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Sample records for chitinase-like proteins abundantly

  1. Chitinase-like proteins with antifungal activity from emperor banana fruits.

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    Ho, Vincent S M; Ng, Tzi Bun

    2007-01-01

    Two 30-kDa proteins with N-terminal sequence homology to chitinases have been isolated from fruits of the emperor banana by using a protocol that involved (NH(4))(2)SO(4) precipitation, affinity chromatography on Affi-gel blue gel, ion exchange chromatography by fast protein liquid chromatography (FPLC) on Mono S and gel filtration by FPLC on Superdex 75. The proteins were adsorbed on Affi-gel blue gel and Mono S. They both inhibited mycelial growth in Fusarium oxysporum but not in Mycosphaerella arachidicola. The chitinase-like protein more strongly bound on Mono S was obtained with a slightly lower yield and exhibited a higher antifungal potency toward F. oxysporum when compared with the less strongly bound chitinase-like protein.

  2. The chitinase-like protein YKL-40 increases mucin5AC production in human bronchial epithelial cells

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    Liu, Chunyi; Li, Qi [Division of Respiratory Medicine, Second Affiliated Hospital, Chongqing Medical University, No. 74, Linjiang Road, Yuzhong District, Chongqing 400010 (China); Zhou, Xiangdong, E-mail: zxd999@263.net [Division of Respiratory Medicine, Second Affiliated Hospital, Chongqing Medical University, No. 74, Linjiang Road, Yuzhong District, Chongqing 400010 (China); Kolosov, Victor P.; Perelman, Juliy M. [Far Eastern Scientific Center of Physiology and Pathology of Respiration, Siberian Branch, Russian Academy of Medical Sciences, Blagoveshchensk (Russian Federation)

    2013-11-01

    Mucus overproduction is an important feature in patients with chronic inflammatory airway diseases. However, the regulatory mechanisms that mediate excessive mucin production remain elusive. Recently, the level of YKL-40, a chitinase-like protein, has been found to be significantly increased in chronic inflammatory airway diseases and has been shown to be associated with the severity of these diseases. In this study, we sought to explore the effect of YKL-40 on mucin5AC (MUC5AC) production in chronic inflammatory airway diseases and the potential signaling pathways involved in this process. We found that elevated YKL-40 levels increased the mRNA and protein expression of MUC5AC in a dose- and time-dependent manner, in association with the phosphorylation of extracellular signal-regulated kinase (ERK) and nuclear factor κB (NF-κB), reflecting their activation. These responses were significantly suppressed by the knockdown of protease-activating receptor 2 (PAR2) with specific small interfering RNA or the inhibitors of ERK and NF-κB. YKL-40-induced MUC5AC overproduction was also effectively attenuated by the inhibitor of focal adhesion kinase (FAK). Taken together, these results imply that YKL-40 can stimulate excessive MUC5AC production through PAR2- and FAK-mediated mechanisms. - Highlights: • MUC5AC is the major secreted mucin in chronic inflammatory airway diseases. • YKL-40 is a prototype of the chitinase-like protein in mammals. • YKL-40 is an active player in chronic inflammatory airway diseases. • YKL-40 can increase MUC5AC production via PAR2-mediated pathway. • FAK is another candidate to mediate YKL-40-induced MUC5AC overexpression.

  3. A new chitinase-like xylanase inhibitor protein (XIP from coffee (Coffea arabica affects Soybean Asian rust (Phakopsora pachyrhizi spore germination

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    Mehta Angela

    2011-02-01

    Full Text Available Abstract Background Asian rust (Phakopsora pachyrhizi is a common disease in Brazilian soybean fields and it is difficult to control. To identify a biochemical candidate with potential to combat this disease, a new chitinase-like xylanase inhibitor protein (XIP from coffee (Coffea arabica (CaclXIP leaves was cloned into the pGAPZα-B vector for expression in Pichia pastoris. Results A cDNA encoding a chitinase-like xylanase inhibitor protein (XIP from coffee (Coffea arabica (CaclXIP, was isolated from leaves. The amino acid sequence predicts a (β/α8 topology common to Class III Chitinases (glycoside hydrolase family 18 proteins; GH18, and shares similarity with other GH18 members, although it lacks the glutamic acid residue essential for catalysis, which is replaced by glutamine. CaclXIP was expressed as a recombinant protein in Pichia pastoris. Enzymatic assay showed that purified recombinant CaclXIP had only residual chitinolytic activity. However, it inhibited xylanases from Acrophialophora nainiana by approx. 60% when present at 12:1 (w/w enzyme:inhibitor ratio. Additionally, CaclXIP at 1.5 μg/μL inhibited the germination of spores of Phakopsora pachyrhizi by 45%. Conclusions Our data suggests that CaclXIP belongs to a class of naturally inactive chitinases that have evolved to act in plant cell defence as xylanase inhibitors. Its role on inhibiting germination of fungal spores makes it an eligible candidate gene for the control of Asian rust.

  4. Comparative genomic analysis of chitinase and chitinase-like genes in the African malaria mosquito (Anopheles gambiae.

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    Jianzhen Zhang

    Full Text Available Chitinase is an important enzyme responsible for chitin metabolism in a wide range of organisms including bacteria, yeasts and other fungi, nematodes and arthropods. However, current knowledge on chitinolytic enzymes, especially their structures, functions and regulation is very limited. In this study we have identified 20 chitinase and chitinase-like genes in the African malaria mosquito, Anopheles gambiae, through genome-wide searching and transcript profiling. We assigned these genes into eight different chitinase groupings (groups I-VIII. Domain analysis of their predicted proteins showed that all contained at least one catalytic domain. However, only seven (AgCht4, AgCht5-1, AgCht6, AgCht7, AgCht8, AgCht10 and AgCht23 displayed one or more chitin-binding domains. Analyses of stage- and tissue-specific gene expression revealed that most of these genes were expressed in larval stages. However, AgCht8 was mainly expressed in the pupal and adult stages. AgCht2 and AgCht12 were specifically expressed in the foregut, whereas AgCht13 was only expressed in the midgut. The high diversity and complexity of An. gambiae chitinase and chitinase-like genes suggest their diverse functions during different developmental stages and in different tissues of the insect. A comparative genomic analysis of these genes along with those present in Drosophila melanogaster, Tribolium castaneum and several other insect species led to a uniform classification and nomenclature of these genes. Our investigation also provided important information for conducting future studies on the functions of chitinase and chitinase-like genes in this important malaria vector and other species of arthropods.

  5. Chitinase-like (CTL) and cellulose synthase (CESA) gene expression in gelatinous-type cellulosic walls of flax (Linum usitatissimum L.) bast fibers.

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    Mokshina, Natalia; Gorshkova, Tatyana; Deyholos, Michael K

    2014-01-01

    Plant chitinases (EC 3.2.1.14) and chitinase-like (CTL) proteins have diverse functions including cell wall biosynthesis and disease resistance. We analyzed the expression of 34 chitinase and chitinase-like genes of flax (collectively referred to as LusCTLs), belonging to glycoside hydrolase family 19 (GH19). Analysis of the transcript expression patterns of LusCTLs in the stem and other tissues identified three transcripts (LusCTL19, LusCTL20, LusCTL21) that were highly enriched in developing bast fibers, which form cellulose-rich gelatinous-type cell walls. The same three genes had low relative expression in tissues with primary cell walls and in xylem, which forms a xylan type of secondary cell wall. Phylogenetic analysis of the LusCTLs identified a flax-specific sub-group that was not represented in any of other genomes queried. To provide further context for the gene expression analysis, we also conducted phylogenetic and expression analysis of the cellulose synthase (CESA) family genes of flax, and found that expression of secondary wall-type LusCESAs (LusCESA4, LusCESA7 and LusCESA8) was correlated with the expression of two LusCTLs (LusCTL1, LusCTL2) that were the most highly enriched in xylem. The expression of LusCTL19, LusCTL20, and LusCTL21 was not correlated with that of any CESA subgroup. These results defined a distinct type of CTLs that may have novel functions specific to the development of the gelatinous (G-type) cellulosic walls.

  6. Chitinase-like (CTL and cellulose synthase (CESA gene expression in gelatinous-type cellulosic walls of flax (Linum usitatissimum L. bast fibers.

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    Natalia Mokshina

    Full Text Available Plant chitinases (EC 3.2.1.14 and chitinase-like (CTL proteins have diverse functions including cell wall biosynthesis and disease resistance. We analyzed the expression of 34 chitinase and chitinase-like genes of flax (collectively referred to as LusCTLs, belonging to glycoside hydrolase family 19 (GH19. Analysis of the transcript expression patterns of LusCTLs in the stem and other tissues identified three transcripts (LusCTL19, LusCTL20, LusCTL21 that were highly enriched in developing bast fibers, which form cellulose-rich gelatinous-type cell walls. The same three genes had low relative expression in tissues with primary cell walls and in xylem, which forms a xylan type of secondary cell wall. Phylogenetic analysis of the LusCTLs identified a flax-specific sub-group that was not represented in any of other genomes queried. To provide further context for the gene expression analysis, we also conducted phylogenetic and expression analysis of the cellulose synthase (CESA family genes of flax, and found that expression of secondary wall-type LusCESAs (LusCESA4, LusCESA7 and LusCESA8 was correlated with the expression of two LusCTLs (LusCTL1, LusCTL2 that were the most highly enriched in xylem. The expression of LusCTL19, LusCTL20, and LusCTL21 was not correlated with that of any CESA subgroup. These results defined a distinct type of CTLs that may have novel functions specific to the development of the gelatinous (G-type cellulosic walls.

  7. Proteomics characterization of abundant Golgi membrane proteins.

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    Bell, A W; Ward, M A; Blackstock, W P; Freeman, H N; Choudhary, J S; Lewis, A P; Chotai, D; Fazel, A; Gushue, J N; Paiement, J; Palcy, S; Chevet, E; Lafrenière-Roula, M; Solari, R; Thomas, D Y; Rowley, A; Bergeron, J J

    2001-02-16

    A mass spectrometric analysis of proteins partitioning into Triton X-114 from purified hepatic Golgi apparatus (84% purity by morphometry, 122-fold enrichment over the homogenate for the Golgi marker galactosyl transferase) led to the unambiguous identification of 81 proteins including a novel Golgi-associated protein of 34 kDa (GPP34). The membrane protein complement was resolved by SDS-polyacrylamide gel electrophoresis and subjected to a hierarchical approach using delayed extraction matrix-assisted laser desorption ionization mass spectrometry characterization by peptide mass fingerprinting, tandem mass spectrometry to generate sequence tags, and Edman sequencing of proteins. Major membrane proteins corresponded to known Golgi residents, a Golgi lectin, anterograde cargo, and an abundance of trafficking proteins including KDEL receptors, p24 family members, SNAREs, Rabs, a single ARF-guanine nucleotide exchange factor, and two SCAMPs. Analytical fractionation and gold immunolabeling of proteins in the purified Golgi fraction were used to assess the intra-Golgi and total cellular distribution of GPP34, two SNAREs, SCAMPs, and the trafficking proteins GBF1, BAP31, and alpha(2)P24 identified by the proteomics approach as well as the endoplasmic reticulum contaminant calnexin. Although GPP34 has never previously been identified as a protein, the localization of GPP34 to the Golgi complex, the conservation of GPP34 from yeast to humans, and the cytosolically exposed location of GPP34 predict a role for a novel coat protein in Golgi trafficking.

  8. Late Embryogenesis Abundant (LEA proteins in legumes

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    Marina eBattaglia

    2013-06-01

    Full Text Available Plants are exposed to different external conditions that affect growth, development, and productivity. Water deficit is one of these adverse conditions caused by drought, salinity, and extreme temperatures. Plants have developed different responses to prevent, ameliorate or repair the damage inflicted by these stressful environments. One of these responses is the activation of a set of genes encoding a group of hydrophilic proteins that typically accumulate to high levels during seed dehydration, at the last stage of embryogenesis, hence named Late Embryogenesis Abundant (LEA proteins. LEA proteins also accumulate in response to water limitation in vegetative tissues, and have been classified in seven groups based on their amino acid sequence similarity and on the presence of distinctive conserved motifs. These proteins are widely distributed in the plant kingdom, from ferns to angiosperms, suggesting a relevant role in the plant response to this unfavorable environmental condition. In this review, we analyzed the LEA proteins from those legumes whose complete genomes have been sequenced such as Phaseolus vulgaris, Glycine max, Medicago truncatula, Lotus japonicus, Cajanus cajan and Cicer arietinum. Considering their distinctive motifs, LEA proteins from the different groups were identified, and their sequence analysis allowed the recognition of novel legume specific motifs. Moreover, we compile their transcript accumulation patterns based on publicly available data. In spite of the limited information on these proteins in legumes, the analysis and data compiled here confirms the high correlation between their accumulation and water deficit, reinforcing their functional relevance under this detrimental conditions.

  9. Protein abundance profiling of the Escherichia coli cytosol

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    Ishihama, Y.; Schmidt, T.; Rappsilber, J.

    2008-01-01

    PAI approach which takes into account the number of sequenced peptides per protein. The values of abundance are within a broad range and accurately reflect independently measured copy numbers per cell. As expected, the most abundant proteins were those involved in protein synthesis, most notably ribosomal...... sample. Using a combination of LC-MS/MS approaches with protein and peptide fractionation steps we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. A measure of abundance is presented for each of the identified proteins, based on the recently developed em...... protein and mRNA abundance in E. coli cells. Conclusion: Abundance measurements for more than 1000 E. coli proteins presented in this work represent the most complete study of protein abundance in a bacterial cell so far. We show significant associations between the abundance of a protein and its...

  10. Protein Biophysics Explains Why Highly Abundant Proteins Evolve Slowly

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    Adrian W.R. Serohijos

    2012-08-01

    Full Text Available The consistent observation across all kingdoms of life that highly abundant proteins evolve slowly demonstrates that cellular abundance is a key determinant of protein evolutionary rate. However, other empirical findings, such as the broad distribution of evolutionary rates, suggest that additional variables determine the rate of protein evolution. Here, we report that under the global selection against the cytotoxic effects of misfolded proteins, folding stability (ΔG, simultaneous with abundance, is a causal variable of evolutionary rate. Using both theoretical analysis and multiscale simulations, we demonstrate that the anticorrelation between the premutation ΔG and the arising mutational effect (ΔΔG, purely biophysical in origin, is a necessary requirement for abundance–evolutionary rate covariation. Additionally, we predict and demonstrate in bacteria that the strength of abundance–evolutionary rate correlation depends on the divergence time separating reference genomes. Altogether, these results highlight the intrinsic role of protein biophysics in the emerging universal patterns of molecular evolution.

  11. Protein abundance profiling of the Escherichia coli cytosol

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    Mann Matthias

    2008-02-01

    Full Text Available Abstract Background Knowledge about the abundance of molecular components is an important prerequisite for building quantitative predictive models of cellular behavior. Proteins are central components of these models, since they carry out most of the fundamental processes in the cell. Thus far, protein concentrations have been difficult to measure on a large scale, but proteomic technologies have now advanced to a stage where this information becomes readily accessible. Results Here, we describe an experimental scheme to maximize the coverage of proteins identified by mass spectrometry of a complex biological sample. Using a combination of LC-MS/MS approaches with protein and peptide fractionation steps we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. A measure of abundance is presented for each of the identified proteins, based on the recently developed emPAI approach which takes into account the number of sequenced peptides per protein. The values of abundance are within a broad range and accurately reflect independently measured copy numbers per cell. As expected, the most abundant proteins were those involved in protein synthesis, most notably ribosomal proteins. Proteins involved in energy metabolism as well as those with binding function were also found in high copy number while proteins annotated with the terms metabolism, transcription, transport, and cellular organization were rare. The barrel-sandwich fold was found to be the structural fold with the highest abundance. Highly abundant proteins are predicted to be less prone to aggregation based on their length, pI values, and occurrence patterns of hydrophobic stretches. We also find that abundant proteins tend to be predominantly essential. Additionally we observe a significant correlation between protein and mRNA abundance in E. coli cells. Conclusion Abundance measurements for more than 1000 E. coli proteins presented in this work

  12. Fundamental constraints on the abundances of chemotaxis proteins

    CERN Document Server

    Bitbol, Anne-Florence

    2015-01-01

    Flagellated bacteria, such as Escherichia coli, perform directed motion in gradients of concentration of attractants and repellents in a process called chemotaxis. The E. coli chemotaxis signaling pathway is a model for signal transduction, but it has unique features. We demonstrate that the need for fast signaling necessitates high abundances of the proteins involved in this pathway. We show that further constraints on the abundances of chemotaxis proteins arise from the requirements of self-assembly, both of flagellar motors and of chemoreceptor arrays. All these constraints are specific to chemotaxis, and published data confirm that chemotaxis proteins tend to be more highly expressed than their homologs in other pathways. Employing a chemotaxis pathway model, we show that the gain of the pathway at the level of the response regulator CheY increases with overall chemotaxis protein abundances. This may explain why, at least in one E. coli strain, the abundance of all chemotaxis proteins is higher in media w...

  13. On ribosome load, codon bias and protein abundance.

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    Stefan Klumpp

    Full Text Available Different codons encoding the same amino acid are not used equally in protein-coding sequences. In bacteria, there is a bias towards codons with high translation rates. This bias is most pronounced in highly expressed proteins, but a recent study of synthetic GFP-coding sequences did not find a correlation between codon usage and GFP expression, suggesting that such correlation in natural sequences is not a simple property of translational mechanisms. Here, we investigate the effect of evolutionary forces on codon usage. The relation between codon bias and protein abundance is quantitatively analyzed based on the hypothesis that codon bias evolved to ensure the efficient usage of ribosomes, a precious commodity for fast growing cells. An explicit fitness landscape is formulated based on bacterial growth laws to relate protein abundance and ribosomal load. The model leads to a quantitative relation between codon bias and protein abundance, which accounts for a substantial part of the observed bias for E. coli. Moreover, by providing an evolutionary link, the ribosome load model resolves the apparent conflict between the observed relation of protein abundance and codon bias in natural sequences and the lack of such dependence in a synthetic gfp library. Finally, we show that the relation between codon usage and protein abundance can be used to predict protein abundance from genomic sequence data alone without adjustable parameters.

  14. Total protein or high-abundance protein: Which offers the best loading control for Western blotting?

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    Thacker, Jonathan S; Yeung, Derrick H; Staines, W Richard; Mielke, John G

    2016-03-01

    Western blotting routinely involves a control for variability in the amount of protein across immunoblot lanes. Normalizing a target signal to one found for an abundantly expressed protein is widely regarded as a reliable loading control; however, this approach is being increasingly questioned. As a result, we compared blotting for two high-abundance proteins (actin and glyceraldehyde 3-phosphate dehydrogenase [GAPDH]) and two total protein membrane staining methods (Ponceau and Coomassie Brilliant Blue) to determine the best control for loading variability. We found that Ponceau staining optimally balanced accuracy and precision, and we suggest that this approach be considered as an alternative to normalizing with a high-abundance protein.

  15. Depletion of abundant plasma proteins by poly(N-isopropylacrylamide-acrylic acid) hydrogel particles

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    Such-Sanmartín, Gerard; Ventura-Espejo, Estela; Jensen, Ole N

    2014-01-01

    at higher efficiency than low abundance proteins, which are enriched in the supernatants, whereas (2) hydrogel particles incubated with high concentrations of plasma capture and irreversibly trap abundant proteins. During the elution step, irreversibly trapped proteins remain captured while low abundance...... (SRM) liquid chromatography (LC)-MS/MS. This novel use of hydrogel particles opens new perspectives for biomarker analysis based on mass spectrometry....

  16. Regular patterns for proteome-wide distribution of protein abundance across species.

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    Fan Zhong

    Full Text Available A proteome of the bio-entity, including cell, tissue, organ, and organism, consists of proteins of diverse abundance. The principle that determines the abundance of different proteins in a proteome is of fundamental significance for an understanding of the building blocks of the bio-entity. Here, we report three regular patterns in the proteome-wide distribution of protein abundance across species such as human, mouse, fly, worm, yeast, and bacteria: in most cases, protein abundance is positively correlated with the protein's origination time or sequence conservation during evolution; it is negatively correlated with the protein's domain number and positively correlated with domain coverage in protein structure, and the correlations became stronger during the course of evolution; protein abundance can be further stratified by the function of the protein, whereby proteins that act on material conversion and transportation (mass category are more abundant than those that act on information modulation (information category. Thus, protein abundance is intrinsically related to the protein's inherent characters of evolution, structure, and function.

  17. Sensing Small Changes in Protein Abundance: Stimulation of Caco-2 Cells by Human Whey Proteins.

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    Cundiff, Judy K; McConnell, Elizabeth J; Lohe, Kimberly J; Maria, Sarah D; McMahon, Robert J; Zhang, Qiang

    2016-01-04

    Mass spectrometry (MS)-based proteomic approaches have largely facilitated our systemic understanding of cellular processes and biological functions. Cutoffs in protein expression fold changes (FCs) are often arbitrarily determined in MS-based quantification with no demonstrable determination of small magnitude changes in protein expression. Therefore, many biological insights may remain veiled due to high FC cutoffs. Herein, we employ the intestinal epithelial cell (IEC) line Caco-2 as a model system to demonstrate the dynamicity of tandem-mass-tag (TMT) labeling over a range of 5-40% changes in protein abundance, with the variance controls of ± 5% FC for around 95% of TMT ratios when sampling 9-12 biological replicates. We further applied this procedure to examine the temporal proteome of Caco-2 cells upon exposure to human whey proteins (WP). Pathway assessments predict subtle effects due to WP in moderating xenobiotic metabolism, promoting proliferation and various other cellular functions in differentiating enterocyte-like Caco-2 cells. This demonstration of a sensitive MS approach may open up new perspectives in the system-wide exploration of elusive or transient biological effects by facilitating scrutiny of narrow windows of proteome abundance changes. Furthermore, we anticipate this study will encourage more investigations of WP on infant gastrointestinal tract development.

  18. Hexapeptide libraries for enhanced protein PTM identification and relative abundance profiling in whole human saliva

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    Bandhakavi, Sricharan; van Riper, Susan K.; Tawfik, Pierre N; Matthew D Stone; Haddad, Tufia; Rhodus, Nelson L.; Carlis, John V.; Griffin, Timothy J.

    2011-01-01

    Dynamic range compression (DRC) by hexapeptide libraries increases MS/MS-based identification of lower-abundance proteins in complex mixtures. However, two unanswered questions impede fully realizing DRC’s potential in shotgun proteomics. First, does DRC enhance identification of post-translationally modified proteins? Second, can DRC be incorporated into a workflow enabling relative protein abundance profiling? We sought to answer both questions analyzing human whole saliva. Addressing quest...

  19. Identification of Differentially Abundant Proteins of Edwardsiella ictaluri during Iron Restriction.

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    Pradeep R Dumpala

    Full Text Available Edwardsiella ictaluri is a Gram-negative facultative anaerobe intracellular bacterium that causes enteric septicemia in channel catfish. Iron is an essential inorganic nutrient of bacteria and is crucial for bacterial invasion. Reduced availability of iron by the host may cause significant stress for bacterial pathogens and is considered a signal that leads to significant alteration in virulence gene expression. However, the precise effect of iron-restriction on E. ictaluri protein abundance is unknown. The purpose of this study was to identify differentially abundant proteins of E. ictaluri during in vitro iron-restricted conditions. We applied two-dimensional difference in gel electrophoresis (2D-DIGE for determining differentially abundant proteins and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF/TOF MS for protein identification. Gene ontology and pathway-based functional modeling of differentially abundant proteins was also conducted. A total of 50 unique differentially abundant proteins at a minimum of 2-fold (p ≤ 0.05 difference in abundance due to iron-restriction were detected. The numbers of up- and down-regulated proteins were 37 and 13, respectively. We noted several proteins, including EsrB, LamB, MalM, MalE, FdaA, and TonB-dependent heme/hemoglobin receptor family proteins responded to iron restriction in E. ictaluri.

  20. Protein abundance changes of Zygosaccharomyces rouxii in different sugar concentrations.

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    Guo, Hong; Niu, Chen; Liu, Bin; Wei, JianPing; Wang, HuXuan; Yuan, YaHong; Yue, TianLi

    2016-09-16

    Zygosaccharomyces rouxii is a yeast which can cause spoilage in the concentrated juice industries. It exhibits resistance to high sugar concentrations but genome- and proteome-wide studies on Z. rouxii in response to high sugar concentrations have been poorly investigated. Herein, by using a 2-D electrophoresis based workflow, the proteome of a wild strain of Z. rouxii under different sugar concentrations has been analyzed. Proteins were extracted, quantified, and subjected to 2-DE analysis in the pH range 4-7. Differences in growth (lag phase), protein content (13.97-19.23mg/g cell dry weight) and number of resolved spots (196-296) were found between sugar concentrations. ANOVA test showed that 168 spots were different, and 47 spots, corresponding to 40 unique gene products have been identified. These protein species are involved in carbohydrate and energy metabolism, amino acid metabolism, response to stimulus, protein transport and vesicle organization, cell morphogenesis regulation, transcription and translation, nucleotide metabolism, amino-sugar nucleotide-sugar pathways, oxidoreductases balancing, and ribosome biogenesis. The present study provides important information about how Z. rouxii acts to cope with high sugar concentration at molecular levels, which might enhance our global understanding of Z. rouxii's high sugar-tolerance trait.

  1. Overexpression Analysis of emv2 gene coding for Late Embryogenesis Abundant Protein from Vigna radiata (Wilczek

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    Rajesh S.

    2008-10-01

    Full Text Available Late embryogenesis abundant (LEA proteins are speculated to protect against water stress deficit in plants. An over expression system for mungbean late embryogenesis abundant protein, emv2 was constructed in a pET29a vector, designated pET-emv2 which is responsible for higher expression under the transcriptional/translational control of T7/lac promoter incorporated in the Escherichia coli BL21 (DE3.Induction protocol was optimized for pET recombinants harboring the target gene. Overexpressed EMV2 protein was purified to homogeneity and the protein profile monitored by SDS-PAGE.

  2. Two Novel Heat-Soluble Protein Families Abundantly Expressed in an Anhydrobiotic Tardigrade

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    Yamaguchi, Ayami; Tanaka, Sae; Yamaguchi, Shiho; Kuwahara, Hirokazu; Takamura, Chizuko; Imajoh-Ohmi, Shinobu; Horikawa, Daiki D.; Toyoda, Atsushi; Katayama, Toshiaki; Arakawa, Kazuharu; Fujiyama, Asao; Kubo, Takeo; Kunieda, Takekazu

    2012-01-01

    Tardigrades are able to tolerate almost complete dehydration by reversibly switching to an ametabolic state. This ability is called anhydrobiosis. In the anhydrobiotic state, tardigrades can withstand various extreme environments including space, but their molecular basis remains largely unknown. Late embryogenesis abundant (LEA) proteins are heat-soluble proteins and can prevent protein-aggregation in dehydrated conditions in other anhydrobiotic organisms, but their relevance to tardigrade anhydrobiosis is not clarified. In this study, we focused on the heat-soluble property characteristic of LEA proteins and conducted heat-soluble proteomics using an anhydrobiotic tardigrade. Our heat-soluble proteomics identified five abundant heat-soluble proteins. All of them showed no sequence similarity with LEA proteins and formed two novel protein families with distinct subcellular localizations. We named them Cytoplasmic Abundant Heat Soluble (CAHS) and Secretory Abundant Heat Soluble (SAHS) protein families, according to their localization. Both protein families were conserved among tardigrades, but not found in other phyla. Although CAHS protein was intrinsically unstructured and SAHS protein was rich in β-structure in the hydrated condition, proteins in both families changed their conformation to an α-helical structure in water-deficient conditions as LEA proteins do. Two conserved repeats of 19-mer motifs in CAHS proteins were capable to form amphiphilic stripes in α-helices, suggesting their roles as molecular shield in water-deficient condition, though charge distribution pattern in α-helices were different between CAHS and LEA proteins. Tardigrades might have evolved novel protein families with a heat-soluble property and this study revealed a novel repertoire of major heat-soluble proteins in these anhydrobiotic animals. PMID:22937162

  3. Two novel heat-soluble protein families abundantly expressed in an anhydrobiotic tardigrade.

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    Yamaguchi, Ayami; Tanaka, Sae; Yamaguchi, Shiho; Kuwahara, Hirokazu; Takamura, Chizuko; Imajoh-Ohmi, Shinobu; Horikawa, Daiki D; Toyoda, Atsushi; Katayama, Toshiaki; Arakawa, Kazuharu; Fujiyama, Asao; Kubo, Takeo; Kunieda, Takekazu

    2012-01-01

    Tardigrades are able to tolerate almost complete dehydration by reversibly switching to an ametabolic state. This ability is called anhydrobiosis. In the anhydrobiotic state, tardigrades can withstand various extreme environments including space, but their molecular basis remains largely unknown. Late embryogenesis abundant (LEA) proteins are heat-soluble proteins and can prevent protein-aggregation in dehydrated conditions in other anhydrobiotic organisms, but their relevance to tardigrade anhydrobiosis is not clarified. In this study, we focused on the heat-soluble property characteristic of LEA proteins and conducted heat-soluble proteomics using an anhydrobiotic tardigrade. Our heat-soluble proteomics identified five abundant heat-soluble proteins. All of them showed no sequence similarity with LEA proteins and formed two novel protein families with distinct subcellular localizations. We named them Cytoplasmic Abundant Heat Soluble (CAHS) and Secretory Abundant Heat Soluble (SAHS) protein families, according to their localization. Both protein families were conserved among tardigrades, but not found in other phyla. Although CAHS protein was intrinsically unstructured and SAHS protein was rich in β-structure in the hydrated condition, proteins in both families changed their conformation to an α-helical structure in water-deficient conditions as LEA proteins do. Two conserved repeats of 19-mer motifs in CAHS proteins were capable to form amphiphilic stripes in α-helices, suggesting their roles as molecular shield in water-deficient condition, though charge distribution pattern in α-helices were different between CAHS and LEA proteins. Tardigrades might have evolved novel protein families with a heat-soluble property and this study revealed a novel repertoire of major heat-soluble proteins in these anhydrobiotic animals.

  4. Two novel heat-soluble protein families abundantly expressed in an anhydrobiotic tardigrade.

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    Ayami Yamaguchi

    Full Text Available Tardigrades are able to tolerate almost complete dehydration by reversibly switching to an ametabolic state. This ability is called anhydrobiosis. In the anhydrobiotic state, tardigrades can withstand various extreme environments including space, but their molecular basis remains largely unknown. Late embryogenesis abundant (LEA proteins are heat-soluble proteins and can prevent protein-aggregation in dehydrated conditions in other anhydrobiotic organisms, but their relevance to tardigrade anhydrobiosis is not clarified. In this study, we focused on the heat-soluble property characteristic of LEA proteins and conducted heat-soluble proteomics using an anhydrobiotic tardigrade. Our heat-soluble proteomics identified five abundant heat-soluble proteins. All of them showed no sequence similarity with LEA proteins and formed two novel protein families with distinct subcellular localizations. We named them Cytoplasmic Abundant Heat Soluble (CAHS and Secretory Abundant Heat Soluble (SAHS protein families, according to their localization. Both protein families were conserved among tardigrades, but not found in other phyla. Although CAHS protein was intrinsically unstructured and SAHS protein was rich in β-structure in the hydrated condition, proteins in both families changed their conformation to an α-helical structure in water-deficient conditions as LEA proteins do. Two conserved repeats of 19-mer motifs in CAHS proteins were capable to form amphiphilic stripes in α-helices, suggesting their roles as molecular shield in water-deficient condition, though charge distribution pattern in α-helices were different between CAHS and LEA proteins. Tardigrades might have evolved novel protein families with a heat-soluble property and this study revealed a novel repertoire of major heat-soluble proteins in these anhydrobiotic animals.

  5. System wide analyses have underestimated protein abundances and the importance of transcription in mammals

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    Jingyi Jessica Li

    2014-02-01

    Full Text Available Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000–16,000 molecules per cell and that differences in mRNA expression between genes explain only 10–40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated protein abundances and the relative importance of transcription. Using individual measurements for 61 housekeeping proteins to rescale whole proteome data from Schwanhausser et al. (2011, we find that the median protein detected is expressed at 170,000 molecules per cell and that our corrected protein abundance estimates show a higher correlation with mRNA abundances than do the uncorrected protein data. In addition, we estimated the impact of further errors in mRNA and protein abundances using direct experimental measurements of these errors. The resulting analysis suggests that mRNA levels explain at least 56% of the differences in protein abundance for the 4,212 genes detected by Schwanhausser et al. (2011, though because one major source of error could not be estimated the true percent contribution should be higher. We also employed a second, independent strategy to determine the contribution of mRNA levels to protein expression. We show that the variance in translation rates directly measured by ribosome profiling is only 9% of that inferred by Schwanhausser et al. (2011, and that the measured and inferred translation rates correlate poorly (R2 = 0.14. Based on this, our second strategy suggests that mRNA levels explain ∼84% of the variance in protein levels. We also determined the percent contributions of transcription, RNA degradation, translation and protein degradation to the variance in protein abundances using both of our strategies. While the magnitudes of the two estimates vary, they both suggest that transcription plays a more important role than the earlier studies implied and translation

  6. System wide analyses have underestimated protein abundances and the importance of transcription in mammals.

    Science.gov (United States)

    Li, Jingyi Jessica; Bickel, Peter J; Biggin, Mark D

    2014-01-01

    Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000-16,000 molecules per cell and that differences in mRNA expression between genes explain only 10-40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated protein abundances and the relative importance of transcription. Using individual measurements for 61 housekeeping proteins to rescale whole proteome data from Schwanhausser et al. (2011), we find that the median protein detected is expressed at 170,000 molecules per cell and that our corrected protein abundance estimates show a higher correlation with mRNA abundances than do the uncorrected protein data. In addition, we estimated the impact of further errors in mRNA and protein abundances using direct experimental measurements of these errors. The resulting analysis suggests that mRNA levels explain at least 56% of the differences in protein abundance for the 4,212 genes detected by Schwanhausser et al. (2011), though because one major source of error could not be estimated the true percent contribution should be higher. We also employed a second, independent strategy to determine the contribution of mRNA levels to protein expression. We show that the variance in translation rates directly measured by ribosome profiling is only 12% of that inferred by Schwanhausser et al. (2011), and that the measured and inferred translation rates correlate poorly (R(2) = 0.13). Based on this, our second strategy suggests that mRNA levels explain ∼81% of the variance in protein levels. We also determined the percent contributions of transcription, RNA degradation, translation and protein degradation to the variance in protein abundances using both of our strategies. While the magnitudes of the two estimates vary, they both suggest that transcription plays a more important role than the earlier studies implied and translation a much smaller

  7. Evaluation of three high abundance protein depletion kits for umbilical cord serum proteomics

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    Nie Jing

    2011-05-01

    Full Text Available Abstract Background High abundance protein depletion is a major challenge in the study of serum/plasma proteomics. Prior to this study, most commercially available kits for depletion of highly abundant proteins had only been tested and evaluated in adult serum/plasma, while the depletion efficiency on umbilical cord serum/plasma had not been clarified. Structural differences between some adult and fetal proteins (such as albumin make it likely that depletion approaches for adult and umbilical cord serum/plasma will be variable. Therefore, the primary purposes of the present study are to investigate the efficiencies of several commonly-used commercial kits during high abundance protein depletion from umbilical cord serum and to determine which kit yields the most effective and reproducible results for further proteomics research on umbilical cord serum. Results The immunoaffinity based kits (PROTIA-Sigma and 5185-Agilent displayed higher depletion efficiency than the immobilized dye based kit (PROTBA-Sigma in umbilical cord serum samples. Both the PROTIA-Sigma and 5185-Agilent kit maintained high depletion efficiency when used three consecutive times. Depletion by the PROTIA-Sigma Kit improved 2DE gel quality by reducing smeared bands produced by the presence of high abundance proteins and increasing the intensity of other protein spots. During image analysis using the identical detection parameters, 411 ± 18 spots were detected in crude serum gels, while 757 ± 43 spots were detected in depleted serum gels. Eight spots unique to depleted serum gels were identified by MALDI- TOF/TOF MS, seven of which were low abundance proteins. Conclusions The immunoaffinity based kits exceeded the immobilized dye based kit in high abundance protein depletion of umbilical cord serum samples and dramatically improved 2DE gel quality for detection of trace biomarkers.

  8. Two Novel Heat-Soluble Protein Families Abundantly Expressed in an Anhydrobiotic Tardigrade

    OpenAIRE

    Ayami Yamaguchi; Sae Tanaka; Shiho Yamaguchi; Hirokazu Kuwahara; Chizuko Takamura; Shinobu Imajoh-Ohmi; Horikawa, Daiki D.; Atsushi Toyoda; Toshiaki Katayama; Kazuharu Arakawa; Asao Fujiyama; Takeo Kubo; Takekazu Kunieda

    2012-01-01

    Tardigrades are able to tolerate almost complete dehydration by reversibly switching to an ametabolic state. This ability is called anhydrobiosis. In the anhydrobiotic state, tardigrades can withstand various extreme environments including space, but their molecular basis remains largely unknown. Late embryogenesis abundant (LEA) proteins are heat-soluble proteins and can prevent protein-aggregation in dehydrated conditions in other anhydrobiotic organisms, but their relevance to tardigrade a...

  9. Nitrogen 15 abundance in protein fractions of beans fertilized with (15NH42SO4

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    Chaud Saula Goulart

    2002-01-01

    Full Text Available Studies evaluating the protein nutritive value of beans labelled with 15N, ussing nitrogen balance and the quantitation of faecal and urinary endogenous nitrogen, determined by isotopic dilution, have been extensively used. The objective of this research was to verify if the isotopic labelling of raw, freeze dried beans (Phaseolus vulgaris L., cultivar Piratã 1 with 1.394 atoms%15N, resulted in the same abundance of the whole flour and of the protein fractions extracted from the beans with 0.5 mol L-1 NaCl. The isotopic abundance found in the whole bean flour, in the protein extract, in the globulin and albumin fractions were respectively: 1.394 ± 0.011; 1.403 ± 0.012; 1.399 ± 0.007 and 1.399 ± 0.028 atoms % of 15N, presenting no difference (P > 0.05. However, a difference was found (P < 0.05 between the above mentioned abundances and the isotopic abundance found in the nitrogen of the proteins in the extraction residue, which was 0.969 ± 0.084. Since the abundances did not differ, the protein nutritive indexes, such as digestibility and biological value, determined from the nitrogen balance and corrected for isotopic dilution, would not be affected by extracting the proteins from the beans with 0.5 mol L¹ NaCl. If working with the nitrogen balance of the residual proteins after extraction and even with the whole flours, these indexes could present incorrect values, since the isotopic labelling of the residual proteins was less than that of the protein fractions.

  10. Visualization and Dissemination of Multidimensional Proteomics Data Comparing Protein Abundance During Caenorhabditis elegans Development

    Science.gov (United States)

    Riffle, Michael; Merrihew, Gennifer E.; Jaschob, Daniel; Sharma, Vagisha; Davis, Trisha N.; Noble, William S.; MacCoss, Michael J.

    2015-11-01

    Regulation of protein abundance is a critical aspect of cellular function, organism development, and aging. Alternative splicing may give rise to multiple possible proteoforms of gene products where the abundance of each proteoform is independently regulated. Understanding how the abundances of these distinct gene products change is essential to understanding the underlying mechanisms of many biological processes. Bottom-up proteomics mass spectrometry techniques may be used to estimate protein abundance indirectly by sequencing and quantifying peptides that are later mapped to proteins based on sequence. However, quantifying the abundance of distinct gene products is routinely confounded by peptides that map to multiple possible proteoforms. In this work, we describe a technique that may be used to help mitigate the effects of confounding ambiguous peptides and multiple proteoforms when quantifying proteins. We have applied this technique to visualize the distribution of distinct gene products for the whole proteome across 11 developmental stages of the model organism Caenorhabditis elegans. The result is a large multidimensional dataset for which web-based tools were developed for visualizing how translated gene products change during development and identifying possible proteoforms. The underlying instrument raw files and tandem mass spectra may also be downloaded. The data resource is freely available on the web at http://www.yeastrc.org/wormpes/.

  11. Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway.

    Science.gov (United States)

    Shi, Tujin; Niepel, Mario; McDermott, Jason E; Gao, Yuqian; Nicora, Carrie D; Chrisler, William B; Markillie, Lye M; Petyuk, Vladislav A; Smith, Richard D; Rodland, Karin D; Sorger, Peter K; Qian, Wei-Jun; Wiley, H Steven

    2016-07-12

    Various genetic mutations associated with cancer are known to alter cell signaling, but it is not clear whether they dysregulate signaling pathways by altering the abundance of pathway proteins. Using a combination of RNA sequencing and ultrasensitive targeted proteomics, we defined the primary components-16 core proteins and 10 feedback regulators-of the epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) pathway in normal human mammary epithelial cells and then quantified their absolute abundance across a panel of normal and breast cancer cell lines as well as fibroblasts. We found that core pathway proteins were present at very similar concentrations across all cell types, with a variance similar to that of proteins previously shown to display conserved abundances across species. In contrast, EGFR and transcriptionally controlled feedback regulators were present at highly variable concentrations. The absolute abundance of most core proteins was between 50,000 and 70,000 copies per cell, but the adaptors SOS1, SOS2, and GAB1 were found at far lower amounts (2000 to 5000 copies per cell). MAPK signaling showed saturation in all cells between 3000 and 10,000 occupied EGFRs, consistent with the idea that adaptors limit signaling. Our results suggest that the relative stoichiometry of core MAPK pathway proteins is very similar across different cell types, with cell-specific differences mostly restricted to variable amounts of feedback regulators and receptors. The low abundance of adaptors relative to EGFR could be responsible for previous observations that only a fraction of total cell surface EGFR is capable of rapid endocytosis, high-affinity binding, and mitogenic signaling.

  12. [Functions of late embryogenesis abundant proteins in desiccation-tolerance of organisms: a review].

    Science.gov (United States)

    Liu, Yun; Liu, Guobao; Li, Ranhui; Zou, Yongdong; Zheng, Yizhi

    2010-05-01

    Late embryogenesis abundant (LEA) proteins are well associated with the desiccation tolerance in organisms. LEA proteins are categorized into at least seven groups by virtue of similarities in their deduced amino acid sequences. Most of the LEA proteins have the characteristics of high hydrophilicity and thermo-stability. The LEA proteins are in unstructured conformation in aqueous solution. However, they adopted amphiphilic alpha-helix structure during desiccation condition. LEA proteins are localized to the different organelles in the cells, i.e. cytoplasm, endoplasmic reticulum, mitochondria and nucleus. The multi-functional capacity of LEA proteins are suggested, as protein stabilization, protection of enzyme activity, membrane association and stabilization, antioxidant function, metal-ion binding or DNA protection, etc. Here, we review the structural and functional characteristics of LEA proteins to provide a reference platform to understand their protective mechanisms during the adaptive response to desiccation in organisms.

  13. Immunodepletion of high-abundant proteins from acute and chronic wound fluids to elucidate low-abundant regulators in wound healing

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    Chojnacki Caroline

    2010-12-01

    Full Text Available Abstract Background The process of wound healing consists of several well distinguishable and finely tuned phases. For most of these phases specific proteins have been characterized, although the underlying mechanisms of regulation are not yet fully understood. It is an open question as to whether deficits in wound healing can be traced back to chronic illnesses such as diabetes mellitus. Previous research efforts in this field focus largely on a restricted set of marker proteins due to the limitations detection by antibodies imposes. For mechanistic purposes the elucidation of differences in acute and chronic wounds can be addressed by a less restricted proteome study. Mass spectrometric (MS methods, e.g. multi dimensional protein identification technology (MudPIT, are well suitable for this complex theme of interest. The human wound fluid proteome is extremely complex, as is human plasma. Therefore, high-abundant proteins often mask the mass spectrometric detection of lower-abundant ones, which makes a depletion step of such predominant proteins inevitable. Findings In this study a commercially available immunodepletion kit was evaluated for the detection of low-abundant proteins from wound fluids. The dynamic range of the entire workflow was significantly increased to 5-6 orders of magnitude, which makes low-abundant regulatory proteins involved in wound healing accessible for MS detection. Conclusion The depletion of abundant proteins is absolutely necessary in order to analyze highly complex protein mixtures such as wound fluids using mass spectrometry. For this the used immunodepletion kit is a first but important step in order to represent the entire dynamic range of highly complex protein mixtures in the future.

  14. Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway

    Energy Technology Data Exchange (ETDEWEB)

    Shi, T.; Niepel, M.; McDermott, J. E.; Gao, Y.; Nicora, C. D.; Chrisler, W. B.; Markillie, L. M.; Petyuk, V. A.; Smith, R. D.; Rodland, K. D.; Sorger, P. K.; Qian, W. -J.; Wiley, H. S.

    2016-07-12

    It is not known whether cancer cells generally show quantitative differences in the expression of signaling pathway proteins that could dysregulate signal transduction. To explore this issue, we first defined the primary components of the EGF-MAPK pathway in normal human mammary epithelial cells, identifying 16 core proteins and 10 feedback regulators. We then quantified their absolute abundance across a panel of normal and cancer cell lines. We found that core pathway proteins were expressed at very similar levels across all cell types. In contrast, the EGFR and transcriptionally controlled feedback regulators were expressed at highly variable levels. The absolute abundance of most core pathway proteins was between 50,000- 70,000 copies per cell, but the adaptors SOS1, SOS2, and GAB1 were found at far lower levels (2,000-5,000 per cell). MAPK signaling showed saturation in all cells between 3,000-10,000 occupied EGFR, consistent with the idea that low adaptor levels limit signaling. Our results suggest that the core MAPK pathway is essentially invariant across different cell types, with cell- specific differences in signaling likely due to variable levels of feedback regulators. The low abundance of adaptors relative to the EGFR could be responsible for previous observation of saturable signaling, endocytosis, and high affinity EGFR.

  15. Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer.

    Science.gov (United States)

    Landau, Kevin S; Na, Insung; Schenck, Ryan O; Uversky, Vladimir N

    2016-01-01

    Prostatic diseases such as prostate cancer and benign prostatic hyperplasia are highly prevalent among men. The number of studies focused on the abundance and roles of intrinsically disordered proteins in prostate cancer is rather limited. The goal of this study is to analyze the prevalence and degree of disorder in proteins that were previously associated with the prostate cancer pathogenesis and to compare these proteins to the entire human proteome. The analysis of these datasets provides means for drawing conclusions on the roles of disordered proteins in this common male disease. We also hope that the results of our analysis can potentially lead to future experimental studies of these proteins to find novel pathways associated with this disease.

  16. Intake of Meat Proteins Substantially Increased the Relative Abundance of Genus Lactobacillus in Rat Feces.

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    Yingying Zhu

    Full Text Available Diet has been shown to have a critical influence on gut bacteria and host health, and high levels of red meat in diet have been shown to increase colonic DNA damage and thus be harmful to gut health. However, previous studies focused more on the effects of meat than of meat proteins. In order to investigate whether intake of meat proteins affects the composition and metabolic activities of gut microbiota, feces were collected from growing rats that were fed with either meat proteins (from beef, pork or fish or non-meat proteins (casein or soy for 14 days. The resulting composition of gut microbiota was profiled by sequencing the V4-V5 region of the 16S ribosomal RNA genes and the short chain fatty acids (SCFAs were analyzed using gas chromatography. The composition of gut microbiota and SCFA levels were significantly different between the five diet groups. At a recommended dose of 20% protein in the diet, meat protein-fed rats had a higher relative abundance of the beneficial genus Lactobacillus, but lower levels of SCFAs and SCFA-producing bacteria including Fusobacterium, Bacteroides and Prevotella, compared with the soy protein-fed group. Further work is needed on the regulatory pathways linking dietary protein intake to gut microbiota.

  17. Protein abundance of clinically relevant multidrug transporters along the entire length of the human intestine.

    Science.gov (United States)

    Drozdzik, Marek; Gröer, Christian; Penski, Jette; Lapczuk, Joanna; Ostrowski, Marek; Lai, Yurong; Prasad, Bhagwat; Unadkat, Jashvant D; Siegmund, Werner; Oswald, Stefan

    2014-10-01

    Intestinal transporters are crucial determinants in the oral absorption of many drugs. We therefore studied the mRNA expression (N = 33) and absolute protein content (N = 10) of clinically relevant transporters in healthy epithelium of the duodenum, the proximal and distal jejunum and ileum, and the ascending, transversal, descending, and sigmoidal colon of six organ donors (24-54 years). In the small intestine, the abundance of nearly all studied proteins ranged between 0.2 and 1.6 pmol/mg with the exception of those of OCT3 (intestinal segment. ABCB1, ABCG2, PEPT1, and ASBT were significantly more abundant in jejunum and ileum than in colon. In contrast to this, the level of expression of ABCC2, ABCC3, and OCT3 was found to be highest in colon. Site-dependent differences in the levels of gene and protein expression were observed for ABCB1 and ASBT. Significant correlations between mRNA and protein levels have been found for ABCG2, ASBT, OCT3, and PEPT1 in the small intestine. Our data provide further physiological pieces of the puzzle required to predict intestinal drug absorption in humans.

  18. A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast.

    Science.gov (United States)

    Blein-Nicolas, Mélisande; Albertin, Warren; da Silva, Telma; Valot, Benoît; Balliau, Thierry; Masneuf-Pomarède, Isabelle; Bely, Marina; Marullo, Philippe; Sicard, Delphine; Dillmann, Christine; de Vienne, Dominique; Zivy, Michel

    2015-08-01

    Heterosis is a universal phenomenon that has major implications in evolution and is of tremendous agro-economic value. To study the molecular manifestations of heterosis and to find factors that maximize its strength, we implemented a large-scale proteomic experiment in yeast. We analyzed the inheritance of 1,396 proteins in 55 inter- and intraspecific hybrids obtained from Saccharomyces cerevisiae and S. uvarum that were grown in grape juice at two temperatures. We showed that the proportion of heterotic proteins was highly variable depending on the parental strain and on the temperature considered. For intraspecific hybrids, this proportion was higher at nonoptimal temperature. Unexpectedly, heterosis for protein abundance was strongly biased toward positive values in interspecific hybrids but not in intraspecific hybrids. Computer modeling showed that this observation could be accounted for by assuming concave relationships between protein abundances and their controlling factors, in line with the metabolic model of heterosis. These results point to nonlinear processes that could play a central role in heterosis.

  19. A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast*

    Science.gov (United States)

    Blein-Nicolas, Mélisande; Albertin, Warren; da Silva, Telma; Valot, Benoît; Balliau, Thierry; Masneuf-Pomarède, Isabelle; Bely, Marina; Marullo, Philippe; Sicard, Delphine; Dillmann, Christine; de Vienne, Dominique; Zivy, Michel

    2015-01-01

    Heterosis is a universal phenomenon that has major implications in evolution and is of tremendous agro-economic value. To study the molecular manifestations of heterosis and to find factors that maximize its strength, we implemented a large-scale proteomic experiment in yeast. We analyzed the inheritance of 1,396 proteins in 55 inter- and intraspecific hybrids obtained from Saccharomyces cerevisiae and S. uvarum that were grown in grape juice at two temperatures. We showed that the proportion of heterotic proteins was highly variable depending on the parental strain and on the temperature considered. For intraspecific hybrids, this proportion was higher at nonoptimal temperature. Unexpectedly, heterosis for protein abundance was strongly biased toward positive values in interspecific hybrids but not in intraspecific hybrids. Computer modeling showed that this observation could be accounted for by assuming concave relationships between protein abundances and their controlling factors, in line with the metabolic model of heterosis. These results point to nonlinear processes that could play a central role in heterosis. PMID:25971257

  20. An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome.

    Directory of Open Access Journals (Sweden)

    John C Newman

    2008-03-01

    Full Text Available Cockayne syndrome (CS is a devastating progeria most often caused by mutations in the CSB gene encoding a SWI/SNF family chromatin remodeling protein. Although all CSB mutations that cause CS are recessive, the complete absence of CSB protein does not cause CS. In addition, most CSB mutations are located beyond exon 5 and are thought to generate only C-terminally truncated protein fragments. We now show that a domesticated PiggyBac-like transposon PGBD3, residing within intron 5 of the CSB gene, functions as an alternative 3' terminal exon. The alternatively spliced mRNA encodes a novel chimeric protein in which CSB exons 1-5 are joined in frame to the PiggyBac transposase. The resulting CSB-transposase fusion protein is as abundant as CSB protein itself in a variety of human cell lines, and continues to be expressed by primary CS cells in which functional CSB is lost due to mutations beyond exon 5. The CSB-transposase fusion protein has been highly conserved for at least 43 Myr since the divergence of humans and marmoset, and appears to be subject to selective pressure. The human genome contains over 600 nonautonomous PGBD3-related MER85 elements that were dispersed when the PGBD3 transposase was last active at least 37 Mya. Many of these MER85 elements are associated with genes which are involved in neuronal development, and are known to be regulated by CSB. We speculate that the CSB-transposase fusion protein has been conserved for host antitransposon defense, or to modulate gene regulation by MER85 elements, but may cause CS in the absence of functional CSB protein.

  1. Assessment of Label-Free Quantification in Discovery Proteomics and Impact of Technological Factors and Natural Variability of Protein Abundance.

    Science.gov (United States)

    Al Shweiki, Mhd Rami; Mönchgesang, Susann; Majovsky, Petra; Thieme, Domenika; Trutschel, Diana; Hoehenwarter, Wolfgang

    2017-04-07

    We evaluated the state of label-free discovery proteomics focusing especially on technological contributions and contributions of naturally occurring differences in protein abundance to the intersample variability in protein abundance estimates in this highly peptide-centric technology. First, the performance of popular quantitative proteomics software, Proteome Discoverer, Scaffold, MaxQuant, and Progenesis QIP, was benchmarked using their default parameters and some modified settings. Beyond this, the intersample variability in protein abundance estimates was decomposed into variability introduced by the entire technology itself and variable protein amounts inherent to individual plants of the Arabidopsis thaliana Col-0 accession. The technical component was considerably higher than the biological intersample variability, suggesting an effect on the degree and validity of reported biological changes in protein abundance. Surprisingly, the biological variability, protein abundance estimates, and protein fold changes were recorded differently by the software used to quantify the proteins, warranting caution in the comparison of discovery proteomics results. As expected, ∼99% of the proteome was invariant in the isogenic plants in the absence of environmental factors; however, few proteins showed substantial quantitative variability. This naturally occurring variation between individual organisms can have an impact on the causality of reported protein fold changes.

  2. Nanomagnetic competition assay for low-abundance protein biomarker quantification in unprocessed human sera.

    Science.gov (United States)

    Li, Yuanpeng; Srinivasan, Balasubramanian; Jing, Ying; Yao, Xiaofeng; Hugger, Marie A; Wang, Jian-Ping; Xing, Chengguo

    2010-03-31

    A novel giant magnetoresistive sensor and uniform high-magnetic-moment FeCo nanoparticles (12.8 nm)-based detecting platform with minimized detecting distance was developed for rapid biomolecule quantification from body fluids. Such a system demonstrates specific, accurate, and quick detection and quantification of interleukin-6, a low-abundance protein and a potential cancer biomarker, directly in 4 muL of unprocessed human sera. This platform is expected to facilitate the identification and validation of disease biomarkers. It may eventually lead to a low-cost personal medical device for chronic disease early detection, diagnosis, and prognosis.

  3. Protamine sulfate precipitation method depletes abundant plant seed-storage proteins: A case study on legume plants.

    Science.gov (United States)

    Kim, Yu Ji; Wang, Yiming; Gupta, Ravi; Kim, So Wun; Min, Chul Woo; Kim, Yong Chul; Park, Ki Hun; Agrawal, Ganesh Kumar; Rakwal, Randeep; Choung, Myoung-Gun; Kang, Kyu Young; Kim, Sun Tae

    2015-05-01

    Depletion of abundant proteins is one of the effective ways to improve detection and identification of low-abundance proteins. Our previous study showed that protamine sulfate precipitation (PSP) method can deplete abundant ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) from leaf proteins and is suitable for their in-depth proteome investigation. In this study, we provide evidence that the PSP method can also be effectively used for depletion of abundant seed-storage proteins (SSPs) from the total seed proteins of diverse legume plants including soybean, broad bean, pea, wild soybean, and peanut. The 0.05% protamine sulfate (PS) was sufficient to deplete major SSPs from all legumes tested except for peanut where 0.1% PS was required. SDS-PAGE, Western blotting and 2DE analyses of PS-treated soybean and peanut seed proteins showed enriched spots in PS-supernatant than total proteins. Coefficient of variation percentage (%CV) and principal component analysis of 2DE spots support the reproducibility, suitability, and efficacy of the PSP method for quantitative and comparative seed proteome analysis. MALDI-TOF-TOF successfully identified some protein spots from soybean and peanut. Hence, this simple, reproducible, economical PSP method has a broader application in depleting plant abundant proteins including SSPs in addition to RuBisCO, allowing discussion for comprehensive proteome establishment and parallel comparative studies in plants.

  4. Abundantly and rarely expressed Lhc protein genes exhibit distinct regulation patterns in plants.

    Science.gov (United States)

    Klimmek, Frank; Sjödin, Andreas; Noutsos, Christos; Leister, Dario; Jansson, Stefan

    2006-03-01

    We have analyzed gene regulation of the Lhc supergene family in poplar (Populus spp.) and Arabidopsis (Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar (Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting-like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.

  5. Late embryogenesis abundant proteins protect human hepatoma cells during acute desiccation.

    Science.gov (United States)

    Li, Shumin; Chakraborty, Nilay; Borcar, Apurva; Menze, Michael A; Toner, Mehmet; Hand, Steven C

    2012-12-18

    Expression of late embryogenesis abundant (LEA) proteins is highly correlated with desiccation tolerance in anhydrobiotic animals, selected land plants, and bacteria. Genes encoding two LEA proteins, one localized to the cytoplasm/nucleus (AfrLEA2) and one targeted to mitochondria (AfrLEA3m), were stably transfected into human HepG2 cells. A trehalose transporter was used for intracellular loading of this disaccharide. Cells were rapidly and uniformly desiccated to low water content (spin-drying technique. Immediately on rehydration, control cells without LEA proteins or trehalose exhibited 0% membrane integrity, compared with 98% in cells loaded with trehalose and expressing AfrLEA2 or AfrLEA3m; surprisingly, AfrLEA3m without trehalose conferred 94% protection. Cell proliferation across 7 d showed an 18-fold increase for cells dried with AfrLEA3m and trehalose, compared with 27-fold for nondried controls. LEA proteins dramatically enhance desiccation tolerance in mammalian cells and offer the opportunity for engineering biostability in the dried state.

  6. An in vivo detection system for transient and low-abundant protein interactions and their kinetics in budding yeast.

    Science.gov (United States)

    Brezovich, Andrea; Schuschnig, Martina; Ammerer, Gustav; Kraft, Claudine

    2015-03-01

    Methylation tracking (M-Track) is a protein-proximity assay in Saccharomyces cerevisiae, allowing the detection of transient protein-protein interactions in living cells. The bait protein is fused to a histone lysine methyl transferase and the prey protein to a methylation acceptor peptide derived from histone 3. Upon interaction, the histone 3 fragment is stably methylated on lysine 9 and can be detected by methylation-specific antibodies. Since methylation marking is irreversible in budding yeast and only takes place in living cells, the occurrence of artifacts during cell lysate preparation is greatly reduced, leading to a more accurate representation of native interactions. So far, this method has been limited to highly abundant or overexpressed proteins. However, many proteins of interest are low-abundant, and overexpression of proteins may interfere with their function, leading to an artificial situation. Here we report the generation of a toolbox including a novel cleavage-enrichment system for the analysis of very low-abundant proteins at their native expression levels. In addition, we developed a system for the parallel analysis of two prey proteins in a single cell, as well as an inducible methylation system. The inducible system allows precise control over the time during which the interaction is detected and can be used to determine interaction kinetics. Furthermore, we generated a set of constructs facilitating the cloning-free genomic tagging of proteins at their endogenous locus by homologous recombination, and their expression from centromeric plasmids.

  7. Characterization of a group 1 late embryogenesis abundant protein in encysted embryos of the brine shrimp Artemia franciscana.

    Science.gov (United States)

    Sharon, Michelle A; Kozarova, Anna; Clegg, James S; Vacratsis, Panayiotis O; Warner, Alden H

    2009-04-01

    Late embryogenesis abundant (LEA) proteins are hydrophilic molecules that are believed to function in desiccation and low-temperature tolerance in some plants and plant propagules, certain prokaryotes, and several animal species. The brine shrimp Artemia franciscana can produce encysted embryos (cysts) that enter diapause and are resistant to severe desiccation. This ability is based on biochemical adaptations, one of which appears to be the accumulation of the LEA protein that is the focus of this study. The studies described herein characterize a 21 kDa protein in encysted Artemia embryos as a group 1 LEA protein. The amino acid sequence of this protein and its gene have been determined and entered into the NCBI database (no. EF656614). The LEA protein consists of 182 amino acids and it is extremely hydrophilic, with glycine (23%), glutamine (17%), and glutamic acid (12.6%) being the most abundant amino acids. This protein also consists of 8 tandem repeats of a 20 amino acid sequence, which is characteristic of group 1 LEA proteins from non-animal species. The LEA protein and its gene are expressed only in encysted embryos and not in larvae or adults. Evidence is presented to show that the LEA protein functions in the prevention of drying-induced protein aggregation, which supports its functional role in desiccation tolerance. This report describes, for the first time, the purification and characterization of a group 1 LEA protein from an animal species.

  8. Universal stress protein Rv2624c alters abundance of arginine and enhances intracellular survival by ATP binding in mycobacteria

    Science.gov (United States)

    Jia, Qiong; Hu, Xinling; Shi, Dawei; Zhang, Yan; Sun, Meihao; Wang, Jianwei; Mi, Kaixia; Zhu, Guofeng

    2016-01-01

    The universal stress protein family is a family of stress-induced proteins. Universal stress proteins affect latency and antibiotic resistance in mycobacteria. Here, we showed that Mycobacterium smegmatis overexpressing M. tuberculosis universal stress protein Rv2624c exhibits increased survival in human monocyte THP-1 cells. Transcriptome analysis suggested that Rv2624c affects histidine metabolism, and arginine and proline metabolism. LC-MS/MS analysis showed that Rv2624c affects the abundance of arginine, a modulator of both mycobacteria and infected THP-1 cells. Biochemical analysis showed that Rv2624c is a nucleotide-binding universal stress protein, and an Rv2624c mutant incapable of binding ATP abrogated the growth advantage in THP-1 cells. Rv2624c may therefore modulate metabolic pathways in an ATP-dependent manner, changing the abundance of arginine and thus increasing survival in THP-1 cells. PMID:27762279

  9. Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis

    Directory of Open Access Journals (Sweden)

    McDermott Jason E

    2012-04-01

    Full Text Available Abstract Background High-throughput methods for obtaining global measurements of transcript and protein levels in biological samples has provided a large amount of data for identification of 'target' genes and proteins of interest. These targets may be mediators of functional processes involved in disease and therefore represent key points of control for viruses and bacterial pathogens. Genes and proteins that are the most highly differentially regulated are generally considered to be the most important. We present topological analysis of co-abundance networks as an alternative to differential regulation for confident identification of target proteins from two related global proteomics studies of hepatitis C virus (HCV infection. Results We analyzed global proteomics data sets from a cell culture study of HCV infection and from a clinical study of liver biopsies from HCV-positive patients. Using lists of proteins known to be interaction partners with pathogen proteins we show that the most differentially regulated proteins in both data sets are indeed enriched in pathogen interactors. We then use these data sets to generate co-abundance networks that link proteins based on similar abundance patterns in time or across patients. Analysis of these co-abundance networks using a variety of network topology measures revealed that both degree and betweenness could be used to identify pathogen interactors with better accuracy than differential regulation alone, though betweenness provides the best discrimination. We found that though overall differential regulation was not correlated between the cell culture and liver biopsy data, network topology was conserved to an extent. Finally, we identified a set of proteins that has high betweenness topology in both networks including a protein that we have recently shown to be essential for HCV replication in cell culture. Conclusions The results presented show that the network topology of protein co-abundance

  10. Dynamin-related proteins Vps1p and Dnm1p control peroxisome abundance in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Kuravi, Kasinath; Nagotu, Shirisha; Krikken, Arjen M; Sjollema, Klaas; Deckers, Markus; Erdmann, Ralf; Veenhuis, Marten; van der Klei, Ida J

    2006-01-01

    Saccharomyces cerevisiae contains three dynamin-related-proteins, Vps1p, Dnm1p and Mgm1p. Previous data from glucose-grown VPS1 and DNM1 null mutants suggested that Vps1p, but not Dnm1p, plays a role in regulating peroxisome abundance. Here we show that deletion of DNM1 also results in reduction of

  11. Stable isotope labelled mass spectrometry for quantification of the relative abundances for expressed proteins induced by PeaT1

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The protein elicitor from the mycelium of Alternaria tenuissima has been isolated.The elicitor triggered resistance to the tobacco mosaic virus in tobacco by inducing relative oxygen species,but without causing hypersensitive necrosis.The elicitor is reported to impart resistance against Verticillium dahliae and to increase yield in cotton,but its mechanism is not yet clear.In this study,the stable isotope labelled mass spectrometry method was used to quantify the relative abundances of protein expression induced by PeaT1 in Arabidopsis.A significant difference in the relative abundances for the expression of different proteins related to metabolism,modification,regulatory,defense,stress and antioxidation was found in Arabidopsis.

  12. Analysis of the plasma proteome in COPD: Novel low abundance proteins reflect the severity of lung remodeling.

    Science.gov (United States)

    Merali, Salim; Barrero, Carlos A; Bowler, Russell P; Chen, Diane Er; Criner, Gerard; Braverman, Alan; Litwin, Samuel; Yeung, Anthony; Kelsen, Steven G

    2014-04-01

    The search for COPD biomarkers has largely employed a targeted approach that focuses on plasma proteins involved in the systemic inflammatory response and in lung injury and repair. This proof of concept study was designed to test the idea that an open, unbiased, in-depth proteomics approach could identify novel, low abundance plasma proteins i.e., ng/mL concentration, which could serve as potential biomarkers. Differentially expressed proteins were identified in a discovery group with severe COPD (FEV1 <45% predicted; n = 10). Subjects with normal lung function matched for age, sex, ethnicity and smoking history served as controls (n = 10). Pooled plasma from each group was exhaustively immunodepleted of abundant proteins, d separated by 1-D gel electrophoresis and extensively fractionated prior to LC-tandem mass spectroscopy (GeLC-MS). Thirty one differentially expressed proteins were identified in the discovery group including markers of lung defense against oxidant stress, alveolar macrophage activation, and lung tissue injury and repair. Four of the 31 proteins (i.e., GRP78, soluble CD163, IL1AP and MSPT9) were measured in a separate verification group of 80 subjects with varying COPD severity by immunoassay. All 4 were significantly altered in COPD and 2 (GRP78 and soluble CD163) correlated with both FEV1 and the extent of emphysema. In-depth, plasma proteomic analysis identified a group of novel, differentially expressed, low abundance proteins that reflect known pathogenic mechanisms and the severity of lung remodeling in COPD. These proteins may also prove useful as COPD biomarkers.

  13. Region-Specific Protein Abundance Changes in the Brain of MPTP-induced Parkinson’s Disease Mouse Model

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xu; Zhou, Jianying; Chin, Mark H; Schepmoes, Athena A; Petyuk, Vladislav A; Weitz, Karl K; Petritis, Brianne O; Monroe, Matthew E; Camp, David G; Wood, Stephen A; Melega, William P; Bigelow, Diana J; Smith, Desmond J; Qian, Weijun; Smith, Richard D

    2010-02-15

    Parkinson’s disease (PD) is characterized by dopaminergic neurodegeneration in the nigrostriatal region of the brain; however, the neurodegeneration extends well beyond dopaminergic neurons. To gain a better understanding of the molecular changes relevant to PD, we applied two-dimensional LC-MS/MS to comparatively analyze the proteome changes in four brain regions (striatum, cerebellum, cortex, and the rest of brain) using a MPTP-induced PD mouse model with the objective to identify nigrostriatal-specific and other region-specific protein abundance changes. The combined analyses resulted in the identification of 4,895 non-redundant proteins with at least two unique peptides per protein. The relative abundance changes in each analyzed brain region were estimated based on the spectral count information. A total of 518 proteins were observed with significant MPTP-induced changes across different brain regions. 270 of these proteins were observed with specific changes occurring either only in the striatum and/or in the rest of the brain region that contains substantia nigra, suggesting that these proteins are associated with the underlying nigrostriatal pathways. Many of the proteins that exhibit significant abundance changes were associated with dopamine signaling, mitochondrial dysfunction, the ubiquitin system, calcium signaling, the oxidative stress response, and apoptosis. A set of proteins with either consistent change across all brain regions or with changes specific to the cortex and cerebellum regions were also detected. One of the interesting proteins is ubiquitin specific protease (USP9X), a deubiquination enzyme involved in the protection of proteins from degradation and promotion of the TGF-β pathway, which exhibited altered abundances in all brain regions. Western blot validation showed similar spatial changes, suggesting that USP9X is potentially associated with neurodegeneration. Together, this study for the first time presents an overall picture of

  14. Lactate dehydrogenase A as a highly abundant eye lens protein in platypus (Ornithorhynchus anatinus): upsilon (upsilon)-crystallin.

    Science.gov (United States)

    van Rheede, Teun; Amons, Reinout; Stewart, Niall; de Jong, Wilfried W

    2003-06-01

    Vertebrate eye lenses mostly contain two abundant types of proteins, the alpha-crystallins and the beta/gamma-crystallins. In addition, certain housekeeping enzymes are highly expressed as crystallins in various taxa. We now observed an unusual approximately 41-kd protein that makes up 16% to 18% of the total protein in the platypus eye lens. Its cDNA sequence was determined, which identified the protein as muscle-type lactate dehydrogenase A (LDH-A). It is the first observation of LDH-A as a crystallin, and we designate it upsilon (upsilon)-crystallin. Interestingly, the related heart-type LDH-B occurs as an abundant lens protein, known as epsilon-crystallin, in many birds and crocodiles. Thus, two members of the ldh gene family have independently been recruited as crystallins in different higher vertebrate lineages, suggesting that they are particularly suited for this purpose in terms of gene regulatory or protein structural properties. To establish whether platypus LDH-A/upsilon-crystallin has been under different selective constraints as compared with other vertebrate LDH-A sequences, we reconstructed the vertebrate ldh-a gene phylogeny. No conspicuous rate deviations or amino acid replacements were observed.

  15. Abundant class III acidic chitinase homologue in tamarind (Tamarindus indica) seed serves as the major storage protein.

