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Sample records for chitinase-like proteins abundantly

  1. Two chitinase-like proteins abundantly accumulated in latex of mulberry show insecticidal activity

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    Komatsu Aino

    2010-01-01

    Full Text Available Abstract Background Plant latex is the cytoplasm of highly specialized cells known as laticifers, and is thought to have a critical role in defense against herbivorous insects. Proteins abundantly accumulated in latex might therefore be involved in the defense system. Results We purified latex abundant protein a and b (LA-a and LA-b from mulberry (Morus sp. and analyzed their properties. LA-a and LA-b have molecular masses of approximately 50 and 46 kDa, respectively, and are abundant in the soluble fraction of latex. Western blotting analysis suggested that they share sequence similarity with each other. The sequences of LA-a and LA-b, as determined by Edman degradation, showed chitin-binding domains of plant chitinases at the N termini. These proteins showed small but significant chitinase and chitosanase activities. Lectin RCA120 indicated that, unlike common plant chitinases, LA-a and LA-b are glycosylated. LA-a and LA-b showed insecticidal activities when fed to larvae of the model insect Drosophila melanogaster. Conclusions Our results suggest that the two LA proteins have a crucial role in defense against herbivorous insects, possibly by hydrolyzing their chitin.

  2. Role of Chitin and Chitinase/Chitinase-Like Proteins in Inflammation, Tissue Remodeling, and Injury

    Science.gov (United States)

    Lee, Chun Geun; Da Silva, Carla A.; Dela Cruz, Charles S.; Ahangari, Farida; Ma, Bing; Kang, Min-Jong; He, Chuan-Hua; Takyar, Seyedtaghi; Elias, Jack A.

    2013-01-01

    The 18 glycosyl hydrolase family of chitinases is an ancient gene family that is widely expressed from prokaryotes to eukaryotes. In mammals, despite the absence of endogenous chitin, a number of chitinases and chitinase-like proteins (C/CLPs) have been identified. However, their roles have only recently begun to be elucidated. Acidic mammalian chitinase (AMCase) inhibits chitin-induced innate inflammation; augments chitin-free, allergen-induced Th2 inflammation; and mediates effector functions of IL-13. The CLPs BRP-39/YKL-40 (also termed chitinase 3-like 1) inhibit oxidant-induced lung injury, augments adaptive Th2 immunity, regulates apoptosis, stimulates alternative macrophage activation, and contributes to fibrosis and wound healing. In accord with these findings, levels of YKL-40 in the lung and serum are increased in asthma and other inflammatory and remodeling disorders and often correlate with disease severity. Our understanding of the roles of C/CLPs in inflammation, tissue remodeling, and tissue injury in health and disease is reviewed below. PMID:21054166

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

    International Nuclear Information System (INIS)

    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

  4. 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.

  5. 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.

  6. Detecting significant changes in protein abundance

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    Kai Kammers

    2015-06-01

    Full Text Available We review and demonstrate how an empirical Bayes method, shrinking a protein's sample variance towards a pooled estimate, leads to far more powerful and stable inference to detect significant changes in protein abundance compared to ordinary t-tests. Using examples from isobaric mass labelled proteomic experiments we show how to analyze data from multiple experiments simultaneously, and discuss the effects of missing data on the inference. We also present easy to use open source software for normalization of mass spectrometry data and inference based on moderated test statistics.

  7. Late Embryogenesis Abundant (LEA) proteins in legumes.

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    Battaglia, Marina; Covarrubias, Alejandra A

    2013-01-01

    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 confirm the high correlation between their accumulation and water deficit, reinforcing their functional relevance under this detrimental conditions. PMID:23805145

  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

    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. The abundance of short proteins in the mammalian proteome.

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    Martin C Frith

    2006-04-01

    Full Text Available Short proteins play key roles in cell signalling and other processes, but their abundance in the mammalian proteome is unknown. Current catalogues of mammalian proteins exhibit an artefactual discontinuity at a length of 100 aa, so that protein abundance peaks just above this length and falls off sharply below it. To clarify the abundance of short proteins, we identify proteins in the FANTOM collection of mouse cDNAs by analysing synonymous and non-synonymous substitutions with the computer program CRITICA. This analysis confirms that there is no real discontinuity at length 100. Roughly 10% of mouse proteins are shorter than 100 aa, although the majority of these are variants of proteins longer than 100 aa. We identify many novel short proteins, including a "dark matter" subset containing ones that lack detectable homology to other known proteins. Translation assays confirm that some of these novel proteins can be translated and localised to the secretory pathway.

