and δ15N signals in the studied high elevation plants is largely species specific (genetic and insensitive to obvious environmental cues.

  16. The optokinetic reflex as a tool for quantitative analyses of nervous system function in mice: application to genetic and drug-induced variation.

    Directory of Open Access Journals (Sweden)

    Hugh Cahill

    2008-04-01

    Full Text Available The optokinetic reflex (OKR, which serves to stabilize a moving image on the retina, is a behavioral response that has many favorable attributes as a test of CNS function. The OKR requires no training, assesses the function of diverse CNS circuits, can be induced repeatedly with minimal fatigue or adaptation, and produces an electronic record that is readily and objectively quantifiable. We describe a new type of OKR test apparatus in which computer-controlled visual stimuli and streamlined data analysis facilitate a relatively high throughput behavioral assay. We used this apparatus, in conjunction with infrared imaging, to quantify basic OKR stimulus-response characteristics for C57BL/6J and 129/SvEv mouse strains and for genetically engineered lines lacking one or more photoreceptor systems or with an alteration in cone spectral sensitivity. A second generation (F2 cross shows that the characteristic difference in OKR frequency between C57BL/6J and 129/SvEv is inherited as a polygenic trait. Finally, we demonstrate the sensitivity and high temporal resolution of the OKR for quantitative analysis of CNS drug action. These experiments show that the mouse OKR is well suited for neurologic testing in the context of drug discovery and large-scale phenotyping programs.

  17. Analyse quantitative de la consommation en viande de brousse en vue d'une gestion durable de la faune sauvage au Gabon

    Directory of Open Access Journals (Sweden)

    Ngama, S.

    2015-01-01

    Full Text Available Quantitative Analysis of Bush Meat Consumptions for a Sustainable Wildlife Management in Gabon. In Gabon, like everywhere in the Central Africa region, hunting could lead to serious ecological damages in the near future. Yet, quantifying bush meat contribution to local people diet will help to improve the efficiency when operating necessary hunting regulation. The purpose of this study was to provide more data on wildlife contribution to forest people's diet and the influence of related factors. To do so, 36 households were surveyed during one year time in the Ipassa reserve buffer zone inMakokou, Gabon. This study reveals that 53.1% of meats consumed by surveyed people are from wildlife. Moreover, this consumption was influenced by (i the fact that households' chiefs are salaried, farmers or hunters, (ii the distance from households' residences to the reserve and (iii meat prices on markets. In addition, poultry meat appears to be a potential alternative to bushmeat and even constituted 52.4% of consumptions in one of the survey areas where the greatest number ofhouseholds' chiefs were salaried.

  18. Quantitative in vivo fluorescence cross-correlation analyses highlight the importance of competitive effects in the regulation of protein-protein interactions.

    Science.gov (United States)

    Sadaie, Wakako; Harada, Yoshie; Matsuda, Michiyuki; Aoki, Kazuhiro

    2014-09-01

    Computer-assisted simulation is a promising approach for clarifying complicated signaling networks. However, this approach is currently limited by a deficiency of kinetic parameters determined in living cells. To overcome this problem, we applied fluorescence cross-correlation spectrometry (FCCS) to measure dissociation constant (Kd) values of signaling molecule complexes in living cells (in vivo Kd). Among the pairs of fluorescent molecules tested, that of monomerized enhanced green fluorescent protein (mEGFP) and HaloTag-tetramethylrhodamine was most suitable for the measurement of in vivo Kd by FCCS. Using this pair, we determined 22 in vivo Kd values of signaling molecule complexes comprising the epidermal growth factor receptor (EGFR)-Ras-extracellular signal-regulated kinase (ERK) mitogen-activated protein (MAP) kinase pathway. With these parameters, we developed a kinetic simulation model of the EGFR-Ras-ERK MAP kinase pathway and uncovered a potential role played by stoichiometry in Shc binding to EGFR during the peak activations of Ras, MEK, and ERK. Intriguingly, most of the in vivo Kd values determined in this study were higher than the in vitro Kd values reported previously, suggesting the significance of competitive bindings inside cells. These in vivo Kd values will provide a sound basis for the quantitative understanding of signal transduction. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  19. Quantitative x-ray diffraction analyses of samples used for sorption studies by the Isotope and Nuclear Chemistry Division, Los Alamos National Laboratory

    International Nuclear Information System (INIS)

    Chipera, S.J.; Bish, D.L.

    1989-09-01

    Yucca Mountain, Nevada, is currently being investigated to determine its suitability to host our nation's first geologic high-level nuclear waste repository. As part of an effort to determine how radionuclides will interact with rocks at Yucca Mountain, the Isotope and Nuclear Chemistry (INC) Division of Los Alamos National Laboratory has conducted numerous batch sorption experiments using core samples from Yucca Mountain. In order to understand better the interaction between the rocks and radionuclides, we have analyzed the samples used by INC with quantitative x-ray diffraction methods. Our analytical methods accurately determine the presence or absence of major phases, but we have not identified phases present below ∼1 wt %. These results should aid in understanding and predicting the potential interactions between radionuclides and the rocks at Yucca Mountain, although the mineralogic complexity of the samples and the lack of information on trace phases suggest that pure mineral studies may be necessary for a more complete understanding. 12 refs., 1 fig., 1 tab

  20. Applications of quaternary stratigraphic, soil-geomorphic, and quantitative geomorphic analyses to the evaluation of tectonic activity and landscape evolution in the Upper Coastal Plain, South Carolina

    International Nuclear Information System (INIS)

    Hanson, K.L.; Bullard, T.F.; Wit, M.W. de; Stieve, A.L.

    1993-01-01

    Geomorphic analyses combined with mapping of fluvial terraces and upland geomorphic surfaces provide new approaches and data for evaluating the Quaternary activity of post-Cretaceous faults that are recognized in subsurface data at the Savannah River Site in the Upper Coastal Plain of southwestern South Carolina. Analyses of longitudinal stream and terrace profiles, regional slope maps, and drainage basin morphometry indicate long-term uplift and southeast tilt of the site region. Preliminary results of drainage basin characterization suggests an apparent rejuvenation of drainages along the trace of the Pen Branch fault (a Tertiary reactivated reverse fault that initiated as a basin-margin normal fault along the northern boundary of the Triassic Dunbarton Basin). This apparent rejuvenation of drainages may be the result of nontectonic geomorphic processes or local tectonic uplift and tilting within a framework of regional uplift. Longitudinal profiles of fluvial terrace surfaces that are laterally continuous across the projected surface trace of the Pen Branch fault show no obvious evidence of warping or faulting within a resolution of ∼3 m. This combined with the estimated age of the terrace surfaces (350 ka to 1 Ma) indicates that if the Pen Branch fault is active, the Pleistocene rate of slip is very low (0.002 to 0.009 mm/yr)

  1. Contribution of stimulations for the optimization of quantitative electron probe micro analysis of heterogeneous catalysts; Apport de la simulation dans l'optimisation de l'analyse quantitative par microsonde electronique de catalyseurs heterogenes

    Energy Technology Data Exchange (ETDEWEB)

    Sorbier, L.

    2001-11-01

    Electron Probe Micro Analysis (EPMA) is frequently used to measure the local concentration of active elements in heterogeneous catalysts. However, when classical procedures are used, a significant deficit is observed both in local total concentration and mean total concentrations. A Monte Carlo program simulating measured intensities (characteristic lines and continuous background) has been written using PENELOPE routines. We have included in this program models taking into account the different physical phenomena likely to lead to the observed signal loss (insulating properties, roughness, porosity, energy loss at interfaces). Simulation results have shown that an important roughness (Ra>200 nm) was the only parameter apt to lead to a significant total signal loss. This led us to inquire into another origin to explain the signal loss observed on meso-porous samples. Measurements conducted on a meso-porous alumina confirmed that measuring aluminum, oxygen and carbon leads to a correct total of concentrations. Signal loss is thus explained by the contamination of the sample during its preparation, the components of the embedding resin diffusing into the porosity and reacting with the reactive surface of the catalyst support. In the case of macroporous catalysts, local roughness effect is very important. The simulations have shown the efficiency of the Peak to Background method to correct these local roughness effects. Measurements conducted on reforming and hydro-treating catalysts have led to a correct total concentration and confirmed the contribution of the Peak to Background method to achieve local quantitative measurement. (author)

  2. Contribution of stimulations for the optimization of quantitative electron probe micro analysis of heterogeneous catalysts; Apport de la simulation dans l'optimisation de l'analyse quantitative par microsonde electronique de catalyseurs heterogenes

    Energy Technology Data Exchange (ETDEWEB)

    Sorbier, L

    2001-11-01

    Electron Probe Micro Analysis (EPMA) is frequently used to measure the local concentration of active elements in heterogeneous catalysts. However, when classical procedures are used, a significant deficit is observed both in local total concentration and mean total concentrations. A Monte Carlo program simulating measured intensities (characteristic lines and continuous background) has been written using PENELOPE routines. We have included in this program models taking into account the different physical phenomena likely to lead to the observed signal loss (insulating properties, roughness, porosity, energy loss at interfaces). Simulation results have shown that an important roughness (Ra>200 nm) was the only parameter apt to lead to a significant total signal loss. This led us to inquire into another origin to explain the signal loss observed on meso-porous samples. Measurements conducted on a meso-porous alumina confirmed that measuring aluminum, oxygen and carbon leads to a correct total of concentrations. Signal loss is thus explained by the contamination of the sample during its preparation, the components of the embedding resin diffusing into the porosity and reacting with the reactive surface of the catalyst support. In the case of macroporous catalysts, local roughness effect is very important. The simulations have shown the efficiency of the Peak to Background method to correct these local roughness effects. Measurements conducted on reforming and hydro-treating catalysts have led to a correct total concentration and confirmed the contribution of the Peak to Background method to achieve local quantitative measurement. (author)

  3. Quantitative analysis of hydrogen and of its isotopes at the surface of the solids; Analyse quantitative de l'hydrogene et de ses isotopes a la surface des solides

    Energy Technology Data Exchange (ETDEWEB)

    Trocellier, P. [CEA Saclay, Dept. des Materiaux pour le Nucleaire (DEN/DANS/DMN), 91 - Gif-sur-Yvette (France)

    2007-07-01

    For analyzing the hydrogen isotopes, the nature of the probe which allows to excite the considered material and to give the hydrogen answer is multiple and is supported by various physical principles. The different available techniques are presented and several examples are given. To conclude, it is possible to determine the superficial or volume distribution of hydrogen or of one of its two heavy isotopes in choosing the most physico-chemical method. The choice of the technique to use depends of the wanted performance. In order to simplify, we can associate: 1)the sensitivity with mass spectrometry; 2)the depth resolution with the glow discharge, the SIMS and the resonant nuclear reaction; 3)the studied depth with the accelerated ions beams and the AMS; 4)the distribution image with the electrons stimulated desorption, the beta autoradiography and the ERDA; 5)the quantitative profile with the accelerated ions beams techniques; 6)the isotopic analysis with mass spectrometry and the accelerated ions beams. In order to be sure of the relevance of the measurements result, it is indicated to combine the advantages and the performances of several techniques as SIMS and NRA or FTIR and ERDA for instance. (O.M.)

  4. Selection and validation of reference genes for quantitative gene expression analyses in various tissues and seeds at different developmental stages in Bixa orellana L.

    Science.gov (United States)

    Moreira, Viviane S; Soares, Virgínia L F; Silva, Raner J S; Sousa, Aurizangela O; Otoni, Wagner C; Costa, Marcio G C

    2018-05-01

    Bixa orellana L., popularly known as annatto, produces several secondary metabolites of pharmaceutical and industrial interest, including bixin, whose molecular basis of biosynthesis remain to be determined. Gene expression analysis by quantitative real-time PCR (qPCR) is an important tool to advance such knowledge. However, correct interpretation of qPCR data requires the use of suitable reference genes in order to reduce experimental variations. In the present study, we have selected four different candidates for reference genes in B. orellana , coding for 40S ribosomal protein S9 (RPS9), histone H4 (H4), 60S ribosomal protein L38 (RPL38) and 18S ribosomal RNA (18SrRNA). Their expression stabilities in different tissues (e.g. flower buds, flowers, leaves and seeds at different developmental stages) were analyzed using five statistical tools (NormFinder, geNorm, BestKeeper, ΔCt method and RefFinder). The results indicated that RPL38 is the most stable gene in different tissues and stages of seed development and 18SrRNA is the most unstable among the analyzed genes. In order to validate the candidate reference genes, we have analyzed the relative expression of a target gene coding for carotenoid cleavage dioxygenase 1 (CCD1) using the stable RPL38 and the least stable gene, 18SrRNA , for normalization of the qPCR data. The results demonstrated significant differences in the interpretation of the CCD1 gene expression data, depending on the reference gene used, reinforcing the importance of the correct selection of reference genes for normalization.

  5. Qualitative and quantitative aspects of information processing in first psychosis: latent class analyses in patients, at-risk subjects, and controls.

    Science.gov (United States)

    van Tricht, Mirjam J; Bour, Lo J; Koelman, Johannes H T M; Derks, Eske M; Braff, David L; de Wilde, Odette M; Boerée, Thijs; Linszen, Don H; de Haan, Lieuwe; Nieman, Dorien H

    2015-04-01

    We aimed to determine profiles of information processing deficits in the pathway to first psychosis. Sixty-one subjects at ultrahigh risk (UHR) for psychosis were assessed, of whom 18 converted to a first episode of psychosis (FEP) within the follow-up period. Additionally, 47 FEP and 30 control subjects were included. Using 10 neurophysiological parameters associated with information processing, latent class analyses yielded three classes at baseline. Class membership was related to group status. Within the UHR sample, two classes were found. Transition to psychosis was nominally associated with class membership. Neurophysiological profiles were unstable over time, but associations between specific neurophysiological components at baseline and follow-up were found. We conclude that certain constellations of neurophysiological variables aid in the differentiation between controls and patients in the prodrome and after first psychosis. Copyright © 2014 Society for Psychophysiological Research.

  6. Quantitative research.

    Science.gov (United States)

    Watson, Roger

    2015-04-01

    This article describes the basic tenets of quantitative research. The concepts of dependent and independent variables are addressed and the concept of measurement and its associated issues, such as error, reliability and validity, are explored. Experiments and surveys – the principal research designs in quantitative research – are described and key features explained. The importance of the double-blind randomised controlled trial is emphasised, alongside the importance of longitudinal surveys, as opposed to cross-sectional surveys. Essential features of data storage are covered, with an emphasis on safe, anonymous storage. Finally, the article explores the analysis of quantitative data, considering what may be analysed and the main uses of statistics in analysis.

  7. Detection of pork adulteration in processed meat by species-specific PCR-QIAxcel procedure based on D-loop and cytb genes.

    Science.gov (United States)

    Barakat, Hassan; El-Garhy, Hoda A S; Moustafa, Mahmoud M A

    2014-12-01

    Detection of pork meat adulteration in "halal" meat products is a crucial issue in the fields of modern food inspection according to implementation of very strict procedures for halal food labelling. Present study aims at detecting and quantifying pork adulteration in both raw and cooked manufactured sausages. This is by applying an optimized species-specific PCR procedure followed by QIAxcel capillary electrophoresis system. Manufacturing experiment was designed by incorporating pork with beef meat at 0.01 to 10 % substitution levels beside beef and pork sausages as negative and positive controls, respectively. Subsequently, sausages were divided into raw and cooked sausages then subjected to DNA extraction. Results indicated that PCR amplifications of mitochondrial D-loop and cytochrome b (cytb) genes by porcine-specific primers produced 185 and 117 bp pork-specific DNA fragments in sausages, respectively. No DNA fragments were detected when PCR was applied on beef sausage DNA confirming primers specificity. For internal control, a 141-bp DNA fragment of eukaryotic 18S ribosomal RNA (rRNA) gene was amplified from pork and beef DNA templates. Although PCR followed by either QIAxcel or agarose techniques were efficient for targeted DNA fragments differentiation even as low as 0.01 % (pork/meat: w/w). For proficiency, adequacy, and performance, PCR-QIA procedure is highly sensitive, a time-saver, electronically documented, mutagenic-reagent free, of little manual errors, accurate in measuring PCR fragments length, and quantitative data supplier. In conclusion, it can be suggested that optimized PCR-QAI is considered as a rapid and sensitive method for routine pork detection and quantification in raw or processed meat.

  8. Vasculature analysis of patient derived tumor xenografts using species-specific PCR assays: evidence of tumor endothelial cells and atypical VEGFA-VEGFR1/2 signalings

    International Nuclear Information System (INIS)

    Bieche, Ivan; Marangoni, Elisabetta; Roman-Roman, Sergio; Decaudin, Didier; Dangles-Marie, Virginie; Vacher, Sophie; Vallerand, David; Richon, Sophie; Hatem, Rana; De Plater, Ludmilla; Dahmani, Ahmed; Némati, Fariba; Angevin, Eric

    2014-01-01

    Tumor endothelial transdifferentiation and VEGFR1/2 expression by cancer cells have been reported in glioblastoma but remain poorly documented for many other cancer types. To characterize vasculature of patient-derived tumor xenografts (PDXs), largely used in preclinical anti-angiogenic assays, we designed here species-specific real-time quantitative RT-PCR assays. Human and mouse PECAM1/CD31, ENG/CD105, FLT1/VEGFR1, KDR/VEGFR2 and VEGFA transcripts were analyzed in a large series of 150 PDXs established from 8 different tumor types (53 colorectal, 14 ovarian, 39 breast and 15 renal cell cancers, 6 small cell and 5 non small cell lung carcinomas, 13 cutaneous melanomas and 5 glioblastomas) and in two bevacizumab-treated non small cell lung carcinomas xenografts. As expected, mouse cell proportion in PDXs -evaluated by quantifying expression of the housekeeping gene TBP- correlated with all mouse endothelial markers and human VEGFA RNA levels. More interestingly, we observed human PECAM1/CD31 and ENG/CD105 expression in all tumor types, with higher rate in glioblastoma and renal cancer xenografts. Human VEGFR expression profile varied widely depending on tumor types with particularly high levels of human FLT1/VEGFR1 transcripts in colon cancers and non small cell lung carcinomas, and upper levels of human KDR/VEGFR2 transcripts in non small cell lung carcinomas. Bevacizumab treatment induced significant low expression of mouse Pecam1/Cd31, Eng/Cd105, Flt1/Vegfr1 and Kdr/Vefr2 while the human PECAM1/CD31 and VEGFA were upregulated. Taken together, our results strongly suggest existence of human tumor endothelial cells in all tumor types tested and of both stromal and tumoral autocrine VEGFA-VEGFR1/2 signalings. These findings should be considered when evaluating molecular mechanisms of preclinical response and resistance to tumor anti-angiogenic strategies

  9. Quantitative assessment of metal dysregulation in β-thalassemia patients in comparison with healthy controls by ICP-MS and chemometric analyses.

    Science.gov (United States)

    Farooq, Sabiha; Mazhar, Wardah; Siddiqui, Amna Jabbar; Ansari, Saqib Hussain; Musharraf, Syed Ghulam

    2018-01-31

    β-Thalassemia is one of the most common inherited disorders and is widely distributed throughout the world. Owing to severe deficiencies in red blood cell production, blood transfusion is required to correct anemia for normal growth and development but causes additional complications owing to iron overload. The aim of this study is to quantify the biometal dysregulations in β-thalassemia patients as compared with healthy controls. A total of 17 elements were analyzed in serum samples of β-thalassemia patients and healthy controls using ICP-MS followed by chemometric analyses. Out of these analyzed elements, 14 showed a significant difference between healthy and disease groups at p 3. A PLS-DA model revealed an excellent separation with 89.8% sensitivity and 97.2% specificity and the overall accuracy of the model was 92.2%. This metallomic study revealed that there is major difference in metallomic profiling of β-thalassemia patients specifically in Co, Mn, Ni, V and Ba, whereas the fold changes in Co, Mn, V and Ba were found to be greater than that in Fe, providing evidence that, in addition to Fe, other metals are also altered significantly and therefore chelation therapy for other metals may also needed in β-thalassemia patients. Copyright © 2018 John Wiley & Sons, Ltd.

  10. Effect of silver nanoparticles on Mediterranean sea urchin embryonal development is species specific and depends on moment of first exposure.

    Science.gov (United States)

    Burić, Petra; Jakšić, Željko; Štajner, Lara; Dutour Sikirić, Maja; Jurašin, Darija; Cascio, Claudia; Calzolai, Luigi; Lyons, Daniel Mark

    2015-10-01

    With the ever growing use of nanoparticles in a broad range of industrial and consumer applications there is increasing likelihood that such nanoparticles will enter the aquatic environment and be transported through freshwater systems, eventually reaching estuarine or marine waters. Due to silver's known antimicrobial properties and widespread use of silver nanoparticles (AgNP), their environmental fate and impact is therefore of particular concern. In this context we have investigated the species-specific effects of low concentrations of 60 nm AgNP on embryonal development in Mediterranean sea urchins Arbacia lixula, Paracentrotus lividus and Sphaerechinus granularis. The sensitivity of urchin embryos was tested by exposing embryos to nanoparticle concentrations in the 1-100 μg L(-1) range, with times of exposure varying from 30 min to 24 h (1 h-48 h for S. granularis) post-fertilisation which corresponded with fertilized egg, 4 cell, blastula and gastrula development phases. The most sensitive species to AgNP was A. lixula with significant modulation of embryonal development at the lowest AgNP concentrations of 1-10 μg L(-1) with high numbers of malformed embryos or arrested development. The greatest impact on development was noted for those embryos first exposed to nanoparticles at 6 and 24 h post fertilisation. For P. lividus, similar effects were noted at higher concentrations of 50 μg L(-1) and 100 μg L(-1) for all times of first exposure. The S. granularis embryos indicated a moderate AgNP impact, and significant developmental abnormalities were recorded in the concentration range of 10-50 μg L(-1). As later post-fertilisation exposure times to AgNP caused greater developmental changes in spite of a shorter total exposure time led us to postulate on additional mechanisms of AgNP toxicity. The results herein indicate that toxic effects of AgNP are species-specific. The moment at which embryos first encounter AgNP is also shown to be

  11. Electron microscopy and three-dimensional reconstruction of native thin filaments reveal species-specific differences in regulatory strand densities

    Energy Technology Data Exchange (ETDEWEB)

    Cammarato, Anthony, E-mail: acammara@burnham.org [Department of Physiology and Biophysics, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118 (United States); Craig, Roger [Department of Cell Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 (United States); Lehman, William [Department of Physiology and Biophysics, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118 (United States)

    2010-01-01

    Throughout the animal kingdom striated muscle contraction is regulated by the thin filament troponin-tropomyosin complex. Homologous regulatory components are shared among vertebrate and arthropod muscles; however, unique protein extensions and/or components characterize the latter. The Troponin T (TnT) isoforms of Drosophila indirect flight and tarantula femur muscle for example contain distinct C-terminal extensions and are {approx}20% larger overall than their vertebrate counterpart. Using electron microscopy and three-dimensional helical reconstruction of native Drosophila, tarantula and frog muscle thin filaments we have identified species-specific differences in tropomyosin regulatory strand densities. The strands on the arthropod thin filaments were significantly larger in diameter than those from vertebrates, although not significantly different from each other. These findings reflect differences in the regulatory troponin-tropomyosin complex, which are likely due to the larger TnT molecules aligning and extending along much of the tropomyosin strands' length. Such an arrangement potentially alters the physical properties of the regulatory strands and may help establish contractile characteristics unique to certain arthropod muscles.

  12. The tree-species-specific effect of forest bathing on perceived anxiety alleviation of young-adults in urban forests

    Directory of Open Access Journals (Sweden)

    Haoming Guan

    2017-12-01

    Full Text Available Forest bathing, i.e. spending time in a forest to walk, view and breathe in a forest, can alleviate the mental depression of visitors, but the tree-species-specific effect of this function by the urban forest is unknown. In this study, sixty-nine university students (aged 19-22, male ratio: 38% were recruited as participants to visit urban forests dominated by birch (Betula platyphylla Suk., maple (Acer triflorum Komarov and oak (Quercus mongolica Fisch. ex Ledeb trees in a park at the center of Changchun City, Northeast China. In the maple forest only the anxiety from study interest was decreased, while the anxiety from employment pressure was alleviated to the most extent in the birch forest. Participants perceived more anxiety from lesson declined in the oak forest than in the birch forest. Body parameters of weight and age were correlated with the anti-anxiety scores. In the oak forest, female participants can perceive more anxiety alleviation than male participants. For university students, forest bathing in our study can promote their study interest. Forest bathing can be more effective to alleviate the anxiety of young adults with greater weight. The birch forest was recommended to be visited by students to alleviate the pressure of employment worry, and the oak forest was recommended to be visited by girls.

  13. New Method for Simultaneous Species-Specific Identification of Equine Strongyles (Nematoda, Strongylida) by Reverse Line Blot Hybridization▿

    Science.gov (United States)

    Traversa, Donato; Iorio, Raffaella; Klei, Thomas R.; Kharchenko, Vitaliy A.; Gawor, Jakub; Otranto, Domenico; Sparagano, Olivier A. E.

    2007-01-01

    The ability of a reverse line blot (RLB) assay to identify 13 common species of equine small strongyles (cyathostomins) and to discriminate them from three Strongylus spp. (large strongyles) was demonstrated. The assay relied on the specific hybridization of PCR-amplified intergenic spacer DNA fragments of the nuclear ribosomal DNA to membrane-bound species-specific probes. All cyathostomins examined were unequivocally identified and simultaneously discriminated from each other and from three large strongyles (Strongylus edentatus, Strongylus equinus, and Strongylus vulgaris). This assay will enable the accurate and rapid identification of equine cyathostomins irrespective of their life cycle stage, opening important avenues for a better understanding of their biology and epidemiology and of the pathogenesis of cyathostomin-associated disease. In particular, this RLB method promises to be a powerful diagnostic tool to determine the roles of individual species in the pathogenesis of mixed infections and to elucidate some aspects of cyathostominosis. Also, it could represent a basic step toward the development of a rapid and simple molecular test for the early detection of drug-resistant genotypes of horse strongyle species. PMID:17626168

  14. Spatio-temporal and species-specific variation in PBDE levels/patterns in British Columbia's coastal waters

    International Nuclear Information System (INIS)

    Ikonomou, Michael G.; Fernandez, Marc P.; Hickman, Zachary L.

    2006-01-01

    Congener-specific levels of PBDEs were measured in the livers and some muscle tissues of Dungeness crab (Cancer magister), English sole (Pleuronectes vetulus) and spiny dogfish (Squalus acanthias). Highest concentrations (1200-560 ng/g lipid) were found in crab collected near heavily urbanized areas (pop. ∼0.3-1.8 million), followed by moderate levels at pulp/paper mills sites (∼150 ng/g), and lowest levels occurred in areas that were somewhat removed from industrial/populated areas (<24 ng/g). Temporal increases in total PBDEs and particularly in BDE-47 for Dungeness crab collected near pulp and paper and urbanized areas between 1994 and 2000 were observed. These correspond to Canadian and worldwide trends seen for PBDEs in biota. English sole and dogfish showed a pattern similar to that of the Columbia River whitefish samples, which corresponded closely to the patterns in the 'penta' commercial mixture. Conversely, Dungeness crab were enriched in lower chlorinated PBDEs, particularly BDE-47 and BDE-49, compared to the fish and shark species from BC. - PBDEs in biota and sediments from the West Coast of Canada reflect temporal, species-specific and geographic distributions

  15. Immunoreactivity between venoms and commercial antiserums in four Chinese snakes and venom identification by species-specific antibody.

    Science.gov (United States)

    Gao, Jian-Fang; Wang, Jin; Qu, Yan-Fu; Ma, Xiao-Mei; Ji, Xiang

    2013-01-31

    We studied the immunoreactivity between venoms and commercial antiserums in four Chinese venomous snakes, Bungarus multicinctus, Naja atra, Deinagkistrodon acutus and Gloydius brevicaudus. Venoms from the four snakes shared common antigenic components, and most venom components expressed antigenicity in the immunological reaction between venoms and antiserums. Antiserums cross-reacted with heterologous venoms. Homologous venom and antiserum expressed the highest reaction activity in all cross-reactions. Species-specific antibodies (SSAbs) were obtained from four antiserums by immunoaffinity chromatography: the whole antiserum against each species was gradually passed through a medium system coated with heterologous venoms, and the cross-reacting components in antiserum were immunoabsorbed by the common antigens in heterologous venoms; the unbound components (i.e., SSAbs) were collected, and passed through Hitrap G protein column and concentrated. The SSAbs were found to have high specificity by western blot and enzyme-linked immunosorbent assay (ELISA). A 6-well ELISA strip coated with SSAbs was used to assign a venom sample and blood and urine samples from the envenomed rats to a given snake species. Our detections could differentiate positive and negative samples, and identify venoms of a snake species in about 35 min. The ELISA strips developed in this study are clinically useful in rapid and reliable identification of venoms from the above four snake species. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Structural and functional conservation of CLEC-2 with the species-specific regulation of transcript expression in evolution.

    Science.gov (United States)

    Wang, Lan; Ren, Shifang; Zhu, Haiyan; Zhang, Dongmei; Hao, Yuqing; Ruan, Yuanyuan; Zhou, Lei; Lee, Chiayu; Qiu, Lin; Yun, Xiaojing; Xie, Jianhui

    2012-08-01

    CLEC-2 was first identified by sequence similarity to C-type lectin-like molecules with immune functions and has been reported as a receptor for the platelet-aggregating snake venom toxin rhodocytin and the endogenous sialoglycoprotein podoplanin. Recent researches indicate that CLEC-2-deficient mice were lethal at the embryonic stage associated with disorganized and blood-filled lymphatic vessels and severe edema. In view of a necessary role of CLEC-2 in the individual development, it is of interest to investigate its phylogenetic homology and highly conserved functional regions. In this work, we reported that CLEC-2 from different species holds with an extraordinary conservation by sequence alignment and phylogenetic tree analysis. The functional structures including N-linked oligosaccharide sites and ligand-binding domain implement a structural and functional conservation in a variety of species. The glycosylation sites (N120 and N134) are necessary for the surface expression CLEC-2. CLEC-2 from different species possesses the binding activity of mouse podoplanin. Nevertheless, the expression of CLEC-2 is regulated with a species-specific manner. The alternative splicing of pre-mRNA, a regulatory mechanism of gene expression, and the binding sites on promoter for several key transcription factors vary between different species. Therefore, CLEC-2 shares high sequence homology and functional identity. However the transcript expression might be tightly regulated by different mechanisms in evolution.

  17. Species-specific accumulation of polybrominated diphenyl ether flame retardants in birds of prey from the Chesapeake Bay region, USA

    Energy Technology Data Exchange (ETDEWEB)

    Chen Da, E-mail: chen@vims.ed [Department of Environmental and Aquatic Animal Health, Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA 23062 (United States); Hale, Robert C. [Department of Environmental and Aquatic Animal Health, Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA 23062 (United States); Watts, Bryan D. [Center for Conservation Biology, College of William and Mary, Williamsburg, VA 23185 (United States); La Guardia, Mark J.; Harvey, Ellen [Department of Environmental and Aquatic Animal Health, Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA 23062 (United States); Mojica, Elizabeth K. [Center for Conservation Biology, College of William and Mary, Williamsburg, VA 23185 (United States)

    2010-05-15

    Compared to organochlorines, little is known about polybrominated diphenyl ether (PBDE) contamination of birds of prey breeding in the Chesapeake Bay, the largest estuary in the U.S. This study examined and compared PBDE contamination in eggs of osprey, double-crested cormorant, brown pelican and peregrine falcon from this area. Several legacy persistent organic pollutants such as PCBs and DDE were also investigated. The level of urbanization of the landscape appeared to influence the level of PBDE exposure. PBDE congener distribution patterns varied between piscivorous and terrestrial-feeding birds. This suggests individual congeners may be subject to differences in bioaccumulation, biomagnification or metabolism in the aquatic and terrestrial food webs. Biomagnification of PBDEs was studied in the Bay aquatic food chains for the first time. A biomagnification factor of 25.1 was estimated for SIGMAPBDEs for the fish - osprey egg food chain. Hazard quotients, applied as a preliminary evaluation, indicated that PBDEs may pose a moderate hazard to ospreys and peregrine falcons through impairment of reproductive performance. - Birds of prey breeding in the Chesapeake Bay (USA) exhibited species-specific PBDE accumulation patterns.

  18. Species-specific accumulation of polybrominated diphenyl ether flame retardants in birds of prey from the Chesapeake Bay region, USA

    International Nuclear Information System (INIS)

    Chen Da; Hale, Robert C.; Watts, Bryan D.; La Guardia, Mark J.; Harvey, Ellen; Mojica, Elizabeth K.

    2010-01-01

    Compared to organochlorines, little is known about polybrominated diphenyl ether (PBDE) contamination of birds of prey breeding in the Chesapeake Bay, the largest estuary in the U.S. This study examined and compared PBDE contamination in eggs of osprey, double-crested cormorant, brown pelican and peregrine falcon from this area. Several legacy persistent organic pollutants such as PCBs and DDE were also investigated. The level of urbanization of the landscape appeared to influence the level of PBDE exposure. PBDE congener distribution patterns varied between piscivorous and terrestrial-feeding birds. This suggests individual congeners may be subject to differences in bioaccumulation, biomagnification or metabolism in the aquatic and terrestrial food webs. Biomagnification of PBDEs was studied in the Bay aquatic food chains for the first time. A biomagnification factor of 25.1 was estimated for ΣPBDEs for the fish - osprey egg food chain. Hazard quotients, applied as a preliminary evaluation, indicated that PBDEs may pose a moderate hazard to ospreys and peregrine falcons through impairment of reproductive performance. - Birds of prey breeding in the Chesapeake Bay (USA) exhibited species-specific PBDE accumulation patterns.

  19. Species-Specific Antimonial Sensitivity in Leishmania Is Driven by Post-Transcriptional Regulation of AQP1

    Science.gov (United States)

    Mandal, Goutam; Mandal, Srotoswati; Sharma, Mansi; Charret, Karen Santos; Papadopoulou, Barbara; Bhattacharjee, Hiranmoy; Mukhopadhyay, Rita

    2015-01-01

    Leishmania is a digenetic protozoan parasite causing leishmaniasis in humans. The different clinical forms of leishmaniasis are caused by more than twenty species of Leishmania that are transmitted by nearly thirty species of phlebotomine sand flies. Pentavalent antimonials (such as Pentostam or Glucantime) are the first line drugs for treating leishmaniasis. Recent studies suggest that pentavalent antimony (Sb(V)) acts as a pro-drug, which is converted to the more active trivalent form (Sb(III)). However, sensitivity to trivalent antimony varies among different Leishmania species. In general, Leishmania species causing cutaneous leishmaniasis (CL) are more sensitive to Sb(III) than the species responsible for visceral leishmaniasis (VL). Leishmania aquaglyceroporin (AQP1) facilitates the adventitious passage of antimonite down a concentration gradient. In this study, we show that Leishmania species causing CL accumulate more antimonite, and therefore exhibit higher sensitivity to antimonials, than the species responsible for VL. This species-specific differential sensitivity to antimonite is directly proportional to the expression levels of AQP1 mRNA. We show that the stability of AQP1 mRNA in different Leishmania species is regulated by their respective 3’-untranslated regions. The differential regulation of AQP1 mRNA explains the distinct antimonial sensitivity of each species. PMID:25714343

  20. Persistent organochlorines in 13 shark species from offshore and coastal waters of Korea: Species-specific accumulation and contributing factors.

    Science.gov (United States)

    Lee, Hyun-Kyung; Jeong, Yunsun; Lee, Sunggyu; Jeong, Woochang; Choy, Eun-Jung; Kang, Chang-Keun; Lee, Won-Chan; Kim, Sang-Jo; Moon, Hyo-Bang

    2015-05-01

    Data on persistent organochlorines (OCs) in sharks are scarce. Concentrations of OCs such as polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) were determined in the muscle tissue of 13 shark species (n=105) collected from offshore (Indian and Pacific Oceans) and coastal waters of Korea, to investigate species-specific accumulation of OCs and to assess the potential health risks associated with consumption of shark meat. Overall OC concentrations were highly variable not only among species but also within the same species of shark. The concentrations of PCBs, DDTs, chlordanes, hexachlorobenzene, and heptachlor in all shark species ranged from shark in our study were relatively lower than those reported in other studies. Aggressive shark species and species inhabiting the Indian Ocean had the highest levels of OCs. Inter-species differences in the concentrations and accumulation profiles of OCs among shark species could be explained by differences in feeding habit and sampling locations. Several confounding factors such as growth velocity, trophic position, and regional contamination status may affect the bioaccumulation of OCs in sharks. Hazard ratios of non-cancer risk for all the OCs were below one, whereas the hazard ratios of lifetime cancer risks of PCBs and DDTs exceeded one, implying potential carcinogenic effects in the general population in Korea. This is the first report to document the occurrence of OCs in sharks from Korea. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Species-specific differences in adaptive phenotypic plasticity in an ecologically relevant trophic trait: hypertrophic lips in Midas cichlid fishes.

    Science.gov (United States)

    Machado-Schiaffino, Gonzalo; Henning, Frederico; Meyer, Axel

    2014-07-01

    The spectacular species richness of cichlids and their diversity in morphology, coloration, and behavior have made them an ideal model for the study of speciation and adaptive evolution. Hypertrophic lips evolved repeatedly and independently in African and Neotropical cichlid radiations. Cichlids with hypertrophic lips forage predominantly in rocky crevices and it has been hypothesized that mechanical stress caused by friction could result in larger lips through phenotypic plasticity. To test the influence of the environment on the size and development of lips, we conducted a series of breeding and feeding experiments on Midas cichlids. Full-sibs of Amphilophus labiatus (thick-lipped) and Amphilophus citrinellus (thin-lipped) each were split into a control group which was fed food from the water column and a treatment group whose food was fixed to substrates. We found strong evidence for phenotypic plasticity on lip area in the thick-lipped species, but not in the thin-lipped species. Intermediate phenotypic values were observed in hybrids from thick- and thin-lipped species reared under "control" conditions. Thus, both a genetic, but also a phenotypic plastic component is involved in the development of hypertrophic lips in Neotropical cichlids. Moreover, species-specific adaptive phenotypic plasticity was found, suggesting that plasticity is selected for in recent thick-lipped species. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  2. Electron microscopy and three-dimensional reconstruction of native thin filaments reveal species-specific differences in regulatory strand densities

    International Nuclear Information System (INIS)

    Cammarato, Anthony; Craig, Roger; Lehman, William

    2010-01-01

    Throughout the animal kingdom striated muscle contraction is regulated by the thin filament troponin-tropomyosin complex. Homologous regulatory components are shared among vertebrate and arthropod muscles; however, unique protein extensions and/or components characterize the latter. The Troponin T (TnT) isoforms of Drosophila indirect flight and tarantula femur muscle for example contain distinct C-terminal extensions and are ∼20% larger overall than their vertebrate counterpart. Using electron microscopy and three-dimensional helical reconstruction of native Drosophila, tarantula and frog muscle thin filaments we have identified species-specific differences in tropomyosin regulatory strand densities. The strands on the arthropod thin filaments were significantly larger in diameter than those from vertebrates, although not significantly different from each other. These findings reflect differences in the regulatory troponin-tropomyosin complex, which are likely due to the larger TnT molecules aligning and extending along much of the tropomyosin strands' length. Such an arrangement potentially alters the physical properties of the regulatory strands and may help establish contractile characteristics unique to certain arthropod muscles.

  3. Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences.