    Science.gov (United States)

    Rao, Devavratha H; Gowda, Lalitha R

    2008-03-26

    The phyla Leguminosae contains protease inhibitors, lectins, chitinases, and glycohydrolases as major defense proteins in their seeds. Electrophoretic analysis of the seed proteins of tamarind ( Tamarindus indica L.), an agri-waste material, indicated the unusual presence of two major proteins comparable to overexpression of recombinant proteins. These proteins were identified by amino-terminal analysis to be (1) Kunitz-type trypsin inhibitor and (2) class III endochitinase (34000 Da). These two proteins were purified to apparent homogeneity by a single-step chitin bead affinity chromatography and characterized. The Kunitz inhibitor was specific toward inhibiting trypsin with a stoichiometry of 1:1. The 33000 +/- 1000 Da protein, accounting for >50% of the total seed protein, is an acidic glycoprotein exhibiting a very low endotype hydrolytic activity toward chitin derivatives. SDS-PAGE followed by densitometry of tamarind seed germination indicates the disappearance of the chitinase with the concomitant appearance of a cysteine endopeptidase. On the basis of its abundance, accumulation without any pathogenesis-related stimulus, temporal regulation, amino acid composition, and very low enzyme activity, this 34000 Da protein designated "tamarinin" physiologically serves as the major storage protein.

  16. Pharmacological zinc and phytase supplementation enhance metallothionein mRNA abundance and protein concentration in newly weaned pigs.

    Science.gov (United States)

    Martínez, Michelle M; Hill, Gretchen M; Link, Jane E; Raney, Nancy E; Tempelman, Robert J; Ernst, Catherine W

    2004-03-01

    The swine industry feeds pharmacological zinc (Zn) to newly weaned pigs to improve health. Because most swine diets are plant-based with a high phytic acid content, we hypothesized that adding phytase to diets could reduce the amount of Zn required to obtain beneficial responses. The role of metallothionein (MT) in Zn homeostasis could be important in this positive response. Thus, the goal of this study was to investigate the effect of dietary Zn and phytase on relative MT mRNA abundance and protein concentration in newly weaned pigs. Diets containing adequate (150 mg Zn/kg) or pharmacological concentrations of Zn (1000 or 2000 mg Zn/kg), as zinc oxide, with or without phytase [0, 500 phytase units (FTU)/kg, Natuphos, BASF] were fed in a 3 x 2 factorial design. Plasma and tissue minerals were measured in pigs killed after 14 d of dietary intervention. Hepatic and renal relative MT mRNA abundance and protein were greater (P pigs fed 1000 mg Zn/kg with phytase, or 2000 mg Zn/kg with or without phytase vs. the remaining treatments. Intestinal mucosa MT mRNA abundance and protein were greater (P pigs fed 2000 mg Zn/kg with phytase than in pigs fed 2000 mg Zn/kg alone or 1000 mg Zn/kg with phytase. Pigs fed 1000 mg Zn/kg plus phytase or 2000 mg Zn/kg with or without phytase had higher plasma, hepatic, and renal Zn than those fed the adequate Zn diets or 1000 mg Zn/kg. We conclude that feeding 1000 mg Zn/kg with phytase enhances MT mRNA abundance and protein and Zn absorption to the same degree as 2000 mg Zn/kg with and without phytase.

  17. SPAK and OSR1 Sensitive Cell Membrane Protein Abundance and Activity of KCNQ1/E1 K+ Channels

    Directory of Open Access Journals (Sweden)

    Bernat Elvira

    2015-11-01

    Full Text Available Background/Aims: KCNQ1/E1 channels are expressed in diverse tissues and serve a variety of functions including endolymph secretion in the inner ear, cardiac repolarization, epithelial transport and cell volume regulation. Kinases involved in regulation of epithelial transport and cell volume include SPAK (SPS1-related proline/alanine-rich kinase and OSR1 (oxidative stress-responsive kinase 1, which are under control of WNK (with-no-K[Lys] kinases. The present study explored whether KCNQ1/E1 channels are regulated by SPAK and/or OSR1. Methods: cRNA encoding KCNQ1/E1 was injected into Xenopus oocytes with or without additional injection of cRNA encoding wild-type SPAK, constitutively active T233ESPAK, WNK insensitive T233ASPAK, catalytically inactive D212ASPAK, wild-type OSR1, constitutively active T185EOSR1, WNK insensitive T185AOSR1 and catalytically inactive D164AOSR1. Voltage gated K+ channel activity was quantified utilizing dual electrode voltage clamp and KCNQ1/E1 channel protein abundance in the cell membrane utilizing chemiluminescence of KCNQ1/E1 containing an extracellular Flag tag epitope (KCNQ1-Flag/E1. Results: KCNQ1/E1 activity and KCNQ1-Flag/E1 protein abundance were significantly enhanced by wild-type SPAK and T233ESPAK, but not by T233ASPAK and D212ASPAK. Similarly, KCNQ1/E1 activity and KCNQ1-Flag/E1 protein abundance were significantly increased by wild-type OSR1 and T185EOSR1, but not by T185AOSR1 and D164AOSR1. Conclusions: SPAK and OSR1 participate in the regulation of KCNQ1/E1 protein abundance and activity.

  18. Isolation of Low Abundance Proteins and Cells Using Buoyant Glass Microbubble Chromatography

    Directory of Open Access Journals (Sweden)

    Steingrimur Stefansson

    2013-01-01

    Full Text Available Conventional protein affinity chromatography relies on highly porous resins that have large surface areas. These properties are ideal for fast flow separation of proteins from biological samples with maximum yields, but these properties can also lead to increased nonspecific protein binding. In certain applications where the purity of an isolated protein is more important than the yield, using a glass solid phase could be advantageous as glass is nonporous and hydrophilic and has a low surface area and low nonspecific protein binding. As a proof of principle, we used protein A-conjugated hollow glass microbubbles to isolate fluorescently labeled neurofilament heavy chain spiked into serum and compared them to protein A Sepharose and protein A magnetic beads (Dynabeads using an anti-neurofilament protein antibody. As expected, a greater volume of glass bubbles was required to match the binding capacity of the magnetic beads and Sepharose resins. On the other hand, nonspecific protein binding to glass bubbles was greatly reduced compared to the other resins. Additionally, since the glass bubbles are buoyant and transparent, they are well suited for isolating cells from biological samples and staining them in situ.

  19. Analysis of the c-src gene product structure, abundance, and protein kinase activity in human neuroblastoma and glioblastoma cells.

    Science.gov (United States)

    O'Shaughnessy, J; Deseau, V; Amini, S; Rosen, N; Bolen, J B

    1987-01-01

    We have compared in different human neuroblastoma cell lines and human glioblastoma cells the expression level, structure, and tyrosine-specific protein kinase activity of pp60c-src. Our results show that not all human neuroblastoma cell lines express pp60c-src molecules with amino-terminal structural alterations. In neuroblastoma cells which possess pp60c-src with altered gel migration, the diminished polyacrylamide gel mobility of pp60c-src was found not to be dependent upon amino-terminal phosphorylations since extensive treatment of these molecules with phosphatase did not significantly change their gel migration properties. Similar differences in gel migration were observed when RNA from the various neuroblastoma and glioblastoma cells was translated in vitro using either rabbit reticulocyte or wheat germ lysates. White the level of c-src mRNA in the different cells analyzed was found to be similar, the abundance of pp60c-src in these same cells was found to vary by as much as 12-fold. This suggests that the abundance of pp60c-src in human neuroendocrine tumors is regulated through post-transcriptional and/or post-translational events which may be related to the stage of neuronal differentiation of the cells. Based upon determination of pp60c-src abundance by immunoblot analysis, we demonstrate that pp60c-src molecules derived from human neuroblastoma and glioblastoma cells have very similar in vitro protein kinase activities.

  20. Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR).

    Science.gov (United States)

    Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J; Laclette, Juan P; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

    2015-05-19

    Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest.

  1. Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR)

    Science.gov (United States)

    Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J.; Laclette, Juan P.; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

    2015-01-01

    Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest. PMID:25989346

  2. Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein abundances by mass spectrometry.

    Science.gov (United States)

    Ahrné, Erik; Martinez-Segura, Amalia; Syed, Afzal Pasha; Vina-Vilaseca, Arnau; Gruber, Andreas J; Marguerat, Samuel; Schmidt, Alexander

    2015-09-01

    The generation of dynamic models of biological processes critically depends on the determination of precise cellular concentrations of biomolecules. Measurements of system-wide absolute protein levels are particularly valuable information in systems biology. Recently, mass spectrometry based proteomics approaches have been developed to estimate protein concentrations on a proteome-wide scale. However, for very complex proteomes, fractionation steps are required, increasing samples number and instrument analysis time. As a result, the number of full proteomes that can be routinely analyzed is limited. Here we combined absolute quantification strategies with the multiplexing capabilities of isobaric tandem mass tags to determine cellular protein abundances in a high throughput and proteome-wide scale even for highly complex biological systems, such as a whole human cell line. We generated two independent data sets to demonstrate the power of the approach regarding sample throughput, dynamic range, quantitative precision and accuracy as well as proteome coverage in comparison to existing mass spectrometry based strategies.

  3. Effects of EPA and DHA on lipid droplet accumulation and mRNA abundance of PAT proteins in caprine monocytes.

    Science.gov (United States)

    Lecchi, Cristina; Invernizzi, Guido; Agazzi, Alessandro; Modina, Silvia; Sartorelli, Paola; Savoini, Giovanni; Ceciliani, Fabrizio

    2013-04-01

    The present study investigated the in vitro effects on caprine monocytes of two ω-3 PUFAs, namely eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on lipid droplet formation, an emerging process of fundamental importance in innate immunity regulation. The mRNA abundance of PAT protein family (PLIN1, PLIN2 and PLIN3), involved in the formation and trafficking of the droplets, was also assessed. The effects of EPA and DHA on monocyte apoptosis were studied as well. The number of lipid droplets per cell was found to be dependent on both type and concentration of fatty acid. ω-3 PUFAs upregulated PLIN3 and PLIN2 gene expression, as well as apoptosis rate. The present findings suggest that PUFA might modify innate immune functions of goat monocytes by interfering with the formation of lipid droplets and by upregulating proteins belonging to PAT protein family.

  4. Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans.

    Directory of Open Access Journals (Sweden)

    B Anne Neville

    Full Text Available Some Eubacterium and Roseburia species are among the most prevalent motile bacteria present in the intestinal microbiota of healthy adults. These flagellate species contribute "cell motility" category genes to the intestinal microbiome and flagellin proteins to the intestinal proteome. We reviewed and revised the annotation of motility genes in the genomes of six Eubacterium and Roseburia species that occur in the human intestinal microbiota and examined their respective locus organization by comparative genomics. Motility gene order was generally conserved across these loci. Five of these species harbored multiple genes for predicted flagellins. Flagellin proteins were isolated from R. inulinivorans strain A2-194 and from E. rectale strains A1-86 and M104/1. The amino-termini sequences of the R. inulinivorans and E. rectale A1-86 proteins were almost identical. These protein preparations stimulated secretion of interleukin-8 (IL-8 from human intestinal epithelial cell lines, suggesting that these flagellins were pro-inflammatory. Flagellins from the other four species were predicted to be pro-inflammatory on the basis of alignment to the consensus sequence of pro-inflammatory flagellins from the β- and γ- proteobacteria. Many fliC genes were deduced to be under the control of σ(28. The relative abundance of the target Eubacterium and Roseburia species varied across shotgun metagenomes from 27 elderly individuals. Genes involved in the flagellum biogenesis pathways of these species were variably abundant in these metagenomes, suggesting that the current depth of coverage used for metagenomic sequencing (3.13-4.79 Gb total sequence in our study insufficiently captures the functional diversity of genomes present at low (≤1% relative abundance. E. rectale and R. inulinivorans thus appear to synthesize complex flagella composed of flagellin proteins that stimulate IL-8 production. A greater depth of sequencing, improved evenness of sequencing

  5. Diversity, abundance, and sex-specific expression of chemosensory proteins in the reproductive organs of the locust Locusta migratoria manilensis.

    Science.gov (United States)

    Zhou, Xian-Hong; Ban, Li-Ping; Iovinella, Immacolata; Zhao, Li-Jing; Gao, Qian; Felicioli, Antonio; Sagona, Simona; Pieraccini, Giuseppe; Pelosi, Paolo; Zhang, Long; Dani, Francesca Romana

    2013-01-01

    Chemosensory proteins (CSPs) are small soluble proteins often associated with chemosensory organs in insects but include members involved in other functions, such as pheromone delivery and development. Although the CSPs of the sensory organs have been extensively studied, little is known on their functions in other parts of the body. A first screening of the available databases has identified 70 sequences encoding CSPs in the oriental locust Locusta migratoria manilensis. Applying proteomic analysis, we have identified 17 of them abundantly expressed in the female reproductive organs, but only one (CSP91) in male organs. Bacterially expressed CSP91 binds fatty acids with a specificity for oleic and linoleic acid, as well as medium-length alcohols and esters. The same acids have been detected as the main gas chromatographic peaks in the dichloromethane extracts of reproductive organs of both sexes. The abundance and the number of CSPs in female reproductive organs indicates important roles for these proteins. We cannot exclude that different functions can be associated with each of the 17 CSPs, including delivery of semiochemicals, solubilization of hormones, direct control of development, or other unknown tasks.

  6. Ferritin acts as the most abundant binding protein for snowdrop lectin in the midgut of rice brown planthoppers (Nilaparvata lugens).

    Science.gov (United States)

    Du, J; Foissac, X; Carss, A; Gatehouse, A M; Gatehouse, J A

    2000-04-01

    The mannose-specific snowdrop lectin [Galanthus nivalis agglutinin (GNA)] displays toxicity to the rice brown planthopper Nilaparvata lugens. A 26kDa GNA-binding polypeptide from N. lugens midgut was identified by lectin blotting and affinity chromatography, and characterized by N-terminal sequencing. This polypeptide is the most abundant binding protein for GNA in the N. lugens midgut. A cDNA (fersub2) encoding this protein was isolated from an N. lugens cDNA library. The deduced amino acid sequence shows significant homology to ferritin subunits from Manduca sexta and other arthropods, plants and vertebrates, and contains a putative N-glycosylation site. Native ferritin was purified from whole insects as a protein of more than 400kDa in size and characterized biochemically. Three subunits of 20, 26 and 27kDa were released from the native complex. The 26kDa subunit binds GNA, and its N-terminal sequence was identical to that of fersub2. A second cDNA (fersub1), exhibiting strong homology with dipteran ferritin, was identified as an abundant cDNA in an N. lugens midgut-specific cDNA library, and could encode the larger ferritin subunit. The fersub1 cDNA carries a stem-loop structure (iron-responsive element) upstream from the start codon, similar to structures that have been shown to play a role in the control of ferritin synthesis in other insects.

  7. Conformation of a group 2 late embryogenesis abundant protein from soybean. Evidence of poly (L-proline)-type II structure.

    Science.gov (United States)

    Soulages, Jose L; Kim, Kangmin; Arrese, Estela L; Walters, Christina; Cushman, John C

    2003-03-01

    Late embryogenesis abundant (LEA) proteins are members of a large group of hydrophilic, glycine-rich proteins found in plants, algae, fungi, and bacteria known collectively as hydrophilins that are preferentially expressed in response to dehydration or hyperosmotic stress. Group 2 LEA (dehydrins or responsive to abscisic acid) proteins are postulated to stabilize macromolecules against damage by freezing, dehydration, ionic, or osmotic stress. However, the structural and physicochemical properties of group 2 LEA proteins that account for such functions remain unknown. We have analyzed the structural properties of a recombinant form of a soybean (Glycine max) group 2 LEA (rGmDHN1). Differential scanning calorimetry of purified rGmDHN1 demonstrated that the protein does not display a cooperative unfolding transition upon heating. Ultraviolet absorption and circular dichroism spectroscopy revealed that the protein is in a largely hydrated and unstructured conformation in solution. However, ultraviolet absorption and circular dichroism measurements collected at different temperatures showed that the protein exists in equilibrium between two extended conformational states: unordered and left-handed extended helical or poly (L-proline)-type II structures. It is estimated that 27% of the residues of rGmDHN1 adopt or poly (L-proline)-type II-like helical conformation at 12 degrees C. The content of extended helix gradually decreases to 15% as the temperature is increased to 80 degrees C. Studies of the conformation of the protein in solution in the presence of liposomes, trifluoroethanol, and sodium dodecyl sulfate indicated that rGmDHN1 has a very low intrinsic ability to adopt alpha-helical structure and to interact with phospholipid bilayers through amphipathic alpha-helices. The ability of the protein to remain in a highly extended conformation at low temperatures could constitute the basis of the functional role of GmDHN1 in the prevention of freezing, desiccation

  8. Identification of an abundant 56 kDa protein implicated in food allergy as granule-bound starch synthase.

    Science.gov (United States)

    Krishnan, Hari B; Chen, Ming-Hsuan

    2013-06-01

    Rice, the staple food of south and east Asian counties, is considered to be hypoallergenic. However, several clinical studies have documented rice-induced allergy in sensitive patients. Rice proteins with molecular weights of 14-16, 26, 33, and 56 kDa have been identified as allergens. Recently, it was documented that the 56 kDa rice allergen was responsible for rice-induced anaphylaxis. The 14-16 kDa allergens have been identified as α-amylase inhibitors; the 26 kDa protein has been identified as α-globulin; and the 33 kDa protein has been identified as glyoxalase I. However, the identity of the 56 kDa rice allergen has not yet been determined. In this study, we demonstrate that serum from patients allergic to maize shows IgE binding to a 56 kDa protein that was present in both maize and rice but not in the oil seeds soybean and peanut. The 56 kDa IgE-binding protein was abundant in the rice endosperm. We have purified this protein from rice endosperm and demonstrated its reactivity to IgE antibodies from the serum of maize-allergic patients. The purified protein was subjected to matrix-assisted laser desorption ionization-time of flight-tandem mass spectrometry analysis, resulting in identification of this rice allergen as granule-bound starch synthase, a product of the Waxy gene. Immunoblot analysis using protein extracts from a waxy mutant of rice revealed the absence of the 56 kDa IgE-binding protein. Our results demonstrate that the 56 kDa rice allergen is granule-bound starch synthase and raise the possibility of using waxy mutants of rice as a potential source of the hypoallergenic diet for patients sensitized to the 56 kDa rice allergen.

  9. Effects of Tamarindus indica fruit pulp extract on abundance of HepG2 cell lysate proteins and their possible consequential impact on metabolism and inflammation.

    Science.gov (United States)

    Chong, Ursula R W; Abdul-Rahman, Puteri S; Abdul-Aziz, Azlina; Hashim, Onn H; Mat-Junit, Sarni

    2013-01-01

    The fruit pulp extract of Tamarindus indica has been reported for its antioxidant and hypolipidemic properties. In this study, the methanol extract of T. indica fruit pulp was investigated for its effects on the abundance of HepG2 cell lysate proteins. Cell lysate was extracted from HepG2 cells grown in the absence and presence of the methanol extract of T. indica fruit pulp. Approximately 2500 spots were resolved using two-dimensional gel electrophoresis and the abundance of 20 cellular proteins was found to be significantly reduced. Among the proteins of reduced abundance, fourteen, including six proteins involved in metabolism (including ethanolamine phosphate cytidylyltransferase), four mitochondrial proteins (including prohibitin and respiratory chain proteins), and four proteins involved in translation and splicing, were positively identified by mass spectrometry and database search. The identified HepG2 altered abundance proteins, when taken together and analyzed by Ingenuity Pathways Analysis (IPA) software, are suggestive of the effects of T. indica fruit pulp extract on metabolism and inflammation, which are modulated by LXR/RXR. In conclusion, the methanol fruit pulp extract of T. indica was shown to cause reduced abundance of HepG2 mitochondrial, metabolic, and regulatory proteins involved in oxidative phosphorylation, protein synthesis, and cellular metabolism.

  10. Effects of Tamarindus indica Fruit Pulp Extract on Abundance of HepG2 Cell Lysate Proteins and Their Possible Consequential Impact on Metabolism and Inflammation

    Directory of Open Access Journals (Sweden)

    Ursula R. W. Chong

    2013-01-01

    Full Text Available The fruit pulp extract of Tamarindus indica has been reported for its antioxidant and hypolipidemic properties. In this study, the methanol extract of T. indica fruit pulp was investigated for its effects on the abundance of HepG2 cell lysate proteins. Cell lysate was extracted from HepG2 cells grown in the absence and presence of the methanol extract of T. indica fruit pulp. Approximately 2500 spots were resolved using two-dimensional gel electrophoresis and the abundance of 20 cellular proteins was found to be significantly reduced. Among the proteins of reduced abundance, fourteen, including six proteins involved in metabolism (including ethanolamine phosphate cytidylyltransferase, four mitochondrial proteins (including prohibitin and respiratory chain proteins, and four proteins involved in translation and splicing, were positively identified by mass spectrometry and database search. The identified HepG2 altered abundance proteins, when taken together and analyzed by Ingenuity Pathways Analysis (IPA software, are suggestive of the effects of T. indica fruit pulp extract on metabolism and inflammation, which are modulated by LXR/RXR. In conclusion, the methanol fruit pulp extract of T. indica was shown to cause reduced abundance of HepG2 mitochondrial, metabolic, and regulatory proteins involved in oxidative phosphorylation, protein synthesis, and cellular metabolism.

  11. The highly abundant protein Ag-Ibp55 from Ascaridia galli represents a novel type of lipid-binding proteins

    NARCIS (Netherlands)

    Jordanova, R; Radoslavov, G; Fischer, P; Torda, A; Lottspeich, F; Boteva, R; Walter, RD; Bankov, [No Value; Liebau, E

    2005-01-01

    Lipid-binding proteins exhibit important functions in lipid transport, cellular signaling, gene transcription, and cytoprotection. Their functional analogues in nematodes are nematode polyprotein allergens/antigens and fatty acid and retinoid-binding proteins. This work describes a novel 55-kDa prot

  12. Sodium-pump gene-expression, protein abundance and enzyme activity in isolated nephron segments of the aging rat kidney

    Science.gov (United States)

    Scherzer, Pnina; Gal-Moscovici, Anca; Sheikh-Hamad, David; Popovtzer, Mordecai M

    2015-01-01

    Aging is associated with alteration in renal tubular functions, including sodium handling and concentrating ability. Na-K-ATPase plays a key role in driving tubular transport, and we hypothesized that decreased concentrating ability of the aging kidney is due in part to downregulation of Na-K-ATPase. In this study, we evaluated Na and K balance, aldosterone levels, and Na-K-ATPase gene expression, protein abundance, and activity in aging rat kidney. Na-K-ATPase activity (assayed microfluorometrically), mRNA (RT-PCR), and protein abundance (immunoblotting) were quantitated in the following isolated nephron segments: PCT, PST, MTAL, DCT, and CCD from 2, 8, 15, and 24 month-old-rats. In the course of aging, creatinine clearance decreased from 0.48 ± 0.02 mL/min/100 g BW to 0.28 ± 0.06 (P < 0.001) and aldosterone decreased from 23.6 ± 0.8 ng/dL to 13.2 ± 0.6 (P < 0.001). Serum Na+ and K+ increased by 4.0% and 22.5%, respectively. Na-K-ATPase activity, mRNA, and protein abundance of the α1 subunit displayed similar trends in all assayed segments; increasing in PCT and PST; decreasing in MTAL and DCT; increasing in CCD: in PCT they increased by 40%, 75%, and 250%, respectively; while in PST they increased by 80%, 50%, and 100%, respectively (P < 0.001). In MTAL they declined by 36%, 24%, and 34%, respectively, and in DCT by 38%, 59%, and 60%, respectively (P < 0.001). They were higher in CCD by 110%, 115%, and 246%, respectively (P < 0.001). Rats maintained Na/K balance; however with a steady state elevated serum K+. These results reveal quantitative changes in axial distribution of Na-K-ATPase at the level of gene expression, protein abundance, and activity in the nephrons of aging animals and may explain, in part, the pathophysiology of the senescent kidney. PMID:26056060

  13. One-step non-chromatography purification of a low abundant fucosylated protein from complex plant crude extract

    Directory of Open Access Journals (Sweden)

    Lindsay Arnold

    2015-08-01

    Full Text Available Effective methods for isolation and purification of glycoproteins and other glycoconjugates are important to biopharmaceutical industry and diagnostic industry. They are also critical to an emerging field of glycoproteomics. In this work, we applied the newly-developed affinity ligand, a fusion protein of elastic like polymer (ELP and a bacterial lectin, in an affinity precipitation process to purify soybean peroxidase (SBP based on the presence of fucoseon the protein surface. We addressed, in particular, the challenge of purifying a low abundant protein from a complex dilute crude plant extract. The novel affinity precipitation developed in this work was very promising. One step binding and precipitation resulted in >95% recovery yield directly from crude extract and a 22.7 fold purification, giving a specific activity of 420 U/mg. The SBP isolated using this affinity precipitation meets or exceeds the quality specifications of reagent grade products by Sigma. We showed that the recovery yield had a strong dependence on the molar ratio of ligand to target fucosylated protein, with a ratio of three giving nearly full recovery, which could be predicted based on the total fucose content per protein molecule and the number of binding site per ligand molecule. We additionally developed a method of ligand regeneration and investigated its reuse. A simple wash with pH buffer was shown to be effective to regenerate the binding capacity for the ligand, and the ligand could be used for 10 times, giving an averaged 80% isolation yield based on initial input of soybean peroxidase. Taken together, an effective method of affinity precipitation was developed, which could be used to enrich a low abundant target glycoprotein from a complex mixture with a high recovery yield. The high selectivity for fucosylated protein and its ease of operation make this method particularly useful for purification of low abundant glycoprotein from natural sources. This work

  14. Chernobyl seed project. Advances in the identification of differentially abundant proteins in a radio-contaminated environment

    Directory of Open Access Journals (Sweden)

    Namik Mammad Oglu Rashydov

    2015-07-01

    Full Text Available Plants have the ability to grow and successfully reproduce in radio-contaminated environments, which has been highlighted by nuclear accidents at Chernobyl (1986 and Fukushima (2011. The main aim of this article is to summarize the advances of the Chernobyl seed project which has the purpose to provide proteomic characterization of plants grown in the Chernobyl area. We present a summary of comparative proteomic studies on soybean and flax seeds harvested from radio-contaminated Chernobyl areas during two successive generations. Using experimental design developed for radio-contaminated areas, altered abundances of glycine betaine, seed storage proteins, and proteins associated with carbon assimilation into fatty acids were detected. Similar studies in Fukushima radio-contaminated areas might complement these data. The results from these Chernobyl experiments can be viewed in a user-friendly format at a dedicated web-based database freely available at www.chernobylproteomics.sav.sk.

  15. Characterization of threonine side chain dynamics in an antifreeze protein using natural abundance {sup 13}C NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Daley, Margaret E.; Sykes, Brian D. [University of Alberta, Department of Biochemistry, CIHR Group in Protein Structure and Function and Protein Engineering Network of Centres of Excellence (Canada)

    2004-06-15

    The dynamics of threonine side chains of the Tenebrio molitor antifreeze protein (TmAFP) were investigated using natural abundance {sup 13}C NMR. In TmAFP, the array of threonine residues on one face of the protein is responsible for conferring its ability to bind crystalline ice and inhibit its growth. Heteronuclear longitudinal and transverse relaxation rates and the {sup 1}H-{sup 13}C NOE were determined in this study. The C{alpha}H relaxation measurements were compared to the previously measured {sup 15}N backbone parameters and these are found to be in agreement. For the analysis of the threonine side chain motions, the model of restricted rotational diffusion about the {chi}{sub 1} dihedral angle was employed [London and Avitabile (1978) J. Am. Chem. Soc., 100, 7159-7165]. We demonstrate that the motion experienced by the ice binding threonine side chains is highly restricted, with an approximate upper limit of less than {+-}25 deg.

  16. Study of model systems to test the potential function of Artemia group 1 late embryogenesis abundant (LEA) proteins.

    Science.gov (United States)

    Warner, Alden H; Guo, Zhi-hao; Moshi, Sandra; Hudson, John W; Kozarova, Anna

    2016-01-01

    Embryos of the brine shrimp, Artemia franciscana, are genetically programmed to develop either ovoviparously or oviparously depending on environmental conditions. Shortly upon their release from the female, oviparous embryos enter diapause during which time they undergo major metabolic rate depression while simultaneously synthesize proteins that permit them to tolerate a wide range of stressful environmental events including prolonged periods of desiccation, freezing, and anoxia. Among the known stress-related proteins that accumulate in embryos entering diapause are the late embryogenesis abundant (LEA) proteins. This large group of intrinsically disordered proteins has been proposed to act as molecular shields or chaperones of macromolecules which are otherwise intolerant to harsh conditions associated with diapause. In this research, we used two model systems to study the potential function of the group 1 LEA proteins from Artemia. Expression of the Artemia group 1 gene (AfrLEA-1) in Escherichia coli inhibited growth in proportion to the number of 20-mer amino acid motifs expressed. As well, clones of E. coli, transformed with the AfrLEA-1 gene, expressed multiple bands of LEA proteins, either intrinsically or upon induction with isopropyl-β-thiogalactoside (IPTG), in a vector-specific manner. Expression of AfrLEA-1 in E. coli did not overcome the inhibitory effects of high concentrations of NaCl and KCl but modulated growth inhibition resulting from high concentrations of sorbitol in the growth medium. In contrast, expression of the AfrLEA-1 gene in Saccharomyces cerevisiae did not alter the growth kinetics or permit yeast to tolerate high concentrations of NaCl, KCl, or sorbitol. However, expression of AfrLEA-1 in yeast improved its tolerance to drying (desiccation) and freezing. Under our experimental conditions, both E. coli and S. cerevisiae appear to be potentially suitable hosts to study the function of Artemia group 1 LEA proteins under environmentally

  17. Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium, Ruminococcus flavefaciens FD-1.

    Directory of Open Access Journals (Sweden)

    Marco T Rincon

    Full Text Available BACKGROUND: The cellulosome is a multi-enzyme machine, which plays a key role in the breakdown of plant cell walls in many anaerobic cellulose-degrading microorganisms. Ruminococcus flavefaciens FD-1, a major fiber-degrading bacterium present in the gut of herbivores, has the most intricate cellulosomal organization thus far described. Cellulosome complexes are assembled through high-affinity cohesin-dockerin interactions. More than two-hundred dockerin-containing proteins have been identified in the R. flavefaciens genome, yet the reason for the expansion of these crucial cellulosomal components is yet unknown. METHODOLOGY/PRINCIPAL FINDINGS: We have explored the full spectrum of 222 dockerin-containing proteins potentially involved in the assembly of cellulosome-like complexes of R. flavefaciens. Bioinformatic analysis of the various dockerin modules showed distinctive conservation patterns within their two Ca(2+-binding repeats and their flanking regions. Thus, we established the conceptual framework for six major groups of dockerin types, according to their unique sequence features. Within this framework, the modular architecture of the parent proteins, some of which are multi-functional proteins, was evaluated together with their gene expression levels. Specific dockerin types were found to be associated with selected groups of functional components, such as carbohydrate-binding modules, numerous peptidases, and/or carbohydrate-active enzymes. In addition, members of other dockerin groups were linked to structural proteins, e.g., cohesin-containing proteins, belonging to the scaffoldins. CONCLUSIONS/SIGNIFICANCE: This report profiles the abundance and sequence diversity of the R. flavefaciens FD-1 dockerins, and provides the molecular basis for future understanding of the potential for a wide array of cohesin-dockerin specificities. Conserved differences between dockerins may be reflected in their stability, function or expression within

  18. A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast*

    OpenAIRE

    Blein-Nicolas, Mélisande; Albertin, Warren; Da Silva, Telma; Valot, Benoît; Balliau, Thierry; Masneuf-Pomarède, Isabelle; Bely, Marina; Marullo, Philippe; Sicard, Delphine; Dillmann, Christine; de Vienne, Dominique; Zivy, Michel

    2015-01-01

    Heterosis is a universal phenomenon that has major implications in evolution and is of tremendous agro-economic value. To study the molecular manifestations of heterosis and to find factors that maximize its strength, we implemented a large-scale proteomic experiment in yeast. We analyzed the inheritance of 1,396 proteins in 55 inter- and intraspecific hybrids obtained from Saccharomyces cerevisiae and S. uvarum that were grown in grape juice at two temperatures. We showed that the proportion...

  19. BacS: an abundant bacteroid protein in Rhizobium etli whose expression ex planta requires nifA.

    Science.gov (United States)

    Jahn, Olivia J; Davila, Guillermo; Romero, David; Noel, K Dale

    2003-01-01

    Rhizobium etli CFN42 bacteroids from bean nodules possessed an abundant 16-kDa protein (BacS) that was found in the membrane pellet after cell disruption. This protein was not detected in bacteria cultured in tryptone-yeast extract. In minimal media, it was produced at low oxygen concentration but not in a mutant whose nifA was disrupted. N-terminal sequencing of the protein led to isolation of a bacS DNA fragment. DNA hybridization and nucleotide sequencing revealed three copies of the bacS gene, all residing on the main symbiotic plasmid of strain CFN42. A stretch of 304 nucleotides, exactly conserved upstream of all three bacS open reading frames, had very close matches with the NifA and sigma 54 consensus binding sequences. The only bacS homology in the genetic sequence databases was to three hypothetical proteins of unknown function, all from rhizobial species. Mutation and genetic complementation indicated that each of the bacS genes gives rise to a BacS polypeptide. Mutants disrupted or deleted in all three genes did not produce the BacS polypeptide but were Nod+ and Fix+ on Phaseolus vulgaris.

  20. Molecular evolution of myelin basic protein, an abundant structural myelin component.

    Science.gov (United States)

    Nawaz, Schanila; Schweitzer, Jörn; Jahn, Olaf; Werner, Hauke B

    2013-08-01

    Rapid nerve conduction in jawed vertebrates is facilitated by the myelination of axons, which evolved in ancient cartilaginous fish. We aim to understand the coevolution of myelin and the major myelin proteins. We found that myelin basic protein (MBP) derived from living cartilaginous fish (sharks and rays) associated with the plasma membrane of glial cells similar to the phosphatidylinositol (4,5)-bisphosphate (PIP₂)-binding marker PH-PLCδ1, and that ionomycin-induced PIP₂-hydrolysis led to its cellular redistribution. We identified two paralogous mbp genes in multiple teleost species, consistent with a genome duplication at the root of the teleost clade. Zebrafish mbpb is organized in a complex transcription unit together with the unrelated gene-of-the-oligodendrocyte-lineage (golli) while mbpa does not encode GOLLI. Moreover, the embryonic expression of mbpa and mbpb differed, indicating functional specialization after duplication. However, both mbpa and mbpb-mRNAs were detected in mature oligodendrocytes and Schwann cells, MBPa and MBPb were mass spectrometrically identified in zebrafish myelin, both associated with the plasma membrane via PIP₂, and the ratio of nonsynonymous to synonymous nucleotide-substitution rates (Ka/Ks) was low. Together, this indicates selective pressure to conserve many aspects of the cellular expression and function of MBP across vertebrate species. We propose that the PIP₂-binding function of MBP is evolutionarily old and that its emergence in ancient gnathostomata provided glial cells with the competence to myelinate.

  1. Assessment of current mass spectrometric workflows for the quantification of low abundant proteins and phosphorylation sites

    Directory of Open Access Journals (Sweden)

    Manuel Bauer

    2015-12-01

    Full Text Available The data described here provide a systematic performance evaluation of popular data-dependent (DDA and independent (DIA mass spectrometric (MS workflows currently used in quantitative proteomics. We assessed the limits of identification, quantification and detection for each method by analyzing a dilution series of 20 unmodified and 10 phosphorylated synthetic heavy labeled reference peptides, respectively, covering six orders of magnitude in peptide concentration with and without a complex human cell digest background. We found that all methods performed very similarly in the absence of background proteins, however, when analyzing whole cell lysates, targeted methods were at least 5–10 times more sensitive than directed or DDA methods. In particular, higher stage fragmentation (MS3 of the neutral loss peak using a linear ion trap increased dynamic quantification range of some phosphopeptides up to 100-fold. We illustrate the power of this targeted MS3 approach for phosphopeptide monitoring by successfully quantifying 9 phosphorylation sites of the kinetochore and spindle assembly checkpoint component Mad1 over different cell cycle states from non-enriched pull-down samples. The data are associated to the research article ‘Evaluation of data-dependent and data-independent mass spectrometric workflows for sensitive quantification of proteins and phosphorylation sites׳ (Bauer et al., 2014 [1]. The mass spectrometry and the analysis dataset have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org via the PRIDE partner repository with the dataset identifier PXD000964.

  2. Norvaline and Norleucine May Have Been More Abundant Protein Components during Early Stages of Cell Evolution

    Science.gov (United States)

    Alvarez-Carreño, Claudia; Becerra, Arturo; Lazcano, Antonio

    2013-10-01

    The absence of the hydrophobic norvaline and norleucine in the inventory of protein amino acids is readdressed. The well-documented intracellular accumulation of these two amino acids results from the low-substrate specificity of the branched-chain amino acid biosynthetic enzymes that act over a number of related α-ketoacids. The lack of absolute substrate specificity of leucyl-tRNA synthase leads to a mischarged norvalyl-tRNALeu that evades the translational proofreading activites and produces norvaline-containing proteins, (cf. Apostol et al. J Biol Chem 272:28980-28988, 1997). A similar situation explains the presence of minute but detectable amounts of norleucine in place of methionine. Since with few exceptions both leucine and methionine are rarely found in the catalytic sites of most enzymes, their substitution by norvaline and norleucine, respectively, would have not been strongly hindered in small structurally simple catalytic polypeptides during the early stages of biological evolution. The report that down-shifts of free oxygen lead to high levels of intracellular accumulation of pyruvate and the subsequent biosynthesis of norvaline (Soini et al. Microb Cell Factories 7:30, 2008) demonstrates the biochemical and metabolic consequences of the development of a highly oxidizing environment. The results discussed here also suggest that a broader definition of biomarkers in the search for extraterrestrial life may be required.

  3. Differential protein abundance and function of UT-B urea transporters in human colon.

    Science.gov (United States)

    Collins, D; Winter, D C; Hogan, A M; Schirmer, L; Baird, A W; Stewart, G S

    2010-03-01

    Facilitative UT-B urea transporters enable the passage of urea across cell membranes. Gastrointestinal urea transporters are thought to play a significant role in the urea nitrogen salvaging process that occurs between mammalian hosts and their gut bacteria. This study investigated the expression of UT-B urea transporters in different segments of human colon. Immunoblot analysis showed that human colon expressed a 35-kDa glycosylated UT-B protein in the colonic mucosa. The 35-kDa UT-B transporter was predominantly located in plasma membrane-enriched samples (P UT-B transporters were located throughout colonocytes situated in the upper portion of the colonic crypts. Bidirectional trans-epithelial urea transport was significantly greater in the ascending colon than the descending colon (P UT-B protein in different sections of the human colon, strongly correlating to regions that contain the largest populations of intestinal bacteria. This study suggests an important role for UT-B urea transporters in maintaining the symbiotic relationship between humans and their gut bacteria.

  4. The effect of cryopreservation on DNA damage, gene expression and protein abundance in vertebrate

    Directory of Open Access Journals (Sweden)

    Sujune Tsai

    2012-01-01

    Full Text Available Cryopreservation techniques allow the long-term storage of a wide variety of biological material without significant deterioration in quality. Immediate post-thaw survival is most often used to assess the effect of the freeze-thaw process on cells. However, this parameter provides no information on possible subtle effects of cryopreservation, including DNA damage, alteration of mRNA levels and protein function that may not be evident immediately post thaw. These potential adverse effects don’t necessarily result in cell death. While there are many comprehensive reviews of gamete and embryo cryopreservation in vertebrate species, we review here the publications relating to cryopreservation impact on the genome of sperm, embryos and oocytes.

  5. Group 3 late embryogenesis abundant proteins from embryos of Artemia franciscana: structural properties and protective abilities during desiccation.

    Science.gov (United States)

    Boswell, Leaf C; Menze, Michael A; Hand, Steven C

    2014-01-01

    Group 3 late embryogenesis abundant (LEA) proteins are highly hydrophilic, and their expression is associated with desiccation tolerance in both plants and animals. Here we show that two LEA proteins from embryos of Artemia franciscana, AfrLEA2 and AfrLEA3m, are intrinsically disordered in solution but upon desiccation gain secondary structure, as measured by circular dichroism. Trifluoroethanol and sodium dodecyl sulfate are both shown to induce α-helical structure in AfrLEA2 and AfrLEA3m. Bioinformatic predictions of secondary-structure content for both proteins correspond most closely to conformations measured in the dry state. Because some LEA proteins afford protection to desiccation-sensitive proteins during drying and subsequent rehydration, we tested for this capacity in AfrLEA2 and AfrLEA3m. The protective capacities vary, depending on the target enzyme. For the cytoplasmic enzyme lactate dehydrogenase, neither AfrLEA2 nor AfrLEA3m, with or without trehalose present, was able to afford protection better than that provided by bovine serum albumin (BSA) under the same conditions. However, for another cytoplasmic enzyme, phosphofructokinase, both AfrLEA2 and AfrLEA3m in the presence of trehalose were able to afford protection far greater than that provided by BSA with trehalose. Finally, for the mitochondrial enzyme citrate synthase, 400-μg/mL AfrLEA3m without trehalose provided significantly more protection than the same concentration of either AfrLEA2 or BSA.

  6. Increased Abundance of Proteins Involved in Phytosiderophore Production in Boron-Tolerant Barley1[C][W

    Science.gov (United States)

    Patterson, John; Ford, Kris; Cassin, Andrew; Natera, Siria; Bacic, Antony

    2007-01-01

    Boron (B) phytotoxicity affects cereal-growing regions worldwide. Although B-tolerant barley (Hordeum vulgare) germplasm is available, molecules responsible for this tolerance mechanism have not been defined. We describe and use a new comparative proteomic technique, iTRAQ peptide tagging (iTRAQ), to compare the abundances of proteins from B-tolerant and -intolerant barley plants from a ‘Clipper’ × ‘Sahara’ doubled-haploid population selected on the basis of a presence or absence of two B-tolerance quantitative trait loci. iTRAQ was used to identify three enzymes involved in siderophore production (Iron Deficiency Sensitive2 [IDS2], IDS3, and a methylthio-ribose kinase) as being elevated in abundance in the B-tolerant plants. Following from this result, we report a potential link between iron, B, and the siderophore hydroxymugineic acid. We believe that this study highlights the potency of the iTRAQ approach to better understand mechanisms of abiotic stress tolerance in cereals, particularly when applied in conjunction with bulked segregant analysis. PMID:17478636

  7. Rapid and individual-specific glycoprofiling of the low abundance N-glycosylated protein tissue inhibitor of metalloproteinases-1

    DEFF Research Database (Denmark)

    Thaysen-Andersen, Morten; Thøgersen, Ida B.; Nielsen, Hans Jørgen

    2007-01-01

    A gel-based method for a mass spectrometric site-specific glycoanalysis was developed using a recombinant glycoprotein expressed in two different cell lines. Hydrophilic interaction liquid chromatography at nanoscale level was used to enrich for glycopeptides prior to MS. The glycoprofiling...... glycoprofiling of a low abundance glycoprotein performed in an individual-specific manner allows for future studies of glycosylated biomarkers for person-specific detection of altered glycosylation and may thus allow early detection and monitoring of diseases....... was performed using matrix-assisted laser desorption/ionization MS and MS/MS. The method proved to be fast and sensitive and furthermore yielded a comprehensive site-specific glycan analysis, allowing a differentiation of the glycoprofiles of the two sources of recombinant protein, both comprising N...

  8. Late Embryogenesis Abundant Proteins

    NARCIS (Netherlands)

    Shih, M.D.; Hoekstra, F.A.; Hsing, Y.I.C.

    2008-01-01

    During the late maturation stage of seed development, water content decreases greatly. One of the most striking characteristics of mature orthodox seeds is their ability to withstand severe desiccation. Mechanisms of plant drought/desiccation tolerance have been studied by numerous groups, and a bro

  9. Expression Profiles of 12 Late Embryogenesis Abundant Protein Genes from Tamarix hispida in Response to Abiotic Stress

    Directory of Open Access Journals (Sweden)

    Caiqiu Gao

    2014-01-01

    Full Text Available Twelve embryogenesis abundant protein (LEA genes (named ThLEA-1 to -12 were cloned from Tamarix hispida. The expression profiles of these genes in response to NaCl, PEG, and abscisic acid (ABA in roots, stems, and leaves of T. hispida were assessed using real-time reverse transcriptase-polymerase chain reaction (RT-PCR. These ThLEAs all showed tissue-specific expression patterns in roots, stems, and leaves under normal growth conditions. However, they shared a high similar expression patterns in the roots, stems, and leaves when exposed to NaCl and PEG stress. Furthermore, ThLEA-1, -2, -3, -4, and -11 were induced by NaCl and PEG, but ThLEA-5, -6, -8, -10, and -12 were downregulated by salt and drought stresses. Under ABA treatment, some ThLEA genes, such as ThLEA-1, -2, and -3, were only slightly differentially expressed in roots, stems, and leaves, indicating that they may be involved in the ABA-independent signaling pathway. These findings provide a basis for the elucidation of the function of LEA genes in future work.

  10. Combining Phytate/Ca2+Fractionation with Trichloroacetic Acid/Acetone Precipitation Improved Separation of Low-Abundant Proteins of Wheat (Triticum aestivum L.) Leaf for Proteomic Analysis

    Institute of Scientific and Technical Information of China (English)

    Muhammad A R F Sultan; LIU Hui; CHENG Yu-Feng; ZHANG Pei-pei; ZHAO Hui-xian

    2013-01-01

    Proteomic assessment of low-abundance leaf proteins is hindered by the large quantity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) present within plant leaf tissues. In the present study, total proteins were extracted from wheat (Triticum aestivum L.) leaves by a conventional trichloroacetic acid (TCA)/acetone method and a protocol first developed in this work. Phytate/Ca2+fractionation and TCA/acetone precipitation were combined to design an improved TCA/acetone method. The extracted proteins were analysed by two-dimensional gel electrophoresis (2-DE). The resulting 2-DE images were compared to reveal major differences. The results showed that large quantities of Rubisco were deleted from wheat leaf proteins prepared by the improved method. As many as (758±4) protein spots were detected from 2-DE images of protein extracts obtained by the improved method, 130 more than those detected by the TCA/acetone method. Further analysis indicated that more protein spots could be detected at regions of pI 4.00-4.99 and 6.50-7.00 in the improved method-based 2-DE images. Our findings indicated that the improved method is an efficient protein preparation protocol for separating low-abundance proteins in wheat leaf tissues by 2-DE analysis. The proposed protocol is simple, fast, inexpensive and also applicable to protein preparations of other plants.

  11. Interleukin (IL)-1 in rat parturition: IL-1 receptors 1 and 2 and accessory proteins abundance in pregnant rat uterus at term - regulation by progesterone.

    Science.gov (United States)

    Ishiguro, Tomohito; Takeda, Jun; Fang, Xin; Bronson, Heather; Olson, David M

    2016-07-01

    The role of interleukin-1 (IL-1), a pro-inflammatory cytokine, in parturition is typically noted by changes in its concentrations. Studying the expression of its receptor family, IL-1 receptor (IL-1R) 1, IL-1R2, IL-1R accessory protein (IL-1RAcP), and its predominantly brain isoform, IL-1RAcPb, during late gestation in the uterus in the Long-Evans rat is another. We assessed changes in their mRNA and protein relative abundance in the uterus and compared IL-1RAcP and IL-1RAcPb mRNA abundance in uterus, cervix, ovaries, placenta, and whole blood of Long-Evans rats during late gestation or in RU486 and progesterone-treated dams using quantitative real-time PCR and western immunoblotting. IL-1R1, IL-1RAcP, and IL-1RAcPb mRNA abundance significantly increased in the uterus at delivery whereas IL-1R2 mRNA abundance significantly decreased. IL-1R1 protein increased at term and IL-1R2 protein decreased at term compared to nonpregnant uteri. IL1-RAcPb mRNA abundance was less than IL-1RAcP, but in the lower uterine segment it was the highest of all tissues examined. RU486 stimulated preterm delivery and an increase in IL-1R1 mRNA abundance whereas progesterone administration extended pregnancy and suppressed the increase in IL-1R1. These data suggest that changes in uterine sensitivity to IL-1 occur during late gestation and suggest another level of regulation for the control of delivery. The roles for IL-1RAcP and IL-1RAcPb need to be determined, but may relate to different intracellular signaling pathways.

  12. Effects of dietary nitrogen concentration on messenger RNA expression and protein abundance of urea transporter-B and aquaporins in ruminal papillae from lactating Holstein cows

    DEFF Research Database (Denmark)

    Røjen, Betina Amdisen; Poulsen, Søren Brandt; Theil, Peter Kappel;

    2011-01-01

    To test the hypothesis that dietary N concentrations affect gut epithelial urea transport by modifying the expression of urea transporter B (UT-B) and aquaporins (AQP), the mRNA expression and protein abundance of UT-B and AQP3, AQP7, AQP8, and AQP10 were investigated in ruminal papillae from 9 l....... In conclusion, AQP3, 7, and 8 were found to be expressed in bovine rumen papillae. None of the investigated transcripts or proteins correlated to the increased rumen epithelial urea permeability observed with low dietary N concentration.......To test the hypothesis that dietary N concentrations affect gut epithelial urea transport by modifying the expression of urea transporter B (UT-B) and aquaporins (AQP), the mRNA expression and protein abundance of UT-B and AQP3, AQP7, AQP8, and AQP10 were investigated in ruminal papillae from 9...... lactating dairy cows. Ruminal papillae were harvested from cows fed low N (12.9% crude protein) and high N (17.1% crude protein) diets in a crossover design with 21-d periods. The mRNA expression was determined by real-time reverse transcription-PCR and protein abundance by immunoblotting. The m...

  13. Detection and quantitation of twenty-seven cytokines, chemokines and growth factors pre- and post-high abundance protein depletion in human plasma

    Directory of Open Access Journals (Sweden)

    Seong-Beom Ahn

    2014-06-01

    Full Text Available Cytokines, chemokines and growth factors (CCGFs in human plasma are analyzed for identification of biomarkers. However concentrations of CCGFs are very low; it is difficult to identify and quantify low abundance proteins in the presence of the high abundance proteins (HAPs unless HAPs are removed prior to analysis. However, there is a concern that the low abundance proteins such as CCGFs may also be removed during the HAP depletion process. In this study, we have examined whether or not depletion of the HAPs enhances detection of the CCGFs by immuno-assays. Top 14 HAPs were depleted from 10 healthy volunteers’ plasma using MARS-14 immuno-depletion column and a total of 27 CCGFs were analyzed by bead-based multiplexed immuno-assay. All 27 CCGFs were detected in neat plasma (NP, 25 were detected in flow through fraction (FT and 21 were detected in bound protein (BP fraction. Concentrations of 22 CCGFs were significantly higher in NP compared to FT and BP. Only one CCGF had higher concentration in FT compared to NP. The remaining 2 CCGFs were not different between NP and FT. It was counter-productive for the detection of 24 CCGFs after HAP removal, primarily due to post-depletion protein precipitation and/or re-suspension of pellets.

  14. SOLiD-SAGE of endophyte-infected red fescue reveals numerous effects on host transcriptome and an abundance of highly expressed fungal secreted proteins.

    Directory of Open Access Journals (Sweden)

    Karen V Ambrose

    Full Text Available One of the most important plant-fungal symbiotic relationships is that of cool season grasses with endophytic fungi of the genera Epichloë and Neotyphodium. These associations often confer benefits, such as resistance to herbivores and improved drought tolerance, to the hosts. One benefit that appears to be unique to fine fescue grasses is disease resistance. As a first step towards understanding the basis of the endophyte-mediated disease resistance in Festuca rubra we carried out a SOLiD-SAGE quantitative transcriptome comparison of endophyte-free and Epichloë festucae-infected F. rubra. Over 200 plant genes involved in a wide variety of physiological processes were statistically significantly differentially expressed between the two samples. Many of the endophyte expressed genes were surprisingly abundant, with the most abundant fungal tag representing over 10% of the fungal mapped tags. Many of the abundant fungal tags were for secreted proteins. The second most abundantly expressed fungal gene was for a secreted antifungal protein and is of particular interest regarding the endophyte-mediated disease resistance. Similar genes in Penicillium and Aspergillus spp. have been demonstrated to have antifungal activity. Of the 10 epichloae whole genome sequences available, only one isolate of E. festucae and Neotyphodium gansuense var inebrians have an antifungal protein gene. The uniqueness of this gene in E. festucae from F. rubra, its transcript abundance, and the secreted nature of the protein, all suggest it may be involved in the disease resistance conferred to the host, which is a unique feature of the fine fescue-endophyte symbiosis.

  15. SOLiD-SAGE of endophyte-infected red fescue reveals numerous effects on host transcriptome and an abundance of highly expressed fungal secreted proteins.

    Science.gov (United States)

    Ambrose, Karen V; Belanger, Faith C

    2012-01-01

    One of the most important plant-fungal symbiotic relationships is that of cool season grasses with endophytic fungi of the genera Epichloë and Neotyphodium. These associations often confer benefits, such as resistance to herbivores and improved drought tolerance, to the hosts. One benefit that appears to be unique to fine fescue grasses is disease resistance. As a first step towards understanding the basis of the endophyte-mediated disease resistance in Festuca rubra we carried out a SOLiD-SAGE quantitative transcriptome comparison of endophyte-free and Epichloë festucae-infected F. rubra. Over 200 plant genes involved in a wide variety of physiological processes were statistically significantly differentially expressed between the two samples. Many of the endophyte expressed genes were surprisingly abundant, with the most abundant fungal tag representing over 10% of the fungal mapped tags. Many of the abundant fungal tags were for secreted proteins. The second most abundantly expressed fungal gene was for a secreted antifungal protein and is of particular interest regarding the endophyte-mediated disease resistance. Similar genes in Penicillium and Aspergillus spp. have been demonstrated to have antifungal activity. Of the 10 epichloae whole genome sequences available, only one isolate of E. festucae and Neotyphodium gansuense var inebrians have an antifungal protein gene. The uniqueness of this gene in E. festucae from F. rubra, its transcript abundance, and the secreted nature of the protein, all suggest it may be involved in the disease resistance conferred to the host, which is a unique feature of the fine fescue-endophyte symbiosis.

  16. Sequential extraction results in improved proteome profiling of medicinal plant Pinellia ternata tubers, which contain large amounts of high-abundance proteins.

    Directory of Open Access Journals (Sweden)

    Xiaolin Wu

    Full Text Available Pinellia ternata tuber is one of the well-known Chinese traditional medicines. In order to understand the pharmacological properties of tuber proteins, it is necessary to perform proteome analysis of P. ternata tubers. However, a few high-abundance proteins (HAPs, mainly mannose-binding lectin (agglutinin, exist in aggregates of various sizes in the tubers and seriously interfere with proteome profiling by two-dimensional electrophoresis (2-DE. Therefore, selective depletion of these HAPs is a prerequisite for enhanced proteome analysis of P. ternata tubers. Based on differential protein solubility, we developed a novel protocol involving two sequential extractions for depletion of some HAPs and prefractionation of tuber proteins prior to 2-DE. The first extraction using 10% acetic acid selectively extracted acid-soluble HAPs and the second extraction using the SDS-containing buffer extracted remaining acid-insoluble proteins. After application of the protocol, 2-DE profiles of P. ternata tuber proteins were greatly improved and more protein spots were detected, especially low-abundance proteins. Moreover, the subunit composition of P. ternata lectin was analyzed by electrophoresis. Native lectin consists of two hydrogen-bonded subunits (11 kDa and 25 kDa and the 11 kDa subunit was a glycoprotein. Subsequently, major HAPs in the tubers were analyzed by mass spectrometry, with nine protein spots being identified as lectin isoforms. The methodology was easy to perform and required no specialized apparatus. It would be useful for proteome analysis of other tuber plants of Araceae.

  17. Proteomic analysis reveals differential accumulation of small heat shock proteins and late embryogenesis abundant proteins between ABA-deficient mutant vp5 seeds and wild-type Vp5 seeds in maize

    Directory of Open Access Journals (Sweden)

    Xiaolin eWu

    2015-01-01

    Full Text Available ABA is a major plant hormone that plays important roles during many phases of plant life cycle, including seed development, maturity and dormancy, and especially the acquisition of desiccation tolerance. Understanding of the molecular basis of ABA-mediated plant response to stress is of interest not only in basic research on plant adaptation but also in applied research on plant productivity. Maize mutant viviparous-5 (vp5, deficient in ABA biosynthesis in seeds, is a useful material for studying ABA-mediated response in maize. Due to carotenoid deficiency, vp5 endosperm is white, compared to yellow Vp5 endosperm. However, the background difference at proteome level between vp5 and Vp5 seeds is unclear. This study aimed to characterize proteome alterations of maize vp5 seeds and to identify ABA-dependent proteins during seed maturation. We compared the embryo and endosperm proteomes of vp5 and Vp5 seeds by gel-based proteomics. Up to 46 protein spots, most in embryos, were found to be differentially accumulated between vp5 and Vp5. The identified proteins included small heat shock proteins (sHSPs, late embryogenesis abundant (LEA proteins, stress proteins, storage proteins and enzymes among others. However, EMB564, the most abundant LEA protein in maize embryo, accumulated in comparable levels between vp5 and Vp5 embryos, which contrasted to previously characterized, greatly lowered expression of emb564 mRNA in vp5 embryos. Moreover, LEA proteins and sHSPs displayed differential accumulations in vp5 embryos: six out of eight identified LEA proteins decreased while nine sHSPs increased in abundance. Finally, we discussed the possible causes of global proteome alterations, especially the observed differential accumulation of identified LEA proteins and sHSPs in vp5 embryos. The data derived from this study provides new insight into ABA-dependent proteins and ABA-mediated response during maize seed maturation.

  18. A gestational high protein diet affects the abundance of muscle transcripts related to cell cycle regulation throughout development in porcine progeny.

    Directory of Open Access Journals (Sweden)

    Michael Oster

    Full Text Available BACKGROUND: In various animal models pregnancy diets have been shown to affect offspring phenotype. Indeed, the underlying programming of development is associated with modulations in birth weight, body composition, and continual diet-dependent modifications of offspring metabolism until adulthood, producing the hypothesis that the offspring's transcriptome is permanently altered depending on maternal diet. METHODOLOGY/PRINCIPAL FINDINGS: To assess alterations of the offspring's transcriptome due to gestational protein supply, German Landrace sows were fed isoenergetic diets containing protein levels of either 30% (high protein--HP or 12% (adequate protein--AP throughout their pregnancy. Offspring muscle tissue (M. longissimus dorsi was collected at 94 days post conception (dpc, and 1, 28, and 188 days post natum (dpn for use with Affymetrix GeneChip Porcine Genome Arrays and subsequent statistical and Ingenuity pathway analyses. Numerous transcripts were found to have altered abundance at 94 dpc and 1 dpn; at 28 dpn no transcripts were altered, and at 188 dpn only a few transcripts showed a different abundance between diet groups. However, when assessing transcriptional changes across developmental time points, marked differences were obvious among the dietary groups. Depending on the gestational dietary exposure, short- and long-term effects were observed for mRNA expression of genes related to cell cycle regulation, energy metabolism, growth factor signaling pathways, and nucleic acid metabolism. In particular, the abundance of transcripts related to cell cycle remained divergent among the groups during development. CONCLUSION: Expression analysis indicates that maternal protein supply induced programming of the offspring's genome; early postnatal compensation of the slight growth retardation obvious at birth in HP piglets resulted, as did a permanently different developmental alteration and responsiveness to the common environment of the

  19. Heterologous Expression of MeLEA3: A 10 kDa Late Embryogenesis Abundant Protein of Cassava, Confers Tolerance to Abiotic Stress in Escherichia coli with Recombinant Protein Showing In Vitro Chaperone Activity.

    Science.gov (United States)

    Barros, Nicolle L F; da Silva, Diehgo T; Marques, Deyvid N; de Brito, Fabiano M; dos Reis, Savio P; de Souza, Claudia R B

    2015-01-01

    Late embryogenesis abundant (LEA) proteins are small molecular weight proteins involved in acquisition of tolerance to drought, salinity, high temperature, cold, and freezing stress in many plants. Previous studies revealed a cDNA sequence coding for a 10 kDa atypical LEA protein, named MeLEA3, predicted to be located into mitochondria with potential role in salt stress response of cassava (Manihot esculenta Crantz). Here we aimed to produce the recombinant MeLEA3 protein by heterologous expression in Escherichia coli and evaluate the tolerance of bacteria expressing this protein under abiotic stress. Our result revealed that the recombinant MeLEA3 protein conferred a protective function against heat and salt stress in bacterial cells. Also, the recombinant MeLEA3 protein showed in vitro chaperone activity by protection of NdeI restriction enzyme activity under heat stress.

  20. Dietary Yeast Cell Wall Extract Alters the Proteome of the Skin Mucous Barrier in Atlantic Salmon (Salmo salar): Increased Abundance and Expression of a Calreticulin-Like Protein.

    Science.gov (United States)

    Micallef, Giulia; Cash, Phillip; Fernandes, Jorge M O; Rajan, Binoy; Tinsley, John W; Bickerdike, Ralph; Martin, Samuel A M; Bowman, Alan S

    2017-01-01

    In order to improve fish health and reduce use of chemotherapeutants in aquaculture production, the immunomodulatory effect of various nutritional ingredients has been explored. In salmon, there is evidence that functional feeds can reduce the abundance of sea lice. This study aimed to determine if there were consistent changes in the skin mucus proteome that could serve as a biomarker for dietary yeast cell wall extract. The effect of dietary yeast cell wall extract on the skin mucus proteome of Atlantic salmon was examined using two-dimensional gel electrophoresis. Forty-nine spots showed a statistically significant change in their normalised volumes between the control and yeast cell wall diets. Thirteen spots were successfully identified by peptide fragment fingerprinting and LC-MS/MS and these belonged to a variety of functions and pathways. To assess the validity of the results from the proteome approach, the gene expression of a selection of these proteins was studied in skin mRNA from two different independent feeding trials using yeast cell wall extracts. A calreticulin-like protein increased in abundance at both the protein and transcript level in response to dietary yeast cell wall extract. The calreticulin-like protein was identified as a possible biomarker for yeast-derived functional feeds since it showed the most consistent change in expression in both the mucus proteome and skin transcriptome. The discovery of such a biomarker is expected to quicken the pace of research in the application of yeast cell wall extracts.

  1. Dietary Yeast Cell Wall Extract Alters the Proteome of the Skin Mucous Barrier in Atlantic Salmon (Salmo salar): Increased Abundance and Expression of a Calreticulin-Like Protein

    Science.gov (United States)

    Micallef, Giulia; Cash, Phillip; Fernandes, Jorge M. O.; Rajan, Binoy; Tinsley, John W.; Bickerdike, Ralph

    2017-01-01

    In order to improve fish health and reduce use of chemotherapeutants in aquaculture production, the immunomodulatory effect of various nutritional ingredients has been explored. In salmon, there is evidence that functional feeds can reduce the abundance of sea lice. This study aimed to determine if there were consistent changes in the skin mucus proteome that could serve as a biomarker for dietary yeast cell wall extract. The effect of dietary yeast cell wall extract on the skin mucus proteome of Atlantic salmon was examined using two-dimensional gel electrophoresis. Forty-nine spots showed a statistically significant change in their normalised volumes between the control and yeast cell wall diets. Thirteen spots were successfully identified by peptide fragment fingerprinting and LC-MS/MS and these belonged to a variety of functions and pathways. To assess the validity of the results from the proteome approach, the gene expression of a selection of these proteins was studied in skin mRNA from two different independent feeding trials using yeast cell wall extracts. A calreticulin-like protein increased in abundance at both the protein and transcript level in response to dietary yeast cell wall extract. The calreticulin-like protein was identified as a possible biomarker for yeast-derived functional feeds since it showed the most consistent change in expression in both the mucus proteome and skin transcriptome. The discovery of such a biomarker is expected to quicken the pace of research in the application of yeast cell wall extracts. PMID:28046109

  2. Purification and in vitro chaperone activity of a class I small heat-shock protein abundant in recalcitrant chestnut seeds.

    Science.gov (United States)

    Collada, C; Gomez, L; Casado, R; Aragoncillo, C

    1997-09-01

    A 20-kD protein has been purified from cotyledons of recalcitrant (desiccation-sensitive) chestnut (Castanea sativa) seeds, where it accumulates at levels comparable to those of major seed storage proteins. This protein, termed Cs smHSP 1, forms homododecameric complexes under nondenaturing conditions and appears to be homologous to cytosolic class I small heat-shock proteins (smHSPs) from plant sources. In vitro evidence has been obtained that the isolated protein can function as a molecular chaperone; it increases, at stoichiometric levels, the renaturation yields of chemically denatured citrate synthase and also prevents the irreversible thermal inactivation of this enzyme. Although a role in desiccation tolerance has been hypothesized for seed smHSPs, this does not seem to be the case for Cs smHSP 1. We have investigated the presence of immunologically related proteins in orthodox and recalcitrant seeds of 13 woody species. Our results indicate that the presence of Cs smHSP 1-like proteins, even at high levels, is not enough to confer desiccation tolerance, and that the amount of these proteins does not furnish a reliable criterion to identify desiccation-sensitive seeds. Additional proteins or mechanisms appear necessary to keep the viability of orthodox seeds upon shedding.

  3. Bee bread increases honeybee haemolymph protein and promote better survival despite of causing higher Nosema ceranae abundance in honeybees.

    Science.gov (United States)

    Basualdo, Marina; Barragán, Sergio; Antúnez, Karina

    2014-08-01

    Adequate protein nutrition supports healthy honeybees and reduces the susceptibility to disease. However little is known concerning the effect of the diet on Nosema ceranae development, an obligate intracellular parasite that disturbs the protein metabolism of honeybees (Apis mellifera). Here we tested the effect of natural (bee bread) and non-natural protein diets (substitute) on haemolymph proteins titers of honeybee and N. ceranae spore production. The natural diet induced higher levels of protein and parasite development, but the survival of bees was also higher than with non-natural diets. The data showed that the administration of an artificially high nutritious diet in terms of crude protein content is not sufficient to promote healthy bees; rather the protein ingested should be efficiently assimilated. The overall results support the idea that the physiological condition of the bees is linked to protein levels in the haemolymph, which affects the tolerance to parasite; consequently the negative impact of the parasite on host fitness is not associated only with the level of infection.

  4. Aestivation Induces Changes in the mRNA Expression Levels and Protein Abundance of Two Isoforms of Urea Transporters in the Gills of the African Lungfish, Protopterus annectens

    Science.gov (United States)

    Chng, You R.; Ong, Jasmine L. Y.; Ching, Biyun; Chen, Xiu L.; Hiong, Kum C.; Wong, Wai P.; Chew, Shit F.; Lam, Siew H.; Ip, Yuen K.

    2017-01-01

    The African lungfish, Protopterus annectens, is ammonotelic in water despite being ureogenic. When it aestivates in mucus cocoon on land, ammonia is detoxified to urea. During the maintenance phase of aestivation, urea accumulates in the body, which is subsequently excreted upon arousal. Urea excretion involves urea transporters (UT/Ut). This study aimed to clone and sequence the ut isoforms from the gills of P. annectens, and to test the hypothesis that the mRNA and/or protein expression levels of ut/Ut isoforms could vary in the gills of P. annectens during the induction, maintenance, and arousal phases of aestivation. Two isoforms of ut, ut-a2a and ut-a2b, were obtained from the gills of P. annectens. ut-a2a consisted of 1227 bp and coded for 408 amino acids with an estimated molecular mass of 44.7 kDa, while ut-a2b consisted of 1392 bp and coded for 464 amino acids with an estimated molecular mass of 51.2 kDa. Ut-a2a and Ut-a2b of P. annectens had a closer phylogenetic relationship with Ut/UT of tetrapods than Ut of fishes. While the mRNA expression pattern of ut-a2a and ut-a2b across various tissues of P. annectens differed, the transcript levels of ut-a2a and ut-a2b in the gills were comparable, indicating that they might be equally important for branchial urea excretion during the initial arousal phase of aestivation. During the maintenance phase of aestivation, the transcript level of ut-a2a increased significantly, but the protein abundance of Ut-a2a remained unchanged in the gills of P. annectens. This could be an adaptive feature to prepare for an increase in the production of Ut-a2a upon arousal. Indeed, arousal led to a significant increase in the branchial Ut-a2a protein abundance. Although the transcript level of ut-a2b remained unchanged, there were significant increases in the protein abundance of Ut-a2b in the gills of P. annectens throughout the three phases of aestivation. The increase in the protein abundance of Ut-a2b during the maintenance

  5. KvLEA, a New Isolated Late Embryogenesis Abundant Protein Gene from Kosteletzkya virginica Responding to Multiabiotic Stresses.

    Science.gov (United States)

    Tang, Xiaoli; Wang, Hongyan; Chu, Liye; Shao, Hongbo

    2016-01-01

    The LEA proteins are a kind of hydrophilic proteins, playing main functions in desiccation tolerance. However, their importance as a kind of stress proteins in abiotic stress is being clarified little by little. In this study we isolated, cloned, and identified the first KvLEA gene in Kosteletzkya virginica. Bioinformatic analysis showed that the protein encoded by this gene had common properties of LEA proteins and the multiple sequences alignment and phylogenetic analysis further showed that this protein had high homology with two Arabidopsis LEA proteins. Gene expression analysis revealed that this gene had a higher expression in root and it was induced obviously by salt stress. Moreover, the transcripts of KvLEA were also induced by other abiotic stresses including drought, high temperature, chilling, and ABA treatment. Among these abiotic stresses, ABA treatment brought about the biggest changes to this gene. Collectively, our research discovered a novel LEA gene and uncovered its involvement in multiabiotic stresses in K. virginica. This research not only enriched studies on LEA gene in plant but also would accelerate more studies on K. virginica in the future.

  6. Foetal life protein restriction in male mink (Neovison vison) kits lowers post-weaning protein oxidation and the relative abundance of hepatic fructose-1,6-bisphosphatase mRNA.

    Science.gov (United States)

    Matthiesen, C F; Blache, D; Thomsen, P D; Tauson, A-H

    2012-01-01

    Foetal life malnutrition has been studied intensively in a number of animal models. Results show that especially foetal life protein malnutrition can lead to metabolic changes later in life. This might be of particular importance for strict carnivores, for example, cat and mink (Neovison vison) because of their higher protein requirement than in other domestic mammals. This study aimed to investigate the effects of low protein provision during foetal life to male mink kits on their protein metabolism during the early post-weaning period of rapid growth and to investigate whether foetal life protein deficiency affects the response to adequate or deficient protein provision post weaning. Further, we intended to study whether the changes in the gene expression of key enzymes in foetal hepatic tissue caused by maternal protein deficiency were manifested post-weaning. A total of 32 male mink kits born to mothers fed either a low-protein diet (LP), that is, 14% of metabolizable energy (ME) from protein (foetal low - FL), n = 16, or an adequate-protein (AP) diet, that is, 29% of ME from protein (foetal adequate - FA), n = 16) in the last 16.3 ± 1.8 days of pregnancy were used. The FL offspring had lower birth weight and lower relative abundance of fructose-1,6-bisphosphatase (Fru-1,6-P2ase) and pyruvate kinase mRNA in foetal hepatic tissue than FA kits. The mothers were fed a diet containing adequate protein until weaning. At weaning (7 weeks of age), half of the kits from each foetal treatment group were fed an AP diet (32% of ME from protein; n = 8 FA and 8 FL) and the other half were fed a LP diet (18% of ME from protein; n = 8 FA and 8 FL) until 9.5 weeks of age, yielding four treatment groups (i.e. FA-AP, FA-LP, FL-AP and FL-LP). Low protein provision in foetal life lowered the protein oxidation post-weaning compared with the controls (P = 0.006), indicating metabolic flexibility and a better ability to conserve protein. This could not, however, be supported by

  7. Proteomic Characterization of Differential Abundant Proteins Accumulated between Lower and Upper Epidermises of Fleshy Scales in Onion (Allium cepa L.) Bulbs

    Science.gov (United States)

    Wu, Xiaolin

    2016-01-01

    The onion (Allium cepa L.) is widely planted worldwide as a valuable vegetable crop. The scales of an onion bulb are a modified type of leaf. The one-layer-cell epidermis of onion scales is commonly used as a model experimental material in botany and molecular biology. The lower epidermis (LE) and upper epidermis (UE) of onion scales display obvious differences in microscopic structure, cell differentiation and pigment synthesis; however, associated proteomic differences are unclear. LE and UE can be easily sampled as single-layer-cell tissues for comparative proteomic analysis. In this study, a proteomic approach based on 2-DE and mass spectrometry (MS) was applied to compare LE and UE of fleshy scales from yellow and red onions. We identified 47 differential abundant protein spots (representing 31 unique proteins) between LE and UE in red and yellow onions. These proteins are mainly involved in pigment synthesis, stress response, and cell division. Particularly, the differentially accumulated chalcone-flavanone isomerase and flavone O-methyltransferase 1-like in LE may result in the differences in the onion scale color between red and yellow onions. Moreover, stress-related proteins abundantly accumulated in both LE and UE. In addition, the differential accumulation of UDP-arabinopyranose mutase 1-like protein and β-1,3-glucanase in the LE may be related to the different cell sizes between LE and UE of the two types of onion. The data derived from this study provides new insight into the differences in differentiation and developmental processes between onion epidermises. This study may also make a contribution to onion breeding, such as improving resistances and changing colors. PMID:28036352

  8. Quantification of intermediate-abundance proteins in serum by multiple reaction monitoring mass spectrometry in a single-quadrupole ion trap.

    Science.gov (United States)

    Lin, Shanhua; Shaler, Thomas A; Becker, Christopher H

    2006-08-15

    A method is presented to quantify intermediate-abundance proteins in human serum using a single-quadrupole linear ion trap mass spectrometer-in contrast, for example, to a triple-quadrupole mass spectrometer. Stable-isotope-labeled (tryptic) peptides are spiked into digested protein samples as internal standards, aligned with the traditional isotope dilution approach. As a proof-of-concept experiment, four proteins of intermediate abundance were selected, coagulation factor V, adiponectin, C-reactive protein (CRP), and thyroxine binding globulin. Stable-isotope-labeled peptides were synthesized with one tryptic sequence from each of these proteins. The normal human serum concentration ranges of these proteins are from 1 to 30 microg/mL (or 20 to 650 pmol/mL). These labeled peptides and their endogenous counterparts were analyzed by LC-MS/MS using multiple reaction monitoring, a multiplexed form of the selected reaction monitoring technique. For these experiments, only one chromatographic dimension (on-line reversed-phase capillary column) was used. Improved limits of detection will result with multidimensional chromatographic methods utilizing more material per sample. Standard curves of the spiked calibrants were generated with concentrations ranging from 3 to 700 pmol/mL using both neat solutions and peptides spiked into the complex matrix of digested serum protein solution where ion suppression effects and interferences are common. Endogenous protein concentrations were determined by comparing MS/MS peak areas of the endogenous peptides to the isotopically labeled internal calibrants. The derived concentrations from a normal human serum pool (neglecting loss of material during sample processing) were 9.2, 110, 120, and 246 pmol/mL for coagulation factor V, adiponectin, CRP, and thyroxine binding globulin, respectively. These concentrations generally agree with the reported normal ranges for these proteins. As a measure of analytical reproducibility of this

  9. The highly abundant chlorophyll-protein complex of iron-deficient Synechococcus sp. PCC7942 (CP43') is encoded by the isiA gene.

    Science.gov (United States)

    Burnap, R L; Troyan, T; Sherman, L A

    1993-11-01

    A chlorophyll (Chl)-protein complex designated CPVI-4 becomes the major pigment-protein complex in Synechococcus sp. PCC7942 cells grown under conditions of iron limitation. Work by Laudenbach et al. (J Bacteriol [1988] 170: 5018-5026) has identified an iron-repressible operon, designated isiAB, containing the flavodoxin gene and a gene predicted to encode a Chl-binding protein resembling CP43 of photosystem II. To test the hypothesis that the CP43-like protein is a component of the CPVI-4 complex, we have inactivated the isiAB operon in Synechococcus sp. PCC7942 using directed insertional mutagenesis. Mutant cells grown under conditions of iron limitation exhibit pronounced changes in their spectroscopic and photosynthetic properties relative to similarly grown wild-type cells. Notably, the strong 77 K fluorescence emission at 685 nm, which dominates the spectrum of iron-deficient wild-type cells, is dramatically reduced in the mutant. The loss of this emission appears to unmask the otherwise obscured photosystem II emissions at 685 and 695 nm. Most importantly, mildly denaturing gel electrophoresis shows that mutant cells no longer express the CPVI-4 complex, indicating that the isiA gene encodes a component of this abundant Chl-protein complex.

  10. Depth-specific fluctuations of gene expression and protein abundance modulate the photophysiology in the seagrass Posidonia oceanica

    Science.gov (United States)

    Procaccini, Gabriele; Ruocco, Miriam; Marín-Guirao, Lázaro; Dattolo, Emanuela; Brunet, Christophe; D’Esposito, Daniela; Lauritano, Chiara; Mazzuca, Silvia; Serra, Ilia Anna; Bernardo, Letizia; Piro, Amalia; Beer, Sven; Björk, Mats; Gullström, Martin; Buapet, Pimchanok; Rasmusson, Lina M.; Felisberto, Paulo; Gobert, Sylvie; Runcie, John W.; Silva, João; Olivé, Irene; Costa, Monya M.; Barrote, Isabel; Santos, Rui

    2017-02-01

    Here we present the results of a multiple organizational level analysis conceived to identify acclimative/adaptive strategies exhibited by the seagrass Posidonia oceanica to the daily fluctuations in the light environment, at contrasting depths. We assessed changes in photophysiological parameters, leaf respiration, pigments, and protein and mRNA expression levels. The results show that the diel oscillations of P. oceanica photophysiological and respiratory responses were related to transcripts and proteins expression of the genes involved in those processes and that there was a response asynchrony between shallow and deep plants probably caused by the strong differences in the light environment. The photochemical pathway of energy use was more effective in shallow plants due to higher light availability, but these plants needed more investment in photoprotection and photorepair, requiring higher translation and protein synthesis than deep plants. The genetic differentiation between deep and shallow stands suggests the existence of locally adapted genotypes to contrasting light environments. The depth-specific diel rhythms of photosynthetic and respiratory processes, from molecular to physiological levels, must be considered in the management and conservation of these key coastal ecosystems.

  11. Depth-specific fluctuations of gene expression and protein abundance modulate the photophysiology in the seagrass Posidonia oceanica

    Science.gov (United States)

    Procaccini, Gabriele; Ruocco, Miriam; Marín-Guirao, Lázaro; Dattolo, Emanuela; Brunet, Christophe; D’Esposito, Daniela; Lauritano, Chiara; Mazzuca, Silvia; Serra, Ilia Anna; Bernardo, Letizia; Piro, Amalia; Beer, Sven; Björk, Mats; Gullström, Martin; Buapet, Pimchanok; Rasmusson, Lina M.; Felisberto, Paulo; Gobert, Sylvie; Runcie, John W.; Silva, João; Olivé, Irene; Costa, Monya M.; Barrote, Isabel; Santos, Rui

    2017-01-01

    Here we present the results of a multiple organizational level analysis conceived to identify acclimative/adaptive strategies exhibited by the seagrass Posidonia oceanica to the daily fluctuations in the light environment, at contrasting depths. We assessed changes in photophysiological parameters, leaf respiration, pigments, and protein and mRNA expression levels. The results show that the diel oscillations of P. oceanica photophysiological and respiratory responses were related to transcripts and proteins expression of the genes involved in those processes and that there was a response asynchrony between shallow and deep plants probably caused by the strong differences in the light environment. The photochemical pathway of energy use was more effective in shallow plants due to higher light availability, but these plants needed more investment in photoprotection and photorepair, requiring higher translation and protein synthesis than deep plants. The genetic differentiation between deep and shallow stands suggests the existence of locally adapted genotypes to contrasting light environments. The depth-specific diel rhythms of photosynthetic and respiratory processes, from molecular to physiological levels, must be considered in the management and conservation of these key coastal ecosystems. PMID:28211527

  12. Increased reactive oxygen species production and lower abundance of complex I subunits and carnitine palmitoyltransferase 1B protein despite normal mitochondrial respiration in insulin-resistant human skeletal muscle

    DEFF Research Database (Denmark)

    Lefort, Natalie; Glancy, Brian; Bowen, Benjamin

    2010-01-01

    the higher ROS production. Tandem mass spectrometry identified protein abundance differences per mitochondrial mass in insulin resistance, including lower abundance of complex I subunits and enzymes involved in the oxidation of branched-chain amino acids (BCAA) and fatty acids (e.g., carnitine...... palmitoyltransferase 1B). CONCLUSIONS: We provide data suggesting normal oxidative capacity of mitochondria in insulin-resistant skeletal muscle in parallel with high rates of ROS production. Furthermore, we show specific abundance differences in proteins involved in fat and BCAA oxidation that might contribute...... to the accumulation of lipid and BCAA frequently associated with the pathogenesis of insulin resistance....

  13. Na+/K+-ATPase α1 identified as an abundant protein in the blood-labyrinth barrier that plays an essential role in the barrier integrity.

    Directory of Open Access Journals (Sweden)

    Yue Yang

    Full Text Available The endothelial-blood/tissue barrier is critical for maintaining tissue homeostasis. The ear harbors a unique endothelial-blood/tissue barrier which we term "blood-labyrinth-barrier". This barrier is critical for maintaining inner ear homeostasis. Disruption of the blood-labyrinth-barrier is closely associated with a number of hearing disorders. Many proteins of the blood-brain-barrier and blood-retinal-barrier have been identified, leading to significant advances in understanding their tissue specific functions. In contrast, capillaries in the ear are small in volume and anatomically complex. This presents a challenge for protein analysis studies, which has resulted in limited knowledge of the molecular and functional components of the blood-labyrinth-barrier. In this study, we developed a novel method for isolation of the stria vascularis capillary from CBA/CaJ mouse cochlea and provided the first database of protein components in the blood-labyrinth barrier as well as evidence that the interaction of Na(+/K(+-ATPase α1 (ATP1A1 with protein kinase C eta (PKCη and occludin is one of the mechanisms of loud sound-induced vascular permeability increase.Using a mass-spectrometry, shotgun-proteomics approach combined with a novel "sandwich-dissociation" method, more than 600 proteins from isolated stria vascularis capillaries were identified from adult CBA/CaJ mouse cochlea. The ion transporter ATP1A1 was the most abundant protein in the blood-labyrinth barrier. Pharmacological inhibition of ATP1A1 activity resulted in hyperphosphorylation of tight junction proteins such as occludin which increased the blood-labyrinth-barrier permeability. PKCη directly interacted with ATP1A1 and was an essential mediator of ATP1A1-initiated occludin phosphorylation. Moreover, this identified signaling pathway was involved in the breakdown of the blood-labyrinth-barrier resulting from loud sound trauma.The results presented here provide a novel method for

  14. CpLEA5, the Late Embryogenesis Abundant Protein Gene from Chimonanthus praecox, Possesses Low Temperature and Osmotic Resistances in Prokaryote and Eukaryotes

    Directory of Open Access Journals (Sweden)

    Yiling Liu

    2015-11-01

    Full Text Available Plants synthesize and accumulate a series of stress-resistance proteins to protect normal physiological activities under adverse conditions. Chimonanthus praecox which blooms in freezing weather accumulates late embryogenesis abundant proteins (LEAs in flowers, but C. praecox LEAs are little reported. Here, we report a group of five LEA genes of C. praecox (CpLEA5, KT727031. Prokaryotic-expressed CpLEA5 was employed in Escherichia coli to investigate bioactivities and membrane permeability at low-temperature. In comparison with the vacant strains, CpLEA5-containing strains survived in a 20% higher rate; and the degree of cell membrane damage in CpLEA5-containing strains was 55% of that of the vacant strains according to a conductivity test, revealing the low-temperature resistance of CpLEA5 in bacteria. CpLEA5 was also expressed in Pichia pastoris. Interestingly, besides low-temperature resistance, CpLEA5 conferred high resistance to salt and alkali in CpLEA5 overexpressing yeast. The CpLEA5 gene was transferred into Arabidopsis thaliana to also demonstrate CpLEA5 actions in plants. As expected, the transgenic lines were more resistant against low-temperature and drought while compared with the wild type. Taken together, CpLEA5-conferred resistances to several conditions in prokaryote and eukaryotes could have great value as a genetic technology to enhance osmotic stress and low-temperature tolerance.

  15. Steroidogenic acute regulatory protein in white sturgeon (Acipenser transmontanus): cDNA cloning, sites of expression and transcript abundance in corticosteroidogenic tissue after an acute stressor.

    Science.gov (United States)

    Kusakabe, Makoto; Zuccarelli, Micah D; Nakamura, Ikumi; Young, Graham

    2009-06-01

    The white sturgeon, Acipenser transmontanus, is a primitive bony fish that is recognized as an important emerging species for aquaculture. However, many aspects of its stress and reproductive physiology remain unclear. These processes are controlled by various steroid hormones. In order to investigate the regulation of steroidogenesis associated with acute stress in sturgeon, a cDNA-encoding steroidogenic acute regulatory protein (StAR) was isolated from white sturgeon. The putative amino acid sequence of sturgeon StAR shares high homology (over 60%) with other vertebrates. Phylogenetic analysis grouped sturgeon StAR within Actinopterygii, but it was clearly segregated from teleost StARs. RT-PCR analysis revealed that transcripts were most abundant in yellow corpuscles found throughout the kidney and weaker signals were detected in gonad and kidney. Very weak signals were also detected in brain and spleen by quantitative real-time PCR. In situ hybridization revealed that StAR is expressed in the cells of yellow corpuscles. No significant changes in StAR gene expression were detected in response to an acute handling stress. These results suggest that StAR is highly conserved throughout vertebrates, but the expression of the functional protein during the stress response may be partially regulated post-transcriptionally.

  16. A late embryogenesis abundant protein HVA1 regulated by an inducible promoter enhances root growth and abiotic stress tolerance in rice without yield penalty.

    Science.gov (United States)

    Chen, Yi-Shih; Lo, Shuen-Fang; Sun, Peng-Kai; Lu, Chung-An; Ho, Tuan-Hua D; Yu, Su-May

    2015-01-01

    Regulation of root architecture is essential for maintaining plant growth under adverse environment. A synthetic abscisic acid (ABA)/stress-inducible promoter was designed to control the expression of a late embryogenesis abundant protein (HVA1) in transgenic rice. The background of HVA1 is low but highly inducible by ABA, salt, dehydration and cold. HVA1 was highly accumulated in root apical meristem (RAM) and lateral root primordia (LRP) after ABA/stress treatments, leading to enhanced root system expansion. Water-use efficiency (WUE) and biomass also increased in transgenic rice, likely due to the maintenance of normal cell functions and metabolic activities conferred by HVA1 which is capable of stabilizing proteins, under osmotic stress. HVA1 promotes lateral root (LR) initiation, elongation and emergence and primary root (PR) elongation via an auxin-dependent process, particularly by intensifying asymmetrical accumulation of auxin in LRP founder cells and RAM, even under ABA/stress-suppressive conditions. We demonstrate a successful application of an inducible promoter in regulating the spatial and temporal expression of HVA1 for improving root architecture and multiple stress tolerance without yield penalty.

  17. Integrated proteomic and N-glycoproteomic analyses of doxorubicin sensitive and resistant ovarian cancer cells reveal glycoprotein alteration in protein abundance and glycosylation.

    Science.gov (United States)

    Ji, Yanlong; Wei, Shasha; Hou, Junjie; Zhang, Chengqian; Xue, Peng; Wang, Jifeng; Chen, Xiulan; Guo, Xiaojing; Yang, Fuquan

    2017-01-06

    Ovarian cancer is one of the most common cancer among women in the world, and chemotherapy remains the principal treatment for patients. However, drug resistance is a major obstacle to the effective treatment of ovarian cancers and the underlying mechanism is not clear. An increased understanding of the mechanisms that underline the pathogenesis of drug resistance is therefore needed to develop novel therapeutics and diagnostic. Herein, we report the comparative analysis of the doxorubicin sensitive OVCAR8 cells and its doxorubicin-resistant variant NCI/ADR-RES cells using integrated global proteomics and N-glycoproteomics. A total of 1525 unique N-glycosite-containing peptides from 740 N-glycoproteins were identified and quantified, of which 253 N-glycosite-containing peptides showed significant change in the NCI/ADR-RES cells. Meanwhile, stable isotope labeling by amino acids in cell culture (SILAC) based comparative proteomic analysis of the two ovarian cancer cells led to the quantification of 5509 proteins. As about 50% of the identified N-glycoproteins are low-abundance membrane proteins, only 44% of quantified unique N-glycosite-containing peptides had corresponding protein expression ratios. The comparison and calibration of the N-glycoproteome versus the proteome classified 14 change patterns of N-glycosite-containing peptides, including 8 up-regulated N-glycosite-containing peptides with the increased glycosylation sites occupancy, 35 up-regulated N-glycosite-containing peptides with the unchanged glycosylation sites occupancy, 2 down-regulated N-glycosite-containing peptides with the decreased glycosylation sites occupancy, 46 down-regulated N-glycosite-containing peptides with the unchanged glycosylation sites occupancy. Integrated proteomic and N-glycoproteomic analyses provide new insights, which can help to unravel the relationship of N-glycosylation and multidrug resistance (MDR), understand the mechanism of MDR, and discover the new diagnostic and

  18. Quantitative analysis of low-abundance serological proteins with peptide affinity-based enrichment and pseudo-multiple reaction monitoring by hybrid quadrupole time-of-flight mass spectrometry.

    Science.gov (United States)

    Kim, Kwang Hoe; Ahn, Yeong Hee; Ji, Eun Sun; Lee, Ju Yeon; Kim, Jin Young; An, Hyun Joo; Yoo, Jong Shin

    2015-07-02

    Multiple reaction monitoring (MRM) is commonly used for the quantitative analysis of proteins during mass pectrometry (MS), and has excellent specificity and sensitivity for an analyte in a complex sample. In this study, a pseudo-MRM method for the quantitative analysis of low-abundance serological proteins was developed using hybrid quadrupole time-of-flight (hybrid Q-TOF) MS and peptide affinity-based enrichment. First, a pseudo-MRM-based analysis using hybrid Q-TOF MS was performed for synthetic peptides selected as targets and spiked into tryptic digests of human serum. By integrating multiple transition signals corresponding to fragment ions in the full scan MS/MS spectrum of a precursor ion of the target peptide, a pseudo-MRM MS analysis of the target peptide showed an increased signal-to-noise (S/N) ratio and sensitivity, as well as an improved reproducibility. The pseudo-MRM method was then used for the quantitative analysis of the tryptic peptides of two low-abundance serological proteins, tissue inhibitor of metalloproteinase 1 (TIMP1) and tissue-type protein tyrosine phosphatase kappa (PTPκ), which were prepared with peptide affinity-based enrichment from human serum. Finally, this method was used to detect femtomolar amounts of target peptides derived from TIMP1 and PTPκ, with good coefficients of variation (CV 2.7% and 9.8%, respectively), using a few microliters of human serum from colorectal cancer patients. The results suggest that pseudo-MRM using hybrid Q-TOF MS, combined with peptide affinity-based enrichment, could become a promising alternative for the quantitative analysis of low-abundance target proteins of interest in complex serum samples that avoids protein depletion.

  19. Improved method for identification of low abundance proteins using 2D-gel electrophoresis, MALDI-TOF and TOF/TOF

    Science.gov (United States)

    Introduction: Differential protein expression studies have been routinely performed in our laboratory to determine the health effects of environmentally-important chemicals. In this abstract, improvements in the in-gel protein digestion, MALDI plate spotting and data acquisition...

  20. The MRC-5 human embryonal lung fibroblast two-dimensional gel cellular protein database: quantitative identification of polypeptides whose relative abundance differs between quiescent, proliferating and SV40 transformed cells

    DEFF Research Database (Denmark)

    Celis, J E; Dejgaard, K; Madsen, Peder;

    1990-01-01

    (1323 with isoelectric focusing and 572 with nonequilibrium pH gradient electrophoresis) are recorded in this database, containing quantitative and qualitative data on the relative abundance of cellular proteins synthesized by quiescent, proliferating and SV40 transformed MRC-5 fibroblasts. Of the 592...... proteins quantitated so far, the levels of 138 were up- or down-regulated (51 and 87, respectively) by two times or more in the transformed cells as compared to their normal proliferating counterparts, while only 14 behaved similarly in quiescent cells. Seven MRC-5 SV40 proteins, including plastin and two...... cells (AMA) database (Celis et al., Electrophoresis 1990, 11, 989-1071) for those polypeptides of known and unknown identity that have been matched to AMA polypeptides. As more information is gathered in this and other laboratories, including data on oncogene proteins and transcription factors...

  1. Raccoon abundance inventory report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the results of a raccoon abundance inventory on Clarence Cannon National Wildlife Refuge in 2012. Determining raccoon abundance allows for...

  2. 甲醇沉淀法去除人血清高丰度蛋白质的实验研究%Establishment of methyl alcohol precipitation method for removing high abundant proteins in human serum

    Institute of Scientific and Technical Information of China (English)

    曹璐颖; 李克; 郑文杰

    2012-01-01

    Objective The common method of depleting the high abundant proteins in human serum is too complicated and ex -pensive to be applied to clinical practice . In this study, an effective and simple method of methyl alcohol precipitation was established for the removal of serum high abundant proteins. Methods The serum albumin of healthy controls was precipitated by different volume methyl alcohol. The removal effect was analyzed with one -dimensional sodium dodecyl sulfate -polyacrylamide gel electrophoresis ( SDS-PAGE) and quantitative method of albumin. Results Compared with the gel images of the original serum , the band of protein with molecular weight between 50000-80000 was removed. The results showed that the average concentration of albumin in the serum was de -creased from (47.65-.35) g/L to (1.16-.08) g/L. The removal ratio of protein was over 97% and the percentage of albumin in the total protein of serum was decreased from 65.4% to49.3%. The significantly statistical differences were observed (P<0.001). And the low abundance proteins could be seen and reserved . Conclusion The methyl alcohol depletion strategy may offer an effective and simple method to remove albumin from human serum , which provided a technical support for further study of serum proteomics .%目的 常用人血清高丰度蛋白质(high abundant proteins,HAP)去除方法操作较繁且成本高,文中探索建立简便有效的甲醇沉淀法去除人血清HAP.方法 用不同体积的甲醇处理血清样品,然后与原血清样品上样进行十二烷基磺酸钠聚丙烯酰胺凝胶电泳(sodium dodecyl sulfate-polyacrylamide gel electrophoresis,SDS-PAGE)分析,并对去除HAP后的样品进行蛋白定量检测.结果 SDS-PAGE显示,经甲醇处理过的血清样品与原血清电泳结果 相比,相对分子质量在50000~80000 间的清蛋白等HAP被明显去除,血清清蛋白平均浓度显著降低,由(47.65±0.35)g /L下降至(1.16±0.08)g /L,去除率达97%以上,

  3. High abundance of Serine/Threonine-rich regions predicted to be hyper-O-glycosylated in the secretory proteins coded by eight fungal genomes

    Directory of Open Access Journals (Sweden)

    González Mario

    2012-09-01

    Full Text Available Abstract Background O-glycosylation of secretory proteins has been found to be an important factor in fungal biology and virulence. It consists in the addition of short glycosidic chains to Ser or Thr residues in the protein backbone via O-glycosidic bonds. Secretory proteins in fungi frequently display Ser/Thr rich regions that could be sites of extensive O-glycosylation. We have analyzed in silico the complete sets of putatively secretory proteins coded by eight fungal genomes (Botrytis cinerea, Magnaporthe grisea, Sclerotinia sclerotiorum, Ustilago maydis, Aspergillus nidulans, Neurospora crassa, Trichoderma reesei, and Saccharomyces cerevisiae in search of Ser/Thr-rich regions as well as regions predicted to be highly O-glycosylated by NetOGlyc (http://www.cbs.dtu.dk. Results By comparison with experimental data, NetOGlyc was found to overestimate the number of O-glycosylation sites in fungi by a factor of 1.5, but to be quite reliable in the prediction of highly O-glycosylated regions. About half of secretory proteins have at least one Ser/Thr-rich region, with a Ser/Thr content of at least 40% over an average length of 40 amino acids. Most secretory proteins in filamentous fungi were predicted to be O-glycosylated, sometimes in dozens or even hundreds of sites. Residues predicted to be O-glycosylated have a tendency to be grouped together forming hyper-O-glycosylated regions of varying length. Conclusions About one fourth of secretory fungal proteins were predicted to have at least one hyper-O-glycosylated region, which consists of 45 amino acids on average and displays at least one O-glycosylated Ser or Thr every four residues. These putative highly O-glycosylated regions can be found anywhere along the proteins but have a slight tendency to be at either one of the two ends.

  4. Snow-mold-induced apoplastic proteins in winter rye leaves lack antifreeze activity

    Science.gov (United States)

    Hiilovaara-Teijo; Hannukkala; Griffith; Yu; Pihakaski-Maunsbach

    1999-10-01

    During cold acclimation, winter rye (Secale cereale L.) plants secrete antifreeze proteins that are similar to pathogenesis-related (PR) proteins. In this experiment, the secretion of PR proteins was induced at warm temperatures by infection with pink snow mold (Microdochium nivale), a pathogen of overwintering cereals. A comparison of cold-induced and pathogen-induced proteins showed that PR proteins accumulated in the leaf apoplast to a greater level in response to cold. The PR proteins induced by cold and by snow mold were similar when separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and examined by immunoblotting. Both groups of PR proteins contained glucanase-like, chitinase-like, and thaumatin-like proteins, and both groups exhibited similar levels of glucanase and chitinase activities. However, only the PR proteins induced by cold exhibited antifreeze activity. Our findings suggest that the cold-induced PR proteins may be isoforms that function as antifreeze proteins to modify the growth of ice during freezing while also providing resistance to the growth of low-temperature pathogens in advance of infection. Both functions of the cold-induced PR proteins may improve the survival of overwintering cereals.

  5. Cloning and Characterization of a Novel cDNA Encoding Late Embryogenesis-Abundant Protein 5 Like (LEA-5) Gene from Cara Cara Navel Orange Fruit(Citrus sinensis Osbeck)

    Institute of Scientific and Technical Information of China (English)

    TAO Neng-guo; YE Jun-li; XU Juan; DENG Xiu-xin

    2006-01-01

    LEA5 gene was postulated related with both stress and hormone responses. In an attempt to find genes exclusively expressed during fruit ripening of Cara Cara navel orange, a novel cDNA clone encoding late embryogenesis-abundant protein 5 like gene (CitLEA5-1) was obtained. It was 582 bp in length, containing 97 deduced amino acids. Compared with the stress-induced LEA5 from leaves of Citrus sinensis, CitLEA5-1 had a shorter 3' untranslated region (UTR). Semiquantitative RT-PCR analysis revealed that CitLEA5-1 was transcriptional regulated during fruit ripening of Cara Cara navel orange.

  6. The absence of protein Y4yS affects negatively the abundance of T3SS Mesorhizobium loti secretin, RhcC2, in bacterial membranes.

    Science.gov (United States)

    Mercante, Virginia; Duarte, Cecilia M; Sánchez, Cintia M; Zalguizuri, Andrés; Caetano-Anollés, Gustavo; Lepek, Viviana C

    2015-01-01

    Mesorhizobium loti MAFF303099 has a functional type III secretion system (T3SS) that is involved in the determination of nodulation competitiveness on Lotus. The M. loti T3SS cluster contains gene y4yS (mlr8765) that codes for a protein of unknown function (Y4yS). A mutation in the y4yS gene favors the M. loti symbiotic competitive ability on Lotus tenuis cv. Esmeralda and affects negatively the secretion of proteins through T3SS. Here we localize Y4yS in the bacterial membrane using a translational reporter peptide fusion. In silico analysis indicated that this protein presents a tetratricopeptide repeat (TPR) domain, a signal peptide and a canonical lipobox LGCC in the N-terminal sequence. These features that are shared with proteins required for the formation of the secretin complex in type IV secretion systems and in the Tad system, together with its localization, suggest that the y4yS-encoded protein is required for the formation of the M. loti T3SS secretin (RhcC2) complex. Remarkably, analysis of RhcC2 in the wild-type and M. loti y4yS mutant strains indicated that the absence of Y4yS affects negatively the accumulation of normal levels of RhcC2 in the membrane.

  7. The absence of protein Y4yS affects negatively the abundance of T3SS Mesorhizobium loti secretin, RhcC2, in bacterial membranes

    Directory of Open Access Journals (Sweden)

    Virginia eMercante

    2015-01-01

    Full Text Available Mesorhizobium loti MAFF303099 has a functional type III secretion system (T3SS that is involved in the determination of nodulation competitiveness on Lotus. The M. loti T3SS cluster contains gene y4yS (mlr8765 that codes for a protein of unknown function (Y4yS. A mutation in the y4yS gene favors the M. loti symbiotic competitive ability on Lotus tenuis cv. Esmeralda and affects negatively the secretion of proteins through T3SS. Here we localize Y4yS in the bacterial membrane using a translational reporter peptide fusion. In silico analysis indicated that this protein presents a tetratricopeptide repeat (TPR domain, a signal peptide and a canonical lipobox LGCC in the N-terminal sequence. These features that are shared with proteins required for the formation of the secretin complex in type IV secretion systems and in the Tad system, together with its localization, suggest that the y4yS-encoded protein is required for the formation of the M. loti T3SS secretin (RhcC2 complex. Remarkably, analysis of RhcC2 in the wild-type and M. loti y4yS mutant strains indicated that the absence of Y4yS affects negatively the accumulation of normal levels of RhcC2 in the membrane.

  8. Precision Chemical Abundance Measurements

    DEFF Research Database (Denmark)

    Yong, David; Grundahl, Frank; Meléndez, Jorge;

    2012-01-01

    This talk covers preliminary work in which we apply a strictly differential line-by-line chemical abundance analysis to high quality UVES spectra of the globular cluster NGC 6752. We achieve extremely high precision in the measurement of relative abundance ratios. Our results indicate that the ob......This talk covers preliminary work in which we apply a strictly differential line-by-line chemical abundance analysis to high quality UVES spectra of the globular cluster NGC 6752. We achieve extremely high precision in the measurement of relative abundance ratios. Our results indicate...... that the observed abundance dispersion exceeds the measurement uncertainties and that many pairs of elements show significant correlations when plotting [X1/H] vs. [X2/H]. Our tentative conclusions are that either NGC 6752 is not chemically homogeneous at the ~=0.03 dex level or the abundance variations...

  9. Abundant immunohistochemical expression of dopamine D{sub 2} receptor and p53 protein in meningiomas: follow-up, relation to gender, age, tumor grade, and recurrence

    Energy Technology Data Exchange (ETDEWEB)

    Trott, G.; Pereira-Lima, J.F.S.; Leães, C.G.S. [Programa de Graduação em Patologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS (Brazil); Centro de Neuroendocrinologia, Complexo Hospitalar Santa Casa de Porto Alegre, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS (Brazil); Ferreira, N.P. [Centro de Neuroendocrinologia, Complexo Hospitalar Santa Casa de Porto Alegre, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS (Brazil); Barbosa-Coutinho, L.M. [Programa de Graduação em Patologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS (Brazil); Oliveira, M.C. [Programa de Graduação em Patologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS (Brazil); Centro de Neuroendocrinologia, Complexo Hospitalar Santa Casa de Porto Alegre, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS (Brazil)

    2015-03-03

    Meningiomas are common, usually benign tumors, with a high postoperative recurrence rate. However, the genesis and development of these tumors remain controversial. We aimed to investigate the presence and implications of a mutated p53 protein and dopamine D{sub 2} receptor in a representative series of meningiomas and to correlate these findings with age, gender, tumor grade, and recurrence. Tumor tissue samples of 157 patients diagnosed with meningioma (37 males and 120 females, mean age 53.6±14.3 years) who underwent surgical resection between 2003 and 2012 at our institution were immunohistochemically evaluated for the presence of p53 protein and dopamine D{sub 2} receptor and were followed-up to analyze tumor recurrence or regrowth. Tumors were classified as grades I (n=141, 89.8%), II (n=13, 8.3%), or grade III (n=3, 1.9%). Dopamine D{sub 2} receptor and p53 protein expression were positive in 93.6% and 49.7% of the cases, respectively. Neither of the markers showed significant expression differences among different tumor grades or recurrence or regrowth statuses. Our findings highlight the potential role of p53 protein in meningioma development and/or progression. The high positivity of dopamine D{sub 2} receptor observed in this study warrants further investigation of the therapeutic potential of dopamine agonists in the evolution of meningiomas.

  10. Small-Molecule Transport by CarO, an Abundant Eight-Stranded β-Barrel Outer Membrane Protein from Acinetobacter baumannii.

    Science.gov (United States)

    Zahn, Michael; D'Agostino, Tommaso; Eren, Elif; Baslé, Arnaud; Ceccarelli, Matteo; van den Berg, Bert

    2015-07-17

    Outer membrane (OM) β-barrel proteins composed of 12-18 β-strands mediate cellular entry of small molecules in Gram-negative bacteria. Small OM proteins with barrels of 10 strands or less are not known to transport small molecules. CarO (carbapenem-associated outer membrane protein) from Acinetobacter baumannii is a small OM protein that has been implicated in the uptake of ornithine and carbapenem antibiotics. Here we report crystal structures of three isoforms of CarO. The structures are very similar and show a monomeric eight-stranded barrel lacking an open channel. CarO has a substantial extracellular domain resembling a glove that contains all the divergent residues between the different isoforms. Liposome swelling experiments demonstrate that full-length CarO and a "loop-less" truncation mutant mediate small-molecule uptake at low levels but that they are unlikely to mediate passage of carbapenem antibiotics. These results are confirmed by biased molecular dynamics simulations that allowed us to quantitatively model the transport of selected small molecules.

  11. Foetal life protein restriction in male mink (Neovison vison) kits lowers post-weaning protein oxidation and the relative abundance of hepatic fructose-1,6-bisphosphatase mRNA

    DEFF Research Database (Denmark)

    Matthiesen, Connie Marianne Frank; Blache, D.; Thomsen, Preben Dybdahl;

    2012-01-01

    protein deficiency affects the response to adequate or deficient protein provision post weaning. Further, we intended to study whether the changes in the gene expression of key enzymes in foetal hepatic tissue caused by maternal protein deficiency were manifested post-weaning. A total of 32 male mink kits...... (P restriction leads to changes in post-weaning protein metabolism through lower protein oxidation of male mink kits....

  12. Abundances of iron-binding photosynthetic and nitrogen-fixing proteins of Trichodesmium both in culture and in situ from the North Atlantic.

    Directory of Open Access Journals (Sweden)

    Sophie Richier

    Full Text Available Marine cyanobacteria of the genus Trichodesmium occur throughout the oligotrophic tropical and subtropical oceans, where they can dominate the diazotrophic community in regions with high inputs of the trace metal iron (Fe. Iron is necessary for the functionality of enzymes involved in the processes of both photosynthesis and nitrogen fixation. We combined laboratory and field-based quantifications of the absolute concentrations of key enzymes involved in both photosynthesis and nitrogen fixation to determine how Trichodesmium allocates resources to these processes. We determined that protein level responses of Trichodesmium to iron-starvation involve down-regulation of the nitrogen fixation apparatus. In contrast, the photosynthetic apparatus is largely maintained, although re-arrangements do occur, including accumulation of the iron-stress-induced chlorophyll-binding protein IsiA. Data from natural populations of Trichodesmium spp. collected in the North Atlantic demonstrated a protein profile similar to iron-starved Trichodesmium in culture, suggestive of acclimation towards a minimal iron requirement even within an oceanic region receiving a high iron-flux. Estimates of cellular metabolic iron requirements are consistent with the availability of this trace metal playing a major role in restricting the biomass and activity of Trichodesmium throughout much of the subtropical ocean.

  13. Abiotic stress induces change in Cinnamoyl CoA Reductase (CCR) protein abundance and lignin deposition in developing seedlings of Leucaena leucocephala.

    Science.gov (United States)

    Srivastava, Sameer; Vishwakarma, Rishi K; Arafat, Yasir Ali; Gupta, Sushim K; Khan, Bashir M

    2015-04-01

    Aboitic stress such as drought and salinity are class of major threats, which plants undergo through their lifetime. Lignin deposition is one of the responses to such abiotic stresses. The gene encoding Cinnamoyl CoA Reductase (CCR) is a key gene for lignin biosynthesis, which has been shown to be over-expressed under stress conditions. In the present study, developing seedlings of Leucaena leucocephala (Vernacular name: Subabul, White popinac) were treated with 1 % mannitol and 200 mM NaCl to mimic drought and salinity stress conditions, respectively. Enzyme linked immunosorbant assay (ELISA) based expression pattern of CCR protein was monitored coupled with Phlorogucinol/HCl activity staining of lignin in transverse sections of developing L. leucocephala seedlings under stress. Our result suggests a differential lignification pattern in developing root and stem under stress conditions. Increase in lignification was observed in mannitol treated stems and corresponding CCR protein accumulation was also higher than control and salt stress treated samples. On the contrary CCR protein was lower in NaCl treated stems and corresponding lignin deposition was also low. Developing root tissue showed a high level of CCR content and lignin deposition than stem samples under all conditions tested. Overall result suggested that lignin accumulation was not affected much in case of developing root however developing stems were significantly affected under drought and salinity stress condition.

  14. Dietary whey protein lowers serum C-peptide concentration and duodenal SREBP-1c mRNA abundance, and reduces occurrence of duodenal tumors and colon aberrant crypt foci in azoxymethane-treated male rats.

    Science.gov (United States)

    Xiao, Rijin; Carter, Julie A; Linz, Amanda L; Ferguson, Matthew; Badger, Thomas M; Simmen, Frank A

    2006-09-01

    We evaluated partially hydrolyzed whey protein (WPH) for inhibitory effects on the development of colon aberrant crypt foci (ACF) and intestinal tumors in azoxymethane (AOM)-treated rats. Pregnant Sprague-Dawley rats and their progeny were fed AIN-93G diets containing casein (CAS, control diet) or WPH as the sole protein source. Colons and small intestines from the male progeny were obtained at 6, 12, 20 and 23 weeks after AOM treatment. At 6 and 23 weeks, post-AOM, WPH-fed rats had fewer ACF than did CAS-fed rats. Intestinal tumors were most frequent at 23 weeks, post-AOM. At this time point, differences in colon tumor incidence with diet were not observed; however, WPH-fed rats had fewer tumors in the small intestine (7.6% vs. 26% incidence, P=.004). Partially hydrolized whey protein suppressed circulating C-peptide concentration (a stable indicator of steady-state insulin secretion) at all four time points relative to the corresponding CAS-fed animals. The relative mRNA abundance for the insulin-responsive, transcription factor gene, SREBP-1c, was reduced by WPH in the duodenum but not colon. Results indicate potential physiological linkages of dietary protein type with circulating C-peptide (and by inference insulin), local expression of SREBP-1c gene and propensity for small intestine tumorigenesis.

  15. Perturbations of amino acid metabolism associated with glyphosate-dependent inhibition of shikimic acid metabolism affect cellular redox homeostasis and alter the abundance of proteins involved in photosynthesis and photorespiration.

    Science.gov (United States)

    Vivancos, Pedro Diaz; Driscoll, Simon P; Bulman, Christopher A; Ying, Liu; Emami, Kaveh; Treumann, Achim; Mauve, Caroline; Noctor, Graham; Foyer, Christine H

    2011-09-01

    The herbicide glyphosate inhibits the shikimate pathway of the synthesis of amino acids such as phenylalanine, tyrosine, and tryptophan. However, much uncertainty remains concerning precisely how glyphosate kills plants or affects cellular redox homeostasis and related processes in glyphosate-sensitive and glyphosate-resistant crop plants. To address this issue, we performed an integrated study of photosynthesis, leaf proteomes, amino acid profiles, and redox profiles in the glyphosate-sensitive soybean (Glycine max) genotype PAN809 and glyphosate-resistant Roundup Ready Soybean (RRS). RRS leaves accumulated much more glyphosate than the sensitive line but showed relatively few changes in amino acid metabolism. Photosynthesis was unaffected by glyphosate in RRS leaves, but decreased abundance of photosynthesis/photorespiratory pathway proteins was observed together with oxidation of major redox pools. While treatment of a sensitive genotype with glyphosate rapidly inhibited photosynthesis and triggered the appearance of a nitrogen-rich amino acid profile, there was no evidence of oxidation of the redox pools. There was, however, an increase in starvation-associated and defense proteins. We conclude that glyphosate-dependent inhibition of soybean leaf metabolism leads to the induction of defense proteins without sustained oxidation. Conversely, the accumulation of high levels of glyphosate in RRS enhances cellular oxidation, possibly through mechanisms involving stimulation of the photorespiratory pathway.

  16. OXYGEN ABUNDANCES IN CEPHEIDS

    Energy Technology Data Exchange (ETDEWEB)

    Luck, R. E.; Andrievsky, S. M. [Department of Astronomy, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-7215 (United States); Korotin, S. N.; Kovtyukh, V. V., E-mail: luck@fafnir.astr.cwru.edu, E-mail: serkor@skyline.od.ua, E-mail: val@deneb1.odessa.ua, E-mail: scan@deneb1.odessa.ua [Department of Astronomy and Astronomical Observatory, Odessa National University, Isaac Newton Institute of Chile, Odessa Branch, Shevchenko Park, 65014 Odessa (Ukraine)

    2013-07-01

    Oxygen abundances in later-type stars, and intermediate-mass stars in particular, are usually determined from the [O I] line at 630.0 nm, and to a lesser extent, from the O I triplet at 615.7 nm. The near-IR triplets at 777.4 nm and 844.6 nm are strong in these stars and generally do not suffer from severe blending with other species. However, these latter two triplets suffer from strong non-local thermodynamic equilibrium (NLTE) effects and thus see limited use in abundance analyses. In this paper, we derive oxygen abundances in a large sample of Cepheids using the near-IR triplets from an NLTE analysis, and compare those abundances to values derived from a local thermodynamic equilibrium (LTE) analysis of the [O I] 630.0 nm line and the O I 615.7 nm triplet as well as LTE abundances for the 777.4 nm triplet. All of these lines suffer from line strength problems making them sensitive to either measurement complications (weak lines) or to line saturation difficulties (strong lines). Upon this realization, the LTE results for the [O I] lines and the O I 615.7 nm triplet are in adequate agreement with the abundance from the NLTE analysis of the near-IR triplets.

  17. Real-time RT-PCR quantification of pregnancy-associated plasma protein-A mRNA abundance in bovine granulosa and theca cells: effects of hormones in vitro.

    Science.gov (United States)

    Aad, Pauline Y; Voge, Justin L; Santiago, Consuelo A; Malayer, Jerry R; Spicer, Leon J

    2006-11-01

    Ovarian follicular growth and dominance are controlled by a series of hormonal and intraovarian events including a decrease in intrafollicular IGF-binding proteins -2, -4 and -5 levels. Proteolytic enzymes such as pregnancy-associated plasma protein-A (PAPP-A) degrade IGFBPs and increase bioavailability of IGF-I and -II during follicular development. The objective of this study was to determine the effect of IGF-I, IGF-II, insulin (INS), LH, FSH, estradiol (E2), leptin or cortisol on ovarian PAPP-A mRNA levels. Granulosa (GC) from small (SM) (1-5 mm) and large (LG) (8-22 mm) follicles as well as theca cells (TC) from LG follicles were collected from bovine ovaries and cultured for 48 h in medium containing 10% FCS and then treated with various hormones in serum-free medium for an additional 24 h. Cells were treated with various concentrations (3-500 ng/ml) and combinations of IGF-I, IGF-II, FSH, LH, E2, INS, leptin and (or) cortisol for 24 h (Experiments 1-10). PAPP-A mRNA levels were measured using quantitative real-time RT-PCR. In SM-GC and LG-GC, none of the treatments significantly affected (P>0.10) PAPP-A mRNA abundance. In LG-TC, IGF-I, LH or cortisol did not affect (P>0.10) PAPP-A mRNA levels, whereas INS with or without LH decreased (P<0.05) PAPP-A mRNA. E2 alone decreased PAPP-A mRNA levels in LG-TC, and E2 amplified the insulin-induced inhibition of PAPP-A mRNA abundance in LG-TC. We conclude that control of PAPP-A mRNA abundance in granulosa and theca cells differs, and that E2 may be part of an intraovarian negative feedback system which may reduce the bioavailable IGFs in the theca layer during growth and selection of follicles.

  18. The impaired intestinal mucosal immune system by valine deficiency for young grass carp (Ctenopharyngodon idella) is associated with decreasing immune status and regulating tight junction proteins transcript abundance in the intestine.

    Science.gov (United States)

    Luo, Jian-Bo; Feng, Lin; Jiang, Wei-Dan; Liu, Yang; Wu, Pei; Jiang, Jun; Kuang, Sheng-Yao; Tang, Ling; Zhang, Yong-An; Zhou, Xiao-Qiu

    2014-09-01

    This study investigated the effects of dietary valine on the growth, intestinal immune response, tight junction proteins transcript abundance and gene expression of immune-related signaling molecules in the intestine of young grass carp (Ctenopharyngodon idella). Six iso-nitrogenous diets containing graded levels of valine (4.3-19.1 g kg(-)(1) diet) were fed to the fish for 8 weeks. The results showed that percentage weight gain (PWG), feed intake and feed efficiency of fish were the lowest in fish fed the valine-deficient diet (P valine deficiency decreased lysozyme, acid phosphatase activities and complement 3 content in the intestine (P valine deficiency significantly decreased transcript of Occludin, Claudin b, Claudin c, Claudin 3, and ZO-1 (P valine did not have a significant effect on expression of Claudin 12 in the intestine of grass carp (P > 0.05). In conclusion, valine deficiency decreased fish growth and intestinal immune status, as well as regulated gene expression of tight junction proteins, NF-κB P65, IκBα and TOR in the fish intestine. Based on the quadratic regression analysis of lysozyme activity or PWG, the dietary valine requirement of young grass carp (268-679 g) were established to be 14.47 g kg(-1) diet (4.82 g 100 g(-1) CP) or 14.00 g kg(-1) diet (4.77 g 100 g(-1) CP), respectively.

  19. Deuterium abundance and cosmology

    CERN Document Server

    Vidal-Madjar, A; Lemoine, M

    1996-01-01

    We review the status of the measurements of the deuterium abundance from the local interstellar medium to the solar system and high redshifts absorbers toward quasars. We present preliminary results toward a white dwarf and a QSO. We conclude that the deuterium evolution from the Big-Bang to now is still not properly understood.

  20. Interaction of unsaturated fat or coconut oil with monensin in lactating dairy cows fed 12 times daily. I. Protozoal abundance, nutrient digestibility, and microbial protein flow to the omasum.

    Science.gov (United States)

    Reveneau, C; Karnati, S K R; Oelker, E R; Firkins, J L

    2012-04-01

    Monensin (tradename: Rumensin) should reduce the extent of amino acid deamination in the rumen, and supplemental fat should decrease protozoal abundance and intraruminal N recycling. Because animal-vegetable (AV) fat can be biohydrogenated in the rumen and decrease its effectiveness as an anti-protozoal agent, we included diets supplemented with coconut oil (CNO) to inhibit protozoa. In a 6 × 6 Latin square design with a 2 × 3 factorial arrangement of treatments, 6 rumen-cannulated cows were fed diets without or with Rumensin (12 g/909 kg) and either no fat (control), 5% AV fat, or 5% CNO. The log10 concentrations (cells/mL) of total protozoa were not different between control (5.97) and AV fat (5.95) but were decreased by CNO (4.79; main effect of fat source). Entodinium and Dasytricha decreased as a proportion of total cells from feeding CNO, whereas Epidinium was unchanged in total abundance and thus increased proportionately. Total volatile fatty acid concentration was not affected by diet, but the acetate:propionate ratio decreased for CNO (1.85) versus control (2.95) or AV fat (2.58). Feeding CNO (23.8%) decreased ruminal neutral detergent fiber digestibility compared with control (31.1%) and AV fat (30.5%). The total-tract digestibility of NDF was lower for CNO (45.8%) versus control (57.0%) and AV fat (54.6%), with no difference in apparent organic matter digestibility (averaging 69.8%). The omasal flows of microbial N and non-ammonia N were lower for CNO versus control and AV fat, but efficiency of microbial protein synthesis was not affected. The dry matter intake was 4.5 kg/d lower with CNO, which decreased milk production by 3.1 kg/d. Main effect means of dry matter intake and milk yield tended to decrease by 0.7 and 1.2 kg/d, respectively, when Rumensin was added. Both percentage and production of milk fat decreased for CNO (main effect of fat source). An interaction was observed such that AV decreased milk fat yield more when combined with Rumensin

  1. Protein

    Science.gov (United States)

    ... Food Service Resources Additional Resources About FAQ Contact Protein Protein is found throughout the body—in muscle, ... the heart and respiratory system, and death. All Protein Isn’t Alike Protein is built from building ...

  2. Short-chain fatty acid-supplemented total parenteral nutrition alters intestinal structure, glucose transporter 2 (GLUT2) mRNA and protein, and proglucagon mRNA abundance in normal rats.

    Science.gov (United States)

    Tappenden, K A; Drozdowski, L A; Thomson, A B; McBurney, M I

    1998-07-01

    Intestinal adaptation is a complex physiologic process that is not completely understood. Intravenous short-chain fatty acids (SCFAs) enhance intestinal adaptation after 80% enterectomy in rats. The purpose of this study was to examine rapid responses to SCFA-supplemented total parenteral nutrition (TPN) in the normal small intestine. After jugular catheterization, 31 Sprague-Dawley rats (weighing 258 +/- 3 g) were randomly assigned to receive standard TPN or an isoenergetic, isonitrogenous TPN solution supplemented with SCFAs (TPN+SCFA). Intestinal samples were obtained after 24 or 72 h of nutrient infusion. TPN+SCFA for 24 h increased (P SCFA for 72 h increased (P SCFA infusion and returned to levels seen with control TPN by 72 h. Glucose transporter 2 (GLUT2) mRNA was significantly higher (P SCFA groups at both time points when compared with control TPN groups. Ileal GLUT2 protein abundance in the 72-h TPN+SCFA group was significantly higher (P SCFA than after 24 h, whereas the 24- and 72-h TPN groups did not differ. In summary, SCFAs led to rapid changes in ileal proglucagon and glucose transporter expression in rats receiving TPN and provide insights into therapeutic management of individuals with short bowel syndrome or intestinal malabsorption syndromes.

  3. hebp3, a novel member of the heme-binding protein gene family, is expressed in the medaka meninges with higher abundance in females due to a direct stimulating action of ovarian estrogens.

    Science.gov (United States)

    Nakasone, Kiyoshi; Nagahama, Yoshitaka; Okubo, Kataaki

    2013-02-01

    The brains of teleost fish exhibit remarkable sexual plasticity throughout their life span. To dissect the molecular basis for the development and reversal of sex differences in the teleost brain, we screened for genes differentially expressed between sexes in the brain of medaka (Oryzias latipes). One of the genes identified in the screen as being preferentially expressed in females was found to be a new member of the heme-binding protein gene family that includes hebp1 and hebp2 and was designated here as hebp3. The medaka hebp3 is expressed in the meninges with higher abundance in females, whereas there is no expression within the brain parenchyma. This female-biased expression of hebp3 is not attributable to the direct action of sex chromosome genes but results from the transient and reversible action of estrogens derived from the ovary. Moreover, estrogens directly activate the transcription of hebp3 via a palindromic estrogen-responsive element in the hebp3 promoter. Taken together, our findings demonstrate that hebp3 is a novel transcriptional target of estrogens, with female-biased expression in the meninges. The definite but reversible sexual dimorphism of the meningeal hebp3 expression may contribute to the development and reversal of sex differences in the teleost brain.

  4. Flare Plasma Iron Abundance

    Science.gov (United States)

    Dennis, Brian R.; Dan, Chau; Jain, Rajmal; Schwartz, Richard A.; Tolbert, Anne K.

    2008-01-01

    The equivalent width of the iron-line complex at 6.7 keV seen in flare X-ray spectra suggests that the iron abundance of the hottest plasma at temperatures >approx.10 MK may sometimes be significantly lower than the nominal coronal abundance of four times the photospheric value that is commonly assumed. This conclusion is based on X-ray spectral observations of several flares seen in common with the Ramaty High Energy Solar Spectroscopic Imager (RHESSI) and the Solar X-ray Spectrometer (SOXS) on the second Indian geostationary satellite, GSAT-2. The implications of this will be discussed as it relates to the origin of the hot flare plasma - either plasma already in the corona that is directly heated during the flare energy release process or chromospheric plasma that is heated by flare-accelerated particles and driven up into the corona. Other possible explanations of lower-than-expected equivalent widths of the iron-line complex will also be discussed.

  5. Primordial Deuterium Abundance Measurements

    CERN Document Server

    Levshakov, S A; Takahara, F; Levshakov, Sergei A.; Kegel, Wilhelm H.; Takahara, Fumio

    1997-01-01

    Deuterium abundances measured recently from QSO absorption-line systems lie in the range from 3 10^{-5} to 3 10^{-4}, which shed some questions on standard big bang theory. We show that this discordance may simply be an artifact caused by inadequate analysis ignoring spatial correlations in the velocity field in turbulent media. The generalized procedure (accounting for such correlations) is suggested to reconcile the D/H measurements. An example is presented based on two high-resolution observations of Q1009+2956 (low D/H) [1,2] and Q1718+4807 (high D/H) [8,9]. We show that both observations are compatible with D/H = 4.1 - 4.6 10^{-5}, and thus support SBBN. The estimated mean value = 4.4 10^{-5} corresponds to the baryon-to-photon ratio during SBBN eta = 4.4 10^{-10} which yields the present-day baryon density Omega_b h^2 = 0.015.

  6. Structure of Human Chitotriosidase. Implications for Specific Inhibitor Design and Function of Mammalian Chitinase-like Lectins

    NARCIS (Netherlands)

    Fusetti, Fabrizia; Moeller, Holger von; Houston, Douglas; Rozeboom, Henriëtte J.; Dijkstra, Bauke W.; Boot, Rolf G.; Aerts, Johannes M.F.G.; Aalten, Daan M.F. van

    2002-01-01

    Chitin hydrolases have been identified in a variety of organisms ranging from bacteria to eukaryotes. They have been proposed to be possible targets for the design of novel chemotherapeutics against human pathogens such as fungi and protozoan parasites as mammals were not thought to possess chitin-p

  7. Cloning of the Bacillus thuringiensis serovar sotto chitinase (Schi gene and characterization of its protein

    Directory of Open Access Journals (Sweden)

    Wan-Fang Zhong

    2005-12-01

    Full Text Available Chitinase plays a positive role in the pathogenicity of Bacillus thuringiensis to insect pests. We used touchdown PCR to clone the chitinase (Schi gene from Bacillus thuringiensis serovar sotto (Bt sotto chromosomal DNA. Our DNA sequencing analysis revealed that the Bt sotto Schi gene consists of an open reading frame (ORF of 2067 nucleotides with codes for the chitinase precursor. We also found that the putative promoter consensus sequences (the -35 and -10 regions of the Bt soto Schi gene are identical to those of the chiA71 gene from Bt Pakistani, the chiA74 gene from Bt kenyae and the ichi gene from Bt israelensis. The Schi chitinase precursor is 688 amino acids long with an estimated molecular mass of 75.75 kDa and a theoretical isoelectric point of 5.74, and contains four domains, which are, in sequence, a signal peptide, an N-terminal catalytic domain, a fibronectin type III like domain and a C-terminal chitin-binding domain. Sequence comparison and the evolutionary relationship of the Bt sotto Schi chitinase to other chitinase and chitinase-like proteins are also discussed.

  8. Gaseous abundances in M82

    CERN Document Server

    Ranalli, P; Origlia, L; Maiolino, R; Makishima, K; Ranalli, Piero; Comastri, Andrea; Origlia, Livia; Maiolino, Roberto; Makishima, Kazuo

    2005-01-01

    We present the preliminary analysis of a deep (100ks) XMM-Newton observation of M82. The spatial distribution of the abundances of chemical elements (Fe, O, Ne, Mg, Si, S) is investigated through narrow-band imaging analisys and spatially-resolved spectroscopy. We find that the abundances of alpha-elements follow a bipolar distribution, these elements being more abundant in the gaseous outflow than in the galaxy centre. This behaviour is found to be more marked for lighter elements (O, Ne) than for heavier elements.

  9. Protein inference: A protein quantification perspective.

    Science.gov (United States)

    He, Zengyou; Huang, Ting; Liu, Xiaoqing; Zhu, Peijun; Teng, Ben; Deng, Shengchun

    2016-08-01

    In mass spectrometry-based shotgun proteomics, protein quantification and protein identification are two major computational problems. To quantify the protein abundance, a list of proteins must be firstly inferred from the raw data. Then the relative or absolute protein abundance is estimated with quantification methods, such as spectral counting. Until now, most researchers have been dealing with these two processes separately. In fact, the protein inference problem can be regarded as a special protein quantification problem in the sense that truly present proteins are those proteins whose abundance values are not zero. Some recent published papers have conceptually discussed this possibility. However, there is still a lack of rigorous experimental studies to test this hypothesis. In this paper, we investigate the feasibility of using protein quantification methods to solve the protein inference problem. Protein inference methods aim to determine whether each candidate protein is present in the sample or not. Protein quantification methods estimate the abundance value of each inferred protein. Naturally, the abundance value of an absent protein should be zero. Thus, we argue that the protein inference problem can be viewed as a special protein quantification problem in which one protein is considered to be present if its abundance is not zero. Based on this idea, our paper tries to use three simple protein quantification methods to solve the protein inference problem effectively. The experimental results on six data sets show that these three methods are competitive with previous protein inference algorithms. This demonstrates that it is plausible to model the protein inference problem as a special protein quantification task, which opens the door of devising more effective protein inference algorithms from a quantification perspective. The source codes of our methods are available at: http://code.google.com/p/protein-inference/.

  10. Chlorine Abundances in Cool Stars

    CERN Document Server

    Maas, Z G; Hinkle, K

    2016-01-01

    Chlorine abundances are reported in 15 evolved giants and one M dwarf in the solar neighborhood. The Cl abundance was measured using the vibration-rotation 1-0 P8 line of H$^{35}$Cl at 3.69851 $\\mu$m. The high resolution L-band spectra were observed using the Phoenix infrared spectrometer on the Kitt Peak Mayall 4m telescope. The average [$^{35}$Cl/Fe] abundance in stars with --0.72$<$[Fe/H]$<$0.20 is [$^{35}$Cl/Fe]=(--0.10$\\pm$0.15) dex. The mean difference between the [$^{35}$Cl/Fe] ratios measured in our stars and chemical evolution model values is (0.16$\\pm$0.15) dex. The [$^{35}$Cl/Ca] ratio has an offset of $\\sim$0.35 dex above model predictions suggesting chemical evolution models are under producing Cl at the high metallicity range. Abundances of C, N, O, Si, and Ca were also measured in our spectral region and are consistent with F and G dwarfs. The Cl versus O abundances from our sample match Cl abundances measured in planetary nebula and \\ion{H}{2} regions. In one star where both H$^{35}$Cl a...

  11. Construction of a two-dimensional liquid chromatography separation system for high abundance proteins depletion in human plasma%去除血浆中高丰度蛋白质的二维液相色谱体系的建立

    Institute of Scientific and Technical Information of China (English)

    朱绍春; 张学洋; 高明霞; 晏国全; 张祥民

    2011-01-01

    High abundance proteins existing in human plasma severely impede the detection of low abundance proteins. This is one of the most difficult problems encountered in plasma pro-teomics research. We developed a two-dimensional liquid chromatography system with strong anion exchange chromatography-reversed-phase liquid chromatography ( SAX-RPLC) for the extensive separation of plasma proteins and selective depletion of high abundance proteins. TSKgel SuperQ-5PW was selected as the first dimensional separation column for crude human plasma fractionation and Jupiter C4 column was selected as the second dimensional separation column. Separation gradients of the two-dimensional liquid chromatography system were optimized to ensure an extensive separation of plasma proteins. Ten peaks with high signal intensities ( >20 mAU) at 215 nm during the second dimensional separation were collected and identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). As a result, 32 proteins, all of which were reported to be high abundance proteins in plasma, including human serum albumin (HAS), immunoglobulin G (IgG) and so on were successfully identified. This system provides an effective method for future depletion of more high abundance proteins and in-depth research in human plasma proteomics.%血浆中高丰度蛋白质的存在严重干扰低丰度蛋白质的检测,是困扰血浆蛋白质组学研究的技术瓶颈之一.针对这一热点问题,建立了一种二维液相色谱(强阴离子交换色谱-反相高效液相色谱)分离系统,对血浆中的高丰度蛋白质进行了色谱定位并进行去除.选择TSKgel SuperQ-5PW为第一维色谱分离柱,第二维色谱分离采用Jupiter C4柱,对第一维的馏分进行进一步的分离.通过梯度优化,血浆样品经过二维系统得到充分分离.第二维分离过程中从紫外信号强度高(215 nm,大于20 mAU)的峰中选择10个峰,利用液相色谱-串联质谱鉴定出32种高丰度蛋白质,

  12. Association between ferritin, high sensitivity C-reactive protein (hsCRP) and relative abundance of Hepcidin mRNA with the risk of type 2 diabetes in obese subjects.

    Science.gov (United States)

    Andrews Guzmán, Mónica; Arredondo Olguín, Miguel

    2014-09-01

    Obesity and Type 2 diabetes mellitus share a strong pro-inflammatory profile. It has been observed that iron is a risk factor in the development of type 2 diabetes. The aim of this study was to evaluate the relationship between iron nutritional status and inflammation with the risk of type 2 diabetes development in obese subjects. We studied 30 obese men with type 2 diabetes (OBDM); 30 obese subjects without diabetes (OB) and 30 healthy subjects (Cn). We isolated peripheral mononuclear cells (PMCs) and challenged them with high Fe concentrations. Total mRNA was isolated and relative abundance of TNF-, IL-6 and hepcidin were determined by qPCR. Iron status, biochemical, inflammatory and oxidative stress parameters were also characterized. OBDM and OB patients showed increased hsCRP levels compared to the Cn group. OBDM subjects showed higher levels of ferritin than the Cn group. TNF-α and IL-6 mRNA relative abundances were increased in OBDM PMCs treated with high/Fe. Hepcidin mRNA was increased with basal and high iron concentration. We found that the highest quartile of ferritin was associated with an increased risk of type 2 diabetes when it was adjusted to BMI and HOMA-IR; this association was independent of the inflammatory status. The highest level of hepcidin gene expression also showed a trend of increased risk of diabetes, however it was not significant. Levels of hsCRP over 2 mg/L showed a significant trend of increasing the risk of diabetes. In conclusion, iron may stimulate the expression of pro-inflammatory genes (TNF-α and IL- 6), and both hepcidin and ferritin gene expression levels could be a risk factor for the development of type 2 diabetes. Subjects that have an increased cardiovascular risk also have a major risk to develop type 2 diabetes, which is independent of the BMI and insulin resistance state.

  13. Association between ferritin, high sensitivity c-reactive protein (hsCRP and relative abundance of Hepcidin mRNA with the risk of type 2 diabetes in obese subjects

    Directory of Open Access Journals (Sweden)

    Mónica Andrews Guzmán

    Full Text Available Obesity and Type 2 diabetes mellitus share a strong pro-inflammatory profile. It has been observed that iron is a risk factor in the development of type 2 diabetes. The aim of this study was to evaluate the relationship between iron nutritional status and inflammation with the risk of type 2 diabetes development in obese subjects. We studied 30 obese men with type 2 diabetes (OBDM; 30 obese subjects without diabetes (OB and 30 healthy subjects (Cn. We isolated peripheral mononuclear cells (PMCs and challenged them with high Fe concentrations. Total mRNA was isolated and relative abundance of TNF-αIL-6 and hepcidin were determined by qPCR. Iron status, biochemical, inflammatory and oxidative stress parameters were also characterized. OBDM and OB patients showed increased hsCRP levels compared to the Cn group. OBDM subjects showed higher levels of ferritin than the Cn group. TNF-α and IL-6 mRNA relative abundances were increased in OBDM PMCs treated with high/Fe. Hepcidin mRNA was increased with basal and high iron concentration. We found that the highest quartile of ferritin was associated with an increased risk of type 2 diabetes when it was adjusted to BMI and HOMA-IR; this association was independent of the inflammatory status. The highest level of hepcidin gene expression also showed a trend of increased risk of diabetes, however it was not significant. Levels of hsCRP over 2 mg/L showed a significant trend of increasing the risk of diabetes. In conclusion, iron may stimulate the expression of pro-inflammatory genes (TNF-α and IL-6, and both hepcidin and ferritin gene expression levels could be a risk factor for the development of type 2 diabetes. Subjects that have an increased cardiovascular risk also have a major risk to develop type 2 diabetes, which is independent of the BMI and insulin resistance state.

  14. Hf Transition Probabilities and Abundances

    CERN Document Server

    Lawler, J E; Labby, Z E; Sneden, C; Cowan, J J; Ivans, I I

    2006-01-01

    Radiative lifetimes from laser-induced fluorescence measurements, accurate to about +/- 5 percent, are reported for 41 odd-parity levels of Hf II. The lifetimes are combined with branching fractions measured using Fourier transform spectrometry to determine transition probabilities for 150 lines of Hf II. Approximately half of these new transition probabilities overlap with recent independent measurements using a similar approach. The two sets of measurements are found to be in good agreement for measurements in common. Our new laboratory data are applied to refine the hafnium photospheric solar abundance and to determine hafnium abundances in 10 metal-poor giant stars with enhanced r-process abundances. For the Sun we derive log epsilon (Hf) = 0.88 +/- 0.08 from four lines; the uncertainty is dominated by the weakness of the lines and their blending by other spectral features. Within the uncertainties of our analysis, the r-process-rich stars possess constant Hf/La and Hf/Eu abundance ratios, log epsilon (Hf...

  15. Gd Transition Probabilities and Abundances

    CERN Document Server

    Den Hartog, E A; Sneden, C; Cowan, J J

    2006-01-01

    Radiative lifetimes, accurate to +/- 5%, have been measured for 49 even-parity and 14 odd-parity levels of Gd II using laser-induced fluorescence. The lifetimes are combined with branching fractions measured using Fourier transform spectrometry to determine transition probabilities for 611 lines of Gd II. This work is the largest-scale laboratory study to date of Gd II transition probabilities and the first using a high performance Fourier transform spectrometer. This improved data set has been used to determine a new solar photospheric Gd abundance, log epsilon = 1.11 +/- 0.03. Revised Gd abundances have also been derived for the r-process-rich metal-poor giant stars CS 22892-052, BD+17 3248, and HD 115444. The resulting Gd/Eu abundance ratios are in very good agreement with the solar-system r-process ratio. We have employed the increasingly accurate stellar abundance determinations, resulting in large part from the more precise laboratory atomic data, to predict directly the Solar System r-process elemental...

  16. Changes in protein abundance between tender and tough meat from bovine Longissimus thoracis muscle assessed by isobaric Tag for Relative and Absolute Quantitation (iTRAQ) and 2-dimensional gel electrophoresis analysis

    DEFF Research Database (Denmark)

    Bjarnadóttir, S G; Hollung, K; Høy, M

    2012-01-01

    -DE analysis (P flux through the tricarboxylate cycle [2......The aim of this study was to find potential biomarkers for meat tenderness in bovine Longissimus thoracis muscle and to compare results from isobaric Tag for Relative and Absolute Quantitation (iTRAQ) and 2-dimensional gel electrophoresis (2-DE) analysis. The experiment included 4 tender and 4......-oxoglutarate dehydrogenase complex component E2 (OGDC-E2)], apoptosis (galectin-1) and regulatory role in the release of Ca2+ from intracellular stores (annexin A6). Even though the overlap in significantly changing proteins was relatively low between iTRAQ and 2-DE analysis, certain proteins predicted to have...

  17. Coho Abundance - Point Features [ds182

    Data.gov (United States)

    California Department of Resources — The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. Beginning in 1998, the Pacific States Marine...

  18. Chinook Abundance - Point Features [ds180

    Data.gov (United States)

    California Department of Resources — The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. Beginning in 1998, the Pacific States Marine...

  19. Coho Abundance - Linear Features [ds183

    Data.gov (United States)

    California Department of Resources — The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. Beginning in 1998, the Pacific States Marine...

  20. Steelhead Abundance - Point Features [ds184

    Data.gov (United States)

    California Department of Resources — The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. Beginning in 1998, the Pacific States Marine...

  1. Steelhead Abundance - Linear Features [ds185

    Data.gov (United States)

    California Department of Resources — The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. Beginning in 1998, the Pacific States Marine...

  2. Abundance estimation and Conservation Biology

    Directory of Open Access Journals (Sweden)

    Nichols, J. D.

    2004-06-01

    Full Text Available Abundance is the state variable of interest in most population–level ecological research and in most programs involving management and conservation of animal populations. Abundance is the single parameter of interest in capture–recapture models for closed populations (e.g., Darroch, 1958; Otis et al., 1978; Chao, 2001. The initial capture–recapture models developed for partially (Darroch, 1959 and completely (Jolly, 1965; Seber, 1965 open populations represented efforts to relax the restrictive assumption of population closure for the purpose of estimating abundance. Subsequent emphases in capture–recapture work were on survival rate estimation in the 1970’s and 1980’s (e.g., Burnham et al., 1987; Lebreton et al.,1992, and on movement estimation in the 1990’s (Brownie et al., 1993; Schwarz et al., 1993. However, from the mid–1990’s until the present time, capture–recapture investigators have expressed a renewed interest in abundance and related parameters (Pradel, 1996; Schwarz & Arnason, 1996; Schwarz, 2001. The focus of this session was abundance, and presentations covered topics ranging from estimation of abundance and rate of change in abundance, to inferences about the demographic processes underlying changes in abundance, to occupancy as a surrogate of abundance. The plenary paper by Link & Barker (2004 is provocative and very interesting, and it contains a number of important messages and suggestions. Link & Barker (2004 emphasize that the increasing complexity of capture–recapture models has resulted in large numbers of parameters and that a challenge to ecologists is to extract ecological signals from this complexity. They offer hierarchical models as a natural approach to inference in which traditional parameters are viewed as realizations of stochastic processes. These processes are governed by hyperparameters, and the inferential approach focuses on these hyperparameters. Link & Barker (2004 also suggest that

  3. Abundance estimation and conservation biology

    Science.gov (United States)

    Nichols, J.D.; MacKenzie, D.I.