    Science.gov (United States)

    Zhang, Huimin; He, Hongkui; Yu, Xiujuan; Xu, Zhaohui; Zhang, Zhizhou

    2016-11-01

    It remains an unsolved problem to quantify a natural microbial community by rapidly and conveniently measuring multiple species with functional significance. Most widely used high throughput next-generation sequencing methods can only generate information mainly for genus-level taxonomic identification and quantification, and detection of multiple species in a complex microbial community is still heavily dependent on approaches based on near full-length ribosome RNA gene or genome sequence information. In this study, we used near full-length rRNA gene library sequencing plus Primer-Blast to design species-specific primers based on whole microbial genome sequences. The primers were intended to be specific at the species level within relevant microbial communities, i.e., a defined genomics background. The primers were tested with samples collected from the Daqu (also called fermentation starters) and pit mud of a traditional Chinese liquor production plant. Sixteen pairs of primers were found to be suitable for identification of individual species. Among them, seven pairs were chosen to measure the abundance of microbial species through quantitative PCR. The combination of near full-length ribosome RNA gene library sequencing and Primer-Blast may represent a broadly useful protocol to quantify multiple species in complex microbial population samples with species-specific primers.

  4. Contribution to the micro-calorimetric study of the characteristics of radio-elements and to their qualitative and quantitative analysis; Contribution a l'etude microcalorimetrique des caracteristiques des radio-elements et a leurs analyses qualitative et quantitative

    Energy Technology Data Exchange (ETDEWEB)

    Ozias, Y [Centre de Production de Plutonium de Marcoule, 30 (France)

    1964-10-01

    equal to that obtained by mass spectrography (destruction of the sample) 1 to 3 per cent, and higher than that obtained by counting techniques (greater than 5 per cent). (author) [French] Le principe de cette etude consiste a enregistrer avec le microcalorimetre E. CALVET le flux d'energie emis par les radioelements en fonction du temps at a partir de cette courbe de determiner soit leurs caracteristiques (periode et energie du rayonnement), soit la composition d'un melange de radioelements. Dans une premiere partie on a adapte les relations theoriques de la radioactivite a l'etude microcalorimetrique. Dans une deuxieme partie on determine experimentalement au microcalorimetre E. CALVET les caracteristiques de divers radioelements, yttrium 90, phosphore 32, soufre 35, iode 131, etc. et leurs melanges. On a etudie plus particulierement l'analyse isotopique du melange de {sup 239}Pu, de {sup 240}Pu et eventuellement de {sup 241}Pu. La methode microcalorimetrique n'a pas la sensibilite des methodes classiques de comptage, sa limite actuelle para etre de l'ordre du micro-watt pour les appareils utilises, mais elle est la plus directe pour les emetteurs de rayonnements facilement absorbables({alpha} et {beta}). Pour les emetteurs {gamma} une partie seulement de l'energie est absorbee par les parois du recipient. La determination de leurs caracteristiques et de leurs masses dans les melanges ne depend ni de la forme, ni de la dilution, ni surtout de l'auto-absorption de la source. Pour des echantillons de forte activite, cette auto-absorption est pour les methodes classiques la source de grosses difficultes entra ant de multiples manipulations: divisions, mise en solution, dilutions qui introduisent autant de causes d'erreur. La methode calorimetrique permet de travailler sur l'echantillon brut. Toutes les mesures ont ete faites avec le microcalorimetre E. CALVET classique; mais pour effectuer une mesure tres precise de' l'energie due au rayonnement {gamma} il faut faire

  5. Visual recognition of age class and preference for infantile features: implications for species-specific vs universal cognitive traits in primates.

    Directory of Open Access Journals (Sweden)

    Anna Sato

    Full Text Available Despite not knowing the exact age of individuals, humans can estimate their rough age using age-related physical features. Nonhuman primates show some age-related physical features; however, the cognitive traits underlying their recognition of age class have not been revealed. Here, we tested the ability of two species of Old World monkey, Japanese macaques (JM and Campbell's monkeys (CM, to spontaneously discriminate age classes using visual paired comparison (VPC tasks based on the two distinct categories of infant and adult images. First, VPCs were conducted in JM subjects using conspecific JM stimuli. When analyzing the side of the first look, JM subjects significantly looked more often at novel images. Based on analyses of total looking durations, JM subjects looked at a novel infant image longer than they looked at a familiar adult image, suggesting the ability to spontaneously discriminate between the two age classes and a preference for infant over adult images. Next, VPCs were tested in CM subjects using heterospecific JM stimuli. CM subjects showed no difference in the side of their first look, but looked at infant JM images longer than they looked at adult images; the fact that CMs were totally naïve to JMs suggested that the attractiveness of infant images transcends species differences. This is the first report of visual age class recognition and a preference for infant over adult images in nonhuman primates. Our results suggest not only species-specific processing for age class recognition but also the evolutionary origins of the instinctive human perception of baby cuteness schema, proposed by the ethologist Konrad Lorenz.

  6. Intramammary infection with coagulase-negative staphylococci at parturition: Species-specific prevalence, risk factors, and effect on udder health.

    Science.gov (United States)

    De Visscher, A; Piepers, S; Haesebrouck, F; De Vliegher, S

    2016-08-01

    Coagulase-negative staphylococci (CNS) are the main cause of bovine intramammary infections (IMI) in many countries. Despite a high prevalence of CNS IMI at parturition, species-specific risk factor studies, relying on accurate identification methods, are lacking. Therefore, this observational study aimed at determining the prevalence and distribution of different CNS species causing IMI in fresh heifers and dairy cows in Flemish dairy herds and identifying associated species- and subgroup-specific risk factors at the herd, cow, and quarter level. The effect on udder health was investigated as well. Staphylococcus chromogenes, S. sciuri, and S. cohnii were the most frequently isolated species. The only CNS species causing IMI in fresh heifers and dairy cows in all herds was Staphylococcus chromogenes, whereas large between-herd differences in distribution were observed for the other species. Quarters from heifers and quarters with an inverted teat end had higher odds of being infected with S. chromogenes, S. simulans, or S. xylosus as well as with S. chromogenes solely. Prepartum teat apex colonization with S. chromogenes increased the likelihood of S. chromogenes IMI in the corresponding quarters at parturition. Quarters with dirty teat apices before calving were more likely to be infected with S. cohnii, S. equorum, S. saprophyticus, or S. sciuri, supporting the environmental nature of these CNS species. Three species (S. chromogenes, S. simulans, and S. xylosus) were associated with a higher quarter somatic cell count at parturition as compared with uninfected quarters. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  7. 2013 Early Career Achievement Award--Proteomics of muscle- and species-specificity in meat color stability.

    Science.gov (United States)

    Suman, S P; Rentfrow, G; Nair, M N; Joseph, P

    2014-03-01

    Meat color is the most important quality trait influencing consumer purchase decisions. The interinfluential interactions between myoglobin and biomolecules govern color stability in meat. The advances in proteomics, such as high throughput analytical tools in mass spectrometry, 2-dimensional electrophoresis, and bioinformatics, offer themselves as robust techniques to characterize the proteome basis of muscle- and species-specific meat color phenomena. Differential abundance of chaperones and antioxidant proteins contributes to muscle-specific color stability in beef; the greater abundance of chaperones and antioxidant proteins in color-stable Longissimus lumborum than in color-labile Psoas major protects myoglobin and contributes to superior color stability of beef Longissimus steaks. Lipid oxidation-induced myoglobin oxidation is more critical to beef color than pork color due to the inherent differences in myoglobin chemistry; the number of nucleophilic histidine residues adducted by reactive aldehydes is greater in beef myoglobin than in pork myoglobin. Preferential adduction of secondary products of lipid oxidation to beef myoglobin accelerates metmyoglobin formation at a greater degree than in its pork counterpart. Mass spectrometric investigations revealed that although cherry-red carboxymyoglobin is more stable than oxymyoglobin, both redox forms undergo lipid oxidation-induced oxidation in model systems. The accuracy of mass spectrometry to detect the molecular mass of proteins has been applied to differentiate myoglobins from closely related meat animals, such as goats and sheep or emu and ostrich. In addition, this approach indicated that turkey myoglobin is 350 Da greater in molecular mass than beef myoglobin, and the unique biochemistry of turkey myoglobin could be responsible for its greater thermostability in model systems as well as the pink color defect observed in fully cooked uncured turkey products.

  8. Organotin persistence in contaminated marine sediments and porewaters: In situ degradation study using species-specific stable isotopic tracers

    Energy Technology Data Exchange (ETDEWEB)

    Furdek, Martina; Mikac, Nevenka [Division for Marine and Environmental Research, Rudjer Boskovic Institute, Bijenicka 54, Zagreb (Croatia); Bueno, Maite; Tessier, Emmanuel; Cavalheiro, Joana [Laboratoire de Chimie Analytique Bio-inorganique et Environnement, Institut Pluridisciplinaire de Recherche sur l’Environnement et les Matériaux, CNRS UMR 5254, Université de Pau et des Pays de l’Adour, Hélioparc Pau Pyrénées, 2, Av. P. Angot, 64053 Pau Cedex 9 (France); Monperrus, Mathilde, E-mail: mathilde.monperrus@univ-pau.fr [Laboratoire de Chimie Analytique Bio-inorganique et Environnement, Institut Pluridisciplinaire de Recherche sur l’Environnement et les Matériaux, CNRS UMR 5254, Université de Pau et des Pays de l’Adour, Hélioparc Pau Pyrénées, 2, Av. P. Angot, 64053 Pau Cedex 9 (France)

    2016-04-15

    Highlights: • Limiting step in OTC degradation in sediments is their desorption into porewater. • TBT persistence in contaminated sediments increases in sediments rich in organic matter. • DBT does not accumulate in sediments as degradation product of TBT. • TBT and DBT degradation in porewaters occurs with half-lives from 2.9 to 9.2 days. • PhTs degradation is slower than BuTs degradation in oxic porewaters. - Abstract: This paper provides a comprehensive study of the persistence of butyltins and phenyltins in contaminated marine sediments and presents the first data on their degradation potentials in porewaters. The study’s aim was to explain the different degradation efficiencies of organotin compounds (OTC) in contaminated sediments. The transformation processes of OTC in sediments and porewaters were investigated in a field experiment using species-specific, isotopically enriched organotin tracers. Sediment characteristics (organic carbon content and grain size) were determined to elucidate their influence on the degradation processes. The results of this study strongly suggest that a limiting step in OTC degradation in marine sediments is their desorption into porewaters because their degradation in porewaters occurs notably fast with half-lives of 9.2 days for tributyltin (TBT) in oxic porewaters and 2.9 ± 0.1 and 9.1 ± 0.9 days for dibutyltin (DBT) in oxic and anoxic porewaters, respectively. By controlling the desorption process, organic matter influences the TBT degradation efficiency and consequently defines its persistence in contaminated sediments, which thus increases in sediments rich in organic matter.

  9. Organotin persistence in contaminated marine sediments and porewaters: In situ degradation study using species-specific stable isotopic tracers

    International Nuclear Information System (INIS)

    Furdek, Martina; Mikac, Nevenka; Bueno, Maite; Tessier, Emmanuel; Cavalheiro, Joana; Monperrus, Mathilde

    2016-01-01

    Highlights: • Limiting step in OTC degradation in sediments is their desorption into porewater. • TBT persistence in contaminated sediments increases in sediments rich in organic matter. • DBT does not accumulate in sediments as degradation product of TBT. • TBT and DBT degradation in porewaters occurs with half-lives from 2.9 to 9.2 days. • PhTs degradation is slower than BuTs degradation in oxic porewaters. - Abstract: This paper provides a comprehensive study of the persistence of butyltins and phenyltins in contaminated marine sediments and presents the first data on their degradation potentials in porewaters. The study’s aim was to explain the different degradation efficiencies of organotin compounds (OTC) in contaminated sediments. The transformation processes of OTC in sediments and porewaters were investigated in a field experiment using species-specific, isotopically enriched organotin tracers. Sediment characteristics (organic carbon content and grain size) were determined to elucidate their influence on the degradation processes. The results of this study strongly suggest that a limiting step in OTC degradation in marine sediments is their desorption into porewaters because their degradation in porewaters occurs notably fast with half-lives of 9.2 days for tributyltin (TBT) in oxic porewaters and 2.9 ± 0.1 and 9.1 ± 0.9 days for dibutyltin (DBT) in oxic and anoxic porewaters, respectively. By controlling the desorption process, organic matter influences the TBT degradation efficiency and consequently defines its persistence in contaminated sediments, which thus increases in sediments rich in organic matter.

  10. Seedling transplants reveal species-specific responses of high-elevation tropical treeline trees to climate change.

    Science.gov (United States)

    Rehm, Evan M; Feeley, Kenneth J

    2016-08-01

    The elevations at which tropical treelines occur are believed to represent the point where low mean temperatures limit the growth of upright woody trees. Consequently, tropical treelines are predicted to shift to higher elevations with global warming. However, treelines throughout the tropics have remained stationary despite increasing global mean temperatures. The goal of the study reported here was to build a more comprehensive understanding of the effects of mean temperature, low-temperature extremes, shading, and their interactions on seedling survival at tropical treelines. We conducted a seedling transplant study using three dominant canopy-forming treeline species in the southern tropical Andes. We found species-specific differences and contrasting responses in seedling survival to changes in mean temperature. The most abundant naturally occurring species at the seedling stage outside the treeline, Weinmannia fagaroides, showed a negative relationship between the survival of transplanted seedlings and mean temperature, the opposite of a priori expectations. Conversely, Clethra cuneata showed increased survival at higher mean temperatures, but survival also increased with higher absolute low temperatures and the presence of shade. Finally, the survival of Gynoxys nitida seedlings was insensitive to temperature but increased under shade. These findings show that multiple factors can determine the upper distributional limit of species forming the current tropical treeline. As such, predictions of future local and regional tropical treeline shifts may need to consider several factors beyond changes in mean temperature. If the treeline remains stationary and cloud forests are unable to expand into higher elevations, there may be severe species loss in this biodiversity hotspot.

  11. Species-specific activation of Cu/Zn SOD by its CCS copper chaperone in the pathogenic yeast Candida albicans.

    Science.gov (United States)

    Gleason, Julie E; Li, Cissy X; Odeh, Hana M; Culotta, Valeria C

    2014-06-01

    Candida albicans is a pathogenic yeast of important public health relevance. Virulence of C. albicans requires a copper and zinc containing superoxide dismutase (SOD1), but the biology of C. albicans SOD1 is poorly understood. To this end, C. albicans SOD1 activation was examined in baker's yeast (Saccharomyces cerevisiae), a eukaryotic expression system that has proven fruitful for the study of SOD1 enzymes from invertebrates, plants, and mammals. In spite of the 80% similarity between S. cerevisiae and C. albicans SOD1 molecules, C. albicans SOD1 is not active in S. cerevisiae. The SOD1 appears incapable of productive interactions with the copper chaperone for SOD1 (CCS1) of S. cerevisiae. C. albicans SOD1 contains a proline at position 144 predicted to dictate dependence on CCS1. By mutation of this proline, C. albicans SOD1 gained activity in S. cerevisiae, and this activity was independent of CCS1. We identified a putative CCS1 gene in C. albicans and created heterozygous and homozygous gene deletions at this locus. Loss of CCS1 resulted in loss of SOD1 activity, consistent with its role as a copper chaperone. C. albicans CCS1 also restored activity to C. albicans SOD1 expressed in S. cerevisiae. C. albicans CCS1 is well adapted for activating its partner SOD1 from C. albicans, but not SOD1 from S. cerevisiae. In spite of the high degree of homology between the SOD1 and CCS1 molecules in these two fungal species, there exists a species-specific barrier in CCS-SOD interactions which may reflect the vastly different lifestyles of the pathogenic versus the noninfectious yeast.

  12. Projections of climate-driven changes in tuna vertical habitat based on species-specific differences in blood oxygen affinity.

    Science.gov (United States)

    Mislan, K A S; Deutsch, Curtis A; Brill, Richard W; Dunne, John P; Sarmiento, Jorge L

    2017-10-01

    Oxygen concentrations are hypothesized to decrease in many areas of the ocean as a result of anthropogenically driven climate change, resulting in habitat compression for pelagic animals. The oxygen partial pressure, pO 2 , at which blood is 50% saturated (P 50 ) is a measure of blood oxygen affinity and a gauge of the tolerance of animals for low ambient oxygen. Tuna species display a wide range of blood oxygen affinities (i.e., P 50 values) and therefore may be differentially impacted by habitat compression as they make extensive vertical movements to forage on subdaily time scales. To project the effects of end-of-the-century climate change on tuna habitat, we calculate tuna P 50 depths (i.e., the vertical position in the water column at which ambient pO 2 is equal to species-specific blood P 50 values) from 21st century Earth System Model (ESM) projections included in the fifth phase of the Climate Model Intercomparison Project (CMIP5). Overall, we project P 50 depths to shoal, indicating likely habitat compression for tuna species due to climate change. Tunas that will be most impacted by shoaling are Pacific and southern bluefin tunas-habitat compression is projected for the entire geographic range of Pacific bluefin tuna and for the spawning region of southern bluefin tuna. Vertical shifts in P 50 depths will potentially influence resource partitioning among Pacific bluefin, bigeye, yellowfin, and skipjack tunas in the northern subtropical and eastern tropical Pacific Ocean, the Arabian Sea, and the Bay of Bengal. By establishing linkages between tuna physiology and environmental conditions, we provide a mechanistic basis to project the effects of anthropogenic climate change on tuna habitats. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

  13. Species-Specific Responses of Juvenile Rockfish to Elevated pCO2: From Behavior to Genomics.

    Directory of Open Access Journals (Sweden)

    Scott L Hamilton

    Full Text Available In the California Current ecosystem, global climate change is predicted to trigger large-scale changes in ocean chemistry within this century. Ocean acidification-which occurs when increased levels of atmospheric CO2 dissolve into the ocean-is one of the biggest potential threats to marine life. In a coastal upwelling system, we compared the effects of chronic exposure to low pH (elevated pCO2 at four treatment levels (i.e., pCO2 = ambient [500], moderate [750], high [1900], and extreme [2800 μatm] on behavior, physiology, and patterns of gene expression in white muscle tissue of juvenile rockfish (genus Sebastes, integrating responses from the transcriptome to the whole organism level. Experiments were conducted simultaneously on two closely related species that both inhabit kelp forests, yet differ in early life history traits, to compare high-CO2 tolerance among species. Our findings indicate that these congeners express different sensitivities to elevated CO2 levels. Copper rockfish (S. caurinus exhibited changes in behavioral lateralization, reduced critical swimming speed, depressed aerobic scope, changes in metabolic enzyme activity, and increases in the expression of transcription factors and regulatory genes at high pCO2 exposure. Blue rockfish (S. mystinus, in contrast, showed no significant changes in behavior, swimming physiology, or aerobic capacity, but did exhibit significant changes in the expression of muscle structural genes as a function of pCO2, indicating acclimatization potential. The capacity of long-lived, late to mature, commercially important fish to acclimatize and adapt to changing ocean chemistry over the next 50-100 years is likely dependent on species-specific physiological tolerances.

  14. SPECIES-SPECIFIC FOREST VARIABLE ESTIMATION USING NON-PARAMETRIC MODELING OF MULTI-SPECTRAL PHOTOGRAMMETRIC POINT CLOUD DATA

    Directory of Open Access Journals (Sweden)

    J. Bohlin

    2012-07-01

    Full Text Available The recent development in software for automatic photogrammetric processing of multispectral aerial imagery, and the growing nation-wide availability of Digital Elevation Model (DEM data, are about to revolutionize data capture for forest management planning in Scandinavia. Using only already available aerial imagery and ALS-assessed DEM data, raster estimates of the forest variables mean tree height, basal area, total stem volume, and species-specific stem volumes were produced and evaluated. The study was conducted at a coniferous hemi-boreal test site in southern Sweden (lat. 58° N, long. 13° E. Digital aerial images from the Zeiss/Intergraph Digital Mapping Camera system were used to produce 3D point-cloud data with spectral information. Metrics were calculated for 696 field plots (10 m radius from point-cloud data and used in k-MSN to estimate forest variables. For these stands, the tree height ranged from 1.4 to 33.0 m (18.1 m mean, stem volume from 0 to 829 m3 ha-1 (249 m3 ha-1 mean and basal area from 0 to 62.2 m2 ha-1 (26.1 m2 ha-1 mean, with mean stand size of 2.8 ha. Estimates made using digital aerial images corresponding to the standard acquisition of the Swedish National Land Survey (Lantmäteriet showed RMSEs (in percent of the surveyed stand mean of 7.5% for tree height, 11.4% for basal area, 13.2% for total stem volume, 90.6% for pine stem volume, 26.4 for spruce stem volume, and 72.6% for deciduous stem volume. The results imply that photogrammetric matching of digital aerial images has significant potential for operational use in forestry.

  15. Potential effects of sea-level rise on plant productivity: Species-specific responses in northeast Pacific tidal marshes

    Science.gov (United States)

    Janousek, Christopher; Buffington, Kevin J.; Thorne, Karen M.; Guntenspergen, Glenn R.; Takekawa, John Y.; Dugger, Bruce D.

    2016-01-01

    Coastal wetland plants are adapted to varying degrees of inundation. However, functional relationships between inundation and productivity are poorly characterized for most species. Determining species-specific tolerances to inundation is necessary to evaluate sea-level rise (SLR) effects on future marsh plant community composition, quantify organic matter inputs to marsh accretion, and inform predictive modeling of tidal wetland persistence. In 2 macrotidal estuaries in the northeast Pacific we grew 5 common species in experimental mesocosms across a gradient of tidal elevations to assess effects on growth. We also tested whether species abundance distributions along elevation gradients in adjacent marshes matched productivity profiles in the mesocosms. We found parabolic relationships between inundation and total plant biomass and shoot counts in Spartina foliosa and Bolboschoenus maritimus in California, USA, and in Carex lyngbyei in Oregon, USA, with maximum total plant biomass occurring at 38, 28, and 15% time submerged, respectively. However, biomass of Salicornia pacifica and Juncus balticus declined monotonically with increasing inundation. Inundation effects on the ratio of belowground to aboveground biomass varied inconsistently among species. In comparisons of field distributions with mesocosm results, B. maritimus, C. lyngbyei and J. balticus were abundant in marshes at or above elevations corresponding with their maximum productivity; however, S. foliosa and S. pacifica were frequently abundant at lower elevations corresponding with sub-optimal productivity. Our findings show species-level differences in how marsh plant growth may respond to future SLR and highlight the sensitivity of high marsh species such as S. pacifica and J. balticus to increases in flooding.

  16. Simultaneous discrimination of species and strains in Lactobacillus rhamnosus using species-specific PCR combined with multiplex mini-sequencing technology.

    Science.gov (United States)

    Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Lina; Chu, Wen-Shen

    2015-12-01

    This study described the use of species-specific PCR in combination with SNaPshot mini-sequencing to achieve species identification and strain differentiation in Lactobacillus rhamnosus. To develop species-specific PCR and strain subtyping primers, the dnaJ gene was used as a target, and its corresponding sequences were analyzed both in Lb. rhamnosus and in a subset of its phylogenetically closest species. The results indicated that the species-specific primer pair was indeed specific for Lb. rhamnosus, and the mini-sequencing assay was able to unambiguously distinguish Lb. rhamnosus strains into different haplotypes. In conclusion, we have successfully developed a rapid, accurate and cost-effective assay for inter- and intraspecies discrimination of Lb. rhamnosus, which can be applied to achieve efficient quality control of probiotic products. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Basic quantitative analyses of medical examinations

    OpenAIRE

    Möltner, A; Schellberg, D; Jünger, J

    2006-01-01

    [english] The evaluation steps are described which are necessary for an elementary test-theoretic analysis of an exam and sufficient as a basis of item-revisions, improvements of the composition of tests and feedback to teaching coordinators and curriculum developers. These steps include the evaluation of the results, the analysis of item difficulty and discrimination and - where appropriate - the corresponding evaluation of single answers. To complete the procedure, the internal consistency ...

  18. Quantitative analyses of empirical fitness landscapes

    International Nuclear Information System (INIS)

    Szendro, Ivan G; Franke, Jasper; Krug, Joachim; Schenk, Martijn F; De Visser, J Arjan G M

    2013-01-01

    The concept of a fitness landscape is a powerful metaphor that offers insight into various aspects of evolutionary processes and guidance for the study of evolution. Until recently, empirical evidence on the ruggedness of these landscapes was lacking, but since it became feasible to construct all possible genotypes containing combinations of a limited set of mutations, the number of studies has grown to a point where a classification of landscapes becomes possible. The aim of this review is to identify measures of epistasis that allow a meaningful comparison of fitness landscapes and then apply them to the empirical landscapes in order to discern factors that affect ruggedness. The various measures of epistasis that have been proposed in the literature appear to be equivalent. Our comparison shows that the ruggedness of the empirical landscape is affected by whether the included mutations are beneficial or deleterious and by whether intragenic or intergenic epistasis is involved. Finally, the empirical landscapes are compared to landscapes generated with the rough Mt Fuji model. Despite the simplicity of this model, it captures the features of the experimental landscapes remarkably well. (paper)

  19. SU-D-207A-02: Possible Characterization of the Brain Tumor Vascular Environment by a Novel Strategy of Quantitative Analysis in Dynamic Contrast Enhanced MR Imaging: A Combination of Both Patlak and Logan Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Yee, S; Chinnaiyan, P; Wloch, J; Pirkola, M; Yan, D [Beaumont Health System, Royal Oak, MI (United States)

    2016-06-15

    Purpose: The majority of quantitative analyses involving dynamic contrast enhanced (DCE) MRI have been performed to obtain kinetic parameters such as Ktrans and ve. Such analyses are generally performed assuming a “reversible” tissue compartment, where the tracer is assumed to be rapidly equilibrated between the plasma and tissue compartments. However, some tumor vascular environments may be more suited for a “non-reversible” tissue compartment, where, as with FDG PET imaging, the tracer is continuously deposited into the tissue compartment (or the return back to the plasma compartment is very slow in the imaging time scale). Therefore, Patlak and Logan analyses, which represent tools for the “non-reversible” and “reversible” modeling, respectively, were performed to better characterize the brain tumor vascular environment. Methods: A voxel-by-voxel analysis was performed to generate both Patlak and Logan plots in two brain tumor patients, one with grade III astrocytoma and the other with grade IV astrocytoma or glioblastoma. The slopes of plots and the r-square were then obtained by linear fitting and compared for each voxel. Results: The 2-dimensional scatter plots of Logan (Y-axis) vs. Patlak slopes (X-axis) clearly showed increased Logan slopes for glioblastoma (Figure 3A). The scatter plots of goodness-of-fit (Figure 3B) also suggested glioblastoma, relative to grade III astrocytoma, might consist of more voxels that are kinetically Logan-like (i.e. rapidly equilibrated extravascular space and active vascular environment). Therefore, the enhanced Logan-like behavior (and the Logan slope) in glioblastoma may imply an increased fraction of active vascular environment, while the enhanced Patlak-like behavior implies the vascular environment permitting a relatively slower washout of the tracer. Conclusion: Although further verification is required, the combination of Patlak and Logan analyses in DCE MRI may be useful in characterizing the tumor

  20. Comparison of GC-ICP-MS and HPLC-ICP-MS for species-specific isotope dilution analysis of tributyltin in sediment after accelerated solvent extraction

    International Nuclear Information System (INIS)

    Wahlen, Raimund; Wolff-Briche, Celine

    2003-01-01

    This study describes a direct comparison of GC and HPLC hyphenated to ICP-MS determination of tributyltin (TBT) in sediment by species-specific isotope dilution analysis (SS-IDMS). The certified reference sediment PACS-2 (NRC, Canada) and a candidate reference sediment (P-18/HIPA-1) were extracted using an accelerated solvent extraction (ASE) procedure. For comparison of GC and LC methods an older bottle of PACS-2 was used, whilst a fresh bottle was taken for demonstration of the accuracy of the methods. The data obtained show good agreement between both methods for both the PACS-2 sediment (LC-ICP-IDMS 828±87 ng g -1 TBT as Sn, GC-ICP-IDMS 848±39 ng g -1 TBT as Sn) and the P-18/ HIPA-1 sediment (LC-ICP-IDMS 78.0±9.7 ng g -1 TBT as Sn, GC-ICP-IDMS 79.2±3.8 ng g -1 TBT as Sn). The analysis by GC-ICP-IDMS offers a greater signal-to-noise ratio and hence a superior detection limit of 0.03 pg TBT as Sn, in the sediment extracts compared to HPLC-ICP-IDMS (3 pg TBT as Sn). A comparison of the uncertainties associated with both methods indicates superior precision of the GC approach. This is related to the better reproducibility of the peak integration, which affects the isotope ratio measurements used for IDMS. The accuracy of the ASE method combined with HPLC-ICP-IDMS was demonstrated during the international interlaboratory comparison P-18 organised by the Comite Consultatif pour la Quantite de Matiere (CCQM). The results obtained by GC-ICP-IDMS for a newly opened bottle of PACS-2 were 1087±77 ng g -1 Sn for DBT and 876±51 ng g -1 Sn for TBT (expanded uncertainties with a coverage factor of 2), which are in good agreement with the certified values of 1090±150 ng g -1 Sn and 980±130 ng g -1 Sn, respectively. (orig.)

  1. Aberration of mitosis by hexavalent chromium in some Fabaceae members is mediated by species-specific microtubule disruption.

    Science.gov (United States)

    Eleftheriou, Eleftherios P; Michalopoulou, Vasiliki A; Adamakis, Ioannis-Dimosthenis S

    2015-05-01

    Because the detrimental effects of chromium (Cr) to higher plants have been poorly investigated, the present study was undertaken to verify the toxic attributes of hexavalent chromium [Cr(VI)] to plant mitotic microtubules (MTs), to determine any differential disruption of MTs during mitosis of taxonomically related species and to clarify the relationship between the visualized chromosomal aberrations and the Cr(VI)-induced MT disturbance. For this purpose, 5-day-old uniform seedlings of Vicia faba, Pisum sativum, Vigna sinensis and Vigna angularis, all belonging to the Fabaceae family, were exposed to 250 μM Cr(VI) supplied as potassium dichromate (K₂Cr₂O₇) for 24, 72 and 120 h and others in distilled water serving as controls. Root tip samples were processed for tubulin immunolabelling (for MT visualization) and DNA fluorescent staining (for chromosomal visualization). Microscopic preparations of cell squashes were then examined and photographed by confocal laser scanning microscopy (CLSM). Cr(VI) halted seedling growth turning roots brown and necrotic. Severe chromosomal abnormalities and differential disturbance of the corresponding MT arrays were found in all mitotic phases. In particular, in V. faba MTs were primarily depolymerized and replaced by atypical tubulin conformations, whereas in P. sativum, V. sinensis and V. angularis they became bundled in a time-dependent manner. In P. sativum, the effects were milder compared to those of the other species, but in all cases MT disturbance adversely affected the proper aggregation of chromosomes on the metaphase plate, their segregation at anaphase and organization of the new nuclei at telophase. Cr(VI) is very toxic to seedling growth. The particular effect depends on the exact stage the cell is found at the time of Cr(VI) entrance and is species-specific. Mitotic MT arrays are differentially deranged by Cr(VI) in the different species examined, even if they are taxonomically related, while their

  2. Species-specific prevalence of vaginal candidiasis among patients with diabetes mellitus and its relation to their glycaemic status.

    Science.gov (United States)

    Goswami, R; Dadhwal, V; Tejaswi, S; Datta, K; Paul, A; Haricharan, R N; Banerjee, U; Kochupillai, N P

    2000-09-01

    Non- C. albicans Candida species are increasingly being recognized as the cause of vulvo-vaginal candidiasis. These species are often less susceptible to antifungal agents. Patients with diabetes mellitus are at risk for vulvo-vaginal candidasis. We assessed the species-specific prevalence rate and risk of candidiasis in patients with diabetes mellitus and healthy controls. Genital tract examination, direct microscopy and fungal cultures of discharge collected by high vaginal swab were undertaken among 78 consecutive patients with diabetes mellitus (mean (+/-sd) age 32+/-12 years and body mass index (BMI) 22.3+/-5.5kg/m(2)) and 88 age- and BMI-matched healthy females. Glycaemic control in the diabetic cohort was assessed by measuring total glycosylated haemoglobin. Candida species were isolated in 36 of 78 (46%) subjects with diabetes mellitus and in 21 of 88 (23%) healthy subjects (Chi-squared 9.11, P=0.0025). The predominant Candida species isolated in diabetics with vulvo-vaginal candidiasis were Candida glabrata (39%), C. albicans (26%) and C. tropicalis (17%). In contrast, in the control group, C. albicans, C. glabrata and C. hemulonii comprised 30% each, with none having C. tropicalis infection (for C. tropicalis: diabetic vs. control; 17% vs. nil, P=0. 05). Among the diabetic group, subjects with vulvo-vaginal candidiasis had significantly higher mean HbA1 when compared to those who had no such infection (12.8+/-2.6% vs. 9.7+/-1.7% respectively, P=0.001). The overall accuracy of direct microscopy and clinical examination for predicting vulvo-vaginal candidiasis was only 77% and 51%, respectively, in the diabetic group, and 83% and 65% in the control group. Patients with diabetes mellitus had a high prevalence rate (46%) of vulvo-vaginal candidiasis with relative risk of 2.45. The non- C. albicans species such as C. glabrata and C. tropicalis were the predominant species isolated among them. There seems to be a significant link between hyperglycaemia and

  3. Cloning and expression of a zebrafish SCN1B ortholog and identification of a species-specific splice variant

    Directory of Open Access Journals (Sweden)

    Slat Emily A

    2007-07-01

    Full Text Available Abstract Background Voltage-gated Na+ channel β1 (Scn1b subunits are multi-functional proteins that play roles in current modulation, channel cell surface expression, cell adhesion, cell migration, and neurite outgrowth. We have shown previously that β1 modulates electrical excitability in vivo using a mouse model. Scn1b null mice exhibit spontaneous seizures and ataxia, slowed action potential conduction, decreased numbers of nodes of Ranvier in myelinated axons, alterations in nodal architecture, and differences in Na+ channel α subunit localization. The early death of these mice at postnatal day 19, however, make them a challenging model system to study. As a first step toward development of an alternative model to investigate the physiological roles of β1 subunits in vivo we cloned two β1-like subunit cDNAs from D. rerio. Results Two β1-like subunit mRNAs from zebrafish, scn1ba_tv1 and scn1ba_tv2, arise from alternative splicing of scn1ba. The deduced amino acid sequences of Scn1ba_tv1 and Scn1ba_tv2 are identical except for their C-terminal domains. The C-terminus of Scn1ba_tv1 contains a tyrosine residue similar to that found to be critical for ankyrin association and Na+ channel modulation in mammalian β1. In contrast, Scn1ba_tv2 contains a unique, species-specific C-terminal domain that does not contain a tyrosine. Immunohistochemical analysis shows that, while the expression patterns of Scn1ba_tv1 and Scn1ba_tv2 overlap in some areas of the brain, retina, spinal cord, and skeletal muscle, only Scn1ba_tv1 is expressed in optic nerve where its staining pattern suggests nodal expression. Both scn1ba splice forms modulate Na+ currents expressed by zebrafish scn8aa, resulting in shifts in channel gating mode, increased current amplitude, negative shifts in the voltage dependence of current activation and inactivation, and increases in the rate of recovery from inactivation, similar to the function of mammalian β1 subunits. In

  4. Species-Specific Monoclonal Antibodies to Escherichia coli-Expressed p36 Cytosolic Protein of Mycoplasma hyopneumoniae

    Science.gov (United States)

    Caron, J.; Sawyer, N.; Moumen, B. Ben Abdel; Bouh, K. Cheikh Saad; Dea, S.

    2000-01-01

    The p36 protein of Mycoplasma hyopneumoniae is a cytosolic protein carrying species-specific antigenic determinants. Based on the genomic sequence of the reference strain ATCC 25934, primers were designed for PCR amplification of the p36-encoding gene (948 bp). These primers were shown to be specific to M. hyopneumoniae since no DNA amplicons could be obtained with other mycoplasma species and pathogenic bacteria that commonly colonize the porcine respiratory tract. The amplified p36 gene was subcloned into the pGEX-4T-1 vector to be expressed in Escherichia coli as a fusion protein with glutathione S-transferase (GST). The GST-p36 recombinant fusion protein was purified by affinity chromatography and cut by thrombin, and the enriched p36 protein was used to immunize female BALB/c mice for the production of anti-p36 monoclonal antibodies (MAbs). The polypeptide specificity of the nine MAbs obtained was confirmed by Western immunoblotting with cell lysates prepared from the homologous strain. Cross-reactivity studies of the anti-p36 MAbs towards two other M. hyopneumoniae reference strains (ATCC 25095 and J strains) and Quebec field strains that had been isolated in culture suggested that these anti-p36 MAbs were directed against a highly conserved epitope, or closely located epitopes, of the p36 protein. No reactivity was demonstrated against other mycoplasma species tested. Clinical signs and lesions suggestive of enzootic pneumonia were reproduced in specific-pathogen-free pigs infected experimentally with a virulent Quebec field strain (IAF-DM9827) of M. hyopneumoniae. The bacteria could be recovered from lung homogenates of pigs that were killed after the 3-week observation period by both PCR and cultivation procedures. Furthermore, the anti-p36 MAbs permitted effective detection by indirect immunofluorescence of M. hyopneumoniae in frozen lung sections from experimentally infected pigs. However, attempts to use the recombinant p36 protein as an antigen in an

  5. Rapid diagnostic tests as a source of DNA for Plasmodium species-specific real-time PCR

    Directory of Open Access Journals (Sweden)

    Van Esbroeck Marjan

    2011-03-01

    Full Text Available Abstract Background This study describes the use of malaria rapid diagnostic tests (RDTs as a source of DNA for Plasmodium species-specific real-time PCR. Methods First, the best method to recover DNA from RDTs was investigated and then the applicability of this DNA extraction method was assessed on 12 different RDT brands. Finally, two RDT brands (OptiMAL Rapid Malaria Test and SDFK60 malaria Ag Plasmodium falciparum/Pan test were comprehensively evaluated on a panel of clinical samples submitted for routine malaria diagnosis at ITM. DNA amplification was done with the 18S rRNA real-time PCR targeting the four Plasmodium species. Results of PCR on RDT were compared to those obtained by PCR on whole blood samples. Results Best results were obtained by isolating DNA from the proximal part of the nitrocellulose component of the RDT strip with a simple DNA elution method. The PCR on RDT showed a detection limit of 0.02 asexual parasites/μl, which was identical to the same PCR on whole blood. For all 12 RDT brands tested, DNA was detected except for one brand when a low parasite density sample was applied. In RDTs with a plastic seal covering the nitrocellulose strip, DNA extraction was hampered. PCR analysis on clinical RDT samples demonstrated correct identification for single species infections for all RDT samples with asexual parasites of P. falciparum (n = 60, Plasmodium vivax (n = 10, Plasmodium ovale (n = 10 and Plasmodium malariae (n = 10. Samples with only gametocytes were detected in all OptiMAL and in 10 of the 11 SDFK60 tests. None of the negative samples (n = 20 gave a signal by PCR on RDT. With PCR on RDT, higher Ct-values were observed than with PCR on whole blood, with a mean difference of 2.68 for OptiMAL and 3.53 for SDFK60. Mixed infections were correctly identified with PCR on RDT in 4/5 OptiMAL tests and 2/5 SDFK60 tests. Conclusions RDTs are a reliable source of DNA for Plasmodium real-time PCR. This study demonstrates the

  6. Development of a multiplex assay for genus- and species-specific detection of Phytophthora based on differences in mitochondrial gene order

    Science.gov (United States)

    G. J. Bilodeau; F. N. Martin; M. D. Coffey; C. L. Blomquist

    2014-01-01

    A molecular diagnostic assay for Phytophthora spp. that is specific, sensitive, has both genus- and species-specific detection capabilities multiplexed, and can be used to systematically develop markers for detection of a wide range of species would facilitate research and regulatory efforts. To address this need, a marker system was developed...