    2004-01-01

    Abundance is the state variable of interest in most population–level ecological research and in most programs involving management and conservation of animal populations. Abundance is the single parameter of interest in capture–recapture models for closed populations (e.g., Darroch, 1958; Otis et al., 1978; Chao, 2001). The initial capture–recapture models developed for partially (Darroch, 1959) and completely (Jolly, 1965; Seber, 1965) open populations represented efforts to relax the restrictive assumption of population closure for the purpose of estimating abundance. Subsequent emphases in capture–recapture work were on survival rate estimation in the 1970’s and 1980’s (e.g., Burnham et al., 1987; Lebreton et al.,1992), and on movement estimation in the 1990’s (Brownie et al., 1993; Schwarz et al., 1993). However, from the mid–1990’s until the present time, capture–recapture investigators have expressed a renewed interest in abundance and related parameters (Pradel, 1996; Schwarz & Arnason, 1996; Schwarz, 2001). The focus of this session was abundance, and presentations covered topics ranging from estimation of abundance and rate of change in abundance, to inferences about the demographic processes underlying changes in abundance, to occupancy as a surrogate of abundance. The plenary paper by Link & Barker (2004) is provocative and very interesting, and it contains a number of important messages and suggestions. Link & Barker (2004) emphasize that the increasing complexity of capture–recapture models has resulted in large numbers of parameters and that a challenge to ecologists is to extract ecological signals from this complexity. They offer hierarchical models as a natural approach to inference in which traditional parameters are viewed as realizations of stochastic processes. These processes are governed by hyperparameters, and the inferential approach focuses on these hyperparameters. Link & Barker (2004) also suggest that our attention

  4. Human baby hair amino acid natural abundance 15N-isotope values are not related to the 15N-isotope values of amino acids in mother's breast milk protein.

    Science.gov (United States)

    Romek, Katarzyna M; Julien, Maxime; Frasquet-Darrieux, Marine; Tea, Illa; Antheaume, Ingrid; Hankard, Régis; Robins, Richard J

    2013-12-01

    Since exclusively breast-suckled infants obtain their nutrient only from their mother's milk, it might be anticipated that a correlation will exist between the (15)N/(14)N isotope ratios of amino acids of protein of young infants and those supplied by their mother. The work presented here aimed to determine whether amino nitrogen transfer from human milk to infant hair protein synthesized within the first month of life conserves the maternal isotopic signature or whether post-ingestion fractionation dominates the nitrogen isotope spectrum. The study was conducted at 1 month post-birth on 100 mother-infant pairs. Isotope ratios (15)N/(14)N and (13)C/(12)C were measured using isotope ratio measurement by Mass Spectrometry (irm-MS) for whole maternal milk, and infant hair and (15)N/(14)N ratios were also measured by GC-irm-MS for the N-pivaloyl-O-isopropyl esters of amino acids obtained from the hydrolysis of milk and hair proteins. The δ(15)N and δ(13)C (‰) were found to be significantly higher in infant hair than in breast milk (δ(15)N, P amino acids in infant hair was also significantly higher than that in maternal milk (P < 0.001). By calculation, the observed shift in isotope ratio was shown not to be accounted for by the amino acid composition of hair and milk proteins, indicating that it is not simply due to differences in the composition in the proteins present. Rather, it would appear that each pool-mother and infant-turns over independently, and that fractionation in infant N-metabolism even in the first month of life dominates over the nutrient N-content.

  5. Sm Transition Probabilities and Abundances

    CERN Document Server

    Lawler, J E; Sneden, C; Cowan, J J

    2005-01-01

    Radiative lifetimes, accurate to +/- 5%, have been measured for 212 odd-parity levels of Sm II using laser-induced fluorescence. The lifetimes are combined with branching fractions measured using Fourier-transform spectrometry to determine transition probabilities for more than 900 lines of Sm II. This work is the largest-scale laboratory study to date of Sm II transition probabilities using modern methods. This improved data set has been used to determine a new solar photospheric Sm abundance, log epsilon = 1.00 +/- 0.03, from 26 lines. The spectra of three very metal-poor, neutron-capture-rich stars also have been analyzed, employing between 55 and 72 Sm II lines per star. The abundance ratios of Sm relative to other rare earth elements in these stars are in agreement, and are consistent with ratios expected from rapid neutron-capture nucleosynthesis (the r-process).

  6. Element abundances at high redshift

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, D.M.; Welty, D.E.; York, D.G. (Northwestern Univ., Evanston, IL (USA); Chicago Univ., IL (USA))

    1989-08-01

    Abundances of Si(+), S(+), Cr(+), Mn(+), Fe( ), and Zn(+) are considered for two absorption-line systems in the spectrum of the QSO PKS 0528 - 250. Zinc and sulfur are underabundant, relative to H, by a factor of 10 compared to their solar and Galactic interstellar abundances. The silicon-, chromium-, iron-, and nickel-to-hydrogen ratios are less than the solar values and comparable to the local interstellar ratios. A straightforward interpretation is that nucleosynthesis in these high-redshift systems has led to only about one-tenth as much heavy production as in the gas clouds around the sun, and that the amount of the observed underabundances attributable to grain depletion is small. The dust-to-gas ratio in these clouds is less than 8 percent of the Galactic value. 25 refs.

  7. Element abundances at high redshift

    Science.gov (United States)

    Meyer, David M.; Welty, D. E.; York, D. G.

    1989-01-01

    Abundances of Si(+), S(+), Cr(+), Mn(+), Fe(_), and Zn(+) are considered for two absorption-line systems in the spectrum of the QSO PKS 0528 - 250. Zinc and sulfur are underabundant, relative to H, by a factor of 10 compared to their solar and Galactic interstellar abundances. The silicon-, chromium-, iron-, and nickel-to-hydrogen ratios are less than the solar values and comparable to the local interstellar ratios. A straightforward interpretation is that nucleosynthesis in these high-redshift systems has led to only about one-tenth as much heavy production as in the gas clouds around the sun, and that the amount of the observed underabundances attributable to grain depletion is small. The dust-to-gas ratio in these clouds is less than 8 percent of the Galactic value.

  8. Abundance analysis of Barium stars

    Institute of Scientific and Technical Information of China (English)

    Guo-Qing Liu; Yan-Chun Liang; Li-Cai Deng

    2009-01-01

    We obtain the chemical abundances of six barium stars and two CH subgiant stars based on the high signal-to-noise ratio and high resolution Echelle spectra. The neu- tron capture process elements Y, Zr, Ba, La and Eu show obvious overabundances relative to the Sun, for example, their [Ba/Fe] values are from 0.45 to 1.27. Other elements, in- cluding Na, Mg, A1, Si, Ca, Sc, Ti, V, Cr, Mn and Ni, show comparable abundances to the Solar ones, and their [Fe/H] covers a range from -0.40 to 0.21, which means they belong to the Galactic disk. The predictions of the theoretical model of wind accretion for bi- nary systems can explain the observed abundance patterns of the neutron capture process elements in these stars, which means that their overabundant heavy-elements could be caused by accreting the ejecta of AGB stars, the progenitors of present-day white dwarf companions in binary systems.

  9. Lead abundance in the uranium star CS 31082-001

    DEFF Research Database (Denmark)

    Plez, B.; Hill, V.; Cayrel, R.;

    2004-01-01

    stars:abundances- physical data and processes: nuclear reactions, nucleosynthesis, abundances- atomic data......stars:abundances- physical data and processes: nuclear reactions, nucleosynthesis, abundances- atomic data...

  10. Surface abundances of ON stars

    CERN Document Server

    Martins, F; Palacios, A; Howarth, I; Georgy, C; Walborn, N R; Bouret, J -C; Barba, R

    2015-01-01

    Massive stars burn hydrogen through the CNO cycle during most of their evolution. When mixing is efficient, or when mass transfer in binary systems happens, chemically processed material is observed at the surface of O and B stars. ON stars show stronger lines of nitrogen than morphologically normal counterparts. Whether this corresponds to the presence of material processed through the CNO cycle or not is not known. Our goal is to answer this question. We perform a spectroscopic analysis of a sample of ON stars with atmosphere models. We determine the fundamental parameters as well as the He, C, N, and O surface abundances. We also measure the projected rotational velocities. We compare the properties of the ON stars to those of normal O stars. We show that ON stars are usually helium-rich. Their CNO surface abundances are fully consistent with predictions of nucleosynthesis. ON stars are more chemically evolved and rotate - on average - faster than normal O stars. Evolutionary models including rotation cann...

  11. Abundance analysis of DAZ white dwarfs

    CERN Document Server

    Kawka, Adela; Dinnbier, Frantisek; Cibulkova, Helena; Nemeth, Peter

    2010-01-01

    We present an abundance analysis of a sample of 33 hydrogen-rich (DA) white dwarfs. We have used archival high-resolution spectra to measure abundances of calcium, magnesium and iron in a set of 30 objects. In addition, we present preliminary calcium abundances in three new white dwarfs based on low-dispersion spectra. We investigate some abundance ratios (Mg/Ca, Fe/Ca) that may help uncover the composition of the accretion source.

  12. Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts

    Energy Technology Data Exchange (ETDEWEB)

    Kleiner, Manuel [Max Planck Institute for Marine Microbiology; Young, Jacque C [ORNL; Shah, Manesh B [ORNL; Verberkmoes, Nathan C [ORNL; Dubilier, Nicole [Max Planck Institute for Marine Microbiology

    2013-01-01

    Transposases, enzymes that catalyze the movement of mobile genetic elements, are the most abundant genes in nature. While many bacteria encode an abundance of transposases in their genomes, the current paradigm is that transposase gene expression is tightly regulated and generally low due to its severe mutagenic effects. In the current study, we detected the highest number of transposase proteins ever reported in bacteria, in symbionts of the gutless marine worm Olavius algarvensis using metaproteomics. At least 26 different transposases from 12 different families were detected and genomic and proteomic analyses suggest many of these are active. This high expression of transposases indicates that the mechanisms for their tight regulation have been disabled or destroyed. Based on recent studies on other symbionts and pathogens that showed high transposase transcription, we speculate that abundant transposase expression might be common in symbionts and pathogens.

  13. Planetary nebulae abundances and stellar evolution

    NARCIS (Netherlands)

    Pottasch, S. R.; Bernard-Salas, J.

    2006-01-01

    A summary is given of planetary nebulae abundances from ISO measurements. It is shown that these nebulae show abundance gradients (with galactocentric distance), which in the case of neon, argon, sulfur and oxygen (with four exceptions) are the same as HII regions and early type star abundance gradi

  14. Planetary nebulae abundances and stellar evolution II

    NARCIS (Netherlands)

    Pottasch, S. R.; Bernard-Salas, J.

    2010-01-01

    Context. In recent years mid-and far infrared spectra of planetary nebulae have been analysed and lead to more accurate abundances. It may be expected that these better abundances lead to a better understanding of the evolution of these objects. Aims. The observed abundances in planetary nebulae are

  15. Origin of Cosmic Chemical Abundances

    CERN Document Server

    Maio, Umberto

    2015-01-01

    Cosmological N-body hydrodynamic computations following atomic and molecular chemistry (e$^-$, H, H$^+$, H$^-$, He, He$^+$, He$^{++}$, D, D$^+$, H$_2$, H$_2^+$, HD, HeH$^+$), gas cooling, star formation and production of heavy elements (C, N, O, Ne, Mg, Si, S, Ca, Fe, etc.) from stars covering a range of mass and metallicity are used to explore the origin of several chemical abundance patterns and to study both the metal and molecular content during simulated galaxy assembly. The resulting trends show a remarkable similarity to up-to-date observations of the most metal-poor damped Lyman-$\\alpha$ absorbers at redshift $z\\gtrsim 2$. These exhibit a transient nature and represent collapsing gaseous structures captured while cooling is becoming effective in lowering the temperature below $\\sim 10^4\\,\\rm K$, before they are disrupted by episodes of star formation or tidal effects. Our theoretical results agree with the available data for typical elemental ratios, such as [C/O], [Si/Fe], [O/Fe], [Si/O], [Fe/H], [O/...

  16. Hydrocarbon Reserves: Abundance or Scarcity

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2005-07-01

    IFP and the OAPEC jointly organize a regular international seminar dealing with world oil-related problems appearing in the news. For the first time, this seminar has been opened to oil and gas company specialists, service companies, research centers and independents. This year's theme concerns oil and gas reserves: are they abundant or are we headed towards the shortages announced by some experts? This theme is especially topical in that: oil and gas currently meet two thirds of world energy needs and almost completely dominate the transport sector; the reserves declared by the OAPEC countries account for nearly half of world reserves; the price of a barrel of oil went through the roof in 2004; world energy demand is growing fast and alternative sources of energy are far from ready to take over from oil and gas in the next few decades. Since the reserves correspond to the volume it is technically and economically viable to produce, the seminar has, of course, dealt with the technical and economic questions that arise in connection with exploration and production, but it has also considered changes in the geopolitical context. Presentations by the leading companies of the OAPEC countries and by the IFP group were completed by presentation from the International Energy Agency (IEA), the United States Geological Survey (USGS), the IHS Energy Group, Total and Gaz de France. This document gathers the transparencies of the following presentations: Hydrocarbon reserves in OAPEC members countries: current and future (M. Al-Lababidi); Non OAPEC liquid reserves and production forecasts (Y. Mathieu); World oil and gas resources and production outlook (K. Chew); Global investments in the upstream (F. Birol); Total's policy in the oil and gas sector (C. de Margerie); Gaz de France's policy in the oil and gas sector (J. Abiteboul); NOC/IOC's opportunities in OPEC countries (I. Sandrea); Relationships between companies, countries and investors: How they may

  17. Climate and local abundance in freshwater fishes

    OpenAIRE

    Knouft, Jason H.; Anthony, Melissa M.

    2016-01-01

    Identifying factors regulating variation in numbers of individuals among populations across a species' distribution is a fundamental goal in ecology. A common prediction, often referred to as the abundant-centre hypothesis, suggests that abundance is highest near the centre of a species' range. However, because of the primary focus on the geographical position of a population, this framework provides little insight into the environmental factors regulating local abundance. While range-wide va...

  18. Protein: MPA6 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available in 30 kDa adipocyte complement-related protein, Adipocyte complement-related 30 kDa protein, Adipocyte, C1q ...and collagen domain-containing protein, Adipose most abundant gene transcript 1 protein, Gelatin-binding protein 9606 Homo sapiens Q15848 9370 9370 Q15848 18054335, 19646806 ...

  19. Abundant Semigroups with a Multiplicative Adequate Transversal

    Institute of Scientific and Technical Information of China (English)

    GUO Xiao Jiang

    2002-01-01

    The aim of this paper is to investigate abundant semigroups with a multiplicative adequate transversal. Some properties and characterizations for such semigroups are obtained. In particular,we establish the structure of this class of abundant semigroups in terms of left normal bands, right normal bands and adequate semigroups with some simple compatibility conditions. Finally, we apply this structure to some special cases.

  20. Climate and local abundance in freshwater fishes.

    Science.gov (United States)

    Knouft, Jason H; Anthony, Melissa M

    2016-06-01

    Identifying factors regulating variation in numbers of individuals among populations across a species' distribution is a fundamental goal in ecology. A common prediction, often referred to as the abundant-centre hypothesis, suggests that abundance is highest near the centre of a species' range. However, because of the primary focus on the geographical position of a population, this framework provides little insight into the environmental factors regulating local abundance. While range-wide variation in population abundance associated with environmental conditions has been investigated in terrestrial species, the relationship between climate and local abundance in freshwater taxa across species' distributions is not well understood. We used GIS-based temperature and precipitation data to determine the relationships between climatic conditions and range-wide variation in local abundance for 19 species of North American freshwater fishes. Climate predicted a portion of the variation in local abundance among populations for 18 species. In addition, the relationship between climatic conditions and local abundance varied among species, which is expected as lineages partition the environment across geographical space. The influence of local habitat quality on species persistence is well documented; however, our results also indicate the importance of climate in regulating population sizes across a species geographical range, even in aquatic taxa.

  1. Resource Abundance and Resource Dependence in China

    NARCIS (Netherlands)

    Ji, K.; Magnus, J.R.; Wang, W.

    2010-01-01

    This paper reconsiders the ‘curse of resources’ hypothesis for the case of China, and distinguishes between resource abundance, resource rents, and resource dependence. Resource abundance and resource rents are shown to be approximately equivalent, and their association with resource dependence vari

  2. Diversity and abundance of ammonia-oxidizing

    NARCIS (Netherlands)

    Cardoso, J.F.M.F.; van Bleijswijk, J.D.L.; Witte, H.; van Duyl, F.C.

    2013-01-01

    We analysed the diversity and abundance of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in the shallow warm-water sponge Halisarca caerulea and the deep cold-water sponges Higginsia thielei and Nodastrella nodastrella. The abundance of AOA and AOB was analysed using catalyzed reporter depositi

  3. Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.

    Directory of Open Access Journals (Sweden)

    Boris Zybailov

    Full Text Available Characterization of the chloroplast proteome is needed to understand the essential contribution of the chloroplast to plant growth and development. Here we present a large scale analysis by nanoLC-Q-TOF and nanoLC-LTQ-Orbitrap mass spectrometry (MS of ten independent chloroplast preparations from Arabidopsis thaliana which unambiguously identified 1325 proteins. Novel proteins include various kinases and putative nucleotide binding proteins. Based on repeated and independent MS based protein identifications requiring multiple matched peptide sequences, as well as literature, 916 nuclear-encoded proteins were assigned with high confidence to the plastid, of which 86% had a predicted chloroplast transit peptide (cTP. The protein abundance of soluble stromal proteins was calculated from normalized spectral counts from LTQ-Obitrap analysis and was found to cover four orders of magnitude. Comparison to gel-based quantification demonstrates that 'spectral counting' can provide large scale protein quantification for Arabidopsis. This quantitative information was used to determine possible biases for protein targeting prediction by TargetP and also to understand the significance of protein contaminants. The abundance data for 550 stromal proteins was used to understand abundance of metabolic pathways and chloroplast processes. We highlight the abundance of 48 stromal proteins involved in post-translational proteome homeostasis (including aminopeptidases, proteases, deformylases, chaperones, protein sorting components and discuss the biological implications. N-terminal modifications were identified for a subset of nuclear- and chloroplast-encoded proteins and a novel N-terminal acetylation motif was discovered. Analysis of cTPs and their cleavage sites of Arabidopsis chloroplast proteins, as well as their predicted rice homologues, identified new species-dependent features, which will facilitate improved subcellular localization prediction. No evidence

  4. Bacterioplankton abundance and production and nanozooplankton abundance in Kenyan coastal waters (Western Indian Ocean)

    NARCIS (Netherlands)

    Goosen, N.K.; Van Rijswijk, P.; De Bie, M.J.M.; Peene, J.; Kromkamp, J.C.

    1997-01-01

    Bacterial abundance, [H-3]thymidine incorporation rate and heterotrophic nanoflagellate abundance were measured in the water column along transects perpendicular to the Kenyan coast (western Indian Ocean) during June-July (SE monsoon) and November-December (intermonsoon) 1992. Bacterial abundance wa

  5. Detecting Abundance Variations in Planetary Nebulae

    Science.gov (United States)

    Monteiro, H.; Santos, P. M.; Falceta-Gonçalves, D.

    2014-04-01

    Empirical methods of investigating chemical abundances are still widely used as a primary tool to study planetary nebulae (PNe) as well as HII regions. In this work we investigate the capacity of the empirical abundance determination methods to recover pre-defined parameters and abundance variations in a realistically modeled planetary nebula. To perform the test we use a threedimensional density structure obtained from a hydrodynamical simulation which is fed through a threedimensional photoionization code. The density structure is an asymetrical and inhomogeneous elongated closed shell. The input parameters used, such as, ionizing source, density, and chemical abundances are typical values of type I PNe. The model emissivities are then projected in the line of sight and emission line maps are generated, which are used to obtain the temperature and density diagnostics. The diagnostics and line emission maps are then used to obtain spatially resolved maps of the abundances. In this work we use the method described above to investigate abundances for two distinct orientations of the density structure. Our results show that for typical signal to noise ratios obtained from long-slit spectroscopy, only large abundance variations can be determined with good precision.

  6. Lithium Abundance of Metal-poor Stars

    Institute of Scientific and Technical Information of China (English)

    Hua-Wei Zhang; Gang Zhao

    2003-01-01

    High-resolution, high signal-to-noise ratio spectra have been obtained for 32 metal-poor stars. The equivalent widths of Li λ6708A were measured and the lithium abundances were derived. The average lithium abundance of 21 stars on the lithium plateau is 2.33±0.02 dex. The Lithium plateau exhibits a marginal trend along metallicity, dA(Li)/d[Fe/H] = 0.12±0.06, and no clear trend with the effective temperature. The trend indicates that the abundance of lithium plateau may not be primordial and that a part of the lithium was produced in Galactic Chemical Evolution (GCE).

  7. Study of the primordial lithium abundance

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Lithium isotopes have attracted an intense interest because the abundance of both 6Li and 6Li from big bang nucleosynthesis (BBN) is one of the puzzles in nuclear astrophysics. Many investigations of both astrophysical observation and nucleosynthesis calculation have been carried out to solve the puzzle, but it is not solved yet. Several nuclear reactions involving lithium have been indirectly measured at China Institute of Atomic Energy, Beijing. The Standard BBN (SBBN) network calculations are then performed to investigate the primordial Lithium abundance. The result shows that these nuclear reactions have minimal effect on the SBBN abundances of 6Li and 7Li.

  8. Screening of differentially expressed Iow-abundance proteins among serum samples from patients with different HBV-related hepatic diseases by SELDI-TOF-MS%小分子差异蛋白在HBV相关性肝病患者血清中的SELDI-TOF-MS筛选

    Institute of Scientific and Technical Information of China (English)

    宁秋悦; 吴继周; 李国坚; 臧宁; 胡蝶飞; 吴健林; 陈茂伟; 万裴琦

    2011-01-01

    AIM: To screen differentially expressed lowabundance proteins among serum samples from patients with different HBV-related hepatic diseases and to evaluate their possible value in the diagnosis of these diseases.METHODS: The surface-enhanced laser desorption or ionization time-of-flight mass spectroscopy (SELDI-TOF-MS) was used to screen differentially expressed proteins among serum samples, in which high-abundance proteins had been removed with acetonitrile, collected from patients with asymptomatic chronic hepatitis B (ASC), chronic hepatitis B (CHB), liver cirrhosis (LC), hepatocellular carcinoma (HCC), and normal controls.Diagnostic models for each disease were then established with differentially expressed proteins.Protein databases were searched to predict the possible structure and function of differentially expressed proteins.RESULTS: Compared with the normal control group, 63 differentially expressed protein peaks were detected in the ASC group, of which 29 were up-regulated and 34 down-regulated (P < 0.05); 57 in the CHB group, of which 29 upregulated and 34 down-regulated; 68 in the LC group, of which 33 up-regulated and 35 downregulated; and 74 in the HCC group, of which 28 up-regulated and 46 down-regulated.A peak with a m/z of 15 889.8 corresponded to a protein whose expression was up-regulated gradually in an order of healthy controls, ASC, CHB and LC patients, and its expression level in the HCC group was lower than those in the CHB group and LC group.The expression of a protein with a m/z of 11 742.2 was higher in the LC group and HCC group than in other groups, and its expression was gradually increased in an order of healthy controls, CHB, and LC patients, or in another order of healthy controls, CHB, and HCC patients.The sensitivity and specificity using the protein peak at 11 742.2 for diagnosis of LC were 90% and 86.67% and for HCC were 93.33% and 83.33%, respectively.%目的:探讨乙型肝炎病毒(HBV)相关性肝病患者血清

  9. Chinook Abundance - Linear Features [ds181

    Data.gov (United States)

    California Department of Resources — The dataset 'ds181_Chinook_ln' is a product of the CalFish Adult Salmonid Abundance Database. Data in this shapefile are collected from stream sections or reaches...

  10. Estimating Squirrel Abundance From Live trapping Data

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — A reprint of an article from the Journal of Wildlife Management entitled "Estimating Squirrel Abundance from Live Trapping Data" by Nixon, Edwards and Eberhardt. The...

  11. SWFSC/MMTD: Vaquita Abundance Survey 1997

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — In 1997, the Southwest Fisheries Science Center (SWFSC) conducted a survey designed to estimate the abundance of vaquita, the Gulf of California harbor porpoise...

  12. Iron abundance in the atmosphere of Arcturus

    CERN Document Server

    Sheminova, V A

    2015-01-01

    Abundance of iron in the atmosphere of Arcturus has been determined from the profiles or regions of the profiles of the weak lines sensitive to iron abundance. The selected lines of Fe I and Fe II were synthesized with the MARCS theoretical models of the atmosphere. From the observed profiles of lines available with a high spectral resolution in the atlas by Hinkle and Wallace (2005), the values of the iron abundance $A = 6.95 \\pm 0.03$ and the radial-tangential macroturbulent velocity $5.6 \\pm 0.2$ km/s were obtained for Arcturus. The same physical quantities were found for the Sun as a star; they are $7.42 \\pm 0.02$ and $3.4 \\pm 0.3$ km/s, respectively. For Arcturus, the iron abundance relative to the solar one was determined with the differential method as [Fe/H] $=-0.48 \\pm 0.02$.

  13. Chemical abundance analysis of 19 barium stars

    CERN Document Server

    Yang, G C; Spite, M; Chen, Y Q; Zhao, G; Zhang, B; Liu, G Q; Liu, Y J; Liu, N; Deng, L C; Spite, F; Hill, V; Zhang, C X

    2016-01-01

    We aim at deriving accurate atmospheric parameters and chemical abundances of 19 barium (Ba) stars, including both strong and mild Ba stars, based on the high signal-to-noise ratio and high resolution Echelle spectra obtained from the 2.16 m telescope at Xinglong station of National Astronomical Observatories, Chinese Academy of Sciences. The chemical abundances of the sample stars were obtained from an LTE, plane-parallel and line-blanketed atmospheric model by inputting the atmospheric parameters (effective temperatures, surface gravities, metallicity and microturbulent velocity) and equivalent widths of stellar absorption lines. These samples of Ba stars are giants indicated by atmospheric parameters, metallicities and kinematic analysis about UVW velocity. Chemical abundances of 17 elements were obtained for these Ba stars. Their light elements (O, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn and Ni) are similar to the solar abundances. Our samples of Ba stars show obvious overabundances of neutron-capture (n-ca...

  14. Coronae of Stars with Supersolar Elemental Abundances

    Science.gov (United States)

    Peretz, Uria; Behar, Ehud; Drake, Stephen A.

    2015-01-01

    Coronal elemental abundances are known to deviate from the photospheric values of their parent star, with the degree of deviation depending on the first ionization potential (FIP). This study focuses on the coronal composition of stars with supersolar photospheric abundances. We present the coronal abundances of six such stars: 11 LMi, iota Hor, HR 7291, tau Boo, and alpha Cen A and B. These stars all have high-statistics X-ray spectra, three of which are presented for the first time. The abundances we measured were obtained using the line-resolved spectra of the Reflection Grating Spectrometer (RGS) in conjunction with the higher throughput EPIC-pn camera spectra onboard the XMM-Newton observatory. A collisionally ionized plasma model with two or three temperature components is found to represent the spectra well. All elements are found to be consistently depleted in the coronae compared to their respective photospheres. For 11 LMi and tau Boo no FIP effect is present, while iota Hor, HR 7291, and alpha Cen A and B show a clear FIP trend. These conclusions hold whether the comparison is made with solar abundances or the individual stellar abundances. Unlike the solar corona, where low-FIP elements are enriched, in these stars the FIP effect is consistently due to a depletion of high-FIP elements with respect to actual photospheric abundances. A comparison with solar (instead of stellar) abundances yields the same fractionation trend as on the Sun. In both cases, a similar FIP bias is inferred, but different fractionation mechanisms need to be invoked.

  15. Does land abundance explain African institutions?

    OpenAIRE

    2012-01-01

    The land abundance view of African history uses sparse population to explain pre-colonial land tenure and slavery. I document the geographic forcing variables that predict land rights, slavery, and population density in a cross section of global societies. I discuss whether these correlations support theories of land rights and slavery, including the land abundance view. I show that pre-colonial institutions predict institutional outcomes in Africa in the present, including land transactions,...

  16. Planetary nebulae abundances and stellar evolution

    CERN Document Server

    Pottasch, S R

    2006-01-01

    A summary is given of planetary nebulae abundances from ISO measurements. It is shown that these nebulae show abundance gradients (with galactocentric distance), which in the case of neon, argon, sulfur and oxygen (with four exceptions) are the same as HII regions and early type star abundance gradients. The abundance of these elements predicted from these gradients at the distance of the Sun from the center are exactly the solar abundance. Sulfur is the exception to this; the reason for this is discussed. The higher solar neon abundance is confirmed; this is discussed in terms of the results of helioseismology. Evidence is presented for oxygen destruction via ON cycling having occurred in the progenitors of four planetary nebulae with bilobal structure. These progenitor stars had a high mass, probably greater than 5 solar masses. This is deduced from the high values of He/H and N/H found in these nebulae. Formation of nitrogen, helium and carbon are discussed. The high mass progenitors which showed oxygen de...

  17. TEA: A Code Calculating Thermochemical Equilibrium Abundances

    Science.gov (United States)

    Blecic, Jasmina; Harrington, Joseph; Bowman, M. Oliver

    2016-07-01

    We present an open-source Thermochemical Equilibrium Abundances (TEA) code that calculates the abundances of gaseous molecular species. The code is based on the methodology of White et al. and Eriksson. It applies Gibbs free-energy minimization using an iterative, Lagrangian optimization scheme. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature-pressure pairs. We tested the code against the method of Burrows & Sharp, the free thermochemical equilibrium code Chemical Equilibrium with Applications (CEA), and the example given by Burrows & Sharp. Using their thermodynamic data, TEA reproduces their final abundances, but with higher precision. We also applied the TEA abundance calculations to models of several hot-Jupiter exoplanets, producing expected results. TEA is written in Python in a modular format. There is a start guide, a user manual, and a code document in addition to this theory paper. TEA is available under a reproducible-research, open-source license via https://github.com/dzesmin/TEA.

  18. Modelling Void Abundance in Modified Gravity

    CERN Document Server

    Voivodic, Rodrigo; Llinares, Claudio; Mota, David F

    2016-01-01

    We use a spherical model and an extended excursion set formalism with drifting diffusive barriers to predict the abundance of cosmic voids in the context of general relativity as well as f(R) and symmetron models of modified gravity. We detect spherical voids from a suite of N-body simulations of these gravity theories and compare the measured void abundance to theory predictions. We find that our model correctly describes the abundance of both dark matter and galaxy voids, providing a better fit than previous proposals in the literature based on static barriers. We use the simulation abundance results to fit for the abundance model free parameters as a function of modified gravity parameters, and show that counts of dark matter voids can provide interesting constraints on modified gravity. For galaxy voids, more closely related to optical observations, we find that constraining modified gravity from void abundance alone may be significantly more challenging. In the context of current and upcoming galaxy surv...

  19. Abundance, distribution and patch formation of zooplankton

    Science.gov (United States)

    Paffenhöfer, Gustav-Adolf; Sherman, Byron K.; Lee, Thomas N.

    The goal of studies described here was to determine the responses of zooplankton taxa to phytoplankton patches which develop in and near intrusions of cold, nutrient-rich Gulf Stream water. To achieve this goal we determined the horizontal and vertical distributions of abundant mesozooplankton taxa on the south-eastern continental shelf of the USA between 29°30‧ and 31°N. The study period was from June 23 to August 16, 1981. Highest concentrations of zooplankton usually occurred in and near patches of phytoplankton. Increased phytoplankton appeared to trigger the formation of patches of the calanoid copepod Temora turbinata and the cyclopoid copepods Oithona spp. and Oncaea spp. The patches of zooplankton had greater alongshore than cross-shelf dimensions. T. turbinata responded rapidly to increased concentrations of phytoplankton by reproducing and aggregating in and above intruded waters. Oithonidae which were often, but not always, abundant in phytoplankton patches eventually attained high concentrations over most of the middle and part of the inner shelf. Their concentration and that of Oncaeidae increased steadily. Oncaeidae were not abundant in recently upwelled waters, as was T. turbinata but reached high concentrations in older intrusions when the abundance of T. turbinata remained level or decreased slowly. Both cyclopoid taxa are thought to reproduce slowly (egg sacs) compared to T. turbinata. Another taxon, the doliolids, became abundant far more rapidly in intruded waters (by asexual reproduction) than did the other three taxa. Doliolids were the most opportunistic intrusion zooplankton form. They do not regularly occur in low abundance on the shelf, as do the three copepod taxa, but develop in pulses in regions where T. turbinata and Oncaea are not abundant. Of the four taxa studied the abundance of doliolids increased and decreased most rapidly, whereas Oithona and Oncaea increased slowly and did not decrease during the study period. T. turbinata

  20. Predicting folivorous primate abundance: validation of a nutritional model.

    Science.gov (United States)

    Chapman, Colin A; Chapman, Lauren J; Naughton-Treves, Lisa; Lawes, Michael J; McDowell, Lee R

    2004-02-01

    Understanding the determinants of animal abundance has become more vital as ecologists are increasingly asked to apply their knowledge to the construction of informed management plans. However, there are few general models are available to explain variation in abundance. Some notable exceptions are studies of folivorous primates, in which the protein-to-fiber ratio of foods has been shown to predict biomass. Here we examine the generality of Milton's [American Naturalist 114:363-378, 1979] protein/fiber model by providing a detailed analysis of diet selection in black-and-white colobus monkeys (Colobus guereza), and applying the model to populations shown to be stable; an assumption not previously examined. Based on observations of two groups of black-and-white colobus in Kibale National Park, Uganda, and one group in a forest fragment, we documented that the animals selected young leaves that had more protein, were more digestible, and had a higher protein-to-fiber ratio than mature leaves. The mature leaves did not differ from young leaves with respect to secondary compounds or mineral content (with the exceptions of copper and zinc). All of the colobus groups selected foods with a high protein-to-fiber ratios. However, one group also selected more digestible foods, and in another group, foraging efforts were positively related to zinc and negatively related to potassium. Previous studies that examined Milton's protein/fiber model did not demonstrate that the study populations were stable. If some populations were not at carrying capacity, then the correlations drawn between food availability and/or quality and folivore biomass may have been spurious. To address this issue, we censused a series of forest fragments in 1995 and again in 2000. We found that the populations in these fragments had declined from 165 in 1995 to 119 animals in 2000. However, based on evidence of population stability and lack of forest disturbance, we concluded that five of the original

  1. The solar photospheric abundance of zirconium

    CERN Document Server

    Caffau, Elisabetta; Ludwig, Hans-Günter; Bonifacio, Piercarlo; Steffen, Matthias

    2010-01-01

    Zirconium (Zr), together with strontium and yttrium, is an important element in the understanding of the Galactic nucleosynthesis. In fact, the triad Sr-Y-Zr constitutes the first peak of s-process elements. Despite its general relevance not many studies of the solar abundance of Zr were conducted. We derive the zirconium abundance in the solar photosphere with the same CO5BOLD hydrodynamical model of the solar atmosphere that we previously used to investigate the abundances of C-N-O. We review the zirconium lines available in the observed solar spectra and select a sample of lines to determine the zirconium abundance, considering lines of neutral and singly ionised zirconium. We apply different line profile fitting strategies for a reliable analysis of Zr lines that are blended by lines of other elements. The abundance obtained from lines of neutral zirconium is very uncertain because these lines are commonly blended and weak in the solar spectrum. However, we believe that some lines of ionised zirconium are...

  2. The iron abundance of the Magellanic Bridge

    CERN Document Server

    Dufton, P L; Thompson, H M A; Street, R A

    2008-01-01

    High-resolution HST ultra-violet spectra for five B-type stars in the Magellanic Bridge and in the Large and Small Magellanic Clouds have been analysed to estimate their iron abundances. Those for the Clouds are lower than estimates obtained from late-type stars or the optical lines in B-type stars by approximately 0.5 dex. This may be due to systematic errors possibly arising from non-LTE effects or from errors in the atomic data as similar low Fe abundances having previously been reported from the analysis of the ultra-violet spectra of Galactic early-type stars. The iron abundance estimates for all three Bridge targets appear to be significantly lower than those found for the SMC and LMC by approximately -0.5 dex and -0.8 dex respectively and these differential results should not be affected by any systematic errors present in the absolute abundance estimates. These differential iron abundance estimates are consistent with the underabundances for C, N, O, Mg and Si of approximately -1.1 dex relative to our...

  3. Abundance differences among G and K giants

    Science.gov (United States)

    Challener, Sharon Lynn Montgomery

    Effective temperatures and surface gravities were derived for 52 G and K giants using model atmosphere. Of these, 33 were called very strong-lined (or VSL) stars primarily because of their CN line strength. We find that when compared to normal stars, the VSL stars show a mean iron overabundance of 0.15 dex. Contrary to earlier suggestions, none of the heavier elements (Z greater than 10) appear selectively enhanced. Red giants are believed to undergo mixing, thereby driving the surface abundances towards those of the stellar interior. Carbon, nitrogen, and oxygen abundances are most sensitive to mixing as they are produced through nucleosynthesis at various depths beneath the star's surface. The CNO abundances (normalized to the iron abundances) of the VSLs appear on average to be normal for G and K giants. This result suggests that the strong CN absorption seen in VSLs is not the result of unusual mixing. Their general overabundance of metal appears instead to be innate, presumably reflecting the metallicity of the gaseous clouds from which they formed. This should be settled once the appropriate number of VSL dwarfs is found. The deviations from the normal population of giants are rather small, however, and certainly not of the magnitude envisioned by Spinrad and Taylor (1969). It is likely that VSLs are merely the stars lying in the tail of the normal abundance distribution.

  4. Oxygen abundance maps of CALIFA galaxies

    CERN Document Server

    Zinchenko, I A; Grebel, E K; Sanchez, S F; Vilchez, J M

    2016-01-01

    We construct maps of the oxygen abundance distribution across the disks of 88 galaxies using CALIFA data release 2 (DR2) spectra. The position of the center of a galaxy (coordinates on the plate) were also taken from the CALIFA DR2. The galaxy inclination, the position angle of the major axis, and the optical radius were determined from the analysis of the surface brightnesses in the SDSS $g$ and $r$ bands of the photometric maps of SDSS data release 9. We explore the global azimuthal abundance asymmetry in the disks of the CALIFA galaxies and the presence of a break in the radial oxygen abundance distribution. We found that there is no significant global azimuthal asymmetry for our sample of galaxies, i.e., the asymmetry is small, usually lower than 0.05 dex. The scatter in oxygen abundances around the abundance gradient has a comparable value, $\\lesssim 0.05$ dex. A significant (possibly dominant) fraction of the asymmetry can be attributed to the uncertainties in the geometrical parameters of these galaxie...

  5. Estimating the relationship between abundance and distribution

    DEFF Research Database (Denmark)

    Rindorf, Anna; Lewy, Peter

    2012-01-01

    Numerous studies investigate the relationship between abundance and distribution using indices reflecting one of the three aspects of distribution: proportion of area occupied, aggregation, and geographical range. Using simulations and analytical derivations, we examine whether these indices...... based on Euclidean distance to the centre of gravity of the spatial distribution. Only the proportion of structurally empty areas, Lloyds index, and indices of the distance to the centre of gravity of the spatial distribution are unbiased at all levels of abundance. The remaining indices generate...... relationships between abundance and distribution even in cases where no underlying relationships exists, although the problem decreases for measures derived from Lorenz curves when samples contain more than four individuals on average. To illustrate the problem, the indices are applied to juvenile North Sea cod...

  6. Chemical Fractionation and Abundances in Coronal Plasma

    CERN Document Server

    Drake, J J

    2003-01-01

    Much of modern astrophysics is grounded on the observed chemical compositions of stars and the diffuse plasma that pervades the space between stars, galaxies and clusters of galaxies. X-ray and EUV spectra of the hot plasma in the outer atmospheres of stars have demonstrated that these environments are subject to chemical fractionation in which the abundances of elements can be enhanced and depleted by an order of magnitude or more. These coronal abundance anomalies are discussed and some of the physical mechanisms that might be responsible for producing them are examined. It is argued that coronal abundances can provide important new diagnostics on physical processes at work in solar and stellar coronae. It seems likely that other hot astrophysical plasmas will be subject to similar effects.

  7. Securing abundance : The politics of energy security

    NARCIS (Netherlands)

    Kester, Johannes

    2016-01-01

    Energy Security is a concept that is known in the literature for its ‘slippery’ nature and subsequent wide range of definitions. Instead of another attempt at grasping the essence of this concept, Securing Abundance reformulates the problem and moves away from a definitional problem to a theoretical

  8. In Abundance: Networked Participatory Practices as Scholarship

    Science.gov (United States)

    Stewart, Bonnie E.

    2015-01-01

    In an era of knowledge abundance, scholars have the capacity to distribute and share ideas and artifacts via digital networks, yet networked scholarship often remains unrecognized within institutional spheres of influence. Using ethnographic methods including participant observation, interviews, and document analysis, this study investigates…

  9. Analysis of 26 Barium Stars I. Abundances

    CERN Document Server

    Allen, D M; Allen, Dinah M.; Barbuy, Beatriz

    2006-01-01

    We present a detailed analysis of 26 barium stars, including dwarf barium stars, providing their atmospheric parameters (Teff, log g, [Fe/H], vt) and elemental abundances. We aim at deriving gravities and luminosity classes of the sample stars, in particular to confirm the existence of dwarf barium stars. Accurate abundances of chemical elements were derived. Abundance ratios between nucleosynthetic processes, by using Eu and Ba as representatives of the r- and s-processes are presented. High-resolution spectra with the FEROS spectrograph at the ESO-1.5m Telescope, and photometric data with Fotrap at the Zeiss telescope at the LNA were obtained. The atmospheric parameters were derived in an iterative way, with temperatures obtained from colour-temperature calibrations. The abundances were derived using spectrum synthesis for Li, Na, Al, alpha-, iron peak, s- and r-elements atomic lines, and C and N molecular lines. Atmospheric parameters in the range 4300 < Teff < 6500, -1.2 < [Fe/H] < 0.0 and 1.4...

  10. Toward reliable estimates of abundance: comparing index methods to assess the abundance of a Mammalian predator.

    Directory of Open Access Journals (Sweden)

    Denise Güthlin

    Full Text Available Due to time and financial constraints indices are often used to obtain landscape-scale estimates of relative species abundance. Using two different field methods and comparing the results can help to detect possible bias or a non monotonic relationship between the index and the true abundance, providing more reliable results. We used data obtained from camera traps and feces counts to independently estimate relative abundance of red foxes in the Black Forest, a forested landscape in southern Germany. Applying negative binomial regression models, we identified landscape parameters that influence red fox abundance, which we then used to predict relative red fox abundance. We compared the estimated regression coefficients of the landscape parameters and the predicted abundance of the two methods. Further, we compared the costs and the precision of the two field methods. The predicted relative abundances were similar between the two methods, suggesting that the two indices were closely related to the true abundance of red foxes. For both methods, landscape diversity and edge density best described differences in the indices and had positive estimated effects on the relative fox abundance. In our study the costs of each method were of similar magnitude, but the sample size obtained from the feces counts (262 transects was larger than the camera trap sample size (88 camera locations. The precision of the camera traps was lower than the precision of the feces counts. The approach we applied can be used as a framework to compare and combine the results of two or more different field methods to estimate abundance and by this enhance the reliability of the result.

  11. An approach to remove albumin for the proteomic analysis of low abundance biomarkers in human serum.

    Science.gov (United States)

    Ahmed, Nuzhat; Barker, Gillian; Oliva, Karen; Garfin, David; Talmadge, Kenneth; Georgiou, Harry; Quinn, Michael; Rice, Greg

    2003-10-01

    Proteomic technologies are being used to discover and identify disease-associated biomarkers. The application of these technologies in the search for potential diagnostic/prognostic biomarkers in the serum of patients has been limited by the presence of highly abundant albumin and immunoglobulins that constitute approximately 60-97% of the total serum proteins. The purpose of the study was to evaluate whether treatment of human serum with Affi-Gel Blue alone or in combination with Protein A (Aurum serum protein mini kit, Bio-Rad) before two-dimensional gel electrophoresis (2-DE) analysis removed high abundance proteins to allow the visualization of low abundant proteins. Serum samples were treated with either Affi-Gel Blue or Aurum kit and then subjected to 2-DE using 11 cm, pH 4-7 isoelectric focussing strips for the first dimension and 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis for second dimension. Protein spots were visualized using a fluorescent protein dye (SYPRO Ruby, Bio-Rad). Comparison between treatment methods showed significant removal of albumin by both Affi-Gel Blue and Aurum kit and considerable differences in the protein profile of the gels after each treatment. Direct comparison between treatments revealed twenty-eight protein spots unique to Affi-Gel Blue while only two spots were unique after Aurum kit treatment. Unique spots in Affi-Gel Blue and Aurum kit treated serum were not visualized in untreated serum. Sixteen hours of Affi-Gel Blue treatment resulted in enhanced visualization of fifty-three protein spots by two-fold, thirty-one by five-fold, twelve by ten-fold and six by twenty-fold. In parallel after Aurum kit treatment two-, five-, ten- and twenty-fold enhancements of thirty, thirteen, eight and five protein spots, respectively, were observed. The pattern of increased visualization of protein spots with both treatment methods was similar. In conclusion, treatment of serum samples with Affi-Gel Blue or Aurum kit before

  12. Non-Salmonid Abundance - Line Features [ds186

    Data.gov (United States)

    California Department of Resources — The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. The "Other Fish" category contains data collected...

  13. Role of Dietary Soy Protein in Obesity

    OpenAIRE

    Manuel T. Velasquez, Sam J. Bhathena

    2007-01-01

    Soy protein is an important component of soybeans and provides an abundant source of dietary protein. Among the dietary proteins, soy protein is considered a complete protein in that it contains ample amounts of all the essential amino acids plus several other macronutrients with a nutritional value roughly equivalent to that of animal protein of high biological value. Soy protein is unique among the plant-based proteins because it is associated with isoflavones, a group of compounds with a v...

  14. Chemical Cartography in the Milky Way with SDSS/APOGEE: Multi-element abundances and abundance ratio variations

    Science.gov (United States)

    Holtzman, Jon A.; Hasselquist, Sten; Johnson, Jennifer; Bird, Jonathan C.; Majewski, Steven R.; SDSS/APOGEE Team

    2017-01-01

    The SDSS/APOGEE project is measuring abundances of multiple elements for several hundred thousand stars across the Milky Way. These allow the mapping of abundances and abundance ratio variations. Results will be presented for multiple abundance ratios across of the Galactic disk. The interpretation of mean abundance maps is complicated by variations in star formation history across the disk and by changing abundance ratios that result from an overall metallicity gradient. Variations in chemical abundance sequences, however, show the potential for using abundance ratios to track the movement of stars through the disk, and provide key information for constraining Galaxy formation and chemical evolution models.

  15. Deuterium Abundance in Consciousness and Current Cosmology

    Science.gov (United States)

    Rauscher, Elizabeth A.

    We utilize the deuterium-hydrogen abundances and their role in setting limits on the mass and other conditions of cosmogenesis and cosmological evolution. We calculate the dependence of a set of physical variables such as density, temperature, energy mass, entropy and other physical variable parameters through the evolution of the universe under the Schwarzschild conditions as a function from early to present time. Reconciliation with the 3°K and missing mass is made. We first examine the Schwarzschild condition; second, the geometrical constraints of a multidimensional Cartesian space on closed cosmologies, and third we will consider the cosmogenesis and evolution of the universe in a multidimensional Cartesian space, obeying the Schwarzschild condition. Implications of this model for matter creation are made. We also examine experimental evidence for closed versus open cosmologies; x-ray detection of the "missing mass" density. Also the interstellar deuterium abundance, along with the value of the Hubble constant set a general criterion on the value of the curvature constant, k. Once the value of the Hubble constant, H is determined, the deuterium abundance sets stringent restrictions on the value of the curvature constant k by an detailed discussion is presented. The experimental evidences for the determination of H and the primary set of coupled equations to determine D abundance is given. 'The value of k for an open, closed, or flat universe will be discussed in terms of the D abundance which will affect the interpretation of the Schwarzschild, black hole universe. We determine cosmology solutions to Einstein's field obeying the Schwarzschild solutions condition. With this model, we can form a reconciliation of the black hole, from galactic to cosmological scale. Continuous creation occurs at the dynamic blackhole plasma field. We term this new model the multiple big bang or "little whimper model". We utilize the deuteriumhydrogen abundances and their role in

  16. Regulation of NHE3, NKCC2, and NCC abundance in kidney during aldosterone escape phenomenon: role of NO.

    Science.gov (United States)

    Turban, Sharon; Wang, Xiao-Yan; Knepper, Mark A

    2003-11-01

    Escape from aldosterone-induced renal NaCl retention is an important homeostatic mechanism in pathophysiological states in which plasma aldosterone levels are inappropriately elevated, e.g., in primary aldosteronism. Our previous studies demonstrated that the escape process occurs largely as a result of a marked suppression of the abundance of the thiazide-sensitive Na-Cl cotransporter (NCC) of the distal convoluted tubule but have also demonstrated a paradoxical increase in the protein abundance of the apical Na/H exchanger of the proximal tubule (NHE3). In the present study, we confirmed the increase in NHE3 and also showed that a similar increase in NHE3 protein abundance occurs in escape from ANG II-mediated NaCl retention. To investigate the potential role of nitric oxide (NO) in the observed upregulation of NHE3, we repeated the aldosterone escape experiment with a superimposed infusion of a NO synthase inhibitor, NG-nitro-l-arginine methyl ester (l-NAME). l-NAME infusion abolished the increase in NHE3 protein abundance. Furthermore, in a different experiment, NO synthase inhibition uncovered an associated decrease in the abundance of the Na-K-2Cl cotransporter (NKCC2) of the thick ascending limb, not seen with simple aldosterone escape. However, NO synthase inhibition did not block the decrease in NCC abundance normally seen with aldosterone escape. Furthermore, l-NAME infusion in aldosterone-treated rats markedly decreased both NHE3 and NKCC2 protein abundance, without changes in the corresponding mRNA levels. We conclude that NHE3 and NKCC2 protein abundances in kidney are positively regulated by NO and that the increase in NHE3 abundance seen in the aldosterone escape phenomenon is NO dependent.

  17. Measurements of Absolute Abundances in Solar Flares

    CERN Document Server

    Warren, Harry P

    2013-01-01

    We present measurements of elemental abundances in solar flares with the EUV Variability Experiment (EVE) on the Solar Dynamics Observatory (SDO). EVE observes both high temperature Fe emission lines (Fe XV-Fe XXIV) and continuum emission from thermal bremsstrahlung that is proportional to the abundance of H. By comparing the relative intensities of line and continuum emission it is possible to determine the enrichment of the flare plasma relative to the composition of the photosphere. This is the first ionization potential or FIP bias ($f$). Since thermal bremsstrahlung at EUV wavelengths is relatively insensitive to the electron temperature, it is important to account for the distribution of electron temperatures in the emitting plasma. We accomplish this by using the observed spectra to infer the differential emission measure distribution and FIP bias simultaneously. In each of the 21 flares that we analyze we find that the observed composition is close to photospheric. The mean FIP bias in our sample is $...

  18. The primordial deuterium abundance problems and prospects

    CERN Document Server

    Levshakov, S A; Kegel, W H; Levshakov, Sergei A.; Takahara, Fumio; Kegel, Wilhelm H.

    1997-01-01

    The current status of extragalactic deuterium abundance is discussed using two examples of `low' and `high' D/H measurements. We show that the discordance of these two types of D abundances may be a consequence of the spatial correlations in the stochastic velocity field. Within the framework of the generalized procedure (accounting for such effects) one finds good agreement between different observations and the theoretical predictions for standard big bang nucleosynthesis (SBBN). In particular, we show that the deuterium absorption seen at z = 2.504 toward Q1009+2956 and the H+D Ly-alpha profile observed at z = 0.701 toward Q1718+4807 are compatible with D/H $\\sim 4.1 - 4.6\\times10^{-5}$. This result supports SBBN and, thus, no inhomogeneity is needed. The problem of precise D/H measurements is discussed.

  19. In Abundance: Networked Participatory Practices as Scholarship

    Directory of Open Access Journals (Sweden)

    Bonnie E Stewart

    2015-06-01

    Full Text Available In an era of knowledge abundance, scholars have the capacity to distribute and share ideas and artifacts via digital networks, yet networked scholarship often remains unrecognized within institutional spheres of influence. Using ethnographic methods including participant observation, interviews, and document analysis, this study investigates networks as sites of scholarship. Its purpose is to situate networked practices within Boyer’s (1990 four components of scholarship – discovery, integration, application, and teaching – and to explore them as a techno-cultural system of scholarship suited to an era of knowledge abundance. Not only does the paper find that networked engagement both aligns with and exceeds Boyer’s model for scholarship, it suggests that networked scholarship may enact Boyer’s initial aim of broadening scholarship itself through fostering extensive cross-disciplinary, public ties and rewarding connection, collaboration, and curation between individuals rather than roles or institutions.

  20. Earth Abundant Element Type I Clathrate Phases

    Directory of Open Access Journals (Sweden)

    Susan M. Kauzlarich

    2016-08-01

    Full Text Available Earth abundant element clathrate phases are of interest for a number of applications ranging from photovoltaics to thermoelectrics. Silicon-containing type I clathrate is a framework structure with the stoichiometry A8-xSi46 (A = guest atom such as alkali metal that can be tuned by alloying and doping with other elements. The type I clathrate framework can be described as being composed of two types of polyhedral cages made up of tetrahedrally coordinated Si: pentagonal dodecahedra with 20 atoms and tetrakaidecahedra with 24 atoms in the ratio of 2:6. The cation sites, A, are found in the center of each polyhedral cage. This review focuses on the newest discoveries in the group 13-silicon type I clathrate family: A8E8Si38 (A = alkali metal; E = Al, Ga and their properties. Possible approaches to new phases based on earth abundant elements and their potential applications will be discussed.

  1. The primordial helium abundance from updated emissivities

    CERN Document Server

    Aver, Erik; Porter, R L; Skillman, Evan D

    2013-01-01

    Observations of metal-poor extragalactic H II regions allow the determination of the primordial helium abundance, Y_p. The He I emissivities are the foundation of the model of the H II region's emission. Porter, Ferland, Storey, & Detisch (2012) have recently published updated He I emissivities based on improved photoionization cross-sections. We incorporate these new atomic data and update our recent Markov Chain Monte Carlo analysis of the dataset published by Izotov, Thuan, & Stasinska (2007). As before, cuts are made to promote quality and reliability, and only solutions which fit the data within 95% confidence level are used to determine the primordial He abundance. The previously qualifying dataset is almost entirely retained and with strong concordance between the physical parameters. Overall, an upward bias from the new emissivities leads to a decrease in Y_p. In addition, we find a general trend to larger uncertainties in individual objects (due to changes in the emissivities) and an increase...

  2. Experimental Limit to Interstellar 244Pu Abundance

    CERN Document Server

    Paul, M; Ahmad, I; Berkovits, D; Bordeanu, C; Ghelberg, S; Hashimoto, Y; Hershcovitch, A I; Jiang, S; Nakanishi, T; Sakamoto, K

    2001-01-01

    Short-lived nuclides, now extinct in the solar system, are expected to be present in the interstellar medium (ISM). Grains of ISM origin were recently discovered in the inner solar system and at Earth orbit and may accrete onto Earth after ablation in the atmosphere. A favorable matrix for detection of such extraterrestrial material is presented by deep open-sea sediments with very low sedimentation rates (0.8-3 mm/kyr). We report here on the measurement of Pu isotopic abundances in a 1-kg deep-sea dry sediment collected in 1992 in the North Pacific. Our measured value of (3+-3)x10^5 244Pu atoms in the Pu-separated fraction of the sample shows no excess over the expected stratospheric nuclear fallout content and under reasonable assumptions we derive a limit of 2x10^-11 g-244Pu/g-ISM for the abundance of 244Pu in ISM.

  3. Detailed Chemical Abundances of Extragalactic Globular Clusters

    CERN Document Server

    Bernstein, R A

    2005-01-01

    We outline a method to measure the detailed chemical composition of extragalactic (unresolved) globular clusters (GCs) from echelle spectra of their integrated light. Our goal is to use this method to measure abundance patterns of GCs in distant spiral and elliptical galaxies to constrain their formation histories. To develop this technique we have obtained a ``training set'' of integrated-light spectra of resolved GCs in the Milky Way and LMC by scanning across the clusters during exposures. Our training set also include spectra of individual stars in those GCs from which abundances can be obtained in the normal way to provide a check on our integrated-light results. We present here the preliminary integrated-light analysis of one GC in our training set, NGC 104 (47 Tuc), and outline some of the techniques utilized and problems encountered in that analysis.

  4. Revised Thorium Abundances for Lunar Red Spots

    Science.gov (United States)

    Hagerty, J. J.; Lawrence, D. J.; Elphic, R. C.; Feldman, W. C.; Vaniman, D. T.; Hawke, B. R.

    2005-01-01

    Lunar red spots are features on the nearside of the Moon that are characterized by high albedo and by a strong absorption in the ultraviolet. These red spots include the Gruithuisen domes, the Mairan domes, Hansteen Alpha, the southern portion of Montes Riphaeus, Darney Chi and Tau, Helmet, and an area near the Lassell crater. It has been suggested that many of the red spots are extrusive, nonmare, volcanic features that could be composed of an evolved lithlogy enriched in thorium. In fact, Hawke et al. used morphological characteristics to show that Hansteen Alpha is a nonmare volcanic construct. However, because the apparent Th abundances (6 - 7 ppm) were lower than that expected for evolved rock types, Hawke et al. concluded that Hansteen Alpha was composed of an unknown rock type. Subsequent studies by Lawrence et al. used improved knowledge of the Th spatial distribution for small area features on the lunar surface to revisit the interpretation of Th abundances at the Hansteen Alpha red spot. As part of their study, Lawrence et al. used a forward modeling technique to show that the Th abundance at Hansteen Alpha is not 6 ppm, but is more likely closer to 25 ppm, a value consistent with evolved lithologies. This positive correlation between the morphology and composition of Hansteen Alpha provides support for the presence of evolved lithologies on the lunar surface. It is possible, however, that Hansteen Alpha represents an isolated occurrence of non-mare volcanism. That is why we have chosen to use the forward modeling technique of Lawrence et al. to investigate the Th abundances at other lunar red spots, starting with the Gruithuisen domes. Additional information is included in the original extended abstract.

  5. Chemical abundances and kinematics of barium stars

    CERN Document Server

    de Castro, D B; Roig, F; Jilinski, E; Drake, N A; Chavero, C; Silva, J V Sales

    2016-01-01

    In this paper we present an homogeneous analysis of photospheric abundances based on high-resolution spectroscopy of a sample of 182 barium stars and candidates. We determined atmospheric parameters, spectroscopic distances, stellar masses, ages, luminosities and scale height, radial velocities, abundances of the Na, Al, $alpha$-elements, iron-peak elements, and s-process elements Y, Zr, La, Ce, and Nd. We employed the local-thermodynamic-equilibrium model atmospheres of Kurucz and the spectral analysis code {\\sc moog}. We found that the metallicities, the temperatures and the surface gravities for barium stars can not be represented by a single gaussian distribution. The abundances of $alpha$-elements and iron peak elements are similar to those of field giants with the same metallicity. Sodium presents some degree of enrichment in more evolved stars that could be attributed to the NeNa cycle. As expected, the barium stars show overabundance of the elements created by the s-process. By measuring the mean heav...

  6. Water Abundance in Molecular Cloud Cores

    CERN Document Server

    Snell, R L; Ashby, M L N; Bergin, E A; Chin, G; Erickson, N R; Goldsmith, P F; Harwit, M; Kleiner, S C; Koch, D G; Neufeld, D A; Patten, B M; Plume, R; Schieder, R; Stauffer, J R; Tolls, V; Wang, Z; Winnewisser, G; Zhang, Y F; Melnick, G J

    2000-01-01

    We present Submillimeter Wave Astronomy Satellite (SWAS) observations of the 1_{10}-1_{01} transition of ortho-water at 557 GHz toward 12 molecular cloud cores. The water emission was detected in NGC 7538, Rho Oph A, NGC 2024, CRL 2591, W3, W3(OH), Mon R2, and W33, and was not detected in TMC-1, L134N, and B335. We also present a small map of the water emission in S140. Observations of the H_2^{18}O line were obtained toward S140 and NGC 7538, but no emission was detected. The abundance of ortho-water relative to H_2 in the giant molecular cloud cores was found to vary between 6x10^{-10} and 1x10^{-8}. Five of the cloud cores in our sample have previous water detections; however, in all cases the emission is thought to arise from hot cores with small angular extents. The water abundance estimated for the hot core gas is at least 100 times larger than in the gas probed by SWAS. The most stringent upper limit on the ortho-water abundance in dark clouds is provided in TMC-1, where the 3-sigma upper limit on the ...

  7. Abundances In Very Metal Poor Dwarf Stars

    CERN Document Server

    Cohen, J G; McWilliam, A; Shectman, S; Thompson, I; Wasserburg, G J; Ivans, I I; Dehn, M; Karlsson, T; Melendez, J; Cohen, Judith G.; Christlieb, Norbert; William, Andrew Mc; Shectman, Steve; Thompson, Ian; Ivans, Inese; Dehn, Matthias; Karlsson, Torgny

    2004-01-01

    We discuss the detailed composition of 28 extremely metal-poor dwarfs, 22 of which are from the Hamburg/ESO Survey, based on Keck Echelle spectra. Our sample has a median [Fe/H] of -2.7 dex, extends to -3.5 dex, and is somewhat less metal-poor than was expected from [Fe/H](HK,HES) determined from low resolution spectra. Our analysis supports the existence of a sharp decline in the distribution of halo stars with metallicity below [Fe/H] = -3.0 dex. So far no additional turnoff stars with [Fe/H]}<-3.5 have been identified in our follow up efforts. For the best observed elements between Mg and Ni, we find that the abundance ratios appear to have reached a plateau, i.e. [X/Fe] is approximately constant as a function of [Fe/H], except for Cr, Mn and Co, which show trends of abundance ratios varying with [Fe/H]. These abundance ratios at low metallicity correspond approximately to the yield expected from Type II SN with a narrow range in mass and explosion parameters; high mass Type II SN progenitors are requir...

  8. A global database of ant species abundances

    Science.gov (United States)

    Gibb, Heloise; Dunn, Rob R.; Sanders, Nathan J.; Grossman, Blair F.; Photakis, Manoli; Abril, Silvia; Agosti, Donat; Andersen, Alan N.; Angulo, Elena; Armbrecht, Ingre; Arnan, Xavier; Baccaro, Fabricio B.; Bishop, Tom R.; Boulay, Raphael; Bruhl, Carsten; Castracani, Cristina; Cerda, Xim; Del Toro, Israel; Delsinne, Thibaut; Diaz, Mireia; Donoso, David A.; Ellison, Aaron M.; Enriquez, Martha L.; Fayle, Tom M.; Feener Jr., Donald H.; Fisher, Brian L.; Fisher, Robert N.; Fitpatrick, Matthew C.; Gomez, Cristanto; Gotelli, Nicholas J.; Gove, Aaron; Grasso, Donato A.; Groc, Sarah; Guenard, Benoit; Gunawardene, Nihara; Heterick, Brian; Hoffmann, Benjamin; Janda, Milan; Jenkins, Clinton; Kaspari, Michael; Klimes, Petr; Lach, Lori; Laeger, Thomas; Lattke, John; Leponce, Maurice; Lessard, Jean-Philippe; Longino, John; Lucky, Andrea; Luke, Sarah H.; Majer, Jonathan; McGlynn, Terrence P.; Menke, Sean; Mezger, Dirk; Mori, Alessandra; Moses, Jimmy; Munyai, Thinandavha Caswell; Pacheco, Renata; Paknia, Omid; Pearce-Duvet, Jessica; Pfeiffer, Martin; Philpott, Stacy M.; Resasco, Julian; Retana, Javier; Silva, Rogerio R.; Sorger, Magdalena D.; Souza, Jorge; Suarez, Andrew V.; Tista, Melanie; Vasconcelos, Heraldo L.; Vonshak, Merav; Weiser, Michael D.; Yates, Michelle; Parr, Catherine L.

    2017-01-01

    What forces structure ecological assemblages? A key limitation to general insights about assemblage structure is the availability of data that are collected at a small spatial grain (local assemblages) and a large spatial extent (global coverage). Here, we present published and unpublished data from 51,388 ant abundance and occurrence records of more than 2693 species and 7953 morphospecies from local assemblages collected at 4212 locations around the world. Ants were selected because they are diverse and abundant globally, comprise a large fraction of animal biomass in most terrestrial communities, and are key contributors to a range of ecosystem functions. Data were collected between 1949 and 2014, and include, for each geo-referenced sampling site, both the identity of the ants collected and details of sampling design, habitat type and degree of disturbance. The aim of compiling this dataset was to provide comprehensive species abundance data in order to test relationships between assemblage structure and environmental and biogeographic factors. Data were collected using a variety of standardised methods, such as pitfall and Winkler traps, and will be valuable for studies investigating large-scale forces structuring local assemblages. Understanding such relationships is particularly critical under current rates of global change. We encourage authors holding additional data on systematically collected ant assemblages, especially those in dry and cold, and remote areas, to contact us and contribute their data to this growing dataset.

  9. Abundance analyses of cool extreme helium stars

    CERN Document Server

    Pandey, G; Lambert, D L; Jeffery, C S; Asplund, M; Pandey, Gajendra; Lambert, David L.; Asplund, Martin

    2001-01-01

    Extreme helium stars (EHe) with effective temperatures from 8000K to 13000K are among the coolest EHe stars and overlap the hotter R CrB stars in effective temperature. The cool EHes may represent an evolutionary link between the hot EHes and the R CrBs. Abundance analyses of four cool EHes are presented. To test for an evolutionary connection, the chemical compositions of cool EHes are compared with those of hot EHes and R CrBs. Relative to Fe, the N abundance of these stars is intermediate between those of hot EHes and R CrBs. For the R CrBs, the metallicity M derived from the mean of Si and S appears to be more consistent with the kinematics than that derived from Fe. When metallicity M derived from Si and S replaces Fe, the observed N abundances of EHes and R CrBs fall at or below the upper limit corresponding to thorough conversion of initial C and O to N. There is an apparent difference between the composition of R CrBs and EHes; the former having systematically higher [N/M] ratios. The material present...

  10. The shape of terrestrial abundance distributions.

    Science.gov (United States)

    Alroy, John

    2015-09-01

    Ecologists widely accept that the distribution of abundances in most communities is fairly flat but heavily dominated by a few species. The reason for this is that species abundances are thought to follow certain theoretical distributions that predict such a pattern. However, previous studies have focused on either a few theoretical distributions or a few empirical distributions. I illustrate abundance patterns in 1055 samples of trees, bats, small terrestrial mammals, birds, lizards, frogs, ants, dung beetles, butterflies, and odonates. Five existing theoretical distributions make inaccurate predictions about the frequencies of the most common species and of the average species, and most of them fit the overall patterns poorly, according to the maximum likelihood-related Kullback-Leibler divergence statistic. Instead, the data support a low-dominance distribution here called the "double geometric." Depending on the value of its two governing parameters, it may resemble either the geometric series distribution or the lognormal series distribution. However, unlike any other model, it assumes both that richness is finite and that species compete unequally for resources in a two-dimensional niche landscape, which implies that niche breadths are variable and that trait distributions are neither arrayed along a single dimension nor randomly associated. The hypothesis that niche space is multidimensional helps to explain how numerous species can coexist despite interacting strongly.

  11. Angel lichen moth abundance and morphology data

    Science.gov (United States)

    Metcalfe, Anya; Kennedy, Theodore A.; Muehlbauer, Jeffrey D.

    2016-01-01

    Two unique datasets on the abundance and morphology of the angel lichen moth ( Cisthene angelus) in Grand Canyon, Arizona, USA were compiled to describe the phenology and life history of this common, but poorly known, species. The abundance data were collected from 2012 to 2013 through a collaboration with river runners in Grand Canyon National Park. These citizen scientists deployed light traps from their campsites for one hour each night of their expedition. Insects were preserved in ethanol on site, and returned to the Southwest Biological Science Center in Flagstaff, Arizona for analysis in the laboratory. A total of 2,437 light trap samples were sorted through, 903 of which contained C. angelus. In total, 73,841 C. angelus were identified and enumerated to create the abundance data set. The morphology dataset is based on a subset of 28 light trap samples from sampling year 2012 (14 from spring and 14 from fall.) It includes gender and forewing lengths for 2,674 individual moths and dry weights for 1,102 of those individuals.

  12. Abundances in Stars with Debris Disks

    CERN Document Server

    Ritchey, Adam M; Stone, Myra; Wallerstein, George

    2013-01-01

    We present preliminary results of a detailed chemical abundance analysis for a sample of solar-type stars known to exhibit excess infrared emission associated with dusty debris disks. Our sample of 28 stars was selected based on results from the Formation and Evolution of Planetary Systems (FEPS) Spitzer Legacy Program, for the purpose of investigating whether the stellar atmospheres have been polluted with planetary material, which could indicate that the metallicity enhancement in stars with planets is due to metal-rich infall in the later stages of star and planet formation. The preliminary results presented here consist of precise abundances for 15 elements (C, O, Na, Mg, Al, Si, S, Ca, Sc, Ti, V, Cr, Fe, Co, and Ni) for half of the stars in our sample. We find that none of the stars investigated so far exhibit the expected trend of increasing elemental abundance with increasing condensation temperature, which would result from the stars having accreted planetary debris. Rather, the slopes of linear least...

  13. Elemental Abundances of Solar Sibling Candidates

    Science.gov (United States)

    Ramírez, I.; Bajkova, A. T.; Bobylev, V. V.; Roederer, I. U.; Lambert, D. L.; Endl, M.; Cochran, W. D.; MacQueen, P. J.; Wittenmyer, R. A.

    2014-06-01

    Dynamical information along with survey data on metallicity and in some cases age have been used recently by some authors to search for candidates of stars that were born in the cluster where the Sun formed. We have acquired high-resolution, high signal-to-noise ratio spectra for 30 of these objects to determine, using detailed elemental abundance analysis, if they could be true solar siblings. Only two of the candidates are found to have solar chemical composition. Updated modeling of the stars' past orbits in a realistic Galactic potential reveals that one of them, HD 162826, satisfies both chemical and dynamical conditions for being a sibling of the Sun. Measurements of rare-element abundances for this star further confirm its solar composition, with the only possible exception of Sm. Analysis of long-term high-precision radial velocity data rules out the presence of hot Jupiters and confirms that this star is not in a binary system. We find that chemical tagging does not necessarily benefit from studying as many elements as possible but instead from identifying and carefully measuring the abundances of those elements that show large star-to-star scatter at a given metallicity. Future searches employing data products from ongoing massive astrometric and spectroscopic surveys can be optimized by acknowledging this fact.

  14. Stellar Mixing and the Primordial Lithium Abundance

    CERN Document Server

    Pinsonneault, M H; Walker, T P; Narayanan, V K

    2002-01-01

    We compare the properties of recent samples of the lithium abundances in halo stars to one another and to the predictions of theoretical models including rotational mixing, and we examine the data for trends with metal abundance. We find from a KS test that in the absence of any correction for chemical evolution, the Ryan, Norris, & Beers (1999} sample is fully consistent with mild rotational mixing induced depletion and, therefore, with an initial lithium abundance higher than the observed value. Tests for outliers depend sensitively on the threshold for defining their presence, but we find a 10$--$45% probability that the RNB sample is drawn from the rotationally mixed models with a 0.2 dex median depletion (with lower probabilities corresponding to higher depletion factors). When chemical evolution trends (Li/H versus Fe/H) are treated in the linear plane we find that the dispersion in the RNB sample is not explained by chemical evolution; the inferred bounds on lithium depletion from rotational mixing...

  15. Relative Abundance Measurements in Plumes and Interplumes

    CERN Document Server

    Guennou, Chloé; Savin, Daniel Wolf

    2015-01-01

    We present measurements of relative elemental abundances in plumes and interplumes. Plumes are bright, narrow structures in coronal holes that extend along open magnetic field lines far out into the corona. Previous work has found that in some coronal structures the abundances of elements with a low first ionization potential (FIP) 10 eV). We have used EIS spectroscopic observations made on 2007 March 13 and 14 over an ~24 hour period to characterize abundance variations in plumes and interplumes. To assess their elemental composition, we have used a differential emission measure (DEM) analysis, which accounts for the thermal structure of the observed plasma. We have used lines from ions of iron, silicon, and sulfur. From these we have estimated the ratio of the iron and silicon FIP bias relative to that for sulfur. From the results, we have created FIP-bias-ratio maps. We find that the FIP-bias ratio is sometimes higher in plumes than in interplumes and that this enhancement can be time dependent. These res...

  16. Elemental abundances of solar sibling candidates

    Energy Technology Data Exchange (ETDEWEB)

    Ramírez, I.; Lambert, D. L.; Endl, M.; Cochran, W. D.; MacQueen, P. J. [McDonald Observatory and Department of Astronomy, University of Texas at Austin, 2515 Speedway, Stop C1400, Austin, Texas 78712-1205 (United States); Bajkova, A. T.; Bobylev, V. V. [Central (Pulkovo) Astronomical Observatory of RAS, 65/1, Pulkovskoye Chaussee, St. Petersburg 196140 (Russian Federation); Roederer, I. U. [Department of Astronomy, University of Michigan, 500 Church Street, Ann Arbor, MI 48109 (United States); Wittenmyer, R. A. [School of Physics, UNSW Australia, Sydney 2052 (Australia)

    2014-06-01

    Dynamical information along with survey data on metallicity and in some cases age have been used recently by some authors to search for candidates of stars that were born in the cluster where the Sun formed. We have acquired high-resolution, high signal-to-noise ratio spectra for 30 of these objects to determine, using detailed elemental abundance analysis, if they could be true solar siblings. Only two of the candidates are found to have solar chemical composition. Updated modeling of the stars' past orbits in a realistic Galactic potential reveals that one of them, HD 162826, satisfies both chemical and dynamical conditions for being a sibling of the Sun. Measurements of rare-element abundances for this star further confirm its solar composition, with the only possible exception of Sm. Analysis of long-term high-precision radial velocity data rules out the presence of hot Jupiters and confirms that this star is not in a binary system. We find that chemical tagging does not necessarily benefit from studying as many elements as possible but instead from identifying and carefully measuring the abundances of those elements that show large star-to-star scatter at a given metallicity. Future searches employing data products from ongoing massive astrometric and spectroscopic surveys can be optimized by acknowledging this fact.

  17. Abundant Solar Nebula Solids in Comets

    Science.gov (United States)

    Messenger, S.; Keller, L. P.; Nakamura-Messenger, K.; Nguyen, A. N.; Clemett, S.

    2016-01-01

    Comets have been proposed to consist of unprocessed interstellar materials together with a variable amount of thermally annealed interstellar grains. Recent studies of cometary solids in the laboratory have shown that comets instead consist of a wide range of materials from across the protoplanetary disk, in addition to a minor complement of interstellar materials. These advances were made possible by the return of direct samples of comet 81P/Wild 2 coma dust by the NASA Stardust mission and recent advances in microscale analytical techniques. Isotopic studies of 'cometary' chondritic porous interplanetary dust particles (CP-IDPs) and comet 81P/Wild 2 Stardust samples show that preserved interstellar materials are more abundant in comets than in any class of meteorite. Identified interstellar materials include sub-micron-sized presolar silicates, oxides, and SiC dust grains and some fraction of the organic material that binds the samples together. Presolar grain abundances reach 1 weight percentage in the most stardust-rich CP-IDPs, 50 times greater than in meteorites. Yet, order of magnitude variations in presolar grain abundances among CP-IDPs suggest cometary solids experienced significant variations in the degree of processing in the solar nebula. Comets contain a surprisingly high abundance of nebular solids formed or altered at high temperatures. Comet 81P/Wild 2 samples include 10-40 micron-sized, refractory Ca- Al-rich inclusion (CAI)-, chondrule-, and ameboid olivine aggregate (AOA)-like materials. The O isotopic compositions of these refractory materials are remarkably similar to their meteoritic counterparts, ranging from 5 percent enrichments in (sup 16) O to near-terrestrial values. Comet 81P/Wild 2 and CP-IDPs also contain abundant Mg-Fe crystalline and amorphous silicates whose O isotopic compositions are also consistent with Solar System origins. Unlike meteorites, that are dominated by locally-produced materials, comets appear to be composed of

  18. Novel Mitochondria-Targeted Heat-Soluble Proteins Identified in the Anhydrobiotic Tardigrade Improve Osmotic Tolerance of Human Cells

    OpenAIRE

    Sae Tanaka; Junko Tanaka; Yoshihiro Miwa; Horikawa, Daiki D.; Toshiaki Katayama; Kazuharu Arakawa; Atsushi Toyoda; Takeo Kubo; Takekazu Kunieda

    2015-01-01

    Tardigrades are able to tolerate almost complete dehydration through transition to a metabolically inactive state, called "anhydrobiosis". Late Embryogenesis Abundant (LEA) proteins are heat-soluble proteins involved in the desiccation tolerance of many anhydrobiotic organisms. Tardigrades, Ramazzottius varieornatus, however, express predominantly tardigrade-unique heat-soluble proteins: CAHS (Cytoplasmic Abundant Heat Soluble) and SAHS (Secretory Abundant Heat Soluble) proteins, which are se...

  19. Can occupancy-abundance models be used to monitor wolf abundance?

    Directory of Open Access Journals (Sweden)

    M Cecilia Latham

    Full Text Available Estimating the abundance of wild carnivores is of foremost importance for conservation and management. However, given their elusive habits, direct observations of these animals are difficult to obtain, so abundance is more commonly estimated from sign surveys or radio-marked individuals. These methods can be costly and difficult, particularly in large areas with heavy forest cover. As an alternative, recent research has suggested that wolf abundance can be estimated from occupancy-abundance curves derived from "virtual" surveys of simulated wolf track networks. Although potentially more cost-effective, the utility of this approach hinges on its robustness to violations of its assumptions. We assessed the sensitivity of the occupancy-abundance approach to four assumptions: variation in wolf movement rates, changes in pack cohesion, presence of lone wolves, and size of survey units. Our simulations showed that occupancy rates and wolf pack abundances were biased high if track surveys were conducted when wolves made long compared to short movements, wolf packs were moving as multiple hunting units as opposed to a cohesive pack, and lone wolves were moving throughout the surveyed landscape. We also found that larger survey units (400 and 576 km2 were more robust to changes in these factors than smaller survey units (36 and 144 km2. However, occupancy rates derived from large survey units rapidly reached an asymptote at 100% occupancy, suggesting that these large units are inappropriate for areas with moderate to high wolf densities (>15 wolves/1,000 km2. Virtually-derived occupancy-abundance relationships can be a useful method for monitoring wolves and other elusive wildlife if applied within certain constraints, in particular biological knowledge of the surveyed species needs to be incorporated into the design of the occupancy surveys. Further, we suggest that the applicability of this method could be extended by directly incorporating some of its

  20. The primordial helium abundance from updated emissivities

    Energy Technology Data Exchange (ETDEWEB)

    Aver, Erik [Department of Physics, Gonzaga University, 502 E Boone Ave, Spokane, WA, 99258 (United States); Olive, Keith A.; Skillman, Evan D. [School of Physics and Astronomy, University of Minnesota, 116 Church St. SE, Minneapolis, MN, 55455 (United States); Porter, R.L., E-mail: aver@gonzaga.edu, E-mail: olive@umn.edu, E-mail: ryanlporter@gmail.com, E-mail: skillman@astro.umn.edu [Department of Physics and Astronomy, University of Georgia, Athens, GA, 30602 (United States)

    2013-11-01

    Observations of metal-poor extragalactic H II regions allow the determination of the primordial helium abundance, Y{sub p}. The He I emissivities are the foundation of the model of the H II region's emission. Porter, Ferland, Storey, and Detisch (2012) have recently published updated He I emissivities based on improved photoionization cross-sections. We incorporate these new atomic data and update our recent Markov Chain Monte Carlo analysis of the dataset published by Izotov, Thuan, and Stasi'nska (2007). As before, cuts are made to promote quality and reliability, and only solutions which fit the data within 95% confidence level are used to determine the primordial He abundance. The previously qualifying dataset is almost entirely retained and with strong concordance between the physical parameters. Overall, an upward bias from the new emissivities leads to a decrease in Y{sub p}. In addition, we find a general trend to larger uncertainties in individual objects (due to changes in the emissivities) and an increased variance (due to additional objects included). From a regression to zero metallicity, we determine Y{sub p} = 0.2465 ± 0.0097, in good agreement with the BBN result, Y{sub p} = 0.2485 ± 0.0002, based on the Planck determination of the baryon density. In the future, a better understanding of why a large fraction of spectra are not well fit by the model will be crucial to achieving an increase in the precision of the primordial helium abundance determination.

  1. Cosmic ray source abundance of calcium

    CERN Document Server

    Perron, C

    1978-01-01

    Re-examines the results of experiments in which ultra-high purity iron targets were irradiated by protons from the two CERN accelerators (600 MeV and 21 GeV); the spallation products were then chemically separated, and their isotopic composition determined by mass spectrometry. Ratios of cross-sections for calcium production by spallation of iron show that /sup 42/Ca, /sup 43/Ca and /sup 44/Ca have about the same abundance, about 10-15% that of iron, confirming earlier studies. (11 refs).

  2. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias.

    Directory of Open Access Journals (Sweden)

    Premal Shah

    2010-09-01

    Full Text Available Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find a consistent positive correlation between tRNA abundances across the genetic code. This work challenges one of the fundamental assumptions made in over 30 years of research on CUB that codons with higher tRNA abundances have lower missense error rates and that missense errors are the primary selective force responsible for CUB.

  3. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias.

    Science.gov (United States)

    Shah, Premal; Gilchrist, Michael A

    2010-09-16

    Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB) assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find a consistent positive correlation between tRNA abundances across the genetic code. This work challenges one of the fundamental assumptions made in over 30 years of research on CUB that codons with higher tRNA abundances have lower missense error rates and that missense errors are the primary selective force responsible for CUB.

  4. Metal Abundances of KISS Galaxies. V. Nebular Abundances of Fifteen Intermediate Luminosity Star-Forming Galaxies

    CERN Document Server

    Hirschauer, Alec S; Bresolin, Fabio; Saviane, Ivo; Yegorova, Irina

    2015-01-01

    We present high S/N spectroscopy of 15 emission-line galaxies (ELGs) cataloged in the KPNO International Spectroscopic Survey (KISS), selected for their possession of high equivalent width [O III] lines. The primary goal of this study was to attempt to derive direct-method ($T_e$) abundances for use in constraining the upper-metallicity branch of the $R_{23}$ relation. The spectra cover the full optical region from [O II]{\\lambda}{\\lambda}3726,3729 to [S III]{\\lambda}{\\lambda}9069,9531 and include the measurement of [O III]{\\lambda}4363 in 13 objects. From these spectra, we determine abundance ratios of helium, nitrogen, oxygen, neon, sulfur, and argon. We find these galaxies to predominantly possess oxygen abundances in the range of 8.0 $\\lesssim$ 12+log(O/H) $\\lesssim$ 8.3. We present a comparison of direct-method abundances with empirical SEL techniques, revealing several discrepancies. We also present a comparison of direct-method oxygen abundance calculations using electron temperatures determined from e...

  5. VLT\\/UVES Abundances in Four Nearby Dwarf Spheroidal Galaxies I. Nucleosynthesis and Abundance Ratios

    CERN Document Server

    Shetrone, M; Tolstoy, E; Primas, F; Hill, V; Kaufer, A

    2003-01-01

    We have used UVES on VLT-UT2 to take spectra of 15 red giants in the Sculptor, Fornax, Carina and Leo I dwarf spheroidal galaxies. We measure the abundances of alpha, iron peak, s and r-process elements. No dSph giants in our sample show the deep mixing abundance pattern seen in nearly all globular clusters. At a given metallicity, the dSph giants exhibit lower [el/Fe] abundance ratios for the alpha elements than stars in the Galactic halo. This can be caused by a slow star formation rate and contribution from Type Ia SN, and/or a small star formation event (low total mass) and mass dependent Type II SN yields. Differences in the even-Z [el/Fe] ratios between these galaxies, as well as differences in the evolution of the s&r-process elements are interpreted in terms of their star formation histories. Comparison of the dSph abundances with those of the Galactic halo reveals some consistencies. In particular, we find stars that mimic the abundance pattern found by Nissen & Shuster (1997) for metal-rich,...

  6. Non-additive effects of genotypic diversity increase floral abundance and abundance of floral visitors.

    Directory of Open Access Journals (Sweden)

    Mark A Genung

    Full Text Available BACKGROUND: In the emerging field of community and ecosystem genetics, genetic variation and diversity in dominant plant species have been shown to play fundamental roles in maintaining biodiversity and ecosystem function. However, the importance of intraspecific genetic variation and diversity to floral abundance and pollinator visitation has received little attention. METHODOLOGY/PRINCIPAL FINDINGS: Using an experimental common garden that manipulated genotypic diversity (the number of distinct genotypes per plot of Solidago altissima, we document that genotypic diversity of a dominant plant can indirectly influence flower visitor abundance. Across two years, we found that 1 plant genotype explained 45% and 92% of the variation in flower visitor abundance in 2007 and 2008, respectively; and 2 plant genotypic diversity had a positive and non-additive effect on floral abundance and the abundance of flower visitors, as plots established with multiple genotypes produced 25% more flowers and received 45% more flower visits than would be expected under an additive model. CONCLUSIONS/SIGNIFICANCE: These results provide evidence that declines in genotypic diversity may be an important but little considered factor for understanding plant-pollinator dynamics, with implications for the global decline in pollinators due to reduced plant diversity in both agricultural and natural ecosystems.

  7. Absolute Abundance Measurements in Solar Flares

    Science.gov (United States)

    Warren, Harry

    2014-06-01

    We present measurements of elemental abundances in solar flares with EVE/SDO and EIS/Hinode. EVE observes both high temperature Fe emission lines Fe XV-XXIV and continuum emission from thermal bremsstrahlung that is proportional to the abundance of H. By comparing the relative intensities of line and continuum emission it is possible to determine the enrichment of the flare plasma relative to the composition of the photosphere. This is the first ionization potential or FIP bias (F). Since thermal bremsstrahlung at EUV wavelengths is relatively insensitive to the electron temperature it is important to account for the distribution of electron temperatures in the emitting plasma. We accomplish this by using the observed spectra to infer the differential emission measure distribution and FIP bias simultaneously. In each of the 21 flares that we analyze we find that the observed composition is close to photospheric. The mean FIP bias in our sample is F=1.17+-0.22. Furthermore, we have compared the EVE measurements with corresponding flare observations of intermediate temperature S, Ar, Ca, and Fe emission lines taken with EIS. Our initial calculations also indicate a photospheric composition for these observations. This analysis suggests that the bulk of the plasma evaporated during a flare comes from deep in the chromosphere, below the region where elemental fractionation in the non-flaring corona occurs.

  8. Measurements of Absolute Abundances in Solar Flares

    Science.gov (United States)

    Warren, Harry P.

    2014-05-01

    We present measurements of elemental abundances in solar flares with the EUV Variability Experiment (EVE) on the Solar Dynamics Observatory. EVE observes both high temperature Fe emission lines (Fe XV-Fe XXIV) and continuum emission from thermal bremsstrahlung that is proportional to the abundance of H. By comparing the relative intensities of line and continuum emission it is possible to determine the enrichment of the flare plasma relative to the composition of the photosphere. This is the first ionization potential or FIP bias (f). Since thermal bremsstrahlung at EUV wavelengths is relatively insensitive to the electron temperature, it is important to account for the distribution of electron temperatures in the emitting plasma. We accomplish this by using the observed spectra to infer the differential emission measure distribution and FIP bias simultaneously. In each of the 21 flares that we analyze we find that the observed composition is close to photospheric. The mean FIP bias in our sample is f = 1.17 ± 0.22. This analysis suggests that the bulk of the plasma evaporated during a flare comes from deep in the chromosphere, below the region where elemental fractionation occurs.

  9. Oxygen Abundance Measurements of SHIELD Galaxies

    CERN Document Server

    Haurberg, Nathalie C; Cannon, John M; Marshall, Melissa V

    2015-01-01

    We have derived oxygen abundances for 8 galaxies from the Survey of HI in Extremely Low-mass Dwarfs (SHIELD). The SHIELD survey is an ongoing study of very low-mass galaxies, with M$_{\\rm HI}$ between 10$^{6.5}$ and 10$^{7.5}$ M$_{\\odot}$, that were detected by the Arecibo Legacy Fast ALFA (ALFALFA) survey. H$\\alpha$ images from the WIYN 3.5m telescope show that these 8 SHIELD galaxies each possess one or two active star-forming regions which were targeted with long-slit spectral observations using the Mayall 4m telescope at KPNO. We obtained a direct measurement of the electron temperature by detection of the weak [O III] $\\lambda$4363 line in 2 of the HII regions. Oxygen abundances for the other HII regions were estimated using a strong-line method. When the SHIELD galaxies are plotted on a B-band luminosity-metallicity diagram they appear to suggest a slightly shallower slope to the relationship than normally seen. However, that offset is systematically reduced when the near-infrared luminosity is used ins...

  10. Manganese abundances in Galactic bulge red giants

    CERN Document Server

    Barbuy, B; Zoccali, M; Minniti, D; Renzini, A; Ortolani, S; Gomez, A; Trevisan, M; Dutra, N

    2013-01-01

    Manganese is mainly produced in type II SNe during explosive silicon burning, in incomplete Si-burning regions, and depends on several nucleosynthesis environment conditions, such as mass cut beween the matter ejected and falling back onto the remnant, electron and neutron excesses, mixing fallback, and explosion energy. Manganese is also produced in type Ia SNe. The aim of this work is the study of abundances of the iron-peak element Mn in 56 bulge giants, among which 13 are red clump stars. Four bulge fields along the minor axis are inspected. The study of abundances of Mn-over-Fe as a function of metallicity in the Galactic bulge may shed light on its production mechanisms. High-resolution spectra were obtained using the FLAMES+UVES spectrograph on the Very Large Telescope. The spectra were obtained within a program to observe 800 stars using the GIRAFFE spectrograph, together with the present UVES spectra. We aim at identifying the chemical evolution of manganese, as a function of metallicity, in the Gala...

  11. Occupancy as a surrogate for abundance estimation

    Directory of Open Access Journals (Sweden)

    MacKenzie, D. I.

    2004-06-01

    Full Text Available In many monitoring programmes it may be prohibitively expensive to estimate the actual abundance of a bird species in a defined area, particularly at large spatial scales, or where birds occur at very low densities. Often it may be appropriate to consider the proportion of area occupied by the species as an alternative state variable. However, as with abundance estimation, issues of detectability must be taken into account in order to make accurate inferences: the non-detection of the species does not imply the species is genuinely absent. Here we review some recent modelling developments that permit unbiased estimation of the proportion of area occupied, colonization and local extinction probabilities. These methods allow for unequal sampling effort and enable covariate information on sampling locations to be incorporated. We also describe how these models could be extended to incorporate information from marked individuals, which would enable finer questions of population dynamics (such as turnover rate of nest sites by specific breeding pairs to be addressed. We believe these models may be applicable to a wide range of bird species and may be useful for investigating various questions of ecological interest. For example, with respect to habitat quality, we might predict that a species is more likely to have higher local extinction probabilities, or higher turnover rates of specific breeding pairs, in poor quality habitats.

  12. Automatic abundance analysis of high resolution spectra

    CERN Document Server

    Bonifacio, P; Bonifacio, Piercarlo; Caffau, Elisabetta

    2003-01-01

    We describe an automatic procedure for determining abundances from high resolution spectra. Such procedures are becoming increasingly important as large amounts of data are delivered from 8m telescopes and their high-multiplexing fiber facilities, such as FLAMES on ESO-VLT. The present procedure is specifically targeted for the analysis of spectra of giants in the Sgr dSph; however, the procedure may be, in principle, tailored to analyse stars of any type. Emphasis is placed on the algorithms and on the stability of the method; the external accuracy rests, ultimately, on the reliability of the theoretical models (model-atmospheres, synthetic spectra) used to interpret the data. Comparison of the results of the procedure with the results of a traditional analysis for 12 Sgr giants shows that abundances accurate at the level of 0.2 dex, comparable with that of traditional analysis of the same spectra, may be derived in a fast and efficient way. Such automatic procedures are not meant to replace the traditional ...

  13. Beryllium abundances in stars hosting giant planets

    CERN Document Server

    Santos, N C; Israelian, G; Mayor, M; Rebolo, R; García-Gíl, A; Pérez de Taoro, M R; Randich, S

    2002-01-01

    We have derived beryllium abundances in a wide sample of stars hosting planets, with spectral types in the range F7V-K0V, aimed at studying in detail the effects of the presence of planets on the structure and evolution of the associated stars. Predictions from current models are compared with the derived abundances and suggestions are provided to explain the observed inconsistencies. We show that while still not clear, the results suggest that theoretical models may have to be revised for stars with Teff<5500K. On the other hand, a comparison between planet host and non-planet host stars shows no clear difference between both populations. Although preliminary, this result favors a ``primordial'' origin for the metallicity ``excess'' observed for the planetary host stars. Under this assumption, i.e. that there would be no differences between stars with and without giant planets, the light element depletion pattern of our sample of stars may also be used to further investigate and constraint Li and Be deple...

  14. Elemental Abundances of Solar Sibling Candidates

    CERN Document Server

    Ramirez, I; Bobylev, V V; Roederer, I U; Lambert, D L; Endl, M; Cochran, W D; MacQueen, P J; Wittenmyer, R A

    2014-01-01

    Dynamical information along with survey data on metallicity and in some cases age have been used recently by some authors to search for candidates of stars that were born in the cluster where the Sun formed. We have acquired high resolution, high signal-to-noise ratio spectra for 30 of these objects to determine, using detailed elemental abundance analysis, if they could be true solar siblings. Only two of the candidates are found to have solar chemical composition. Updated modeling of the stars' past orbits in a realistic Galactic potential reveals that one of them, HD162826, satisfies both chemical and dynamical conditions for being a sibling of the Sun. Measurements of rare-element abundances for this star further confirm its solar composition, with the only possible exception of Sm. Analysis of long-term high-precision radial velocity data rules out the presence of hot Jupiters and confirms that this star is not in a binary system. We find that chemical tagging does not necessarily benefit from studying a...

  15. Abundance Anomalies In Tidal Disruption Events

    CERN Document Server

    Kochanek, C S

    2015-01-01

    The ~10% of tidal disruption events (TDEs) due to stars more massive than the Sun should show abundance anomalies due to stellar evolution in helium, carbon and nitrogen, but not oxygen. Helium is always enhanced, but only by up to ~25% on average because it becomes inaccessible once it is sequestered in the high density core as the star leaves the main sequence. However, portions of the debris associated with the disrupted core of a main sequence star can be enhanced in helium by factors of 2-3 for debris at a common orbital period. These helium abundance variations may be a contributor to the observed diversity of hydrogen and helium line strengths in TDEs. A still more striking anomaly is the rapid enhancement of nitrogen and the depletion of carbon due to the CNO cycle -- stars more massive than the Sun quickly show an increase in their average N/C ratio by factors of 3-10. Because low mass stars evolve slowly and high mass stars are rare, TDEs showing high N/C will almost all be due to 1-2Msun stars disr...

  16. New Elemental Abundances for V1974 Cygni

    CERN Document Server

    Vanlandingham, K M; Shore, S N; Starrfield, S; Wagner, R M

    2005-01-01

    We present a new analysis of existing optical and ultraviolet spectra of the ONeMg nova V1974 Cygni 1992. Using these data and the photoionization code Cloudy, we have determined the physical parameters and elemental abundances for this nova. Many of the previous studies of this nova have made use of incorrect analyses and hence a new study was required. Our results show that the ejecta are enhanced, relative to solar, in helium, nitrogen, oxygen, neon, magnesium and iron. Carbon was found to be subsolar. We find an ejected mass of ~2x10e-4 solar masses. Our model results fit well with observations taken at IR, radio, sub-millimeter and X-ray wavelengths.

  17. Nitrous Oxide Production by Abundant Benthic Macrofauna

    DEFF Research Database (Denmark)

    Stief, Peter; Schramm, Andreas

    Detritivorous macrofauna species co-ingest large quantities of microorganisms some of which survive the gut passage. Denitrifying bacteria, in particular, become metabolically induced by anoxic conditions, nitrate, and labile organic compounds in the gut of invertebrates. A striking consequence...... of the short-term metabolic induction of gut denitrification is the preferential production of nitrous oxide rather than dinitrogen. On a large scale, gut denitrification in, for instance, Chironomus plumosus larvae can increase the overall nitrous oxide emission of lake sediment by a factor of eight. We...... that do not ingest large quantities of microorganisms produced insignificant amounts of nitrous oxide. Ephemera danica, a very abundant mayfly larva, was monitored monthly in a nitrate-polluted stream. Nitrous oxide production by this filter-feeder was highly dependent on nitrate availability...

  18. An Update of the Primordial Helium Abundance

    Science.gov (United States)

    Peimbert, Antonio; Peimbert, Manuel; Luridiana, Valentina

    2015-08-01

    Three of the best determinations of the primordial helium abundance (Yp) are those obtained from low metallicity HII regions by Aver, Olive, Porter, & Skillman (2013); Izotov, Thuan, & Guseva (2014); and Peimbert, Peimbert, & Luridiana (2007). In this poster we update the Yp determination by Peimbert et al. taking into account, among other aspects, recent advances in the determination of the He atomic physical parameters, the temperature structure, the collisional effects of high temperatures on the Balmer lines, as well as the effect of H and He bound-bound absorption.We compare our results with those of Aver et al. and Izotov et al. and point out possible explanations for the differences among the three determinations. We also compare our results with those obtained with the Plank satellite considering recent measurements of the neutron mean life; this comparison has implications on the determination of the number of light neutrino families.

  19. Forms and genesis of species abundance distributions

    Directory of Open Access Journals (Sweden)

    Evans O. Ochiaga

    2015-12-01

    Full Text Available Species abundance distribution (SAD is one of the most important metrics in community ecology. SAD curves take a hollow or hyperbolic shape in a histogram plot with many rare species and only a few common species. In general, the shape of SAD is largely log-normally distributed, although the mechanism behind this particular SAD shape still remains elusive. Here, we aim to review four major parametric forms of SAD and three contending mechanisms that could potentially explain this highly skewed form of SAD. The parametric forms reviewed here include log series, negative binomial, lognormal and geometric distributions. The mechanisms reviewed here include the maximum entropy theory of ecology, neutral theory and the theory of proportionate effect.

  20. VLT/UVES abundances in four nearby dwarf spheroidal galaxies. I. Nucleosynthesis and abundance ratios

    NARCIS (Netherlands)

    Shetrone, M; Venn, KA; Tolstoy, E; Primas, F; Hill, [No Value; Kaufer, A

    2003-01-01

    We have used the Ultraviolet Echelle Spectrograph (UVES) on Kueyen (UT2) of the Very Large Telescope to take spectra of 15 individual red giants in the Sculptor, Fornax, Carina, and Leo I dwarf spheroidal galaxies (dSph's). We measure the abundances of alpha-, iron peak, first s-process, second s-pr

  1. Abundances of Galactic Anticenter Planetary Nebulae and the Oxygen Abundance Gradient in the Galactic Disk

    CERN Document Server

    Henry, R B C; Jaskot, Anne E; Balick, Bruce; Morrison, Michael A; Milingo, Jacquelynne B

    2010-01-01

    We have obtained spectrophotometric observations of 41 anticenter planetary nebulae (PNe) located in the disk of the Milky Way. Electron temperatures and densities, as well as chemical abundances for He, N, O, Ne, S, Cl, and Ar were determined. Incorporating these results into our existing database of PN abundances yielded a sample of 124 well-observed objects with homogeneously-determined abundances extending from 0.9-21 kpc in galactocentric distance. We performed a detailed regression analysis which accounted for uncertainties in both oxygen abundances and radial distances in order to establish the metallicity gradient across the disk to be: 12+log(O/H)=(9.09+/-.05) - (0.058+/-.006) x Rg, with Rg in kpc. While we see some evidence that the gradient steepens at large galactocentric distances, more objects toward the anticenter need to be observed in order to confidently establish the true form of the metallicity gradient. We find no compelling evidence that the gradient differs between Peimbert Types I and ...

  2. Solar-system abundances of the elements - A new table

    Science.gov (United States)

    Grevesse, Nicolas; Anders, Edward

    1989-01-01

    This paper presents an abridged version of a new abundance compilation (Anders and Grevesse, 1988), representing an update of Anders and Ebihara (1982) and Grevesse (1984). It includes revised meteoritic abundances as well as photospheric and coronal abundances, based on literature through mid-1988.

  3. Abundance of sardine fish species in Bangladesh

    Directory of Open Access Journals (Sweden)

    Roy Bikram Jit

    2012-06-01

    Full Text Available The study was conducted during January, 2012 to December 2012 in the sardine fisheries which is occurred both in artisanal and industrial fishing sector in the marine water of the Bay of Bengal of Bangladesh region. During this study period the total landing amounts by weight of sardines were 7352.99 MT, among these 23.76% (1747.22 MT was exploited by the artisanal mechanized boats and 76.24% (5605.77 MT captured through different industrial fishing trawlers and contributed 17.51% of the total marine fish production by commercial fish trawlers during the study period. 4 sardine species have been recorded from our marine territory. Among them, 2 sardine species are highly abundant, Sardinella fimbriata total production volumes was 5495.79 MT (74.74% contributed 1747.22MT (31.79% from the artisanal and 3748.57MT (68.21% from the industrial sector and Dussumieria acuta production amounts was 1857.20MT (25.26% contributed only from the industrial fishing sector.Species wise contribution shows that S. fimbriata contributed 100% in the artisanal sector and in the industrial fishing S. fimbriata contributed 66.87% and D. acuta contributed the rest 33.13%. The distribution of the S. fimbriata is within 10-20 meters depth and abundance was observed in the southern part of the South patches and South of south patches (N: 210.09// -22, E: 920.04/-07 to N: 200.45/-25, E: 920.18/-56 and 10-50m depth in onshore and off shore areas in the north-west to north-east of Middle ground (Kohinoor point -N: 210.36/.23, E: 900.06/.43 to N: 210.18/.18, E 910.17/.57. The distribution of the D. acuta is within 40-60 m. depth and abundance was observed in the north-west to north-east of Middle ground areas (Kohinoor point - N: 210.36/.23, E: 900.06/.43 to N: 210.18/.18, E 910.17/.57 and south-west to south-east of Middle ground (Kohinoor point- N: 200-17/.29, E: 900.15/.21 to N: 200.29/.56, E: 910.24/.22 in the Bay of Bengal of Bangladesh region. The peak capture season of

  4. Manganese abundances in Galactic bulge red giants

    Science.gov (United States)

    Barbuy, B.; Hill, V.; Zoccali, M.; Minniti, D.; Renzini, A.; Ortolani, S.; Gómez, A.; Trevisan, M.; Dutra, N.

    2013-11-01

    Context. Manganese is mainly produced in type II SNe during explosive silicon burning, in incomplete Si-burning regions, and depends on several nucleosynthesis environment conditions, such as mass cut between the matter ejected and falling back onto the remnant, electron and neutron excesses, mixing fallback, and explosion energy. Manganese is also produced in type Ia SNe. Aims: The aim of this work is the study of abundances of the iron-peak element Mn in 56 bulge giants, among which 13 are red clump stars. Four bulge fields along the minor axis are inspected. The study of abundances of Mn-over-Fe as a function of metallicity in the Galactic bulge may shed light on its production mechanisms. Methods: High-resolution spectra were obtained using the FLAMES+UVES spectrograph on the Very Large Telescope. The spectra were obtained within a program to observe 800 stars using the GIRAFFE spectrograph, together with the present UVES spectra. Results: We aim at identifying the chemical evolution of manganese, as a function of metallicity, in the Galactic bulge. We find [Mn/Fe] ~ -0.7 at [Fe/H] ~ -1.3, increasing to a solar value at metallicities close to solar, and showing a spread around - 0.7 ≲ [Fe/H] ≲ -0.2, in good agreement with other work on Mn in bulge stars. There is also good agreement with chemical evolution models. We find no clear difference in the behaviour of the four bulge fields. Whereas [Mn/Fe] vs. [Fe/H] could be identified with the behaviour of the thick disc stars, [Mn/O] vs. [O/H] has a behaviour running parallel, at higher metallicities, compared to thick disc stars, indicating that the bulge enrichment might have proceeded differently from that of the thick disc. Observations collected at the European Southern Observatory, Paranal, Chile (ESO programmes 71.B-0617A, 73.B0074A, and GTO 71.B-0196).Tables 1-6 and Figs. 1-6 are available in electronic form at http://www.aanda.org

  5. The Solar Heavy Element Abundances: I. Constraints from Stellar Interiors

    CERN Document Server

    Delahaye, F; Delahaye, Franck; Pinsonneault, Marc

    2005-01-01

    The latest solar atmosphere models include non-LTE corrections and 3D hydrodynamic convection simulations. These models predict a significant reduction in the solar metal abundance, which leads to a serious conflict between helioseismic data and the predictions of solar interiors models. We demonstrate that the helioseismic constraints on the surface convection zone depth and helium abundance combined with stellar interiors models can be used to define the goodness of fit for a given chemical composition. After a detailed examination of the errors in the theoretical models we conclude that models constructed with the older solar abundances are consistent (<2 \\sigma) with the seismic data. Models constructed with the proposed new low abundance scale are strongly disfavored, disagreeing at the 15 \\sigma level. We then use the sensitivity of the seismic properties to abundance changes to invert the problem and infer a seismic solar heavy element abundance mix with two components: meteoritic abundances, and th...

  6. Nucleosynthesis: Stellar and Solar Abundances and Atomic Data

    CERN Document Server

    Cowan, J J; Sneden, C; Den Hartog, E A; Collier, J L; Cowan, John J.; Lawler, James E.; Sneden, Christopher; Collier, Jason

    2006-01-01

    Abundance observations indicate the presence of often surprisingly large amounts of neutron capture (i.e., s- and r-process) elements in old Galactic halo and globular cluster stars. These observations provide insight into the nature of the earliest generations of stars in the Galaxy -- the progenitors of the halo stars -- responsible for neutron-capture synthesis. Comparisons of abundance trends can be used to understand the chemical evolution of the Galaxy and the nature of heavy element nucleosynthesis. In addition age determinations, based upon long-lived radioactive nuclei abundances, can now be obtained. These stellar abundance determinations depend critically upon atomic data. Improved laboratory transition probabilities have been recently obtained for a number of elements. These new gf values have been used to greatly refine the abundances of neutron-capture elemental abundances in the solar photosphere and in very metal-poor Galactic halo stars. The newly determined stellar abundances are surprisingl...

  7. Rapid Upregulation of Orai1 Abundance in the Plasma Membrane of Platelets Following Activation with Thrombin and Collagen Related Peptide

    Directory of Open Access Journals (Sweden)

    Guilai Liu

    2015-11-01

    Full Text Available Background: Blood platelets accomplish primary hemostasis following vascular injury and contribute to the orchestration of occlusive vascular disease. Platelets are activated by an increase of cytosolic Ca2+-activity ([Ca2+]i, which is accomplished by Ca2+-release from intracellular stores and subsequent store operated Ca2+ entry (SOCE through Ca2+ release activated Ca2+ channel moiety Orai1. Powerful activators of platelets include thrombin and collagen related peptide (CRP, which are in part effective by activation of small G- protein Rac1. The present study explored the influence of thrombin and CRP on Orai1 protein abundance and cytosolic Ca2+-activity ([Ca2+]i in platelets drawn from wild type mice. Methods: Orai1 protein surface abundance was quantified utilizing CF™488A conjugated antibodies, and [Ca2+]i was determined with Fluo3-fluorescence. Results: In resting platelets, Orai1 protein abundance and [Ca2+]i were low. Thrombin (0.02 U/ml and CRP (5ug/ml within 2 min increased [Ca2+]i and Orai1 protein abundance at the platelet surface. [Ca2+]i was further increased by Ca2+ ionophore ionomycin (1 µM and by store depletion with the sarcoendoplasmatic Ca2+ ATPase inhibitor thapsigargin (1 µM. However, Orai1 protein abundance at the platelet surface was not significantly affected by ionomycin and only slightly increased by thapsigargin. The effect of thrombin and CRP on Orai1 abundance and [Ca2+]i was significantly blunted by Rac1 inhibitor NSC23766 (50 µM. Conclusion: The increase of [Ca2+]i following stimulation of platelets with thrombin and collagen related peptide is potentiated by ultrarapid Rac1 sensitive translocation of Orai1 into the cell membrane.

  8. Comparing halo bias from abundance and clustering

    CERN Document Server

    Hoffmann, Kai; Gaztanaga, Enrique

    2015-01-01

    We model the abundance of haloes in the $\\sim(3 \\ \\text{Gpc}/h)^3$ volume of the MICE Grand Challenge simulation by fitting the universal mass function with an improved Jack-Knife error covariance estimator that matches theory predictions. We present unifying relations between different fitting models and new predictions for linear ($b_1$) and non-linear ($c_2$ and $c_3$) halo clustering bias. Different mass function fits show strong variations in their overall poor performance when including the low mass range ($M_h \\lesssim 3 \\ 10^{12} \\ M_{\\odot}/h$) in the analysis, which indicates noisy friends-of-friends halo detection given the MICE resolution ($m_p \\simeq 3 \\ 10^{10} \\ M_{\\odot}$/h). Together with fits from the literature we find an overall variance in the amplitudes of around $10%$ in the low mass and up to $50%$ in the high mass (galaxy cluster) range ($M_h > 10^{14} \\ M_{\\odot}/h$). These variations propagate into a $10%$ change in $b_1$ predictions and a $50%$ change in $c_2$ or $c_3$. Despite the...

  9. Quasar Elemental Abundances at High Redshifts

    CERN Document Server

    Dietrich, M; Shields, J C; Constantin, A; Heidt, J; Jäger, K; Vestergaard, M; Wagner, S J

    2003-01-01

    We examine rest-frame ultraviolet spectra of 70 high redshift quasars (z>3.5) to study the chemical enrichment history of the gas closely related to the quasars, and thereby estimate the epoch of first star formation. The fluxes of several ultraviolet emission lines were investigated within the framework of the most recent photoionization models to estimate the metallicity of the gas associated with the high-z quasars. Standard photoionization parameters and the assumption of secondary nitrogen enrichment indicate an average abundance of Z/Z_sol = 4 to 5 in the line emitting gas. Assuming a time scale of t_evol = 0.5 - 0.8 Gyrs for the chemical enrichment of the gas, the first major star formation for quasars with z>=4 should have started at a redshift of z_f = 6 - 8, corresponding to an age of the universe of several 10^8 yrs (H_o = 65 km/s/Mpc, Omega_M = 0.3, Omega_Lambda = 0.7). We note that this also appears to be the era of re-ionization of the universe. Finally, there is some evidence for a positive lum...

  10. Nitrogen Abundances in High-z DLAs

    CERN Document Server

    Molaro, P; D'Odorico, V; Péroux, C

    2003-01-01

    Determination of chemical abundances for elements produced mainly by Type I SNae and intermediate mass stars in high redshift DLAs probes the early chemical build-up on time-scales comparable with their production. Nitrogen shows a peculiar behaviour never detected before in any other class of objects. For [N/H] < -3 there is a plateau with [N/Si]= -1.45(\\pm 0.05). We interpret this as empirical evidence for primary N production by massive stars in young systems where AGB stars have not yet had time to make their contribution. The plateau provides the observational integrated yields for N production by massive stars which are theoretically rather uncertain. High N/Si and solar [alpha/iron-peak] ratios are observed at high redshift and place at an earlier epoch the onset of star formation. On the other hand, low N/Si, i.e. young objects, are observed also at relatively low redshifts. These evidences suggest that DLAs started to be formed at a very early epoch but their formation has been extended up to late...

  11. Bacterial bile metabolising gene abundance in Crohn's, ulcerative colitis and type 2 diabetes metagenomes.

    Directory of Open Access Journals (Sweden)

    Alain Labbé

    Full Text Available We performed an analysis to determine the importance of bile acid modification genes in the gut microbiome of inflammatory bowel disease and type 2 diabetic patients. We used publicly available metagenomic datasets from the Human Microbiome Project and the MetaHIT consortium, and determined the abundance of bile salt hydrolase gene (bsh, 7 alpha-dehydroxylase gene (adh and 7-alpha hydroxysteroid dehydrogenase gene (hsdh in fecal bacteria in diseased populations of Crohn's disease (CD, Ulcerative Colitis (UC and Type 2 diabetes mellitus (T2DM. Phylum level abundance analysis showed a significant reduction in Firmicute-derived bsh in UC and T2DM patients but not in CD patients, relative to healthy controls. Reduction of adh and hsdh genes was also seen in UC and T2DM patients, while an increase was observed in the CD population as compared to healthy controls. A further analysis of the bsh genes showed significant differences in the correlations of certain Firmicutes families with disease or healthy populations. From this observation we proceeded to analyse BSH protein sequences and identified BSH proteins clusters representing the most abundant strains in our analysis of Firmicute bsh genes. The abundance of the bsh genes corresponding to one of these protein clusters was significantly reduced in all disease states relative to healthy controls. This cluster includes bsh genes derived from Lachospiraceae, Clostridiaceae, Erysipelotrichaceae and Ruminococcaceae families. This metagenomic analysis provides evidence of the importance of bile acid modifying enzymes in health and disease. It further highlights the importance of identifying gene and protein clusters, as the same gene may be associated with health or disease, depending on the strains expressing the enzyme, and differences in the enzymes themselves.

  12. The Origin of Element Abundance Variations in Solar Energetic Particles

    Science.gov (United States)

    Reames, Donald V.

    2016-08-01

    Abundance enhancements, during acceleration and transport in both gradual and impulsive solar energetic particle (SEP) events, vary approximately as power laws in the mass-to-charge ratio [A/Q] of the ions. Since the Q-values depend upon the electron temperature of the source plasma, this has allowed a determination of this temperature from the pattern of element-abundance enhancements and a verification of the expected inverse-time dependence of the power of A/Q for diffusive transport of ions from the SEP events, with scattering mean free paths found to be between 0.2 and 1 AU. SEP events derived from plasma of different temperatures map into different regions in typical cross-plots of abundances, spreading the distributions. In comparisons of SEP events with temperatures above 2 MK, impulsive events show much broader non-thermal variation of abundances than do gradual events. The extensive shock waves accelerating ions in gradual events may average over much of an active region where numerous but smaller magnetic reconnections, "nanojets", produce suprathermal seed ions, thus averaging over varying abundances, while an impulsive SEP event only samples one local region of abundance variations. Evidence for a reference He/O-abundance ratio of 91, rather than 57, is also found for the hotter plasma. However, while this is similar to the solar-wind abundance of He/O, the solar-wind abundances otherwise provide an unacceptably poor reference for the SEP-abundance enhancements, generating extremely large errors.

  13. Protein Crystal Serum Albumin

    Science.gov (United States)

    1998-01-01

    As the most abundant protein in the circulatory system albumin contributes 80% to colloid osmotic blood pressure. Albumin is also chiefly responsible for the maintenance of blood pH. It is located in every tissue and bodily secretion, with extracellular protein comprising 60% of total albumin. Perhaps the most outstanding property of albumin is its ability to bind reversibly to an incredible variety of ligands. It is widely accepted in the pharmaceutical industry that the overall distribution, metabolism, and efficiency of many drugs are rendered ineffective because of their unusually high affinity for this abundant protein. An understanding of the chemistry of the various classes of pharmaceutical interactions with albumin can suggest new approaches to drug therapy and design. Principal Investigator: Dan Carter/New Century Pharmaceuticals

  14. Housing system influences abundance of Pax3 and Pax7 in postnatal chicken skeletal muscles.

    Science.gov (United States)

    Yin, H D; Li, D Y; Zhang, L; Yang, M Y; Zhao, X L; Wang, Y; Liu, Y P; Zhu, Q

    2014-06-01

    Paired box (Pax) proteins 3 and 7 are associated with activation of muscle satellite cells and play a major role in hyperplastic and hypertrophic growth in postnatal skeletal muscle fibers. The objective of this study was to evaluate the effect of housing system on abundance of Pax3 and Pax7 in postnatal chicken skeletal muscles. At 42 d, 1,200 chickens with similar BW were randomly assigned to cage, pen, and free-range group. The mRNA abundance was measured in pectoralis major and thigh muscle at d 56, 70, and 84, and the protein expression was quantified at d 84. Increases in mRNA abundance of PAX3 and PAX7 with age were less pronounced in caged system chickens than in pen and free-range chickens from d 56 to 84, and free-range chickens showed a more pronounced increase in gene expression with age compared with penned chickens. At d 84, quantities of PAX3 and PAX7 mRNA and protein were highest in both pectoralis major and thigh muscle of chickens raised in the free-range group, lowest in penned chickens, and intermediate in caged chickens (P chicken skeletal muscles.

  15. Fiber type effects on contraction-stimulated glucose uptake and GLUT4 abundance in single fibers from rat skeletal muscle.

    Science.gov (United States)

    Castorena, Carlos M; Arias, Edward B; Sharma, Naveen; Bogan, Jonathan S; Cartee, Gregory D

    2015-02-01

    To fully understand skeletal muscle at the cellular level, it is essential to evaluate single muscle fibers. Accordingly, the major goals of this study were to determine if there are fiber type-related differences in single fibers from rat skeletal muscle for: 1) contraction-stimulated glucose uptake and/or 2) the abundance of GLUT4 and other metabolically relevant proteins. Paired epitrochlearis muscles isolated from Wistar rats were either electrically stimulated to contract (E-Stim) or remained resting (No E-Stim). Single fibers isolated from muscles incubated with 2-deoxy-d-[(3)H]glucose (2-DG) were used to determine fiber type [myosin heavy chain (MHC) isoform protein expression], 2-DG uptake, and abundance of metabolically relevant proteins, including the GLUT4 glucose transporter. E-Stim, relative to No E-Stim, fibers had greater (P GLUT4, tethering protein containing a UBX domain for GLUT4 (TUG), cytochrome c oxidase IV (COX IV), and filamin C protein levels were significantly greater (P GLUT4 levels for MHC-IIax fibers exceeded MHC-IIxb fibers. GLUT4, COX IV, filamin C, and TUG abundance in single fibers was significantly (P GLUT4 abundance among the fiber types were not accompanied by significant differences in contraction-stimulated glucose uptake.

  16. Radial molecular abundances and gas cooling in starless cores

    CERN Document Server

    Sipilä, O

    2012-01-01

    Aims: We aim to simulate radial profiles of molecular abundances and the gas temperature in cold and heavily shielded starless cores by combining chemical and radiative transfer models. Methods: A determination of the dust temperature in a modified Bonnor-Ebert sphere is used to calculate initial radial molecular abundance profiles. The abundances of selected cooling molecules corresponding to two different core ages are then extracted to determine the gas temperature at two time steps. The calculation is repeated in an iterative process yielding molecular abundances consistent with the gas temperature. Line emission profiles for selected substances are calculated using simulated abundance profiles. Results: The gas temperature is a function of time; the gas heats up as the core gets older because the cooling molecules are depleted onto grain surfaces. The contributions of the various cooling molecules to the total cooling power change with time. Radial chemical abundance profiles are non-trivial: different s...

  17. Evolution of dispersion in the cosmic deuterium abundance

    CERN Document Server

    Dvorkin, Irina; Silk, Joseph; Petitjean, Patrick; Olive, Keith A

    2016-01-01

    Deuterium is created during Bing Bang Nucleosynthesis, and, in contrast to the other light stable nuclei, can only be destroyed thereafter by fusion in stellar interiors. In this paper we study the cosmic evolution of the deuterium abundance in the interstellar medium and its dispersion using realistic galaxy evolution models. We find that models that reproduce the observed metal abundance are compatible with observations of the deuterium abundance in the local ISM and z ~ 3 absorption line systems. In particular, we reproduce the low astration factor which we attribute to a low global star formation efficiency. We calculate the dispersion in deuterium abundance arising from different structure formation histories in different parts of the Universe. Our model also predicts an extremely tight correlation between deuterium and metal abundances which could be used to measure the primordial deuterium abundance.

  18. TEA: A Code for Calculating Thermochemical Equilibrium Abundances

    CERN Document Server

    Blecic, Jasmina; Bowman, M Oliver

    2015-01-01

    We present an open-source Thermochemical Equilibrium Abundances (TEA) code that calculates the abundances of gaseous molecular species. The code is based on the methodology of White et al. (1958) and Eriksson (1971). It applies Gibbs free-energy minimization using an iterative, Lagrangian optimization scheme. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature-pressure pairs. We tested the code against the method of Burrows & Sharp (1999), the free thermochemical equilibrium code CEA (Chemical Equilibrium with Applications), and the example given by White et al. (1958). Using their thermodynamic data, TEA reproduces their final abundances, but with higher precision. We also applied the TEA abundance calculations to models of several hot-Jupiter exoplanets, producing expected results. TEA is written in Python in a modular format. There is a start guide, a user manual, and a code document in addition to this theory paper. TEA is ...

  19. Shallow extra mixing in solar twins inferred from Be abundances

    CERN Document Server

    Maia, M Tucci; Castro, M; Asplund, M; Ramírez, I; Monroe, T R; Nascimento, J D do; Yong, D

    2015-01-01

    Lithium and beryllium are destroyed at different temperatures in stellar interiors. As such, their relative abundances offer excellent probes of the nature and extent of mixing processes within and below the convection zone. We determine Be abundances for a sample of eight solar twins for which Li abundances have previously been determined. The analyzed solar twins span a very wide range of age, 0.5-8.2 Gyr, which enables us to study secular evolution of Li and Be depletion. We gathered high-quality UVES/VLT spectra and obtained Be abundances by spectral synthesis of the Be II 313 nm doublet. The derived beryllium abundances exhibit no significant variation with age. The more fragile Li, however, exhibits a monotonically decreasing abundance with increasing age. Therefore, relatively shallow extra mixing below the convection zone is necessary to simultaneously account for the observed Li and Be behavior in the Sun and solar twins.

  20. Abundances of metals in five nearby open clusters

    CERN Document Server

    Hui-Bon-Hoa, A

    1998-01-01

    Abundances of Mg, Ca, Sc, Cr, Fe, and Ni are derived for A stars of five nearby open clusters of various ages using high resolution spectroscopy. We point out a correlation between the abundance of Ca and that of Sc, suggesting that the abundance anomalies of these elements arise from the same physical process. Pronounced Am patterns are rather found in the oldest cluster stars whereas younger targets show weaker Am anomalies and atypical patterns for some of them.

  1. The Stellar Oxygen Abundance Gradient in M33

    Science.gov (United States)

    Monteverde, M. I.; Herrero, A.; Lennon, D. J.; Kudritzki, R.-P.

    1997-01-01

    We report here first results concerning stellar oxygen abundances in M33. Non-LTE model atmosphere and non-LTE line formation calculations were used to determine the oxygen abundance of B-type supergiants. By choosing stars located at different projected radial distances to the center of M33, we are able to determine the oxygen abundance gradient, for which we obtain a value of -0.16 +/- 0.06 dex kpc-1. This is the first time that the oxygen stellar abundance gradient has been determined in a spiral galaxy other than the Milky Way.

  2. Regulation of YKL-40 expression by corticosteroids : effect on pro-inflammatory macrophages in vitro and its modulation in COPD in vivo

    NARCIS (Netherlands)

    Kunz, L. I. Z.; van't Wout, E. F. A.; van Schadewijk, A.; Postma, D. S.; Kerstjens, H. A. M.; Sterk, P. J.; Hiemstra, P. S.

    2015-01-01

    Background: Macrophages constitute a heterogeneous cell population with pro-(M Phi 1) and anti-inflammatory (M Phi 2) cells. The soluble chitinase-like-protein YKL-40 is expressed in macrophages and various other cell types, and has been linked to a variety of inflammatory diseases, including COPD.

  3. Herbivore regulation of plant abundance in aquatic ecosystems.

    Science.gov (United States)

    Wood, Kevin A; O'Hare, Matthew T; McDonald, Claire; Searle, Kate R; Daunt, Francis; Stillman, Richard A

    2017-05-01

    Herbivory is a fundamental process that controls primary producer abundance and regulates energy and nutrient flows to higher trophic levels. Despite the recent proliferation of small-scale studies on herbivore effects on aquatic plants, there remains limited understanding of the factors that control consumer regulation of vascular plants in aquatic ecosystems. Our current knowledge of the regulation of primary producers has hindered efforts to understand the structure and functioning of aquatic ecosystems, and to manage such ecosystems effectively. We conducted a global meta-analysis of the outcomes of plant-herbivore interactions using a data set comprised of 326 values from 163 studies, in order to test two mechanistic hypotheses: first, that greater negative changes in plant abundance would be associated with higher herbivore biomass densities; second, that the magnitude of changes in plant abundance would vary with herbivore taxonomic identity. We found evidence that plant abundance declined with increased herbivore density, with plants eliminated at high densities. Significant between-taxa differences in impact were detected, with insects associated with smaller reductions in plant abundance than all other taxa. Similarly, birds caused smaller reductions in plant abundance than echinoderms, fish, or molluscs. Furthermore, larger reductions in plant abundance were detected for fish relative to crustaceans. We found a positive relationship between herbivore species richness and change in plant abundance, with the strongest reductions in plant abundance reported for low herbivore species richness, suggesting that greater herbivore diversity may protect against large reductions in plant abundance. Finally, we found that herbivore-plant nativeness was a key factor affecting the magnitude of herbivore impacts on plant abundance across a wide range of species assemblages. Assemblages comprised of invasive herbivores and native plant assemblages were associated with

  4. Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods.

    Directory of Open Access Journals (Sweden)

    Huhe

    Full Text Available In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P < 0.002 and P < 0.03, respectively. The present study elucidates the ecology of bacteria that mediate the nitrogen cycle in recently abandoned croplands.

  5. Latitudinal patterns in the abundance of major marine bacterioplankton groups

    DEFF Research Database (Denmark)

    Wietz, Matthias; Gram, Lone; Jørgensen, Bo

    2010-01-01

    ) and Gammaproteobacteria (polar stations) varied between major oceanic regions (biomes), as did absolute abundances of Roseobacter (peaking at temperate and polar stations). For almost all groups absolute abundances were positively correlated with nutrient concentrations in warmer oceans, and negatively with oxygen...

  6. Detecting novel low-abundant transcripts in Drosophila

    DEFF Research Database (Denmark)

    Lee, Sanggyu; Bao, Jingyue; Zhou, Guolin;

    2005-01-01

    Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244...

  7. Variation in rank abundance replicate samples and impact of clustering

    NARCIS (Netherlands)

    Neuteboom, J.H.; Struik, P.C.

    2005-01-01

    Calculating a single-sample rank abundance curve by using the negative-binomial distribution provides a way to investigate the variability within rank abundance replicate samples and yields a measure of the degree of heterogeneity of the sampled community. The calculation of the single-sample rank a

  8. A protocol for sampling vascular epiphyte richness and abundance

    NARCIS (Netherlands)

    Wolf, J.H.D.; Gradstein, S.R.; Nadkarni, N.M.

    2009-01-01

    The sampling of epiphytes is fraught with methodological difficulties. We present a protocol to sample and analyse vascular epiphyte richness and abundance in forests of different structure (SVERA). Epiphyte abundance is estimated as biomass by recording the number of plant components in a range of

  9. Abundance sensitive points of line profiles in the stellar spectra

    CERN Document Server

    Sheminova, V A

    2014-01-01

    Many abundance studies are based on spectrum synthesis and $\\chi$-squared differences between the synthesized and an observed spectrum. Much of the spectra so compared depend only weakly on the elemental abundances. Logarithmic plots of line depths rather than relative flux make this more apparent. We present simulations that illustrate a simple method for finding regions of the spectrum most sensitive to abundance, and also some caveats for using such information. As expected, we find that weak features are the most sensitive. Equivalent widths of weak lines are ideal features, because of their sensitivity to abundances, and insensitivity to factors that broaden the line profiles. The wings of strong lines can also be useful, but it is essential that the broadening mechanisms be accurately known. The very weakest features, though sensitive to abundance, should be avoided or used with great caution because of uncertainty of continuum placement as well as numerical uncertainties associated with the subtraction...

  10. Abundance Survey of M and K Dwarf Stars

    Energy Technology Data Exchange (ETDEWEB)

    Woolf, Vincent M. [Astronomy Department, University of Washington, Seattle, WA 98133 (United States); Wallerstein, George [Astronomy Department, University of Washington, Seattle, WA 98133 (United States)

    2005-07-25

    We report the measurement of chemical abundances in 35 low-mass main sequence (M and K dwarf) stars. We have measured the abundance of 12 elements in Kapteyn's Star, a nearby halo M subdwarf. The abundances indicate an iron abundance of [Fe/H] = -0.98, which is about 0.5 dex smaller than that measured in the only previous published measurement using atomic absorption lines. We have measured Fe and Ti abundances in 35 M and K dwarfs with -2.39 [Fe/H] +0.21 using atomic absorption lines, mostly in the 8000A <{lambda} < 8850A range. These will be used to calibrate photometric and low-resolution spectrum metallicity indices for low mass dwarfs, which will make metallicity estimates for these stars more certain. We also describe some difficulties encountered which are not normally necessary to consider when studying warmer stars.

  11. Ionized Gaseous Nebulae Abundance Determination from the Direct Method

    Science.gov (United States)

    Pérez-Montero, Enrique

    2017-04-01

    This tutorial explains the procedure used to analyze an optical emission-line spectrum produced by a nebula ionized by massive star formation. Particularly, the methodology used to derive physical properties, such as electron density and temperature, and the ionic abundances of the most representative elements whose emission lines are present in the optical spectrum is described. The main focus is on the direct method, which is based on the measurement of the electron temperature to derive the abundances, given that the ionization and thermal equilibrium of the ionized gas is dominated by the metallicity. The ionization correction factors used to obtain total abundances from the abundances of some of their ions are also given. Finally, some strong-line methods to derive abundances are described. Such methods are used when no estimation of the temperature can be derived, but which can be consistent with the direct method if they are empirically calibrated.

  12. The Detailed Chemical Abundance Patterns of M31 Globular Clusters

    CERN Document Server

    Colucci, J E; Cohen, J

    2012-01-01

    We present detailed chemical abundances for $>$20 elements in $\\sim$30 globular clusters in M31. These results have been obtained using high resolution ($\\lambda/\\Delta\\lambda\\sim$24,000) spectra of their integrated light and analyzed using our original method. The globular clusters have galactocentric radii between 2.5 kpc and 117 kpc, and therefore provide abundance patterns for different phases of galaxy formation recorded in the inner and outer halo of M31. We find that the clusters in our survey have a range in metallicity of $-2.2$20 kpc have a small range in abundance of [Fe/H]$=-1.6 \\pm 0.10$. We also measure abundances of alpha, r- and s-process elements. These results constitute the first abundance pattern constraints for old populations in M31 that are comparable to those known for the Milky Way halo.

  13. Star formation and the interstellar medium in low surface brightness galaxies; 1, Oxygen abundances and abundance gradients in low surface brightness disk galaxies

    NARCIS (Netherlands)

    Blok, W. J. G. de; Hulst, J. M. van der

    1998-01-01

    Submitted to: Astron. Astrophys. Abstract: We present measurements of the oxygen abundances in 64 HII regions in 12 LSB galaxies. We find that oxygen abundances are low. No regions with solar abundance have been found, and most have oxygen abundances $sim 0.5$ to 0.1 solar. The oxygen abundance appe

  14. Evidences of abundant hemocyanin variants in shrimp Litopenaeus vannamei.

    Science.gov (United States)

    Zhao, Xianliang; Guo, Lingling; Lu, Xin; Lu, Hui; Wang, Fan; Zhong, Mingqi; Chen, Jiehui; Zhang, Yueling

    2016-09-01

    Hemocyanin (HMC) is a multifunctional immune molecule present in mollusks and arthropods and functions as an important antigen non-specific immune protein. Our previous evidences demonstrated that Litopenaeus vannamei HMC might display extensive molecular diversities. In this study, bioinformatics analysis showed dozens of variant sequences of the HMC subunit with higher molecular weight from L. vannamei (LvHMC). Three variant fragments, named as LvHMCV1-3, which shared 85-99% nucleotide identity with that of the classical form of LvHMC (AJ250830.1), were cloned and characterized. Spatial expression profiles showed that LvHMCV1-3 had different tissue-specific distribution, which were affected by stimulation with six pathogenic bacteria, including Escherichia coli K12, Vibrio parahaemolyticus, Vibrio alginolyticus, Vibrio fluvialis, Streptococcus pyogenes and Staphylococcus aureus, with each variant fragment showing a specific stress pattern to different bacterial pathogens. Full length cDNA of LvHMCV3 was further cloned and characterized. The deduced amino acid sequence shared 92% identity with that of LvHMC, possessed a conserved structure characteristic of the HMC family and could be clustered into one branch along with other arthropod HMC in a phylogenetic tree. In addition, the recombinant protein of LvHMCV3 (rLvHMCV3) showed obvious agglutination activities against three aquaculture pathogenic bacteria including E. coli K12, V. parahaemolyticus and S.aureus at concentrations ranging from 31.25-62.5g/mL. It also showed obvious antibacterial activity against V. parahaemolyticus at concentrations 0.02-0.5mg/mL, and possessed the best inhibitive effects compared with those of rLvHMCV4 and rLvHMC. Co-injection of V. parahaemolyticus and rLvHMCV3 in L. vannamei showed significant decrease of the mortality rate at 24-72h after injection. Therefore, these studies suggested that L. vannamei had abundant HMC variants, which possessed obvious resistance to pathogenic

  15. Dam removal increases American eel abundance in distant headwater streams

    Science.gov (United States)

    Hitt, Nathaniel P.; Eyler, Sheila; Wofford, John E.B.

    2012-01-01

    American eel Anguilla rostrata abundances have undergone significant declines over the last 50 years, and migration barriers have been recognized as a contributing cause. We evaluated eel abundances in headwater streams of Shenandoah National Park, Virginia, to compare sites before and after the removal of a large downstream dam in 2004 (Embrey Dam, Rappahannock River). Eel abundances in headwater streams increased significantly after the removal of Embrey Dam. Observed eel abundances after dam removal exceeded predictions derived from autoregressive models parameterized with data prior to dam removal. Mann–Kendall analyses also revealed consistent increases in eel abundances from 2004 to 2010 but inconsistent temporal trends before dam removal. Increasing eel numbers could not be attributed to changes in local physical habitat (i.e., mean stream depth or substrate size) or regional population dynamics (i.e., abundances in Maryland streams or Virginia estuaries). Dam removal was associated with decreasing minimum eel lengths in headwater streams, suggesting that the dam previously impeded migration of many small-bodied individuals (dams may influence eel abundances in headwater streams up to 150 river kilometers distant, and that dam removal may provide benefits for eel management and conservation at the landscape scale.

  16. Model reduction for stochastic chemical systems with abundant species

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Stephen; Cianci, Claudia; Grima, Ramon [School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH93JR, Scotland (United Kingdom)

    2015-12-07

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

  17. Beryllium Abundances in Stars of One-Solar-Mass

    CERN Document Server

    Boesgaard, Ann Merchant

    2008-01-01

    We have determined Be abundances in 50 F and G dwarfs in the mass range of 0.9 $\\leq$ M$_\\odot$ $\\leq$ 1.1 as determined by Lambert & Reddy. The effective temperatures are 5600 to 6400 K and metallicities from $-$0.65 to +0.11. The spectra were taken primarily with Keck I + HIRES. The Be abundances were found via spectral synthesis of Be II lines near 3130 \\AA. The Be abundances were investigated as a function of age, temperature, metallicity and Li abundance in this narrow mass range. Even though our stars are similar in mass, they show a range in Be abundances of a factor of $>$40. We find that [Be/Fe] has no dependence on temperature, but does show a spread of a factor of 6 at a given temperature. The reality of the spread is shown by two identical stars which differ from each other by a factor of two only in their abundances of Li and Be. Our thin-disk-star sample fits the trend between Be abundance and [Fe/H] found for halo and thick disk stars, extending it to about 4 orders of magnitude in the two ...

  18. Stellar abundances in the solar neighborhood: The Hypatia Catalog

    Energy Technology Data Exchange (ETDEWEB)

    Hinkel, Natalie R.; Timmes, F.X.; Young, Patrick A.; Pagano, Michael D. [School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287 (United States); Turnbull, Margaret C. [Global Science Institute, P.O. Box 252, Antigo, WI 54409 (United States)

    2014-09-01

    We compile spectroscopic abundance data from 84 literature sources for 50 elements across 3058 stars in the solar neighborhood, within 150 pc of the Sun, to produce the Hypatia Catalog. We evaluate the variability of the spread in abundance measurements reported for the same star by different surveys. We also explore the likely association of the star within the Galactic disk, the corresponding observation and abundance determination methods for all catalogs in Hypatia, the influence of specific catalogs on the overall abundance trends, and the effect of normalizing all abundances to the same solar scale. The resulting stellar abundance determinations in the Hypatia Catalog are analyzed only for thin-disk stars with observations that are consistent between literature sources. As a result of our large data set, we find that the stars in the solar neighborhood may reveal an asymmetric abundance distribution, such that a [Fe/H]-rich group near the midplane is deficient in Mg, Si, S, Ca, Sc II, Cr II, and Ni as compared to stars farther from the plane. The Hypatia Catalog has a wide number of applications, including exoplanet hosts, thick- and thin-disk stars, and stars with different kinematic properties.

  19. Geographical range and local abundance of tree species in China.

    Directory of Open Access Journals (Sweden)

    Haibao Ren

    Full Text Available Most studies on the geographical distribution of species have utilized a few well-known taxa in Europe and North America, with little research in China and its wide range of climate and forest types. We assembled large datasets to quantify the geographic ranges of tree species in China and to test several biogeographic hypotheses: 1 whether locally abundant species tend to be geographically widespread; 2 whether species are more abundant towards their range-centers; and 3 how abundances are correlated between sites. Local abundances of 651 species were derived from four tree plots of 20-25 ha where all individuals ≥1 cm in stem diameter were mapped and identified taxonomically. Range sizes of these species across China were then estimated from over 460,000 geo-referenced records; a Bayesian approach was used, allowing careful measures of error of each range estimate. The log-transformed range sizes had a bell-shaped distribution with a median of 703,000 km(2, and >90% of 651 species had ranges >10(5 km(2. There was no relationship between local abundance and range size, and no evidence for species being more abundant towards their range-centers. Finally, species' abundances were positively correlated between sites. The widespread nature of most tree species in China suggests few are vulnerable to global extinction, and there is no indication of the double-peril that would result if rare species also had narrow ranges.

  20. (Un)true deuterium abundance in the Galactic disk

    Science.gov (United States)

    Prodanović, Tijana; Steigman, Gary; Fields, Brian D.

    2010-04-01

    Deuterium has a special place in cosmology, nuclear astrophysics, and galactic chemical evolution, because of its unique property that it is only created in the big bang nucleosynthesis while all other processes result in its net destruction. For this reason, among other things, deuterium abundance measurements in the interstellar medium (ISM) allow us to determine the fraction of interstellar gas that has been cycled through stars, and set constraints and learn about different Galactic chemical evolution (GCE) models. However, recent indications that deuterium might be preferentially depleted onto dust grains complicate our understanding about the meaning of measured ISM deuterium abundances. For this reason, recent estimates by Linsky et al. (2006) have yielded a lower bound to the “true”, undepleted, ISM deuterium abundance that is very close to the primordial abundance, indicating a small deuterium astration factor contrary to the demands of many GCE models. To avoid any prejudice about deuterium dust depletion along different lines of sight that are used to determine the “true” D abundance, we propose a model-independent, statistical Bayesian method to address this issue and determine in a model-independent manner the undepleted ISM D abundance. We find the best estimate for the gas-phase ISM deuterium abundance to be (D/H)ISM ≥ (2.0 ± 0.1) × 10-5. Presented are the results of Prodanović et al. (2009).

  1. Cloning and Expression Analysis of a Late Embryogenesis Abundant Protein Gene SpLea5 from Sesuviumportulacastrum%海马齿胚胎发育晚期丰富蛋白基因SpLea5的克隆与表达分析

    Institute of Scientific and Technical Information of China (English)

    付桂; 范伟; 畅文军; 张治礼

    2011-01-01

    根据筛选文库时获得的EST序列信息,利用RACE技术从海马齿根中分离获得了一个海马齿胚胎发育晚期丰富蛋白基因的全长cDNA,命名为SeLea5.序列分析结果表明,SpLea5基因cDNA全长685 bp,含有一个294 bD的完整开放阅读框,编码97个氨基酸残基;推测编码的氨基酸序列与柽柳、杨木樨、烟草、甜橙、温州蜜柑、麻风树和陆地棉中相廊基因的氨基酸序列一致性为54%、52%、48%、47%、47%、46%、44%、41%,在聚类分析时与高等植物聚为一类.SpLea5在海马齿植株中呈组成型表达,但根中表达最为丰富,茎和叶次之:海水、NaCl、PEG、ABA处理均能够诱导根部SpLea5基凶的表达.这些结果表明,SpLea5基因可能参与了海马齿对盐和十旱胁迫的分子响应.%Based on the EST sequences from a differentially expressed eDNA library of Sesuvium portulacastrum roots, the full-length eDNA of a late embryogenesis abundant pnotein gene designated as SpLea5 was cloned from S. portulacastrum roots. Sequence analysis showed that the SpLea5 eDNA contained 685 bp with an open reading frame (ORF) of 294 bp and encoded 97 amino acid residues. The deduced amino acid sequence shared the identity of 54%, 52%, 48%, 47%, 47%,46%, 46%, 44% and 41% with that from Tamarix androssowii, Populus suaveolens, Nicotiana tabacum, Citrus sinensis,Citrus unshiu, Jatropha curcas, Gossypium hirsutum, Glycine max and Ricinus communis, respectively. In phylogenetic tree the SpLea5 and other plant-derived Leas were grouped into one large cluster. Semi-quantitative RT-PCR analysis revealed that the SPLea5 was constitutively expressed in all tested organs but at different levels. The SpLea5 was strongly expressed in roots, but weakly in leaves and stems. The expression of SpLea5 was strongly regulated by seawater, NaCI, PEG and ABA, suggesting that the SpLea5 in S.portulacastrum may be involved in responses to salt stress and drought.