  7. Development of SCAR markers and PCR assays for single or simultaneous species-specific detection of Phytophthora nicotianae and Pythium helicoides in ebb-and-flow irrigated kalanchoe.

    Science.gov (United States)

    Ahonsi, Monday O; Ling, Yin; Kageyama, Koji

    2010-11-01

    Phytophthora nicotianae and Pythium helicoides are important water-borne oomycete pathogens of irrigated ornamentals particularly ebb-and-flow irrigated kalanchoe in Japan. We developed novel PCR-based sequence characterized amplified region markers and assays for rapid identification and species-specific detection of both pathogens in separate PCR reactions or simultaneously in a duplex PCR.

  8. Halocarbon emissions by selected tropical seaweeds: species-specific and compound-specific responses under changing pH.

    Science.gov (United States)

    Mithoo-Singh, Paramjeet Kaur; Keng, Fiona S-L; Phang, Siew-Moi; Leedham Elvidge, Emma C; Sturges, William T; Malin, Gill; Abd Rahman, Noorsaadah

    2017-01-01

    Five tropical seaweeds, Kappaphycus alvarezii (Doty) Doty ex P.C. Silva, Padina australis Hauck, Sargassum binderi Sonder ex J. Agardh (syn. S. aquifolium (Turner) C. Agardh), Sargassum siliquosum J. Agardh and Turbinaria conoides (J. Agardh) Kützing, were incubated in seawater of pH 8.0, 7.8 (ambient), 7.6, 7.4 and 7.2, to study the effects of changing seawater pH on halocarbon emissions. Eight halocarbon species known to be emitted by seaweeds were investigated: bromoform (CHBr 3 ), dibro-momethane (CH 2 Br 2 ), iodomethane (CH 3 I), diiodomethane (CH 2 I 2 ), bromoiodomethane (CH 2 BrI), bromochlorometh-ane (CH 2 BrCl), bromodichloromethane (CHBrCl 2 ), and dibro-mochloromethane (CHBr 2 Cl). These very short-lived halocarbon gases are believed to contribute to stratospheric halogen concentrations if released in the tropics. It was observed that the seaweeds emit all eight halocarbons assayed, with the exception of K. alvarezii and S. binderi for CH 2 I 2 and CH 3 I respectively, which were not measurable at the achievable limit of detection. The effect of pH on halocarbon emission by the seaweeds was shown to be species-specific and compound specific. The highest percentage changes in emissions for the halocarbons of interest were observed at the lower pH levels of 7.2 and 7.4 especially in Padina australis and Sargassum spp., showing that lower seawater pH causes elevated emissions of some halocarbon compounds. In general the seaweed least affected by pH change in terms of types of halocarbon emission, was P. australis . The commercially farmed seaweed K. alvarezii was very sensitive to pH change as shown by the high increases in most of the compounds in all pH levels relative to ambient. In terms of percentage decrease in maximum quantum yield of photosynthesis ( F v ∕ F m ) prior to and after incubation, there were no significant correlations with the various pH levels tested for all seaweeds. The correlation between percentage decrease in the maximum

  9. Halocarbon emissions by selected tropical seaweeds: species-specific and compound-specific responses under changing pH

    Directory of Open Access Journals (Sweden)

    Paramjeet Kaur Mithoo-Singh

    2017-01-01

    Full Text Available Five tropical seaweeds, Kappaphycus alvarezii (Doty Doty ex P.C. Silva, Padina australis Hauck, Sargassum binderi Sonder ex J. Agardh (syn. S. aquifolium (Turner C. Agardh, Sargassum siliquosum J. Agardh and Turbinaria conoides (J. Agardh Kützing, were incubated in seawater of pH 8.0, 7.8 (ambient, 7.6, 7.4 and 7.2, to study the effects of changing seawater pH on halocarbon emissions. Eight halocarbon species known to be emitted by seaweeds were investigated: bromoform (CHBr3, dibro­momethane (CH2Br2, iodomethane (CH3I, diiodomethane (CH2I2, bromoiodomethane (CH2BrI, bromochlorometh­ane (CH2BrCl, bromodichloromethane (CHBrCl2, and dibro­mochloromethane (CHBr2Cl. These very short-lived halocarbon gases are believed to contribute to stratospheric halogen concentrations if released in the tropics. It was observed that the seaweeds emit all eight halocarbons assayed, with the exception of K. alvarezii and S. binderi for CH2I2 and CH3I respectively, which were not measurable at the achievable limit of detection. The effect of pH on halocarbon emission by the seaweeds was shown to be species-specific and compound specific. The highest percentage changes in emissions for the halocarbons of interest were observed at the lower pH levels of 7.2 and 7.4 especially in Padina australis and Sargassum spp., showing that lower seawater pH causes elevated emissions of some halocarbon compounds. In general the seaweed least affected by pH change in terms of types of halocarbon emission, was P. australis. The commercially farmed seaweed K. alvarezii was very sensitive to pH change as shown by the high increases in most of the compounds in all pH levels relative to ambient. In terms of percentage decrease in maximum quantum yield of photosynthesis (Fv∕Fm prior to and after incubation, there were no significant correlations with the various pH levels tested for all seaweeds. The correlation between percentage decrease in the maximum quantum yield of

  10. Do the Golden-winged Warbler and Blue-winged Warbler Exhibit Species-specific Differences in their Breeding Habitat Use?

    Directory of Open Access Journals (Sweden)

    Laura L. Patton

    2010-12-01

    Full Text Available We compared habitat features of Golden-winged Warbler (Vermivora chrysoptera territories in the presence and absence of the Blue-winged Warbler (V. cyanoptera on reclaimed coal mines in southeastern Kentucky, USA. Our objective was to determine whether there are species specific differences in habitat that can be manipulated to encourage population persistence of the Golden-winged Warbler. When compared with Blue-winged Warblers, Golden-winged Warblers established territories at higher elevations and with greater percentages of grass and canopy cover. Mean territory size (minimum convex polygon was 1.3 ha (se = 0.1 for Golden-winged Warbler in absence of Blue-winged Warbler, 1.7 ha (se = 0.3 for Golden-winged Warbler coexisting with Blue-winged Warbler, and 2.1 ha (se = 0.3 for Blue-winged Warbler. Territory overlap occurred within and between species (18 of n = 73 territories, 24.7%. All Golden-winged and Blue-winged Warblers established territories that included an edge between reclaimed mine land and mature forest, as opposed to establishing territories in open grassland/shrubland habitat. The mean distance territories extended from a forest edge was 28.0 m (se = 3.8 for Golden-winged Warbler in absence of Blue-winged Warbler, 44.7 m (se = 5.7 for Golden-winged Warbler coexisting with Blue-winged Warbler, and 33.1 m (se = 6.1 for Blue-winged Warbler. Neither territory size nor distances to forest edges differed significantly between Golden-winged Warbler in presence or absence of Blue-winged Warbler. According to Monte Carlo analyses, orchardgrass (Dactylis glomerata, green ash (Fraxinus pennsylvanica seedlings and saplings, and black locust (Robinia pseudoacacia saplings were indicative of sites with only Golden-winged Warblers. Sericea lespedeza, goldenrod (Solidago spp., clematis vine (Clematis spp., and blackberry (Rubus spp. were indicative of sites where both species occurred. Our findings complement recent genetic studies and add

  11. Mutant p97 exhibits species-specific changes of its ATPase activity and compromises the UBXD9-mediated monomerisation of p97 hexamers.

    Science.gov (United States)

    Rijal, Ramesh; Arhzaouy, Khalid; Strucksberg, Karl-Heinz; Cross, Megan; Hofmann, Andreas; Schröder, Rolf; Clemen, Christoph S; Eichinger, Ludwig

    2016-01-01

    p97 (VCP) is a homo-hexameric triple-A ATPase that exerts a plethora of cellular processes. Heterozygous missense mutations of p97 cause at least five human neurodegenerative disorders. However, the specific molecular consequences of p97 mutations are hitherto widely unknown. Our in silico structural models of human and Dictyostelium p97 showed that the disease-causing human R93C, R155H, and R155C as well as Dictyostelium R154C, E219K, R154C/E219K p97 mutations constitute variations in surface-exposed locations. In-gel ATPase activity measurements of p97 monomers and hexamers revealed significant mutation- and species-specific differences. While all human p97 mutations led to an increase in ATPase activity, no changes could be detected for the Dictyostelium R154C mutant, which is orthologous to human R155C. The E219K mutation led to an almost complete loss of activity, which was partially recuperated in the R154C/E219K double-mutant indicating p97 inter-domain communication. By means of co-immunoprecipitation experiments we identified an UBX-domain containing Dictyostelium protein as a novel p97 interaction partner. We categorized all UBX-domain containing Dictyostelium proteins and named the interaction partner UBXD9. Pull-down assays and surface plasmon resonance analyses of Dictyostelium UBXD9 or the human orthologue TUG/ASPL/UBXD9 demonstrated direct interactions with p97 as well as species-, mutation- and ATP-dependent differences in the binding affinities. Sucrose density gradient assays revealed that both human and Dictyostelium UBXD9 proteins very efficiently disassembled wild-type, but to a lesser extent mutant p97 hexamers into monomers. Our results are consistent with a scenario in which p97 point mutations lead to differences in enzymatic activities and molecular interactions, which in the long-term result in a late-onset and progressive multisystem disease. Copyright © 2016 The Authors. Published by Elsevier GmbH.. All rights reserved.

  12. Lack of association between PKLR rs3020781 and NOS1AP rs7538490 and type 2 diabetes, overweight, obesity and related metabolic phenotypes in a Danish large-scale study: case-control studies and analyses of quantitative traits

    Directory of Open Access Journals (Sweden)

    Almind Katrine

    2008-12-01

    Full Text Available Abstract Background Several studies in multiple ethnicities have reported linkage to type 2 diabetes on chromosome 1q21-25. Both PKLR encoding the liver pyruvate kinase and NOS1AP encoding the nitric oxide synthase 1 (neuronal adaptor protein (CAPON are positioned within this chromosomal region and are thus positional candidates for the observed linkage peak. The C-allele of PKLR rs3020781 and the T-allele of NOS1AP rs7538490 are reported to strongly associate with type 2 diabetes in various European-descent populations comprising a total of 2,198 individuals with a combined odds ratio (OR of 1.33 [1.16–1.54] and 1.53 [1.28–1.81], respectively. Our aim was to validate these findings by investigating the impact of the two variants on type 2 diabetes and related quantitative metabolic phenotypes in a large study sample of Danes. Further, we intended to expand the analyses by examining the effect of the variants in relation to overweight and obesity. Methods PKLR rs3020781 and NOS1AP rs7538490 were genotyped, using TaqMan allelic discrimination, in a combined study sample comprising a total of 16,801 and 16,913 individuals, respectively. The participants were ascertained from four different study groups; the population-based Inter99 cohort (nPKLR = 5,962, nNOS1AP = 6,008, a type 2 diabetic patient group (nPKLR = 1,873, nNOS1AP = 1,874 from Steno Diabetes Center, a population-based study sample (nPKLR = 599, nNOS1AP = 596 from Steno Diabetes Center and the ADDITION Denmark screening study cohort (nPKLR = 8,367, nNOS1AP = 8,435. Results In case-control studies we evaluated the potential association between rs3020781 and rs7538490 and type 2 diabetes and obesity. No significant associations were observed for type 2 diabetes (rs3020781: pAF = 0.49, OR = 1.02 [0.96–1.10]; rs7538490: pAF = 0.84, OR = 0.99 [0.93–1.06]. Neither did we show association with overweight or obesity. Additionally, the PKLR and the NOS1AP genotypes were demonstrated not

  13. Recombinant major outer membrane protein (MOMP) of Chlamydophila abortus, Chlamydophila pecorum, and Chlamydia suis as antigens to distinguish chlamydial species-specific antibodies in animal sera.

    Science.gov (United States)

    Hoelzle, Ludwig E; Hoelzle, Katharina; Wittenbrink, Max M

    2004-10-05

    Recombinant major outer membrane proteins (rMOMP) of Chlamydophila (Ch.) abortus, Ch. pecorum, and Chlamydia (C.) suis were used as antigens to distinguish chlamydial species-specific antibodies in (i) immune sera from six rabbits and three pigs raised against native purified elementary bodies, (ii) serum samples from 25 sows vaccinated with Ch. abortus, and (iii) 40 serum samples from four heifers experimentally infected with Ch. abortus. All post-exposition sera contained chlamydial antibodies as confirmed by strong ELISA seroreactivities against the chlamydial LPS. For the rMOMP ELISA mean IgG antibody levels were at least 5.8-fold higher with the particular rMOMP homologous to the chlamydial species used for immunisation or infection than with heterologous rMOMPs (P <0.001). Preferential rMOMP ELISA reactivities of sera were confirmed by Western blotting. The results suggest that the entire chlamydial rMOMP could provide a species-specific serodiagnostic antigen.

  14. Discrimination of the Lactobacillus acidophilus group using sequencing, species-specific PCR and SNaPshot mini-sequencing technology based on the recA gene.

    Science.gov (United States)

    Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Mu-Chiou; Wang, Li-Tin; Huang, Lina; Lee, Fwu-Ling

    2012-10-01

    To clearly identify specific species and subspecies of the Lactobacillus acidophilus group using phenotypic and genotypic (16S rDNA sequence analysis) techniques alone is difficult. The aim of this study was to use the recA gene for species discrimination in the L. acidophilus group, as well as to develop a species-specific primer and single nucleotide polymorphism primer based on the recA gene sequence for species and subspecies identification. The average sequence similarity for the recA gene among type strains was 80.0%, and most members of the L. acidophilus group could be clearly distinguished. The species-specific primer was designed according to the recA gene sequencing, which was employed for polymerase chain reaction with the template DNA of Lactobacillus strains. A single 231-bp species-specific band was found only in L. delbrueckii. A SNaPshot mini-sequencing assay using recA as a target gene was also developed. The specificity of the mini-sequencing assay was evaluated using 31 strains of L. delbrueckii species and was able to unambiguously discriminate strains belonging to the subspecies L. delbrueckii subsp. bulgaricus. The phylogenetic relationships of most strains in the L. acidophilus group can be resolved using recA gene sequencing, and a novel method to identify the species and subspecies of the L. delbrueckii and L. delbrueckii subsp. bulgaricus was developed by species-specific polymerase chain reaction combined with SNaPshot mini-sequencing. Copyright © 2012 Society of Chemical Industry.

  15. New view on the age-specificity of pig Cryptosporidium by species-specific primers for distinguishing Cryptosporidium suis and Cryptosporidium pig genotype II

    Czech Academy of Sciences Publication Activity Database

    Jeníková, M.; Němejc, K.; Sak, Bohumil; Květoňová, Dana; Kváč, Martin

    2011-01-01

    Roč. 176, 2/3 (2011), 120-125 ISSN 0304-4017 R&D Projects: GA ČR GP523/07/P117 Institutional research plan: CEZ:AV0Z60220518 Keywords : Cryptosporidium suis * Cryptosporidium pig genotype II * Mixed infection * Age-specificity * Species-specific primers Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 2.579, year: 2011

  16. Quantification of Different Eubacterium spp. in Human Fecal Samples with Species-Specific 16S rRNA-Targeted Oligonucleotide Probes

    OpenAIRE

    Schwiertz, Andreas; Le Blay, Gwenaelle; Blaut, Michael

    2000-01-01

    Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E. hadrum, E. lentum, E. limosum, E. moniliforme, and E. ventriosum. The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none...

  17. Development of a Species-specific PCR Assay for Three Xanthomonas Species, Causing Bulb and Flower Diseases, Based on Their Genome Sequences

    Directory of Open Access Journals (Sweden)

    Chang-Gi Back

    2015-09-01

    Full Text Available In this study, we developed a species-specific PCR assay for rapid and accurate detection of three Xanthomonas species, X. axonopodis pv. poinsettiicola (XAP, X. hyacinthi (XH and X. campestris pv. zantedeschiae (XCZ, based on their draft genome sequences. XAP, XH and XCZ genomes consist of single chromosomes that contain 5,221, 4,395 and 7,986 protein coding genes, respectively. Species-specific primers were designed from variable regions of the draft genome sequence data and assessed by a PCR-based detection method. These primers were also tested for specificity against 17 allied Xanthomonas species as well as against the host DNA and the microbial community of the host surface. Three primer sets were found to be very specific and no amplification product was obtained with the host DNA and the microbial community of the host surface. In addition, a detection limit of 1 pg/μl per PCR reaction was detected when these primer sets were used to amplify corresponding bacterial DNAs. Therefore, these primer sets and the developed species-specific PCR assay represent a valuable, sensitive, and rapid diagnostic tool that can be used to detect three specific pathogens at early stages of infection and may help control diseases.

  18. Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes.

    Science.gov (United States)

    Schwiertz, A; Le Blay, G; Blaut, M

    2000-01-01

    Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E. hadrum, E. lentum, E. limosum, E. moniliforme, and E. ventriosum. The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none of the probes showed cross-hybridization under stringent conditions. The species-specific probes were applied to fecal samples obtained from 12 healthy volunteers. E. biforme, E. cylindroides, E. hadrum, E. lentum, and E. ventriosum could be determined. All other Eubacterium species for which probes had been designed were under the detection limit of 10(7) cells g (dry weight) of feces(-1). The cell counts obtained are essentially in accordance with the literature data, which are based on colony counts. This shows that whole-cell in situ hybridization with species-specific probes is a valuable tool for the enumeration of Eubacterium species in feces.

  19. A novel synthetic peptide microarray assay detects Chlamydia species-specific antibodies in animal and human sera.

    Science.gov (United States)

    Sachse, Konrad; Rahman, Kh Shamsur; Schnee, Christiane; Müller, Elke; Peisker, Madlen; Schumacher, Thomas; Schubert, Evelyn; Ruettger, Anke; Kaltenboeck, Bernhard; Ehricht, Ralf

    2018-03-16

    Serological analysis of Chlamydia (C.) spp. infections is still mainly based on micro-immunofluorescence and ELISA. To overcome the limitations of conventional serology, we have designed a novel microarray carrying 52 synthetic peptides representing B-cell epitopes from immunodominant proteins of all 11 chlamydial species. The new assay has been validated using monospecific mouse hyperimmune sera. Subsequently, serum samples from cattle, sheep and humans with a known history of chlamydial infection were examined. For instance, the specific humoral response of sheep to treatment with a C. abortus vaccine has been visualized against a background of C. pecorum carriership. In samples from humans, dual infection with C. trachomatis and C. pneumoniae could be demonstrated. The experiments revealed that the peptide microarray assay was capable of simultaneously identifying specific antibodies to each Chlamydia spp. The actual assay represents an open platform test that can be complemented through future advances in Chlamydia proteome research. The concept of the highly parallel multi-antigen microarray proven in this study has the potential to enhance our understanding of antibody responses by defining not only a single quantitative response, but also the pattern of this response. The added value of using peptide antigens will consist in unprecedented serodiagnostic specificity.

  20. Hawaiʻi Coral Disease database (HICORDIS: species-specific coral health data from across the Hawaiian archipelago

    Directory of Open Access Journals (Sweden)

    Jamie M. Caldwell

    2016-09-01

    Full Text Available The Hawaiʻi Coral Disease database (HICORDIS houses data on colony-level coral health condition observed across the Hawaiian archipelago, providing information to conduct future analyses on coral reef health in an era of changing environmental conditions. Colonies were identified to the lowest taxonomic classification possible (species or genera, measured and assessed for visual signs of health condition. Data were recorded for 286,071 coral colonies surveyed on 1819 transects at 660 sites between 2005 and 2015. The database contains observations for 60 species from 22 genera with 21 different health conditions. The goals of the HICORDIS database are to: i provide open access, quality controlled and validated coral health data assembled from disparate surveys conducted across Hawaiʻi; ii facilitate appropriate crediting of data; and iii encourage future analyses of coral reef health. In this article, we describe and provide data from the HICORDIS database. The data presented in this paper were used in the research article “Satellite SST-based Coral Disease Outbreak Predictions for the Hawaiian Archipelago” (Caldwell et al., 2016 [1]. Keywords: Marine biology, Coral, Reefs, Disease, Hawaii

  1. Development of a multiplex assay for genus- and species-specific detection of Phytophthora based on differences in mitochondrial gene order.

    Science.gov (United States)

    Bilodeau, Guillaume J; Martin, Frank N; Coffey, Michael D; Blomquist, Cheryl L

    2014-07-01

    A molecular diagnostic assay for Phytophthora spp. that is specific, sensitive, has both genus- and species-specific detection capabilities multiplexed, and can be used to systematically develop markers for detection of a wide range of species would facilitate research and regulatory efforts. To address this need, a marker system was developed based on the high copy sequences of the mitochondrial DNA utilizing gene orders that were highly conserved in the genus Phytophthora but different in the related genus Pythium and plants to reduce the importance of highly controlled annealing temperatures for specificity. An amplification primer pair designed from conserved regions of the atp9 and nad9 genes produced an amplicon of ≈340 bp specific for the Phytophthora spp. tested. The TaqMan probe for the genus-specific Phytophthora test was designed from a conserved portion of the atp9 gene whereas variable intergenic spacer sequences were used for designing the species-specific TaqMan probes. Specific probes were developed for 13 species and the P. citricola species complex. In silico analysis suggests that species-specific probes could be developed for at least 70 additional described and provisional species; the use of locked nucleic acids in TaqMan probes should expand this list. A second locus spanning three tRNAs (trnM-trnP-trnM) was also evaluated for genus-specific detection capabilities. At 206 bp, it was not as useful for systematic development of a broad range of species-specific probes as the larger 340-bp amplicon. All markers were validated against a test panel that included 87 Phytophthora spp., 14 provisional Phytophthora spp., 29 Pythium spp., 1 Phytopythium sp., and 39 plant species. Species-specific probes were validated further against a range of geographically diverse isolates to ensure uniformity of detection at an intraspecific level, as well as with other species having high levels of sequence similarity to ensure specificity. Both diagnostic

  2. Determination of the species specificity of the primers for the detection of chicken and turkey meat by realtime PCR method

    Directory of Open Access Journals (Sweden)

    Lenka Maršálková

    2014-07-01

    Full Text Available The aim of this work was to use TaqMan Real-Time PCR for quantitative authentication of chicken and turkey meat. To meet this purpose, a specific pair of primers and TaqMan probe was used. The test was aimed at identifying the reaction cycle of turkey and chicken meat using by two sets of primers. With first set of primer designed for chicken we obtained the following results: Cp = 16.18 for 100% chicken DNA Cp = 29, 18 100% turkey DNA It was also amplified DNA of pig that exceeded the detection threshold fluorescence intensities in the 31.07 cycle (Cp = 31.07. Using primers designed for turkey we obtained the following results Cp = 31.16 for 100% CHDNA, Cp =16.18 100% TDNA. It was also amplified the 100% DNA of rabbit in 31.63 cycle (Cp = 31.63 and deer in cycle 32 (Cp = 32. The DNA of all other animal species was amplificated after more than 35 cycles (Cp >35. It follows that the second detection primer pair is specific enough to unrelated species of animals by 30 cycles of the reaction. Species authentication based on DNA analysis from this perspective overcomes all the shortcomings of proteins. At present, DNA analysis use different types of PCR. Is the most progressive Real-time PCR, which is suitable for the specific use of detection (primers and TaqMan probe. The TaqMan Real-time PCR is within the sensitivity and specificity, clearly one of the best methods for identifying the species of chicken and turkey meat. The specificity of this method, however, depends primarily on the specificity of the primers and TaqMan probe. The 30 cycle reaction was chosen by us as the threshold for specificity using primers for authentication chicken and turkey meat.

  3. Laser Beam Focus Analyser

    DEFF Research Database (Denmark)

    Nielsen, Peter Carøe; Hansen, Hans Nørgaard; Olsen, Flemming Ove

    2007-01-01

    the obtainable features in direct laser machining as well as heat affected zones in welding processes. This paper describes the development of a measuring unit capable of analysing beam shape and diameter of lasers to be used in manufacturing processes. The analyser is based on the principle of a rotating......The quantitative and qualitative description of laser beam characteristics is important for process implementation and optimisation. In particular, a need for quantitative characterisation of beam diameter was identified when using fibre lasers for micro manufacturing. Here the beam diameter limits...... mechanical wire being swept through the laser beam at varying Z-heights. The reflected signal is analysed and the resulting beam profile determined. The development comprised the design of a flexible fixture capable of providing both rotation and Z-axis movement, control software including data capture...

  4. Species-specific considerations in using the fish embryo test as an alternative to identify endocrine disruption.

    Science.gov (United States)

    Schiller, Viktoria; Zhang, Xiaowei; Hecker, Markus; Schäfers, Christoph; Fischer, Rainer; Fenske, Martina

    2014-10-01

    A number of regulations have been implemented that aim to control the release of potentially adverse endocrine disrupters into the aquatic environment based on evidence from laboratory studies. Currently, such studies rely on testing approaches with adult fish because reliable alternatives have not been validated so far. Fish embryo tests have been proposed as such an alternative, and here we compared two species (medaka and zebrafish) to determine their suitability for the assessment of substances with estrogenic and anti-androgenic activity. Changes in gene expression (in here the phrase gene expression is used synonymously to gene transcription, although it is acknowledged that gene expression is additionally regulated, e.g., by translation and protein stability) patterns between the two species were compared in short term embryo exposure tests (medaka: 7-day post fertilization [dpf]; zebrafish: 48 and 96h post fertilization [hpf]) by using relative quantitative real-time RT-PCR. The tested genes were related to the hypothalamic-gonadal-axis and early steroidogenesis. Test chemicals included 17α-ethinylestradiol and flutamide as estrogenic and anti-androgenic reference compounds, respectively, as well as five additional substances with endocrine activities, namely bisphenol A, genistein, prochloraz, linuron and propanil. Estrogenic responses were comparable in 7-dpf medaka and 48/96-hpf zebrafish embryos and included transcriptional upregulation of aromatase b, vitellogenin 1 as well as steroidogenic genes, suggesting that both species reliably detected exposure to estrogenic compounds. However, anti-androgenic responses differed between the two species, with each species providing specific information concerning the mechanism of anti-androgenic disruption in fish embryos. Although small but significant changes in the expression of selected genes was observed in 48-hpf zebrafish embryos, exposure prolonged to 96hpf was necessary to obtain a response indicative

  5. Microscopy and image analysis based approaches for the species-specific identification of bovine and swine bone containing material

    Directory of Open Access Journals (Sweden)

    Matteo Ottoboni

    2014-05-01

    Full Text Available The aim of this study was to evaluate the potential of image analysis measurements in combination with the official analytical method for the detection of constituents of animal origin in feedstuffs, in distinguishing between bovine and swine (bone containing material. Authentic samples of controlled origin containing bovine or swine meat and bone meals were analysed by the microscopic method, in accordance with the official analytical method. Sediment fractions of each sample were observed with a compound microscope at X40. A total of 362 bone fragment lacunae images were recorded and processed through image analysis software, deriving 30 geometric variables for each lacuna. Results indicated that not only were most variables significantly (P<0.001 different between bovine and swine samples, but also that two thirds of the same variables were bigger in bovine than in swine. This information, however, does not seem to be so effective in practice since bovine and swine features and measurements overlapped. It can be concluded that the microscopic method even when combined with image analysis does not fit all the requirements for accurately identifying prohibited ingredients of animal origin. A combined approach with other methods is therefore recommended.

  6. Undressing of Waddlia chondrophila to enrich its outer membrane proteins to develop a new species-specific ELISA

    Directory of Open Access Journals (Sweden)

    J. Lienard

    2014-01-01

    Full Text Available Waddlia chondrophila, an obligate intracellular bacterium of the Chlamydiales order, is considered as an agent of bovine abortion and a likely cause of miscarriage in humans. Its role in respiratory diseases was questioned after the detection of its DNA in clinical samples taken from patients suffering from pneumonia or bronchiolitis. To better define the role of Waddlia in both miscarriage and pneumonia, a tool allowing large-scale serological investigations of Waddlia seropositivity is needed. Therefore, enriched outer membrane proteins of W. chondrophila were used as antigens to develop a specific ELISA. After thorough analytical optimization, the ELISA was validated by comparison with micro-immunofluorescence and it showed a sensitivity above 85% with 100% specificity. The ELISA was subsequently applied to human sera to specify the role of W. chondrophila in pneumonia. Overall, 3.6% of children showed antibody reactivity against W. chondrophila but no significant difference was observed between children with and without pneumonia. Proteomic analyses were then performed using mass spectrometry, highlighting members of the outer membrane protein family as the dominant proteins. The major Waddlia putative immunogenic proteins were identified by immunoblot using positive and negative human sera. The new ELISA represents an efficient tool with high throughput applications. Although no association with pneumonia and Waddlia seropositivity was observed, this ELISA could be used to specify the role of W. chondrophila in miscarriage and in other diseases.

  7. Individual and species-specific traits explain niche size and functional role in spiders as generalist predators.

    Science.gov (United States)

    Sanders, Dirk; Vogel, Esther; Knop, Eva

    2015-01-01

    The function of a predator within a community is greatly based on its trophic niche, that is the number and the strength of feeding links. In generalist predators, which feed on a wide range of prey, the size and position of the trophic niche is likely determined by traits such as hunting mode, the stratum they occur in, their body size and age. We used stable isotope analyses ((13)C and (15)N) to measure the trophic niche size of nine spider species within a forest hedge community and tested for species traits and individual traits that influence stable isotope enrichment, niche size and resource use. The spiders Enoplognatha, Philodromus, Floronia, and Heliophanus had large isotopic niches, which correspond to a more generalistic feeding behaviour. In contrast, Araneus, Metellina and Agelena, as top predators in the system, had rather narrow niches. We found a negative correlation between trophic position and niche size. Differences in trophic position in spiders were explained by body size, hunting modes and stratum, while niche size was influenced by hunting mode. In Philodromus, the size of the trophic niche increased significantly with age. Fitting spiders to functional groups according to their mean body size, hunting mode and their habitat domain resulted in largely separated niches, which indicates that these traits are meaningful for separating functional entities in spiders. Functional groups based on habitat domain (stratum) caught the essential functional differences between the species with species higher up in the vegetation feeding on flying insects and herb and ground species also preying on forest floor decomposers. Interestingly, we found a gradient from large species using a higher habitat domain and having a smaller niche to smaller species foraging closer to the ground and having a larger niche. This shows that even within generalist predators, such as spiders, there is a gradient of specialism that can be predicted by functional traits.

  8. Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts

    Directory of Open Access Journals (Sweden)

    Lewin Harris A

    2009-04-01

    Full Text Available Abstract Background Bidirectional promoters are shared regulatory regions that influence the expression of two oppositely oriented genes. This type of regulatory architecture is found more frequently than expected by chance in the human genome, yet many specifics underlying the regulatory design are unknown. Given that the function of most orthologous genes is similar across species, we hypothesized that the architecture and regulation of bidirectional promoters might also be similar across species, representing a core regulatory structure and enabling annotation of these regions in additional mammalian genomes. Results By mapping the intergenic distances of genes in human, chimpanzee, bovine, murine, and rat, we show an enrichment for pairs of genes equal to or less than 1,000 bp between their adjacent 5' ends ("head-to-head" compared to pairs of genes that fall in the same orientation ("head-to-tail" or whose 3' ends are side-by-side ("tail-to-tail". A representative set of 1,369 human bidirectional promoters was mapped to orthologous sequences in other mammals. We confirmed predictions for 5' UTRs in nine of ten manual picks in bovine based on comparison to the orthologous human promoter set and in six of seven predictions in human based on comparison to the bovine dataset. The two predictions that did not have orthology as bidirectional promoters in the other species resulted from unique events that initiated transcription in the opposite direction in only those species. We found evidence supporting the independent emergence of bidirectional promoters from the family of five RecQ helicase genes, which gained their bidirectional promoters and partner genes independently rather than through a duplication process. Furthermore, by expanding our comparisons from pairwise to multispecies analyses we developed a map representing a core set of bidirectional promoters in mammals. Conclusion We show that the orthologous positions of bidirectional

  9. Standardization of a two-step real-time polymerase chain reaction based method for species-specific detection of medically important Aspergillus species.

    Science.gov (United States)

    Das, P; Pandey, P; Harishankar, A; Chandy, M; Bhattacharya, S; Chakrabarti, A

    2017-01-01

    Standardization of Aspergillus polymerase chain reaction (PCR) poses two technical challenges (a) standardization of DNA extraction, (b) optimization of PCR against various medically important Aspergillus species. Many cases of aspergillosis go undiagnosed because of relative insensitivity of conventional diagnostic methods such as microscopy, culture or antigen detection. The present study is an attempt to standardize real-time PCR assay for rapid sensitive and specific detection of Aspergillus DNA in EDTA whole blood. Three nucleic acid extraction protocols were compared and a two-step real-time PCR assay was developed and validated following the recommendations of the European Aspergillus PCR Initiative in our setup. In the first PCR step (pan-Aspergillus PCR), the target was 28S rDNA gene, whereas in the second step, species specific PCR the targets were beta-tubulin (for Aspergillus fumigatus, Aspergillus flavus, Aspergillus terreus), gene and calmodulin gene (for Aspergillus niger). Species specific identification of four medically important Aspergillus species, namely, A. fumigatus, A. flavus, A. niger and A. terreus were achieved by this PCR. Specificity of the PCR was tested against 34 different DNA source including bacteria, virus, yeast, other Aspergillus sp., other fungal species and for human DNA and had no false-positive reactions. The analytical sensitivity of the PCR was found to be 102 CFU/ml. The present protocol of two-step real-time PCR assays for genus- and species-specific identification for commonly isolated species in whole blood for diagnosis of invasive Aspergillus infections offers a rapid, sensitive and specific assay option and requires clinical validation at multiple centers.

  10. COMPARISON OF A GENUS-SPECIFIC CONVENTIONAL PCR AND A SPECIES-SPECIFIC NESTED-PCR FOR MALARIA DIAGNOSIS USING FTA COLLECTED SAMPLES FROM KINGDOM OF SAUDI ARABIA.

    Science.gov (United States)

    Al-Harthi, Saeed A

    2015-12-01

    Molecular tools are increasingly accepted as the most sensitive and reliable techniques for malaria diagnosis and epidemiological surveys. Also, collection of finger prick blood spots onto filter papers is the most simple and affordable method for samples preservation and posterior molecular analysis, especially in rural endemic regions where malaria remains a major health problem. Two malaria molecular diagnostic tests, a Plasmodium genus-specific conventional PCR and a Plasmodium species-specific Nested PCR, were evaluated using DNA templates prepared from Whatman-FTA cards' dry blood spots using both, Methanol-fixation/Heat-extraction and FTA commercial purification kit. A total of 121 blood samples were collected from six Saudi south-western endemic districts both, as thick and thin films for routine microscopic screening and onto FTA cards for molecular studies. Out of the 121 samples, 75 were P. falciparum positive by at least one technique. No other species of Plasmodium were detected. P. falciparum parasites were identified in 69/75 (92%) samples by microscopic screening in health care centers. P. genus-specific PCR was able to amplify P. falciparum DNA in 41/75 (55%) and 59/75 (79%) samples using Methanol-fixation/Heat-extraction and FTA purification kit, respectively. P. species-specific Nested PCR revealed 68/75 (91%) and 75/75 (100%) positive samples using DNA templates were isolated by Methanol-fixation/Heat- extraction and FTA purification methods, respectively. The species-specific Nested PCR applied to Whatman-FTA preserved and processed blood samples represents the best alternative to classical microscopy for malaria diagnosis, particularly in epidemiological screening.

  11. Design of a species-specific PCR method for the detection of the heat-resistant fungi Talaromyces macrosporus and Talaromyces trachyspermus.

    Science.gov (United States)

    Yamashita, S; Nakagawa, H; Sakaguchi, T; Arima, T-H; Kikoku, Y

    2018-01-01

    Heat-resistant fungi occur sporadically and are a continuing problem for the food and beverage industry. The genus Talaromyces, as a typical fungus, is capable of producing the heat-resistant ascospores responsible for the spoilage of processed food products. Isocitrate lyase, a signature enzyme of the glyoxylate cycle, is required for the metabolism of non-fermentable carbon compounds, like acetate and ethanol. Here, species-specific primer sets for detection and identification of DNA derived from Talaromyces macrosporus and Talaromyces trachyspermus were designed based on the nucleotide sequences of their isocitrate lyase genes. Polymerase chain reaction (PCR) using a species-specific primer set amplified products specific to T. macrosporus and T. trachyspermus. Other fungal species, such as Byssochlamys fulva and Hamigera striata, which cause food spoilage, were not detected using the Talaromyces-specific primer sets. The detection limit for each species-specific primer set was determined as being 50 pg of template DNA, without using a nested PCR method. The specificity of each species-specific primer set was maintained in the presence of 1,000-fold amounts of genomic DNA from other fungi. The method also detected fungal DNA extracted from blueberry inoculated with T. macrosporus. This PCR method provides a quick, simple, powerful and reliable way to detect T. macrosporus and T. trachyspermus. Polymerase chain reaction (PCR)-based detection is rapid, convenient and sensitive compared with traditional methods of detecting heat-resistant fungi. In this study, a PCR-based method was developed for the detection and identification of amplification products from Talaromyces macrosporus and Talaromyces trachyspermus using primer sets that target the isocitrate lyase gene. This method could be used for the on-site detection of T. macrosporus and T. trachyspermus in the near future, and will be helpful in the safety control of raw materials and in food and beverage

  12. [The comparative assessment of the practical value of the currently employed methods for the recognition and species specificity of the blood].

    Science.gov (United States)

    Grezina, N Iu; Suleĭmenova, G M

    2011-01-01

    The objective of the present study was to evaluate sensitivity and specificity of the HemDirect method on test-plates (Seratec) for detecting human hemoglobin (HHb). These characteristics were compared with those of other widely used methods designed for the detection of blood traces, viz. thin layer chromatography, hemotest, spectrofluorimetry, and identification of blood species specificity (by countercurrent immunoelectrophoresis in agar and on the acetate-cellulose film). It was shown that the HemDirect test is highly specific and far more sensitive than other techniques used for the same purpose in the practical work. It can be recommended as the method of choice for the detection of blood microtraces.

  13. Species-specific sensitivity to selenium-induced impairment of cortisol secretion in adrenocortical cells of rainbow trout (Oncorhynchus mykiss) and brook trout (Salvelinus fontinalis)

    International Nuclear Information System (INIS)

    Miller, L.L.; Hontela, A.

    2011-01-01

    Species differences in physiological and biochemical attributes exist even among closely related species and may underlie species-specific sensitivity to toxicants. Rainbow trout (RT) are more sensitive than brook trout (BT) to the teratogenic effects of selenium (Se), but it is not known whether all tissues exhibit this pattern of vulnerability. In this study, primary cultures of RT and BT adrenocortical cells were exposed to selenite (Na 2 SO 3 ) and selenomethionine (Se-Met) to compare cell viability and ACTH-stimulated cortisol secretion in the two fish species. Cortisol, the primary stress hormone in fish, facilitates maintenance of homeostasis when fish are exposed to stressors, including toxicants. Cell viability was not affected by Se, but selenite impaired cortisol secretion, while Se-Met did not (RT and BT EC 50 > 2000 mg/L). RT cells were more sensitive (EC 50 = 8.7 mg/L) to selenite than BT cells (EC 50 = 90.4 mg/L). To identify the targets where Se disrupts cortisol synthesis, selenite-impaired RT and BT cells were stimulated with ACTH, dbcAMP, OH-cholesterol, and pregnenolone. Selenite acted at different steps in the cortisol biosynthesis pathway in RT and BT cells, confirming a species-specific toxicity mechanism. To test the hypothesis that oxidative stress mediates Se-induced toxicity, selenite-impaired RT cells were exposed to NAC, BSO and antioxidants (DETCA, ATA, Vit A, and Vit E). Inhibition of SOD by DETCA enhanced selenite-induced cortisol impairment, indicating that oxidative stress plays a role in Se toxicity; however, modifying GSH content of the cells did not have an effect. The results of this study, with two closely related salmonids, provided additional evidence for species-specific differences in sensitivity to Se which should be considered when setting thresholds and water quality guidelines. - Research Highlights: → We investigated species-specific sensitivity to Se in trout adrenocortical cells. → Selenite, not Se-Met, disrupts

  14. Thermophilic Alkaline Fermentation Followed by Mesophilic Anaerobic Digestion for Efficient Hydrogen and Methane Production from Waste-Activated Sludge: Dynamics of Bacterial Pathogens as Revealed by the Combination of Metagenomic and Quantitative PCR Analyses.

    Science.gov (United States)

    Wan, Jingjing; Jing, Yuhang; Rao, Yue; Zhang, Shicheng; Luo, Gang

    2018-03-15

    Thermophilic alkaline fermentation followed by mesophilic anaerobic digestion (TM) for hydrogen and methane production from waste-activated sludge (WAS) was investigated. The TM process was also compared to a process with mesophilic alkaline fermentation followed by a mesophilic anaerobic digestion (MM) and one-stage mesophilic anaerobic digestion (M) process. The results showed that both hydrogen yield (74.5 ml H 2 /g volatile solids [VS]) and methane yield (150.7 ml CH 4 /g VS) in the TM process were higher than those (6.7 ml H 2 /g VS and 127.8 ml CH 4 /g VS, respectively) in the MM process. The lowest methane yield (101.2 ml CH 4 /g VS) was obtained with the M process. Taxonomic results obtained from metagenomic analysis showed that different microbial community compositions were established in the hydrogen reactors of the TM and MM processes, which also significantly changed the microbial community compositions in the following methane reactors compared to that with the M process. The dynamics of bacterial pathogens were also evaluated. For the TM process, the reduced diversity and total abundance of bacterial pathogens in WAS were observed in the hydrogen reactor and were further reduced in the methane reactor, as revealed by metagenomic analysis. The results also showed not all bacterial pathogens were reduced in the reactors. For example, Collinsella aerofaciens was enriched in the hydrogen reactor, which was also confirmed by quantitative PCR (qPCR) analysis. The study further showed that qPCR was more sensitive for detecting bacterial pathogens than metagenomic analysis. Although there were some differences in the relative abundances of bacterial pathogens calculated by metagenomic and qPCR approaches, both approaches demonstrated that the TM process was more efficient for the removal of bacterial pathogens than the MM and M processes. IMPORTANCE This study developed an efficient process for bioenergy (H 2 and CH 4 ) production from WAS and elucidates the

  15. Species-specific diagnostic assays for Bonamia ostreae and B. exitiosa in European flat oyster Ostrea edulis: conventional, real-time and multiplex PCR.

    Science.gov (United States)

    Ramilo, Andrea; Navas, J Ignacio; Villalba, Antonio; Abollo, Elvira

    2013-05-27

    Bonamia ostreae and B. exitiosa have caused mass mortalities of various oyster species around the world and co-occur in some European areas. The World Organisation for Animal Health (OIE) has included infections with both species in the list of notifiable diseases. However, official methods for species-specific diagnosis of either parasite have certain limitations. In this study, new species-specific conventional PCR (cPCR) and real-time PCR techniques were developed to diagnose each parasite species. Moreover, a multiplex PCR method was designed to detect both parasites in a single assay. The analytical sensitivity and specificity of each new method were evaluated. These new procedures were compared with 2 OIE-recommended methods, viz. standard histology and PCR-RFLP. The new procedures showed higher sensitivity than the OIE recommended ones for the diagnosis of both species. The sensitivity of tests with the new primers was higher using oyster gills and gonad tissue, rather than gills alone. The lack of a 'gold standard' prevented accurate estimation of sensitivity and specificity of the new methods. The implementation of statistical tools (maximum likelihood method) for the comparison of the diagnostic tests showed the possibility of false positives with the new procedures, although the absence of a gold standard precluded certainty. Nevertheless, all procedures showed negative results when used for the analysis of oysters from a Bonamia-free area.

  16. Photoadaptations of photosynthesis and carbon metabolism by phytoplankton from McMurdo Sound, Antarctica. I. Species-specific and community responses to reduced irradiances

    International Nuclear Information System (INIS)

    Rivkin, R.B.; Voytek, M.A.

    1987-01-01

    Irradiance-dependent rates of photosynthesis and photosynthate labeling patterns were measured for phytoplankton in McMurdo Sound, Antarctica. Species-specific and traditional whole-water techniques were used to compare the physiological responses of algae collected in a high light environment at the ice edge and from a low light environment under the annual sea ice. There were differences among species within the same sample, for the same species isolated from high and low light environments, and when species-specific responses were compared with that of the natural assemblage. For algae collected beneath the sea ice, photosynthesis generally saturated at a lower irradiance, and the light-limited region of the P vs. I relationship had a steeper slope than for the same species collected at the ice edge. Low-light-adapted algae incorporated significantly less 14 C into proteins and more into low molecular weight compounds and lipids than the same species isolated from a high light environment. Under conditions where reduced rates of protein synthesis were coupled with high rates of carbon uptake, the measurement of photosynthesis may not accurately reflect the physiological condition of the phytoplankton

  17. Species specificity of social reinstatement in Japanese quail Coturnix japonica genetically selected for high or low levels of social reinstatement behaviour.

    Science.gov (United States)

    Mills, A D; Jones, R B; Faure, J M

    1995-05-01

    Divergent lines of Japanese quail Coturnix japonica showing high (HSR) or low (LSR) levels of social reinstatement (SR) behaviour (as measured in a treadmill apparatus) have been developed. However, it was not known if selection had influenced social reinstatement tendencies in a general or a species-specific fashion. Therefore, the present study compared the SR behaviour of quail chicks of the HSR and LSR lines and of a Control line when the goal box of the treadmill was empty or when it contained small, same-species groups of either Japanese quail, domestic fowl or Guinea fowl chicks. The results clearly demonstrated that the SR behaviour of Japanese quail chicks is species-specific and that this specificity has not been influenced during genetic selection, over sixteen generations, of the HSR and LSR lines. The HSR chicks showed more locomotor activity in the treadmill than did those of the other lines regardless of the nature of the goal-box stimulus. The results are discussed in terms of general activity, underlying fearfulness and social motivation.

  18. U2504 Determines the Species Specificity of the A-site Cleft Antibiotics: The sStructures of Tiamulin, Homoharringtonine and Bruceantin Bound to the Ribosome

    Energy Technology Data Exchange (ETDEWEB)

    Gurel, G.; Blaha, G; Moore, P; Steitz,

    2009-01-01

    Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 {angstrom}. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

  19. U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.

    Science.gov (United States)

    Gürel, Güliz; Blaha, Gregor; Moore, Peter B; Steitz, Thomas A

    2009-05-29

    Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 A. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

  20. U2504 Determines the Species Specificity of the A-site Cleft Antibiotics. The Structures of Tiamulin, Homoharringtonine and Bruceantin Bound to the Ribosome

    Science.gov (United States)

    Gürel, Güliz; Blaha, Gregor; Moore, Peter B.; Steitz, Thomas A.

    2009-01-01

    Structures have been obtained for the complexes tiamulin, homoharringtonine and bruceatin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.8 to 3.2 Å. They show that these inhibitors all block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl transferase center, which is universally conserved. In addition these structures support the hypothesis that the species-specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (E. coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms. PMID:19362093

  1. U2504 Determines the Species Specificity of the A-Site Cleft Antibiotics: The Structures of Tiamulin, Homoharringtonine, and Bruceantin Bound to the Ribosome

    Energy Technology Data Exchange (ETDEWEB)

    Gürel, Güliz; Blaha, Gregor; Moore, Peter B.; Steitz, Thomas A.; Yale

    2009-06-30

    Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 {angstrom}. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the Asite cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

  2. Application of a Reverse Line Blot hybridisation assay for the species-specific identification of cyathostomins (Nematoda, Strongylida) from benzimidazole-treated horses in the Slovak Republic.

    Science.gov (United States)

    Cernanská, Dana; Paoletti, Barbara; Králová-Hromadová, Ivica; Iorio, Raffaella; Cudeková, Patrícia; Milillo, Piermarino; Traversa, Donato

    2009-03-09

    Five horse farms located in eastern Slovakia were investigated for the presence of benzimidazole-resistant strongyles by faecal egg count reduction test and egg hatch assay. Coprocultures were prepared for each farm from faecal samples taken pre- and post-treatment and harvested larvae were molecularly examined with a Reverse Line Blot assay. Faecal egg count reduction values ranged from 0 to 52.5% and all farms were positive for benzimidazole-resistant cyathostomins. Seven benzimidazole-resistant cyathostomin species were molecularly identified on farms before and also after treatment. These data demonstrate that resistance to benzimidazoles is well established in cyathostomin populations from horse farms in the Slovak Republic and that the molecular assay was able to determine the species-specific distribution of resistant cyathostomins under field conditions.

  3. Live Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis activate the inflammatory response trhough Toll-like receptors 2, 4, and 9 in species-specific patterns

    DEFF Research Database (Denmark)

    Mogensen, T.H.; Paludan, Søren Riis; Kilian, Mogens

    2006-01-01

    activation by live bacteria. Here, we demonstrate that live Streptococcus pneumoniae, Haemophilus influenzae type b, and Neisseria meningitidis, the three principal causes of bacterial meningitis, use distinct sets of TLRs to trigger the inflammatory response. Using human embryonic kidney 293 cell lines......, each overexpressing one type of TLR, we found that S. pneumoniae triggered activation of the transcription factor nuclear factor-kappaB and expression of interleukin-8, only in cells expressing TLR2 or -9. The same response was evoked by H. influenzae in cells expressing TLR2 or -4 and by N...... and confirmed the essential role of these TLRs and also identified differential functions of TLRs in activation of the inflammatory response. Collectively, we here demonstrate that S. pneumoniae, H. influenzae, and N. meningitidis each activate several TLRs in species-specific patterns and show that infection...

  4. Identification of S-glutathionylation sites in species-specific proteins by incorporating five sequence-derived features into the general pseudo-amino acid composition.

    Science.gov (United States)

    Zhao, Xiaowei; Ning, Qiao; Ai, Meiyue; Chai, Haiting; Yang, Guifu

    2016-06-07

    As a selective and reversible protein post-translational modification, S-glutathionylation generates mixed disulfides between glutathione (GSH) and cysteine residues, and plays an important role in regulating protein activity, stability, and redox regulation. To fully understand S-glutathionylation mechanisms, identification of substrates and specific S-Glutathionylated sites is crucial. Experimental identification of S-glutathionylated sites is labor-intensive and time consuming, so establishing an effective computational method is much desirable due to their convenient and fast speed. Therefore, in this study, a new bioinformatics tool named SSGlu (Species-Specific identification of Protein S-glutathionylation Sites) was developed to identify species-specific protein S-glutathionylated sites, utilizing support vector machines that combine multiple sequence-derived features with a two-step feature selection. By 5-fold cross validation, the performance of SSGlu was measured with an AUC of 0.8105 and 0.8041 for Homo sapiens and Mus musculus, respectively. Additionally, SSGlu was compared with the existing methods, and the higher MCC and AUC of SSGlu demonstrated that SSGlu was very promising to predict S-glutathionylated sites. Furthermore, a site-specific analysis showed that S-glutathionylation intimately correlated with the features derived from its surrounding sites. The conclusions derived from this study might help to understand more of the S-glutathionylation mechanism and guide the related experimental validation. For public access, SSGlu is freely accessible at http://59.73.198.144:8080/SSGlu/. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Immunophenotypical characterization of canine mesenchymal stem cells from perivisceral and subcutaneous adipose tissue by a species-specific panel of antibodies.

    Science.gov (United States)

    Ivanovska, Ana; Grolli, Stefano; Borghetti, Paolo; Ravanetti, Francesca; Conti, Virna; De Angelis, Elena; Macchi, Francesca; Ramoni, Roberto; Martelli, Paolo; Gazza, Ferdinando; Cacchioli, Antonio

    2017-10-01

    Immunophenotypical characterization of mesenchymal stem cells is fundamental for the design and execution of sound experimental and clinical studies. The scarce availability of species-specific antibodies for canine antigens has hampered the immunophenotypical characterization of canine mesenchymal stem cells (MSC). The aim of this study was to select a panel of species-specific direct antibodies readily useful for canine mesenchymal stem cells characterization. They were isolated from perivisceral and subcutaneous adipose tissue samples collected during regular surgeries from 8 dogs. Single color flow cytometric analysis of mesenchymal stem cells (P3) deriving from subcutaneous and perivisceral adipose tissue with a panel of 7 direct anti-canine antibodies revealed two largely homogenous cell populations with a similar pattern: CD29 + , CD44 + , CD73 + , CD90 + , CD34 - , CD45 - and MHC-II - with no statistically significant differences among them. Antibody reactivity was demonstrated on canine peripheral blood mononuclear cells. The similarities are reinforced by their in vitro cell morphology, trilineage differentiation ability and RT-PCR analysis (CD90 + , CD73 + , CD105 + , CD44 + , CD13 + , CD29 + , Oct-4 + gene and CD31 - and CD45 - expression). Our results report for the first time a comparison between the immunophenotypic profile of canine MSC deriving from perivisceral and subcutaneous adipose tissue. The substantial equivalence between the two populations has practical implication on clinical applications, giving the opportunity to choose the source depending on the patient needs. The results contribute to routine characterization of MSC populations grown in vitro, a mandatory process for the definition of solid and reproducible laboratory and therapeutic procedures. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Predicting incursion of plant invaders into Kruger National Park, South Africa: the interplay of general drivers and species-specific factors.

    Directory of Open Access Journals (Sweden)

    Vojtěch Jarošík

    Full Text Available BACKGROUND: Overcoming boundaries is crucial for incursion of alien plant species and their successful naturalization and invasion within protected areas. Previous work showed that in Kruger National Park, South Africa, this process can be quantified and that factors determining the incursion of invasive species can be identified and predicted confidently. Here we explore the similarity between determinants of incursions identified by the general model based on a multispecies assemblage, and those identified by species-specific models. We analyzed the presence and absence of six invasive plant species in 1.0×1.5 km segments along the border of the park as a function of environmental characteristics from outside and inside the KNP boundary, using two data-mining techniques: classification trees and random forests. PRINCIPAL FINDINGS: The occurrence of Ageratum houstonianum, Chromolaena odorata, Xanthium strumarium, Argemone ochroleuca, Opuntia stricta and Lantana camara can be reliably predicted based on landscape characteristics identified by the general multispecies model, namely water runoff from surrounding watersheds and road density in a 10 km radius. The presence of main rivers and species-specific combinations of vegetation types are reliable predictors from inside the park. CONCLUSIONS: The predictors from the outside and inside of the park are complementary, and are approximately equally reliable for explaining the presence/absence of current invaders; those from the inside are, however, more reliable for predicting future invasions. Landscape characteristics determined as crucial predictors from outside the KNP serve as guidelines for management to enact proactive interventions to manipulate landscape features near the KNP to prevent further incursions. Predictors from the inside the KNP can be used reliably to identify high-risk areas to improve the cost-effectiveness of management, to locate invasive plants and target them for

  7. Predicting Incursion of Plant Invaders into Kruger National Park, South Africa: The Interplay of General Drivers and Species-Specific Factors

    Science.gov (United States)

    Jarošík, Vojtěch; Pyšek, Petr; Foxcroft, Llewellyn C.; Richardson, David M.; Rouget, Mathieu; MacFadyen, Sandra

    2011-01-01

    Background Overcoming boundaries is crucial for incursion of alien plant species and their successful naturalization and invasion within protected areas. Previous work showed that in Kruger National Park, South Africa, this process can be quantified and that factors determining the incursion of invasive species can be identified and predicted confidently. Here we explore the similarity between determinants of incursions identified by the general model based on a multispecies assemblage, and those identified by species-specific models. We analyzed the presence and absence of six invasive plant species in 1.0×1.5 km segments along the border of the park as a function of environmental characteristics from outside and inside the KNP boundary, using two data-mining techniques: classification trees and random forests. Principal Findings The occurrence of Ageratum houstonianum, Chromolaena odorata, Xanthium strumarium, Argemone ochroleuca, Opuntia stricta and Lantana camara can be reliably predicted based on landscape characteristics identified by the general multispecies model, namely water runoff from surrounding watersheds and road density in a 10 km radius. The presence of main rivers and species-specific combinations of vegetation types are reliable predictors from inside the park. Conclusions The predictors from the outside and inside of the park are complementary, and are approximately equally reliable for explaining the presence/absence of current invaders; those from the inside are, however, more reliable for predicting future invasions. Landscape characteristics determined as crucial predictors from outside the KNP serve as guidelines for management to enact proactive interventions to manipulate landscape features near the KNP to prevent further incursions. Predictors from the inside the KNP can be used reliably to identify high-risk areas to improve the cost-effectiveness of management, to locate invasive plants and target them for eradication. PMID:22194893

  8. PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor

    Directory of Open Access Journals (Sweden)

    Leyla Esfandiari

    2016-07-01

    Full Text Available A PCR-free, optics-free device is used for the detection of Escherichia coli (E. coli 16S rRNA at 10 fM, which corresponds to ~100–1000 colony forming units/mL (CFU/mL depending on cellular rRNA levels. The development of a rapid, sensitive, and cost-effective nucleic acid detection platform is sought for the detection of pathogenic microbes in food, water and body fluids. Since 16S rRNA sequences are species specific and are present at high copy number in viable cells, these nucleic acids offer an attractive target for microbial pathogen detection schemes. Here, target 16S rRNA of E. coli at 10 fM concentration was detected against a total RNA background using a conceptually simple approach based on electromechanical signal transduction, whereby a step change reduction in ionic current through a pore indicates blockage by an electrophoretically mobilized bead-peptide nucleic acid probe conjugate hybridized to target nucleic acid. We investigated the concentration detection limit for bacterial species-specific 16S rRNA at 1 pM to 1 fM and found a limit of detection of 10 fM for our device, which is consistent with our previous finding with single-stranded DNA of similar length. In addition, no false positive responses were obtained with control RNA and no false negatives with target 16S rRNA present down to the limit of detection (LOD of 10 fM. Thus, this detection scheme shows promise for integration into portable, low-cost systems for rapid detection of pathogenic microbes in food, water and body fluids.

  9. Species-specific effects of live roots and shoot litter on soil decomposer abundances do not forecast plant litter-nitrogen uptake.

    Science.gov (United States)

    Saj, Stéphane; Mikola, Juha; Ekelund, Flemming

    2009-08-01

    Plant species produce litter of varying quality and differ in the quality and quantity of compounds they release from live roots, which both can induce different decomposer growth in the soil. To test whether differences in decomposer growth can forecast the amount of N species acquire from plant litter, as suggested by theory, we grew individuals of three grassland plants-Holcus lanatus, Plantago lanceolata and Lotus corniculatus-in soils into which (15)N-labelled litter of either Holcus, Plantago or Lotus was added. We measured the effects of live roots and litter of each species on soil microbes and their protozoan and nematode feeders, and to link decomposer growth and plant nutrient uptake, we measured the amount of N taken up by plants from the added litter. We hypothesised that those species that induce the highest growth of microbes, and especially that of microbial feeders, will also take up the highest amount of N from the litter. We found, however, that although numbers of bacterial-feeding Protozoa and nematodes were on average lower after addition of Holcus than Plantago or Lotus litter, N uptake was higher from Holcus litter. Further, although the effects on Protozoa and bacterial- and fungal-feeding nematodes did not differ between the live plants, litter-N uptake differed, with Holcus being the most efficient compared to Plantago and Lotus. Hence, although microbes and their feeders unquestionably control N mineralization in the soil, and their growth differs among plant species, these differences cannot predict differences in litter-N uptake among plant species. A likely reason is that for nutrient uptake, other species-specific plant traits, such as litter chemistry, root proliferation ability and competitiveness for soil N, override in significance the species-specific ability of plants to induce decomposer growth.

  10. Au-based/electrochemically etched cavity-microelectrodes as optimal tool for quantitative analyses on finely dispersed electrode materials: Pt/C, IrO2-SnO2 and Ag catalysts

    International Nuclear Information System (INIS)

    Minguzzi, Alessandro; Locatelli, Cristina; Lugaresi, Ottavio; Vertova, Alberto; Rondinini, Sandra

    2013-01-01

    In this work, we report the preparation and properties of Au-based cavity-microelectrodes. The use of gold as cavity current collector allows obtaining a regular cylindrical recess, whose volume is easily determined with good accuracy and precision. This in turn leads to an improved and much more reliable use of the cavity microelectrode (C-ME) as a tool for the quantitative characterization of finely dispersed materials and for their quantitative rapid screening. The features of Au/C-MEs are well demonstrated by the good linear correlation between the cavity volume (determined by electrochemical methods) and the quantity of charge related to the amount of electroactive powder inserted into the cavity. To prove this point, we adopted two different test systems: Pt/C and an IrO 2 -based material. Finally, we proved the adequacy of Au/C-MEs in the case of Ag particles as electrocatalysts for the hydrodehalogenation of trichloromethane. In this last part, C-ME interestingly appears as a flexible and versatile tool that presents peculiar features: the voltammetric signal can be controlled by either the electron transfer or by mass transport and can be associated to the outer surface or to the whole amount of material inserted into the cavity. This means that C-MEs can be used either as a microdisk of a desired material (that is very useful, especially in scanning electrochemical microscopy) or for precise quantitative studies of the material inserted inside it

  11. Species-specific and seasonal differences in chlorophyll fluorescence and photosynthetic light response among three evergreen species in a Madrean sky island mixed conifer forest

    Science.gov (United States)

    Potts, D. L.; Minor, R. L.; Braun, Z.; Barron-Gafford, G. A.

    2012-12-01

    Unlike the snowmelt-dominated hydroclimate of more northern mountainous regions, the hydroclimate of the Madrean sky islands is characterized by snowmelt and convective storms associated with the North American Monsoon. These mid-summer storms trigger biological activity and are important drivers of primary productivity. For example, at the highest elevations where mixed conifer forests occur, ecosystem carbon balance is influenced by monsoon rains. Whereas these storms' significance is increasingly recognized at the ecosystem scale, species-specific physiological responses to the monsoon are poorly known. Prior to and following monsoon onset, we measured pre-dawn and light-adapted chlorophyll fluorescence as well as photosynthetic light response in southwestern white pine (Pinus strobiformis), ponderosa pine (Pinus ponderosa), and Douglas fir (Pseudotsuga menziesii) in a Madrean sky island mixed conifer forest near Tucson, Arizona. Photochemical quenching (qp), an indicator of the proportion of open PSII reaction centers, was greatest in P. strobiformis and least in P. menziesii and increased in response to monsoon rains (repeated-measures ANOVA; species, F2,14 = 6.17, P = 0.012; time, F2,14= 8.17, P = 0.013). In contrast, non-photochemical quenching (qN), an indicator of heat dissipation ability, was greatest in P. ponderosa and least in P. menziesii, but was not influenced by monsoon onset (repeated-measures ANOVA; species, F2,12 = 4.18, P = 0.042). Estimated from leaf area-adjusted photosynthetic light response curves, maximum photosynthetic rate (Amax) was greatest in P. ponderosa and least in P. menziesii (repeated-measures ANOVA; species, F2,8= 40.8, P = 0.001). Surprisingly, while the monsoon positively influenced Amax among P. ponderosa and P. strobiformis, Amax of P. menziesii declined with monsoon onset (repeated-measures ANOVA; species x time, F2,8 = 13.8, P = 0.002). Calculated as the initial slope of the photosynthetic light response curve, light

  12. Species-specific physiological response by the cold-water corals Lophelia pertusa and Madrepora oculata to variations within their natural temperature range

    Science.gov (United States)

    Naumann, Malik S.; Orejas, Covadonga; Ferrier-Pagès, Christine

    2014-01-01

    The scleractinian cold-water corals (CWC) Lophelia pertusa and Madrepora oculata represent two major deep-sea reef-forming species that act as key ecosystem engineers over a wide temperature range, extending from the northern Atlantic (ca. 5-9 °C) to the Mediterranean Sea (ca. 11-13 °C). Recent research suggests that environmental parameters, such as food supply, settling substrate availability or aragonite saturation state may represent important precursors controlling habitat suitability for CWC. However, the effect of one principal environmental factor, temperature, on CWC key physiological processes is still unknown. In order to evaluate this effect on calcification, respiration, and dissolved organic carbon (DOC) net flux, colonies of Mediterranean L. pertusa and M. oculata were acclimated in aquaria to three temperatures (12, 9 and 6 °C), by consecutive decrements of 1 month duration. L. pertusa and M. oculata maintained at Mediterranean control conditions (i.e. 12 °C) displayed constant rates, on average respiring 4.8 and 4.0 μmol O2 cm-2 coral surface area d-1, calcifying 22.3 and 12.3 μmol CaCO3 g-1 skeletal dry weight d-1 and net releasing 2.6 and 3.1 μmol DOC cm-2 coral surface area d-1, respectively. Respiration of L. pertusa was not affected by lowered temperatures, while M. oculata respiration declined significantly (by 48%) when temperature decreased to 9 °C and 6 °C relative to controls. L. pertusa calcification at 9 °C was similar to controls, but decreased significantly (by 58%) at 6 °C. For M. oculata, calcification declined by 41% at 9 °C and by 69% at 6 °C. DOC net flux was similar throughout the experiment for both CWC. These findings reveal species-specific physiological responses by CWC within their natural temperature range. L. pertusa shows thermal acclimation in respiration and calcification, while these mechanisms appear largely absent in M. oculata. Conclusively, species-specific thermal acclimation may significantly affect

  13. Study of Sylvilagus rabbit TRIM5α species-specific domain: how ancient endoviruses could have shaped the antiviral repertoire in Lagomorpha

    Directory of Open Access Journals (Sweden)

    Areal Helena

    2011-10-01

    Full Text Available Abstract Background Since the first report of the antiretroviral restriction factor TRIM5α in primates, several orthologs in other mammals have been described. Recent studies suggest that leporid retroviruses like RELIK, the first reported endogenous lentivirus ever, may have imposed positive selection in TRIM5α orthologs of the European rabbit and European brown hare. Considering that RELIK must already have been present in a common ancestor of the leporid genera Lepus, Sylvilagus and Oryctolagus, we extended the study of evolutionary patterns of TRIM5α to other members of the Leporidae family, particularly to the genus Sylvilagus. Therefore, we obtained the TRIM5α nucleotide sequences of additional subspecies and species of the three leporid genera. We also compared lagomorph TRIM5α deduced protein sequences and established TRIM5α gene and TRIM5α protein phylogenies. Results The deduced protein sequence of Iberian hare TRIM5α was 89% identical to European rabbit TRIM5α, although high divergence was observed at the PRYSPRY v1 region between rabbit and the identified alleles from this hare species (allele 1: 50% divergence; allele 2: 53% divergence. A high identity was expected between the Sylvilagus and Oryctolagus TRIM5α proteins and, in fact, the Sylvilagus TRIM5α was 91% identical to the Oryctolagus protein. Nevertheless, the PRYSPRY v1 region was only 50% similar between these genera. Selection analysis of Lagomorpha TRIM5α proteins identified 25 positively-selected codons, 11 of which are located in the PRYSPRY v1 region, responsible for species specific differences in viral capsid recognition. Conclusions By extending Lagomorpha TRIM5α studies to an additional genus known to bear RELIK, we verified that the divergent species-specific pattern observed between the Oryctolagus and Lepus PRYSPRY-domains is also present in Sylvilagus TRIM5α. This work is one of the first known studies that compare the evolution of the

  14. Analyse quantitative détaillée des distillats moyens par couplage CG/SM. Application à l'étude des schémas réactionnels du procédé d'hydrotraitement Quantitative Analysis of Middle Distillats by Gc/Ms Coupling. Application to Hydrotreatment Process Mechanisms

    Directory of Open Access Journals (Sweden)

    Fafet A.

    2006-11-01

    Full Text Available L'analyse détaillée des distillats moyens est une étape indispensable à la compréhension des mécanismes réactionnels et à la cinétique de certains procédés de raffinage comme l'hydrotraitement. Une nouvelle méthode associant, d'une part un couplage chromatographie en phase gazeuse/spectrométrie de masse (CG/SM et, d'autre part une analyse quantitative par famille chimique par spectrométrie de masse a été développée. La chromatographie en phase gazeuse, réalisée sur une colonne apolaire, effectue la distillation des composés présents dans le gazole et la spectrométrie de masse quantifie les familles chimiques par intervalle de nombre d'atomes de carbone ou de point d'ébullition. Elle permet d'accéder ainsi à la répartition par nombre d'atomes de carbone de chaque famille chimique (alcanes, cycloalcanes, hydrocarbures aromatiques à un ou plusieurs noyaux, hydrocarbures aromatiques soufrés. Cette méthode a été validée et appliquée à une charge et à une recette d'hydrotraitement. A detailed analysis of middle distillates is essential for understanding the reaction mechanism and for studying the kinetics of refining processes such hydrotreatment. In fact, when we see the complexity of saturated and aromatic hydrocarbon mixtures appearing in gas oil, we realize that it's necessary to have a very detailed analysis of those cuts to understand the mechanisms involved in refining processes and to be able to describe their kinetics. Each gas oil has a very different composition and therefore a specific reactivity. That is why we have tried to develop predictive kinetic models to avoid experimenting in pilot plants, which is very expensive. But, even if all the compounds of a gasoline (PI-200°C have now been identified and quantified, using gas chromatography (1, such is not the case for heavier cuts. Only an overall characterization can be made, by chemical family. The techniques employed are, for example, HPLC (3,4 or

  15. The role of the arachidonic acid cascade in the species-specific X-ray-induced inflammation of the rabbit eye

    International Nuclear Information System (INIS)

    Bito, L.Z.; Klein, E.M.

    1982-01-01

    To identify the mediator(s) of the apparently species-specific X-ray-induced inflammation of the rabbit eye, inhibitors of the synthesis and/or release of known or putative mediators of ocular inflammation were administered prior to irradiation. The X-ray-induced ocular inflammation, particularly the rise in intraocular pressure, was found to be inhibited by intravenous pretreatment of rabbits with flurbiprofen, indomethacin, or imidazole (1, 10, and 100 mg/kg i.v., respectively), or by combined intravitreal and topical administration of flurbiprofen. Systemic, intravitreal, and/or topical pretreatment with prednisolone or disodium cromoglycate or the retrobulbar injection of ethyl alcohol or capsaicin failed to block the inflammatory response, whereas vitamin E apparently exerted some protective effect. These findings show that the X-ray-induced inflammation of the rabbit eye is mediated, at least in part, by prostaglandins (PGs) and/or related autacoids. In addition, these results suggest that the unique sensitivity of the rabbit eye to X-ray-induced inflammation is due either to the presence in this species of a unique or uniquely effective triggering mechanism for the release of PG precursors or to the greater sensitivity of this species to the ocular inflammatory effects of PGs. Thus the rabbit eye may provide a unique model for studying some aspects of arachidonic acid release or ocular PG effects, but extreme caution must be exercised in generalizing such findings to other species

  16. Spatio-temporal and species-specific variation in PBDE levels/patterns in British Columbia's coastal waters

    Energy Technology Data Exchange (ETDEWEB)

    Ikonomou, Michael G. [Marine Environmental Quality, Institute of Ocean Sciences, Fisheries and Oceans Canada, 9860 W. Saanich Road, Sidney, British Columbia V8L 4B2 (Canada)]. E-mail: ikonomoum@dfo-mpo.gc.ca; Fernandez, Marc P. [Marine Environmental Quality, Institute of Ocean Sciences, Fisheries and Oceans Canada, 9860 W. Saanich Road, Sidney, British Columbia V8L 4B2 (Canada); Hickman, Zachary L. [College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032 (United States)

    2006-03-15

    Congener-specific levels of PBDEs were measured in the livers and some muscle tissues of Dungeness crab (Cancer magister), English sole (Pleuronectes vetulus) and spiny dogfish (Squalus acanthias). Highest concentrations (1200-560 ng/g lipid) were found in crab collected near heavily urbanized areas (pop. {approx}0.3-1.8 million), followed by moderate levels at pulp/paper mills sites ({approx}150 ng/g), and lowest levels occurred in areas that were somewhat removed from industrial/populated areas (<24 ng/g). Temporal increases in total PBDEs and particularly in BDE-47 for Dungeness crab collected near pulp and paper and urbanized areas between 1994 and 2000 were observed. These correspond to Canadian and worldwide trends seen for PBDEs in biota. English sole and dogfish showed a pattern similar to that of the Columbia River whitefish samples, which corresponded closely to the patterns in the 'penta' commercial mixture. Conversely, Dungeness crab were enriched in lower chlorinated PBDEs, particularly BDE-47 and BDE-49, compared to the fish and shark species from BC. - PBDEs in biota and sediments from the West Coast of Canada reflect temporal, species-specific and geographic distributions.

  17. Species-specific guidelines for choosing forest regeneration material for northern Sweden; Beslutsunderlag foer val av skogsodlingsmaterial i norra Sverige med traedslagsvisa guider

    Energy Technology Data Exchange (ETDEWEB)

    Rosvall, O.; Andersson, Bengt; Ericsson, Tore

    1998-05-01

    To facilitate the selection of suitable seed-orchard and natural-stand regeneration material for sites in northern Sweden, a conceptual model was developed which includes a specification of the sites and genetic material, seed source transfer effects on various tree characters, and delineation of suitable utilization-areas for specific regeneration materials and management objectives. The most important site characteristics are photoperiod, temperature sum and local-climate pattern, specified by latitude, elevation and topography. The regeneration material is characterised by its specific properties, such as breeding value, and potential reaction to changes in the photoperiod (standardised latitudinal origin). A specification of transfer effects was made by the changes in the characteristics of a population when moved along photoperiod (latitudinal) or temperature (elevation) gradients. Optimum latitudinal seed-source transfer distances can be calculated for each temperature climate and management objective based on the economic value of the population characteristics and the species-specific transfer effects. On the basis of what were assessed to be common requirements, we drew up a baseline option whereby suitable utilization areas for seed-orchard and natural-stand progenies were delineated. An analysis was made of the consequences of the baseline option and the background information was reviewed and summarised for Pinus sylvestris, Pinus contorta, Picea abies and Betula pendula 95 refs, 24 figs, 16 tabs

  18. Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers.

    Science.gov (United States)

    Zhou, L X; Xiao, Y; Xia, W; Yang, Y D

    2015-12-08

    Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species.

  19. The nuclear higher-order structure defined by the set of topological relationships between DNA and the nuclear matrix is species-specific in hepatocytes.

    Science.gov (United States)

    Silva-Santiago, Evangelina; Pardo, Juan Pablo; Hernández-Muñoz, Rolando; Aranda-Anzaldo, Armando

    2017-01-15

    During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions. However, if the topological relationships between DNA and the NM were the subject of any biological constraint with functional significance then they must be adaptive and thus be positively selected by natural selection and they should be reasonably conserved, at least within closely related species. We carried out a coarse-grained, comparative evaluation of the DNA-NM topological relationships in primary hepatocytes from two closely related mammals: rat and mouse, by determining the relative position to the NM of a limited set of target sequences corresponding to highly-conserved genomic regions that also represent a sample of distinct chromosome territories within the interphase nucleus. Our results indicate that the pattern of topological relationships between DNA and the NM is not conserved between the hepatocytes of the two closely related species, suggesting that the NHOS, like the karyotype, is species-specific. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. A regional composite-face effect for species-specific recognition: Upper and lower halves play different roles in holistic processing of monkey faces.

    Science.gov (United States)

    Wang, Zhe; Quinn, Paul C; Jin, Haiyang; Sun, Yu-Hao P; Tanaka, James W; Pascalis, Olivier; Lee, Kang

    2018-04-25

    Using a composite-face paradigm, we examined the holistic processing induced by Asian faces, Caucasian faces, and monkey faces with human Asian participants in two experiments. In Experiment 1, participants were asked to judge whether the upper halves of two faces successively presented were the same or different. A composite-face effect was found for Asian faces and Caucasian faces, but not for monkey faces. In Experiment 2, participants were asked to judge whether the lower halves of the two faces successively presented were the same or different. A composite-face effect was found for monkey faces as well as for Asian faces and Caucasian faces. Collectively, these results reveal that own-species (i.e., own-race and other-race) faces engage holistic processing in both upper and lower halves of the face, but other-species (i.e., monkey) faces engage holistic processing only when participants are asked to match the lower halves of the face. The findings are discussed in the context of a region-based holistic processing account for the species-specific effect in face recognition. Copyright © 2018 Elsevier Ltd. All rights reserved.

  1. Phytoplankton IF-FISH: Species-specific labeling of cellular proteins by immunofluorescence (IF) with simultaneous species identification by fluorescence immunohybridization (FISH).

    Science.gov (United States)

    Meek, Megan E; Van Dolah, Frances M

    2016-05-01

    Phytoplankton rarely occur as unialgal populations. Therefore, to study species-specific protein expression, indicative of physiological status in natural populations, methods are needed that will both assay for a protein of interest and identify the species expressing it. Here we describe a protocol for IF-FISH, a dual labeling procedure using immunofluorescence (IF) labeling of a protein of interest followed by fluorescence in situ hybridization (FISH) to identify the species expressing that protein. The protocol was developed to monitor expression of the cell cycle marker proliferating cell nuclear antigen (PCNA) in the red tide dinoflagellate, Karenia brevis, using a large subunit (LSU) rRNA probe to identify K. brevis in a mixed population of morphologically similar Karenia species. We present this protocol as proof of concept that IF-FISH can be successfully applied to phytoplankton cells. This method is widely applicable for the analysis of single-cell protein expression of any protein of interest within phytoplankton communities. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. A five-amino-acid motif in the undefined region of the TLR8 ectodomain is required for species-specific ligand recognition.

    Science.gov (United States)

    Liu, Jin; Xu, Congfeng; Hsu, Li-Chung; Luo, Yunping; Xiang, Rong; Chuang, Tsung-Hsien

    2010-02-01

    Toll-like receptors play important roles in regulating immunity against microbial infections. Toll-like receptor 8 (TLR8) belongs to a subfamily comprising TLR7, TLR8 and TLR9. Human TLR8 mediates anti-viral immunity by recognizing ssRNA viruses, and triggers potent anti-viral and antitumor immune responses upon ligation by synthetic small molecular weight ligands. Interestingly, distinct from human TLR8, mouse TLR8 was not responsive to ligand stimulation in the absence of polyT-oligodeoxynucleotides (polyT-ODN). The molecular basis for this distinct ligand recognition is still unclear. In the present study, we compared the activation of TLR8 from different species including mouse, rat, human, bovine, porcine, horse, sheep, and cat by ligand ligations. Only the TLR8s from the rodent species (i.e., mouse and rat TLR8s) failed to respond to ligand stimulation in the absence of polyT-ODN. Multiple sequence alignment analysis suggested that these two rodent TLR8s lack a five-amino-acid motif that is conserved in the non-rodent species with varied sequence. This small motif is located in an undefined region of the hTLR8 ectodomain, immediately following LRR-14. Deletion mutation analysis suggested that this motif is essential for the species-specific ligand recognition of hTLR8, whereas it is not required for self-dimerization and intracellular localization of this receptor. (c) 2009 Elsevier Ltd. All rights reserved.