  2. How ants drop out: ant abundance on tropical mountains.

    Directory of Open Access Journals (Sweden)

    John T Longino

    Full Text Available In tropical wet forests, ants are a large proportion of the animal biomass, but the factors determining abundance are not well understood. We characterized ant abundance in the litter layer of 41 mature wet forest sites spread throughout Central America (Chiapas, Guatemala, Honduras, Nicaragua, and Costa Rica and examined the impact of elevation (as a proxy for temperature and community species richness. Sites were intentionally chosen to minimize variation in precipitation and seasonality. From sea level to 1500 m ant abundance very gradually declined, community richness declined more rapidly than abundance, and the local frequency of the locally most common species increased. These results suggest that within this elevational zone, density compensation is acting, maintaining high ant abundance as richness declines. In contrast, in sites above 1500 m, ant abundance dropped abruptly to much lower levels. Among these high montane sites, community richness explained much more of the variation in abundance than elevation, and there was no evidence of density compensation. The relative stability of abundance below 1500 m may be caused by opposing effects of temperature on productivity and metabolism. Lower temperatures may decrease productivity and thus the amount of food available for consumers, but slower metabolisms of consumers may allow maintenance of higher biomass at lower resource supply rates. Ant communities at these lower elevations may be highly interactive, the result of continuous habitat presence over geological time. High montane sites may be ephemeral in geological time, resulting in non-interactive communities dominated by historical and stochastic processes. Abundance in these sites may be determined by the number of species that manage to colonize and/or avoid extinction on mountaintops.

  3. Understanding and reducing statistical uncertainties in nebular abundance determinations

    Science.gov (United States)

    Wesson, R.; Stock, D. J.; Scicluna, P.

    2012-06-01

    Whenever observations are compared to theories, an estimate of the uncertainties associated with the observations is vital if the comparison is to be meaningful. However, many or even most determinations of temperatures, densities and abundances in photoionized nebulae do not quote the associated uncertainty. Those that do typically propagate the uncertainties using analytical techniques which rely on assumptions that generally do not hold. Motivated by this issue, we have developed Nebular Empirical Analysis Tool (NEAT), a new code for calculating chemical abundances in photoionized nebulae. The code carries out a standard analysis of lists of emission lines using long-established techniques to estimate the amount of interstellar extinction, calculate representative temperatures and densities, compute ionic abundances from both collisionally excited lines and recombination lines, and finally to estimate total elemental abundances using an ionization correction scheme. NEATuses a Monte Carlo technique to robustly propagate uncertainties from line flux measurements through to the derived abundances. We show that, for typical observational data, this approach is superior to analytic estimates of uncertainties. NEAT also accounts for the effect of upward biasing on measurements of lines with low signal-to-noise ratio, allowing us to accurately quantify the effect of this bias on abundance determinations. We find not only that the effect can result in significant overestimates of heavy element abundances derived from weak lines, but also that taking it into account reduces the uncertainty of these abundance determinations. Finally, we investigate the effect of possible uncertainties in R, the ratio of selective-to-total extinction, on abundance determinations. We find that the uncertainty due to this parameter is negligible compared to the statistical uncertainties due to typical line flux measurement uncertainties.

  4. Core-shell hydrogel particles harvest, concentrate and preserve labile low abundance biomarkers.

    Directory of Open Access Journals (Sweden)

    Caterina Longo

    Full Text Available BACKGROUND: The blood proteome is thought to represent a rich source of biomarkers for early stage disease detection. Nevertheless, three major challenges have hindered biomarker discovery: a candidate biomarkers exist at extremely low concentrations in blood; b high abundance resident proteins such as albumin mask the rare biomarkers; c biomarkers are rapidly degraded by endogenous and exogenous proteinases. METHODOLOGY AND PRINCIPAL FINDINGS: Hydrogel nanoparticles created with a N-isopropylacrylamide based core (365 nm-shell (167 nm and functionalized with a charged based bait (acrylic acid were studied as a technology for addressing all these biomarker discovery problems, in one step, in solution. These harvesting core-shell nanoparticles are designed to simultaneously conduct size exclusion and affinity chromatography in solution. Platelet derived growth factor (PDGF, a clinically relevant, highly labile, and very low abundance biomarker, was chosen as a model. PDGF, spiked in human serum, was completely sequestered from its carrier protein albumin, concentrated, and fully preserved, within minutes by the particles. Particle sequestered PDGF was fully protected from exogenously added tryptic degradation. When the nanoparticles were added to a 1 mL dilute solution of PDGF at non detectable levels (less than 20 picograms per mL the concentration of the PDGF released from the polymeric matrix of the particles increased within the detection range of ELISA and mass spectrometry. Beyond PDGF, the sequestration and protection from degradation for a series of additional very low abundance and very labile cytokines were verified. CONCLUSIONS AND SIGNIFICANCE: We envision the application of harvesting core-shell nanoparticles to whole blood for concentration and immediate preservation of low abundance and labile analytes at the time of venipuncture.

  5. A metastable equilibrium model for the relative abundances of microbial phyla in a hot spring.

    Directory of Open Access Journals (Sweden)

    Jeffrey M Dick

    Full Text Available Many studies link the compositions of microbial communities to their environments, but the energetics of organism-specific biomass synthesis as a function of geochemical variables have rarely been assessed. We describe a thermodynamic model that integrates geochemical and metagenomic data for biofilms sampled at five sites along a thermal and chemical gradient in the outflow channel of the hot spring known as "Bison Pool" in Yellowstone National Park. The relative abundances of major phyla in individual communities sampled along the outflow channel are modeled by computing metastable equilibrium among model proteins with amino acid compositions derived from metagenomic sequences. Geochemical conditions are represented by temperature and activities of basis species, including pH and oxidation-reduction potential quantified as the activity of dissolved hydrogen. By adjusting the activity of hydrogen, the model can be tuned to closely approximate the relative abundances of the phyla observed in the community profiles generated from BLAST assignments. The findings reveal an inverse relationship between the energy demand to form the proteins at equal thermodynamic activities and the abundance of phyla in the community. The distance from metastable equilibrium of the communities, assessed using an equation derived from energetic considerations that is also consistent with the information-theoretic entropy change, decreases along the outflow channel. Specific divergences from metastable equilibrium, such as an underprediction of the relative abundances of phototrophic organisms at lower temperatures, can be explained by considering additional sources of energy and/or differences in growth efficiency. Although the metabolisms used by many members of these communities are driven by chemical disequilibria, the results support the possibility that higher-level patterns of chemotrophic microbial ecosystems are shaped by metastable equilibrium states that

  6. Proteoglycans in Leiomyoma and Normal Myometrium: Abundance, Steroid Hormone Control, and Implications for Pathophysiology.

    Science.gov (United States)

    Barker, Nichole M; Carrino, David A; Caplan, Arnold I; Hurd, William W; Liu, James H; Tan, Huiqing; Mesiano, Sam

    2016-03-01

    Uterine leiomyoma are a common benign pelvic tumors composed of modified smooth muscle cells and a large amount of extracellular matrix (ECM). The proteoglycan composition of the leiomyoma ECM is thought to affect pathophysiology of the disease. To test this hypothesis, we examined the abundance (by immunoblotting) and expression (by quantitative real-time polymerase chain reaction) of the proteoglycans biglycan, decorin, and versican in leiomyoma and normal myometrium and determined whether expression is affected by steroid hormones and menstrual phase. Leiomyoma and normal myometrium were collected from women (n = 17) undergoing hysterectomy or myomectomy. In vitro studies were performed on immortalized leiomyoma (UtLM) and normal myometrial (hTERT-HM) cells with and without exposure to estradiol and progesterone. In leiomyoma tissue, abundance of decorin messenger RNA (mRNA) and protein were 2.6-fold and 1.4-fold lower, respectively, compared with normal myometrium. Abundance of versican mRNA was not different between matched samples, whereas versican protein was increased 1.8-fold in leiomyoma compared with myometrium. Decorin mRNA was 2.4-fold lower in secretory phase leiomyoma compared with proliferative phase tissue. In UtLM cells, progesterone decreased the abundance of decorin mRNA by 1.3-fold. Lower decorin expression in leiomyoma compared with myometrium may contribute to disease growth and progression. As decorin inhibits the activity of specific growth factors, its reduced level in the leiomyoma cell microenvironment may promote cell proliferation and ECM deposition. Our data suggest that decorin expression in leiomyoma is inhibited by progesterone, which may be a mechanism by which the ovarian steroids affect leiomyoma growth and disease progression.

  7. Chemical Protein Modification through Cysteine.

    Science.gov (United States)

    Gunnoo, Smita B; Madder, Annemieke

    2016-04-01

    The modification of proteins with non-protein entities is important for a wealth of applications, and methods for chemically modifying proteins attract considerable attention. Generally, modification is desired at a single site to maintain homogeneity and to minimise loss of function. Though protein modification can be achieved by targeting some natural amino acid side chains, this often leads to ill-defined and randomly modified proteins. Amongst the natural amino acids, cysteine combines advantageous properties contributing to its suitability for site-selective modification, including a unique nucleophilicity, and a low natural abundance--both allowing chemo- and regioselectivity. Native cysteine residues can be targeted, or Cys can be introduced at a desired site in a protein by means of reliable genetic engineering techniques. This review on chemical protein modification through cysteine should appeal to those interested in modifying proteins for a range of applications.

  8. The determination of electron abundances in interstellar clouds

    Science.gov (United States)

    Wootten, A.; Snell, R.; Glassgold, A. E.

    1979-01-01

    An independent method is proposed for the determination of electron abundances in dense clouds based upon the abundance ratio of HCO(+) and CO. The method is derived from a simple application of gas phase ion molecule interstellar chemistry. It is noted that unlike the fractionation of deuterated molecules, it applies to warm as well as to cool clouds. The method is illustrated with the results of the recent abundance survey of Wooten et al. (1978). Finally, it is shown that in cases where deuterium enhancement is measured, an upper limit can be obtained for the cosmic ray ionization rate.

  9. Trace-element abundances in several new ureilites

    Science.gov (United States)

    Boynton, William V.; Hill, Dolores H.

    1993-01-01

    Four new ureilites are analyzed for trace-element abundances. Frontier Mountain (FRO) 90054 is an augite-rich ureilite and has high rare earth element (REE) abundances with a pattern expected of augite. FRO 90036 and Acfer 277 have REE patterns similar to the V-shape pattern of other ureilites. Nuevo Mercurio (b) has very high REE abundances, but they look like they are due to terrestrial alteration. The siderophile-element pattern of these ureilites are similar to those of known ureilites.

  10. Oxygen and nitrogen abundances in Virgo and field spirals

    OpenAIRE

    Pilyugin, L. S.; Molla, Mercedes; Ferrini, Federico; Vilchez, Jose M.

    2001-01-01

    The oxygen and nitrogen abundances in the HII regions of the nine Virgo spirals of the sample from Skillman et al (1996) and in nine field spiral galaxies are re-determined with the recently suggested P - method. We confirm that there is an abundance segregation in the sample of Virgo spirals in the sense that the HI deficient Virgo spirals near the core of the cluster have higher oxygen abundances in comparison to the spirals at the periphery of the Virgo cluster. At the same time both the V...

  11. Dust formation in a galaxy with primitive abundances.

    Science.gov (United States)

    Sloan, G C; Matsuura, M; Zijlstra, A A; Lagadec, E; Groenewegen, M A T; Wood, P R; Szyszka, C; Bernard-Salas, J; van Loon, J Th

    2009-01-16

    Interstellar dust plays a crucial role in the evolution of galaxies. It governs the chemistry and physics of the interstellar medium. In the local universe, dust forms primarily in the ejecta from stars, but its composition and origin in galaxies at very early times remain controversial. We report observational evidence of dust forming around a carbon star in a nearby galaxy with a low abundance of heavy elements, 25 times lower than the solar abundance. The production of dust by a carbon star in a galaxy with such primitive abundances raises the possibility that carbon stars contributed carbonaceous dust in the early universe.

  12. Understanding and reducing statistical uncertainties in nebular abundance determinations

    CERN Document Server

    Wesson, R; Scicluna, P

    2012-01-01

    Whenever observations are compared to theories, an estimate of the uncertainties associated with the observations is vital if the comparison is to be meaningful. However, many determinations of temperatures, densities and abundances in photoionized nebulae do not quote the associated uncertainty. Those that do typically propagate the uncertainties using analytical techniques which rely on assumptions that generally do not hold. Motivated by this issue, we have developed NEAT (Nebular Empirical Analysis Tool), a new code for calculating chemical abundances in photoionized nebulae. The code carries out an analysis of lists of emission lines using long-established techniques to estimate the amount of interstellar extinction, calculate representative temperatures and densities, compute ionic abundances from both collisionally excited lines and recombination lines, and finally to estimate total elemental abundances using an ionization correction scheme. NEAT uses a Monte Carlo technique to robustly propagate uncer...

  13. Relative abundance of desert tortoises on the Nevada Test Site

    Energy Technology Data Exchange (ETDEWEB)

    Rautenstrauch, K.R.; O`Farrell, T.P.

    1993-12-31

    Seven hundred fifty-nine transects having a total length of 1,191 km were walked during 1981--1986 to determine the distribution and relative abundance of desert tortoises (Gopherus agassizii) on the Nevada Test Site (NTS). The abundance of tortoises on NTS was low to very low relative to other populations in the Mojave Desert. Sign of tortoises was found from 880 to 1,570 m elevation and was more abundant above 1,200 m than has been reported previously for Nevada. Tortoises were more abundant on NTS on the upper alluvial fans and slopes of mountains than in valley bottoms. They also were more common on or near limestone and dolomite mountains than on mountains of volcanic origin.

  14. FAMA: An automatic code for stellar parameter and abundance determination

    CERN Document Server

    Magrini, Laura; Friel, Eileen; Spina, Lorenzo; Jacobson, Heather; Cantat-Gaudin, Tristan; Donati, Paolo; Baglioni, Roberto; Maiorca, Enrico; Bragaglia, Angela; Sordo, Rosanna; Vallenari, Antonella

    2013-01-01

    The large amount of spectra obtained during the epoch of extensive spectroscopic surveys of Galactic stars needs the development of automatic procedures to derive their atmospheric parameters and individual element abundances. Starting from the widely-used code MOOG by C. Sneden, we have developed a new procedure to determine atmospheric parameters and abundances in a fully automatic way. The code FAMA (Fast Automatic MOOG Analysis) is presented describing its approach to derive atmospheric stellar parameters and element abundances. The code, freely distributed, is written in Perl and can be used on different platforms. The aim of FAMA is to render the computation of the atmospheric parameters and abundances of a large number of stars using measurements of equivalent widths as automatic and as independent of any subjective approach as possible. It is based on the simultaneous search for three equilibria: excitation equilibrium, ionization balance, and the relationship between \\fei\\ and the reduced equivalent ...

  15. Determining the forsterite abundance of the dust around AGB stars

    CERN Document Server

    de Vries, B L; Waters, L B F M; Blommaert, J A D L; Kemper, F

    2010-01-01

    We present a diagnostic tool to determine the forsterite abundance of the dust ejected by AGB stars. Our method is based on a comparison between the observed strength of spectral bands of forsterite and model calculations. We show that the 11.3 {\\mu}m forsterite band is a robust indicator of the forsterite abundance of the current mass-loss period for AGB stars with an optically thick dust shell. The 33.6 {\\mu}m band of forsterite is sensitive to changes in the density and the geometry of the emitting dust shell, and so a less robust indicator. We apply this method to six high mass-loss rate AGB stars, showing that AGB stars can have forsterite abundances of 12% by mass and higher, which is more than the previously found maximum abundance of 5%.

  16. THE ATOMIC WEIGHTS COMMISSION AND ISOTOPIC ABUNDANCE RATIO DETERMINATIONS.

    Energy Technology Data Exchange (ETDEWEB)

    HOLDEN, N.E.

    2005-08-07

    Following Thomson's discovery of stable isotopes in non-radioactive chemical elements, the derivation of atomic weight values from mass spectrometric measurements of isotopic abundance ratios moved very slowly. Forty years later, only 3 1/2 % of the recommended values were based on mass spectrometric measurements and only 38% in the first half century. It might be noted that two chemical elements (tellurium and mercury) are still based on chemical measurements, where the atomic weight value calculated from the relative isotopic abundance measurement either agrees with the value from the chemical measurement or the atomic weight value calculated from the relative isotopic abundance measurement falls within the uncertainty of the chemical measurement of the atomic weight. Of the 19 chemical elements, whose atomic weight is based on non-corrected relative isotopic abundance measurements, five of these are two isotope systems (indium, iridium, lanthanum, lutetium and tantalum) and one is a three-isotope system (oxygen).

  17. Unit scale abundance and habitat data - Calawah River Riverscape Study

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The objective of this study was to identify the patterns of juvenile salmonid distribution and relative abundance in relation to habitat correlates. It is the first...

  18. Abundance of Asymmetric Dark Matter in Brane World Cosmology

    Science.gov (United States)

    Abdusattar, Haximjan; Iminniyaz, Hoernisa

    2016-09-01

    Relic abundance of asymmetric Dark Matter particles in brane world cosmological scenario is investigated in this article. Hubble expansion rate is enhanced in brane world cosmology and it affects the relic abundance of asymmetric Dark Matter particles. We analyze how the relic abundance of asymmetric Dark Matter is changed in this model. We show that in such kind of nonstandard cosmological scenario, indirect detection of asymmetric Dark Matter is possible if the cross section is small enough which let the anti-particle abundance kept in the same amount with the particle. We show the indirect detection signal constraints can be used to such model only when the cross section and the 5-dimensional Planck mass scale are in appropriate values. Supported by the National Natural Science Foundation of China under Grant No. 11365022

  19. The RAVE Catalog of Stellar Elemental Abundances: First Data Release

    NARCIS (Netherlands)

    Boeche, C.; Siebert, A.; Williams, M.; de Jong, R. S.; Steinmetz, M.; Fulbright, J. P.; Ruchti, G. R.; Bienaymé, O.; Bland-Hawthorn, J.; Campbell, R.; Freeman, K. C.; Gibson, B. K.; Gilmore, G.; Grebel, E. K.; Helmi, A.; Munari, U.; Navarro, J. F.; Parker, Q. A.; Reid, W.; Seabroke, G. M.; Siviero, A.; Watson, F. G.; Wyse, R. F. G.; Zwitter, T.

    2011-01-01

    We present chemical elemental abundances for 36,561 stars observed by the RAdial Velocity Experiment (RAVE), an ambitious spectroscopic survey of our Galaxy at Galactic latitudes |b| > 25° and with magnitudes in the range 9

  20. A Comparison of Stellar Elemental Abundance Techniques and Measurements

    CERN Document Server

    Hinkel, Natalie R; Pagano, Michael D; Desch, Steven J; Anbar, Ariel D; Adibekyan, Vardan; Blanco-Cuaresma, Sergi; Carlberg, Joleen K; Mena, Elisa Delgado; Liu, Fan; Nordlander, Thomas; Sousa, Sergio G; Korn, Andreas; Gruyters, Pieter; Heiter, Ulrike; Jofre, Paula; Santos, Nuno C; Soubiran, Caroline

    2016-01-01

    Stellar elemental abundances are important for understanding the fundamental properties of a star or stellar group, such as age and evolutionary history, as well as the composition of an orbiting planet. However, as abundance measurement techniques have progressed, there has been little standardization between individual methods and their comparisons. As a result, different stellar abundance procedures determine measurements that vary beyond quoted error for the same elements within the same stars (Hinkel et al. 2014). The purpose of this paper is to better understand the systematic variations between methods and offer recommendations for producing more accurate results in the future. We have invited a number of participants from around the world (Australia, Portugal, Sweden, Switzerland, and USA) to calculate ten element abundances (C, O, Na, Mg, Al, Si, Fe, Ni, Ba, and Eu) using the same stellar spectra for four stars (HD361, HD10700, HD121504, HD202206). Each group produced measurements for each of the sta...

  1. Solar models with new low-metal abundances

    CERN Document Server

    Yang, Wuming

    2016-01-01

    In the last decade, the photospheric abundances of the Sun had been revised several times by many observers. The standard solar models (SSM) constructed with the new low-metal abundances disagree with helioseismic results and detected neutrino fluxes. The solar model problem has been puzzled some stellar physicists for more than ten years. Rotation, enhanced diffusion, convection overshoot, and magnetic fields are used to reconcile the new abundances with helioseismology. The \\textbf{too} low-helium \\textbf{subsurface abundance} in enhanced diffusion models can be improved by the mixing caused by rotation and magnetic fields. The problem of the depth of the convective zone in rotating models can be resolved by convection overshoot. Consequently the Asplund-Grevesse-Sauval rotation model including overshooting (AGSR) reproduces the seismically inferred sound-speed and density profiles, and the convection zone depth as well as the Grevesse and Sauval (GS98) model computed before. But this model fails to reprodu...

  2. Whooping Crane Winter Abundance Survey Protocol Aransas National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This protocol is primarily designed to provide a mechanism for monitoring trends in whooping crane abundance on their wintering grounds along the Texas gulf coast....

  3. Relative Abundance of Breeding Birds in the Dismal Swamp 1982

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — To obtain an idea of the relative abundance of breeding birds in the predominant mixed swamp hardwoods forest of the Dismal Swamp in southeastern Virginia, a...

  4. Abundances of PNe in the Outer Disk of M31

    CERN Document Server

    Kwitter, Karen B; Balick, Bruce; Henry, R B C

    2012-01-01

    We present spectroscopic observations and chemical abundances of 16 planetary nebulae (PNe) in the outer disk of M31. The [O III] 4363 line is detected in all objects, allowing a direct measurement of the nebular temperature essential for accurate abundance determinations. Our results show that the abundances in these M31 PNe display the same correlations and general behaviors as Type II PNe in the Milky Way Galaxy. We also calculate photoionization models to derive estimates of central star properties. From these we infer that our sample PNe, all near the peak of the Planetary Nebula Luminosity Function, originated from stars near 2 M_sun. Finally, under the assumption that these PNe are located in M31's disk, we plot the oxygen abundance gradient, which appears shallower than the gradient in the Milky Way.

  5. A Differential Abundance Analysis of HD219175 A and B

    Institute of Scientific and Technical Information of China (English)

    Hua-Wei Zhang; Gang Zhao

    2005-01-01

    The abundances of the wide binary pair HD 219175 A and B are determined and compared using a line-by-line differential analysis. No evidence for difference has been found in the abundances of Fe, O, Na, Mg, Al, Si, K, Ca, Sc,Ti, V, Cr, Mn, Ni, Cu and Ba. Our results support a physical relation between the two components of HD 219175.

  6. Literature survey of isotopic abundance data for 1987-1989

    Energy Technology Data Exchange (ETDEWEB)

    Holden, N.E. (Brookhaven National Lab., Upton, NY (USA))

    1989-08-09

    I have compiled all of the data on isotopic abundance measurements and their variation in nature for the time period since the last General Assembly. Most of the data deals with the variations in the abundances as given by per mil deviations from some standard. As such, they are not of major interest to the Atomic Weights Commission. However, there were some measurements which are of general interest in this list.

  7. The Open Cluster Chemical Abundances from Spanish Observatories survey (OCCASO)

    CERN Document Server

    Carrera, R; Balaguer-Núñez, L; Jordi, C; Pancino, E; Allende-Prieto, C; Blanco-Cuaresma, S; Mártinez-Vázquez, C E; Murabito, S; del Pino, A; Aparicio, A; Gallart, C; Recio-Blanco, A

    2014-01-01

    We present the motivation, design and current status of the Open Cluster Chemical Abundances from Spanish Observatories survey (OCCASO). Using the high resolution spectroscopic facilities available at Spanish observatories, OCCASO will derive chemical abundances in a sample of 20 to 25 open clusters older than 0.5 Gyr. This sample will be used to study in detail the formation and evolution of the Galactic disc using open clusters as tracers.

  8. Harbour porpoise Phocoena phocoena abundance in the southwestern Baltic Sea

    OpenAIRE

    Scheidat, M.; Gilles, A.; Kock, K. H.; Siebert, U

    2008-01-01

    Harbour porpoise Phocoena phocoena is the only cetacean species resident in the Baltic Sea. At least 2 different subpopulations occur in this area, with a presumed demarcation line in the western Baltic Sea. Aerial surveys were conducted during different seasons in the years 2002 to 2006, to obtain estimates of porpoise abundance for the southwestern Baltic. Within the survey area, 3 strata were defined. In total, 46 surveys were completed for these strata. Abundance estimates and correspondi...

  9. New Abundant Microbial Groups in Aquatic Hypersaline Environments

    OpenAIRE

    Ghai, Rohit; Pašić, Lejla; Fernández González, Ana Beatriz; Martín Cuadrado, Ana Belén; Megumi Mizuno, Carolina; McMahon, Katherine D.; Papke, R Thane; Stepanauskas, Ramunas; Rodríguez Brito, Beltrán; Rohwer, Forest; Sánchez-Porro Álvarez, Cristina; Ventosa Ucero, Antonio; Rodríguez Valera, Francisco

    2011-01-01

    We describe the microbiota of two hypersaline saltern ponds, one of intermediate salinity (19%) and a NaCl saturated crystallizer pond (37%) using pyrosequencing. The analyses of these metagenomes (nearly 784 Mb) reaffirmed the vast dominance of Haloquadratum walsbyi but also revealed novel, abundant and previously unsuspected microbial groups. We describe for the first time, a group of low GC Actinobacteria, related to freshwater Actinobacteria, abundant in low and intermediate salinities. M...

  10. Beryllium, Lithium and Oxygen Abundances in F-type Stars

    CERN Document Server

    García-López, R J; Pérez de Taoro, M R; Casares, C; Rasilla, J L; Rebolo, R; Allende-Prieto, C

    1997-01-01

    Beryllium and oxygen abundances have been derived in a sample of F-type field stars for which lithium abundances had been measured previously, with the aim of obtaining observational constraints to discriminate between the different mixing mechanisms proposed. Mixing associated with the transport of angular momentum in the stellar interior and internal gravity waves within the framework of rotating evolutionary models, appear to be promising ways to explain the observations.

  11. The Open Cluster Chemical Abundances from Spanish Observatories Survey (OCCASO)

    Science.gov (United States)

    Carrera, R.; Casamiquela, L.; Balaguer-Núñez, L.; Jordi, C.; Pancino, E.; Allende-Prieto, C.; Blanco-Cuaresma, S.; Martínez-Vázquez, C. E.; Murabito, S.; del Pino, A.; Aparicio, A.; Gallart, C.; Recio-Blanco, A.

    2016-10-01

    We present the motivation, design and current status of the Open Cluster Chemical Abundances from Spanish Observatories survey (OCCASO). Using the high resolution spectroscopic facilities available at Spanish observatories, OCCASO will derive chemical abundances in a sample of 20 to 25 OCs older than 0.5 Gyr. This sample will be used to study in detail the formation and evolution of the Galactic disk using OCs as tracers.

  12. Causality of the relationship between geographic distribution and species abundance

    DEFF Research Database (Denmark)

    Borregaard, Michael Krabbe; Rahbek, Carsten

    2010-01-01

    The positive relationship between a species' geographic distribution and its abundance is one of ecology's most well-documented patterns, yet the causes behind this relationship remain unclear. Although many hypotheses have been proposed to account for distribution-abundance relationships none ha......, in a framework that facilitates a comparison between them. We identify and discuss the central factors governing the individual mechanisms, and elucidate their effect on empirical patterns....

  13. Chemical abundances from planetary nebulae in local spiral galaxies

    CERN Document Server

    Richer, M G

    2015-01-01

    While the chemical abudances observed in bright planetary nebulae in local spiral galaxies are less varied than their counterparts in dwarfs, they provide new insight. Their helium abundances are typically enriched by less than 50\\% compared to the primordial abundance. Nitrogen abundances always show some level of secondary enrichment, but the absolute enrichment is not extreme. In particular, type I PNe are rare among the bright PNe in local spirals. The oxygen and neon abundances are very well correlated and follow the relation between these abundances observed in star-forming galaxies, implying that either the progenitor stars of these PNe modify neither abundance substantially or that they modify both to maintain the ratio (not predicted by theory). According to theory, these results imply that the progenitor stars of bright PNe in local spirals have masses of about $2\\,\\mathrm M_{\\odot}$ or less. If so, the progenitors of these PNe have substantial lifetimes that allow us to use them to study the recent...

  14. Chromospheric Models and the Oxygen Abundance in Giant Stars

    Science.gov (United States)

    Dupree, A. K.; Avrett, E. H.; Kurucz, R. L.

    2016-04-01

    Realistic stellar atmospheric models of two typical metal-poor giant stars in Omega Centauri, which include a chromosphere (CHR), influence the formation of optical lines of O i: the forbidden lines (λ6300, λ6363) and the infrared triplet (λλ7771-7775). One-dimensional semi-empirical non-local thermodynamic equilibrium (LTE) models are constructed based on observed Balmer lines. A full non-LTE formulation is applied for evaluating the line strengths of O i, including photoionization by the Lyman continuum and photoexcitation by Lyα and Lyβ. Chromospheric models (CHR) yield forbidden oxygen transitions that are stronger than those in radiative/convective equilibrium (RCE) models. The triplet oxygen lines from high levels also appear stronger than those produced in an RCE model. The inferred oxygen abundance from realistic CHR models for these two stars is decreased by factors of ˜3 as compared to values derived from RCE models. A lower oxygen abundance suggests that intermediate-mass AGB stars contribute to the observed abundance pattern in globular clusters. A change in the oxygen abundance of metal-poor field giants could affect models of deep mixing episodes on the red giant branch. Changes in the oxygen abundance can impact other abundance determinations that are critical to astrophysics, including chemical tagging techniques and galactic chemical evolution.

  15. Element Abundances in Solar Energetic Particles and the Solar Corona

    CERN Document Server

    Reames, Donald V

    2013-01-01

    This is a study of abundances of the elements He, C, N, O, Ne, Mg, Si, S, Ar, Ca, and Fe in solar energetic particles (SEPs) in the 2 - 15 MeV amu-1 region measured on the Wind spacecraft during 54 large SEP events occurring between November 1994 and June 2012. The origin of most of the temporal and spatial variations in abundances of the heavier elements lies in rigidity-dependent scattering during transport of the particles away from the site of acceleration at shock waves driven out from the Sun by coronal mass ejections (CMEs). Variation in the abundance of Fe is correlated with the Fe spectral index, as expected from scattering theory but not previously noted. Clustering of Fe abundances during the "reservoir" period, late in SEP events, is also newly reported. Transport-induced enhancements in one region are balanced by depletions in another, thus, averaging over these variations produces SEP abundances that are energy independent, confirms previous SEP abundances in this energy region, and provides a c...

  16. Carbon and Strontium Abundances of Metal-Poor Stars

    CERN Document Server

    Lai, David K; Bolte, Michael; Lucatello, Sara

    2007-01-01

    We present carbon and strontium abundances for 100 metal-poor stars measured from R$\\sim $7000 spectra obtained with the Echellette Spectrograph and Imager at the Keck Observatory. Using spectral synthesis of the G-band region, we have derived carbon abundances for stars ranging from [Fe/H]$=-1.3$ to [Fe/H]$=-3.8$. The formal errors are $\\sim 0.2$ dex in [C/Fe]. The strontium abundance in these stars was measured using spectral synthesis of the resonance line at 4215 {\\AA}. Using these two abundance measurments along with the barium abundances from our previous study of these stars, we show it is possible to identify neutron-capture-rich stars with our spectra. We find, as in other studies, a large scatter in [C/Fe] below [Fe/H]$ = -2$. Of the stars with [Fe/H]$<-2$, 9$\\pm$4% can be classified as carbon-rich metal-poor stars. The Sr and Ba abundances show that three of the carbon-rich stars are neutron-capture-rich, while two have normal Ba and Sr. This fraction of carbon enhanced stars is consistent with ...

  17. The abundance of silicon in the solar atmosphere

    Science.gov (United States)

    Shaltout, A. M. K.; Beheary, M. M.; Bakry, A.; Ichimoto, K.

    2013-04-01

    High-resolution solar spectra were used to determine the silicon abundance (εSi) content by comparison with Si line synthesis relying on realistic hydrodynamical simulations of the solar surface convection, as 3D inhomogeneous model of the solar photosphere. Based on a set of 19 Si I and 2 Si II lines, with accurate transition probabilities as well as accurate observational data available, the solar photospheric Si abundance has been determined to be log εSi(3D) = 7.53 ± 0.07. Here we derive the photospheric silicon abundance taking into account non-LTE effects based on 1D solar model, the non-LTE abundance value we find is log εSi (1D) = 7.52 ± 0.08. The photospheric Si abundance agrees well with the results of Asplund and more recently published by Asplund et al. relative to previous 3D-based abundances, the consistency given that the quoted errors here are (±0.07 dex).

  18. Abundance profiles and cool cores in galaxy groups

    CERN Document Server

    Johnson, Ria; Ponman, Trevor J; Rasmussen, Jesper; Sanderson, Alastair J R

    2011-01-01

    Using data from the Two Dimensional XMM-Newton Group Survey (2dXGS), we have examined the abundance profile properties of both cool core (CC) and non cool core (NCC) galaxy groups. The ten NCC systems in our sample represent a population which to date has been poorly studied in the group regime. Fitting the abundance profiles as a linear function of log radius, we find steep abundance gradients in cool core (CC) systems, with a slope of -0.54+/-0.07. In contrast, non cool core (NCC) groups have profiles consistent with uniform metallicity. Many CC groups show a central abundance dip or plateau, and we find evidence for anticorrelation between the core abundance gradient and the 1.4 GHz radio power of the brightest group galaxy (BGG) in CC systems. This may indicate the effect of AGN-driven mixing within the central ~0.1r_500. It is not possible to discern whether such behaviour is present in the NCC groups, due to the small and diverse sample with the requisite radio data. The lack of strong abundance gradien...

  19. CHROMOSPHERIC MODELS AND THE OXYGEN ABUNDANCE IN GIANT STARS

    Energy Technology Data Exchange (ETDEWEB)

    Dupree, A. K.; Avrett, E. H.; Kurucz, R. L., E-mail: dupree@cfa.harvard.edu [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA 02138 (United States)

    2016-04-10

    Realistic stellar atmospheric models of two typical metal-poor giant stars in Omega Centauri, which include a chromosphere (CHR), influence the formation of optical lines of O i: the forbidden lines (λ6300, λ6363) and the infrared triplet (λλ7771−7775). One-dimensional semi-empirical non-local thermodynamic equilibrium (LTE) models are constructed based on observed Balmer lines. A full non-LTE formulation is applied for evaluating the line strengths of O i, including photoionization by the Lyman continuum and photoexcitation by Lyα and Lyβ. Chromospheric models (CHR) yield forbidden oxygen transitions that are stronger than those in radiative/convective equilibrium (RCE) models. The triplet oxygen lines from high levels also appear stronger than those produced in an RCE model. The inferred oxygen abundance from realistic CHR models for these two stars is decreased by factors of ∼3 as compared to values derived from RCE models. A lower oxygen abundance suggests that intermediate-mass AGB stars contribute to the observed abundance pattern in globular clusters. A change in the oxygen abundance of metal-poor field giants could affect models of deep mixing episodes on the red giant branch. Changes in the oxygen abundance can impact other abundance determinations that are critical to astrophysics, including chemical tagging techniques and galactic chemical evolution.

  20. New calibrations for abundance determinations in HII regions

    CERN Document Server

    Pilyugin, L S

    2016-01-01

    Simple relations for deriving the oxygen abundance in HII regions with intensities of the three strong emission lines R_2, R_3, and N_2 (R calibration) or S_2, R_3, and N_2 (S calibration) in their spectra are suggested. A sample of 313 reference HII regions of the counterpart method is used as calibrating data points. Relations for the determination of nitrogen abundances, the R calibration, are also constructed. We find that the oxygen and nitrogen abundances in high-metallicity HII regions can be estimated using the intensities of the two strong lines R_2 and N_2 (or S_2 and N_2 for oxygen) only. The corresponding two-dimensional relations are provided. There are considerable advantages of the suggested calibration relations as compared to the existing ones. First, the oxygen and nitrogen abundances estimated through the suggested calibrations agree with the Te-based abundances within ~0.1 dex over the whole metallicity range, i.e., the relative accuracy of the calibration-based abundances is 0.1 dex. Alth...

  1. Global abundance of planktonic heterotrophic protists in the deep ocean.

    Science.gov (United States)

    Pernice, Massimo C; Forn, Irene; Gomes, Ana; Lara, Elena; Alonso-Sáez, Laura; Arrieta, Jesus M; del Carmen Garcia, Francisca; Hernando-Morales, Victor; MacKenzie, Roy; Mestre, Mireia; Sintes, Eva; Teira, Eva; Valencia, Joaquin; Varela, Marta M; Vaqué, Dolors; Duarte, Carlos M; Gasol, Josep M; Massana, Ramon

    2015-03-01

    The dark ocean is one of the largest biomes on Earth, with critical roles in organic matter remineralization and global carbon sequestration. Despite its recognized importance, little is known about some key microbial players, such as the community of heterotrophic protists (HP), which are likely the main consumers of prokaryotic biomass. To investigate this microbial component at a global scale, we determined their abundance and biomass in deepwater column samples from the Malaspina 2010 circumnavigation using a combination of epifluorescence microscopy and flow cytometry. HP were ubiquitously found at all depths investigated down to 4000 m. HP abundances decreased with depth, from an average of 72±19 cells ml(-1) in mesopelagic waters down to 11±1 cells ml(-1) in bathypelagic waters, whereas their total biomass decreased from 280±46 to 50±14 pg C ml(-1). The parameters that better explained the variance of HP abundance were depth and prokaryote abundance, and to lesser extent oxygen concentration. The generally good correlation with prokaryotic abundance suggested active grazing of HP on prokaryotes. On a finer scale, the prokaryote:HP abundance ratio varied at a regional scale, and sites with the highest ratios exhibited a larger contribution of fungi molecular signal. Our study is a step forward towards determining the relationship between HP and their environment, unveiling their importance as players in the dark ocean's microbial food web.

  2. Mitochondrial abundance and efficiency contribute to lean color of dark cutting beef.

    Science.gov (United States)

    McKeith, Russell O; King, D Andy; Grayson, Adria L; Shackelford, Steven D; Gehring, Kerri B; Savell, Jeffrey W; Wheeler, Tommy L

    2016-06-01

    Beef carcasses exhibiting four levels of dark cutting severity (DCS): Severe, Moderate, Mild, and Shady were compared to Control carcasses to investigate biochemical traits contributing to the dark cutting condition. Color attributes of Longissimus lumborum (LL) were measured after grading and during simulated retail display. Mitochondrial abundance and efficiency, bloomed oxymyoglobin, reducing ability, glycolytic potential, myoglobin concentration, and protein solubility and oxidation were determined. Glycolytic potential and lactate concentrations decreased (Pdark cutting condition is associated with greater oxidative metabolism coupled with less efficient mitochondria resulting in depletion of glycogen during stress.

  3. A Search for Stars of Very Low Metal Abundance. VI. Detailed Abundances of 313 Metal-Poor Stars

    CERN Document Server

    Roederer, Ian U; Thompson, Ian B; Shectman, Stephen A; Sneden, Christopher; Burley, Gregory S; Kelson, Daniel D

    2014-01-01

    We present radial velocities, equivalent widths, model atmosphere parameters, and abundances or upper limits for 53 species of 48 elements derived from high resolution optical spectroscopy of 313 metal-poor stars. A majority of these stars were selected from the metal-poor candidates of the HK Survey of Beers, Preston, and Shectman. We derive detailed abundances for 61% of these stars for the first time. Spectra were obtained during a 10-year observing campaign using the Magellan Inamori Kyocera Echelle spectrograph on the Magellan Telescopes at Las Campanas Observatory, the Robert G. Tull Coude Spectrograph on the Harlan J. Smith Telescope at McDonald Observatory, and the High Resolution Spectrograph on the Hobby-Eberly Telescope at McDonald Observatory. We perform a standard LTE abundance analysis using MARCS model atmospheres, and we apply line-by-line statistical corrections to minimize systematic abundance differences arising when different sets of lines are available for analysis. We identify several ab...

  4. Combination of hydrogel nanoparticles and proteomics to reveal secreted proteins associated with decidualization of human uterine stromal cells

    Directory of Open Access Journals (Sweden)

    Stephens Andrew N

    2011-09-01

    Full Text Available Abstract Background Identification of secreted proteins of low abundance is often limited by abundant and high molecular weight (MW proteins. We have optimised a procedure to overcome this limitation. Results Low MW proteins in the conditioned media of cultured cells were first captured using dual-size exclusion/affinity hydrogel nanoparticles and their identities were then revealed by proteomics. Conclusions This technique enables the analysis of secreted proteins of cultured cells low MW and low abundance.

  5. A search for stars of very low metal abundance. VI. Detailed abundances of 313 metal-poor stars

    Energy Technology Data Exchange (ETDEWEB)

    Roederer, Ian U.; Preston, George W.; Thompson, Ian B.; Shectman, Stephen A.; Burley, Gregory S.; Kelson, Daniel D. [Carnegie Observatories, 813 Santa Barbara Street, Pasadena, CA 91101 (United States); Sneden, Christopher, E-mail: iur@umich.edu [Department of Astronomy, University of Texas at Austin, 1 University Station, C1400, Austin, TX 78712 (United States)

    2014-06-01

    We present radial velocities, equivalent widths, model atmosphere parameters, and abundances or upper limits for 53 species of 48 elements derived from high resolution optical spectroscopy of 313 metal-poor stars. A majority of these stars were selected from the metal-poor candidates of the HK Survey of Beers, Preston, and Shectman. We derive detailed abundances for 61% of these stars for the first time. Spectra were obtained during a 10 yr observing campaign using the Magellan Inamori Kyocera Echelle spectrograph on the Magellan Telescopes at Las Campanas Observatory, the Robert G. Tull Coudé Spectrograph on the Harlan J. Smith Telescope at McDonald Observatory, and the High Resolution Spectrograph on the Hobby-Eberly Telescope at McDonald Observatory. We perform a standard LTE abundance analysis using MARCS model atmospheres, and we apply line-by-line statistical corrections to minimize systematic abundance differences arising when different sets of lines are available for analysis. We identify several abundance correlations with effective temperature. A comparison with previous abundance analyses reveals significant differences in stellar parameters, which we investigate in detail. Our metallicities are, on average, lower by ≈0.25 dex for red giants and ≈0.04 dex for subgiants. Our sample contains 19 stars with [Fe/H] ≤–3.5, 84 stars with [Fe/H] ≤–3.0, and 210 stars with [Fe/H] ≤–2.5. Detailed abundances are presented here or elsewhere for 91% of the 209 stars with [Fe/H] ≤–2.5 as estimated from medium resolution spectroscopy by Beers, Preston, and Shectman. We will discuss the interpretation of these abundances in subsequent papers.

  6. Potential Health Effects of Enzymatic Protein Hydrolysates from Chlorella vulgaris

    OpenAIRE

    2016-01-01

    Background and Objective: Chlorella vulgaris is a multi-cellular edible algal species with abundant proteins. Extraction of high value protein fractions for pharmaceutical and nutritional applications can significantly increase the commercial value of microalga biomasses. There is no known report on the anticancer peptides derived from the Chlorella vulgaris abundant protein.Materials and Methods: This study examined the antimicrobial and anticancer effects of peptides from a hydrolyzed Chlor...

  7. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers......, are reported. The aim is to depict how the elucidation of the interplay of structures requires the interplay of methods....

  8. Spatial patterns in the abundance of the coastal horned lizard

    Science.gov (United States)

    Fisher, Robert N.; Suarez, Andrew V.; Case, Ted J.

    2002-01-01

    Coastal horned lizards (   Phrynosoma coronatum) have undergone severe declines in southern California and are a candidate species for state and federal listing under the Endangered Species Act. Quantitative data on their habitat use, abundance, and distribution are lacking, however. We investigated the determinants of abundance for coastal horned lizards at multiple spatial scales throughout southern California. Specifically, we estimated lizard distribution and abundance by establishing 256 pitfall trap arrays clustered within 21 sites across four counties. These arrays were sampled bimonthly for 2–3 years. At each array we measured 26 “local” site descriptors and averaged these values with other “regional” measures to determine site characteristics. Our analyses were successful at identifying factors within and among sites correlated with the presence and abundance of coastal horned lizards. These factors included the absence of the invasive Argentine ant (  Linepithema humile) (and presence of native ant species eaten by the lizards), the presence of chaparral community plants, and the presence of sandy substrates. At a regional scale the relative abundance of Argentine ants was correlated with the relative amount of developed edge around a site. There was no evidence for spatial autocorrelation, even at the scale of the arrays within sites, suggesting that the determinants of the presence or absence and abundance of horned lizard can vary over relatively small spatial scales ( hundreds of meters). Our results suggest that a gap-type approach may miss some of the fine-scale determinants of species abundance in fragmented habitats.

  9. Songbird abundance and parasitism differ between urban and rural shrublands.

    Science.gov (United States)

    Burhans, Dirk E; Thompson, Frank R

    2006-02-01

    Many studies have examined differences in avian community composition between urban and rural habitats, but few, if any, have looked at nesting success of urban shrubland birds in a replicated fashion while controlling for habitat. We tested factors affecting nest survival, parasitism by the Brown-headed Cowbird (Molothrus ater), and species abundance in shrubland habitat in rural and urban landscapes. We found no support for our hypothesis that nest survival was lower in urban landscapes, but strong support for the hypothesis that survival increased with nest height. We found strong support for our hypothesis that cowbird parasitism was greater in urban than rural landscapes; parasitism in urban sites was at least twice that of rural sites. We found strong support for an urban landscape effect on abundance for several species; Northern Cardinal (Cardinalis cardinalis) and Brown-headed Cowbirds were more abundant in urban landscapes, whereas Field Sparrow (Spizella pusilla) and Blue-winged Warbler (Vermivora pinus) were more abundant in rural sites. There was support for lower abundances of Blue-gray Gnatcatcher (Polioptila caerulea) and Indigo Bunting (Passerina cyanea) with increased housing density. For six other species, edge and trail density or vegetation parameters best explained abundance. Lower abundances and greater parasitism in habitat patches in urban landscapes are evidence that, for some species, these urban landscapes do not fulfill the same role as comparable habitats in rural landscapes. Regional bird conservation planning and local habitat management in urban landscapes may need to consider these effects in efforts to sustain bird populations at regional and local scales.

  10. Change in avian abundance predicted from regional forest inventory data

    Science.gov (United States)

    Twedt, Daniel J.; Tirpak, John M.; Jones-Farrand, D. Todd; Thompson, Frank R.; Uihlein, William B.; Fitzgerald, Jane A.

    2010-01-01

    An inability to predict population response to future habitat projections is a shortcoming in bird conservation planning. We sought to predict avian response to projections of future forest conditions that were developed from nationwide forest surveys within the Forest Inventory and Analysis (FIA) program. To accomplish this, we evaluated the historical relationship between silvicolous bird populations and FIA-derived forest conditions within 25 ecoregions that comprise the southeastern United States. We aggregated forest area by forest ownership, forest type, and tree size-class categories in county-based ecoregions for 5 time periods spanning 1963-2008. We assessed the relationship of forest data with contemporaneous indices of abundance for 24 silvicolous bird species that were obtained from Breeding Bird Surveys. Relationships between bird abundance and forest inventory data for 18 species were deemed sufficient as predictive models. We used these empirically derived relationships between regional forest conditions and bird populations to predict relative changes in abundance of these species within ecoregions that are anticipated to coincide with projected changes in forest variables through 2040. Predicted abundances of these 18 species are expected to remain relatively stable in over a quarter (27%) of the ecoregions. However, change in forest area and redistribution of forest types will likely result in changed abundance of some species within many ecosystems. For example, abundances of 11 species, including pine warbler (Dendroica pinus), brown-headed nuthatch (Sitta pusilla), and chuckwills- widow (Caprimulgus carolinensis), are projected to increase within more ecoregions than ecoregions where they will decrease. For 6 other species, such as blue-winged warbler (Vermivora pinus), Carolina wren (Thryothorus ludovicianus), and indigo bunting (Passerina cyanea), we projected abundances will decrease within more ecoregions than ecoregions where they will

  11. On the influence of the environment on galactic chemical abundances

    Science.gov (United States)

    Pilyugin, L. S.; Grebel, E. K.; Zinchenko, I. A.; Nefedyev, Y. A.; Mattsson, L.

    2017-02-01

    We examine the influence of the environment on the chemical abundances of late-type galaxies with masses of 109.1-1011 M⊙ using data from the Sloan Digital Sky Survey. We find that the environmental influence on galactic chemical abundances is strongest for galaxies with masses of 109.1-109.6 M⊙. The galaxies in the densest environments may exceed the average oxygen abundances by about ˜0.05 dex (the median value of the overabundances for 101 galaxies in the densest environments) and show higher abundances in nitrogen by about ˜0.1. The abundance excess decreases with increasing galaxy mass and with decreasing environmental density. Since only a small fraction of late-type galaxies is located in high-density environments, these galaxies do not have a significant influence on the general X/H-M relation. The metallicity-mass relations for isolated galaxies and for galaxies with neighbours are very similar. The mean shift of non-isolated galaxies around the metallicity-mass relation traced by the isolated galaxies is less than ˜0.01 dex for oxygen and less than ˜0.02 dex for nitrogen. The scatter in the galactic chemical abundances is large for any number of neighbour galaxies (at any environmental density), i.e. galaxies with both enhanced and reduced abundances can be found at any environmental density. This suggests that environmental effects do not play a key role in evolution of late-type galaxies, as was also concluded in some of the previous studies.

  12. Microbial abundance in surface ice on the Greenland Ice Sheet

    Directory of Open Access Journals (Sweden)

    Marek eStibal

    2015-03-01

    Full Text Available Measuring microbial abundance in glacier ice and identifying its controls is essential for a better understanding and quantification of biogeochemical processes in glacial ecosystems. However, cell enumeration of glacier ice samples is challenging due to typically low cell numbers and the presence of interfering mineral particles. We quantified for the first time the abundance of microbial cells in surface ice from geographically distinct sites on the Greenland Ice Sheet, using three enumeration methods: epifluorescence microscopy (EFM, flow cytometry (FCM and quantitative polymerase chain reaction (qPCR. In addition, we reviewed published data on microbial abundance in glacier ice and tested the three methods on artificial ice samples of realistic cell (10^2 – 10^7 cells ml-1 and mineral particle (0.1 – 100 mg/ml concentrations, simulating a range of glacial ice types, from clean subsurface ice to surface ice to sediment-laden basal ice. We then used multivariate statistical analysis to identify factors responsible for the variation in microbial abundance on the ice sheet. EFM gave the most accurate and reproducible results of the tested methodologies, and was therefore selected as the most suitable technique for cell enumeration of ice containing dust. Cell numbers in surface ice samples, determined by EFM, ranged from ca 2 x 10^3 to ca 2 x 10^6 cells/ml while dust concentrations ranged from 0.01 to 2 mg/ml. The lowest abundances were found in ice sampled from the accumulation area of the ice sheet and in samples affected by fresh snow; these samples may be considered as a reference point of the cell abundance of precipitants that are deposited on the ice sheet surface. Dust content was the most significant variable to explain the variation in the abundance data, which suggests a direct association between deposited dust particles and cells and/or by their provision of limited nutrients to microbial communities on the Greenland Ice Sheet.

  13. Urban warming drives insect pest abundance on street trees.

    Directory of Open Access Journals (Sweden)

    Emily K Meineke

    Full Text Available Cities profoundly alter biological communities, favoring some species over others, though the mechanisms that govern these changes are largely unknown. Herbivorous arthropod pests are often more abundant in urban than in rural areas, and urban outbreaks have been attributed to reduced control by predators and parasitoids and to increased susceptibility of stressed urban plants. These hypotheses, however, leave many outbreaks unexplained and fail to predict variation in pest abundance within cities. Here we show that the abundance of a common insect pest is positively related to temperature even when controlling for other habitat characteristics. The scale insect Parthenolecanium quercifex was 13 times more abundant on willow oak trees in the hottest parts of Raleigh, NC, in the southeastern United States, than in cooler areas, though parasitism rates were similar. We further separated the effects of heat from those of natural enemies and plant quality in a greenhouse reciprocal transplant experiment. P. quercifex collected from hot urban trees became more abundant in hot greenhouses than in cool greenhouses, whereas the abundance of P. quercifex collected from cooler urban trees remained low in hot and cool greenhouses. Parthenolecanium quercifex living in urban hot spots succeed with warming, and they do so because some demes have either acclimatized or adapted to high temperatures. Our results provide the first evidence that heat can be a key driver of insect pest outbreaks on urban trees. Since urban warming is similar in magnitude to global warming predicted in the next 50 years, pest abundance on city trees may foreshadow widespread outbreaks as natural forests also grow warmer.

  14. Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

    Science.gov (United States)

    Gorochowski, Thomas E.; Ignatova, Zoya; Bovenberg, Roel A.L.; Roubos, Johannes A.

    2015-01-01

    Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement. PMID:25765653

  15. Didehydrophenylalanine, an abundant modification in the beta subunit of plant polygalacturonases

    Science.gov (United States)

    Printz, Bruno; Gutsch, Annelie; Behr, Marc; Renaut, Jenny; Hausman, Jean-Francois

    2017-01-01

    The structure and the activity of proteins are often regulated by transient or stable post- translational modifications (PTM). Different from well-known, abundant modifications such as phosphorylation and glycosylation some modifications are limited to one or a few proteins across a broad range of related species. Although few examples of the latter type are known, the evolutionary conservation of these modifications and the enzymes responsible for their synthesis suggest an important physiological role. Here, the first observation of a new, fold-directing PTM is described. During the analysis of alfalfa cell wall proteins a -2Da mass shift was observed on phenylalanine residues in the repeated tetrapeptide FxxY of the beta-subunit of polygalacturonase. This modular protein is known to be involved in developmental and stress-responsive processes. The presence of this modification was confirmed using in-house and external datasets acquired by different commonly used techniques in proteome studies. Based on these analyses it was found that all identified phenylalanine residues in the sequence FxxY of this protein were modified to α,β-didehydro-Phe (ΔPhe). Besides showing the reproducible identification of ΔPhe in different species arguments that substantiate the fold-determining role of ΔPhe are given. PMID:28207764

  16. New aerial survey and hierarchical model to estimate manatee abundance

    Science.gov (United States)

    Langimm, Cahterine A.; Dorazio, Robert M.; Stith, Bradley M.; Doyle, Terry J.

    2011-01-01

    Monitoring the response of endangered and protected species to hydrological restoration is a major component of the adaptive management framework of the Comprehensive Everglades Restoration Plan. The endangered Florida manatee (Trichechus manatus latirostris) lives at the marine-freshwater interface in southwest Florida and is likely to be affected by hydrologic restoration. To provide managers with prerestoration information on distribution and abundance for postrestoration comparison, we developed and implemented a new aerial survey design and hierarchical statistical model to estimate and map abundance of manatees as a function of patch-specific habitat characteristics, indicative of manatee requirements for offshore forage (seagrass), inland fresh drinking water, and warm-water winter refuge. We estimated the number of groups of manatees from dual-observer counts and estimated the number of individuals within groups by removal sampling. Our model is unique in that we jointly analyzed group and individual counts using assumptions that allow probabilities of group detection to depend on group size. Ours is the first analysis of manatee aerial surveys to model spatial and temporal abundance of manatees in association with habitat type while accounting for imperfect detection. We conducted the study in the Ten Thousand Islands area of southwestern Florida, USA, which was expected to be affected by the Picayune Strand Restoration Project to restore hydrology altered for a failed real-estate development. We conducted 11 surveys in 2006, spanning the cold, dry season and warm, wet season. To examine short-term and seasonal changes in distribution we flew paired surveys 1–2 days apart within a given month during the year. Manatees were sparsely distributed across the landscape in small groups. Probability of detection of a group increased with group size; the magnitude of the relationship between group size and detection probability varied among surveys. Probability

  17. On the influence of the environment on galactic chemical abundances

    CERN Document Server

    Pilyugin, L S; Zinchenko, I A; Nefedyev, Y A; Mattsson, L

    2016-01-01

    We examine the influence of the environment on the chemical abundances of late-type galaxies with masses of 10^9.1 M_sun - 10^11 M_sun using data from the Sloan Digital Sky Survey(SDSS). We find that the environmental influence on galactic chemical abundances is strongest for galaxies with masses of 10^9.1 M_sun to 10^9.6 Msun. The galaxies in the densest environments may exceed the average oxygen abundances by about 0.05 dex (the median value of the overabundances for 101 galaxies in the densest environments) and show higher abundances in nitrogen by about 0.1. The abundance excess decreases with increasing galaxy mass and with decreasing environmental density. Since only a small fraction of late-type galaxies is located in high-density environments these galaxies do not have a significant influence on the general X/H - M relation. The metallicity - mass relations for isolated galaxies and for galaxies with neighbors are very similar. The mean shift of non-isolated galaxies around the metallicity - mass rela...

  18. Spectroscopic Study on the Beryllium Abundances of Red Giant Stars

    CERN Document Server

    Takeda, Yoichi

    2014-01-01

    An extensive spectroscopic study was carried out for the beryllium abundances of 200 red giants (mostly of late G and early K type), which were determined from the near-UV Be II 3131.066 line based on high-dispersion spectra obtained by Subaru/HDS, with an aim of investigating the nature of surface Be contents in these evolved giants; e.g., dependence upon stellar parameters, degree of peculiarity along with its origin and build-up timing. We found that Be is considerably deficient (to widely different degree from star to star) in the photosphere of these evolved giants by ~1-3 dex (or more) compared to the initial abundance. While the resulting Be abundances (A(Be)) appear to weakly depend upon T_eff, log g, [Fe/H], M, age, and v_sin i, this may be attributed to the metallicity dependence of A(Be) coupled with the mutual correlation between these stellar parameters, since such tendencies almost disappear in the metallicity-scaled Be abundance ([Be/Fe]). By comparing the Be abundances (as well as their correl...

  19. Detailed photospheric abundances of 28 Peg and HD 202240

    CERN Document Server

    Elmasli, Asli; Kilicoglu, Tolgahan; Unal, Kubraozge; Nasolo, Yahya; Albayrak, Berahitdin

    2015-01-01

    The atmospheric parameters and chemical abundances of two neglected A-type stars, 28 Peg and HD 202240, were derived using high resolution spectra obtained at the TUBITAK National Observatory. We determined the photospheric abundances of eleven elements for 28 Peg and twenty for HD 202240, using equivalent-width measurement and spectral synthesis methods. Their abundance patterns are in good agreement with those of chemically normal A-type stars having similar atmospheric parameters. We pinpoint the position of these stars on the H-R diagram and estimate their masses and ages as; $2.60\\pm0.10\\ M_\\odot$ and $650\\pm50\\ Myr$ for 28 Peg and $4.50\\pm0.09\\ M_\\odot$ and $150\\pm10\\ Myr$ for HD 202240. To compare our abundance determinations with those of stars having similar ages and atmospheric parameters, we select members of open clusters. We notice that our target stars exhibit similar abundance patterns with these members.

  20. Lithium isotopic abundances in metal-poor halo stars

    CERN Document Server

    Asplund, M; Nissen, P E; Primas, F; Smith, V V; Asplund, Martin; Lambert, David L.; Nissen, Poul Erik; Primas, Francesca; Smith, Verne V.

    2005-01-01

    Very high-quality spectra of 24 metal-poor halo dwarfs and subgiants have been acquired with ESO's VLT/UVES for the purpose of determining Li isotopic abundances. The derived 1D, non-LTE 7Li abundances from the LiI 670.8nm line reveal a pronounced dependence on metallicity but with negligible scatter around this trend. Very good agreement is found between the abundances from the LiI 670.8nm line and the LiI 610.4nm line. The estimated primordial 7Li abundance is $7Li/H = 1.1-1.5 x 10^-10, which is a factor of three to four lower than predicted from standard Big Bang nucleosynthesis with the baryon density inferred from the cosmic microwave background. Interestingly, 6Li is detected in nine of our 24 stars at the >2sigma significance level. Our observations suggest the existence of a 6Li plateau at the level of log 6Li = 0.8; however, taking into account predictions for 6Li destruction during the pre-main sequence evolution tilts the plateau such that the 6Li abundances apparently increase with metallicity. Ou...

  1. Correlation between lithium abundances and ages of solar twin stars

    CERN Document Server

    Carlos, Marilia; Melendez, Jorge

    2016-01-01

    We want to determine the lithium abundances of solar twin stars as a function of stellar age to provide constraints for stellar evolutions models and to investigate whether there is a connection between low Li abundance and the occurrence of planets. For a sample of 21 solar twins observed with the HARPS spectrograph at high spectral resolution (R~115.000) and very high signal-to-noise ratio (600 < S/N < 2400), precise lithium abundances were obtained by spectral synthesis of the LiI 6707.8 A line and compared to stellar ages, masses, and metallicities determined from a spectroscopic analysis of the same set of HARPS spectra. We show that for the large majority of the solar twins there is a strong correlation between lithium abundance and stellar age. As the age increases from 1 to 9 Gyr, the Li abundance decreases by a factor of ~ 50. The relation agrees fairly well with predictions from non-standard stellar evolution models of Li destruction at the bottom of the upper convection zone. Two stars deviat...

  2. Study on the Abundance Discrepancy Problem in the Magellanic Clouds

    CERN Document Server

    Cipriano, L Toribio San; Domínguez-Guzmán, G; García-Rojas, J

    2016-01-01

    We present chemical abundances of carbon (C) and oxygen (O) in the Large and Small Magellanic Clouds from deep and high-quality optical spectra of HII regions. The data have been taken using the Ultraviolet-Visual Echelle Spectrograph at the 8.2-m Very Large Telescope with the goal of detecting the faint CII and OII recombination lines. For all the objects of the sample, we determine C^2+ abundances from recombination lines and O^2+ abundances from recombination lines and collisionally excited lines. In addition, we calculate the abundance discrepancy factors (ADFs) for O^2+ and C^2+, as well as the O/H, C/H and C/O ratios. We study the behaviour of the ADF comparing the values obtained in the Magellanic Clouds with those obtained for other HII regions in different galaxies. We also compare the nebular and stellar abundances in two regions of the sample. Finally, we discuss the chemical evolution of the MCs through the O/H, C/H and C/O radial gradients and the changes of the C/O ratio as a function of O/H.

  3. Neutron-Capture Element Abundances in Magellanic Cloud Planetary Nebulae

    CERN Document Server

    Mashburn, A L; Madonna, S; Dinerstein, H L; Roederer, I U; Geballe, T

    2016-01-01

    We present near-infrared spectra of ten planetary nebulae (PNe) in the Large and Small Magellanic Clouds (LMC and SMC), acquired with the FIRE and GNIRS spectrometers on the 6.5-m Baade and 8.1-m Gemini South Telescopes, respectively. We detect Se and/or Kr emission lines in eight of these objects, the first detections of n-capture elements in Magellanic Cloud PNe. Our abundance analysis shows large s-process enrichments of Kr (0.6-1.3 dex) in the six PNe in which it was detected, and Se is enriched by 0.5-0.9 dex in five objects. We also estimate upper limits to Rb and Cd abundances in these objects. Our abundance results for the LMC are consistent with the hypothesis that PNe with 2--3 M$_{\\odot}$ progenitors dominate the bright end of the PN luminosity function in young gas-rich galaxies. We find no significant correlations between s-process enrichments and other elemental abundances, central star temperature, or progenitor mass, though this is likely due to our small sample size. We determine S abundances...

  4. Factors affecting Culicoides species composition and abundance in avian nests.

    Science.gov (United States)

    Martínez-de la Puente, J; Merino, S; Tomás, G; Moreno, J; Morales, J; Lobato, E; Talavera, S; Sarto I Monteys, V

    2009-08-01

    Mechanisms affecting patterns of vector distribution among host individuals may influence the population and evolutionary dynamics of vectors, hosts and the parasites transmitted. We studied the role of different factors affecting the species composition and abundance of Culicoides found in nests of the blue tit (Cyanistes caeruleus). We identified 1531 females and 2 males of 7 different Culicoides species in nests, with C. simulator being the most abundant species, followed by C. kibunensis, C. festivipennis, C. segnis, C. truncorum, C. pictipennis and C. circumscriptus. We conducted a medicationxfumigation experiment randomly assigning bird's nests to different treatments, thereby generating groups of medicated and control pairs breeding in fumigated and control nests. Medicated pairs were injected with the anti-malarial drug Primaquine diluted in saline solution while control pairs were injected with saline solution. The fumigation treatment was carried out using insecticide solution or water for fumigated and control nests respectively. Brood size was the main factor associated with the abundance of biting midges probably because more nestlings may produce higher quantities of vector attractants. In addition, birds medicated against haemoparasites breeding in non-fumigated nests supported a higher abundance of C. festivipennis than the rest of the groups. Also, we found that the fumigation treatment reduced the abundance of engorged Culicoides in both medicated and control nests, thus indicating a reduction of feeding success produced by the insecticide. These results represent the first evidence for the role of different factors in affecting the Culicoides infracommunity in wild avian nests.

  5. Chemical abundances of stars with brown-dwarf companions

    CERN Document Server

    Sánchez, D Mata; Israelian, G; Santos, N C; Sahlmann, J; Udry, S

    2014-01-01

    It is well-known that stars with giant planets are on average more metal-rich than stars without giant planets, whereas stars with detected low-mass planets do not need to be metal-rich. With the aim of studying the weak boundary that separates giant planets and brown dwarfs (BDs) and their formation mechanism, we analyze the spectra of a sample of stars with already confirmed BD companions both by radial velocity and astrometry. We employ standard and automatic tools to perform an EW-based analysis and to derive chemical abundances from CORALIE spectra of stars with BD companions. We compare these abundances with those of stars without detected planets and with low-mass and giant-mass planets. We find that stars with BDs do not have metallicities and chemical abundances similar to those of giant-planet hosts but they resemble the composition of stars with low-mass planets. The distribution of mean abundances of $\\alpha$-elements and iron peak elements of stars with BDs exhibit a peak at about solar abundance...

  6. Abundances and diffusion of elements in M67 stars

    CERN Document Server

    Önehag, Anna; Korn, Andreas

    2013-01-01

    We present a spectroscopic study at high resolution, R~50,000, of 14 stars located on the main sequence, at the turn-off point and on the early subgiant branch in the cluster M67 in order to investigate its detailed chemical composition, for comparison with the Sun and solar twins in the solar neighbourhood, and to explore selective atomic diffusion of chemical elements as predicted by stellar-structure theory. We have obtained VLT/FLAMES-UVES spectra and analysed these strictly differentially in order to explore chemical-abundance similarities and differences between the M67 stars and the Sun, and among the M67 stars themselves. Individual abundances of 19 different chemical elements are obtained for the stars. They are found to agree very well with solar abundances, with abundance ratios closer to solar than those of most solar twins in the solar neighbourhood. An exception is Li which shows a considerable scatter among the cluster stars. There is a tendency for the cluster-star abundances to be depleted re...

  7. Carbon and Oxygen abundances across the Hertzsprung gap

    CERN Document Server

    Adamczak, Jens

    2014-01-01

    We derived atmospheric parameters and spectroscopic abundances for C and O for a large sample of stars located in the Hertzsprung gap in the Hertzsprung-Russell Diagram in order to detect chemical peculiarities and get a comprehensive overview of the population of stars in this evolutionary state. We have observed and analyzed high resolution spectra (R = 60 000) of 188 stars in the mass range 2 - 5 Msun with the 2.7 m Harlan J. Smith Telescope at the McDonald Observatory including 28 stars previously identified as Am/Ap stars. We find that the C and O abundances of the majority of stars in the Hertzsprung gap are in accordance with abundances derived for local lower mass dwarfs but detect expected peculiarities for the Am/Ap stars. The C and O abundances of stars with Teff < 6500 K are slightly lower than for the hotter objects but the C/O ratio is constant in the analyzed temperature domain. No indication of an alteration of the C and O abundances of the stars by mixing during the evolution across the He...

  8. New Radial Abundance Gradients for NGC 628 and NGC 2403

    CERN Document Server

    Berg, Danielle A; Garnett, Donald R; Croxall, Kevin V; Marble, Andrew R; Smith, J D; Gordon, Karl; Kennicutt, Robert C

    2013-01-01

    Motived by recent ISM studies, we present high quality MMT and Gemini spectroscopic observations of H II regions in the nearby spiral galaxies NGC 628 and NGC 2403 in order to measure their chemical abundance gradients. Using long-slit and multi-object mask optical spectroscopy, we obtained measurements of the temperature sensitive auroral lines [O III] {\\lambda}4363 and/or [N II] {\\lambda}5755 at a strength of 4{\\sigma} or greater in 11 H II regions in NGC 628 and 7 regions in NGC 2403. These observations allow us, for the first time, to derive an oxygen abundance gradient in NGC 628 based solely on "direct" oxygen abundances of H II regions: 12 + log(O/H) = (8.43+/-0.03) + (-0.017+/-0.002) x Rg (dex/kpc), with a dispersion in log(O/H) of {\\sigma} = 0.10 dex, from 14 regions with a radial coverage of ~2-19 kpc. This is a significantly shallower slope than found by previous "strong-line" abundance studies. In NGC 2403, we derive an oxygen abundance gradient of 12 + log(O/H) = (8.48+/-0.04) + (-0.032+/-0.007) ...

  9. Stellar chemical abundances: in pursuit of the highest achievable precision

    Energy Technology Data Exchange (ETDEWEB)

    Bedell, Megan; Bean, Jacob L. [Department of Astronomy and Astrophysics, University of Chicago, 5640 S. Ellis Avenue, Chicago, IL 60637 (United States); Meléndez, Jorge; Leite, Paulo [Departamento de Astronomia do IAG/USP, Universidade de São Paulo, Rua do Matão 1226, Cidade Universitária, São Paulo, SP 05508-900 (Brazil); Ramírez, Ivan [McDonald Observatory and Department of Astronomy, University of Texas at Austin, Austin, TX 78712-1206 (United States); Asplund, Martin, E-mail: mbedell@oddjob.uchicago.edu [Research School of Astronomy and Astrophysics, The Australian National University, Cotter Road, Weston, ACT 2611 (Australia)

    2014-11-01

    The achievable level of precision on photospheric abundances of stars is a major limiting factor on investigations of exoplanet host star characteristics, the chemical histories of star clusters, and the evolution of the Milky Way and other galaxies. While model-induced errors can be minimized through the differential analysis of spectrally similar stars, the maximum achievable precision of this technique has been debated. As a test, we derive differential abundances of 19 elements from high-quality asteroid-reflected solar spectra taken using a variety of instruments and conditions. We treat the solar spectra as being from unknown stars and use the resulting differential abundances, which are expected to be zero, as a diagnostic of the error in our measurements. Our results indicate that the relative resolution of the target and reference spectra is a major consideration, with use of different instruments to obtain the two spectra leading to errors up to 0.04 dex. Use of the same instrument at different epochs for the two spectra has a much smaller effect (∼0.007 dex). The asteroid used to obtain the solar standard also has a negligible effect (∼0.006 dex). Assuming that systematic errors from the stellar model atmospheres have been minimized, as in the case of solar twins, we confirm that differential chemical abundances can be obtained at sub-0.01 dex precision with due care in the observations, data reduction, and abundance analysis.

  10. Generalized estimators of avian abundance from count survey data

    Directory of Open Access Journals (Sweden)

    Royle, J. A.

    2004-01-01

    Full Text Available I consider modeling avian abundance from spatially referenced bird count data collected according to common protocols such as capture-recapture, multiple observer, removal sampling and simple point counts. Small sample sizes and large numbers of parameters have motivated many analyses that disregard the spatial indexing of the data, and thus do not provide an adequate treatment of spatial structure. I describe a general framework for modeling spatially replicated data that regards local abundance as a random process, motivated by the view that the set of spatially referenced local populations (at the sample locations constitute a metapopulation. Under this view, attention can be focused on developing a model for the variation in local abundance independent of the sampling protocol being considered. The metapopulation model structure, when combined with the data generating model, define a simple hierarchical model that can be analyzed using conventional methods. The proposed modeling framework is completely general in the sense that broad classes of metapopulation models may be considered, site level covariates on detection and abundance may be considered, and estimates of abundance and related quantities may be obtained for sample locations, groups of locations, unsampled locations. Two brief examples are given, the first involving simple point counts, and the second based on temporary removal counts. Extension of these models to open systems is briefly discussed.

  11. Influence of edge on predator prey distribution and abundance

    Science.gov (United States)

    Ferguson, Steven H.

    2004-03-01

    I investigated the effect of spatial configuration on distribution and abundance of invertebrate trophic groups by counting soil arthropods under boxes (21 × 9.5 cm) arranged in six different patterns that varied in the amount of edge (137-305 cm). I predicted fewer individuals from the consumer trophic group (Collembola) in box groups with greater amount of edge. This prediction was based on the assumption that predators (mites, ants, spiders, centipedes) select edge during foraging and thereby reduce abundance of the less mobile consumer group under box patterns with greater edge. Consumer abundance (Collembola) was not correlated with amount of edge. Among the predator groups, mite, ant and centipede abundance related to the amount of edge of box groups. However, in contrast to predictions, abundance of these predators was negatively correlated with amount of edge in box patterns. All Collembola predators, with the exception of ants, were less clumped in distribution than Collembola. The results are inconsistent with the view that predators used box edges to predate the less mobile consumer trophic group. Alternative explanations for the spatial patterns other than predator-prey relations include (1) a negative relationship between edge and moisture, (2) a positive relationship between edge and detritus decomposition (i.e. mycelium as food for the consumer group), and (3) a negative relationship between edge and the interstices between adjacent boxes. Landscape patterns likely affect microclimate, food, and predator-prey relations and, therefore, future experimental designs need to control these factors individually to distinguish among alternative hypotheses.

  12. Sulfur and zinc abundances of red giant stars

    CERN Document Server

    Takeda, Yoichi; Harakawa, Hiroki; Sato, Bun'ei

    2016-01-01

    Sulfur and zinc are chemically volatile elements, which play significant roles as depletion-free tracers in studying galactic chemical evolution. However, regarding red giants having evolved off the main sequence, reliable abundance determinations of S and Zn seem to be difficult despite that a few studies have been reported so far. Given this situation, we tried to establish the abundances of these elements for an extensive sample of 239 field GK giants (-0.8 < [Fe/H] < +0.2), by applying the spectrum-fitting technique to S I 8694-5, S I 6757, and Zn I 6362 lines and by taking into account the non-LTE effect. Besides, similar abundance analysis was done for 160 FGK dwarfs to be used for comparison. The non-LTE corrections for the S and Zn abundances derived from these lines turned out < 0.1(-0.2) dex for most cases and not very significant. It revealed that the S I 6757 feature is more reliable as an abundance indicator than S I 8694-5 for the case of red giants, because the latter suffers blending ...

  13. Enhanced Abundances in Spiral Galaxies of the Pegasus I Cluster

    CERN Document Server

    Robertson, Paul; Blanc, Guillermo A

    2011-01-01

    We study the influence of cluster environment on the chemical evolution of spiral galaxies in the Pegasus I cluster. We determine the gas-phase heavy element abundances of six galaxies in Pegasus derived from H II region spectra obtained from integral-field spectroscopy. These abundances are analyzed in the context of Virgo, whose spirals are known to show increasing interstellar metallicity as a function of H I deficiency. The galaxies in the Pegasus cluster, despite its lower density and velocity dispersion, also display gas loss due to ISM-ICM interaction, albeit to a lesser degree. Based on the abundances of 3 H I deficient spirals and 2 H I normal spirals, we observe a heavy element abundance offset of +0.13\\pm0.07 dex for the H I deficient galaxies. This abundance differential is consistent with the differential observed in Virgo for galaxies with a similar H I deficiency, and we observe a correlation between log(O/H) and the H I deficiency parameter DEF for the two clusters analyzed together. Our resul...

  14. Synergistic effects of high fat feeding and apolipoprotein E deletion on enterocytic amyloid-beta abundance

    Directory of Open Access Journals (Sweden)

    Dhaliwal Satvinder S

    2008-04-01

    Full Text Available Abstract Background Amyloid-β (Aβ, a key protein found in amyloid plaques of subjects with Alzheimer's disease is expressed in the absorptive epithelial cells of the small intestine. Ingestion of saturated fat significantly enhances enterocytic Aβ abundance whereas fasting abolishes expression. Apolipoprotein (apo E has been shown to directly modulate Aβ biogenesis in liver and neuronal cells but it's effect in enterocytes is not known. In addition, apo E modulates villi length, which may indirectly modulate Aβ as a consequence of differences in lipid absorption. This study compared Aβ abundance and villi length in wild-type (WT and apo E knockout (KO mice maintained on either a low-fat or high-fat diet. Wild-type C57BL/6J and apo E KO mice were randomised for six-months to a diet containing either 4% (w/w unsaturated fats, or chow comprising 16% saturated fats and 1% cholesterol. Quantitative immunohistochemistry was used to assess Aβ abundance in small intestinal enterocytes. Apo E KO mice given the low-fat diet had similar enterocytic Aβ abundance compared to WT controls. Results The saturated fat diet substantially increased enterocytic Aβ in WT and in apo E KO mice, however the effect was greater in the latter. Villi height was significantly greater in apo E KO mice than for WT controls when given the low-fat diet. However, WT mice had comparable villi length to apo E KO when fed the saturated fat and cholesterol enriched diet. There was no effect of the high-fat diet on villi length in apo E KO mice. Conclusion The findings of this study are consistent with the notion that lipid substrate availability modulates enterocytic Aβ. Apo E may influence enterocytic lipid availability by modulating absorptive capacity.

  15. Carbon abundances of sdO stars from SPY

    Science.gov (United States)

    Hirsch, Heiko; Heber, Uli

    2009-06-01

    Ströer et al. (2007) recently suggested a classification of sdOs according to supersolar and subsolar helium abundances, with only the helium-enriched stars showing signes of carbon and/or nitrogen in their optical spectra. We aim to derive reliable carbon and nitrogen abundances by fitting synthetic spectra to data obtained with the UVES spectrograph at ESO. Here we present our first results of the analysis of carbon abundances in hot subdwarf O stars. By constructing a grid of model atmospheres consisting of hydrogen, helium and carbon we were able to derive atmospheric parameters of nine carbon rich sdOs. We find log(NC/Ntotal) up to ten times higher than the solar value, while the mean value for the effective temperature and the surface gravity is slightly lower than derived by helium-hydrogen models only. Surprisingly, we also find three fast rotators among our program stars.

  16. Abundance of atomic carbon /C I/ in dense interstellar clouds

    Science.gov (United States)

    Phillips, T. G.; Huggins, P. J.

    1981-01-01

    The abundance of interstellar neutral atomic carbon is investigated by means of its ground state fine-structure line emission at 492 GHz using the 91.5 cm telescope of NASAs Kuiper Airborne Observatory. Atomic carbon is found to be very abundant in dense interstellar molecular clouds with column densities of about 10 to the 19th per sq cm. Because the observations have considerably greater column densities than current theories of carbon chemistry, it is suggested that the physical conditions of these clouds are not as simple as assumed in the models. Various situations are discussed which would lead to large C I abundances, including the possibility that the chemical lifetimes of the clouds are relatively short.

  17. O, Na, Ba and Eu abundance patterns in open clusters

    CERN Document Server

    MacLean, B T; Lattanzio, J

    2014-01-01

    Open clusters are historically regarded as single-aged stellar populations representative of star formation within the Galactic disk. Recent literature has questioned this view, based on discrepant Na abundances relative to the field, and concerns about the longevity of bound clusters contributing to a selection bias: perhaps long-lived open clusters are chemically different to the star formation events that contributed to the Galactic disk. We explore a large sample of high resolution Na, O, Ba & Eu abundances from the literature, homogenized as much as reasonable including accounting for NLTE effects, variations in analysis and choice of spectral lines. Compared to a template globular cluster and representative field stars, we find no significant abundance trends, confirming that the process producing the Na-O anti-correlation in globular clusters is not present in open clusters. Furthermore, previously reported Na-enhancement of open clusters is found to be an artefact of NLTE effects, with the open cl...

  18. Elemental abundances of intermediate age open cluster NGC 3680

    CERN Document Server

    Mitschang, A W; Zucker, D B

    2012-01-01

    We present a new abundance analysis of the intermediate age Galactic open cluster NGC 3680, based on high resolution, high signal-to-noise VLT/UVES spectroscopic data. Several element abundances are presented for this cluster for the first time, but most notably we derive abundances for the light and heavy s-process elements Y, Ba, La, and Nd. The serendipitous measurement of the rare-earth r-process element Gd is also reported. This cluster exhibits a significant enhancement of Na in giants as compared to dwarfs, which may be a proxy for an O to Na anti-correlation as observed in Galactic globular clusters but not open clusters. We also observe a step-like enhancement of heavy s-process elements towards higher atomic number, contrary to expectations from AGB nucleosynthesis models, suggesting that the r-process played a significant role in the generation of both La and Nd in this cluster

  19. An MCMC determination of the primordial helium abundance

    CERN Document Server

    Aver, Erik; Skillman, Evan D

    2011-01-01

    Spectroscopic observations of the chemical abundances in metal-poor H II regions provide an independent method for estimating the primordial helium abundance. H II regions are described by several physical parameters such as electron density, electron temperature, and reddening, in addition to y, the ratio of helium to hydrogen. It had been customary to estimate or determine self-consistently these parameters to calculate y. Frequentist analyses of the parameter space have been shown to be successful in these determinations, and Markov Chain Monte Carlo (MCMC) techniques have proven to be very efficient in sampling this parameter space. Nevertheless, accurate determination of the primordial helium abundance from observations of H II regions is constrained by both systematic and statistical uncertainties. In an attempt to better reduce the latter, and better characterize the former, we apply MCMC methods to the large dataset recently compiled by Izotov, Thuan, & Stasinska (2007). To improve the reliability...

  20. The effects of He I 10830 on helium abundance determinations

    CERN Document Server

    Aver, Erik; Skillman, Evan D

    2015-01-01

    Observations of helium and hydrogen emission lines from metal-poor extragalactic H II regions provide an independent method for determining the primordial helium abundance, Y_p. Traditionally, the emission lines employed are in the visible wavelength range, and the number of suitable lines is limited. Furthermore, when using these lines, large systematic uncertainties in helium abundance determinations arise due to the degeneracy of physical parameters, such as temperature and density. Recently, Izotov, Thuan, & Guseva (2014) have pioneered adding the He 10830 infrared emission line in helium abundance determinations. The strong electron density dependence of He 10830 makes it ideal for better constraining density, potentially breaking the degeneracy with temperature. We revisit our analysis of the dataset published by Izotov, Thuan, & Stasinska (2007) and incorporate the newly available observations of He 10830 by scaling them using the observed-to-theoretical Paschen-gamma ratio. The solutions are b...

  1. Accurate Enthalpies of Formation of Astromolecules: Energy, Stability and Abundance

    CERN Document Server

    Etim, Emmanuel E

    2016-01-01

    Accurate enthalpies of formation are reported for known and potential astromolecules using high level ab initio quantum chemical calculations. A total of 130 molecules comprising of 31 isomeric groups and 24 cyanide/isocyanide pairs with atoms ranging from 3 to 12 have been considered. The results show an interesting, surprisingly not well explored, relationship between energy, stability and abundance (ESA) existing among these molecules. Among the isomeric species, isomers with lower enthalpies of formation are more easily observed in the interstellar medium compared to their counterparts with higher enthalpies of formation. Available data in literature confirm the high abundance of the most stable isomer over other isomers in the different groups considered. Potential for interstellar hydrogen bonding accounts for the few exceptions observed. Thus, in general, it suffices to say that the interstellar abundances of related species are directly proportional to their stabilities. The immediate consequences of ...

  2. Element abundances in X-ray emitting plasmas in stars

    CERN Document Server

    Testa, Paola

    2010-01-01

    Studies of element abundances in stars are of fundamental interest for their impact in a wide astrophysical context, from our understanding of galactic chemistry and its evolution, to their effect on models of stellar interiors, to the influence of the composition of material in young stellar environments on the planet formation process. We review recent results of studies of abundance properties of X-ray emitting plasmas in stars, ranging from the corona of the Sun and other solar-like stars, to pre-main sequence low-mass stars, and to early-type stars. We discuss the status of our understanding of abundance patterns in stellar X-ray plasmas, and recent advances made possible by accurate diagnostics now accessible thanks to the high resolution X-ray spectroscopy with Chandra and XMM-Newton.

  3. Oxygen Abundance Methods in SDSS: View from Modern Statistics

    Indian Academy of Sciences (India)

    Fei Shi; Gang Zhao; James Wicker

    2010-09-01

    Our purpose is to find which is the most reliable one among various oxygen abundance determination methods. We will test the validity of several different oxygen abundance determination methods using methods of modern statistics. These methods include Bayesian analysis and information scoring. We will analyze a sample of ∼ 6000 HII galaxies from the Sloan Digital Sky Survey (SDSS) spectroscopic observations data release four. All methods that we used drew the same conclusion that the method is a more reliable oxygen abundance determination method than the Bayesian metallicity method under the existing telescope ability. The ratios of the likelihoods between the different kinds of methods tell us that the , , and 32 methods are consistent with each other because the and 32 methods are calibrated by method. The Bayesian and 23 methods are consistent with each other because both are calibrated by a galaxy model. In either case, the 2 method is an unreliable method.

  4. Relative species abundance of replicator dynamics with sparse interactions

    CERN Document Server

    Obuchi, Tomoyuki; Tokita, Kei

    2016-01-01

    A theory of relative species abundance on sparsely-connected networks is presented by investigating the replicator dynamics with symmetric interactions. Sparseness of a network involves difficulty in analyzing the fixed points of the equation, and we avoid this problem by treating large self interaction $u$, which allows us to construct a perturbative expansion. Based on this perturbation, we find that the nature of the interactions is directly connected to the abundance distribution, and some characteristic behaviors, such as multiple peaks in the abundance distribution and all species coexistence at moderate values of $u$, are discovered in a wide class of the distribution of the interactions. The all species coexistence collapses at a critical value of $u$, $u_c$, and this collapsing is regarded as a phase transition. To get more quantitative information, we also construct a non-perturbative theory on random graphs based on techniques of statistical mechanics. The result shows those characteristic behavior...

  5. La and Eu Abundances in Metal-poor Halo Stars

    Science.gov (United States)

    Cardillo, Harrison; Burris, Debra L.

    2016-01-01

    Elements with atomic number greater than Z=26 (the Iron Peak) cannot be formed through fusion in a star's core; the majority of these elements are produced through one of two neutron-capture processes. Early in the history of the Galaxy, the rapid neutron-capture process (r-process) is believed to be responsible for the production of elements Z=56 and beyond. These elements require at least one generation of stars to have completed their life cycle in order to be synthesized. Therefore, if we observe the heavy metal abundances in what are called Population II stars (metal-poor stars), then we can begin to make inferences about the chemistry of the earliest stars in the Galaxy. To contribute to this picture of the early universe, the Lanthanum and Europium abundances of low-metallicity stars will be measured and trends in these abundances based on comparisons to existing related literature will be sought.

  6. Functional environmental proteomics: elucidating the role of a c-type cytochrome abundant during uranium bioremediation.

    Science.gov (United States)

    Yun, Jiae; Malvankar, Nikhil S; Ueki, Toshiyuki; Lovley, Derek R

    2016-02-01

    Studies with pure cultures of dissimilatory metal-reducing microorganisms have demonstrated that outer-surface c-type cytochromes are important electron transfer agents for the reduction of metals, but previous environmental proteomic studies have typically not recovered cytochrome sequences from subsurface environments in which metal reduction is important. Gel-separation, heme-staining and mass spectrometry of proteins in groundwater from in situ uranium bioremediation experiments identified a putative c-type cytochrome, designated Geobacter subsurface c-type cytochrome A (GscA), encoded within the genome of strain M18, a Geobacter isolate previously recovered from the site. Homologs of GscA were identified in the genomes of other Geobacter isolates in the phylogenetic cluster known as subsurface clade 1, which predominates in a diversity of Fe(III)-reducing subsurface environments. Most of the gscA sequences recovered from groundwater genomic DNA clustered in a tight phylogenetic group closely related to strain M18. GscA was most abundant in groundwater samples in which Geobacter sp. predominated. Expression of gscA in a strain of Geobacter sulfurreducens that lacked the gene for the c-type cytochrome OmcS, thought to facilitate electron transfer from conductive pili to Fe(III) oxide, restored the capacity for Fe(III) oxide reduction. Atomic force microscopy provided evidence that GscA was associated with the pili. These results demonstrate that a c-type cytochrome with an apparent function similar to that of OmcS is abundant when Geobacter sp. are abundant in the subsurface, providing insight into the mechanisms for the growth of subsurface Geobacter sp. on Fe(III) oxide and suggesting an approach for functional analysis of other Geobacter proteins found in the subsurface.

  7. Hepatic cytochrome P450 activity, abundance, and expression throughout human development

    Energy Technology Data Exchange (ETDEWEB)

    Sadler, Natalie C.; Nandhikonda, Premchendar; Webb-Robertson, Bobbie-Jo M.; Ansong, Charles; Anderson, Lindsey N.; Smith, Jordan N.; Corley, Richard A.; Wright, Aaron T.

    2016-07-01

    Cytochrome P450s are Phase I metabolic enzymes that play critical roles in the biotransformation of endogenous compounds and xenobiotics. The expression and activity of P450 enzymes can vary considerably throughout human development, especially when comparing fetal development to neonates, children, and adults. In an effort to develop a more comprehensive understanding of the ontogeny of P450 expression and activity we employed a multi-omic characterization of P450 transcript expression, protein abundance, and functional activity. To quantify the functional activity of individual P450s we employ activity-based protein profiling, which uses modified mechanism-based inhibitors of P450s as chemical probes, in tandem with proteomic analyses to quantify activity. Our results reveal life-stage-dependent variability in P450 expression, abundance, and activity throughout human development and frequent discordant relationships between expression and activity. The results were used to distribute P450s into three general classes based upon developmental stage of expression and activity. We have significantly expanded the knowledge of P450 ontogeny, particularly at the level of individual P450 activity. We anticipate that our ontogeny results will be useful for enabling predictive therapeutic dosing, and for avoiding potentially adverse and harmful reactions during maturation from both therapeutic drugs and environmental xenobiotics.

  8. The decoupling of abundance and species richness in lizard communities.

    Science.gov (United States)

    Nimmo, Dale G; James, Simon G; Kelly, Luke T; Watson, Simon J; Bennett, Andrew F

    2011-05-01

    1. Patterns of species richness often correlate strongly with measures of energy. The more individuals hypothesis (MIH) proposes that this relationship is facilitated by greater resources supporting larger populations, which are less likely to become extinct. Hence, the MIH predicts that community abundance and species richness will be positively related. 2. Recently, Buckley & Jetz (2010, Journal of Animal Ecology, 79, 358-365) documented a decoupling of community abundance and species richness in lizard communities in south-west United States, such that richer communities did not contain more individuals. They predicted, as a consequence of the mechanisms driving the decoupling, a more even distribution of species abundances in species-rich communities, evidenced by a positive relationship between species evenness and species richness. 3. We found a similar decoupling of the relationship between abundance and species richness for lizard communities in semi-arid south-eastern Australia. However, we note that a positive relationship between evenness and richness is expected because of the nature of the indices used. We illustrate this mathematically and empirically using data from both sets of lizard communities. When we used a measure of evenness, which is robust to species richness, there was no relationship between evenness and richness in either data set. 4. For lizard communities in both Australia and the United States, species dominance decreased as species richness increased. Further, with the iterative removal of the first, second and third most dominant species from each community, the relationship between abundance and species richness became increasingly more positive. 5. Our data support the contention that species richness in lizard communities is not directly related to the number of individuals an environment can support. We propose an alternative hypothesis regarding how the decoupling of abundance and richness is accommodated; namely, an inverse

  9. Baade's window and APOGEE. Metallicities, ages, and chemical abundances

    Science.gov (United States)

    Schultheis, M.; Rojas-Arriagada, A.; García Pérez, A. E.; Jönsson, H.; Hayden, M.; Nandakumar, G.; Cunha, K.; Allende Prieto, C.; Holtzman, J. A.; Beers, T. C.; Bizyaev, D.; Brinkmann, J.; Carrera, R.; Cohen, R. E.; Geisler, D.; Hearty, F. R.; Fernandez-Tricado, J. G.; Maraston, C.; Minnitti, D.; Nitschelm, C.; Roman-Lopes, A.; Schneider, D. P.; Tang, B.; Villanova, S.; Zasowski, G.; Majewski, S. R.

    2017-03-01

    Context. Baade's window (BW) is one of the most observed Galactic bulge fields in terms of chemical abundances. Owing to its low and homogeneous interstellar absorption it is considered the perfect calibration field for Galactic bulge studies. Aims: In the era of large spectroscopic surveys, calibration fields such as BW are necessary for cross calibrating the stellar parameters and individual abundances of the APOGEE survey. Methods: We use the APOGEE BW stars to derive the metallicity distribution function (MDF) and individual abundances for α- and iron-peak elements of the APOGEE ASPCAP pipeline (DR13), as well as the age distribution for stars in BW. Results: We determine the MDF of APOGEE stars in BW and find a remarkable agreement with that of the Gaia-ESO survey (GES). Both exhibit a clear bimodal distribution. We also find that the Mg-metallicity planes of the two surveys agree well, except for the metal-rich part ([Fe/H] > 0.1), where APOGEE finds systematically higher Mg abundances with respect to the GES. The ages based on the [C/N] ratio reveal a bimodal age distribution, with a major old population at 10 Gyr, with a decreasing tail towards younger stars. A comparison of stellar parameters determined by APOGEE and those determined by other sources reveals detectable systematic offsets, in particular for spectroscopic surface gravity estimates. In general, we find a good agreement between individual abundances of O, Na, Mg, Al, Si, K, Ca, Cr, Mn, Co, and Ni from APOGEE with that of literature values. Conclusions: We have shown that in general APOGEE data show a good agreement in terms of MDF and individual chemical abundances with respect to literature works. Using the [C/N] ratio we found a significant fraction of young stars in BW.

  10. A Comparison of Stellar Elemental Abundance Techniques and Measurements

    Science.gov (United States)

    Hinkel, Natalie R.; Young, Patrick A.; Pagano, Michael D.; Desch, Steven J.; Anbar, Ariel D.; Adibekyan, Vardan; Blanco-Cuaresma, Sergi; Carlberg, Joleen K.; Delgado Mena, Elisa; Liu, Fan; Nordlander, Thomas; Sousa, Sergio G.; Korn, Andreas; Gruyters, Pieter; Heiter, Ulrike; Jofré, Paula; Santos, Nuno C.; Soubiran, Caroline

    2016-09-01

    Stellar elemental abundances are important for understanding the fundamental properties of a star or stellar group, such as age and evolutionary history, as well as the composition of an orbiting planet. However, as abundance measurement techniques have progressed, there has been little standardization between individual methods and their comparisons. As a result, different stellar abundance procedures determine measurements that vary beyond the quoted error for the same elements within the same stars. The purpose of this paper is to better understand the systematic variations between methods and offer recommendations for producing more accurate results in the future. We invited a number of participants from around the world (Australia, Portugal, Sweden, Switzerland, and the United States) to calculate 10 element abundances (C, O, Na, Mg, Al, Si, Fe, Ni, Ba, and Eu) using the same stellar spectra for four stars (HD 361, HD 10700, HD 121504, and HD 202206). Each group produced measurements for each star using (1) their own autonomous techniques, (2) standardized stellar parameters, (3) a standardized line list, and (4) both standardized parameters and a line list. We present the resulting stellar parameters, absolute abundances, and a metric of data similarity that quantifies the homogeneity of the data. We conclude that standardization of some kind, particularly stellar parameters, improves the consistency between methods. However, because results did not converge as more free parameters were standardized, it is clear there are inherent issues within the techniques that need to be reconciled. Therefore, we encourage more conversation and transparency within the community such that stellar abundance determinations can be reproducible as well as accurate and precise.

  11. Sulfur and zinc abundances of red giant stars†

    Science.gov (United States)

    Takeda, Yoichi; Omiya, Masashi; Harakawa, Hiroki; Sato, Bun'ei

    2016-10-01

    Sulfur and zinc are chemically volatile elements, which play significant roles as depletion-free tracers in studying galactic chemical evolution. However, regarding red giants having evolved off the main sequence, reliable abundance determinations of S and Zn seem to be difficult, despite the several studies that have been reported so far. Given this situation, we tried to establish the abundances of these elements for an extensive sample of 239 field GK giants ( - 0.8 ≲ [Fe/H] ≲ +0.2), by applying the spectrum-fitting technique to S I 8694-5, S I 6757, and Zn I 6362 lines and by taking into account the non-LTE effect. Besides, similar abundance analysis was done for 160 FGK dwarfs to be used for comparison. The non-LTE corrections for the S and Zn abundances derived from these lines turned out to be ≲ 0.1(-0.2) dex for most cases and not very significant. It revealed that the S I 6757 feature is more reliable as an abundance indicator than S I 8694-5 for the case of red giants, because the latter suffers blending of unidentified lines. The finally resulting [S/Fe]-[Fe/H] and [Zn/Fe]-[Fe/H] relations for GK giants were confirmed to be in good agreement with those for FGK dwarfs, indicating that S and Zn abundances of red giants are reliably determinable from the S I 6757 and Zn I 6362 lines. Accordingly, not only main-sequence stars but also evolved red giant stars are usable for tracing the chemical evolution history of S and Zn in the regime of disk metallicity by using these lines.

  12. Relationships between sedimentary subseafloor microbial abundance and sedimentation rate

    Science.gov (United States)

    Kallmeyer, J.

    2015-12-01

    Cell count data for estimates of global subseafloor microbial abundance need to be simplified in order to be used for model calculations All models rely on regressions of cell counts vs. depth. Different strategies are being used for simplifying the data, e.g. averaging over highly variable data from different oceanic provinces or excluding individual datasets that cannot be described by a single regression. While providing global estimates, these models fail to identify the finer details of the controls on subseafloor microbial abundance. Most subseafloor microbes are heterotrophic and gain energy by degrading buried organic matter. Because sedimentation rate is usually positively correlated with primary productivity and organic matter flux to the seafloor, it determines how much organic matter is deposited on the sea floor and how fast it is buried and reaches greater depths. At the same depth, in environments with low sed. rates the organic matter is older, more degraded and supports less metabolic activity than in those with high sed. rates. As a result, sed. rates control penetration depth of oxygen and other electron acceptors. Oxygen penetration remains in the mm to cm range over most sed. rates and it only penetrates significantly deeper at very low rates of ca. 1 mm/kyr or less. However, microbial abundance correlates with sed. rate over a wider range. In order to take a more detailed look at the influence of sed. rate and therefore sediment age on cell abundance, ages and additional geochemical information were assigned to individual cell counts. The new dataset shows the strong influence of sed. rates or rather sediment age on microbial abundance, while oxygen concentrations seem to have only a minor influence. Using data from IODP drill sites that have moved from high to low productivity zones or vice versa helps to differentiate between different factors that control microbial cell abundance.

  13. Mangroves Enhance Reef Fish Abundance at the Caribbean Regional Scale.

    Directory of Open Access Journals (Sweden)

    Joseph E Serafy

    Full Text Available Several studies conducted at the scale of islands, or small sections of continental coastlines, have suggested that mangrove habitats serve to enhance fish abundances on coral reefs, mainly by providing nursery grounds for several ontogenetically-migrating species. However, evidence of such enhancement at a regional scale has not been reported, and recently, some researchers have questioned the mangrove-reef subsidy effect. In the present study, using two different regression approaches, we pursued two questions related to mangrove-reef connectivity at the Caribbean regional scale: (1 Are reef fish abundances limited by mangrove forest area?; and (2 Are mean reef fish abundances proportional to mangrove forest area after taking human population density and latitude into account? Specifically, we tested for Caribbean-wide mangrove forest area effects on the abundances of 12 reef fishes that have been previously characterized as "mangrove-dependent". Analyzed were data from an ongoing, long-term (20-year citizen-scientist fish monitoring program; coastal human population censuses; and several wetland forest information sources. Quantile regression results supported the notion that mangrove forest area limits the abundance of eight of the 12 fishes examined. Linear mixed-effects regression results, which considered potential human (fishing and habitat degradation and latitudinal influences, suggested that average reef fish densities of at least six of the 12 focal fishes were directly proportional to mangrove forest area. Recent work questioning the mangrove-reef fish subsidy effect likely reflects a failure to: (1 focus analyses on species that use mangroves as nurseries, (2 consider more than the mean fish abundance response to mangrove forest extent; and/or (3 quantitatively account for potentially confounding human impacts, such as fishing pressure and habitat degradation. Our study is the first to demonstrate at a large regional scale (i

  14. First Stellar Abundances in the Dwarf Irregular Galaxy IC 1613

    Science.gov (United States)

    Tautvaišienė, Gražina; Geisler, Doug; Wallerstein, George; Borissova, Jura; Bizyaev, Dmitry; Pagel, Bernard E. J.; Charbonnel, Corinne; Smith, Verne

    2007-12-01

    Chemical abundances in three M supergiants in the Local Group dwarf irregular galaxy IC 1613 have been determined using high-resolution spectra obtained with the UVES spectrograph on the ESO 8.2 m Kueyen telescope. A detailed synthetic-spectrum analysis has been used to determine the atmospheric parameters and abundances of O, Na, Mg, Al, Si, Ca, Sc, Ti, Cr, Fe, Co, Ni, La, and Eu. We find the overall metallicity of the stars to be [Fe/H] = -0.67 ± 0.09 and the age 9-13 Myr, which is in excellent agreement with the present-day values in the age-metallicity relationship model of IC 1613 by Skillman et al. We have found that the three supergiants investigated have a mean [α/Fe] equal to about -0.1, which is lower than seen in Galactic stars at the same metallicity and is in agreement with the results obtained in other dwarf irregular galaxies. The oxygen abundances are in agreement with the upper values of the nebular oxygen determinations in IC 1613. The abundance ratios of s- and r-process elements to iron are enhanced relative to solar by about 0.3 dex. The abundance pattern of the elements studied is similar to that of the Small Magellanic Cloud, except for Co and Ni, which are underabundant in the SMC. The observed elemental abundances are generally in very good agreement with the recent chemical evolution model of Yuk and Lee. Based on observations collected with the Very Large Telescope and the 2.2 m Telescope of the European Southern Observatory within the Observing Programs 70.B-0361(A) and 072.D-0113(D).

  15. LITERATURE SURVEY ON ISOTOPIC ABUNDANCE RATIO MEASUREMENTS - 2001-2005

    Energy Technology Data Exchange (ETDEWEB)

    HOLDEN, N.E.

    2005-08-13

    Along with my usual weekly review of the published literature for new nuclear data, I also search for new candidates for best measurements of isotopic abundances from a single source. Most of the published articles, that I previously had found in the Research Library at the Brookhaven Lab, have already been sent to the members of the Atomic Weights Commission, by either Michael Berglund or Thomas Walczyk. In the last few days, I checked the published literature for any other articles in the areas of natural variations in isotopic abundance ratios, measurements of isotopic abundance ratios on samples of extra-terrestrial material and isotopic abundance ratio measurements performed using ICPMS instruments. Hopefully this information will be of interest to members of the Commission, the sub-committee on isotopic abundance measurements (SIAM), members of the former sub-committee on natural isotopic fractionation (SNIF), the sub-committee on extra-terrestrial isotope ratios (SETIR), the RTCE Task Group and the Guidelines Task Group, who are dealing with ICPMS and TIMS comparisons. In the following report, I categorize the publications in one of four areas. Measurements performed using either positive or negative ions with Thermal Ionization Mass Spectrometer, TIMS, instruments; measurements performed on Inductively Coupled Plasma Mass Spectrometer, ICPMS, instruments; measurements of natural variations of the isotopic abundance ratios; and finally measurements on extra-terrestrial samples with instrumentation of either type. There is overlap in these areas. I selected out variations and ET results first and then categorized the rest of the papers by TIMS and ICPMS.

  16. Chemical Abundances for Seven Giant Stars in M68 (NGC 4590) A Globular Cluster with Abnormal Silicon and Titanium Abundances

    CERN Document Server

    Lee, J W; Habgood, M J; Lee, Jae-Woo; Carney, Bruce W.

    2004-01-01

    We present a detailed chemical abundance study of seven giant stars in M68 including six red giants and one post-AGB star. We find significant differences in the gravities determined using photometry and those obtained from ionization balance, which suggests that non-LTE effects are important for these low-gravity, metal-poor stars. We adopt an iron abundance using photometric gravities and Fe II lines to minimize those effects, finding [Fe/H] = -2.16 +/- 0.02. For element-to-iron ratios,we rely on neutral lines vs. Fe I and ionized lines vs. FeII (except for [O/Fe]) to also minimize non-LTE effects. We find variations in the abundances of sodium among the program stars. However, there is no correlation (or anti-correlation) with the oxygen abundances. Further, the post-AGB star has a normal (low) abundance of sodium. Both of these facts add further support to the idea that the variations seen among some light elements within individual globular clusters arises from primordial variations, and not from deep mi...

  17. Asteroseismic estimate of helium abundance of 16 Cyg A, B

    Directory of Open Access Journals (Sweden)

    Verma Kuldeep

    2015-01-01

    Full Text Available The helium ionization zone in a star leaves a characteristic signature on its oscillation frequencies, which can be used to estimate the helium content in the envelope of the star. We use the oscillation frequencies of 16 Cyg A and B, obtained using 2.5 years of Kepler data, to estimate the envelope helium abundance of these stars. We find the envelope helium abundance to lie in the range 0.231–0.251 for 16 Cyg A and 0.218–0.266 for 16 Cyg B.

  18. Distribution and abundance of West Greenland humpback whales ( Megaptera novaeangliae )

    DEFF Research Database (Denmark)

    Larsen, Finn; Hammond, P.S.

    2004-01-01

    Photo-identification surveys of humpback whales Megaptera novaeangliae were conducted at West Greenland during 1988-93, the last 2 years of which were part of the internationally coordinated humpback whale research programme YoNAH, with the primary aim of estimating abundance for the West Greenland...... effort. A total of 670 groups of humpback whales was encountered leading to the identification of 348 individual animals. Three areas of concentration were identified: an area off Nuuk; an area at c. 63degrees30'N; and an area off Frederikshab. Sequential Petersen capture-recapture estimates of abundance...

  19. Dark Matter Relic Abundance and Light Sterile Neutrinos

    CERN Document Server

    Tang, Yi-Lei

    2016-01-01

    In this paper, we calculate the relic abundance of the dark matter particles when they can annihilate into sterile neutrinos with the mass $\\lesssim 100 \\text{ GeV}$ in a simple model. Unlike the usual standard calculations, the sterile neutrino may fall out of the thermal equilibrium with the thermal bath before the dark matter freezes out. In such case, if the Yukawa coupling between Higgs and sterile neutrino $y_N$ is small, this process gives rise to a larger $\\Omega_{\\text{DM}} h^2$ so we need a larger coupling between dark matter and the sterile neutrino for a correct relic abundance.

  20. Fe-peak element abundances in disk and halo stars

    CERN Document Server

    Bergemann, Maria

    2009-01-01

    At present none of Galactic chemical evolution (GCE) models provides a self-consistent description of observed trends for all iron-peak elements with metallicity simultaneously. The question is whether the discrepancy is due to deficiencies of GCE models, such as stellar yields, or due to erroneous spectroscopically-determined abundances of these elements in metal-poor stars. The present work aims at a critical reevaluation of the abundance trends for several odd and even-Z Fe-peak elements, which are important for understanding explosive nucleosynthesis in supernovae.

  1. New functionalities in abundant element oxides: ubiquitous element strategy.

    Science.gov (United States)

    Hosono, Hideo; Hayashi, Katsuro; Kamiya, Toshio; Atou, Toshiyuki; Susaki, Tomofumi

    2011-06-01

    While most ceramics are composed of ubiquitous elements (the ten most abundant elements within the Earth's crust), many advanced materials are based on rare elements. A 'rare-element crisis' is approaching owing to the imbalance between the limited supply of rare elements and the increasing demand. Therefore, we propose a 'ubiquitous element strategy' for materials research, which aims to apply abundant elements in a variety of innovative applications. Creation of innovative oxide materials and devices based on conventional ceramics is one specific challenge. This review describes the concept of ubiquitous element strategy and gives some highlights of our recent research on the synthesis of electronic, thermionic and structural materials using ubiquitous elements.

  2. Carbon Abundances in the Small Magellanic Cloud Planetary Nebulae

    CERN Document Server

    Lee, T H; Shaw, R A; Balick, B; Villaver, E

    2006-01-01

    As an ongoing study of Magellanic Cloud PNe we have obtained UV spectra of 9 PNe in the SMC to measure their carbon abundances. The spectra have been acquired with ACS HRC/PR200L and SBC/PR130L. The ACS prisms give a reasonable resolution in the range of 1200 -- 2500 A to detect the C IV, C III], and C II] nebular emission, essential for chemical studies of the PNe. The carbon abundances of SMC PNe, together with those of the LMC previously determined with STIS spectroscopy, will allow a comparative study of nebular enrichment and provide the basis for comparison with stellar evolution models at various metallicity.

  3. Suppressing the QCD axion abundance by hidden monopoles

    Energy Technology Data Exchange (ETDEWEB)

    Kawasaki, Masahiro [Tokyo Univ., Chiba (Japan). Inst. for Cosmic Ray Research; Tokyo Univ., Chiba (Japan). Kavli IPMU (WPI), UTIAS; Takahashi, Fuminobu [Tokyo Univ., Miyagi (Japan). Dept. of Physics; Tokyo Univ., Chiba (Japan). Kavli IPMU (WPI), UTIAS; Yamada, Masaki [Tokyo Univ., Chiba (Japan). Inst. for Cosmic Ray Research; Tokyo Univ., Chiba (Japan). Kavli IPMU (WPI), UTIAS; DESY Hamburg (Germany)

    2015-11-15

    We study the Witten effect of hidden monopoles on the QCD axion dynamics, and show that its abundance as well as isocurvature perturbations can be significantly suppressed if there is a sufficient amount of hidden monopoles. When the hidden monopoles make up a significant fraction of dark matter, the Witten effect suppresses the abundance of axion with the decay constant smaller than 10{sup 12} GeV. The cosmological domain wall problem of the QCD axion can also be avoided, relaxing the upper bound on the decay constant when the Peccei-Quinn symmetry is spontaneously broken after inflation.

  4. Suppressing the QCD axion abundance by hidden monopoles

    Directory of Open Access Journals (Sweden)

    Masahiro Kawasaki

    2016-02-01

    Full Text Available We study the Witten effect of hidden monopoles on the QCD axion dynamics, and show that its abundance as well as isocurvature perturbations can be significantly suppressed if there is a sufficient amount of hidden monopoles. When the hidden monopoles make up a significant fraction of dark matter, the Witten effect suppresses the abundance of axion with the decay constant smaller than 1012GeV. The cosmological domain wall problem of the QCD axion can also be avoided, relaxing the upper bound on the decay constant when the Peccei–Quinn symmetry is spontaneously broken after inflation.

  5. Trace Element Abundance Measurements on Cosmic Dust Particles

    Science.gov (United States)

    Flynn, George

    1996-01-01

    The X-Ray Microprobe on beamline X-26A at the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory was used to determine the abundances of elements from Cr through Sr in individual interplanetary dust particles (IDPs) collected from the Earth's stratosphere and the Scanning Transmission X-ray Microscope (STXM) on beamline X-1A at the NSLS was used to determine the carbon abundances and spatial distributions in IDPs. In addition, modeling was performed in an attempt to associate particular types of IDPs with specific types of parent bodies, and thus to infer the chemistry, mineralogy, and structural properties of those parent bodies.

  6. ANALYSIS OF RICIN TOXIN PREPARATIONS FOR CARBOHYDRATE AND FATTY ACID ABUNDANCE AND ISOTOPE RATIO INFORMATION

    Energy Technology Data Exchange (ETDEWEB)

    Wunschel, David S.; Kreuzer-Martin, Helen W.; Antolick, Kathryn C.; Colburn, Heather A.; Moran, James J.; Melville, Angela M.

    2009-12-01

    This report describes method development and preliminary evaluation for analyzing castor samples for signatures of purifying ricin. Ricin purification from the source castor seeds is essentially a problem of protein purification using common biochemical methods. Indications of protein purification will likely manifest themselves as removal of the non-protein fractions of the seed. Two major, non-protein, types of biochemical constituents in the seed are the castor oil and various carbohydrates. The oil comprises roughly half the seed weight while the carbohydrate component comprises roughly half of the remaining “mash” left after oil and hull removal. Different castor oil and carbohydrate components can serve as indicators of specific toxin processing steps. Ricinoleic acid is a relatively unique fatty acid in nature and is the most abundant component of castor oil. The loss of ricinoleic acid indicates a step to remove oil from the seeds. The relative amounts of carbohydrates and carbohydrate-like compounds, including arabinose, xylose, myo-inositol fucose, rhamnose, glucosamine and mannose detected in the sample can also indicate specific processing steps. For instance, the differential loss of arabinose relative to mannose and N-acetyl glucosamine indicates enrichment for the protein fraction of the seed using protein precipitation. The methods developed in this project center on fatty acid and carbohydrate extraction from castor samples followed by derivatization to permit analysis by gas chromatography-mass spectrometry (GC-MS). Method descriptions herein include: the source and preparation of castor materials used for method evaluation, the equipment and description of procedure required for chemical derivatization, and the instrument parameters used in the analysis. Two types of derivatization methods describe analysis of carbohydrates and one procedure for analysis of fatty acids. Two types of GC-MS analysis is included in the method development, one

  7. Economical evolution: microbes reduce the synthetic cost of extracellular proteins.

    Science.gov (United States)

    Smith, Daniel R; Chapman, Matthew R

    2010-08-24

    Protein evolution is not simply a race toward improved function. Because organisms compete for limited resources, fitness is also affected by the relative economy of an organism's proteome. Indeed, many abundant proteins contain relatively high percentages of amino acids that are metabolically less taxing for the cell to make, thus reducing cellular cost. However, not all abundant proteins are economical, and many economical proteins are not particularly abundant. Here we examined protein composition and found that the relative synthetic cost of amino acids constrains the composition of microbial extracellular proteins. In Escherichia coli, extracellular proteins contain, on average, fewer energetically expensive amino acids independent of their abundance, length, function, or structure. Economic pressures have strategically shaped the amino acid composition of multicomponent surface appendages, such as flagella, curli, and type I pili, and extracellular enzymes, including type III effector proteins and secreted serine proteases. Furthermore, in silico analysis of Pseudomonas syringae, Mycobacterium tuberculosis, Saccharomyces cerevisiae, and over 25 other microbes spanning a wide range of GC content revealed a broad bias toward more economical amino acids in extracellular proteins. The synthesis of any protein, especially those rich in expensive aromatic amino acids, represents a significant investment. Because extracellular proteins are lost to the environment and not recycled like other cellular proteins, they present a greater burden on the cell, as their amino acids cannot be reutilized during translation. We hypothesize that evolution has optimized extracellular proteins to reduce their synthetic burden on the cell.

  8. Affected by abundant PLTP : the atherogenic role of a lipid transfer protein in transgenic mice

    NARCIS (Netherlands)

    H.M.E. Samyn (Hannelore); M. Moerland (Matthijs)

    2009-01-01

    markdownabstract__Abstract__ Atherosclerosis is a progressive disease of the large and medium-sized arteries. The disease is characterised by endothelial dysfunction, inflammation and the accumulation of fatty and fibrous substances in the vessel wall, resulting in thickening and loss of elasticity

  9. Abundant Semigroups Which Are Disjoint Unions of Multiplicative Adequate Transversals

    Institute of Scientific and Technical Information of China (English)

    Haijun LIU; Xiaojiang GUO

    2013-01-01

    The aim of this paper is to study abundant semigroups which are disjoint unions of multiplicative adequate tranversals.After obtaining some properties of such semigroup,we prove that a semigroup is a disjoint union of multiplicative adequate transversals if and only if it is isomorphic to the direct product of a rectangular band and an adequate semigroup.

  10. Monitoring the abundance of plastic debris in the marine environment

    NARCIS (Netherlands)

    Ryan, P.G.; Moore, C.J. C.J.; Franeker, van J.A.; Moloney, C.L.

    2009-01-01

    Plastic debris has significant environmental and economic impacts in marine systems. Monitoring is crucial to assess the efficacy of measures implemented to reduce the abundance of plastic debris, but it is complicated by large spatial and temporal heterogeneity in the amounts of plastic debris and

  11. Accurate genome relative abundance estimation based on shotgun metagenomic reads.

    Directory of Open Access Journals (Sweden)

    Li C Xia

    Full Text Available Accurate estimation of microbial community composition based on metagenomic sequencing data is fundamental for subsequent metagenomics analysis. Prevalent estimation methods are mainly based on directly summarizing alignment results or its variants; often result in biased and/or unstable estimates. We have developed a unified probabilistic framework (named GRAMMy by explicitly modeling read assignment ambiguities, genome size biases and read distributions along the genomes. Maximum likelihood method is employed to compute Genome Relative Abundance of microbial communities using the Mixture Model theory (GRAMMy. GRAMMy has been demonstrated to give estimates that are accurate and robust across both simulated and real read benchmark datasets. We applied GRAMMy to a collection of 34 metagenomic read sets from four metagenomics projects and identified 99 frequent species (minimally 0.5% abundant in at least 50% of the data-sets in the human gut samples. Our results show substantial improvements over previous studies, such as adjusting the over-estimated abundance for Bacteroides species for human gut samples, by providing a new reference-based strategy for metagenomic sample comparisons. GRAMMy can be used flexibly with many read assignment tools (mapping, alignment or composition-based even with low-sensitivity mapping results from huge short-read datasets. It will be increasingly useful as an accurate and robust tool for abundance estimation with the growing size of read sets and the expanding database of reference genomes.

  12. Dilaton could affect abundance of dark matter particles

    CERN Multimedia

    2007-01-01

    "The amount of dark matter left over from the early universe may be less than previously believed. new research shows that the "relic abundance" of stable dark matter particles such as the neutralino may be reduced as compared to standard cosmology theories due to the effects of the "dilaton", a particle with zero spin in the gravitational sector of strings." (1 page)

  13. Lead abundance in the uranium star CS 31082-001

    CERN Document Server

    Plez, B; Cayrel, R; Spite, M; Barbuy, B; Beers, T C; Bonifacio, P; Primas, F; Nordström, B

    2004-01-01

    In a previous paper we were able to measure the abundance of uranium and thorium in the very-metal poor halo giant BPS CS 31082-001, but only obtained an upper limit for the abundance of lead (Pb). We have got from ESO 17 hours of additional exposure on this star in order to secure a detection of the minimum amount of lead expected to be present in CS 31082-001, the amount arising from the decay of the original content of Th and U in the star. We report here this successful detection. We find an LTE abundance log(Pb/H)+12=-0.55 \\pm 0.15 dex, one dex below the upper limits given by other authors for the similar stars CS 22892-052 and BD +17d3248, also enhanced in r-process elements. From the observed present abundances of Th and U in the star, the expected amount of Pb produced by the decay of 232Th, and 238U alone, over 12-15 Gyr is -0.73\\pm 0.17 dex. The decay of 235U is more difficult to estimate, but is probably slightly below the contribution of 238U, making the contribution of the 3 actinides only slight...

  14. Morphological change in Newfoundland caribou: Effects of abundance and climate

    Directory of Open Access Journals (Sweden)

    Shane P. Mahoney

    2011-04-01

    Full Text Available The demographic and environmental influences on large mammal morphology are central questions in ecology. We investigated the effects of population abundance and climate on body size and number of male antler points for the La Poile and Middle Ridge caribou (Rangifer tarandus, L. 1758 herds, Newfoundland, Canada. Across 40 years and 20-fold changes in abundance, adult males and females exhibited diminished stature as indicated by jawbone size (diastema and total mandible length and the number of antler points at the time of harvest. Associations between jawbone size and population abundance at birth were consistently negative for both herds, both sexes, and all age classes. Large-scale climate patterns, as measured by the North Atlantic Oscillation in the winter prior to birth, were also negatively associated with jawbone size. Declines in male antler size, as measured by the number of antler points, were not well predicted by either abundance or climate, suggesting other factors (e.g., current, rather than latent, foraging conditions may be involved. We conclude that these morphological changes indicate competition for food resources.

  15. Abundances in the metal poor dwarf Ross 451

    Science.gov (United States)

    Spiesman, William J.

    1990-01-01

    High dispersion echelle spectra of the high velocity subdwarf Ross 451 (= G236-080) were obtained using the 4-m telescope at Kitt Peak. Initial abundance determinations for six elements are presented, using absolute oscillator strengths and metal-poor stellar-atmosphere models.

  16. Determining Boundaries between Abundance Biozones Using Minimal Equipment

    Directory of Open Access Journals (Sweden)

    Brent Wilson

    2010-01-01

    Full Text Available The areal extent of a biological community is usually determined using statistical techniques that only give reliable results where samples contain similar and high numbers of specimens. This paper presents a simple, inexpensive method for determining the geographical limits of biological communities applicable where adjacent samples contain widely differing numbers of specimens. The method is a development of SHE Analysis, which discerns boundaries between adjacent abundance biozones (ABs, an AB being an area with a distinct community structure. As originally conceived, SHEbi (SHE Analysis for the identification of Biozones commences with species' absolute abundances and works best with large samples of equal sizes. If the variance in (per sample is high, SHEbi may place AB boundaries in unexpected locations. A modification, based on proportional abundances, is developed here using species' proportional abundances (=/ for each sample where is the number of specimens in the ith species in the sample. For intertidal foraminifera from the Caroni Swamp, Trinidad, where , the number of specimens, fluctuates widely between samples, the modification (SHEbip gives ecologically more sensible results than does traditional SHEbi.

  17. Teaching Old Dogs New Tricks: The Luxury of Digital Abundance

    Science.gov (United States)

    O'Brien, David; Scharber, Cassandra

    2010-01-01

    Today we thrive on an abundance of relatively cheap computing power and have the luxury of wasting most of it. It is quickly becoming not only possible but also financially sound, for educators to significantly complement, supplement, or even replace traditional print curricula with digital print and media, online curricula and websites, and…

  18. The abundance of (not just) dark matter haloes

    CERN Document Server

    Sawala, Till; Crain, Robert A; Jenkins, Adrian; Schaye, Joop; Theuns, Tom; Zavala, Jesus

    2012-01-01

    We study the effect of baryons on the abundance of structures and substructures in a Lambda-CDM cosmology, using a pair of high resolution cosmological simulations from the GIMIC project. Both simulations use identical initial conditions, but while one contains only dark matter, the other also includes baryons. We find that gas pressure, reionisation, supernova feedback, stripping, and truncated accretion systematically reduce the total mass and the abundance of structures below ~10^12 solar masses compared to the pure dark matter simulation. Taking this into account and adopting an appropriate detection threshold lowers the abundance of observed galaxies with maximum circular velocities below 100 km/s, significantly reducing the reported discrepancy between Lambda-CDM and the measured HI velocity function of the ALFALFA survey. We also show that the stellar-to-total mass ratios of galaxies with stellar masses of ~10^5 - 10^7 solar masses inferred from abundance matching of the (sub)halo mass function to the ...

  19. A catalogue of helium abundance indicators from globular cluster photometry

    Science.gov (United States)

    Sandquist, Eric L.

    2000-04-01

    We present a survey of helium abundance indicators derived from a comprehensive study of globular cluster photometry in the literature. For each of the three indicators used, we conduct a thorough error analysis, and identify systematic errors in the computational procedures. For the population ratio RNHBNRGB, we find that there is no evidence of a trend with metallicity, although there appears to be real scatter in the values derived. Although this indicator is the one best able to provide useful absolute helium abundances, the mean value is Y~0.20, indicating the probable presence of additional systematic error. For the magnitude difference from the horizontal branch to the main sequence Δ and the RR Lyrae mass-luminosity exponent A, it is only possible to determine relative helium abundances reliably. This is due to continuing uncertainties in the absolute metallicity scale for Δ, and uncertainty in the RR Lyrae temperature scale for A. Both indicators imply that the helium abundance is approximately constant as a function of [Fe/H]. According to the A indicator, both Oosterhoff I and II group clusters have constant values independent of [Fe/H] and horizontal branch type. In addition, the two groups have slopes dlog/d[Fe/H] that are consistent with each other, but significantly smaller than the slope for the combined sample.

  20. Lithium Abundance Of The Solar-Type Superflare Stars

    Science.gov (United States)

    Honda, Satoshi; Notsu, Yuta; Maehara, Hiroyuki; Notsu, Shota; Shibayama, Takuya; Nogami, Daisaku; Shibata, Kazunari

    2016-07-01

    We performed the high dispersion spectroscopy of solar-type superflare stars by Subaru/HDS, and estimate the stellar parameters and lithium abundance of the stars to compare with the Sun. Our spectroscopic analysis of superflare stars show more than half of targets have no evidence of binary system and the stellar parameters are in the range of solar-type stars (Notsu et al. 2015a&b). We also investigate the correlations of Lithium abundance with stellar atmospheric parameters, rotational velocity, and superflare activities to understand the nature of superflare stars and the possibility of the nucleosynthesis of lithium by superflares. The derived lithium abundance in superflare stars do not show the correlation with stellar parameters. As compared with the lithium abundance in Hyades cluster which is younger than the sun, it is suggested that half of observed stars are young. However, there are some objects which show the low lithium and slowly rotate from the estimated v sin(i) and period of brightness variation. These results indicate that the superflare stars are not only young stars but also old stars like our sun. In our observations, we could not find the any evidence of lithium productions by superflare.

  1. The Origin of Element Abundance Variations in Solar Energetic Particles

    CERN Document Server

    Reames, Donald V

    2016-01-01

    Abundance enhancements, during acceleration and transport in both gradual and impulsive solar energetic particle (SEP) events, vary approximately as power laws in the mass-to-charge ratio A/Q of the ions. Since the Q values depend upon the electron temperature of the source plasma, this has allowed a determination of this temperature from the pattern of element abundance enhancements and a verification of the expected inverse-time dependence of the power of A/Q for diffusive transport of ions from the SEP events, with scattering mean free paths found to be between 0.2 and 1 AU. SEP events derived from plasma of different temperatures map into different regions in typical cross-plots of abundances, spreading the distributions. In comparisons of SEP events with temperatures above 2 MK, impulsive events show much broader non-thermal variation of abundances than do gradual events. The extensive shock waves accelerating ions in gradual events may average over much of an active region where numerous but smaller mag...

  2. High-resolution abundance analysis of HD 140283

    CERN Document Server

    Siqueira-Mello, C; Barbuy, B; Spite, M; Spite, F; Korotin, S A

    2015-01-01

    HD 140283 is a reference subgiant that is metal poor and confirmed to be a very old star. The abundances of this type of old star can constrain the nature and nucleosynthesis processes that occurred in its (even older) progenitors. The present study may shed light on nucleosynthesis processes yielding heavy elements early in the Galaxy. A detailed abundance analysis of a high-quality spectrum is carried out, with the intent of providing a reference on stellar lines and abundances of a very old, metal-poor subgiant. We aim to derive abundances from most available and measurable spectral lines. The analysis is carried out using high-resolution (R = 81 000) and high signal-to-noise ratio (800 < S/N/pixel < 3400) spectrum, in the wavelength range 3700 - 10475, obtained with a seven-hour exposure time, using the ESPaDOnS at the CFHT. The calculations in LTE were performed with the OSMARCS 1D atmospheric model and the spectrum synthesis code Turbospectrum, while the analysis in NLTE is based on the MULTI code...

  3. Mars atmospheric water vapor abundance: 1996-1997

    Science.gov (United States)

    Sprague, A. L.; Hunten, D. M.; Doose, L. R.; Hill, R. E.

    2003-05-01

    Measurements of martian atmospheric water vapor made throughout Ls = 18.0°-146.4° (October 3, 1996-July 12, 1997) show changes in Mars humidity on hourly, daily, and seasonal time scales. Because our observing program during the 1996-1997 Mars apparition did not include concomitant measurement of nearby CO 2 bands, high northern latitude data were corrected for dust and aerosol extinction assuming an optical depth of 0.8, consistent with ground-based and HST imaging of northern dust storms. All other measurements with airmass greater than 3.5 were corrected using a total optical depth of 0.5. Three dominant results from this data set are as follows: (1) pre- and post-opposition measurements made with the slit crossing many hours of local time on Mars' Earth-facing disk show a distinct diurnal pattern with highest abundances around and slightly after noon with low abundances in the late afternoon, (2) measurements of water vapor over the Mars Pathfinder landing site (Carl Sagan Memorial Station) on July 12, 1997, found 21 ppt μm in the spatial sector centered near 19° latitude, 36° longitude while abundances around the site varied from as low as 6 to as high as 28 ppt μm, and (3) water vapor abundance is patchy on hourly and daily time scales but follows the usual seasonal trends.

  4. Abundance of eukaryotic microbes in the deep subtropical North Atlantic

    NARCIS (Netherlands)

    Morgan-Smith, D.; Herndl, G.J.; van Aken, H.M.; Bochdansky, A.B.

    2011-01-01

    The meso- and bathypelagic ocean comprises the largest habitat on earth, yet we know very little about the distribution and activity of protists in this environment. These small eukaryotes are responsible for controlling bacterial abundance in the surface ocean and are major players in the material

  5. Direct Oxygen Abundances for Low Luminosity LVL Galaxies

    CERN Document Server

    Berg, Danielle A; Marble, Andrew R; van Zee, Liese; Engelbracht, Charles W; Lee, Janice C; Kennicutt, Robert C; Jr.,; Calzetti, Daniela; Dale, Daniel A; Johnson, Benjamin D

    2012-01-01

    We present MMT spectroscopic observations of HII regions in 42 low luminosity galaxies in the LVL. For 31 galaxies, we measured the temperature sensitive [O III] line at a strength of 4 sigma or greater, and thus determine direct oxygen abundances. Our results provide the first direct estimates of oxygen abundance for 19 galaxies. Oxygen abundances were compared to B-band and 4.5 micron luminosities and stellar masses in order to characterize the luminosity-metallicity (L-Z) and mass-metallicity (M-Z) relationships at low-luminosity. We present and analyze a "Combined Select" sample composed of 38 objects (drawn from our parent sample and the literature) with direct oxygen abundances and reliable distance determinations (TRGB or Ceph). Consistent with previous studies, the B-band and 4.5 micron L-Z relationships were found to be 12+log(O/H)=(6.27+/-0.21)+(-0.11+/-0.01)M_B and 12+log(O/H)=(6.10+/-0.21)+(-0.10+/-0.01)M_[4.5] (sigma=0.15 and 0.14). For this sample, we derive a M-Z relationship of 12+log(O/H)=(5....

  6. A complete dataset of copper for investigation of element abundance

    Science.gov (United States)

    Zeng, Jiaolong; Liu, Yanpeng; Yuan, Jianmin

    2014-05-01

    The abundance of copper plays an important role in the chemical evolution of various stars, such as giant stars and solar-type stars. Accurate determination of its abundance helps to clarify a number of problems including the quite different behavior from other Fe-peak elements both in our Galaxy and extragalactic systems and the [Cu/Fe] ratios in Galactic stars. To accurately determine the copper abundance, it is necessary to include the non-local thermodynamic equilibrium (NLTE) effects, which depend on a complete dataset of atomic data. However, the complexity of electronic structure of copper makes the accurate prediction of a complete set of atomic data difficult. For both atomic Cu and the first ionized Cu II, the energies of 3d and 4s orbitals are very close and their competition results in complex energy levels. The excitation energy of 3d orbital is very low resulting in an opening 3d atomic system which is difficult to deal with theoretically due to the strong electron correlations. We present a complete set of atomic data including the energy levels, oscillator strengths, and photoionization cross sections of Cu I for the NLTE modeling in copper abundance investigation of astrophysical objects. The calculations are performed with the R-matrix method.

  7. Potential retention effect at fish farms boosts zooplankton abundance

    Science.gov (United States)

    Fernandez-Jover, D.; Toledo-Guedes, K.; Valero-Rodríguez, J. M.; Fernandez-Gonzalez, V.; Sanchez-Jerez, P.

    2016-11-01

    Coastal aquaculture activities influence wild macrofauna in natural environments due to the introduction of artificial structures, such as floating cages, that provide structural complexity in the pelagic system. This alters the abundance and distribution of the affected species and also their feeding behaviour and diet. Despite this, the effects of coastal aquaculture on zooplankton assemblages and the potential changes in their abundance and distribution remain largely unstudied. Traditional plankton sampling hauls between the farm mooring systems entail some practical difficulties. As an alternative, light traps were deployed at 2 farms in the SW Mediterranean during a whole warm season. Total zooplankton capture by traps at farms was higher than at control locations on every sampling night. It ranged from 3 to 10 times higher for the taxonomic groups: bivalvia, cladocera, cumacea, fish early-life-stages, gastropoda, polychaeta and tanaidacea; 10-20 times higher for amphipoda, chaetognatha, isopoda, mysidacea and ostracoda, and 22 times higher for copepoda and the crustacean juvenile stages zoea and megalopa. Permutational analysis showed significant differences for the most abundant zooplankton groups (copepoda, crustacean larvae, chaetognatha, cladocera, mysidacea and polychaeta). This marked incremental increase in zooplankton taxa at farms was consistent, irrespective of the changing environmental variables registered every night. Reasons for the greater abundance of zooplankton at farms are discussed, although results suggest a retention effect caused by cage structures rather than active attraction through physical or chemical cues.

  8. Interaction of detritus with abundance of cyanobacteria and microalgae

    NARCIS (Netherlands)

    Gons, H.J.

    1995-01-01

    Detritus particles interact with phytoplankton growth through light attenuation and nutrient retention. A model is described for predicting abundance of cyanobacteria and microalgae in relation to the detritus dynamics in shallow lakes with varying phosphorus load. Steady-state P distribution among

  9. "Capture" Me if You Can: Estimating Abundance of Dolphin Populations

    Science.gov (United States)

    Thompson, Jessica; Curran, Mary Carla; Cox, Tara

    2016-01-01

    Animal populations are monitored over time to assess the effects of environmental disaster and disease, as well as the efficacy of laws designed to protect them. Determining the abundance of a species within a defined area is one method of monitoring a population. In "Capture" Me if You Can, middle school students will use data collected…

  10. Abundance of bacterial and diatom fouling on various surfaces

    Digital Repository Service at National Institute of Oceanography (India)

    PrabhaDevi

    of exposure and thereafter an irreversible attachment was observed until the end of sampling (144 hr). Nitzschia sp was found to be most abundant on surfaces as well as in the subsurface waters. The other forms present included Navicula sp, Grammatophora sp...

  11. Chemical abundances of distant extremely metal-poor unevolved stars

    CERN Document Server

    Bonifacio, P; Caffau, E; Ludwig, H -G; Spite, M; Hernández, J I González; Behara, N T

    2012-01-01

    Aims: The purpose of our study is to determine the chemical composition of a sample of 16 candidate Extremely Metal-Poor (EMP) dwarf stars, extracted from the Sloan Digital Sky Survey (SDSS). There are two main purposes: in the first place to verify the reliability of the metallicity estimates derived from the SDSS spectra; in the second place to see if the abundance trends found for the brighter nearer stars studied previously also hold for this sample of fainter, more distant stars. Methods: We used the UVES at the VLT to obtain high-resolution spectra of the programme stars. The abundances were determined by an automatic analysis with the MyGIsFOS code, with the exception of lithium, for which the abundances were determined from the measured equivalent widths of the Li I resonance doublet. Results: All candidates are confirmed to be EMP stars, with [Fe/H]<= -3.0. The chemical composition of the sample of stars is similar to that of brighter and nearer samples. We measured the lithium abundance for 12 st...

  12. Terrestrial salamander abundance on reclaimed mountaintop removal mines

    Science.gov (United States)

    Wood, Petra Bohall; Williams, Jennifer M.

    2013-01-01

    Mountaintop removal mining, a large-scale disturbance affecting vegetation, soil structure, and topography, converts landscapes from mature forests to extensive grassland and shrubland habitats. We sampled salamanders using drift-fence arrays and coverboard transects on and near mountaintop removal mines in southern West Virginia, USA, during 2000–2002. We compared terrestrial salamander relative abundance and species richness of un-mined, intact forest with habitats on reclaimed mountaintop removal mines (reclaimed grassland, reclaimed shrubland, and fragmented forest). Salamanders within forests increased in relative abundance with increasing distance from reclaimed mine edge. Reclaimed grassland and shrubland habitats had lower relative abundance and species richness than forests. Characteristics of reclaimed habitats that likely contributed to lower salamander abundance included poor soils (dry, compacted, little organic matter, high rock content), reduced vertical structure of vegetation and little tree cover, and low litter and woody debris cover. Past research has shown that salamander populations reduced by clearcutting may rebound in 15–24 years. Time since disturbance was 7–28 years in reclaimed habitats on our study areas and salamander populations had not reached levels found in adjacent mature forests.

  13. Relative species abundance of replicator dynamics with sparse interactions

    Science.gov (United States)

    Obuchi, Tomoyuki; Kabashima, Yoshiyuki; Tokita, Kei

    2016-11-01

    A theory of relative species abundance on sparsely-connected networks is presented by investigating the replicator dynamics with symmetric interactions. Sparseness of a network involves difficulty in analyzing the fixed points of the equation, and we avoid this problem by treating large self interaction u, which allows us to construct a perturbative expansion. Based on this perturbation, we find that the nature of the interactions is directly connected to the abundance distribution, and some characteristic behaviors, such as multiple peaks in the abundance distribution and all species coexistence at moderate values of u, are discovered in a wide class of the distribution of the interactions. The all species coexistence collapses at a critical value of u, u c , and this collapsing is regarded as a phase transition. To get more quantitative information, we also construct a non-perturbative theory on random graphs based on techniques of statistical mechanics. The result shows those characteristic behaviors are sustained well even for not large u. For even smaller values of u, extinct species start to appear and the abundance distribution becomes rounded and closer to a standard functional form. Another interesting finding is the non-monotonic behavior of diversity, which quantifies the number of coexisting species, when changing the ratio of mutualistic relations Δ . These results are examined by numerical simulations, which show that our theory is exact for the case without extinct species, but becomes less and less precise as the proportion of extinct species grows.

  14. Chemical Abundance Analysis of Moving Group W11450 (Latham 1)

    CERN Document Server

    O'Connell, Julia E; Frinchaboy, Peter M

    2016-01-01

    We present elemental abundances for all seven stars in Moving Group W11450 (Latham 1) to determine if they may be chemically related. These stars appear to be both spatially and kinematically related, but no spectroscopic abundance analysis exists in literature. Abundances for eight elements were derived via equivalent width analyses of high resolution (R $\\sim$60,000), high signal-to-noise ratio ($\\langle$SNR$\\rangle\\sim$100) spectra obtained with the Otto Struve 2.1m telescope and Sandiford Echelle Spectrograph at McDonald Observatory. The large star-to-star scatter in metallicity, -0.55 $\\leq$ [Fe/H] $\\leq$ 0.06 dex ($\\sigma$= 0.25), implies these stars were not produced from the same chemically homogeneous molecular cloud, and are therefore not part of a remnant or open cluster as previously proposed. Prior to this analysis, it was suggested that two stars in the group, W11449 & W11450, are possible wide binaries. The candidate wide binary pair show similar chemical abundance patterns with not only ir...

  15. GASEOUS CO ABUNDANCE-AN EVOLUTIONARY TRACER FOR MOLECULAR CLOUDS

    Energy Technology Data Exchange (ETDEWEB)

    Liu Tie; Wu Yuefang; Zhang Huawei, E-mail: liutiepku@gmail.com, E-mail: ywu@pku.edu.cn [Department of Astronomy, Peking University, Beijing 100871 (China)

    2013-09-20

    Planck cold clumps are among the most promising objects to investigate the initial conditions of the evolution of molecular clouds. In this work, by combing the dust emission data from the survey of the Planck satellite with the molecular data of {sup 12}CO/{sup 13}CO/C{sup 18}O (1-0) lines from observations with the Purple Mountain Observatory 13.7 m telescope, we investigate the CO abundance, CO depletion, and CO-to-H{sub 2} conversion factor of 674 clumps in the early cold cores sample. The median and mean values of the CO abundance are 0.89 Multiplication-Sign 10{sup -4} and 1.28 Multiplication-Sign 10{sup -4}, respectively. The mean and median of CO depletion factor are 1.7 and 0.9, respectively. The median value of X{sub CO-to-H{sub 2}} for the whole sample is 2.8 Multiplication-Sign 10{sup 20} cm{sup -2} K{sup -1} km{sup -1} s. The CO abundance, CO depletion factor, and CO-to-H{sub 2} conversion factor are strongly (anti-)correlated to other physical parameters (e.g., dust temperature, dust emissivity spectral index, column density, volume density, and luminosity-to-mass ratio). To conclude, the gaseous CO abundance can be used as an evolutionary tracer for molecular clouds.