  3. The potential of species-specific tagatose-6-phosphate (T6P) pathway in Lactobacillus casei group for galactose reduction in fermented dairy foods.

    Science.gov (United States)

    Wu, Qinglong; Shah, Nagendra P

    2017-04-01

    Residual lactose and galactose in fermented dairy foods leads to several industrial and health concerns. There is very little information pertaining to manufacture of fermented dairy foods that are low in lactose and galactose. In the present study, comparative genomic survey demonstrated the constant presence of chromosome-encoded tagatose-6-phosphate (T6P) pathway in Lactobacillus casei group. Lactose/galactose utilization tests and β-galactosidase assay suggest that PTS Gal system, PTS Lac system and T6P pathway are major contributors for lactose/galactose catabolism in this group of organisms. In addition, it was found than lactose catabolism by Lb. casei group accumulated very limited galactose in the MRS-lactose medium and in reconstituted skim milk, whereas Streptococcus thermophilus and Lb. delbrueckii subsp. bulgaricus (Lb. bulgaricus) strains secreted high amount of galactose extracellularly. Moreover, co-culturing Lb. casei group with Str. thermophilus showed significant reduction in galactose content, while co-culturing Lb. casei group with Lb. bulgaricus showed significant reduction in lactose content but significant increase in galactose content in milk. Overall, the present study highlighted the potential of Lb. casei group for reducing galactose accumulation in fermented milks due to its species-specific T6P pathway. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Intérêts et limites de l'analyse de la moelle osseuse en toxicologie médicolégale : contribution à l'interprétation quantitative des concentrations médullaires

    OpenAIRE

    Cartiser , Nathalie

    2011-01-01

    The aim of this work was to evaluate the interest of bone marrow (BM) analysis in forensic toxicology, as an alternative matrix to blood. An analytical method was developed and validated for the quantification of citalopram, diazepam, and its main metabolites (nordazepam, temazepam, oxazepam) in BM and 10 others matrices of forensic interest. This procedure was successfully applied to real cases for putrified sample analyses and to establish a tissue kinetic in rabbit samples for a pharmacoki...

  5. Quantitative habitability.

    Science.gov (United States)

    Shock, Everett L; Holland, Melanie E

    2007-12-01

    A framework is proposed for a quantitative approach to studying habitability. Considerations of environmental supply and organismal demand of energy lead to the conclusions that power units are most appropriate and that the units for habitability become watts per organism. Extreme and plush environments are revealed to be on a habitability continuum, and extreme environments can be quantified as those where power supply only barely exceeds demand. Strategies for laboratory and field experiments are outlined that would quantify power supplies, power demands, and habitability. An example involving a comparison of various metabolisms pursued by halophiles is shown to be well on the way to a quantitative habitability analysis.

  6. Hymenoptera venom allergy: analysis of double positivity to honey bee and Vespula venom by estimation of IgE antibodies to species-specific major allergens Api m1 and Ves v5.

    Science.gov (United States)

    Müller, U R; Johansen, N; Petersen, A B; Fromberg-Nielsen, J; Haeberli, G

    2009-04-01

    In patients with hymenoptera venom allergy diagnostic tests are often positive with honey bee and Vespula venom causing problems in selection of venoms for immunotherapy. 100 patients each with allergic reactions to Vespula or honey bee stings and positive i.e. skin tests to the respective venom, were analysed for serum IgE to bee venom, Vespula venom and crossreacting carbohydrate determinants (CCDs) by UNICAP (CAP) and ADVIA Centaur (ADVIA). IgE-antibodies to species specific recombinant major allergens (SSMA) Api m1 for bee venom and Ves v5 for Vespula venom, were determined by ADVIA. 30 history and skin test negative patients served as controls. By CAP sensitivity was 1.0 for bee and 0.91 for Vespula venom, by ADVIA 0.99 for bee and 0.91 for Vespula venom. None of the controls were positive with either test. Double positivity was observed in 59% of allergic patients by CAP, in 32% by ADVIA. slgE to Api m1 was detected in 97% of bee and 17% of Vespula venom allergic patients, slgE to Ves v5 in 87% of Vespula and 17% of bee venom allergic patients. slgE to CCDs were present in 37% of all allergic patients and in 56% of those with double positivity and were more frequent in bee than in Vespula venom allergic patients. Double positivity of IgE to bee and Vespula venom is often caused by crossreactions, especially to CCDs. IgE to both Api m1 and Ves v5 indicates true double sensitization and immunotherapy with both venoms.

  7. Simultaneous multi-species determination of trimethyllead, monomethylmercury and three butyltin compounds by species-specific isotope dilution GC-ICP-MS in biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Poperechna, Nataliya; Heumann, Klaus G. [Johannes Gutenberg-University Mainz (Germany). Institute of Inorganic Chemistry and Analytical Chemistry

    2005-09-01

    An accurate and sensitive multi-species species-specific isotope dilution GC-ICP-MS method was developed for the simultaneous determination of trimethyllead (Me{sub 3}Pb{sup +}), monomethylmercury (MeHg{sup +}) and the three butyltin species Bu{sub 3}Sn{sup +}, Bu{sub 2}Sn{sup 2+}, and BuSn{sup 3+} in biological samples. The method was validated by three biological reference materials (CRM 477, mussel tissue certified for butyltins; CRM 463, tuna fish certified for MeHg{sup +}; DORM 2, dogfish muscle certified for MeHg{sup +}). Under certain conditions, and with minor modifications of the sample pretreatment procedure, this method could also be transferred to environmental samples such as sediments, as demonstrated by analyzing sediment reference material BCR 646 (freshwater sediment, certified for butyltins). The detection limits of the multi-species GC-ICP-IDMS method for biological samples were 1.4 ng g{sup -1} for MeHg{sup +}, 0.06 ng g{sup -1} for Me{sub 3}Pb{sup +}, 0.3 ng g{sup -1} for BuSn{sup 3+} and Bu{sub 3}Sn{sup +}, and 1.2 ng g{sup -1} for Bu{sub 2}Sn{sup 2+}. Because of the high relevance of these heavy metal alkyl species to the quality assurance of seafood, the method was also applied to corresponding samples purchased from a supermarket. The methylated lead fraction in these samples, correlated to total lead, varied over a broad range (from 0.01% to 7.6%). On the other hand, the MeHg{sup +} fraction was much higher, normally in the range of 80-100%. Considering that we may expect tighter legislative limitations on MeHg{sup +} levels in seafood in the future, we found the highest methylmercury contents (up to 10.6 {mu}g g{sup -1}) in two shark samples, an animal which is at the end of the marine food chain, whereas MeHg{sup +} contents of less than 0.2 {mu}g g{sup -1} were found in most other seafood samples; these results correlate with the idea that MeHg{sup +} is usually of biological origin in the marine environment. The concentration of

  8. Is splash erosion potential species specific? Measuring of splash erosion potential under forest in different succession stages along a biodiversity gradient in the humid subtropics

    Science.gov (United States)

    Geißler, C.; Kühn, P.; Scholten, T.

    2009-04-01

    It is widely accepted that (forest) vegetation is a key control for the type and intensity of soil erosion. The current paradigm is that natural or quasi-natural vegetation protects the soil from erosion and that agricultural vegetation or land use generally enhances erosion. The latter was in focus of most research during the last decades and less interest was paid on natural systems, which are more difficult to study. Nevertheless, afforestation is widely used as a measure of soil protection against soil erosion. Rainfall can be highly erosive particularly in the humid subtropics. Regarding climate change, also precipitation regime may change in direction to even more severe storms and higher rainfall intensities; it is a research field of growing importance. Key mechanisms of a vegetation cover in reducing or enhancing erosion are modifications of drop-size distribution, retention of raindrop impact on the soil and changes in amount and spatial distribution of rainfall at the ground surface. Controlling determinants are rainfall intensity, drop size distribution, drop fall velocity, height of the canopy as well as density of the canopy, crown and leaf traits, LAI and coverage by a litter layer. Large drops are supposed to be significant sources of splash detachment in forests (Brandt 1989; Vis 1986). However, the mechanisms of reducing (or enhancing?) splash detachment under forest in relation to species richness and species composition are not well understood. Some studies indicate that raindrop impact is species specific (Calder 2001; Nanko et al. 2006) and some neglect the effects of species specific impacts (Foot & Morgan 2005). Our research uses different methods of rainfall characterization (splash cups, tipping-bucket rain gauge, laser distrometer) to reveal the described mechanisms from the canopy through different vegetation layers to the ground. First results of splash cup measurements (revised after Ellison 1947) show that sand loss under vegetation

  9. PCR-based molecular discrimination of Pandora neoaphidis isolates from related entomopathogenic fungi and development of species-specific diagnostic primers.

    Science.gov (United States)

    Tymon, Anna M; Shah, Paresh A; Pell, Judith K

    2004-04-01

    Studies were performed to assess the genetic variation amongst isolates of the aphid-pathogenic fungus Pandora neoaphidis (syn. Erynia neoaphidis). 37 isolates were examined, from a range of pest and non-pest aphid species, as well as 21 from eight other entomophthoralean species. Universal primers were used to amplify the ITS rDNA regions and all of the species tested produced discrete ITS groups, with the exception of Conidiobolus spp. Neighbour-joining analysis of the ITS2 regions from P. neoaphidis, P. kondoiensis and Zoophthora radicans demonstrated that these three species formed distinct groups with sequence identities of 58-82% between the groups. An ITS size of ca 1,100 bp was diagnostic for P. neoaphidis, while ca 1,450 bp was characteristic of P. kondoiensis. ITS-RFLP analysis failed to yield intraspecific polymorphisms in any of the P. neoaphidis isolates screened, although it was useful in distinguishing between different entomophthoralean species. Some intraspecific variation in the ITS region was detected in a number of isolates of Z. radicans and Conidiobolus spp. We propose that two isolates previously identified as P. neoaphidis based on conidia morphology, are actually P. kondoiensis based on molecular studies. Sequencing analysis of the complete ITS region from P. neoaphidis and P. kondoiensis allowed species-specific primers to be developed for P. neoaphidis and P. kondoiensis. These were used to screen aphids infected in laboratory bioassays and from field-collected samples, without prior isolation of the fungus. The primers are useful tools for quantifying the epizootiology of P. neoaphidis in aphid populations, as well as assessing competitive interactions between these two species.

  10. Species-specific diagnostics of Apis mellifera trypanosomatids: A nine-year survey (2007-2015) for trypanosomatids and microsporidians in Serbian honey bees.

    Science.gov (United States)

    Stevanovic, Jevrosima; Schwarz, Ryan S; Vejnovic, Branislav; Evans, Jay D; Irwin, Rebecca E; Glavinic, Uros; Stanimirovic, Zoran

    2016-09-01

    In this study, honey bees collected in Serbia over 9 consecutive years (2007-2015) were retrospectively surveyed to determine the prevalence of eukaryotic gut parasites by molecular screening of archival DNA samples. We developed species-specific primers for PCR to detect the two known honey bee trypanosomatid species, Crithidia mellificae and the recently described Lotmaria passim. These primers were validated for target specificity under single and mixed-species conditions as well as against the bumblebee trypanosomatid Crithidia bombi. Infections by Nosema apis and Nosema ceranae (Microsporidia) were also determined using PCR. Samples from 162 colonies (18 from each year) originating from 57 different localities were surveyed. L. passim was detected in every year with an overall frequency of 62.3% and annual frequencies ranging from 38.9% to 83.3%. This provides the earliest confirmed record to date for L. passim and the first report of this species in Serbia. N. ceranae was ubiquitous, occurring in every year and at 95.7% overall frequency, ranging annually from 83.3% to 100%. The majority of colonies (60.5%) were co-infected with L. passim and N. ceranae, but colony infections by each species were statistically independent of one another over the nine years. Although C. mellificae and N. apis have both been reported recently at low frequency in Europe, neither of these species was detected in Serbia. These results support the hypothesis that L. passim has predominated over C. mellificae in A. mellifera during the past decade. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. In-Depth N-Glycosylation Reveals Species-Specific Modifications and Functions of the Royal Jelly Protein from Western (Apis mellifera) and Eastern Honeybees (Apis cerana).

    Science.gov (United States)

    Feng, Mao; Fang, Yu; Han, Bin; Xu, Xiang; Fan, Pei; Hao, Yue; Qi, Yuping; Hu, Han; Huo, Xinmei; Meng, Lifeng; Wu, Bin; Li, Jianke

    2015-12-04

    Royal jelly (RJ), secreted by honeybee workers, plays diverse roles as nutrients and defense agents for honeybee biology and human health. Despite being reported to be glycoproteins, the glycosylation characterization and functionality of RJ proteins in different honeybee species are largely unknown. An in-depth N-glycoproteome analysis and functional assay of RJ produced by Apis mellifera lingustica (Aml) and Apis cerana cerana (Acc) were conducted. RJ produced by Aml yielded 80 nonredundant N-glycoproteins carrying 190 glycosites, of which 23 novel proteins harboring 35 glycosites were identified. For Acc, all 43 proteins glycosylated at 138 glycosites were reported for the first time. Proteins with distinct N-glycoproteomic characteristics in terms of glycoprotein species, number of N-glycosylated sites, glycosylation motif, abundance level of glycoproteins, and N-glycosites were observed in this two RJ samples. The fact that the low inhibitory efficiency of N-glycosylated major royal jelly protein 2 (MRJP2) against Paenibacillus larvae (P. larvae) and the absence of antibacterial related glycosylated apidaecin, hymenoptaecin, and peritrophic matrix in the Aml RJ compared to Acc reveal the mechanism for why the Aml larvae are susceptible to P. larvae, the causative agent of a fatal brood disease (American foulbrood, AFB). The observed antihypertension activity of N-glycosylated MRJP1 in two RJ samples and a stronger activity found in Acc than in Aml reveal that specific RJ protein and modification are potentially useful for the treatment of hypertensive disease for humans. Our data gain novel understanding that the western and eastern bees have evolved species-specific strategies of glycosylation to fine-tune protein activity for optimizing molecular function as nutrients and immune agents for the good of honeybee and influence on the health promoting activity for human as well. This serves as a valuable resource for the targeted probing of the biological

  12. Loss of memory CD4+ T-cells in semi-wild mandrills (Mandrillus sphinx) naturally infected with species-specific simian immunodeficiency virus SIVmnd-1.

    Science.gov (United States)

    Greenwood, Edward J D; Schmidt, Fabian; Liégeois, Florian; Kondova, Ivanela; Herbert, Anaïs; Ngoubangoye, Barthelemy; Rouet, François; Heeney, Jonathan L

    2014-01-01

    Simian immunodeficiency virus (SIV) infection is found in a number of African primate species and is thought to be generally non-pathogenic. However, studies of wild primates are limited to two species, with SIV infection appearing to have a considerably different outcome in each. Further examination of SIV-infected primates exposed to their natural environment is therefore warranted. We performed a large cross-sectional study of a cohort of semi-wild mandrills with naturally occurring SIV infection, including 39 SIV-negative and 33 species-specific SIVmnd-1-infected animals. This study was distinguished from previous reports by considerably greater sample size, examination of exclusively naturally infected animals in semi-wild conditions and consideration of simian T-lymphotropic virus (STLV) status in addition to SIVmnd-1 infection. We found that SIVmnd-1 infection was associated with a significant and progressive loss of memory CD4(+) T-cells. Limited but significant increases in markers of immune activation in the T-cell populations, significant increases in plasma neopterin and changes to B-cell subsets were also observed in SIV-infected animals. However, no increase in plasma soluble CD14 was observed. Histological examination of peripheral lymph nodes suggested that SIVmnd-1 infection was not associated with a significant disruption of the lymph node architecture. Whilst this species has evolved numerous strategies to resist the development of AIDS, significant effects of SIV infection could be observed when examined in a natural environment. STLVmnd-1 infection also had significant effects on some markers relevant to understanding SIV infection and thus should be considered in studies of SIV infection of African primates where present.

  13. Species specificity of bacteria associated to the brown seaweeds Lobophora (Dictyotales, Phaeophyceae and their potential for induction of rapid coral bleaching in Acropora muricata

    Directory of Open Access Journals (Sweden)

    Christophe William Vieira

    2016-03-01

    Full Text Available While reef degradation is occurring worldwide, it is not uncommon to see phase shifts from coral to macroalgal dominated reefs. Numerous studies have addressed the mechanisms by which macroalgae may outcompete corals and a few recent studies highlighted the putative role of bacteria at the interface between macroalgae and corals. Some studies suggest that macroalgae may act as vectors and/or foster proliferation of microorganisms pathogenic for corals. Using a combination of high throughput sequencing, bacterial culturing and in situ bioassays we question if the adversity of macroalgal-associated bacteria to corals is mediated by specific bacterial taxa. Using Illumina sequencing, we characterized and compared the bacterial community from two Lobophora (Dictyotales, Phaeophyceae species. The two species presented distinctive bacterial communities. Both species shared approximately half of their OTUs, mainly the most abundant bacteria. Species-specific OTUs belong to Planctomycetes, Proteobacteria and Bacteroidetes. In total, 16 culturable bacterial strain were isolated and identified from the Lobophora surface, consisting of 10 genera (from 9 families, 4 classes and 3 phyla, some of which are not known as, but are related to pathogens involved in coral diseases, and others naturally associated to corals. When patches of marine agar with 24 h cultures of each of these bacteria were placed in direct contact with the branches of the scleractinian coral Acropora muricata, they caused severe bleaching after 24 h exposure. Results suggest that regardless of taxonomic affinities, increase in density of any bacteria can be adverse to corals. Nevertheless, the microbial community associated to macroalgal surface may not represent a threat to corals, because the specific bacterial screening and control exerted by the alga preventing specific bacterial proliferation.

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

    Directory of Open Access Journals (Sweden)

    O'Gara Fergal

    2010-11-01

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

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

    Science.gov (United States)

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

    2010-11-25

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

  16. The human immunodeficiency virus-1 protein Tat and its discrete fragments evoke selective release of acetylcholine from human and rat cerebrocortical terminals through species-specific mechanisms.

    Science.gov (United States)

    Feligioni, Marco; Raiteri, Luca; Pattarini, Roberto; Grilli, Massimo; Bruzzone, Santina; Cavazzani, Paolo; Raiteri, Maurizio; Pittaluga, Anna

    2003-07-30

    The effect of the human immunodeficiency virus-1 protein Tat was investigated on neurotransmitter release from human and rat cortical nerve endings. Tat failed to affect the release of several neurotransmitters, such as glutamate, GABA, norepinephrine, and others, but it evoked the release of [3H]ACh via increase of cytosolic [Ca2+]. In human nerve terminals, the Tat effect partly depends on Ca2+ entry through voltage-sensitive Ca2+ channels, because Cd2+ halved the Tat-evoked release. Activation of group I metabotropic glutamate receptors (mGluR) and mobilization of Ca2+ from IP3-sensitive intraterminal stores are also involved, because the Tat effect was prevented by mGluR antagonists 2-methyl-6-(phenylethynyl)pyridine hydrochloride and 7-(hydroxyimino)cyclopropa[b]chromen-1a-carboxylate ethyl ester and by the IP3 receptor antagonists heparin and xestospongin C. Furthermore, the group I selective mGlu agonist (RS)-3,5-dihydroxyphenylglycine enhanced [3H]ACh release. In rat nerve terminals, the Tat-evoked release neither depends on external Ca2+ ions entry nor on IP3-mediated mechanisms. Tat seems to cause mobilization of Ca2+ from ryanodine-sensitive internal stores because its effect was prevented by both 8-bromo-cyclic adenosine diphosphate-ribose and dantrolene. The Tat-evoked release from human synaptosomes was mimicked by the peptide sequences Tat 32-62, Tat 49-86, and Tat 41-60. In contrast, the Tat 49-86 and Tat 61-80 fragments, but not the Tat 32-62 fragment, were active in rat synaptosomes. In conclusion, Tat elicits Ca2+-dependent [3H]ACh release by species-specific intraterminal mechanisms by binding via discrete amino acid sequences to different receptive sites on human and rat cholinergic terminals.

  17. Species-Specific and Drug-Specific Differences in Susceptibility of Candida Biofilms to Echinocandins: Characterization of Less Common Bloodstream Isolates

    Science.gov (United States)

    Simitsopoulou, Maria; Peshkova, Pavla; Tasina, Efthymia; Katragkou, Aspasia; Kyrpitzi, Daniela; Velegraki, Aristea; Walsh, Thomas J.

    2013-01-01

    Candida species other than Candida albicans are increasingly recognized as causes of biofilm-associated infections. This is a comprehensive study that compared the in vitro activities of all three echinocandins against biofilms formed by different common and infrequently identified Candida isolates. We determined the activities of anidulafungin (ANID), caspofungin (CAS), and micafungin (MFG) against planktonic cells and biofilms of bloodstream isolates of C. albicans (15 strains), Candida parapsilosis (6 strains), Candida lusitaniae (16 strains), Candida guilliermondii (5 strains), and Candida krusei (12 strains) by XTT [2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide] assay. Planktonic and biofilm MICs were defined as ≥50% fungal damage. Planktonic cells of all Candida species were susceptible to the three echinocandins, with MICs of ≤1 mg/liter. By comparison, differences in the MIC profiles of biofilms in response to echinocandins existed among the Candida species. Thus, C. lusitaniae and C. guilliermondii biofilms were highly recalcitrant to all echinocandins, with MICs of ≥32 mg/liter. In contrast, the MICs of all three echinocandins for C. albicans and C. krusei biofilms were relatively low (MICs ≤ 1 mg/liter). While echinocandins exhibited generally high MICs against C. parapsilosis biofilms, MFG exhibited the lowest MICs against these isolates (4 mg/liter). A paradoxical growth effect was observed with CAS concentrations ranging from 8 to 64 mg/liter against C. albicans and C. parapsilosis biofilms but not against C. krusei, C. lusitaniae, or C. guilliermondii. While non-albicans Candida planktonic cells were susceptible to all echinocandins, there were drug- and species-specific differences in susceptibility among biofilms of the various Candida species, with C. lusitaniae and C. guilliermondii exhibiting profiles of high MICs of the three echinocandins. PMID:23529739

  18. Bacteria in the vaginal microbiome alter the innate immune response and barrier properties of the human vaginal epithelia in a species-specific manner.

    Science.gov (United States)

    Doerflinger, Sylvie Y; Throop, Andrea L; Herbst-Kralovetz, Melissa M

    2014-06-15

    Bacterial vaginosis increases the susceptibility to sexually transmitted infections and negatively affects women's reproductive health. To investigate host-vaginal microbiota interactions and the impact on immune barrier function, we colonized 3-dimensional (3-D) human vaginal epithelial cells with 2 predominant species of vaginal microbiota (Lactobacillus iners and Lactobacillus crispatus) or 2 prevalent bacteria associated with bacterial vaginosis (Atopobium vaginae and Prevotella bivia). Colonization of 3-D vaginal epithelial cell aggregates with vaginal microbiota was observed with direct attachment to host cell surface with no cytotoxicity. A. vaginae infection yielded increased expression membrane-associated mucins and evoked a robust proinflammatory, immune response in 3-D vaginal epithelial cells (ie, expression of CCL20, hBD-2, interleukin 1β, interleukin 6, interleukin 8, and tumor necrosis factor α) that can negatively affect barrier function. However, P. bivia and L. crispatus did not significantly upregulate pattern-recognition receptor-signaling, mucin expression, antimicrobial peptides/defensins, or proinflammatory cytokines in 3-D vaginal epithelial cell aggregates. Notably, L. iners induced pattern-recognition receptor-signaling activity, but no change was observed in mucin expression or secretion of interleukin 6 and interleukin 8. We identified unique species-specific immune signatures from vaginal epithelial cells elicited by colonization with commensal and bacterial vaginosis-associated bacteria. A. vaginae elicited a signature that is consistent with significant disruption of immune barrier properties, potentially resulting in enhanced susceptibility to sexually transmitted infections during bacterial vaginosis. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. Species-specific control of cellular proliferation and the impact of large animal models for the use of olfactory ensheathing cells and Schwann cells in spinal cord repair.

    Science.gov (United States)

    Wewetzer, Konstantin; Radtke, Christine; Kocsis, Jeffery; Baumgärtner, Wolfgang

    2011-05-01

    Autologous transplantation of olfactory ensheathing cells (OECs) and Schwann cells (SCs) is considered a promising option to promote axonal regrowth and remyelination after spinal cord injury in humans. However, if the experimental data from the rodent model can be directly extrapolated to humans, as widely believed, remains to be established. While limitations of the rodent system have recently been discussed with regard to the distinct organization of the motor systems, the question whether OECs and SCs may display species-specific properties has not been fully addressed. Prompted by recent studies on canine and porcine glia, we performed a detailed analysis of the in vitro and in vivo properties of OECs and SCs and show that rodent but not human, monkey, porcine, and canine glia require mitogens for in vitro expansion, display a complex response to elevated intracellular cAMP, and undergo spontaneous immortalization upon prolonged mitogen stimulation. These data indicate fundamental inter-species differences of the control of cellular proliferation. Whether OECs and SCs from large animals and humans share growth-promoting in vivo properties with their rodent counterpart is not yet clear. Autologous implantation studies in humans did not reveal adverse effects of cell transplantation so far. However, in vivo studies of large animal or human glia and rodent recipients mainly focused on the remyelinating potential of the transplanted cells. Thus, further experimental in vivo studies in large animals are essential to fully define the axonal growth-promoting potential of OECs and SCs. Based on the homology of the in vitro growth control between porcine, canine and human glia, it is concluded that these species may serve as valuable translational models for scaling up human procedures. This article is part of a Special Issue entitled: Understanding olfactory ensheathing glia and their prospect for nervous system repair. Copyright © 2010 Elsevier Inc. All rights

  20. Crystal structure of ryanodine receptor N-terminal domain from Plutella xylostella reveals two potential species-specific insecticide-targeting sites.

    Science.gov (United States)

    Lin, Lianyun; Liu, Chen; Qin, Juan; Wang, Jie; Dong, Shengjie; Chen, Wei; He, Weiyi; Gao, Qingzhi; You, Minsheng; Yuchi, Zhiguang

    2018-01-01

    Ryanodine receptors (RyRs) are large calcium-release channels located in sarcoplasmic reticulum membrane. They play a central role in excitation-contraction coupling of muscle cells. Three commercialized insecticides targeting pest RyRs generate worldwide sales over 2 billion U.S. dollars annually, but the structure of insect RyRs remains elusive, hindering our understanding of the mode of action of RyR-targeting insecticides and the development of insecticide resistance in pests. Here we present the crystal structure of RyR N-terminal domain (NTD) (residue 1-205) at 2.84 Å resolution from the diamondback moth (DBM), Plutella xylostella, a destructive pest devouring cruciferous crops all over the world. Similar to its mammalian homolog, DBM RyR NTD consists of a beta-trefoil folding motif and a flanking alpha helix. Interestingly, two regions in NTD interacting with neighboring domains showed distinguished conformations in DBM relative to mammalian RyRs. Using homology modeling and molecular dynamics simulation, we created a structural model of the N-terminal three domains, showing two unique binding pockets that could be targeted by potential species-specific insecticides. Thermal melt experiment showed that the stability of DBM RyR NTD was higher than mammalian RyRs, probably due to a stable intra-domain disulfide bond observed in the crystal structure. Previously DBM NTD was shown to be one of the two critical regions to interact with insecticide flubendiamide, but isothermal titration calorimetry experiments negated DBM NTD alone as a major binding site for flubendiamide. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Molecular characterization and chromosomal distribution of a species-specific transcribed centromeric satellite repeat from the olive fruit fly, Bactrocera oleae.

    Directory of Open Access Journals (Sweden)

    Konstantina T Tsoumani

    Full Text Available Satellite repetitive sequences that accumulate in the heterochromatin consist a large fraction of a genome and due to their properties are suggested to be implicated in centromere function. Current knowledge of heterochromatic regions of Bactrocera oleae genome, the major pest of the olive tree, is practically nonexistent. In our effort to explore the repetitive DNA portion of B. oleae genome, a novel satellite sequence designated BoR300 was isolated and cloned. The present study describes the genomic organization, abundance and chromosomal distribution of BoR300 which is organized in tandem, forming arrays of 298 bp-long monomers. Sequence analysis showed an AT content of 60.4%, a CENP-B like-motif and a high curvature value based on predictive models. Comparative analysis among randomly selected monomers demonstrated a high degree of sequence homogeneity (88%-97% of BoR300 repeats, which are present at approximately 3,000 copies per haploid genome accounting for about 0.28% of the total genomic DNA, based on two independent qPCR approaches. In addition, expression of the repeat was also confirmed through RT-PCR, by which BoR300 transcripts were detected in both sexes. Fluorescence in situ hybridization (FISH of BoR300 on mitotic metaphases and polytene chromosomes revealed signals to the centromeres of two out of the six chromosomes which indicated a chromosome-specific centromeric localization. Moreover, BoR300 is not conserved in the closely related Bactrocera species tested and it is also absent in other dipterans, but it's rather restricted to the B. oleae genome. This feature of species-specificity attributed to BoR300 satellite makes it a good candidate as an identification probe of the insect among its relatives at early development stages.

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

    LENUS (Irish Health Repository)

    Browne, Patrick

    2010-11-25

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

  3. Quantitative Finance

    Science.gov (United States)

    James, Jessica

    2017-01-01

    Quantitative finance is a field that has risen to prominence over the last few decades. It encompasses the complex models and calculations that value financial contracts, particularly those which reference events in the future, and apply probabilities to these events. While adding greatly to the flexibility of the market available to corporations and investors, it has also been blamed for worsening the impact of financial crises. But what exactly does quantitative finance encompass, and where did these ideas and models originate? We show that the mathematics behind finance and behind games of chance have tracked each other closely over the centuries and that many well-known physicists and mathematicians have contributed to the field.

  4. Certification of butyltins and phenyltins in marine sediment certified reference material by species-specific isotope-dilution mass spectrometric analysis using synthesized {sup 118}Sn-enriched organotin compounds

    Energy Technology Data Exchange (ETDEWEB)

    Inagaki, Kazumi; Takatsu, Akiko; Watanabe, Takuro; Aoyagi, Yoshie; Yarita, Takashi; Okamoto, Kensaku; Chiba, Koichi [National Institute of Advanced Industrial Science and Technology (AIST), Environmental Standard Section, National Metrology Institute of Japan (NMIJ), Tsukuba, Ibaraki (Japan)

    2007-04-15

    A new marine sediment certified reference material, NMIJ CRM 7306-a, for butyltin and phenyltin analysis has been prepared and certified by the National Metrological Institute of Japan at the National Institute of Advanced Industrial Science and Technology (NMIJ/AIST). Candidate sediment material was collected at a bay near industrial activity in Japan. After air-drying, sieving, and mixing the material was sterilized with {gamma}-ray irradiation. The material was re-mixed and packaged into 250 glass bottles (15 g each) and these were stored in a freezer at -30 C. Certification was performed by use of three different types of species-specific isotope-dilution mass spectrometry (SSID-MS) - SSID-GC-ICP-MS, SSID-GC-MS, and SSID-LC-ICP-MS, with {sup 118}Sn-enriched organotin compounds synthesized from {sup 118}Sn-enriched metal used as a spike. The {sup 118}Sn-enriched mono-butyltin (MBT), dibutyltin (DBT), and tributyltin (TBT) were synthesized as a mixture whereas the {sup 118}Sn-enriched di-phenyltin (DPhT) and triphenyltin (TPhT) were synthesized individually. Four different extraction methods, mechanical shaking, ultrasonic, microwave-assisted, and pressurized liquid extraction, were adopted to avoid possible analytical bias caused by non-quantitative extraction and degradation or inter-conversion of analytes in sample preparations. Tropolone was used as chelating agent in all the extraction methods. Certified values are given for TBT 44{+-}3 {mu}g kg{sup -1} as Sn, DBT 51 {+-} 2 {mu}g kg{sup -1} as Sn, MBT 67 {+-} 3 {mu}g kg{sup -1} as Sn, TPhT 6.9 {+-} 1.2 {mu}g kg{sup -1} as Sn, and DPhT 3.4 {+-} 1.2 {mu}g kg{sup -1} as Sn. These levels are lower than in other sediment CRMs currently available for analysis of organotin compounds. (orig.)

  5. Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life.

    Science.gov (United States)

    Xiong, Weili; Brown, Christopher T; Morowitz, Michael J; Banfield, Jillian F; Hettich, Robert L

    2017-07-10

    ) utilization and short-chain fatty acid production. Overall, this study reports species-specific proteome profiles and metabolic functions of human gut microbiota during early colonization. In particular, our work contributes to reveal microbiota-associated shifts and variations in the metabolism of three major nutrient sources and short-chain fatty acid during colonization of preterm infant gut.

  6. Species-specific ecological niche modelling predicts different range contractions for Lutzomyia intermedia and a related vector of Leishmania braziliensis following climate change in South America.

    Science.gov (United States)

    McIntyre, Shannon; Rangel, Elizabeth F; Ready, Paul D; Carvalho, Bruno M

    2017-03-24

    findings indicate that climate change will not always lead to range expansion of disease vectors such as sand flies. Ecological niche models should be species specific, carefully selected and combined in an ensemble approach.

  7. Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae.

    Science.gov (United States)

    Szczecińska, Monika; Sawicki, Jakub

    2015-09-15

    plastid genome and nuclear rRNA cluster sequences in three species of the genus Pulsatilla is an important contribution to our knowledge of the evolution and phylogeography of those endangered taxa. The resulting data can be used to identify regions that are particularly useful for barcoding, phylogenetic and phylogeographic studies. The investigated taxa can be identified at each stage of development based on their species-specific SNPs. The nuclear and plastid genomic resources enable advanced studies on hybridization, including identification of parent species, including their roles in that process. The identified nonsynonymous mutations could play an important role in adaptations to changing environments. The results of the study will also provide valuable information about the evolution of the plastome structure in the family Ranunculaceae.

  8. HDP2: a ribosomal DNA (NTS-ETS) sequence as a target for species-specific molecular diagnosis of intestinal taeniasis in humans.

    Science.gov (United States)

    Flores, María D; Gonzalez, Luis M; Hurtado, Carolina; Motta, Yamileth Monje; Domínguez-Hidalgo, Cristina; Merino, Francisco Jesús; Perteguer, María J; Gárate, Teresa

    2018-02-27

    Taenia solium, T. asiatica and T. saginata tapeworms cause human taeniasis and are the origin of porcine and bovine cysticercosis. Furthermore, T. solium eggs can cause human cysticercosis, with neurocysticercosis being the most serious form of the disease. These helminth infections are neglected tropical diseases and are endemic in several countries in the Americas, Asia and Africa. As a result of globalization, migration in particular, the infections have been extending to non-endemic territories. Species-specific diagnosis of taeniasis is subject to drawbacks that could be resolved using molecular approaches. In the present study, conventional and real-time amplification protocols (cPCR and qPCR) based on the T. saginata HDP2 sequence were applied in the differential diagnosis of taeniasis (T. saginata, T. solium) in both fecal samples and proglottids expelled by patients. The HDP2 homolog in T. solium was cloned and characterized. Semi-nested cPCR and qPCR (Sn-HDP2 cPCR and Sn-HDP2 qPCR) amplified T. saginata and T. solium DNA, with an analytical sensitivity of 40 and 400 fg, respectively, and identically in both protocols. Eighteen taeniasis patients were diagnosed directly with T. saginata or T. solium, either from proglottids or fecal samples with/without eggs (detected using microscopy), based on the optimized Sn-HDP2 qPCR. After cloning, the T. solium HDP2 homolog sequence was confirmed to be a ribosomal sequence. The HDP2 fragment corresponded to a non-transcribed sequence/external transcribed repeat (NTS/ETS) of ribosomal DNA. Compared with the T. saginata HDP2 homolog, the T solium HDP2 sequence lacked the first 900 nt at the 5' end and showed nucleotide substitutions and small deletions. Sn-HDP2 cPCR and Sn-HDP2 qPCR were set up for the diagnosis of human taeniasis, using proglottids and fecal samples from affected patients. The new Sn-HDP2 qPCR protocol was the best option, as it directly differentiated T. saginata from T. solium. The diagnosis of

  9. Liver volume, intrahepatic fat and body weight in the course of a lifestyle interventional study. Analysis with quantitative MR-based methods; Lebervolumen, Leberfettanteil und Koerpergewicht im Verlauf einer Lebensstilinterventionsstudie. Eine Analyse mit quantitativen MR-basierten Methoden

    Energy Technology Data Exchange (ETDEWEB)

    Bongers, M.N. [Klinikum der Eberhard-Karls-Universitaet Tuebingen, Abteilung fuer Diagnostische und Interventionelle Radiologie, Tuebingen (Germany); Universitaetsklinikum Tuebingen, Sektion fuer Experimentelle Radiologie der Abteilung fuer Diagnostische und Interventionelle Radiologie, Tuebingen (Germany); Stefan, N.; Fritsche, A.; Haering, H.U. [Universitaetsklinikum Tuebingen, Innere Medizin IV - Endokrinologie und Diabetologie, Angiologie, Nephrologie und Klinische Chemie, Tuebingen (Germany); Helmholtz-Zentrum Muenchen an der Universitaet Tuebingen, Institut fuer Diabetes-Forschung und Metabolische Erkrankungen (IDM), Tuebingen (Germany); Nikolaou, K. [Klinikum der Eberhard-Karls-Universitaet Tuebingen, Abteilung fuer Diagnostische und Interventionelle Radiologie, Tuebingen (Germany); Schick, F. [Universitaetsklinikum Tuebingen, Sektion fuer Experimentelle Radiologie der Abteilung fuer Diagnostische und Interventionelle Radiologie, Tuebingen (Germany); Machann, J. [Universitaetsklinikum Tuebingen, Sektion fuer Experimentelle Radiologie der Abteilung fuer Diagnostische und Interventionelle Radiologie, Tuebingen (Germany); Helmholtz-Zentrum Muenchen an der Universitaet Tuebingen, Institut fuer Diabetes-Forschung und Metabolische Erkrankungen (IDM), Tuebingen (Germany); Deutsches Zentrum fuer Diabetesforschung (DZD), Neuherberg (Germany)

    2015-04-01

    The aim of this study was to investigate potential associations between changes in liver volume, the amount of intrahepatic lipids (IHL) and body weight during lifestyle interventions. In a prospective study 150 patients with an increased risk for developing type 2 diabetes mellitus were included who followed a caloric restriction diet for 6 months. In the retrospective analysis 18 women and 9 men (age range 22-71 years) with an average body mass index (BMI) of 32 kg/m{sup 2} were enrolled. The liver volume was determined at the beginning and after 6 months by three-dimensional magnetic resonance imaging (3D-MRI, echo gradient, opposed-phase) and IHLs were quantified by volume-selective MR spectroscopy in single voxel stimulated echo acquisition mode (STEAM). Univariable and multivariable correlation analyses between changes of liver volume (Δliver volume), intrahepatic lipids (ΔIHL) and body weight (ΔBW) were performed. Univariable correlation analysis in the whole study cohort showed associations between ΔIHL and ΔBW (r = 0.69; p < 0.0001), ΔIHL and Δliver volume (r = 0.66; p = 0.0002) as well as ΔBW and Δliver volume (r = 0.5; p = 0.0073). Multivariable correlation analysis revealed that changes of liver volume are primarily determined by changes in IHL independent of changes in body weight (β = 0.0272; 95 % CI: 0.0155-0.034; p < 0.0001). Changes of liver volume during lifestyle interventions are independent of changes of body weight primarily determined by changes of IHL. These results show the reversibility of augmented liver volume in steatosis if it is possible to reduce IHLs during lifestyle interventions. (orig.) [German] Lassen sich Zusammenhaenge zwischen den Aenderungen des Lebervolumens, des Anteils intrahepatischer Lipide und des Koerpergewichts waehrend einer Lebensstilintervention feststellen ?In einer prospektiven Interventionsstudie unterzogen sich 150 Probanden mit erhoehtem Diabetesrisiko fuer 6 Monate einer diaetetischen

  10. Development and Characterization of A Multiplexed RT-PCR Species Specific Assay for Bovine and one for Porcine Foot-and-Mouth Disease Virus Rule-Out

    Energy Technology Data Exchange (ETDEWEB)

    Smith, S M; Danganan, L; Tammero, L; Vitalis, B; Lenhoff, R; Naraghi-arani, P; Hindson, B

    2007-08-06

    Lawrence Livermore National Laboratory (LLNL), in collaboration with the Department of Homeland Security (DHS) and the United States Department of Agriculture (USDA), Animal and Plant Health Inspection Services (APHIS) has developed candidate multiplexed assays that may potentially be used within the National Animal Health Laboratory Network (NAHLN), the National Veterinary Services Laboratory (Ames, Iowa) and the Plum Island Animal Disease Center (PIADC). This effort has the ability to improve our nation's capability to discriminate between foreign animal diseases and those that are endemic using a single assay, thereby increasing our ability to protect food and agricultural resources with a diagnostic test which could enhance the nation's capabilities for early detection of a foreign animal disease. In FY2005 with funding from the DHS, LLNL developed the first version (Version 1.0) of a multiplexed (MUX) nucleic-acid-based RT-PCR assay that included signatures for foot-and-mouth disease virus (FMDV) detection with rule-out tests for two other foreign animal diseases (FADs) of swine, Vesicular Exanthema of Swine (VESV) and Swine Vesicular Disease Virus (SVDV), and four other domestic viral diseases Bovine Viral Diarrhea Virus (BVDV), Bovine Herpes Virus 1 (BHV-1), Bluetongue virus (BTV) and Parapox virus complex (which includes Bovine Papular Stomatitis Virus [BPSV], Orf of sheep, and Pseudocowpox). In FY06, LLNL has developed Bovine and Porcine species-specific panel which included existing signatures from Version 1.0 panel as well as new signatures. The MUX RT-PCR porcine assay for detection of FMDV includes the FADs, VESV and SVD in addition to vesicular stomatitis virus (VSV) and porcine reproductive and respiratory syndrome (PRRS). LLNL has also developed a MUX RT-PCR bovine assay for detection of FMDV with rule out tests for the two bovine FADs malignant catarrhal fever (MCF), rinderpest virus (RPV) and the domestic diseases vesicular stomatitis

  11. DNA barcoding of freshwater fishes and the development of a quantitative qPCR assay for the species-specific detection and quantification of fish larvae from plankton samples.

    Science.gov (United States)

    Loh, W K W; Bond, P; Ashton, K J; Roberts, D T; Tibbetts, I R

    2014-08-01

    The barcoding of mitochondrial cytochrome c oxidase subunit 1 (coI) gene was amplified and sequenced from 16 species of freshwater fishes found in Lake Wivenhoe (south-eastern Queensland, Australia) to support monitoring of reservoir fish populations, ecosystem function and water health. In this study, 630-650 bp sequences of the coI barcoding gene from 100 specimens representing 15 genera, 13 families and two subclasses of fishes allowed 14 of the 16 species to be identified and differentiated. The mean ± s.e. Kimura 2 parameter divergence within and between species was 0.52 ± 0.10 and 23.8 ± 2.20% respectively, indicating that barcodes can be used to discriminate most of the fish species accurately. The two terapontids, Amniataba percoides and Leiopotherapon unicolor, however, shared coI DNA sequences and could not be differentiated using this gene. A barcoding database was established and a qPCR assay was developed using coI sequences to identify and quantify proportional abundances of fish species in ichthyoplankton samples from Lake Wivenhoe. These methods provide a viable alternative to the time-consuming process of manually enumerating and identifying ichthyoplankton samples. © 2014 The Fisheries Society of the British Isles.

  12. Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae

    Directory of Open Access Journals (Sweden)

    Monika Szczecińska

    2015-09-01

    patens and Pulsatilla vernalis. Conclusions/significance: The determination of complete plastid genome and nuclear rRNA cluster sequences in three species of the genus Pulsatilla is an important contribution to our knowledge of the evolution and phylogeography of those endangered taxa. The resulting data can be used to identify regions that are particularly useful for barcoding, phylogenetic and phylogeographic studies. The investigated taxa can be identified at each stage of development based on their species-specific SNPs. The nuclear and plastid genomic resources enable advanced studies on hybridization, including identification of parent species, including their roles in that process. The identified nonsynonymous mutations could play an important role in adaptations to changing environments. The results of the study will also provide valuable information about the evolution of the plastome structure in the family Ranunculaceae.

  13. Using Inequality Measures to Incorporate Environmental Justice into Regulatory Analyses

    Science.gov (United States)

    Abstract: Formally evaluating how specific policy measures influence environmental justice is challenging, especially in the context of regulatory analyses in which quantitative comparisons are the norm. However, there is a large literature on developing and applying quantitative...

  14. Quantitative radiography

    International Nuclear Information System (INIS)

    Brase, J.M.; Martz, H.E.; Waltjen, K.E.; Hurd, R.L.; Wieting, M.G.

    1986-01-01

    Radiographic techniques have been used in nondestructive evaluation primarily to develop qualitative information (i.e., defect detection). This project applies and extends the techniques developed in medical x-ray imaging, particularly computed tomography (CT), to develop quantitative information (both spatial dimensions and material quantities) on the three-dimensional (3D) structure of solids. Accomplishments in FY 86 include (1) improvements in experimental equipment - an improved microfocus system that will give 20-μm resolution and has potential for increased imaging speed, and (2) development of a simple new technique for displaying 3D images so as to clearly show the structure of the object. Image reconstruction and data analysis for a series of synchrotron CT experiments conducted by LLNL's Chemistry Department has begun

  15. Quantitative lymphography

    International Nuclear Information System (INIS)

    Mostbeck, A.; Lofferer, O.; Kahn, P.; Partsch, H.; Koehn, H.; Bialonczyk, Ch.; Koenig, B.

    1984-01-01

    Labelled colloids and macromolecules are removed lymphatically. The uptake of tracer in the regional lymphnodes is a parameter of lymphatic flow. Due to great variations in patient shape - obesity, cachexia - and accompanying variations in counting efficiencies quantitative measurements with reasonable accuracy have not been reported to date. A new approach to regional absorption correction is based on the combination of transmission and emission scans for each patient. The transmission scan is used for calculation of an absorption correction matrix. Accurate superposition of the correction matrix and the emission scan is achieved by computing the centers of gravity of point sources and - in the case of aligning opposite views - by cross correlation of binary images. In phantom studies the recovery was high (98.3%) and the coefficient of variation of repeated measurement below 1%. In patient studies a standardized stress is a prerequisite for reliable and comparable results. Discrimination between normals (14.3 +- 4.2D%) and patients with lymphedema (2.05 +- 2.5D%) was highly significant using praefascial lymphography and sc injection. Clearence curve analysis of the activities at the injection site, however, gave no reliable data for this purpose. In normals, the uptake in lymphnodes after im injection is by one order of magnitude lower then the uptake after sc injection. The discrimination between normals and patients with postthromboic syndrome was significant. Lymphography after ic injection was in the normal range in 2/3 of the patients with lymphedema and is therefore of no diagnostic value. The difference in uptake after ic and sc injection demonstrated for the first time by our quantitative method provides new insights into the pathophysiology of lymphedema and needs further investigation. (Author)

  16. Application of multivariable analysis methods to the quantitative detection of gas by tin dioxide micro-sensors; Application des methodes d'analyse multivariables a la detection quantitative de gaz par microcapteurs a base de dioxyde d'etain

    Energy Technology Data Exchange (ETDEWEB)

    Perdreau, N.

    2000-01-17

    The electric conductivity of tin dioxide depends on the temperature of the material and on the nature and environment of the surrounding gas. This work shows that the treatment by multivariable analysis methods of electric conductance signals of one sensor allows to determine concentrations of binary or ternary mixtures of ethanol (0-80 ppm), carbon monoxide (0-300 ppm) and methane (0-1000 ppm). A part of this study has consisted of the design and the implementation of an automatic testing bench allowing to acquire the electric conductance of four sensors in thermal cycle and under gaseous cycles. It has also revealed some disturbing effects (humidity,..) of the measurement. Two techniques of sensor fabrication have been used to obtain conductances (depending of temperature) distinct for each gas, reproducible for the different sensors and enough stable with time to allow the exploitation of the signals by multivariable analysis methods (tin dioxide under the form of thin layers obtained by reactive evaporation or under the form of sintered powder bars). In a last part, it has been shown that the quantitative determination of gas by the application of chemo-metry methods is possible although the relation between the electric conductances in one part and the temperatures and concentrations in another part is non linear. Moreover, the modelling with the 'Partial Least Square' method and a pretreatment allows to obtain performance data comparable to those obtained with neural networks. (O.M.)

  17. Quantitative Thermochronology

    Science.gov (United States)

    Braun, Jean; van der Beek, Peter; Batt, Geoffrey

    2006-05-01

    Thermochronology, the study of the thermal history of rocks, enables us to quantify the nature and timing of tectonic processes. Quantitative Thermochronology is a robust review of isotopic ages, and presents a range of numerical modeling techniques to allow the physical implications of isotopic age data to be explored. The authors provide analytical, semi-analytical, and numerical solutions to the heat transfer equation in a range of tectonic settings and under varying boundary conditions. They then illustrate their modeling approach built around a large number of case studies. The benefits of different thermochronological techniques are also described. Computer programs on an accompanying website at www.cambridge.org/9780521830577 are introduced through the text and provide a means of solving the heat transport equation in the deforming Earth to predict the ages of rocks and compare them directly to geological and geochronological data. Several short tutorials, with hints and solutions, are also included. Numerous case studies help geologists to interpret age data and relate it to Earth processes Essential background material to aid understanding and using thermochronological data Provides a thorough treatise on numerical modeling of heat transport in the Earth's crust Supported by a website hosting relevant computer programs and colour slides of figures from the book for use in teaching

  18. Knowledge management for efficient quantitative analyses during regulatory reviews.

    Science.gov (United States)

    Krudys, Kevin; Li, Fang; Florian, Jeffry; Tornoe, Christoffer; Chen, Ying; Bhattaram, Atul; Jadhav, Pravin; Neal, Lauren; Wang, Yaning; Gobburu, Joga; Lee, Peter I D

    2011-11-01

    Knowledge management comprises the strategies and methods employed to generate and leverage knowledge within an organization. This report outlines the activities within the Division of Pharmacometrics at the US FDA to effectively manage knowledge with the ultimate goal of improving drug development and advancing public health. The infrastructure required for pharmacometric knowledge management includes provisions for data standards, queryable databases, libraries of modeling tools, archiving of analysis results and reporting templates for effective communication. Two examples of knowledge management systems developed within the Division of Pharmacometrics are used to illustrate these principles. The benefits of sound knowledge management include increased productivity, allowing reviewers to focus on research questions spanning new drug applications, such as improved trial design and biomarker development. The future of knowledge management depends on the collaboration between the FDA and industry to implement data and model standards to enhance sharing and dissemination of knowledge.

  19. Quantitative Analyses of the Modes of Deformation in Engineering Thermoplastics

    Science.gov (United States)

    Landes, B. G.; Bubeck, R. A.; Scott, R. L.; Heaney, M. D.

    1998-03-01

    Synchrotron-based real-time small-angle X-ray scattering (RTSAXS) studies have been performed on rubber-toughened engineering thermoplastics with amorphous and semi-crystalline matrices. Scattering patterns are measured at successive time intervals of 3 ms were analyzed to determine the plastic strain due to crazing. Simultaneous measurements of the absorption of the primary beam by the sample permits the total plastic strain to be concurrently computed. The plastic strain due to other deformation mechanisms (e.g., particle cavitation and macroscopic shear yield can be determined from the difference between the total and craze-derived plastic strains. The contribution from macroscopic shear deformation can be determined from video-based optical data measured simultaneously with the X-ray data. These types of time-resolved experiments result in the generation of prodigious quantities of data, the analysis of which can considerably delay the determination of key results. A newly developed software package that runs in WINDOWSa 95 permits the rapid analysis of the relative contributions of the deformation modes from these time-resolved experiments. Examples of using these techniques on ABS-type and QUESTRAa syndiotactic polystyrene type engineering resins will be given.

  20. Object-oriented fault tree evaluation program for quantitative analyses

    Science.gov (United States)

    Patterson-Hine, F. A.; Koen, B. V.

    1988-01-01

    Object-oriented programming can be combined with fault free techniques to give a significantly improved environment for evaluating the safety and reliability of large complex systems for space missions. Deep knowledge about system components and interactions, available from reliability studies and other sources, can be described using objects that make up a knowledge base. This knowledge base can be interrogated throughout the design process, during system testing, and during operation, and can be easily modified to reflect design changes in order to maintain a consistent information source. An object-oriented environment for reliability assessment has been developed on a Texas Instrument (TI) Explorer LISP workstation. The program, which directly evaluates system fault trees, utilizes the object-oriented extension to LISP called Flavors that is available on the Explorer. The object representation of a fault tree facilitates the storage and retrieval of information associated with each event in the tree, including tree structural information and intermediate results obtained during the tree reduction process. Reliability data associated with each basic event are stored in the fault tree objects. The object-oriented environment on the Explorer also includes a graphical tree editor which was modified to display and edit the fault trees.

  1. Differentiation of Actinobacillus pleuropneumoniae strains by sequence analysis of 16S rDNA and ribosomal intergenic regions, and development of a species specific oligonucleotide for in situ detection

    DEFF Research Database (Denmark)

    Fussing, Vivian; Paster, Bruce J.; Dewhirst, Floyd E.

    1998-01-01

    . The larger RIS's were different between the 3 species tested. The sequence of the 16S ribosomal gene was determined for 8 serotypes of A. pleuropneumoniae. These sequences showed only minor base differences, indicating a close genetic relatedness of these serotypes within the species. An oligonucleotide DNA...... probe designed from the 16S rRNA gene sequence of A. pleuropneumoniae was specific for all strains of the target species and did not cross react with A. lignieresii, the closest known relative of A. pleuropneumoniae. This species-specific DNA probe labeled with fluorescein was used for in situ......The aims of this study were to characterize and determine intraspecies and interspecies relatedness of Actinobacillus pleuropneumoniae to Actinobacillus lignieresii and Actinobacillus suis by sequence analysis of the ribosomal operon and to find a species-specific area for in situ detection of A...

  2. The quantitative Morse theorem

    OpenAIRE

    Loi, Ta Le; Phien, Phan

    2013-01-01

    In this paper, we give a proof of the quantitative Morse theorem stated by {Y. Yomdin} in \\cite{Y1}. The proof is based on the quantitative Sard theorem, the quantitative inverse function theorem and the quantitative Morse lemma.

  3. Theory and Practice in Quantitative Genetics

    DEFF Research Database (Denmark)

    Posthuma, Daniëlle; Beem, A Leo; de Geus, Eco J C

    2003-01-01

    With the rapid advances in molecular biology, the near completion of the human genome, the development of appropriate statistical genetic methods and the availability of the necessary computing power, the identification of quantitative trait loci has now become a realistic prospect for quantitative...... geneticists. We briefly describe the theoretical biometrical foundations underlying quantitative genetics. These theoretical underpinnings are translated into mathematical equations that allow the assessment of the contribution of observed (using DNA samples) and unobserved (using known genetic relationships......) genetic variation to population variance in quantitative traits. Several statistical models for quantitative genetic analyses are described, such as models for the classical twin design, multivariate and longitudinal genetic analyses, extended twin analyses, and linkage and association analyses. For each...

  4. Genomics of a Metamorphic Timing QTL: met1 Maps to a Unique Genomic Position and Regulates Morph and Species-Specific Patterns of Brain Transcription

    Science.gov (United States)

    Page, Robert B.; Boley, Meredith A.; Kump, David K.; Voss, Stephen R.

    2013-01-01

    Very little is known about genetic factors that regulate life history transitions during ontogeny. Closely related tiger salamanders (Ambystoma species complex) show extreme variation in metamorphic timing, with some species foregoing metamorphosis altogether, an adaptive trait called paedomorphosis. Previous studies identified a major effect quantitative trait locus (met1) for metamorphic timing and expression of paedomorphosis in hybrid crosses between the biphasic Eastern tiger salamander (Ambystoma tigrinum tigrinum) and the paedomorphic Mexican axolotl (Ambystoma mexicanum). We used existing hybrid mapping panels and a newly created hybrid cross to map the met1 genomic region and determine the effect of met1 on larval growth, metamorphic timing, and gene expression in the brain. We show that met1 maps to the position of a urodele-specific chromosome rearrangement on linkage group 2 that uniquely brought functionally associated genes into linkage. Furthermore, we found that more than 200 genes were differentially expressed during larval development as a function of met1 genotype. This list of differentially expressed genes is enriched for proteins that function in the mitochondria, providing evidence of a link between met1, thyroid hormone signaling, and mitochondrial energetics associated with metamorphosis. Finally, we found that met1 significantly affected metamorphic timing in hybrids, but not early larval growth rate. Collectively, our results show that met1 regulates species and morph-specific patterns of brain transcription and life history variation. PMID:23946331

  5. Chitinase mRNA Levels Determined by QPCR in Crab-Eating Monkey (Macaca fascicularis) Tissues: Species-Specific Expression of Acidic Mammalian Chitinase and Chitotriosidase.

    Science.gov (United States)

    Uehara, Maiko; Tabata, Eri; Ishii, Kazuhiro; Sawa, Akira; Ohno, Misa; Sakaguchi, Masayoshi; Matoska, Vaclav; Bauer, Peter O; Oyama, Fumitaka

    2018-05-09

    Mice and humans express two active chitinases: acidic mammalian chitinase (AMCase) and chitotriosidase (CHIT1). Both chitinases are thought to play important roles in specific pathophysiological conditions. The crab-eating monkey ( Macaca fascicularis ) is one of the most frequently used nonhuman primate models in basic and applied biomedical research. Here, we performed gene expression analysis of two chitinases in normal crab-eating monkey tissues by way of quantitative real-time polymerase chain reaction (qPCR) using a single standard DNA molecule. Levels of AMCase and CHIT1 messenger RNAs (mRNAs) were highest in the stomach and the lung, respectively, when compared to other tissues. Comparative gene expression analysis of mouse, monkey, and human using monkey⁻mouse⁻human hybrid standard DNA showed that the AMCase mRNA levels were exceptionally high in mouse and monkey stomachs while very low in the human stomach. As for the CHIT1 mRNA, we detected higher levels in the monkey lung when compared with those of mouse and human. The differences of mRNA expression between the species in the stomach tissues were basically reflecting the levels of the chitinolytic activities. These results indicate that gene expression of AMCase and CHIT1 differs between mammalian species and requiring special attention in handling data in chitinase-related studies in particular organisms.

  6. Quantitative clinical radiobiology

    International Nuclear Information System (INIS)

    Bentzen, S.M.

    1993-01-01

    Based on a series of recent papers, a status is given of our current ability to quantify the radiobiology of human tumors and normal tissues. Progress has been made in the methods of analysis. This includes the introduction of 'direct' (maximum likelihood) analysis, incorporation of latent-time in the analyses, and statistical approaches to allow for the many factors of importance in predicting tumor-control probability of normal-tissue complications. Quantitative clinical radiobiology of normal tissues is reviewed with emphasis on fractionation sensitivity, repair kinetics, regeneration, latency, and the steepness of dose-response curves. In addition, combined modality treatment, functional endpoints, and the search for a correlation between the occurrence of different endpoints in the same individual are discussed. For tumors, quantitative analyses of fractionation sensitivity, repair kinetics, reoxygenation, and regeneration are reviewed. Other factors influencing local control are: Tumor volume, histopathologic differentiation and hemoglobin concentration. Also, the steepness of the dose-response curve for tumors is discussed. Radiobiological strategies for improving radiotherapy are discussed with emphasis on non-standard fractionation and individualization of treatment schedules. (orig.)

  7. De Novo Transcriptomes of Forsythia koreana Using a Novel Assembly Method: Insight into Tissue- and Species-Specific Expression of Lignan Biosynthesis-Related Gene.

    Directory of Open Access Journals (Sweden)

    Akira Shiraishi

    Full Text Available Forsythia spp. are perennial woody plants which are one of the most extensively used medicinal sources of Chinese medicines and functional diets owing to their lignan contents. Lignans have received widespread attention as leading compounds in the development of antitumor drugs and healthy diets for reducing the risks of lifestyle-related diseases. However, the molecular basis of Forsythia has yet to be established. In this study, we have verified de novo deep transcriptome of Forsythia koreana leaf and callus using the Illumina HiSeq 1500 platform. A total of 89 million reads were assembled into 116,824 contigs using Trinity, and 1,576 of the contigs displayed the sequence similarity to the enzymes responsible for plant specialized metabolism including lignan biosynthesis. Notably, gene ontology (GO analysis indicated the remarkable enrichment of lignan-biosynthetic enzyme genes in the callus transcriptome. Nevertheless, precise annotation and molecular phylogenetic analyses were hindered by partial sequences of open reading frames (ORFs of the Trinity-based contigs. To obtain more numerous contigs harboring a full-length ORF, we developed a novel overlapping layout consensus-based procedure, virtual primer-based sequence reassembly (VP-seq. VP-seq elucidated 709 full-length ORFs, whereas only 146 full-length ORFs were assembled by Trinity. The comparison of expression profiles of leaf and callus using VP-seq-based full-length ORFs revealed 50-fold upregulation of secoisolariciresinol dehydrogenase (SIRD in callus. Expression and phylogenetic cluster analyses predicted candidates for matairesinol-glucosylating enzymes. We also performed VP-seq analysis of lignan-biosynthetic enzyme genes in the transcriptome data of other lignan-rich plants, Linum flavum, Linum usitatissimum and Podophyllum hexandrum. The comparative analysis indicated both common gene clusters involved in biosynthesis upstream of matairesinol such as SIRD and plant lineage

  8. Cytological and molecular relationships between Larix decidua, L. leptolepis and Larix x eurolepis: identification of species-specific Chromosoms and synchronization of mitotic cells.

    Science.gov (United States)

    Nkongolo, K K; Klimaszewska, K

    1995-05-01

    The effects of different concentrations of hydroxyurea (HU) and aphidicolin (APH) on the mitotic index (MI) were compared in cells of embryogenic cultures of Larix decidua, L. leptolepis, and L. decidua x L. leptolepis (Larix x eurolepis). The highest enhancement of the MI was obtained with HU at 1.25 mM and 0.6% colchicine. In general the MI decreased with an increase of HU or APH concentration (over 1.25 mM for HU and 5 μM for APH). Detailed karyotype analyses were made on the somatic complement of L. decidua, L. leptolepis, and their hybrid. These karyotypes were asymmetrical and advanced, with the smaller chromosomes being more submedian than the larger ones. The topography of chromosome 7 of L. decidua and chromosome 9 of L. leptolepis was found to be the most significant cytotaxonomic characteristic in differentiating these two species. Cytological data indicate that Japanese larch (L. leptolepis) is phylogenetically closer to European larch (L. decidua) than the Siberian larch group (L. sibirica and L. sukaczewii). Chromosomes with unusually long kinetochores were found in both species and the hybrid. Hyperploid cells (2n = 25) were observed in the hybrid (Larix x eurolepis) material analyzed. A genomic L. decidua probe hybridized strongly to dots of DNA from L. leptolepis indicating that there is high sequence homology between these two species.

  9. Assessment of species-specific and temporal variations of major, trace and rare earth elements in vineyard ambient using moss bags.

    Science.gov (United States)

    Milićević, Tijana; Aničić Urošević, Mira; Vuković, Gordana; Škrivanj, Sandra; Relić, Dubravka; Frontasyeva, Marina V; Popović, Aleksandar

    2017-10-01

    Since the methodological parameters of moss bag biomonitoring have rarely been investigated for the application in agricultural areas, two mosses, Sphagnum girgensohnii (a species of the most recommended biomonitoring genus) and Hypnum cupressiforme (commonly available), were verified in a vineyard ambient. The moss bags were exposed along transects in six vineyard parcels during the grapevine season (March‒September 2015). To select an appropriate period for the reliable 'signal' of the element enrichment in the mosses, the bags were simultaneously exposed during five periods (3 × 2 months, 1 × 4 months, and 1 × 6 months). Assuming that vineyard is susceptible to contamination originated from different agricultural treatments, a wide range of elements (41) were determined in the moss and topsoil samples. The mosses were significantly enriched by the elements during the 2-month bag exposure which gradually increasing up to 6 months, but Cu and Ni exhibited the noticeable fluctuations during the grapevine season. However, the 6-month exposure of moss bags could be recommended for comparative studies among different vineyards because it reflects the ambient pollution comprising unpredictable treatments of grapevine applied during the whole season. Although higher element concentrations were determined in S. girgensohnii than H. cupressiforme, both species reflected the spatio-temporal changes in the ambient element content. Moreover, the significant correlation of the element (Cr, Cu, Sb, and Ti) concentrations between the mosses, and the same pairs of the elements correlated within the species, imply the comparable use of S. girgensohnii and H. cupressiforme in the vineyard (agricultural) ambient. Finally, both the moss bags and the soil analyses suggest that vineyard represents a dominant diffuse pollution source of As, Cr, Cu, Ni, Fe, and V. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Salmonella Typhimurium-specific bacteriophage ΦSH19 and the origins of species specificity in the Vi01-like phage family

    Directory of Open Access Journals (Sweden)

    Wilson Ray

    2011-11-01

    Full Text Available Abstract Background Whole genome sequencing of bacteriophages suitable for biocontrol of pathogens in food products is a pre-requisite to any phage-based intervention procedure. Trials involving the biosanitization of Salmonella Typhimurium in the pig production environment identified one such candidate, ΦSH19. Results This phage was sequenced and analysis of its 157,785 bp circular dsDNA genome revealed a number of interesting features. ΦSH19 constitutes another member of the recently-proposed Myoviridae Vi01-like family of phages, containing S. Typhi-specific Vi01 and Shigella-specific SboM-AG3. At the nucleotide level ΦSH19 is highly similar to phage Vi01 (80-98% pairwise identity over the length of the genome, with the major differences lying in the region associated with host-range determination. Analyses of the proteins encoded within this region by ΦSH19 revealed a cluster of three putative tail spikes. Of the three tail spikes, two have protein domains associated with the pectate lyase family of proteins (Tsp2 and P22 tail spike family (Tsp3 with the prospect that these enable Salmonella O antigen degradation. Tail spike proteins of Vi01 and SboM-AG3 are predicted to contain conserved right-handed parallel β-helical structures but the internal protein domains are varied allowing different host specificities. Conclusions The addition or exchange of tail spike protein modules is a major contributor to host range determination in the Vi01-like phage family.

  11. Whole-transcriptome analysis of verocytotoxigenic Escherichia coli O157:H7 (Sakai suggests plant-species-specific metabolic responses on exposure to spinach and lettuce extracts.

    Directory of Open Access Journals (Sweden)

    Louise Crozier

    2016-07-01

    Full Text Available Verocytotoxigenic Escherichia coli (VTEC can contaminate crop plants, potentially using them as secondary hosts, which can lead to food-borne infection. Currently, little is known about the influence of the specific plant species on the success of bacterial colonisation. As such, we compared the ability of the VTEC strain, E. coli O157:H7 ‘Sakai’, to colonise the roots and leaves of four leafy vegetables: spinach (Spinacia oleracea, lettuce (Lactuca sativa, vining green pea (Pisum sativum and prickly lettuce (L. serriola, a wild relative of domesticated lettuce. Also, to determine the drivers of the initial response on interaction with plant tissue, the whole transcriptome of E. coli O157:H7 Sakai was analysed following exposure to plant extracts of varying complexity (spinach leaf lysates or root exudates, and leaf cell wall polysaccharides from spinach or lettuce. Plant extracts were used to reduce heterogeneity inherent in plant-microbe interactions and remove the effect of plant immunity. This dual approach provided information on the initial adaptive response of E. coli O157:H7 Sakai to the plant environment together with the influence of the living plant during bacterial establishment and colonisation. Results showed that both the plant tissue type and the plant species strongly influence the short-term (1 hour transcriptional response to extracts as well as longer-term (10 days plant colonisation or persistence. We show that propagation temperature (37 versus 18 oC has a major impact on the expression profile and therefore pre-adaptation of bacteria to a plant-relevant temperature is necessary to avoid misleading temperature-dependent wholescale gene-expression changes in response to plant material. For each of the plant extracts tested, the largest group of (annotated differentially regulated genes were associated with metabolism. However, large-scale differences in the metabolic and biosynthetic pathways between treatment types

  12. Identification of amino acid residues in the ligand-binding domain of the aryl hydrocarbon receptor causing the species-specific response to omeprazole: possible determinants for binding putative endogenous ligands.

    Science.gov (United States)

    Shiizaki, Kazuhiro; Ohsako, Seiichiroh; Kawanishi, Masanobu; Yagi, Takashi

    2014-02-01

    Omeprazole (OME) induces the expression of genes encoding drug-metabolizing enzymes, such as CYP1A1, via activation of the aryl hydrocarbon receptor (AhR) both in vivo and in vitro. However, the precise mechanism of OME-mediated AhR activation is still under investigation. While elucidating species-specific susceptibility to dioxin, we found that OME-mediated AhR activation was mammalian species specific. Moreover, we previously reported that OME has inhibitory activity toward CYP1A1 enzymes. From these observations, we speculated that OME-mediated AhR target gene transcription is due to AhR activation by increasing amounts of putative AhR ligands in serum by inhibition of CYP1A1 activity. We compared the amino acid sequences of OME-sensitive rabbit AhR and nonsensitive mouse AhR to identify the residues responsible for the species-specific response. Chimeric AhRs were constructed by exchanging domains between mouse and rabbit AhRs to define the region required for the response to OME. OME-mediated transactivation was observed only with the chimeric AhR that included the ligand-binding domain (LBD) of the rabbit AhR. Site-directed mutagenesis revealed three amino acids (M328, T353, and F367) in the rabbit AhR that were responsible for OME-mediated transactivation. Replacing these residues with those of the mouse AhR abolished the response of the rabbit AhR. In contrast, substitutions of these amino acids with those of the rabbit AhR altered nonsensitive mouse AhR to become sensitive to OME. These results suggest that OME-mediated AhR activation requires a specific structure within LBD that is probably essential for binding with enigmatic endogenous ligands.

  13. Quantitative nature of overexpression experiments

    Science.gov (United States)

    Moriya, Hisao

    2015-01-01

    Overexpression experiments are sometimes considered as qualitative experiments designed to identify novel proteins and study their function. However, in order to draw conclusions regarding protein overexpression through association analyses using large-scale biological data sets, we need to recognize the quantitative nature of overexpression experiments. Here I discuss the quantitative features of two different types of overexpression experiment: absolute and relative. I also introduce the four primary mechanisms involved in growth defects caused by protein overexpression: resource overload, stoichiometric imbalance, promiscuous interactions, and pathway modulation associated with the degree of overexpression. PMID:26543202

  14. Automatic quantitative metallography

    International Nuclear Information System (INIS)

    Barcelos, E.J.B.V.; Ambrozio Filho, F.; Cunha, R.C.

    1976-01-01

    The quantitative determination of metallographic parameters is analysed through the description of Micro-Videomat automatic image analysis system and volumetric percentage of perlite in nodular cast irons, porosity and average grain size in high-density sintered pellets of UO 2 , and grain size of ferritic steel. Techniques adopted are described and results obtained are compared with the corresponding ones by the direct counting process: counting of systematic points (grid) to measure volume and intersections method, by utilizing a circunference of known radius for the average grain size. The adopted technique for nodular cast iron resulted from the small difference of optical reflectivity of graphite and perlite. Porosity evaluation of sintered UO 2 pellets is also analyzed [pt

  15. Digital image analyser for autoradiography

    International Nuclear Information System (INIS)

    Muth, R.A.; Plotnick, J.

    1985-01-01

    The most critical parameter in quantitative autoradiography for assay of tissue concentrations of tracers is the ability to obtain precise and accurate measurements of optical density of the images. Existing high precision systems for image analysis, rotating drum densitometers, are expensive, suffer from mechanical problems and are slow. More moderately priced and reliable video camera based systems are available, but their outputs generally do not have the uniformity and stability necessary for high resolution quantitative autoradiography. The authors have designed and constructed an image analyser optimized for quantitative single and multiple tracer autoradiography which the authors refer to as a memory-mapped charged-coupled device scanner (MM-CCD). The input is from a linear array of CCD's which is used to optically scan the autoradiograph. Images are digitized into 512 x 512 picture elements with 256 gray levels and the data is stored in buffer video memory in less than two seconds. Images can then be transferred to RAM memory by direct memory-mapping for further processing. Arterial blood curve data and optical density-calibrated standards data can be entered and the optical density images can be converted automatically to tracer concentration or functional images. In double tracer studies, images produced from both exposures can be stored and processed in RAM to yield ''pure'' individual tracer concentration or functional images. Any processed image can be transmitted back to the buffer memory to be viewed on a monitor and processed for region of interest analysis

  16. Cloning and expression of porcine Colony Stimulating Factor-1 (CSF-1) and Colony Stimulating Factor-1 Receptor (CSF-1R) and analysis of the species specificity of stimulation by CSF-1 and Interleukin 34

    Science.gov (United States)

    Gow, Deborah J.; Garceau, Valerie; Kapetanovic, Ronan; Sester, David P.; Fici, Greg J.; Shelly, John A.; Wilson, Thomas L.; Hume, David A.

    2012-01-01

    Macrophage Colony Stimulating Factor (CSF-1) controls the survival, differentiation and proliferation of cells of the mononuclear phagocyte system. A second ligand for the CSF-1R, Interleukin 34 (IL-34), has been described, but its physiological role is not yet known. The domestic pig provides an alternative to traditional rodent models for evaluating potential therapeutic applications of CSF-1R agonists and antagonists. To enable such studies, we cloned and expressed active pig CSF-1. To provide a bioassay, pig CSF-1R was expressed in the factor-dependent Ba/F3 cell line. On this transfected cell line, recombinant porcine CSF-1 and human CSF-1 had identical activity. Mouse CSF-1 does not interact with the human CSF-1 receptor but was active on pig. By contrast, porcine CSF-1 was active on mouse, human, cat and dog cells. IL-34 was previously shown to be species-specific, with mouse and human proteins demonstrating limited cross-species activity. The pig CSF-1R was equally responsive to both mouse and human IL-34. Based upon the published crystal structures of CSF-1/CSF-1R and IL34/CSF-1R complexes, we discuss the molecular basis for the species specificity. PMID:22974529

  17. A New Diagnostic system for Ultra Sensitive and Specific Detection and Quantitation of “Candidatus Liberibacter asiaticus”, the Bacterium Associated with Citrus Huanglongbing

    Science.gov (United States)

    In this study, an ultra sensitive and quantitative diagnostic system for “Candidatus Liberibacter asiaticus” was developed. This system adapts a nested PCR and Taq-Man PCR in a single closed tube. The procedure involves two steps of PCR using the species specific outer and inner primer pairs. Differ...

  18. Species-specific challenges in dog cloning.

    Science.gov (United States)

    Kim, G A; Oh, H J; Park, J E; Kim, M J; Park, E J; Jo, Y K; Jang, G; Kim, M K; Kim, H J; Lee, B C

    2012-12-01

    Somatic cell nuclear transfer (SCNT) is now an established procedure used in cloning of several species. SCNT in dogs involves multiple steps including the removal of the nuclear material, injection of a donor cell, fusion, activation of the reconstructed oocytes and finally transfer to a synchronized female recipient. There are therefore many factors that contribute to cloning efficiency. By performing a retrospective analysis of 2005-2012 published papers regarding dog cloning, we define the optimum procedure and summarize the specific feature for dog cloning. © 2012 Blackwell Verlag GmbH.

  19. Analysing User Lifetime in Voluntary Online Collaboration

    DEFF Research Database (Denmark)

    McHugh, Ronan; Larsen, Birger

    2010-01-01

    This paper analyses persuasion in online collaboration projects. It introduces a set of heuristics that can be applied to such projects and combines these with a quantitative analysis of user activity over time. Two example sites are studies, Open Street Map and The Pirate Bay. Results show that ...

  20. NOAA's National Snow Analyses

    Science.gov (United States)

    Carroll, T. R.; Cline, D. W.; Olheiser, C. M.; Rost, A. A.; Nilsson, A. O.; Fall, G. M.; Li, L.; Bovitz, C. T.

    2005-12-01

    NOAA's National Operational Hydrologic Remote Sensing Center (NOHRSC) routinely ingests all of the electronically available, real-time, ground-based, snow data; airborne snow water equivalent data; satellite areal extent of snow cover information; and numerical weather prediction (NWP) model forcings for the coterminous U.S. The NWP model forcings are physically downscaled from their native 13 km2 spatial resolution to a 1 km2 resolution for the CONUS. The downscaled NWP forcings drive an energy-and-mass-balance snow accumulation and ablation model at a 1 km2 spatial resolution and at a 1 hour temporal resolution for the country. The ground-based, airborne, and satellite snow observations are assimilated into the snow model's simulated state variables using a Newtonian nudging technique. The principle advantages of the assimilation technique are: (1) approximate balance is maintained in the snow model, (2) physical processes are easily accommodated in the model, and (3) asynoptic data are incorporated at the appropriate times. The snow model is reinitialized with the assimilated snow observations to generate a variety of snow products that combine to form NOAA's NOHRSC National Snow Analyses (NSA). The NOHRSC NSA incorporate all of the available information necessary and available to produce a "best estimate" of real-time snow cover conditions at 1 km2 spatial resolution and 1 hour temporal resolution for the country. The NOHRSC NSA consist of a variety of daily, operational, products that characterize real-time snowpack conditions including: snow water equivalent, snow depth, surface and internal snowpack temperatures, surface and blowing snow sublimation, and snowmelt for the CONUS. The products are generated and distributed in a variety of formats including: interactive maps, time-series, alphanumeric products (e.g., mean areal snow water equivalent on a hydrologic basin-by-basin basis), text and map discussions, map animations, and quantitative gridded products

  1. Risico-analyse brandstofpontons

    NARCIS (Netherlands)

    Uijt de Haag P; Post J; LSO

    2001-01-01

    A generic, quantitative risk assessment was carried out according to the standard method in the 'Purple Book' to determine the risks posed by pontoons used for supplying fuel to watercraft. The pontoon is assumed to be situated in a yacht basin accessible only to pleasure boats, and the tank lorry

  2. Quantitative investment analysis

    CERN Document Server

    DeFusco, Richard

    2007-01-01

    In the "Second Edition" of "Quantitative Investment Analysis," financial experts Richard DeFusco, Dennis McLeavey, Jerald Pinto, and David Runkle outline the tools and techniques needed to understand and apply quantitative methods to today's investment process.