  16. NEW RADIAL ABUNDANCE GRADIENTS FOR NGC 628 AND NGC 2403

    Energy Technology Data Exchange (ETDEWEB)

    Berg, Danielle A.; Skillman, Evan D. [Department of Astronomy, University of Minnesota, 116 Church St. SE, Minneapolis, MN 55455 (United States); Croxall, Kevin V. [Ohio State University, 140 West 18th Avenue, Columbus, OH 43210 (United States); Marble, Andrew R. [National Solar Observatory, 950 N Cherry Avenue, Tucson, AZ 85719 (United States); Smith, J. D. [Ritter Astrophysical Observatory, University of Toledo, Toledo, OH 43606 (United States); Gordon, Karl [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Kennicutt, Robert C. Jr. [Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA (United Kingdom); Garnett, Donald R., E-mail: berg@astro.umn.edu, E-mail: skillman@astro.umn.edu, E-mail: croxall.5@osu.edu, E-mail: amarble@nso.edu, E-mail: jd.smith@utoledo.edu, E-mail: kgordon@stsci.edu, E-mail: robk@ast.cam.ac.uk

    2013-10-01

    Motivated by recent interstellar medium studies, we present high quality MMT and Gemini spectroscopic observations of H II regions in the nearby spiral galaxies NGC 628 and NGC 2403 in order to measure their chemical abundance gradients. Using long-slit and multi-object mask optical spectroscopy, we obtained measurements of the temperature sensitive auroral lines [O III] λ4363 and/or [N II] λ5755 at a strength of 4σ or greater in 11 H II regions in NGC 628 and 7 regions in NGC 2403. These observations allow us, for the first time, to derive an oxygen abundance gradient in NGC 628 based solely on 'direct' oxygen abundances of H II regions: 12 + log(O/H) = (8.43 ± 0.03) + (–0.017 ± 0.002) × R{sub g} (dex kpc{sup –1}), with a dispersion in log(O/H) of σ = 0.10 dex, from 14 regions with a radial coverage of ∼2-19 kpc. This is a significantly shallower slope than found by previous 'strong-line' abundance studies. In NGC 2403, we derive an oxygen abundance gradient of 12 + log(O/H) = (8.48 ± 0.04) + (–0.032 ± 0.007)× R{sub g} (dex kpc{sup –1}), with a dispersion in log(O/H) of σ = 0.07 dex, from seven H II with a radial coverage of ∼1-10 kpc. Additionally, we measure the N, S, Ne, and Ar abundances. We find the N/O ratio decreases with increasing radius for the inner disk, but reaches a plateau past R{sub 25} in NGC 628. NGC 2403 also has a negative N/O gradient with radius, but we do not sample the outer disk of the galaxy past R{sub 25} and so do not see evidence for a plateau. This bi-modal pattern measured for NGC 628 indicates dominant contributions from secondary nitrogen inside of the R{sub 25} transition and dominantly primary nitrogen farther out. As expected for α-process elements, S/O, Ne/O, and Ar/O are consistent with constant values over a range in oxygen abundance.

  17. Sulfur activation-related extracellular proteins of Acidithiobacillus ferrooxidans

    Institute of Scientific and Technical Information of China (English)

    ZHANG Cheng-gui; ZHANG Rui-yong; XIA Jin-lan; ZHANG Qian; NIE Zhen-yuan

    2008-01-01

    The fractions of the extracellular proteins of Acidithiobacillus ferrooxidans grown on two different energy substrates,elemental sulfur and ferrous sulfate,were selectively prepared with hot water treatment and distinctly shown by two-dimensional gel electrophoresis.Some protein spots with apparently higher abundance in sulfur energy substrate than in ferrous sulfate energy substrate were identified by using MALDI-TOF/TOF.Based on peptide mass fingerprints and bioinformatical analysis,the extracellular proteins were classified according to their functions as conjugal transfer protein,pilin,vacJ lipoprotein,polysaccharide deacetylase family protein,Ser/Thr protein phosphatase family protein and hypothetical proteins.Several extracellular proteins were found abundant in thiol groups and with CXXC functional motif,these proteins may be directly involved in the sulfur activation by use of their thiol group (Pr-SH) to bond the elemental sulfur.

  18. Sponging of Cellular Proteins by Viral RNAs

    OpenAIRE

    Charley, Phillida A.; Wilusz, Jeffrey

    2014-01-01

    Viral RNAs accumulate to high levels during infection and interact with a variety of cellular factors including miRNAs and RNA-binding proteins. Although many of these interactions exist to directly modulate replication, translation and decay of viral transcripts, evidence is emerging that abundant viral RNAs may in certain cases serve as a sponge to sequester host non coding RNAs and proteins. By effectively reducing the ability of cellular RNA binding proteins to regulate host cell gene exp...

  19. A role of peripheral myelin protein 2 in lipid homeostasis of myelinating Schwann cells.

    NARCIS (Netherlands)

    Zenker, Jennifer; ruskamo, salla; domenech-estevez, Enric; medard, jean-jacques; Verheijen, M.H.; Brouwers, Jos; Kursula, Petri; kieseier, bernd; Chrast, Roman

    2014-01-01

    Peripheral myelin protein 2 (Pmp2, P2 or Fabp8), a member of the fatty acid binding protein family, was originally described together with myelin basic protein (Mbp or P1) and myelin protein zero (Mpz or P0) as one of the most abundant myelin proteins in the peripheral nervous system (PNS). Although

  20. Estimating abundance in the presence of species uncertainty

    Science.gov (United States)

    Chambert, Thierry A; Hossack, Blake R.; Fishback, LeeAnn; Davenport, Jon M.

    2016-01-01

    1.N-mixture models have become a popular method for estimating abundance of free-ranging animals that are not marked or identified individually. These models have been used on count data for single species that can be identified with certainty. However, co-occurring species often look similar during one or more life stages, making it difficult to assign species for all recorded captures. This uncertainty creates problems for estimating species-specific abundance and it can often limit life stages to which we can make inference. 2.We present a new extension of N-mixture models that accounts for species uncertainty. In addition to estimating site-specific abundances and detection probabilities, this model allows estimating probability of correct assignment of species identity. We implement this hierarchical model in a Bayesian framework and provide all code for running the model in BUGS-language programs. 3.We present an application of the model on count data from two sympatric freshwater fishes, the brook stickleback (Culaea inconstans) and the ninespine stickleback (Pungitius pungitius), ad illustrate implementation of covariate effects (habitat characteristics). In addition, we used a simulation study to validate the model and illustrate potential sample size issues. We also compared, for both real and simulated data, estimates provided by our model to those obtained by a simple N-mixture model when captures of unknown species identification were discarded. In the latter case, abundance estimates appeared highly biased and very imprecise, while our new model provided unbiased estimates with higher precision. 4.This extension of the N-mixture model should be useful for a wide variety of studies and taxa, as species uncertainty is a common issue. It should notably help improve investigation of abundance and vital rate characteristics of organisms’ early life stages, which are sometimes more difficult to identify than adults.

  1. Abundance and bathymetric distribution of Bahrain (Arabian Gulf) reef ichthyofaunas

    Science.gov (United States)

    Smith, Gregory B.; Saleh, Mostafa A.

    1987-03-01

    Species composition and relative abundance of reef-fish assemblages at 4-7, 7-10, and 13-15 m depths off Bahrain (Arabian Gulf) were surveyed using SCUBA and the species/time, random count technique. A total of 55 species within 22 families was recorded from all reef stations. The most diverse reef-fish families were the Pomacentridae (5 spp.), Carangidae (4 spp.), Haemulidae (4 spp.), Sparidae (4 spp.), and Gobiidae (4 spp.). Species richness increased with depth, ranging from 37 species at the shallowest station to 43 species at the deepest station. Species composition and abundance exhibited quantitative and qualitative differences between the three depth intervals. Ten species were found only at the deepest station; 12 species were found only at the shallower stations. The abundance of many additional species progressively increased or decreased with increasing depth. A total of 10 species received maximum abundance scores. Of these, Pomacentrus trichourus received maximum abundance scores at all three stations. Pomacentrus aquilus and Diplodus sargus received maximum scores at both shallower stations. In addition, Amblygobius albimaculatus, Lutjanus fulviflammus, and Pseudochromis dutoiti received maximum scores at the shallowest station as did Scolopsis ghanam, S. taeniatus, Epinephelus malabaricus, and Neopomacentrus sindensis at the deepest station. Low species richness and equitability characterize the Bahrain reef ichthyofauna and undoubtedly relate to stressful environmental conditions within the Arabian Gulf. Most species are widely distributed through either the Western Indian Ocean Province or Indo-Polynesian Province of the Indo-West Pacific Region; several species, however, exhibit far more restricted distributions and confer a certain distinctiveness upon the Arabian Gulf ichthyofauna.

  2. Neutron-capture Element Abundances in Magellanic Cloud Planetary Nebulae

    Science.gov (United States)

    Mashburn, A. L.; Sterling, N. C.; Madonna, S.; Dinerstein, Harriet L.; Roederer, I. U.; Geballe, T. R.

    2016-11-01

    We present near-infrared spectra of 10 planetary nebulae (PNe) in the Large and Small Magellanic Clouds (LMC and SMC), acquired with the FIRE and GNIRS spectrometers on the 6.5 m Baade and 8.1 m Gemini South Telescopes, respectively. We detect Se and/or Kr emission lines in eight of these objects, the first detections of n-capture elements in Magellanic Cloud PNe. Our abundance analysis shows large s-process enrichments of Kr (0.6–1.3 dex) in the six PNe in which it was detected, and Se is enriched by 0.5–0.9 dex in five objects. We also estimate upper limits to Rb and Cd abundances in these objects. Our abundance results for the LMC are consistent with the hypothesis that PNe with 2–3 M ⊙ progenitors dominate the bright end of the PN luminosity function in young gas-rich galaxies. We find no significant correlations between s-process enrichments and other elemental abundances, central star temperature, or progenitor mass, though this is likely due to our small sample size. We determine S abundances from our spectra and find that [S/H] agrees with [Ar/H] to within 0.2 dex for most objects, but is lower than [O/H] by 0.2–0.4 dex in some PNe, possibly due to O enrichment via third dredge-up. Our results demonstrate that n-capture elements can be detected in PNe belonging to nearby galaxies with ground-based telescopes, allowing s-process enrichments to be studied in PN populations with well-determined distances. This paper includes data obtained with the 6.5-m Magellan Telescopes located at Las Campanas Observatory, Chile, and with the Gemini-South Telescope at Cerro Pachon, Chile.

  3. Abundance modelling of invasive and indigenous Culicoides species in Spain

    Directory of Open Access Journals (Sweden)

    Els Ducheyne

    2013-11-01

    Full Text Available In this paper we present a novel methodology applied in Spain to model spatial abundance patterns of potential vectors of disease at a medium spatial resolution of 5 x 5 km using a countrywide database with abundance data for five Culicoides species, random regression Forest modelling and a spatial dataset of ground measured and remotely sensed eco-climatic and environmental predictor variables. First the probability of occurrence was computed. In a second step a direct regression between the probability of occurrence and trap abundance was established to verify the linearity of the relationship. Finally the probability of occurrence was used in combination with the set of predictor variables to model abundance. In each case the variable importance of the predictors was used to biologically interpret results and to compare both model outputs, and model performance was assessed using four different accuracy measures. Results are shown for C. imicola, C. newsteadii, C. pulicaris group, C. punctatus and C. obsoletus group. In each case the probability of occurrence is a good predictor of abundance at the used spatial resolution of 5 x 5 km. In addition, the C. imicola and C. obsoletus group are highly driven by summer rainfall. The spatial pattern is inverse between the two species, indicating that the lower and upper thresholds are different. C. pulicaris group is mainly driven by temperature. The patterns for C. newsteadii and C. punctatus are less clear. It is concluded that the proposed methodology can be used as an input to transmission-infection-recovery (TIR models and R0 models. The methodology will become available to the general public as part of the VECMAPTM software.

  4. Identification of prophages in bacterial genomes by dinucleotide relative abundance difference.

    Directory of Open Access Journals (Sweden)

    K V Srividhya

    Full Text Available BACKGROUND: Prophages are integrated viral forms in bacterial genomes that have been found to contribute to interstrain genetic variability. Many virulence-associated genes are reported to be prophage encoded. Present computational methods to detect prophages are either by identifying possible essential proteins such as integrases or by an extension of this technique, which involves identifying a region containing proteins similar to those occurring in prophages. These methods suffer due to the problem of low sequence similarity at the protein level, which suggests that a nucleotide based approach could be useful. METHODOLOGY: Earlier dinucleotide relative abundance (DRA have been used to identify regions, which deviate from the neighborhood areas, in genomes. We have used the difference in the dinucleotide relative abundance (DRAD between the bacterial and prophage DNA to aid location of DNA stretches that could be of prophage origin in bacterial genomes. Prophage sequences which deviate from bacterial regions in their dinucleotide frequencies are detected by scanning bacterial genome sequences. The method was validated using a subset of genomes with prophage data from literature reports. A web interface for prophage scan based on this method is available at http://bicmku.in:8082/prophagedb/dra.html. Two hundred bacterial genomes which do not have annotated prophages have been scanned for prophage regions using this method. CONCLUSIONS: The relative dinucleotide distribution difference helps detect prophage regions in genome sequences. The usefulness of this method is seen in the identification of 461 highly probable loci pertaining to prophages which have not been annotated so earlier. This work emphasizes the need to extend the efforts to detect and annotate prophage elements in genome sequences.

  5. Proteomic characterization of human milk whey proteins during a twelve-month lactation period.

    Science.gov (United States)

    Liao, Yalin; Alvarado, Rudy; Phinney, Brett; Lönnerdal, Bo

    2011-04-01

    Human milk is a rich source of bioactive proteins that support the early growth and development of the newborn. Although the major components of the protein fraction in human milk have been studied, the expression and relative abundance of minor components have received limited attention. We examined the expression of low-abundance proteins in the whey fraction of human milk and their dynamic changes over a twelve-month lactation period. The low-abundance proteins were enriched by ProteoMiner beads, and protein identification was performed by liquid chromatography tandem mass spectrometry. One hundred and fifteen proteins were identified, thirty-eight of which have not been previously reported in human colostrum or milk. We also for the first time described differences in protein patterns among the low-abundance proteins during lactation. These results enhance our knowledge about the complexity of the human milk proteome, which constitutes part of the advantages to the breast-fed infant.

  6. High Mobility Group Proteins and Their Post-Translational Modifications

    OpenAIRE

    Zhang, Qingchun; Wang, Yinsheng

    2008-01-01

    The high mobility group (HMG) proteins, including HMGA, HMGB and HMGN, are abundant and ubiquitous nuclear proteins that bind to DNA, nucleosome and other multi-protein complexes in a dynamic and reversible fashion to regulate DNA processing in the context of chromatin. All HMG proteins, like histone proteins, are subjected to extensive post-translational modifications (PTMs), such as lysine acetylation, arginine/lysine methylation and serine/threonine phosphorylation, to modulate their inter...

  7. Correlation of mRNA and protein in complex biological samples.

    Science.gov (United States)

    Maier, Tobias; Güell, Marc; Serrano, Luis

    2009-12-17

    The correlation between mRNA and protein abundances in the cell has been reported to be notoriously poor. Recent technological advances in the quantitative analysis of mRNA and protein species in complex samples allow the detailed analysis of this pathway at the center of biological systems. We give an overview of available methods for the identification and quantification of free and ribosome-bound mRNA, protein abundances and individual protein turnover rates. We review available literature on the correlation of mRNA and protein abundances and discuss biological and technical parameters influencing the correlation of these central biological molecules.

  8. Review of Big Bang Nucleosynthesis and Primordial Abundances

    Science.gov (United States)

    Tytler, David; O'Meara, John M.; Suzuki, Nao; Lubin, Dan

    2001-03-01

    Big Bang Nucleosynthesis (BBN) is the synthesis of the light nuclei, Deuterium (D or 2H), 3He, 4He and 7Li during the first few minutes of the universe. This review concentrates on recent improvements in the measurement of the primordial (after BBN, and prior to modification) abundances of these nuclei. We mention improvement in the standard theory, and the non-standard extensions which are limited by the data. We have achieved an order of magnitude improvement in the precision of the measurement of primordial D/H, using the HIRES spectrograph on the W. M. Keck telescope to measure D in gas with very nearly primordial abundances towards quasars. From 1994 - 1996, it appeared that there could be a factor of ten range in primordial D/H, but today four examples of low D are secure. High D/H should be much easier to detect, and since there are no convincing examples, it must be extremely rare or non-existent. All data are consistent with a single low value for D/H, and the examples which are consistent with high D/H are readily interpreted as H contamination near the position of D. The new D/H measurements give the most accurate value for the baryon to photon ratio, η, and hence the cosmological baryon density. A similar density is required to explain the amount of Lyα absorption from neutral Hydrogen in the intergalactic medium (IGM) at redshift z ≃ 3, and to explain the fraction of baryons in local clusters of galaxies. The D/H measurements lead to predictions for the abundances of the other light nuclei, which generally agree with measurements. The remaining differences with some measurements can be explained by a combination of measurement and analysis errors or changes in the abundances after BBN. The measurements do not require physics beyond the standard BBN model. Instead, the agreement between the abundances is used to limit the non-standard physics. New measurements are giving improved understanding of the difficulties in estimating the abundances of all

  9. Protein Condensation

    Science.gov (United States)

    Gunton, James D.; Shiryayev, Andrey; Pagan, Daniel L.

    2014-07-01

    Preface; 1. Introduction; 2. Globular protein structure; 3. Experimental methods; 4. Thermodynamics and statistical mechanics; 5. Protein-protein interactions; 6. Theoretical studies of equilibrium; 7. Nucleation theory; 8. Experimental studies of nucleation; 9. Lysozyme; 10. Some other globular proteins; 11. Membrane proteins; 12. Crystallins and cataracts; 13. Sickle hemoglobin and sickle cell anemia; 14, Alzheimer's disease; Index.

  10. Relative quantification of several plasma proteins during liver transplantation surgery.

    Science.gov (United States)

    Parviainen, Ville; Joenväärä, Sakari; Tukiainen, Eija; Ilmakunnas, Minna; Isoniemi, Helena; Renkonen, Risto

    2011-01-01

    Plasma proteome is widely used in studying changes occurring in human body during disease or other disturbances. Immunological methods are commonly used in such studies. In recent years, mass spectrometry has gained popularity in high-throughput analysis of plasma proteins. In this study, we tested whether mass spectrometry and iTRAQ-based protein quantification might be used in proteomic analysis of human plasma during liver transplantation surgery to characterize changes in protein abundances occurring during early graft reperfusion. We sampled blood from systemic circulation as well as blood entering and exiting the liver. After immunodepletion of six high-abundant plasma proteins, trypsin digestion, iTRAQ labeling, and cation-exchange fractionation, the peptides were analyzed by reverse phase nano-LC-MS/MS. In total, 72 proteins were identified of which 31 could be quantified in all patient specimens collected. Of these 31 proteins, ten, mostly medium-to-high abundance plasma proteins with a concentration range of 50-2000 mg/L, displayed relative abundance change of more than 10%. The changes in protein abundance observed in this study allow further research on the role of several proteins in ischemia-reperfusion injury during liver transplantation and possibly in other surgery.

  11. Relative Quantification of Several Plasma Proteins during Liver Transplantation Surgery

    Directory of Open Access Journals (Sweden)

    Ville Parviainen

    2011-01-01

    Full Text Available Plasma proteome is widely used in studying changes occurring in human body during disease or other disturbances. Immunological methods are commonly used in such studies. In recent years, mass spectrometry has gained popularity in high-throughput analysis of plasma proteins. In this study, we tested whether mass spectrometry and iTRAQ-based protein quantification might be used in proteomic analysis of human plasma during liver transplantation surgery to characterize changes in protein abundances occurring during early graft reperfusion. We sampled blood from systemic circulation as well as blood entering and exiting the liver. After immunodepletion of six high-abundant plasma proteins, trypsin digestion, iTRAQ labeling, and cation-exchange fractionation, the peptides were analyzed by reverse phase nano-LC-MS/MS. In total, 72 proteins were identified of which 31 could be quantified in all patient specimens collected. Of these 31 proteins, ten, mostly medium-to-high abundance plasma proteins with a concentration range of 50–2000 mg/L, displayed relative abundance change of more than 10%. The changes in protein abundance observed in this study allow further research on the role of several proteins in ischemia-reperfusion injury during liver transplantation and possibly in other surgery.

  12. Protein found to promote DNA repair, prevent cancer

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ An abundant chromosomal protein that binds to damaged DNA prevents cancer development by enhancing DNA repair, researchers at University of Texas reported on-line in the Proceedings of the National Academies of Science.

  13. Abundance ratios in the hot ISM of elliptical galaxies

    CERN Document Server

    Pipino, A

    2011-01-01

    To constrain the recipes put forth to solve the theoretical Fe discrepancy in the hot interstellar medium of elliptical galaxies and at the same time explain the [alpha/Fe] ratios. In order to do so we use the latest theoretical nucleosynthetic yields, we incorporate the dust, we explore differing SNIa progenitor scenarios by means of a self-consistent chemical evolution model which reproduces the properties of the stellar populations in elliptical galaxies. Models with Fe-only dust and/or a lower effective SNIa rate achieve a better agreement with the observed Fe abundance. However, a suitable modification to the SNIa yield with respect to the standard W7 model is needed to fully match the abundance ratio pattern. The 2D explosion model C-DDT by Maeda et al. (2010) is a promising candidate for reproducing the [Fe/H] and the [alpha/Fe] ratios. (A&A format)

  14. Comparing Amino Acid Abundances and Distributions Across Carbonaceous Chondrite Groups

    Science.gov (United States)

    Burton, Aaron S.; Callahan, Michael P.; Glavin, Daniel P.; Elsila, Jamie E.; Dworkin, Jason P.

    2012-01-01

    Meteorites are grouped according to bulk properties such as chemical composition and mineralogy. These parameters can vary significantly among the different carbonaceous chondrite groups (CI, CM, CO, CR, CH, CB, CV and CK). We have determined the amino acid abundances of more than 30 primary amino acids in meteorites from each of the eight groups, revealing several interesting trends. There are noticeable differences in the structural diversity and overall abundances of amino acids between meteorites from the different chondrite groups. Because meteorites may have been an important source of amino acids to the prebiotic Earth and these organic compounds are essential for life as we know it, the observed variations of these molecules may have been important for the origins of life.

  15. On the statistical mechanics of species abundance distributions.

    Science.gov (United States)

    Bowler, Michael G; Kelly, Colleen K

    2012-09-01

    A central issue in ecology is that of the factors determining the relative abundance of species within a natural community. The proper application of the principles of statistical physics to species abundance distributions (SADs) shows that simple ecological properties could account for the near universal features observed. These properties are (i) a limit on the number of individuals in an ecological guild and (ii) per capita birth and death rates. They underpin the neutral theory of Hubbell (2001), the master equation approach of Volkov et al. (2003, 2005) and the idiosyncratic (extreme niche) theory of Pueyo et al. (2007); they result in an underlying log series SAD, regardless of neutral or niche dynamics. The success of statistical mechanics in this application implies that communities are in dynamic equilibrium and hence that niches must be flexible and that temporal fluctuations on all sorts of scales are likely to be important in community structure.

  16. Chemical Abundance Patterns and the Early Environment of Dwarf Galaxies

    CERN Document Server

    Corlies, Lauren; Tumlinson, Jason; Bryan, Greg

    2013-01-01

    Recent observations suggest that abundance pattern differences exist between low metallicity stars in the Milky Way stellar halo and those in the dwarf satellite galaxies. This paper takes a first look at what role the early environment for pre-galactic star formation might have played in shaping these stellar populations. In particular, we consider whether differences in cross-pollution between the progenitors of the stellar halo and the satellites could help to explain the differences in abundance patterns. Using an N-body simulation, we find that the progenitor halos of the main halo are primarily clustered together at z=10 while the progenitors of the satellite galaxies remain on the outskirts of this cluster. Next, analytically modeled supernova-driven winds show that main halo progenitors cross-pollute each other more effectively while satellite galaxy progenitors remain more isolated. Thus, inhomogeneous cross-pollution as a result of different high-z spatial locations of each system's progenitors can ...

  17. Generating potassium abundance variations in the Solar Nebula

    CERN Document Server

    Hubbard, Alexander

    2016-01-01

    An intriguing aspect of chondritic meteorites is that they are complementary: while their separate components have wildly varying abundances, bulk chondrites have nearly solar composition. This implies that the nearly-solar reservoirs in which chondrites were born were in turn assembled from sub-reservoirs of differing compositions that birthed the different components. We focus on explaining the potassium abundance variations between chondrules even within a single chondrite, while maintaining the observed CI $^{41}$K to $^{39}$K ratios. This requires physically separating potassium and chondrules while the temperature is high enough for K to be in the gas phase. We examine several mechanisms which could drive the dust through gas and show that to do so locally would have required long (sub-orbital to many orbits) time scales; with shortest potassium depletion time scales occurring in a scenario where chondrules formed high above the midplane and settled out of the evaporated potassium. While orbital time sc...

  18. Peculiarities of {\\alpha}-element abundances in Galactic open clusters

    CERN Document Server

    Marsakov, V A; Koval', V V; Shpigel', L V

    2016-01-01

    A catalog compiling the parameters of 346 open clusters, including their metallicities, positions, ages, and velocities has been composed. The elements of the Galactic orbits for 272 of the clusters have been calculated. Spectroscopic determinations of the relative abundances, [el/Fe], for 14 elements synthesized in various nuclear processes averaged over data from 109 publications are presented for 90 clusters. Since no systematic effects distorting the relative abundances of the studied elements in these clusters have been found, these difference suggest real differences between clusters with high, elongated orbits and field stars. In particular, this supports the earlier conclusion, based on an analysis of the elements of the Galactic orbits, that some clusters formed as a result of interactions between high-velocity, metal-poor clouds and the interstellar medium of the Galactic thin disk. On average, clusterswith high, elongated orbits and metallicities ${\\rm [Fe/H]} - 0.1$ formed as a result of interact...

  19. Atmospheric parameters and abundances of sdB stars

    CERN Document Server

    Heber, U

    2004-01-01

    We summarize recent results of quantitative spectral analyses using NLTE and metal line-blanketed LTE model atmospheres. Temperatures and gravities derived for hundreds of sdB stars are now available and allow us to investigate systematic uncertainties of teff, log g scales and to test the theory of stellar evolution and pulsations. Surface abundance patterns of about two dozen sdB stars are surprisingly homogenous. In particular the iron abundance is almost solar for most sdBs. We highlight one iron deficient and three super metal-rich sdBs, a challenge to diffusion theory. SdB stars are slowly rotating stars unless they are in close binary systems which is hard to understand if the sdB stars were formed in merger events. The only exception is the pulsator PG 1605+072 rotating at v sin i = 39km/s. Signatures of stellar winds from sdB stars have possibly been found.

  20. Multiple peaks of species abundance distributions induced by sparse interactions

    CERN Document Server

    Obuchi, Tomoyuki; Tokita, Kei

    2016-01-01

    We investigate the replicator dynamics with "sparse" symmetric interactions which represent specialist-specialist interactions in ecological communities. By considering a large self interaction $u$, we conduct a perturbative expansion which manifests that the nature of the interactions has a direct impact on the species abundance distribution. The central results are all species coexistence in a realistic range of the model parameters and that a certain discrete nature of the interactions induces multiple peaks in the species abundance distribution, providing the possibility of theoretically explaining multiple peaks observed in various field studies. To get more quantitative information, we also construct a non-perturbative theory which becomes exact on tree-like networks if all the species coexist, providing exact critical values of $u$ below which extinct species emerge. Numerical simulations in various different situations are conducted and they clarify the robustness of the presented mechanism of all spe...

  1. ASPCAP: The Apogee Stellar Parameter and Chemical Abundances Pipeline

    CERN Document Server

    Pérez, Ana E García; Holtzman, Jon A; Shetrone, Matthew; Mészáros, Szabolcs; Bizyaev, Dmitry; Carrera, Ricardo; Cunha, Katia; García-Hernández, D A; Johnson, Jennifer A; Majewski, Steven R; Nidever, David L; Schiavon, Ricardo P; Shane, Neville; Smith, Verne V; Sobeck, Jennifer; Troup, Nicholas; Zamora, Olga; Bovy, Jo; Eisenstein, Daniel J; Feuillet, Diane; Frinchaboy, Peter M; Hayden, Michael R; Hearty, Fred R; Nguyen, Duy C; O'Connell, Robert W; Pinsonneault, Marc H; Weinberg, David H; Wilson, John C; Zasowski, Gail

    2015-01-01

    The Apache Point Observatory Galactic Evolution Experiment (APOGEE) has built the largest moderately high-resolution (R=22, 500) spectroscopic map of the stars across the Milky Way, and including dust-obscured areas. The APOGEE Stellar Parameter and Chemical Abundances Pipeline (ASPCAP) is the software developed for the automated analysis of these spectra. ASPCAP determines atmospheric parameters and chemical abundances from observed spectra by comparing observed spectra to libraries of theoretical spectra, using chi-2 minimization in a multidimensional parameter space. The package consists of a fortran90 code that does the actual minimization, and a wrapper IDL code for book-keeping and data handling. This paper explains in detail the ASPCAP components and functionality, and presents results from a number of tests designed to check its performance. ASPCAP provides stellar effective temperatures, surface gravities, and metallicities precise to 2%, 0.1 dex, and 0.05 dex, respectively, for most APOGEE stars, wh...

  2. The Curious Conundrum Regarding Sulfur Abundances In Planetary Nebulae

    CERN Document Server

    Henry, R B C; Karakas, A I; Ferland, G J; Maguire, M

    2012-01-01

    Sulfur abundances derived from optical emission line measurements and ionization correction factors in planetary nebulae are systematically lower than expected for the objects' metallicities. We have carefully considered a large range of explanations for this "sulfur anomaly", including: (1) correlations between the size of the sulfur deficit and numerous nebular and central star properties; (2) ionization correction factors which under-correct for unobserved ions; (3) effects of dielectronic recombination on the sulfur ionization balance; (4) sequestering of S into dust and/or molecules; and (5) excessive destruction of S or production of O by AGB stars. It appears that all but the second scenario can be ruled out. However, we find evidence that the sulfur deficit is generally reduced but not eliminated when S^+3 abundances determined directly from IR measurements are used in place of the customary sulfur ionization correction factor. We tentatively conclude that the sulfur anomaly is caused by the inability...

  3. Iron Abundance Diagnostics in High-Redshift QSOs

    CERN Document Server

    Corbin, M R; Freduling, N K W; Corbin, Michael R.; Korista, Kirk T.; Freduling, Nalaka Kodituwakku & Wolfram

    2004-01-01

    The abundance of alpha-process elements such as magnesium and carbon relative to iron measured from the broad emission lines of QSOs can serve as a diagnostic of the star formation and chemical enrichment histories of their host galaxies. We investigate the relationship between Fe/Mg and Fe/C abundance ratios and the resulting Fe II / Mg II 2800A and Fe II / 1900A-blend flux ratios, both of which have been measured in QSOs out to redshifts of approximately six. Using a galactic chemical evolution model based on a starburst in a giant elliptical galaxy, we find that these flux ratios are good tracers of the chemical enrichment of the nuclei. However, the values of these ratios measured in objects at redshifts of approximately six suggest that iron enrichment has occurred more rapidly in these objects than predicted by the assumed elliptical starburst model, under currently favored cosmologies.

  4. Can solid body destruction explain abundance discrepancies in planetary nebulae?

    CERN Document Server

    Henney, William J

    2010-01-01

    In planetary nebulae, abundances of oxygen and other heavy elements derived from optical recombination lines are systematically higher than those derived from collisionally excited lines. We investigate the hypothesis that the destruction of solid bodies may produce pockets of cool, high-metallicity gas that could explain these abundance discrepancies. Under the assumption of maximally efficient radiative ablation, we derive two fundamental constraints that the solid bodies must satisfy in order that their evaporation during the planetary nebula phase should generate a high enough gas phase metallicity. A local constraint implies that the bodies must be larger than tens of meters, while a global constraint implies that the total mass of the solid body reservoir must exceed a few hundredths of a solar mass. This mass greatly exceeds the mass of any population of comets or large debris particles expected to be found orbiting evolved low- to intermediate-mass stars. We therefore conclude that contemporaneous sol...

  5. Chemical Abundances of the S star GZ Peg

    CERN Document Server

    Pompéia, Luciana

    2009-01-01

    The chemical compositions of stars from the Asymptotic Giant Branch are still poorly known due to the low temperatures of their atmospheres and therefore the presence of many molecular transitions hampering the analysis of atomic lines. One way to overcome this difficulty is by the study of lines in regions free from molecular contamination. We have chosen some of those regions to study the chemical abundance of the S-type star GZ Peg. Stellar parameters are derived from spectroscopic analysis and a metallicity of -0.77 dex is found. Chemical abundances of 8 elements are reported and an enhancement of s-process elements is inferred, typical to that of an S-type star.

  6. ELSA: An Integrated, Semi-Automated Nebular Abundance Package

    CERN Document Server

    Johnson, M D; Henry, R B C; Kwitter, K B

    2006-01-01

    We present ELSA, a new modular software package, written in C, to analyze and manage spectroscopic data from emission-line objects. In addition to calculating plasma diagnostics and abundances from nebular emission lines, the software provides a number of convenient features including the ability to ingest logs produced by IRAF's splot task, to semi-automatically merge spectra in different wavelength ranges, and to automatically generate various data tables in machine-readable or LaTeX format. ELSA features a highly sophisticated interstellar reddening correction scheme that takes into account temperature and density effects as well as He II contamination of the hydrogen Balmer lines. Abundance calculations are performed using a 5-level atom approximation with recent atomic data, based on R. Henry's ABUN program. Improvements planned in the near future include use of a three-region ionization model, similar to IRAF's nebular package, error propagation, and the addition of ultraviolet and infrared line analysi...

  7. Revisiting the Interpretation of Thorium Abundances at Hansteen Alpha

    Science.gov (United States)

    Lawrence, D. J.; Hawke, B. R.; Elphic, R. C.; Feldman, W. C.; Prettyman, T. H.; Vaniman, D. T.

    2004-01-01

    Hansteen Alpha is one of the few remaining locations on the Moon thought to be formed by highlands volcanism. Hansteen Alpha is a triangular shaped feature located in the southern portion of Oceanus Procellarum (12 degrees W, 50 degrees S) and its size is approximately 25 km on each side. As described by Hawke et al., there is clear evidence that: 1) Hansteen Alpha was emplaced by extrusive volcanic processes; and 2) it was formed by a viscous lava that should be enriched in Th. However, in the study of Hawke et al. using available Lunar Prospector (LP) Th data, it was concluded that the Hansteen Alpha region was not greatly enriched in Th as would be expected for a highly evolved, viscous lava. It was further concluded based on other compositional data that the magma that formed Hansteen Alpha did not correspond to any known rock type. Here we revisit the interpretation of Th abundances at Hansteen Alpha for a couple of reasons. First, the size of Hansteen Alpha is smaller than the spatial resolution of the LP Gamma-ray Spectrometer (LP-GRS) from which the Th abundances were derived. Therefore, the LP-GRS pixels covering Hansteen Alpha may not truly represent the Th abundance of the Hansteen Alpha feature. Second, recent work has led to a much greater understanding of the Th spatial distribution for small-area features on the lunar surface. In particular, using forward modeling techniques, we have developed the ability to obtain information about Th abundances for features that are at or smaller than the FWHM spatial resolution (approximately [80 square kilometers]) of the LP-GRS data.

  8. Raptor abundance and northern bobwhite survival and habitat use

    Science.gov (United States)

    Turner, J.; Hernandez, F.; Boal, Clint W.; Ballard, Bart M.; Bryant, Fred C.; Wester, D.B.

    2014-01-01

    Predation risk has a profound influence on prey behavior and habitat use. The Rio Grande Plains ecoregion of Texas, USA, provides a unique opportunity to investigate changes in prey behavior because the ecoregion experiences a high influx of raptors every year during autumn migration. We used an 8-year data set (2000–2008) of radiocollared northern bobwhites (Colinus virginianus) and raptor abundance to test the hypothesis that bobwhites responded to increased raptor abundance via changes in woody-cover use at the home-range scale. Bobwhite survival was negatively correlated with raptor abundance, with red-tailed hawks (Buteo jamaicensis), and northern harriers (Circus cyaneus) accounting for 51% of the variability in bobwhite survival (P raptor migration (6.6% ± 0.5%; n = 73 bobwhites) and non-migration periods (7.1% ± 0.4%; n = 105 bobwhites; P = 0.490). In addition, bobwhites that survived the raptor migration period used similar amounts of woody cover within their home range (6.3% ± 0.6%, n = 58 bobwhites) compared with those dying during the migration period (6.8% ± 0.4%, n = 100 bobwhites; P = 0.530). Our data suggest that bobwhites do not alter their use of woody cover at the home-range scale in response to increasing raptor abundance, but this does not preclude increased use of woody cover at the point-of-use scale.

  9. Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

    KAUST Repository

    Roux, Simon

    2016-05-12

    Ocean microbes drive global-scale biogeochemical cycling, but do so under constraints imposed by viruses on host community composition, metabolism, and evolutionary trajectories. Due to sampling and cultivation challenges, genome-level viral diversity remains poorly described and grossly understudied in nature such that <1% of observed surface ocean viruses, even those that are abundant and ubiquitous, are ?known?. Here we analyze a global map of abundant, double stranded DNA (dsDNA) viruses and viral-encoded auxiliary metabolic genes (AMGs) with genomic and ecological contexts through the Global Ocean Viromes (GOV) dataset, which includes complete genomes and large genomic fragments from both surface and deep ocean viruses sampled during the Tara Oceans and Malaspina research expeditions. A total of 15,222 epi- and mesopelagic viral populations were identified that comprised 867 viral clusters (VCs, approximately genus-level groups). This roughly triples known ocean viral populations, doubles known candidate bacterial and archaeal virus genera, and near-completely samples epipelagic communities at both the population and VC level. Thirty-eight of the 867 VCs were identified as the most impactful dsDNA viral groups in the oceans, as these were locally or globally abundant and accounted together for nearly half of the viral populations in any GOV sample. Most of these were predicted in silico to infect dominant, ecologically relevant microbes, while two thirds of them represent newly described viruses that lacked any cultivated representative. Beyond these taxon-specific ecological observations, we identified 243 viral-encoded AMGs in GOV, only 95 of which were known. Deeper analyses of 4 of these AMGs revealed that abundant viruses directly manipulate sulfur and nitrogen cycling, and do so throughout the epipelagic ocean. Together these data provide a critically-needed organismal catalog and functional context to begin meaningfully integrating viruses into

  10. Lightest sterile neutrino abundance within the nuMSM

    OpenAIRE

    Asaka, Takehiko; Laine, Mikko; Shaposhnikov, Mikhail

    2006-01-01

    We determine the abundance of the lightest (dark matter) sterile neutrinos created in the Early Universe due to active-sterile neutrino transitions from the thermal plasma. Our starting point is the field-theoretic formula for the sterile neutrino production rate, derived in our previous work [JHEP 06(2006)053], which allows to systematically incorporate all relevant effects, and also to analyse various hadronic uncertainties. Our numerical results differ moderately from previous computations...

  11. Palm diversity and abundance in the Colombian Amazon

    DEFF Research Database (Denmark)

    Balslev, Henrik; Copete, Juan Carlos; Pedersen, Dennis

    2017-01-01

    We studied diversity and abundance of palms in the eastern Colombian Amazon in 71 transects, 61 measuring 5×500 m and 10 transects measuring 4×500 m, innventoring a total of 17.25 hectares. We found a total of 74 species in 21 genera. In terra firme we found 68 species in 20 genera and an average...... found in this study (Euterpe precatoria, Oenocarpus bataua, Attalea butyracea, Iriartella setigera) coincide with dominant species in other Amazonian palm communities....

  12. Evolution of lithium abundance in the Sun and solar twins

    Science.gov (United States)

    Thévenin, F.; Oreshina, A. V.; Baturin, V. A.; Gorshkov, A. B.; Morel, P.; Provost, J.

    2017-02-01

    Evolution of the 7Li abundance in the convection zone of the Sun during different stages of its life time is considered to explain its low photospheric value in comparison with that of the solar system meteorites. Lithium is intensively and transiently burned in the early stages of evolution (pre-main sequence, pMS) when the radiative core arises, and then the Li abundance only slowly decreases during the main sequence (MS). We study the rates of lithium burning during these two stages. In a model of the Sun, computed ignoring pMS and without extra-convective mixing (overshooting) at the base of the convection zone, the lithium abundance does not decrease significantly during the MS life time of 4.6 Gyr. Analysis of helioseismic inversions together with post-model computations of chemical composition indicates the presence of the overshooting region and restricts its thickness. It is estimated to be approximately half of the local pressure scale height (0.5HP) which corresponds to 3.8% of the solar radius. Introducing this extra region does not noticeably deplete lithium during the MS stage. In contrast, at the pMS stage, an overshooting region with a value of approximately 0.18HP is enough to produce the observed lithium depletion. If we conclude that the dominant lithium burning takes place during the pMS stage, the dispersion of the lithium abundance in solar twins is explained by different physical conditions, primarily during the early stage of evolution before the MS.

  13. Should Ecosystem Management Involve Active Control of Species Abundances?

    Directory of Open Access Journals (Sweden)

    Timothy E. Essington

    2005-12-01

    Full Text Available We review four case studies in which there is a risk of extinction or severe reduction in highly valued species if we ignore either, or both, of two ecosystem control options. “Symptomatic control” implies direct control of extinction risk through direct harvesting or culling of competitors and predators. “Systemic control” implies treating the causes of the problem that led to an unnaturally high abundance in the first place. We demonstrate, with a discussion of historically observed population trends, how surprising trophic interactions can emerge as a result of alterations to a system. Simulation models were developed for two of the case studies as aids to adaptive policy design, to expose possible abundance changes caused by trophic interactions and to highlight key uncertainties about possible responses to ecosystem management policies involving active intervention to control abundances. With reasonable parameter values, these models predict a wide range of possible responses given available data, but do indicate a good chance that active control would reverse declines and reverse extinction risks. We find that controlling seal (Phoca vitulina populations in the Georgia Strait increases juvenile survival rates of commercial salmon (Oncorhynchus spp. species, but that commensurate increases in hake populations from decreased seal predation could be a compensatory source of predation on juvenile salmon. We also show that wolf (Canis lupus control and moose (Alces alces harvest bring about a recovery in caribou (Rangifer tarandus caribou populations, where simple habitat protection policies fail to recover caribou before wolf predation causes severe declines. The results help address a common problem in disturbed ecosystems, where controlling extinction risks can mean choosing between active control of species abundance or establishing policies of protection, and allowing threatened species to recover naturally.

  14. Abundances and ADFs in PNe with WC central stars

    CERN Document Server

    García-Rojas, Jorge; Morisset, Christophe; Ruiz, Maria Teresa

    2011-01-01

    We present preliminary results obtained from the analysis of very deep echelle spectra of a dozen planetary nebulae with [WC] or weak emission lines (wels) central stars. The computed abundance discrepancy factors (ADFs) are moderate, with values lower than 4. In principle, no evidence of the H-poor metal enriched inclusions proposed by Liu et al. (2000) have been found. However, a detailed analysis of the data is in progress.

  15. Diversity and abundance of photosynthetic sponges in temperate Western Australia

    Directory of Open Access Journals (Sweden)

    Brümmer Franz

    2009-02-01

    Full Text Available Abstract Background Photosynthetic sponges are important components of reef ecosystems around the world, but are poorly understood. It is often assumed that temperate regions have low diversity and abundance of photosynthetic sponges, but to date no studies have investigated this question. The aim of this study was to compare the percentages of photosynthetic sponges in temperate Western Australia (WA with previously published data on tropical regions, and to determine the abundance and diversity of these associations in a range of temperate environments. Results We sampled sponges on 5 m belt transects to determine the percentage of photosynthetic sponges and identified at least one representative of each group of symbionts using 16S rDNA sequencing together with microscopy techniques. Our results demonstrate that photosynthetic sponges are abundant in temperate WA, with an average of 63% of sponge individuals hosting high levels of photosynthetic symbionts and 11% with low to medium levels. These percentages of photosynthetic sponges are comparable to those found on tropical reefs and may have important implications for ecosystem function on temperate reefs in other areas of the world. A diverse range of symbionts sometimes occurred within a small geographic area, including the three "big" cyanobacterial clades, Oscillatoria spongeliae, "Candidatus Synechococcus spongiarum" and Synechocystis species, and it appears that these clades all occur in a wide range of sponges. Additionally, spongin-permeating red algae occurred in at least 7 sponge species. This study provides the first investigation of the molecular phylogeny of rhodophyte symbionts in sponges. Conclusion Photosynthetic sponges are abundant and diverse in temperate WA, with comparable percentages of photosynthetic to non-photosynthetic sponges to tropical zones. It appears that there are three common generalist clades of cyanobacterial symbionts of sponges which occur in a wide

  16. Histogrammatic Method for Determining Relative Abundance of Input Gas Pulse

    Science.gov (United States)

    Mandrake, Lukas; Bornstein, Benjamin J.; Madzunkov, Stojan; MacAskill, John A.

    2012-01-01

    To satisfy the Major Constituents Analysis (MCA) requirements for the Vehicle Cabin Atmosphere Monitor (VCAM), this software analyzes the relative abundance ratios for N2, O2, Ar, and CO2 as a function of time and constructs their best-estimate mean. A histogram is first built of all abundance ratios for each of the species vs time. The abundance peaks corresponding to the intended measurement and any obfuscating background are then separated via standard peak-finding techniques in histogram space. A voting scheme is then used to include/exclude this particular time sample in the final average based on its membership to the intended measurement or the background population. This results in a robust and reasonable estimate of the abundance of trace components such as CO2 and Ar even in the presence of obfuscating backgrounds internal to the VCAM device. VCAM can provide a means for monitoring the air within the enclosed environments, such as the ISS (International Space Station), Crew Exploration Vehicle (CEV), a Lunar Habitat, or another vehicle traveling to Mars. Its miniature pre-concentrator, gas chromatograph (GC), and mass spectrometer can provide unbiased detection of a large number of organic species as well as MCA analysis. VCAM s software can identify the concentration of trace chemicals and whether the chemicals are on a targeted list of hazardous compounds. This innovation s performance and reliability on orbit, along with the ground team s assessment of its raw data and analysis results, will validate its technology for future use and development.

  17. Abundances of metal-weak thick-disc candidates

    CERN Document Server

    Bonifacio, P; Molaro, P

    1999-01-01

    High resolution spectra of 5 candidate metal-weak thick-disc stars suggested by Beers & Sommer-Larsen (1995) are analyzed to determine their chemical abundances. The low abundance of all the objects has been confirmed with metallicity reaching [Fe/H]=-2.9. However, for three objects, the astrometric data from the Hipparcos catalogue suggests they are true halo members. The remaining two, for which proper-motion data are not available, may have disc-like kinematics. It is therefore clear that it is useful to address properties of putative metal-weak thick-disc stars only if they possess full kinematic data. For CS 22894-19 the abundance pattern similar to those of typical halo stars is found, suggesting that chemical composition is not a useful discriminant between thick-disc and halo stars. CS 29529-12 is found to be C enhanced with [C/Fe]=+1.0; other chemical peculiarities involve the s process elements: [Sr/Fe]=-0.65 and [Ba/Fe]=+0.62, leading to a high [Ba/Sr] considerably larger than what is found in ...

  18. Counteracting wetland overgrowth increases breeding and staging bird abundances

    Science.gov (United States)

    Lehikoinen, Petteri; Lehikoinen, Aleksi; Mikkola-Roos, Markku; Jaatinen, Kim

    2017-01-01

    Human actions have led to loss and degradation of wetlands, impairing their suitability as habitat especially for waterbirds. Such negative effects may be mitigated through habitat management. To date scientific evidence regarding the impacts of these actions remains scarce. We studied guild specific abundances of breeding and staging birds in response to habitat management on 15 Finnish wetlands. In this study management actions comprised several means of vegetation removal to thwart overgrowth. Management cost efficiency was assessed by examining the association between site-specific costs and bird abundances. Several bird guilds exhibited positive connections with both habitat management as well as with invested funds. Most importantly, however, red-listed species and species with special conservation concern as outlined by the EU showed positive correlations with management actions, underlining the conservation value of wetland management. The results suggest that grazing was especially efficient in restoring overgrown wetlands. As a whole this study makes it clear that wetland habitat management constitutes a feasible conservation tool. The marked association between invested funds and bird abundance may prove to be a valuable tool for decision makers when balancing costs and impact of conservation measures against one another.

  19. Breeding return times and abundance in capture-recapture models.

    Science.gov (United States)

    Pledger, Shirley; Baker, Edward; Scribner, Kim

    2013-12-01

    For many long-lived animal species, individuals do not breed every year, and are often not accessible during non-breeding periods. Individuals exhibit site fidelity if they return to the same breeding colony or spawning ground when they breed. If capture and recapture is only possible at the breeding site, temporary emigration models are used to allow for only a subset of the animals being present in any given year. Most temporary emigration models require the use of the robust sampling design, and their focus is usually on probabilities of annual survival and of transition between breeding and non-breeding states. We use lake sturgeon (Acipenser fulvescens) data from a closed population where only a simple (one sample per year) sampling scheme is possible, and we also wish to estimate abundance as well as sex-specific survival and breeding return time probabilities. By adding return time parameters to the Schwarz-Arnason version of the Jolly-Seber model, we have developed a new likelihood-based model which yields plausible estimates of abundance, survival, transition and return time parameters. An important new finding from investigation of the model is the overestimation of abundance if a Jolly-Seber model is used when Markovian temporary emigration is present.

  20. Element Abundances and Source Plasma Temperatures of Solar Energetic Particles

    Science.gov (United States)

    Reames, Donald V.

    2016-11-01

    Thirty years ago Breneman and Stone [1] observed that the enhancement or suppression of element abundances in large solar energetic-particle (SEP) events varies as a power of the mass-to-charge ratio, A/Q, of the elements. Since Q during acceleration or transport may depend upon the source plasma temperature T, the pattern of element enhancements can provide a best-fit measure of T. The small SEP events we call 3He-rich or “impulsive” show average enhancements, relative to coronal abundances, rising as the 3.6 power of A/Q to a factor of ∼1000 for (76magnetic reconnection on open field lines in solar flares and jets. It has been recently found that the large shock-accelerated “gradual” SEP events have a broad range of source plasma temperatures; 69% have coronal temperatures of T seed population containing residual impulsive suprathermal ions. Most of the large event-to-event abundance variations and their time variation are largely explained by variations in T magnified by A/Q-dependent fractionation during transport. However, the non-thermal variance of impulsive SEP events (∼30%) exceeds that of the ∼3 MK gradual events (∼10%) so that several small impulsive events must be averaged together with the ambient plasma to form the seed population for shock acceleration in these events.

  1. The Effects of Initial Abundances on Nitrogen in Protoplanetary Disks

    CERN Document Server

    Schwarz, Kamber R

    2014-01-01

    The dominant form of nitrogen provided to most solar system bodies is currently unknown, though available measurements show that the detected nitrogen in solar system rocks and ices is depleted with respect to solar abundances and the interstellar medium. We use a detailed chemical/physical model of the chemical evolution of a protoplanetary disk to explore the evolution and abundance of nitrogen-bearing molecules. Based on this model we analyze how initial chemical abundances, provided as either gas or ice during the early stages of disk formation, influence which species become the dominant nitrogen bearers at later stages. We find that a disk with the majority of its initial nitrogen in either atomic or molecular nitrogen is later dominated by atomic and molecular nitrogen as well as NH$_{3}$ and HCN ices, where the dominant species varies with disk radius. When nitrogen is initially in gaseous ammonia, it later becomes trapped in ammonia ice except in the outer disk where atomic nitrogen dominates. For a ...

  2. Chromospheric Models and the Oxygen Abundance in Giant Stars

    CERN Document Server

    Dupree, A K; Kurucz, R L

    2016-01-01

    Realistic stellar atmospheric models of two typical metal-poor giant stars in Omega Centauri that include a chromosphere influence the formation of optical lines of Oxygen I: the forbidden lines (630nm, 636nm) and the infrared triplet (777.1-777.5 nm). One-dimensional semi-empirical non-LTE models are constructed based on observed Balmer lines. A full non-LTE formulation is applied in evaluating line strengths of O I including photoionization by the Lyman continuum and photoexcitation by Ly-alpha and Ly-beta. Chromospheric models (CHR) yield forbidden oxygen transitions that are stronger than in radiative/convective equilibrium (RCE) models. The triplet oxygen lines from high levels also appear stronger than produced in an RCE model. The inferred oxygen abundance from realistic CHR models for these two stars is decreased by factors ~3 as compared to values derived from RCE models. A lower oxygen abundance suggests that intermediate mass AGB stars contribute to the observed abundance pattern in globular cluste...

  3. Carbon and Oxygen Abundances in Low Metallicity Dwarf Galaxies

    Science.gov (United States)

    Berg, Danielle A.; Skillman, Evan D.; Henry, Richard B. C.; Erb, Dawn K.; Carigi, Leticia

    2016-08-01

    The study of carbon and oxygen abundances yields information on the time evolution and nucleosynthetic origins of these elements, yet they remain relatively unexplored. At low metallicities, (12+log(O/H) complemented by optical SDSS spectra, from which we measured the nebular physical conditions and oxygen abundances using the direct method. At low metallicity, (12+log(O/H) < 8.0), no clear trend is evident in C/O versus O/H for the present sample given the large dispersion observed. When combined with recombination line observations at higher values of O/H, a general trend of increasing C/O with increasing O/H is also viable but with some significant outliers. Additionally, we find the C/N ratio appears to be constant (but with significant scatter) over a large range in oxygen abundance, indicating that carbon is predominantly produced by similar nucleosynthetic mechanisms as nitrogen. If true, and our current understanding of nitrogen production is correct, this would indicate that primary production of carbon (a flat trend) dominates at low metallicity, but quasi-secondary production (an increasing trend) becomes prominent at higher metallicities. A larger sample will be needed to determine the true nature and dispersion of the relation.

  4. Chemical abundances in Galactic Planetary Nebulae with Spitzer spectra

    CERN Document Server

    Garcia-Hernandez, D A

    2014-01-01

    We present new low-resolution (R~800) optical spectra of 22 Galactic PNe with Spitzer spectra. These data are combined with recent optical spectroscopic data available in the literature to construct representative samples of compact (and presumably young) Galactic disc and bulge PNe with Spitzer spectra. Attending to the nature of the dust features seen in their Spitzer spectra, Galactic disc and bulge PNe are classified according to four major dust types (oxygen chemistry or OC, carbon chemistry or CC, double chemistry or DC, featureless or F) and subtypes (amorphous and crystalline, and aliphatic and aromatic). Nebular gas abundances of He, N, O, Ne, S, Cl and Ar, as well as plasma parameters (e.g. Ne, Te) are homogeneously derived and we study the median chemical abundances and nebular properties in Galactic disc and bulge PNe depending on their Spitzer dust types and subtypes. A comparison of the derived median abundance patterns with AGB nucleosynthesis predictions show mainly that: i) DC PNe, both with ...

  5. Highly siderophile element abundances in Eoarchean komatiite and basalt protoliths

    Science.gov (United States)

    Frank, Elizabeth A.; Maier, Wolfgang D.; Mojzsis, Stephen J.

    2016-03-01

    Plume-derived, Mg-rich, volcanic rocks (komatiites, high-Mg basalts, and their metamorphic equivalents) can record secular changes in the highly siderophile element (HSE) abundances of mantle sources. An apparent secular time-dependent enrichment trend in HSE abundances from Paleoarchean to Paleoproterozoic mantle-derived rocks could represent the protracted homogenization of a Late Veneer chondritic contaminant into the pre-Late Veneer komatiite source. To search for a possible time dependence of a late accretion signature in the Eoarchean mantle, we report new data from rare >3700 Myr-old mafic and ultramafic schists locked in supracrustal belts from the Inukjuak domain (Québec, Canada) and the Akilia association (West Greenland). Our analysis shows that some of these experienced HSE mobility and/or include a cumulate component (Touboul et al. in Chem Geol 383:63-75, 2014), whereas several of the oldest samples show some of the most depleted HSE abundances measured for rocks of this composition. We consider these new data for the oldest documented rocks of komatiite protolith in light of the Late Veneer hypothesis.

  6. Relic Abundance in Secluded Dark Matter Scenario with Massive Mediator

    CERN Document Server

    Okawa, Shohei; Yamanaka, Masato

    2016-01-01

    The relic abundance of the dark matter (DM) particle $d$ is studied in a secluded DM scenario, in which the $d$ number decreasing process dominantly occurs not through the pair annihilation of $d$ into the standard model particles, but via the $dd \\to mm$ scattering process with a subsequently decaying mediator particle $m$. It is pointed out that the cosmologically observed relic abundance of DM can be accomplished even with a massive mediator having a mass $m_m$ non-negligibly heavy compared with the DM particle mass $m_d$. In the degenerated $d$-$m$ case ($m_d=m_m$), the DM relic abundance is realized by adjusting the $dd \\to mm$ scattering amplitude large enough and by choosing an appropriate mediator particle life-time. The DM evolution in the early universe exhibits characteristic "terrace" behavior, or two-step number density decreasing behavior, having a "fake" freeze-out at the first step. Based on these observations, a novel possibility of the DM model buildings is introduced in which the mediator p...

  7. The distribution and abundance of interstellar C2H

    Science.gov (United States)

    Huggins, P. J.; Carlson, W. J.; Kinney, A. L.

    1984-01-01

    C2H(N = 1-0) emission has been extensively observed in a variety of molecular clouds, including: 12 hot, dense, cloud cores, 3 bright-rimmed clouds (in NGC 1977, IC 1396, and IC 1848), and across the extended OMC - 1 cloud. It has also been observed in the circumstellar envelopes IRC + 10216 and AFGL 2688. Abundance analyses of the molecular clouds yield C2H/(C-13)O abundance ratios of about 0.01, with little variation (less than about a factor of 4) either between clouds or across individual clouds. In the Orion plateau source, the C2H abundance is enhanced by less than a factor of 4, relative to the extended cloud. The generally high levels of C2H found in the molecular clouds are not readily accounted for by simple, steady-state chemical models, and suggest, as do earlier observations of atomic carbon, that the carbon chemistry in dense clouds is more active than is commonly assumed.

  8. A Catalog of Helium Abundance Indicators from Globular Cluster Photometry

    CERN Document Server

    Sandquist, E L

    1999-01-01

    For each of the three indicators used, we have conducted a thorough error analysis, and identified systematic errors in the computational procedures. For the population ratio R = N_HB / N_RGB, we find that there is no evidence of a trend with metallicity, although there appears to be real scatter in the values derived. Although this indicator is the one best able to provide useful absolute helium abundances, the mean value is Y approximately 0.20, indicating the probable presence of additional systematic error. For the magnitude difference from the horizontal branch to the main sequence Delta and the RR Lyrae mass-luminosity exponent A, it is only possible to reliably determine relative helium abundances. This is due to continuing uncertainties in the absolute metallicity scale for Delta, and uncertainty in the RR Lyrae temperature scale for A. Both indicators imply that the helium abundance is approximately constant as a function of [Fe/H]. According to the A indicator, both Oosterhoff I and II group cluster...

  9. Abundances and kinematics for ten anticentre open clusters

    CERN Document Server

    Cantat-Gaudin, T; Vallenari, A; Sordo, R; Bragaglia, A; Magrini, L

    2016-01-01

    Open clusters are distributed all across the disk and are convenient tracers of its properties. In particular, outer disk clusters bear a key role for the investigation of the chemical evolution of the Galactic disk. The goal of this study is to derive homogeneous elemental abundances for a sample of ten outer disk OCs, and investigate possible links with disk structures such as the Galactic Anticenter Stellar Structure. We analyse high-resolution spectra of red giants, obtained from the HIRES@Keck and UVES@VLT archives. We derive elemental abundances and stellar atmosphere parameters by means of the classical equivalent width method. We also performed orbit integrations using proper motions. The Fe abundances we derive trace a shallow negative radial metallicity gradient of slope -0.027+/-0.007 dex.kpc-1 in the outer 12 kpc of the disk. The [alpha/Fe] gradient appears flat, with a slope of 0.006+/-0.007 dex.kpc-1 . The two outermost clusters (Be 29 and Sau 1) appear to follow elliptical orbits. Be 20 also ex...

  10. Beryllium abundance in turn-off stars of NGC 6752

    CERN Document Server

    Pasquini, L; Randich, S; Galli, D; Gratton, R G; Wolff, B; Pasquini, Luca; Bonifacio, Piercarlo; Randich, Sofia; Galli, Daniele; Gratton, Raffaele G.

    2006-01-01

    Aims: To measure the beryllium abundance in two TO stars of the Globular Cluster NGC 6752, one oxygen rich and sodium poor, the other presumably oxygen poor and sodium rich. Be abundances in these stars are used to put on firmer grounds the hypothesis of Be as cosmochronometer and to investigate the formation of Globular Clusters. Method:We present near UV spectra with resolution R$\\sim 45000$ obtained with the UVES spectrograph on the 8.2m VLT Kueyen telescope, analysed with spectrum synthesis based on plane parallel LTE model atmospheres. Results:Be is detected in the O rich star with log(Be/H)=-12.04 $\\pm$0.15, while Be is not detected in the other star for which we obtain the upper limit log(Be/H)$<$-12.2. A large difference in nitrogen abundance (1.6 dex) is found between the two stars. Conclusions:The Be measurement is compatible with what found in field stars with the same [Fe/H] and [O/H]. The 'Be age' of the cluster is found to be 13.3 Gyrs, in excellent agreement with the results from main sequen...

  11. An Integral Field Study of Abundance Gradients in Nearby LIRGs

    CERN Document Server

    Rich, J A; Kewley, L J; Dopita, M A; Rupke, D S N

    2012-01-01

    We present for the first time metallicity maps generated using data from the Wide Field Spectrograph (WiFeS) on the ANU 2.3m of 9 Luminous Infrared Galaxies (LIRGs) and discuss the abundance gradients and distribution of metals in these systems. We have carried out optical integral field spectroscopy (IFS) of several several LIRGs in various merger phases to investigate the merger process. In a major merger of two spiral galaxies with preexisting disk abundance gradients, the changing distribution of metals can be used as a tracer of gas flows in the merging system as low metallicity gas is transported from the outskirts of each galaxy to their nuclei. We employ this fact to probe merger properties by using the emission lines in our IFS data to calculate the gas-phase metallicity in each system. We create abundance maps and subsequently derive a metallicity gradient from each map. We compare our measured gradients to merger stage as well as several possible tracers of merger progress and observed nuclear abun...

  12. Stellar Chemical Abundances: In Pursuit of the Highest Achievable Precision

    CERN Document Server

    Bedell, M; Bean, J; Ramirez, I; Leite, P; Asplund, M

    2014-01-01

    The achievable level of precision on photospheric abundances of stars is a major limiting factor on investigations of exoplanet host star characteristics, the chemical histories of star clusters, and the evolution of the Milky Way and other galaxies. While model-induced errors can be minimized through the differential analysis of spectrally similar stars, the maximum achievable precision of this technique has been debated. As a test, we derive differential abundances of 19 elements from high-quality asteroid-reflected solar spectra taken using a variety of instruments and conditions. We treat the solar spectra as being from unknown stars and use the resulting differential abundances, which are expected to be zero, as a diagnostic of the error in our measurements. Our results indicate that the relative resolution of the target and reference spectra is a major consideration, with use of different instruments to obtain the two spectra leading to errors up to 0.04 dex. Use of the same instrument at different epoc...

  13. The reasons of metamorphosis and abundance of Kabylian vernacular houses

    Directory of Open Access Journals (Sweden)

    Walid Hamma

    2018-06-01

    Full Text Available Kabylia suffers from the abundance of its ancient villages and the metamorphosis of its traditional houses, which has led to a very advanced degradation and a loss of the authenticity of its old constructions. To understand the phenomenon of exodus, the reasons for its abundant villages and the remodeling of historical buildings, we adopted two approaches, the first is sociological through the use of questionnaire and the second is architectural through use of the method of morphological analysis. After survey, we first highlighted the reasons for the abundant which are economic at 74.89%, educational at 17.00%, social at 4.05%, political at 3.23% and religious at 0.83%. Then, the reasons for the metamorphosis of Kabyle houses, which are structural at 25.20%, functional at 31.70%, spatial at 34.95%, aesthetics at 4.06%, thermal insulation at 2.43% and sound insulation at 1.62%. Finally, the architectural parts changed are the structure at 69.10%, the materials at 13.01%, the roof at 98.37%, the facade at 39.02%, the decoration at 45.52%, the operation at 82.92%, the spaces at 85.63%, the area at 85.63% Thermal insulation at 13.82%, noise insulation at 7.31% and carpentry at 96.74%.

  14. Atmospheric Abundances in Post-AGB candidates of Intermediate Temperature

    CERN Document Server

    Ferro, A A; Mathias, P; Giridhar, Sunetra

    2001-01-01

    Detailed atmospheric abundances have been calculated for a sample of A-G supergiant stars with IR fluxes and/or high galactic latitudes. HD 172481 and HD 158616 show clear indications of being post-AGB stars that have experienced third dredge-up. HD 158616 is carbon-rich while the abundance pattern of HD 172481 and its large Li enhancement gives support to the hot bottom burning scenario that explains paucity of carbon-rich stars among AGB stars. HD 172324 is very likely a hot post-AGB star that shows a strong carbon deficiency. HD 725, HD 218753 and HD 331319 also appear to be evolved objects between the red giant and the AGB. HD 9167, HD 173638 with a few exceptions, reflect solar abundances and no signs of post red giant evolution. They are most likely young massive disk supergiants. Further analysis of proto-Planetary Nebula HDE 341617 reveals that He lines show signs of velocity stratification. The emission lines have weakened considerably since 1993. The envelope expands at 19 km s$^{-1}$ relative to th...

  15. Rotation and surface abundance peculiarities in A-type stars

    CERN Document Server

    Takeda, Yoichi; Kang, Dong-Il; Lee, Byeong-Cheol; Kim, Kang-Min

    2008-01-01

    In an attempt of clarifying the connection between the photospheric abundance anomalies and the stellar rotation as well as of exploring the nature of "normal A" stars, the abundances of seven elements (C, O, Si, Ca, Ti, Fe, and Ba) and the projected rotational velocity for 46 A-type field stars were determined by applying the spectrum-fitting method to the high-dispersion spectral data obtained with BOES at BOAO. We found that the peculiarities (underabundances of C, O, and Ca; an overabundance of Ba) seen in slow rotators efficiently decrease with an increase of rotation, which almost disappear at v_e sin i > 100 km s^-1. This further suggests that stars with sufficiently large rotational velocity may retain the original composition at the surface without being altered. Considering the subsolar tendency (by several tenths dex below) exhibited by the elemental abundances of such rapidly-rotating (supposedly normal) A stars, we suspect that the gas metallicity may have decreased since our Sun was born, contra...

  16. Calibration of Nebular Emission-line Diagnostics; 2, Abundances

    CERN Document Server

    Oey, M S

    2000-01-01

    (Abridged) We examine standard methods of measuring nebular chemical abundances, including estimates based on direct T_e measurements, and also bright-line diagnostics. We use observations of 4 LMC HII regions whose ionizing stars have classifications ranging from O7 to WN3. We assume a 2-zone T_e structure to compute ionic abundances. We compare with photoionization models tailored to the properties of the individual objects, and emphasize the importance of correctly relating T_e in the two zones, which can otherwise cause errors of ~0.2 dex in abundance estimates. There are no spatial variations to within 0.1 - 0.15 dex in any of the objects, even one hosting 3 WR stars. Our data agree with the modeled R23 and S23 diagnostics of O and S. We present the first theoretical tracks for S23, which are in excellent agreement with a larger dataset. However, contrary to earlier suggestions, S23 is much more sensitive to the ionization parameter than is R23, because S23 does not sample S IV. We therefore introduce S2...

  17. Measuring helium abundance difference in giants of NGC 2808

    CERN Document Server

    Pasquini, L; Kaufl, H U; Cacciari, C

    2011-01-01

    Multiple populations have been detected in several globular clusters (GC) that do not display a spread in metallicity. Unusual features of their CMD can be interpreted in terms of differences in the Helium content of the stars belonging to the sub-populations. Differences in He abundance have never been directly observed. We attempt to measure these differences in two giant stars of NGC 2808 with very similar parameters but different Na and O abundances, hence that presumably belong to different sub-populations, by directly comparing their He I 10830 {\\AA} lines. The He 10830 {\\AA} line forms in the upper chromosphere. Our detailed models derive the chromospheric structure using the Ca II and H$\\alpha$, and simulate the corresponding He I 10830 line profiles. We show that, at a given value of He abundance, the He I 10830 equivalent width cannot significantly change without a corresponding much larger change in the Ca II lines. We have used the VLT-CRIRES to obtain high-resolution spectra in the 10830 {\\AA} re...

  18. Molecular abundances in the inner layers of IRC +10216

    CERN Document Server

    Agundez, M; Cernicharo, J; Kahane, C; Daniel, F; Guelin, M

    2012-01-01

    Observations towards IRC +10216 of CS, SiO, SiS, NaCl, KCl, AlCl, AlF, and NaCN have been carried out with the IRAM 30-m telescope in the 80-357.5 GHz frequency range. A large number of rotational transitions covering a wide range of energy levels, including highly excited vibrational states, are detected in emission and serve to trace different regions of the envelope. Radiative transfer calculations based on the LVG formalism have been performed to derive molecular abundances from the innermost out to the outer layers. The excitation calculations include infrared pumping to excited vibrational states and inelastic collisions, for which up-to-date rate coefficients for rotational and, in some cases, ro-vibrational transitions are used. We find that in the inner layers CS, SiO, and SiS have abundances relative to H$_2$ of 4e-6, 1.8e-7, and 3e-6, respectively, and that CS and SiS have significant lower abundances in the outer envelope, which implies that they actively contribute to the formation of dust. Moreo...

  19. Elemental abundances of flaring solar plasma - Enhanced neon and sulfur

    Science.gov (United States)

    Schmelz, J. T.

    1993-01-01

    Elemental abundances of two flares observed with the SMM Flat Crystal Spectrometer are compared and contrasted. The first had a gradual rise and a slow decay, while the second was much more impulsive. Simultaneous spectra of seven bright soft X-ray resonance lines provide information over a broad temperature range and are available throughout both flares, making these events unique in the SMM data base. For the first flare, the plasma seemed to be characterized by coronal abundances but, for the second, the plasma composition could not be coronal, photospheric, or a linear combination of both. A good differential emission measure fit required enhanced neon such that Ne/O = 0.32 +/- 0.02, a value which is inconsistent with the current models of coronal abundances based on the elemental first-ionization potential. Similar values of enhanced neon are found for flaring plasma observed by the SMM gamma-ray spectrometer, in (He-3)-rich solar energetic particle events, and in the decay phase of several long duration soft X-ray events. Sulfur is also enhanced in the impulsive flare, but not as dramatically as neon. These events are compared with two models which attempt to explain the enhanced values of neon and sulfur.

  20. The Origin of Fluorine: Abundances in AGB Carbon Stars Revisited

    CERN Document Server

    Abia, C; Cristallo, S; de Laverny, P

    2015-01-01

    Revised spectroscopic parameters for the HF molecule and a new CN line list in the 2.3 mu region have been recently available, allowing a revision of the F content in AGB stars. AGB carbon stars are the only observationally confirmed sources of fluorine. Nowadays there is not a consensus on the relevance of AGB stars in its Galactic chemical evolution. The aim of this article is to better constrain the contribution of these stars with a more accurate estimate of their fluorine abundances. Using new spectroscopic tools and LTE spectral synthesis, we redetermine fluorine abundances from several HF lines in the K-band in a sample of Galactic and extragalactic AGB carbon stars of spectral types N, J and SC spanning a wide range of metallicities. On average, the new derived fluorine abundances are systematically lower by 0.33 dex with respect to previous determinations. This may derive from a combination of the lower excitation energies of the HF lines and the larger macroturbulence parameters used here as well as...