  3. Rigour in quantitative research.

    Science.gov (United States)

    Claydon, Leica Sarah

    2015-07-22

    This article which forms part of the research series addresses scientific rigour in quantitative research. It explores the basis and use of quantitative research and the nature of scientific rigour. It examines how the reader may determine whether quantitative research results are accurate, the questions that should be asked to determine accuracy and the checklists that may be used in this process. Quantitative research has advantages in nursing, since it can provide numerical data to help answer questions encountered in everyday practice.

  4. Quantitation: clinical applications

    International Nuclear Information System (INIS)

    Britton, K.E.

    1982-01-01

    Single photon emission tomography may be used quantitatively if its limitations are recognized and quantitation is made in relation to some reference area on the image. Relative quantitation is discussed in outline in relation to the liver, brain and pituitary, thyroid, adrenals, and heart. (U.K.)

  5. Quantitative approaches in climate change ecology

    DEFF Research Database (Denmark)

    Brown, Christopher J.; Schoeman, David S.; Sydeman, William J.

    2011-01-01

    Contemporary impacts of anthropogenic climate change on ecosystems are increasingly being recognized. Documenting the extent of these impacts requires quantitative tools for analyses of ecological observations to distinguish climate impacts in noisy data and to understand interactions between...... climate variability and other drivers of change. To assist the development of reliable statistical approaches, we review the marine climate change literature and provide suggestions for quantitative approaches in climate change ecology. We compiled 267 peer‐reviewed articles that examined relationships...

  6. Myxoma Virus dsRNA Binding Protein M029  Inhibits the Type I IFN-Induced Antiviral State in a  Highly Species-Specific Fashion.

    Science.gov (United States)

    Rahman, Masmudur M; McFadden, Grant

    2017-02-02

    Myxoma virus (MYXV) is Leporipoxvirus that possesses a specific rabbit-restricted host tropism but exhibits a much broader  cellular host range in cultured cells. MYXV is able to efficiently  block all aspects of the type I interferon (IFN)-induced  antiviral  state  in rabbit cells, partially in  human  cells  and  very  poorly  in  mouse  cells.  The mechanism(s) of this species-specific inhibition of  type I IFN-induced antiviral state is not well understood. Here we demonstrate that MYXV encoded  protein  M029, a truncated relative of the vaccinia virus (VACV) E3 double-stranded RNA (dsRNA)  binding  protein  that  inhibits  protein  kinase  R (PKR),  can  also  antagonize the type I IFN-induced  antiviral state in a highly species-specific manner. In cells pre-treated with type I IFN prior to  infection,  MYXV  exploits  M029  to  overcome  the  induced  antiviral  state completely in rabbit cells,  partially  in  human  cells,  but  not at all in mouse cells. However, in cells pre-infected with MYXV,  IFN-induced  signaling  is fully  inhibited  even  in the  absence  of M029 in cells from all three species,  suggesting  that  other  MYXV  protein(s)  apart  from  M029  block  IFN  signaling  in  a  speciesindependent  manner.  We  also  show  that  the  antiviral  state  induced in rabbit, human or mouse cells  by  type  I IFN  can  inhibit M029-knockout MYXV even when PKR is genetically knocked-out, suggesting  that  M029  targets  other  host  proteins  for  this  antiviral state inhibition. Thus, the MYXV  dsRNA  binding  protein  M029  not  only  antagonizes  PKR  from  multiple  species  but  also blocks the  type I IFN antiviral state independently of PKR in a highly species-specific fashion.

  7. Analyse of Maintenance Cost in ST

    CERN Document Server

    Jenssen, B W

    2001-01-01

    An analyse has been carried out in ST concerning the total costs for the division. Even though the target was the maintenance costs in ST, the global budget over has been analysed. This has been done since there is close relation between investments & consolidation and the required level for maintenance. The purpose of the analyse was to focus on maintenance cost in ST as a ratio of total maintenance costs over the replacement value of the equipment, and to make some comparisons with other industries and laboratories. Families of equipment have been defined and their corresponding ratios calculated. This first approach gives us some "quantitative" measurements. This analyse should be combined with performance indicators (more "qualitative" measurements) that are telling us how well we are performing. This will help us in defending our budget, make better priorities, and we will satisfy the requirements from our external auditors.

  8. Contesting Citizenship: Comparative Analyses

    DEFF Research Database (Denmark)

    Siim, Birte; Squires, Judith

    2007-01-01

    importance of particularized experiences and multiple ineequality agendas). These developments shape the way citizenship is both practiced and analysed. Mapping neat citizenship modles onto distinct nation-states and evaluating these in relation to formal equality is no longer an adequate approach....... Comparative citizenship analyses need to be considered in relation to multipleinequalities and their intersections and to multiple governance and trans-national organisinf. This, in turn, suggests that comparative citizenship analysis needs to consider new spaces in which struggles for equal citizenship occur...

  9. Determination of artifactual formation of monomethylmercury (CH{sub 3}Hg{sup +}) in environmental samples using stable Hg{sup 2+} isotopes with ICP-MS detection: Calculation of contents applying species specific isotope addition

    Energy Technology Data Exchange (ETDEWEB)

    Hintelmann, H. [Trent University, Environmental Science Centre, Peterborough ON K9J 7B8 (Canada); Falter, R. [Bayreuth Institute for Terrestrial Ecosystem Research (BITOEK), Central Analytics, POB 101251, University of Bayreuth, D-95440 Bayreuth (Germany); Ilgen, G. [Bayreuth Institute for Terrestrial Ecosystem Research (BITOEK), Central Analytics, POB 101251, University of Bayreuth, D-95440 Bayreuth (Germany); Evans, R.D. [Trent University, Environmental Science Centre, Peterborough ON K9J 7B8 (Canada)

    1997-06-01

    Various extraction techniques, as distillation, acid and alkaline extraction, have been tested with regard to their potential to form a monomethylmercury (CH{sub 3}Hg{sup +}) artifact from inorganic Hg during sample preparation. Hg{sup 2+} has been added to different reference materials in the form of enriched stable tracers and the formation of new methylmercury from that tracer has been analyzed by HPLC/ICP-MS and GC/ICP-MS. Both techniques gave comparable results. In particular, the distillation technique was prone to artifact formation. The resulting overestimation of methylmercury in sediments was as high as 80%. Artifact formation in hair, liver and algae samples was less significant, though still observable. Fish muscle tissue showed no artifact formation upon distillation, but some of the inorganic tracer was converted to methylmercury during alkaline extraction. Acid extraction of sediments resulted in low artifact formation rates. Fractionated measurements of sediment distillates revealed high methylmercury formation rates towards the end of the distillation process when acid concentrations in the solution are highest. A technique for correction of the measured apparent methylmercury content applying species specific isotope addition (SSIA) is proposed and the calculation scheme is presented. (orig.). With 6 figs., 3 tabs.

  10. Rapid identification of 11 human intestinal Lactobacillus species by multiplex PCR assays using group- and species-specific primers derived from the 16S-23S rRNA intergenic spacer region and its flanking 23S rRNA.

    Science.gov (United States)

    Song, Y; Kato, N; Liu, C; Matsumiya, Y; Kato, H; Watanabe, K

    2000-06-15

    Rapid and reliable two-step multiplex polymerase chain reaction (PCR) assays were established to identify human intestinal lactobacilli; a multiplex PCR was used for grouping of lactobacilli with a mixture of group-specific primers followed by four multiplex PCR assays with four sorts of species-specific primer mixtures for identification at the species level. Primers used were designed from nucleotide sequences of the 16S-23S rRNA intergenic spacer region and its flanking 23S rRNA gene of members of the genus Lactobacillus which are commonly isolated from human stool specimens: Lactobacillus acidophilus, Lactobacillus crispatus, Lactobacillus delbrueckii (ssp. bulgaricus and ssp. lactis), Lactobacillus fermentum, Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus paracasei (ssp. paracasei and ssp. tolerans), Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus and Lactobacillus salivarius (ssp. salicinius and ssp. salivarius). The established two-step multiplex PCR assays were applied to the identification of 84 Lactobacillus strains isolated from human stool specimens and the PCR results were consistent with the results from the DNA-DNA hybridization assay. These results suggest that the multiplex PCR system established in this study is a simple, rapid and reliable method for the identification of common Lactobacillus isolates from human stool samples.

  11. Quantitative analysis chemistry

    International Nuclear Information System (INIS)

    Ko, Wansuk; Lee, Choongyoung; Jun, Kwangsik; Hwang, Taeksung

    1995-02-01

    This book is about quantitative analysis chemistry. It is divided into ten chapters, which deal with the basic conception of material with the meaning of analysis chemistry and SI units, chemical equilibrium, basic preparation for quantitative analysis, introduction of volumetric analysis, acid-base titration of outline and experiment examples, chelate titration, oxidation-reduction titration with introduction, titration curve, and diazotization titration, precipitation titration, electrometric titration and quantitative analysis.

  12. Quantitative Algebraic Reasoning

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Panangaden, Prakash; Plotkin, Gordon

    2016-01-01

    We develop a quantitative analogue of equational reasoning which we call quantitative algebra. We define an equality relation indexed by rationals: a =ε b which we think of as saying that “a is approximately equal to b up to an error of ε”. We have 4 interesting examples where we have a quantitative...... equational theory whose free algebras correspond to well known structures. In each case we have finitary and continuous versions. The four cases are: Hausdorff metrics from quantitive semilattices; pWasserstein metrics (hence also the Kantorovich metric) from barycentric algebras and also from pointed...

  13. Quantitative autoradiography of neurochemicals

    International Nuclear Information System (INIS)

    Rainbow, T.C.; Biegon, A.; Bleisch, W.V.

    1982-01-01

    Several new methods have been developed that apply quantitative autoradiography to neurochemistry. These methods are derived from the 2-deoxyglucose (2DG) technique of Sokoloff (1), which uses quantitative autoradiography to measure the rate of glucose utilization in brain structures. The new methods allow the measurement of the rate of cerbral protein synthesis and the levels of particular neurotransmitter receptors by quantitative autoradiography. As with the 2DG method, the new techniques can measure molecular levels in micron-sized brain structures; and can be used in conjunction with computerized systems of image processing. It is possible that many neurochemical measurements could be made by computerized analysis of quantitative autoradiograms

  14. Risico-analyse brandstofpontons

    NARCIS (Netherlands)

    Uijt de Haag P; Post J; LSO

    2001-01-01

    Voor het bepalen van de risico's van brandstofpontons in een jachthaven is een generieke risico-analyse uitgevoerd. Er is een referentiesysteem gedefinieerd, bestaande uit een betonnen brandstofponton met een relatief grote inhoud en doorzet. Aangenomen is dat de ponton gelegen is in een

  15. Fast multichannel analyser

    Energy Technology Data Exchange (ETDEWEB)

    Berry, A; Przybylski, M M; Sumner, I [Science Research Council, Daresbury (UK). Daresbury Lab.

    1982-10-01

    A fast multichannel analyser (MCA) capable of sampling at a rate of 10/sup 7/ s/sup -1/ has been developed. The instrument is based on an 8 bit parallel encoding analogue to digital converter (ADC) reading into a fast histogramming random access memory (RAM) system, giving 256 channels of 64 k count capacity. The prototype unit is in CAMAC format.

  16. A fast multichannel analyser

    International Nuclear Information System (INIS)

    Berry, A.; Przybylski, M.M.; Sumner, I.

    1982-01-01

    A fast multichannel analyser (MCA) capable of sampling at a rate of 10 7 s -1 has been developed. The instrument is based on an 8 bit parallel encoding analogue to digital converter (ADC) reading into a fast histogramming random access memory (RAM) system, giving 256 channels of 64 k count capacity. The prototype unit is in CAMAC format. (orig.)

  17. Possible future HERA analyses

    International Nuclear Information System (INIS)

    Geiser, Achim

    2015-12-01

    A variety of possible future analyses of HERA data in the context of the HERA data preservation programme is collected, motivated, and commented. The focus is placed on possible future analyses of the existing ep collider data and their physics scope. Comparisons to the original scope of the HERA pro- gramme are made, and cross references to topics also covered by other participants of the workshop are given. This includes topics on QCD, proton structure, diffraction, jets, hadronic final states, heavy flavours, electroweak physics, and the application of related theory and phenomenology topics like NNLO QCD calculations, low-x related models, nonperturbative QCD aspects, and electroweak radiative corrections. Synergies with other collider programmes are also addressed. In summary, the range of physics topics which can still be uniquely covered using the existing data is very broad and of considerable physics interest, often matching the interest of results from colliders currently in operation. Due to well-established data and MC sets, calibrations, and analysis procedures the manpower and expertise needed for a particular analysis is often very much smaller than that needed for an ongoing experiment. Since centrally funded manpower to carry out such analyses is not available any longer, this contribution not only targets experienced self-funded experimentalists, but also theorists and master-level students who might wish to carry out such an analysis.

  18. Biomass feedstock analyses

    Energy Technology Data Exchange (ETDEWEB)

    Wilen, C.; Moilanen, A.; Kurkela, E. [VTT Energy, Espoo (Finland). Energy Production Technologies

    1996-12-31

    The overall objectives of the project `Feasibility of electricity production from biomass by pressurized gasification systems` within the EC Research Programme JOULE II were to evaluate the potential of advanced power production systems based on biomass gasification and to study the technical and economic feasibility of these new processes with different type of biomass feed stocks. This report was prepared as part of this R and D project. The objectives of this task were to perform fuel analyses of potential woody and herbaceous biomasses with specific regard to the gasification properties of the selected feed stocks. The analyses of 15 Scandinavian and European biomass feed stock included density, proximate and ultimate analyses, trace compounds, ash composition and fusion behaviour in oxidizing and reducing atmospheres. The wood-derived fuels, such as whole-tree chips, forest residues, bark and to some extent willow, can be expected to have good gasification properties. Difficulties caused by ash fusion and sintering in straw combustion and gasification are generally known. The ash and alkali metal contents of the European biomasses harvested in Italy resembled those of the Nordic straws, and it is expected that they behave to a great extent as straw in gasification. Any direct relation between the ash fusion behavior (determined according to the standard method) and, for instance, the alkali metal content was not found in the laboratory determinations. A more profound characterisation of the fuels would require gasification experiments in a thermobalance and a PDU (Process development Unit) rig. (orig.) (10 refs.)

  19. In-vivo quantitative measurement

    International Nuclear Information System (INIS)

    Ito, Takashi

    1992-01-01

    So far by positron CT, the quantitative analyses of oxygen consumption rate, blood flow distribution, glucose metabolic rate and so on have been carried out. The largest merit of using the positron CT is the observation and verification of mankind have become easy. Recently, accompanying the rapid development of the mapping tracers for central nervous receptors, the observation of many central nervous receptors by the positron CT has become feasible, and must expectation has been placed on the elucidation of brain functions. The conditions required for in vitro processes cannot be realized in strict sense in vivo. The quantitative measurement of in vivo tracer method is carried out by measuring the accumulation and movement of a tracer after its administration. The movement model of the mapping tracer for central nervous receptors is discussed. The quantitative analysis using a steady movement model, the measurement of dopamine receptors by reference method, the measurement of D 2 receptors using 11C-Racloprode by direct method, and the possibility of measuring dynamics bio-reaction are reported. (K.I.)

  20. IDENTIFIKASI DAGING BABI MENGGUNAKAN METODE PCR-RFLP GEN Cytochrome b DAN PCR PRIMER SPESIFIK GEN AMELOGENIN (Pork Identification Using PCR-RFLP of Cytochrome b Gene and Species Specific PCR of Amelogenin Gene

    Directory of Open Access Journals (Sweden)

    Yuny Erwanto

    2013-03-01

    Full Text Available A polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP and species specific PCR methods had been applied for identifying pork in mixture of meat. Pork sample in various levels (1, 3, 5 and 10% was prepared in mixture with beef, chicken and mutton. The primary CYTb1 and CYTb2 were designed in the mitochondrial cytochrome b b (cytochrome b gene and PCR successfully amplified fragments of 359 bp. To distinguish pig species existence, the amplified PCR products of mitochondrial DNA were cut by BseDI restriction enzyme. The result showed that pig mitochondrial DNA was cut into 131 and 228 bp fragments. A polymerase chain reaction (PCR method based on the nucleotide sequence variation in the amelogenin gene has been chosen for the specific identification of pork DNAs in mixture meat. The primers designed generated specific fragments of 353 and 312 bp length for pork. The specificity of the primary designed was tested on 4 animal species including pig, cattle, chicken and goat species. Analysis of experimental mixture meat demonstrated that 1% of raw pork tissues could be detected using PCR-RFLP with BseDI restriction enzyme but detection using species-specific PCR showed the cross reactivity to beef, chicken and mutton. The cytochrome b PCR-RFLP species identification assay yielded excellent results for identification of pig species. PCR-RFLP is a potentially reliable technique for detection of the existence of pork in animal food product for Halal authentication. Keywords: Pork identification, cytochrome b, amelogenin, polymerase chain reaction   ABSTRAK   Penelitian ini dilakukan untuk mengaplikasikan metode deteksi daging babi dalam campuan daging dengan sapi, kambing dan ayam melalui PCR-RFLP dan PCR dengan primer spesifik untuk babi. Level kontaminasi daging babi dibuat sebesar 1, 3, 5 dan 10% dari total daging dalam campuran. Metode PCR-RFLP menggunakan sepasang primer yaitu gen cytochrome b dari mitokondria yang

  1. Unusual evolutionary conservation and further species-specific adaptations of a large family of nonclassical MHC class Ib genes across different degrees of genome ploidy in the amphibian subfamily Xenopodinae.

    Science.gov (United States)

    Edholm, Eva-Stina; Goyos, Ana; Taran, Joseph; De Jesús Andino, Francisco; Ohta, Yuko; Robert, Jacques

    2014-06-01

    Nonclassical MHC class Ib (class Ib) genes are a family of highly diverse and rapidly evolving genes wherein gene numbers, organization, and expression markedly differ even among closely related species rendering class Ib phylogeny difficult to establish. Whereas among mammals there are few unambiguous class Ib gene orthologs, different amphibian species belonging to the anuran subfamily Xenopodinae exhibit an unusually high degree of conservation among multiple class Ib gene lineages. Comparative genomic analysis of class Ib gene loci of two divergent (~65 million years) Xenopodinae subfamily members Xenopus laevis (allotetraploid) and Xenopus tropicalis (diploid) shows that both species possess a large cluster of class Ib genes denoted as Xenopus/Silurana nonclassical (XNC/SNC). Our study reveals two distinct phylogenetic patterns among these genes: some gene lineages display a high degree of flexibility, as demonstrated by species-specific expansion and contractions, whereas other class Ib gene lineages have been maintained as monogenic subfamilies with very few changes in their nucleotide sequence across divergent species. In this second category, we further investigated the XNC/SNC10 gene lineage that in X. laevis is required for the development of a distinct semi-invariant T cell population. We report compelling evidence of the remarkable high degree of conservation of this gene lineage that is present in all 12 species of the Xenopodinae examined, including species with different degrees of ploidy ranging from 2, 4, 8 to 12 N. This suggests that the critical role of XNC10 during early T cell development is conserved in amphibians.

  2. Development of a Species-Specific PCR Assay for Detection of Leishmania donovani in Clinical Samples from Patients with Kala-Azar and Post-Kala-Azar Dermal Leishmaniasis

    Science.gov (United States)

    Salotra, Poonam; Sreenivas, G.; Pogue, Gregory P.; Lee, Nancy; Nakhasi, Hira L.; Ramesh, V.; Negi, N. S.

    2001-01-01

    We have developed a PCR assay that is capable of amplifying kinetoplast DNA (kDNA) of Leishmania donovani in a species-specific manner among Old World leishmanias. With Indian strains and isolates of L. donovani the assay was sensitive enough to detect kDNA in an amount equivalent to a single parasite or less. The extreme sensitivity of the assay was reflected in its ability to detect parasite DNA from small volumes of peripheral blood of patients with kala-azar (KA) and from skin lesions from patients with post-KA dermal leishmaniasis (PKDL). A total of 107 clinical leishmaniasis samples were analyzed. Of these 102 (95.3%) were positive by PCR. The test provided a diagnosis of KA with 96% sensitivity using patient whole-blood samples instead of bone marrow or spleen aspirates that are obtained by invasive procedures. The assay was also successful in the diagnosis of 45 of 48 PKDL cases (93.8%). Cross-reactions with pathogens prevalent in the area of endemicity, viz., Mycobacterium tuberculosis, Mycobacterium leprae, and Plasmodium spp., could be ruled out. Eighty-one control samples, including dermal scrapings from healthy portions of skin from patients with PKDL were all negative. Two of twenty controls from the area of endemicity were found positive by PCR assay; however, there was a good possibility that these two were asymptomatic carriers since they were serologically positive for KA. Thus, this PCR assay represents a tool for the diagnosis of KA and PKDL in Indian patients in a noninvasive manner, with simultaneous species identification of parasites in clinical samples. PMID:11230394

  3. AMS analyses at ANSTO

    Energy Technology Data Exchange (ETDEWEB)

    Lawson, E.M. [Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia). Physics Division

    1998-03-01

    The major use of ANTARES is Accelerator Mass Spectrometry (AMS) with {sup 14}C being the most commonly analysed radioisotope - presently about 35 % of the available beam time on ANTARES is used for {sup 14}C measurements. The accelerator measurements are supported by, and dependent on, a strong sample preparation section. The ANTARES AMS facility supports a wide range of investigations into fields such as global climate change, ice cores, oceanography, dendrochronology, anthropology, and classical and Australian archaeology. Described here are some examples of the ways in which AMS has been applied to support research into the archaeology, prehistory and culture of this continent`s indigenous Aboriginal peoples. (author)

  4. AMS analyses at ANSTO

    International Nuclear Information System (INIS)

    Lawson, E.M.

    1998-01-01

    The major use of ANTARES is Accelerator Mass Spectrometry (AMS) with 14 C being the most commonly analysed radioisotope - presently about 35 % of the available beam time on ANTARES is used for 14 C measurements. The accelerator measurements are supported by, and dependent on, a strong sample preparation section. The ANTARES AMS facility supports a wide range of investigations into fields such as global climate change, ice cores, oceanography, dendrochronology, anthropology, and classical and Australian archaeology. Described here are some examples of the ways in which AMS has been applied to support research into the archaeology, prehistory and culture of this continent's indigenous Aboriginal peoples. (author)

  5. Analyses of MHD instabilities

    International Nuclear Information System (INIS)

    Takeda, Tatsuoki

    1985-01-01

    In this article analyses of the MHD stabilities which govern the global behavior of a fusion plasma are described from the viewpoint of the numerical computation. First, we describe the high accuracy calculation of the MHD equilibrium and then the analysis of the linear MHD instability. The former is the basis of the stability analysis and the latter is closely related to the limiting beta value which is a very important theoretical issue of the tokamak research. To attain a stable tokamak plasma with good confinement property it is necessary to control or suppress disruptive instabilities. We, next, describe the nonlinear MHD instabilities which relate with the disruption phenomena. Lastly, we describe vectorization of the MHD codes. The above MHD codes for fusion plasma analyses are relatively simple though very time-consuming and parts of the codes which need a lot of CPU time concentrate on a small portion of the codes, moreover, the codes are usually used by the developers of the codes themselves, which make it comparatively easy to attain a high performance ratio on the vector processor. (author)

  6. Uncertainty Analyses and Strategy

    International Nuclear Information System (INIS)

    Kevin Coppersmith

    2001-01-01

    The DOE identified a variety of uncertainties, arising from different sources, during its assessment of the performance of a potential geologic repository at the Yucca Mountain site. In general, the number and detail of process models developed for the Yucca Mountain site, and the complex coupling among those models, make the direct incorporation of all uncertainties difficult. The DOE has addressed these issues in a number of ways using an approach to uncertainties that is focused on producing a defensible evaluation of the performance of a potential repository. The treatment of uncertainties oriented toward defensible assessments has led to analyses and models with so-called ''conservative'' assumptions and parameter bounds, where conservative implies lower performance than might be demonstrated with a more realistic representation. The varying maturity of the analyses and models, and uneven level of data availability, result in total system level analyses with a mix of realistic and conservative estimates (for both probabilistic representations and single values). That is, some inputs have realistically represented uncertainties, and others are conservatively estimated or bounded. However, this approach is consistent with the ''reasonable assurance'' approach to compliance demonstration, which was called for in the U.S. Nuclear Regulatory Commission's (NRC) proposed 10 CFR Part 63 regulation (64 FR 8640 [DIRS 101680]). A risk analysis that includes conservatism in the inputs will result in conservative risk estimates. Therefore, the approach taken for the Total System Performance Assessment for the Site Recommendation (TSPA-SR) provides a reasonable representation of processes and conservatism for purposes of site recommendation. However, mixing unknown degrees of conservatism in models and parameter representations reduces the transparency of the analysis and makes the development of coherent and consistent probability statements about projected repository

  7. Quantitative film radiography

    International Nuclear Information System (INIS)

    Devine, G.; Dobie, D.; Fugina, J.; Hernandez, J.; Logan, C.; Mohr, P.; Moss, R.; Schumacher, B.; Updike, E.; Weirup, D.

    1991-01-01

    We have developed a system of quantitative radiography in order to produce quantitative images displaying homogeneity of parts. The materials that we characterize are synthetic composites and may contain important subtle density variations not discernible by examining a raw film x-radiograph. In order to quantitatively interpret film radiographs, it is necessary to digitize, interpret, and display the images. Our integrated system of quantitative radiography displays accurate, high-resolution pseudo-color images in units of density. We characterize approximately 10,000 parts per year in hundreds of different configurations and compositions with this system. This report discusses: the method; film processor monitoring and control; verifying film and processor performance; and correction of scatter effects

  8. A simple beam analyser

    International Nuclear Information System (INIS)

    Lemarchand, G.

    1977-01-01

    (ee'p) experiments allow to measure the missing energy distribution as well as the momentum distribution of the extracted proton in the nucleus versus the missing energy. Such experiments are presently conducted on SACLAY's A.L.S. 300 Linac. Electrons and protons are respectively analysed by two spectrometers and detected in their focal planes. Counting rates are usually low and include time coincidences and accidentals. Signal-to-noise ratio is dependent on the physics of the experiment and the resolution of the coincidence, therefore it is mandatory to get a beam current distribution as flat as possible. Using new technologies has allowed to monitor in real time the behavior of the beam pulse and determine when the duty cycle can be considered as being good with respect to a numerical basis

  9. EEG analyses with SOBI.

    Energy Technology Data Exchange (ETDEWEB)

    Glickman, Matthew R.; Tang, Akaysha (University of New Mexico, Albuquerque, NM)

    2009-02-01

    The motivating vision behind Sandia's MENTOR/PAL LDRD project has been that of systems which use real-time psychophysiological data to support and enhance human performance, both individually and of groups. Relevant and significant psychophysiological data being a necessary prerequisite to such systems, this LDRD has focused on identifying and refining such signals. The project has focused in particular on EEG (electroencephalogram) data as a promising candidate signal because it (potentially) provides a broad window on brain activity with relatively low cost and logistical constraints. We report here on two analyses performed on EEG data collected in this project using the SOBI (Second Order Blind Identification) algorithm to identify two independent sources of brain activity: one in the frontal lobe and one in the occipital. The first study looks at directional influences between the two components, while the second study looks at inferring gender based upon the frontal component.

  10. Pathway-based analyses.

    Science.gov (United States)

    Kent, Jack W

    2016-02-03

    New technologies for acquisition of genomic data, while offering unprecedented opportunities for genetic discovery, also impose severe burdens of interpretation and penalties for multiple testing. The Pathway-based Analyses Group of the Genetic Analysis Workshop 19 (GAW19) sought reduction of multiple-testing burden through various approaches to aggregation of highdimensional data in pathways informed by prior biological knowledge. Experimental methods testedincluded the use of "synthetic pathways" (random sets of genes) to estimate power and false-positive error rate of methods applied to simulated data; data reduction via independent components analysis, single-nucleotide polymorphism (SNP)-SNP interaction, and use of gene sets to estimate genetic similarity; and general assessment of the efficacy of prior biological knowledge to reduce the dimensionality of complex genomic data. The work of this group explored several promising approaches to managing high-dimensional data, with the caveat that these methods are necessarily constrained by the quality of external bioinformatic annotation.

  11. Analysing Access Control Specifications

    DEFF Research Database (Denmark)

    Probst, Christian W.; Hansen, René Rydhof

    2009-01-01

    When prosecuting crimes, the main question to answer is often who had a motive and the possibility to commit the crime. When investigating cyber crimes, the question of possibility is often hard to answer, as in a networked system almost any location can be accessed from almost anywhere. The most...... common tool to answer this question, analysis of log files, faces the problem that the amount of logged data may be overwhelming. This problems gets even worse in the case of insider attacks, where the attacker’s actions usually will be logged as permissible, standard actions—if they are logged at all....... Recent events have revealed intimate knowledge of surveillance and control systems on the side of the attacker, making it often impossible to deduce the identity of an inside attacker from logged data. In this work we present an approach that analyses the access control configuration to identify the set...

  12. Network class superposition analyses.

    Directory of Open Access Journals (Sweden)

    Carl A B Pearson

    Full Text Available Networks are often used to understand a whole system by modeling the interactions among its pieces. Examples include biomolecules in a cell interacting to provide some primary function, or species in an environment forming a stable community. However, these interactions are often unknown; instead, the pieces' dynamic states are known, and network structure must be inferred. Because observed function may be explained by many different networks (e.g., ≈ 10(30 for the yeast cell cycle process, considering dynamics beyond this primary function means picking a single network or suitable sample: measuring over all networks exhibiting the primary function is computationally infeasible. We circumvent that obstacle by calculating the network class ensemble. We represent the ensemble by a stochastic matrix T, which is a transition-by-transition superposition of the system dynamics for each member of the class. We present concrete results for T derived from boolean time series dynamics on networks obeying the Strong Inhibition rule, by applying T to several traditional questions about network dynamics. We show that the distribution of the number of point attractors can be accurately estimated with T. We show how to generate Derrida plots based on T. We show that T-based Shannon entropy outperforms other methods at selecting experiments to further narrow the network structure. We also outline an experimental test of predictions based on T. We motivate all of these results in terms of a popular molecular biology boolean network model for the yeast cell cycle, but the methods and analyses we introduce are general. We conclude with open questions for T, for example, application to other models, computational considerations when scaling up to larger systems, and other potential analyses.

  13. Seismic fragility analyses

    International Nuclear Information System (INIS)

    Kostov, Marin

    2000-01-01

    In the last two decades there is increasing number of probabilistic seismic risk assessments performed. The basic ideas of the procedure for performing a Probabilistic Safety Analysis (PSA) of critical structures (NUREG/CR-2300, 1983) could be used also for normal industrial and residential buildings, dams or other structures. The general formulation of the risk assessment procedure applied in this investigation is presented in Franzini, et al., 1984. The probability of failure of a structure for an expected lifetime (for example 50 years) can be obtained from the annual frequency of failure, β E determined by the relation: β E ∫[d[β(x)]/dx]P(flx)dx. β(x) is the annual frequency of exceedance of load level x (for example, the variable x may be peak ground acceleration), P(fI x) is the conditional probability of structure failure at a given seismic load level x. The problem leads to the assessment of the seismic hazard β(x) and the fragility P(fl x). The seismic hazard curves are obtained by the probabilistic seismic hazard analysis. The fragility curves are obtained after the response of the structure is defined as probabilistic and its capacity and the associated uncertainties are assessed. Finally the fragility curves are combined with the seismic loading to estimate the frequency of failure for each critical scenario. The frequency of failure due to seismic event is presented by the scenario with the highest frequency. The tools usually applied for probabilistic safety analyses of critical structures could relatively easily be adopted to ordinary structures. The key problems are the seismic hazard definitions and the fragility analyses. The fragility could be derived either based on scaling procedures or on the base of generation. Both approaches have been presented in the paper. After the seismic risk (in terms of failure probability) is assessed there are several approaches for risk reduction. Generally the methods could be classified in two groups. The

  14. Culture-independent identification and quantification of Gallibacterium anatis (G. anatis) by real-time quantitative PCR

    DEFF Research Database (Denmark)

    Wang, Chong; Robles, Francisco; Ramirez, Saul

    2016-01-01

    Gallibacterium is a genus within the family Pasteurellaceae characterized by a high level of phenotypic and genetic diversity. No diagnostic method has yet been described, which allows species-specific identification of Gallibacterium anatis. The aim of this study was to develop a real...... published conventional PCR method and culture-based identification, respectively. The detection rates were 97%, 78% and 34% for the current qPCR, the conventional PCR and the culture-based identification method, respectively. The qPCR assay was able to detect the gene gyrB in serial dilutions of 10......-time quantitative PCR (qPCR) method allowing species-specific identification and quantification of G. anatis. A G. anatis specific DNA sequence was identified in the gyrase subunit B gene (gyrB) and used to design a TaqMan probe and corresponding primers. The specificity of the assay was tested on 52 bacterial...

  15. Website-analyse

    DEFF Research Database (Denmark)

    Thorlacius, Lisbeth

    2009-01-01

    eller blindgyder, når han/hun besøger sitet. Studier i design og analyse af de visuelle og æstetiske aspekter i planlægning og brug af websites har imidlertid kun i et begrænset omfang været under reflektorisk behandling. Det er baggrunden for dette kapitel, som indleder med en gennemgang af æstetikkens......Websitet er i stigende grad det foretrukne medie inden for informationssøgning,virksomhedspræsentation, e-handel, underholdning, undervisning og social kontakt. I takt med denne voksende mangfoldighed af kommunikationsaktiviteter på nettet, er der kommet mere fokus på at optimere design og...... planlægning af de funktionelle og indholdsmæssige aspekter ved websites. Der findes en stor mængde teori- og metodebøger, som har specialiseret sig i de tekniske problemstillinger i forbindelse med interaktion og navigation, samt det sproglige indhold på websites. Den danske HCI (Human Computer Interaction...

  16. A channel profile analyser

    International Nuclear Information System (INIS)

    Gobbur, S.G.

    1983-01-01

    It is well understood that due to the wide band noise present in a nuclear analog-to-digital converter, events at the boundaries of adjacent channels are shared. It is a difficult and laborious process to exactly find out the shape of the channels at the boundaries. A simple scheme has been developed for the direct display of channel shape of any type of ADC on a cathode ray oscilliscope display. This has been accomplished by sequentially incrementing the reference voltage of a precision pulse generator by a fraction of a channel and storing ADC data in alternative memory locations of a multichannel pulse height analyser. Alternative channels are needed due to the sharing at the boundaries of channels. In the flat region of the profile alternate memory locations are channels with zero counts and channels with the full scale counts. At the boundaries all memory locations will have counts. The shape of this is a direct display of the channel boundaries. (orig.)

  17. Quantitative risk analysis of urban flooding in lowland areas

    NARCIS (Netherlands)

    Ten Veldhuis, J.A.E.

    2010-01-01

    Urban flood risk analyses suffer from a lack of quantitative historical data on flooding incidents. Data collection takes place on an ad hoc basis and is usually restricted to severe events. The resulting data deficiency renders quantitative assessment of urban flood risks uncertain. The study

  18. Bayesian uncertainty analyses of probabilistic risk models

    International Nuclear Information System (INIS)

    Pulkkinen, U.

    1989-01-01

    Applications of Bayesian principles to the uncertainty analyses are discussed in the paper. A short review of the most important uncertainties and their causes is provided. An application of the principle of maximum entropy to the determination of Bayesian prior distributions is described. An approach based on so called probabilistic structures is presented in order to develop a method of quantitative evaluation of modelling uncertainties. The method is applied to a small example case. Ideas for application areas for the proposed method are discussed

  19. Quantitative secondary electron detection

    Science.gov (United States)

    Agrawal, Jyoti; Joy, David C.; Nayak, Subuhadarshi

    2018-05-08

    Quantitative Secondary Electron Detection (QSED) using the array of solid state devices (SSD) based electron-counters enable critical dimension metrology measurements in materials such as semiconductors, nanomaterials, and biological samples (FIG. 3). Methods and devices effect a quantitative detection of secondary electrons with the array of solid state detectors comprising a number of solid state detectors. An array senses the number of secondary electrons with a plurality of solid state detectors, counting the number of secondary electrons with a time to digital converter circuit in counter mode.

  20. [Methods of quantitative proteomics].

    Science.gov (United States)

    Kopylov, A T; Zgoda, V G

    2007-01-01

    In modern science proteomic analysis is inseparable from other fields of systemic biology. Possessing huge resources quantitative proteomics operates colossal information on molecular mechanisms of life. Advances in proteomics help researchers to solve complex problems of cell signaling, posttranslational modification, structure and functional homology of proteins, molecular diagnostics etc. More than 40 various methods have been developed in proteomics for quantitative analysis of proteins. Although each method is unique and has certain advantages and disadvantages all these use various isotope labels (tags). In this review we will consider the most popular and effective methods employing both chemical modifications of proteins and also metabolic and enzymatic methods of isotope labeling.

  1. Development and Characterization of a Multiplexed RT-PCR Species Specific Assay for Bovine and one for Porcine Foot-and-Mouth Disease Virus Rule-Out Supplemental Materials

    Energy Technology Data Exchange (ETDEWEB)

    Smith, S; Danganan, L; Tammero, L; Lenhoff, R; Naraghi-arani, P; Hindson, B

    2007-08-06

    viruses which are of two bovine types bovine papular stomatitis virus (BPSV) and psuedocowpox (PCP). This document provides details of signature generation, evaluation, and testing, as well as the specific methods and materials used. A condensed summary of the development, testing and performance of the multiplexed assay panel was presented in a 126 page separate document, entitled 'Development and Characterization of A Multiplexed RT-PCR Species Specific Assay for Bovine and one for Porcine Foot-and-Mouth Disease Virus Rule-Out'. This supplemental document provides additional details of large amount of data collected for signature generation, evaluation, and testing, as well as the specific methods and materials used for all steps in the assay development and utilization processes. In contrast to last years effort, the development of the bovine and porcine panels is pending additional work to complete analytical characterization of FMDV, VESV, VSV, SVD, RPV and MCF. The signature screening process and final panel composition impacts this effort. The unique challenge presented this year was having strict predecessor limitations in completing characterization, where efforts at LLNL must preceed efforts at PIADC, such challenges were alleviated in the 2006 reporting by having characterization data from the interlaboratory comparison and at Plum Island under AgDDAP project. We will present an addendum at a later date with additional data on the characterization of the porcine and bovine multiplex assays when that data is available.

  2. Quantitative Decision Support Requires Quantitative User Guidance

    Science.gov (United States)

    Smith, L. A.

    2009-12-01

    Is it conceivable that models run on 2007 computer hardware could provide robust and credible probabilistic information for decision support and user guidance at the ZIP code level for sub-daily meteorological events in 2060? In 2090? Retrospectively, how informative would output from today’s models have proven in 2003? or the 1930’s? Consultancies in the United Kingdom, including the Met Office, are offering services to “future-proof” their customers from climate change. How is a US or European based user or policy maker to determine the extent to which exciting new Bayesian methods are relevant here? or when a commercial supplier is vastly overselling the insights of today’s climate science? How are policy makers and academic economists to make the closely related decisions facing them? How can we communicate deep uncertainty in the future at small length-scales without undermining the firm foundation established by climate science regarding global trends? Three distinct aspects of the communication of the uses of climate model output targeting users and policy makers, as well as other specialist adaptation scientists, are discussed. First, a brief scientific evaluation of the length and time scales at which climate model output is likely to become uninformative is provided, including a note on the applicability the latest Bayesian methodology to current state-of-the-art general circulation models output. Second, a critical evaluation of the language often employed in communication of climate model output, a language which accurately states that models are “better”, have “improved” and now “include” and “simulate” relevant meteorological processed, without clearly identifying where the current information is thought to be uninformative and misleads, both for the current climate and as a function of the state of the (each) climate simulation. And thirdly, a general approach for evaluating the relevance of quantitative climate model output

  3. Exergetic and thermoeconomic analyses of power plants

    International Nuclear Information System (INIS)

    Kwak, H.-Y.; Kim, D.-J.; Jeon, J.-S.

    2003-01-01

    Exergetic and thermoeconomic analyses were performed for a 500-MW combined cycle plant. In these analyses, mass and energy conservation laws were applied to each component of the system. Quantitative balances of the exergy and exergetic cost for each component, and for the whole system was carefully considered. The exergoeconomic model, which represented the productive structure of the system considered, was used to visualize the cost formation process and the productive interaction between components. The computer program developed in this study can determine the production costs of power plants, such as gas- and steam-turbines plants and gas-turbine cogeneration plants. The program can be also be used to study plant characteristics, namely, thermodynamic performance and sensitivity to changes in process and/or component design variables

  4. Using Microsoft Office Excel 2007 to conduct generalized matching analyses.

    Science.gov (United States)

    Reed, Derek D

    2009-01-01

    The generalized matching equation is a robust and empirically supported means of analyzing relations between reinforcement and behavior. Unfortunately, no simple task analysis is available to behavior analysts interested in using the matching equation to evaluate data in clinical or applied settings. This technical article presents a task analysis for the use of Microsoft Excel to analyze and plot the generalized matching equation. Using a data-based case example and a step-by-step guide for completing the analysis, these instructions are intended to promote the use of quantitative analyses by researchers with little to no experience in quantitative analyses or the matching law.

  5. USING MICROSOFT OFFICE EXCEL® 2007 TO CONDUCT GENERALIZED MATCHING ANALYSES

    Science.gov (United States)

    Reed, Derek D

    2009-01-01

    The generalized matching equation is a robust and empirically supported means of analyzing relations between reinforcement and behavior. Unfortunately, no simple task analysis is available to behavior analysts interested in using the matching equation to evaluate data in clinical or applied settings. This technical article presents a task analysis for the use of Microsoft Excel to analyze and plot the generalized matching equation. Using a data-based case example and a step-by-step guide for completing the analysis, these instructions are intended to promote the use of quantitative analyses by researchers with little to no experience in quantitative analyses or the matching law. PMID:20514196

  6. Extending Quantitative Easing

    DEFF Research Database (Denmark)

    Hallett, Andrew Hughes; Fiedler, Salomon; Kooths, Stefan

    The notes in this compilation address the pros and cons associated with the extension of ECB quantitative easing programme of asset purchases. The notes have been requested by the Committee on Economic and Monetary Affairs as an input for the February 2017 session of the Monetary Dialogue....

  7. Quantitative Moessbauer analysis

    International Nuclear Information System (INIS)

    Collins, R.L.

    1978-01-01

    The quantitative analysis of Moessbauer data, as in the measurement of Fe 3+ /Fe 2+ concentration, has not been possible because of the different mean square velocities (x 2 ) of Moessbauer nuclei at chemically different sites. A method is now described which, based on Moessbauer data at several temperatures, permits the comparison of absorption areas at (x 2 )=0. (Auth.)

  8. Accuracy of quantitative visual soil assessment

    Science.gov (United States)

    van Leeuwen, Maricke; Heuvelink, Gerard; Stoorvogel, Jetse; Wallinga, Jakob; de Boer, Imke; van Dam, Jos; van Essen, Everhard; Moolenaar, Simon; Verhoeven, Frank; Stoof, Cathelijne

    2016-04-01

    farmers carried out quantitative visual observations all independently from each other. All observers assessed five sites, having a sand, peat or clay soil. For almost all quantitative visual observations the spread of observed values was low (coefficient of variation background of the observer, might influence the outcome of visual assessment of some soil properties. In countries where soil analyses can easily be carried out, VSA might be a good replenishment to available soil chemical analyses, and in countries where it is not feasible to carry out soil analyses, VSA might be a good start to assess soil quality.

  9. Critical Quantitative Inquiry in Context

    Science.gov (United States)

    Stage, Frances K.; Wells, Ryan S.

    2014-01-01

    This chapter briefly traces the development of the concept of critical quantitative inquiry, provides an expanded conceptualization of the tasks of critical quantitative research, offers theoretical explanation and justification for critical research using quantitative methods, and previews the work of quantitative criticalists presented in this…

  10. Gagueira e disfluência comum na infância: análise das manifestações clínicas nos seus aspectos qualitativos e quantitativos Stuttering and common dysfluency in childhood: analyses of clinical manifestations in their qualitative and quantitative aspects

    Directory of Open Access Journals (Sweden)

    Suzana Maria de Amarante Merçon

    2007-06-01

    Full Text Available OBJETIVO: analisar em seus aspectos qualitativos e quantitativos as manifestações clínicas da gagueira e da disfluência comum na faixa etária de dois a seis anos. MÉTODOS: revisão de Literatura Sistemática a partir de livros e artigos científicos de Fonoaudiologia indexados no LILACS e no MEDLINE de 1993 a 2005. RESULTADOS: as diferenças qualitativas mais importantes são: o tipo de unidade lingüística na qual as disfluências ocorrem, tipologias de disfluências, presença ou ausência de esforço físico durante a fala e possíveis dificuldades na linguagem. Pré-escolares com gagueira freqüentemente apresentam dificuldades em competências metalinguísticas, especialmente com as metafonológicas, sendo que mais estudos sobre este aspecto são necessários. A freqüência de sílabas disfluentes e a taxa de elocução verbal estão entre os parâmetros quantitativos significativos. CONCLUSÃO: diferenças na fala e na linguagem parecem ser fatores importantes para distinguir gagueira de disfluências comuns infantis.PURPOSE: to examine the clinical manifestations of stuttering and common dysfluency in their qualitative and quantitative aspects, in children between the ages of two and six years old. METHODS: systematic literature review from books and indexed scientific articles on speech pathology in LILACS and MEDLINE from 1993 to 2005. RESULTS: the most important qualitative differences are: the kind of linguistic unit where dysfluency occur, dysfluency typologies, the presence or absence of physical effort during the speech and possible language difficulties. Preschoolers who stutter very often show difficulties in metalinguistic competencies, especially with the metaphonological ones and more studies about this aspect are needed. The frequency of diffluent syllables and the rate of verbal elocution are among the significant quantitative aspects. CONCLUSION: differences in the speech and in the language seem to be important

  11. Quantitative Assessment of the IT Agile Transformation

    Directory of Open Access Journals (Sweden)

    Orłowski Cezary

    2017-03-01

    Full Text Available The aim of this paper is to present the quantitative perspective of the agile transformation processes in IT organisations. The phenomenon of agile transformation becomes a complex challenge for an IT organisation since it has not been analysed in detail so far. There is no research on the readiness of IT organisations to realise agile transformation processes. Such processes also prove to have uncontrolled character. Therefore, to minimise the risk of failure referring to the realisation of transformation processes, it is necessary to monitor them. It is also necessary to identify and analyse such processes to ensure their continuous character.

  12. Applied quantitative finance

    CERN Document Server

    Chen, Cathy; Overbeck, Ludger

    2017-01-01

    This volume provides practical solutions and introduces recent theoretical developments in risk management, pricing of credit derivatives, quantification of volatility and copula modeling. This third edition is devoted to modern risk analysis based on quantitative methods and textual analytics to meet the current challenges in banking and finance. It includes 14 new contributions and presents a comprehensive, state-of-the-art treatment of cutting-edge methods and topics, such as collateralized debt obligations, the high-frequency analysis of market liquidity, and realized volatility. The book is divided into three parts: Part 1 revisits important market risk issues, while Part 2 introduces novel concepts in credit risk and its management along with updated quantitative methods. The third part discusses the dynamics of risk management and includes risk analysis of energy markets and for cryptocurrencies. Digital assets, such as blockchain-based currencies, have become popular b ut are theoretically challenging...

  13. Quantitative skeletal scintiscanning

    International Nuclear Information System (INIS)

    Haushofer, R.

    1982-01-01

    330 patients were examined by skeletal scintiscanning with sup(99m)Tc pyrophosphate and sup(99m)methylene diphosphonate in the years between 1977 and 1979. Course control examinations were carried out in 12 patients. The collective of patients presented with primary skeletal tumours, metastases, inflammatory and degenerative skeletal diseases. Bone scintiscanning combined with the ''region of interest'' technique was found to be an objective and reproducible technique for quantitative measurement of skeletal radioactivity concentrations. The validity of nuclear skeletal examinations can thus be enhanced as far as diagnosis, course control, and differential diagnosis are concerned. Quantitative skeletal scintiscanning by means of the ''region of interest'' technique has opened up a new era in skeletal diagnosis by nuclear methods. (orig./MG) [de

  14. Quantitative FDG in depression

    Energy Technology Data Exchange (ETDEWEB)

    Chua, P.; O`Keefe, G.J.; Egan, G.F.; Berlangieri, S.U.; Tochon-Danguy, H.J.; Mckay, W.J.; Morris, P.L.P.; Burrows, G.D. [Austin Hospital, Melbourne, VIC (Australia). Dept of Psychiatry and Centre for PET

    1998-03-01

    Full text: Studies of regional cerebral glucose metabolism (rCMRGlu) using positron emission tomography (PET) in patients with affective disorders have consistently demonstrated reduced metabolism in the frontal regions. Different quantitative and semi-quantitative rCMRGlu regions of interest (ROI) comparisons, e.g. absolute metabolic rates, ratios of dorsolateral prefrontal cortex (DLPFC) to ipsilateral hemisphere cortex, have been reported. These studies suffered from the use of a standard brain atlas to define ROls, whereas in this case study, the individual``s magnetic resonance imaging (MRI) scan was registered with the PET scan to enable accurate neuroanatomical ROI definition for the subject. The patient is a 36-year-old female with a six-week history of major depression (HAM-D = 34, MMSE = 28). A quantitative FDG PET study and an MRI scan were performed. Six MRI-guided ROls (DLPFC, PFC, whole hemisphere) were defined. The average rCMRGlu in the DLPFC (left = 28.8 + 5.8 mol/100g/min; right = 25.6 7.0 mol/100g/min) were slightly reduced compared to the ipsilateral hemispherical rate (left = 30.4 6.8 mol/100g/min; right = 29.5 7.2 mol/100g/min). The ratios of DLPFC to ipsilateral hemispheric rate were close to unity (left = 0.95 0.29; right 0.87 0.32). The right to left DLPFC ratio did not show any significant asymmetry (0.91 0.30). These results do not correlate with earlier published results reporting decreased left DLPFC rates compared to right DLPFC, although our results will need to be replicated with a group of depressed patients. Registration of PET and MRI studies is necessary in ROI-based quantitative FDG PET studies to allow for the normal anatomical variation among individuals, and thus is essential for accurate comparison of rCMRGlu between individuals.

  15. Quantitative FDG in depression

    International Nuclear Information System (INIS)

    Chua, P.; O'Keefe, G.J.; Egan, G.F.; Berlangieri, S.U.; Tochon-Danguy, H.J.; Mckay, W.J.; Morris, P.L.P.; Burrows, G.D.

    1998-01-01

    Full text: Studies of regional cerebral glucose metabolism (rCMRGlu) using positron emission tomography (PET) in patients with affective disorders have consistently demonstrated reduced metabolism in the frontal regions. Different quantitative and semi-quantitative rCMRGlu regions of interest (ROI) comparisons, e.g. absolute metabolic rates, ratios of dorsolateral prefrontal cortex (DLPFC) to ipsilateral hemisphere cortex, have been reported. These studies suffered from the use of a standard brain atlas to define ROls, whereas in this case study, the individual''s magnetic resonance imaging (MRI) scan was registered with the PET scan to enable accurate neuroanatomical ROI definition for the subject. The patient is a 36-year-old female with a six-week history of major depression (HAM-D = 34, MMSE = 28). A quantitative FDG PET study and an MRI scan were performed. Six MRI-guided ROls (DLPFC, PFC, whole hemisphere) were defined. The average rCMRGlu in the DLPFC (left = 28.8 + 5.8 mol/100g/min; right = 25.6 7.0 mol/100g/min) were slightly reduced compared to the ipsilateral hemispherical rate (left = 30.4 6.8 mol/100g/min; right = 29.5 7.2 mol/100g/min). The ratios of DLPFC to ipsilateral hemispheric rate were close to unity (left = 0.95 0.29; right 0.87 0.32). The right to left DLPFC ratio did not show any significant asymmetry (0.91 0.30). These results do not correlate with earlier published results reporting decreased left DLPFC rates compared to right DLPFC, although our results will need to be replicated with a group of depressed patients. Registration of PET and MRI studies is necessary in ROI-based quantitative FDG PET studies to allow for the normal anatomical variation among individuals, and thus is essential for accurate comparison of rCMRGlu between individuals

  16. Quantitative traits and diversification.

    Science.gov (United States)

    FitzJohn, Richard G

    2010-12-01

    Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be associated with increased rates of diversification. Here, I present a phylogenetic likelihood-based method (quantitative state speciation and extinction [QuaSSE]) that can be used to test such hypotheses using extant character distributions. This approach assumes that diversification follows a birth-death process where speciation and extinction rates may vary with one or more traits that evolve under a diffusion model. Speciation and extinction rates may be arbitrary functions of the character state, allowing much flexibility in testing models of trait-dependent diversification. I test the approach using simulated phylogenies and show that a known relationship between speciation and a quantitative character could be recovered in up to 80% of the cases on large trees (500 species). Consistent with other approaches, detecting shifts in diversification due to differences in extinction rates was harder than when due to differences in speciation rates. Finally, I demonstrate the application of QuaSSE to investigate the correlation between body size and diversification in primates, concluding that clade-specific differences in diversification may be more important than size-dependent diversification in shaping the patterns of diversity within this group.

  17. Analyse géochimique de la matiére organique extraite des roches sédimentaires. IV. Extraction des roches en faible quantités Geochemical Analysis of Organic Matter Extracted from Sedimentary Rocks Iv. Exraction from Small Amounts of Rock

    Directory of Open Access Journals (Sweden)

    Monin J. C.

    2006-11-01

    Full Text Available L'extraction en Soxhlet est inappllcable lorsque les échantillons de roche sont de trop petite taille. A l'occasion de la mise au point du protocole d'extraction correspondant, on examine l'influence d'un certain nombre de conditions opératoires sur le rendement d'extraction : température, durée nature et quantité du solvant, présence de lumière, présence d'air, procédé d'extraction. Pour les hydrocarbures, tant saturés qu'aromatiques, le facteur essentiel est l'agitation du milieu d'extraction ; la nature du solvant n'est pas critique, à condition de ne pas choisir un très mauvais solvant des hydrocarbures : l'extractibilité est en effet plus fonction du pouvoir désorbant vis-à-vis de la roche que du pouvoir solvant proprement dit. Pour les résines et asphalténes, l'interprétation des résultats est délicate, car la frontière n'est pas nette entre produits simplement dissous, produits de solvolyse et, produits de néoformation par interaction solvant-matière organique-matière minérale. II n'existe donc pas de protocole d'extraction recommandable dans l'absolu. Tout dépend des exigences analytiques et aussi pratiques du laboratoire; à l'Institut Français du Pétrole (IFP le protocole retenu est l'extraction en bécher avec agitation magnétique pendant 20 min dans le chroroforme à 50 °C (approximativement; on donne aussi le protocole d'évaporation du solvant et de récupération de l'extrait, qui doit être étudié soigneusement étant donné les faibles quantités mises en jeu. A Soxhlet extractor cannot be used with rock samples that are too small in size. With the development of on extraction procédure for such cases, this article examines the influence of various operating conditions on extraction yield, i. e. temperature, duration, nature and amount of solvent, presence of light, présence of air and extraction process. For both saturated and aromatic hydrocarbons, the essential factor is the stirring of the

  18. Persuading Collaboration: Analysing Persuasion in Online Collaboration Projects

    DEFF Research Database (Denmark)

    McHugh, Ronan; Larsen, Birger

    2010-01-01

    In this paper we propose that online collaborative production sites can be fruitfully analysed in terms of the general theoretical framework of Persuasive Design. OpenStreetMap and The Pirate Bay are used as examples of collaborative production sites. Results of a quantitative analysis of persuas...

  19. Grey literature in meta-analyses.

    Science.gov (United States)

    Conn, Vicki S; Valentine, Jeffrey C; Cooper, Harris M; Rantz, Marilyn J

    2003-01-01

    In meta-analysis, researchers combine the results of individual studies to arrive at cumulative conclusions. Meta-analysts sometimes include "grey literature" in their evidential base, which includes unpublished studies and studies published outside widely available journals. Because grey literature is a source of data that might not employ peer review, critics have questioned the validity of its data and the results of meta-analyses that include it. To examine evidence regarding whether grey literature should be included in meta-analyses and strategies to manage grey literature in quantitative synthesis. This article reviews evidence on whether the results of studies published in peer-reviewed journals are representative of results from broader samplings of research on a topic as a rationale for inclusion of grey literature. Strategies to enhance access to grey literature are addressed. The most consistent and robust difference between published and grey literature is that published research is more likely to contain results that are statistically significant. Effect size estimates of published research are about one-third larger than those of unpublished studies. Unfunded and small sample studies are less likely to be published. Yet, importantly, methodological rigor does not differ between published and grey literature. Meta-analyses that exclude grey literature likely (a) over-represent studies with statistically significant findings, (b) inflate effect size estimates, and (c) provide less precise effect size estimates than meta-analyses including grey literature. Meta-analyses should include grey literature to fully reflect the existing evidential base and should assess the impact of methodological variations through moderator analysis.

  20. Quantitative ion implantation

    International Nuclear Information System (INIS)

    Gries, W.H.

    1976-06-01

    This is a report of the study of the implantation of heavy ions at medium keV-energies into electrically conducting mono-elemental solids, at ion doses too small to cause significant loss of the implanted ions by resputtering. The study has been undertaken to investigate the possibility of accurate portioning of matter in submicrogram quantities, with some specific applications in mind. The problem is extensively investigated both on a theoretical level and in practice. A mathematical model is developed for calculating the loss of implanted ions by resputtering as a function of the implanted ion dose and the sputtering yield. Numerical data are produced therefrom which permit a good order-of-magnitude estimate of the loss for any ion/solid combination in which the ions are heavier than the solid atoms, and for any ion energy from 10 to 300 keV. The implanted ion dose is measured by integration of the ion beam current, and equipment and techniques are described which make possible the accurate integration of an ion current in an electromagnetic isotope separator. The methods are applied to two sample cases, one being a stable isotope, the other a radioisotope. In both cases independent methods are used to show that the implantation is indeed quantitative, as predicted. At the same time the sample cases are used to demonstrate two possible applications for quantitative ion implantation, viz. firstly for the manufacture of calibration standards for instrumental micromethods of elemental trace analysis in metals, and secondly for the determination of the half-lives of long-lived radioisotopes by a specific activity method. It is concluded that the present study has advanced quantitative ion implantation to the state where it can be successfully applied to the solution of problems in other fields

  1. Quantitative cardiac computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Thelen, M.; Dueber, C.; Wolff, P.; Erbel, R.; Hoffmann, T.

    1985-06-01

    The scope and limitations of quantitative cardiac CT have been evaluated in a series of experimental and clinical studies. The left ventricular muscle mass was estimated by computed tomography in 19 dogs (using volumetric methods, measurements in two axes and planes and reference volume). There was good correlation with anatomical findings. The enddiastolic volume of the left ventricle was estimated in 22 patients with cardiomyopathies; using angiography as a reference, CT led to systematic under-estimation. It is also shown that ECG-triggered magnetic resonance tomography results in improved visualisation and may be expected to improve measurements of cardiac morphology.

  2. F# for quantitative finance

    CERN Document Server

    Astborg, Johan

    2013-01-01

    To develop your confidence in F#, this tutorial will first introduce you to simpler tasks such as curve fitting. You will then advance to more complex tasks such as implementing algorithms for trading semi-automation in a practical scenario-based format.If you are a data analyst or a practitioner in quantitative finance, economics, or mathematics and wish to learn how to use F# as a functional programming language, this book is for you. You should have a basic conceptual understanding of financial concepts and models. Elementary knowledge of the .NET framework would also be helpful.

  3. Quantitative performance monitoring

    International Nuclear Information System (INIS)

    Heller, A.S.

    1987-01-01

    In the recently published update of NUREG/CR 3883, it was shown that Japanese plants of size and design similar to those in the US have significantly fewer trips in a given year of operation. One way to reduce such imbalance is the efficient use of available plant data. Since plant data are recorded and monitored continuously for management feedback and timely resolution of problems, this data should be actively used to increase the efficiency of operations and, ultimately, for a reduction of plant trips in power plants. A great deal of information is lost, however, if the analytical tools available for the data evaluation are misapplied or not adopted at all. This paper deals with a program developed to use quantitative techniques to monitor personnel performance in an operating power plant. Visual comparisons of ongoing performance with predetermined quantitative performance goals are made. A continuous feedback is provided to management for early detection of adverse trends and timely resolution of problems. Ultimately, costs are reduced through effective resource management and timely decision making

  4. Rapid identification of probiotic Lactobacillus species by multiplex PCR using species-specific primers based on the region extending from 16S rRNA through 23S rRNA.

    Science.gov (United States)

    Kwon, Hyuk-Sang; Yang, Eun-Hee; Yeon, Seung-Woo; Kang, Byoung-Hwa; Kim, Tae-Yong

    2004-10-15

    This study aimed to develop a novel multiplex polymerase chain reaction (PCR) primer set for the identification of seven probiotic Lactobacillus species such as Lactobacillus acidophilus, Lactobacillus delbrueckii, Lactobacillus casei, Lactobacillus gasseri, Lactobacillus plantarum, Lactobacillus reuteri and Lactobacillus rhamnosus. The primer set, comprising of seven specific and two conserved primers, was derived from the integrated sequences of 16S and 23S rRNA genes and their rRNA intergenic spacer region of each species. It was able to identify the seven target species with 93.6% accuracy, which exceeds that of the general biochemical methods. The phylogenetic analyses, using 16S rDNA sequences of the probiotic isolates, also provided further support that the results from the multiplex PCR assay were trustworthy. Taken together, we suggest that the multiplex primer set is an efficient tool for simple, rapid and reliable identification of seven Lactobacillus species.

  5. Analysing Terrorism from a Systems Thinking Perspective

    Directory of Open Access Journals (Sweden)

    Lukas Schoenenberger

    2014-02-01

    Full Text Available Given the complexity of terrorism, solutions based on single factors are destined to fail. Systems thinking offers various tools for helping researchers and policy makers comprehend terrorism in its entirety. We have developed a semi-quantitative systems thinking approach for characterising relationships between variables critical to terrorism and their impact on the system as a whole. For a better understanding of the mechanisms underlying terrorism, we present a 16-variable model characterising the critical components of terrorism and perform a series of highly focused analyses. We show how to determine which variables are best suited for government intervention, describing in detail their effects on the key variable—the political influence of a terrorist network. We also offer insights into how to elicit variables that destabilise and ultimately break down these networks. Because we clarify our novel approach with fictional data, the primary importance of this paper lies in the new framework for reasoning that it provides.

  6. Project analysis and integration economic analyses summary

    Science.gov (United States)

    Macomber, H. L.

    1986-01-01

    An economic-analysis summary was presented for the manufacture of crystalline-silicon modules involving silicon ingot/sheet, growth, slicing, cell manufacture, and module assembly. Economic analyses provided: useful quantitative aspects for complex decision-making to the Flat-plate Solar Array (FSA) Project; yardsticks for design and performance to industry; and demonstration of how to evaluate and understand the worth of research and development both to JPL and other government agencies and programs. It was concluded that future research and development funds for photovoltaics must be provided by the Federal Government because the solar industry today does not reap enough profits from its present-day sales of photovoltaic equipment.

  7. Shedding quantitative fluorescence light on novel regulatory mechanisms in skeletal biomedicine and biodentistry.

    Science.gov (United States)

    Lee, Ji-Won; Iimura, Tadahiro

    2017-02-01

    Digitalized fluorescence images contain numerical information such as color (wavelength), fluorescence intensity and spatial position. However, quantitative analyses of acquired data and their validation remained to be established. Our research group has applied quantitative fluorescence imaging on tissue sections and uncovered novel findings in skeletal biomedicine and biodentistry. This review paper includes a brief background of quantitative fluorescence imaging and discusses practical applications by introducing our previous research. Finally, the future perspectives of quantitative fluorescence imaging are discussed.

  8. Quality control in quantitative computed tomography

    International Nuclear Information System (INIS)

    Jessen, K.A.; Joergensen, J.

    1989-01-01

    Computed tomography (CT) has for several years been an indispensable tool in diagnostic radiology, but it is only recently that extraction of quantitative information from CT images has been of practical clinical value. Only careful control of the scan parameters, and especially the scan geometry, allows useful information to be obtained; and it can be demonstrated by simple phantom measurements how sensitive a CT system can be to variations in size, shape and position of the phantom in the gantry aperture. Significant differences exist between systems that are not manifested in normal control of image quality and general performance tests. Therefore an actual system has to be analysed for its suitability for quantitative use of the images before critical clinical applications are justified. (author)

  9. Quantitative analysis of thallium-201 myocardial scintigraphy

    International Nuclear Information System (INIS)

    Kanemoto, Nariaki; Hoer, G.; Johost, S.; Maul, F.-D.; Standke, R.

    1981-01-01

    The method of quantitative analysis of thallium-201 myocardial scintigraphy using computer assisted technique was described. Calculated indices are washout factor, vitality index and redistribution factor. Washout factor is the ratio of counts at certain period of time after exercise and immediately after exercise. This value is neccessary for the evaluation of redistribution to the ischemic areas in serial imagings to correct the Tl-201 washout from the myocardium under the assumption that the washout is constant in the whole myocardium. Vitality index is the ratio between the Tl-201 uptake in the region of interest and that of the maximum. Redistribution factor is the ratio of the redistribution in the region of interest in serial imagings after exercise to that of immediately after exercise. Four examples of exercise Tl-201 myocardial scintigrams and the quantitative analyses before and after the percutaneous transluminal coronary angioplasty were presented. (author)

  10. QTest: Quantitative Testing of Theories of Binary Choice.

    Science.gov (United States)

    Regenwetter, Michel; Davis-Stober, Clintin P; Lim, Shiau Hong; Guo, Ying; Popova, Anna; Zwilling, Chris; Cha, Yun-Shil; Messner, William

    2014-01-01

    The goal of this paper is to make modeling and quantitative testing accessible to behavioral decision researchers interested in substantive questions. We provide a novel, rigorous, yet very general, quantitative diagnostic framework for testing theories of binary choice. This permits the nontechnical scholar to proceed far beyond traditionally rather superficial methods of analysis, and it permits the quantitatively savvy scholar to triage theoretical proposals before investing effort into complex and specialized quantitative analyses. Our theoretical framework links static algebraic decision theory with observed variability in behavioral binary choice data. The paper is supplemented with a custom-designed public-domain statistical analysis package, the QTest software. We illustrate our approach with a quantitative analysis using published laboratory data, including tests of novel versions of "Random Cumulative Prospect Theory." A major asset of the approach is the potential to distinguish decision makers who have a fixed preference and commit errors in observed choices from decision makers who waver in their preferences.

  11. The APOSTEL recommendations for reporting quantitative optical coherence tomography studies

    DEFF Research Database (Denmark)

    Cruz-Herranz, Andrés; Balk, Lisanne J; Oberwahrenbrock, Timm

    2016-01-01

    OBJECTIVE: To develop consensus recommendations for reporting of quantitative optical coherence tomography (OCT) study results. METHODS: A panel of experienced OCT researchers (including 11 neurologists, 2 ophthalmologists, and 2 neuroscientists) discussed requirements for performing and reporting...... quantitative analyses of retinal morphology and developed a list of initial recommendations based on experience and previous studies. The list of recommendations was subsequently revised during several meetings of the coordinating group. RESULTS: We provide a 9-point checklist encompassing aspects deemed...... relevant when reporting quantitative OCT studies. The areas covered are study protocol, acquisition device, acquisition settings, scanning protocol, funduscopic imaging, postacquisition data selection, postacquisition data analysis, recommended nomenclature, and statistical analysis. CONCLUSIONS...

  12. Pathway models for analysing and managing the introduction of alien plant pests - an overview and categorization

    NARCIS (Netherlands)

    Douma, J.C.; Pautasso, M.; Venette, R.C.; Robinet, C.; Hemerik, L.; Mourits, M.C.M.; Schans, J.; Werf, van der W.

    2016-01-01

    Alien plant pests are introduced into new areas at unprecedented rates through global trade, transport, tourism and travel, threatening biodiversity and agriculture. Increasingly, the movement and introduction of pests is analysed with pathway models to provide risk managers with quantitative

  13. The quantitative imaging network: the role of quantitative imaging in radiation therapy

    International Nuclear Information System (INIS)

    Tandon, Pushpa; Nordstrom, Robert J.; Clark, Laurence

    2014-01-01

    The potential value of modern medical imaging methods has created a need for mechanisms to develop, translate and disseminate emerging imaging technologies and, ideally, to quantitatively correlate those with other related laboratory methods, such as the genomics and proteomics analyses required to support clinical decisions. One strategy to meet these needs efficiently and cost effectively is to develop an international network to share and reach consensus on best practices, imaging protocols, common databases, and open science strategies, and to collaboratively seek opportunities to leverage resources wherever possible. One such network is the Quantitative Imaging Network (QIN) started by the National Cancer Institute, USA. The mission of the QIN is to improve the role of quantitative imaging for clinical decision making in oncology by the development and validation of data acquisition, analysis methods, and other quantitative imaging tools to predict or monitor the response to drug or radiation therapy. The network currently has 24 teams (two from Canada and 22 from the USA) and several associate members, including one from Tata Memorial Centre, Mumbai, India. Each QIN team collects data from ongoing clinical trials and develops software tools for quantitation and validation to create standards for imaging research, and for use in developing models for therapy response prediction and measurement and tools for clinical decision making. The members of QIN are addressing a wide variety of cancer problems (Head and Neck cancer, Prostrate, Breast, Brain, Lung, Liver, Colon) using multiple imaging modalities (PET, CT, MRI, FMISO PET, DW-MRI, PET-CT). (author)

  14. Quantitive DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  15. Chinese legal texts – Quantitative Description

    Directory of Open Access Journals (Sweden)

    Ľuboš GAJDOŠ

    2017-06-01

    Full Text Available The aim of the paper is to provide a quantitative description of legal Chinese. This study adopts the approach of corpus-based analyses and it shows basic statistical parameters of legal texts in Chinese, namely the length of a sentence, the proportion of part of speech etc. The research is conducted on the Chinese monolingual corpus Hanku. The paper also discusses the issues of statistical data processing from various corpora, e.g. the tokenisation and part of speech tagging and their relevance to study of registers variation.

  16. Quantitative sexing (Q-Sexing) and relative quantitative sexing (RQ ...

    African Journals Online (AJOL)

    samer

    Key words: Polymerase chain reaction (PCR), quantitative real time polymerase chain reaction (qPCR), quantitative sexing, Siberian tiger. INTRODUCTION. Animal molecular sexing .... 43:3-12. Ellegren H (1996). First gene on the avian W chromosome (CHD) provides a tag for universal sexing of non-ratite birds. Proc.

  17. Quantitative linking hypotheses for infant eye movements.

    Directory of Open Access Journals (Sweden)

    Daniel Yurovsky

    Full Text Available The study of cognitive development hinges, largely, on the analysis of infant looking. But analyses of eye gaze data require the adoption of linking hypotheses: assumptions about the relationship between observed eye movements and underlying cognitive processes. We develop a general framework for constructing, testing, and comparing these hypotheses, and thus for producing new insights into early cognitive development. We first introduce the general framework--applicable to any infant gaze experiment--and then demonstrate its utility by analyzing data from a set of experiments investigating the role of attentional cues in infant learning. The new analysis uncovers significantly more structure in these data, finding evidence of learning that was not found in standard analyses and showing an unexpected relationship between cue use and learning rate. Finally, we discuss general implications for the construction and testing of quantitative linking hypotheses. MATLAB code for sample linking hypotheses can be found on the first author's website.

  18. Sample preparation in foodomic analyses.

    Science.gov (United States)

    Martinović, Tamara; Šrajer Gajdošik, Martina; Josić, Djuro

    2018-04-16

    Representative sampling and adequate sample preparation are key factors for successful performance of further steps in foodomic analyses, as well as for correct data interpretation. Incorrect sampling and improper sample preparation can be sources of severe bias in foodomic analyses. It is well known that both wrong sampling and sample treatment cannot be corrected anymore. These, in the past frequently neglected facts, are now taken into consideration, and the progress in sampling and sample preparation in foodomics is reviewed here. We report the use of highly sophisticated instruments for both high-performance and high-throughput analyses, as well as miniaturization and the use of laboratory robotics in metabolomics, proteomics, peptidomics and genomics. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  19. Deterministic quantitative risk assessment development

    Energy Technology Data Exchange (ETDEWEB)

    Dawson, Jane; Colquhoun, Iain [PII Pipeline Solutions Business of GE Oil and Gas, Cramlington Northumberland (United Kingdom)

    2009-07-01

    Current risk assessment practice in pipeline integrity management is to use a semi-quantitative index-based or model based methodology. This approach has been found to be very flexible and provide useful results for identifying high risk areas and for prioritizing physical integrity assessments. However, as pipeline operators progressively adopt an operating strategy of continual risk reduction with a view to minimizing total expenditures within safety, environmental, and reliability constraints, the need for quantitative assessments of risk levels is becoming evident. Whereas reliability based quantitative risk assessments can be and are routinely carried out on a site-specific basis, they require significant amounts of quantitative data for the results to be meaningful. This need for detailed and reliable data tends to make these methods unwieldy for system-wide risk k assessment applications. This paper describes methods for estimating risk quantitatively through the calibration of semi-quantitative estimates to failure rates for peer pipeline systems. The methods involve the analysis of the failure rate distribution, and techniques for mapping the rate to the distribution of likelihoods available from currently available semi-quantitative programs. By applying point value probabilities to the failure rates, deterministic quantitative risk assessment (QRA) provides greater rigor and objectivity than can usually be achieved through the implementation of semi-quantitative risk assessment results. The method permits a fully quantitative approach or a mixture of QRA and semi-QRA to suit the operator's data availability and quality, and analysis needs. For example, consequence analysis can be quantitative or can address qualitative ranges for consequence categories. Likewise, failure likelihoods can be output as classical probabilities or as expected failure frequencies as required. (author)

  20. Deconvoluting complex tissues for expression quantitative trait locus-based analyses

    DEFF Research Database (Denmark)

    Seo, Ji-Heui; Li, Qiyuan; Fatima, Aquila

    2013-01-01

    Breast cancer genome-wide association studies have pinpointed dozens of variants associated with breast cancer pathogenesis. The majority of risk variants, however, are located outside of known protein-coding regions. Therefore, identifying which genes the risk variants are acting through present...

  1. Assumptions in quantitative analyses of health risks of overhead power lines

    NARCIS (Netherlands)

    de Jong, A.; Wardekker, J.A.; van der Sluijs, J.P.

    2012-01-01

    One of the major issues hampering the formulation of uncontested policy decisions on contemporary risks is the presence of uncertainties in various stages of the policy cycle. In literature, different lines are suggested to address the problem of provisional and uncertain evidence. Reflective

  2. Nonlinear dynamics and stability of boiling water reactors: qualitative and quantitative analyses

    International Nuclear Information System (INIS)

    March-Leuba, J.; Cacuci, D.G.; Perez, R.B.

    1985-01-01

    A phenomenological model has been developed to simulate the qualitative behavior of boiling water reactors (BWRs) in the nonlinear regime under deterministic and stochastic excitations. After the linear stability threshold is crossed, limit cycle oscillations appear due to interactions between two unstable equilibrium points and the phase-space trajectories. This limit cycle becomes unstable when the feedback gain exceeds a certain critical value. Subsequent limit cycle instabilities produce a cascade of period-doubling bifurcations that leads to a periodic pulsed behavior. Under stochastic excitations, BWRs exhibit a single characteristic resonance, at approx.0.5 Hz, in the linear regime. By contrast, this work shows that harmonics of this characteristic frequency appear in the nonlinear regime. Furthermore, this work also demonstrates that amplitudes of the limit cycle oscillations do not depend on the variance of the stochastic excitation and remain bounded at all times. A physical model of nonlinear BWR dynamics has also been developed and employed to calculate the amplitude of limit cycle oscillations and their effects on fuel integrity over a wide range of operating conditions in the Vermont Yankee reactor. These calculations have confirmed that, beyond the threshold for linear stability, the reactor's state variable undergo limit cycle oscillations

  3. Analyses and quantitative determination of the strontium radioisotopes 89 and 90 in milk powder

    International Nuclear Information System (INIS)

    Jeanmaire, L.; Michon, G.

    1959-01-01

    The authors describe a procedure for the determination of the strontium radioisotopes 89 and 90. The concentration of strontium is made possible by the insolubility of its nitrate salt in strong nitric acid which allows the removal of greatest part of calcium. The purification is performed on a cation exchange column. The amount of radioisotope 90 is determined by means of its daughter product yttrium 90 necessary calibrations and computations are treated in special paragraphs. With regard to the reproducibility of the measurements, the fluctuations are less than 20 per cent. This seems satisfaction for such a technique which have great sensibility while being long and necessitative great carefulness. (author) [fr

  4. Quantitative Methods for Analysing Joint Questionnaire Data: Exploring the Role of Joint in Force Design

    Science.gov (United States)

    2015-08-01

    and organisational sciences; organisational psychology and behavioural psychology disciplines; and systems sciences and network centric warfare. From...Kernot and Tim McKay Joint and Operations Analysis Division Defence Science and Technology Organisation DST-Group-TN-1474 ABSTRACT In...dimensional space comprising: Coordination and Organisation ; Social Capital; and Optimisation of the Socio-technical Systems. Given the variability of the

  5. Applying CLSM to increment core surfaces for histometric analyses: A novel advance in quantitative wood anatomy

    OpenAIRE

    Wei Liang; Ingo Heinrich; Gerhard Helle; I. Dorado Liñán; T. Heinken

    2013-01-01

    A novel procedure has been developed to conduct cell structure measurements on increment core samples of conifers. The procedure combines readily available hardware and software equipment. The essential part of the procedure is the application of a confocal laser scanning microscope (CLSM) which captures images directly from increment cores surfaced with the advanced WSL core-microtome. Cell wall and lumen are displayed with a strong contrast due to the monochrome black and green nature of th...

  6. Quantitative Analyses of Transition Pension Liabilities and Solvency Sustainability in China

    Directory of Open Access Journals (Sweden)

    Yueqiang Zhao

    2017-12-01

    Full Text Available In the context of the aging population, the debt risk and solvency situation of China’s pension plan are of major concern for government and individuals. The aim of this paper is to project public pension liabilities and evaluate the solvency sustainability of China’s pension reform during transition periods. By using cohort component and actuarial models, transition debt and solvency sustainability are projected under the existing policy scenario and several sets of hypothetical policy scenarios. We find that the transition liabilities will peak in 2035 and the pension plan will become unsustainable in 2048 under existing policies. In the proposed scenario, postponing retirement age helps to maintain pension plan sust