  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

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    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. Abundant lipid and protein components of drusen.

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    Lan Wang

    Full Text Available BACKGROUND: Drusen are extracellular lesions characteristic of aging and age-related maculopathy, a major retinal disease of the elderly. We determined the relative proportions of lipids and proteins in drusen capped with retinal pigment epithelium (RPE and in RPE isolated from non-macular regions of 36 human retinas with grossly normal maculas obtained <6 hr after death. METHODOLOGY/PRINCIPAL FINDINGS: Druse pellets were examined by light and electron microscopy. Component proteins were extracted using novel methods for preserved tissues, separated, subjected to tryptic digestion and LC-MS(MS(2 analysis using an ion trap mass spectrometer, and identified with reference to databases. Lipid classes were separated using thin layer chromatography and quantified by densitometry. Major druse components were esterified cholesterol (EC, phosphatidylcholine (PC, and protein (37.5+/-13.7, 36.9+/-12.9, and 43.0+/-11.5 ng/druse, respectively. Lipid-containing particles (median diameter, 77 nm occupied 37-44% of druse volume. Major proteins include vitronectin, complement component 9, apoE, and clusterin, previously seen in drusen, and ATP synthase subunit beta, scavenger receptor B2, and retinol dehydrogenase 5, previously seen in RPE. Drusen and RPE had similar protein profiles, with higher intensities and greater variability in drusen. C8, part of the complement membrane attack complex, was localized in drusen by immunofluorescence. CONCLUSIONS/SIGNIFICANCE: At least 40% of druse content is comprised by lipids dominated by EC and PC, 2 components that are potentially accounted for by just one pathway, the secretion of lipoproteins by RPE. Manipulating genes encoding apolipoprotein pathways would be a fruitful approach to producing drusen with high EC content in laboratory animals. Therapies that directly mitigate drusen should prepare for the substantial volume of neutral lipids. The catalog of major druse proteins is nearing completion.

  15. Molecular, Structural and Immunological Characterization of Der p 18, a Chitinase-Like House Dust Mite Allergen

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    Resch, Yvonne; Blatt, Katharina; Malkus, Ursula; Fercher, Christian; Swoboda, Ines; Focke-Tejkl, Margit; Chen, Kuan-Wei; Seiberler, Susanne; Mittermann, Irene; Lupinek, Christian; Rodriguez-Dominguez, Azahara; Zieglmayer, Petra; Zieglmayer, René; Keller, Walter; Krzyzanek, Vladislav; Valent, Peter; Valenta, Rudolf; Vrtala, Susanne

    2016-01-01

    Background The house dust mite (HDM) allergen Der p 18 belongs to the glycoside hydrolase family 18 chitinases. The relevance of Der p 18 for house dust mite allergic patients has only been partly investigated. Objective To perform a detailed characterization of Der p 18 on a molecular, structural and immunological level. Methods Der p 18 was expressed in E. coli, purified to homogeneity, tested for chitin-binding activity and its secondary structure was analyzed by circular dichroism. Der p 18-specific IgG antibodies were produced in rabbits to localize the allergen in mites using immunogold electron microscopy and to search for cross-reactive allergens in other allergen sources (i.e. mites, crustacea, mollusca and insects). IgE reactivity of rDer p 18 was tested with sera from clinically well characterized HDM-allergic patients (n = 98) and its allergenic activity was analyzed in basophil activation experiments. Results Recombinant Der p 18 was expressed and purified as a folded, biologically active protein. It shows weak chitin-binding activity and partial cross-reactivity with Der f 18 from D. farinae but not with proteins from the other tested allergen sources. The allergen was mainly localized in the peritrophic matrix of the HDM gut and to a lower extent in fecal pellets. Der p 18 reacted with IgE from 10% of mite allergic patients from Austria and showed allergenic activity when tested for basophil activation in Der p 18-sensitized patients. Conclusion Der p 18 is a rather genus-specific minor allergen with weak chitin-binding activity but exhibits allergenic activity and therefore should be included in diagnostic test panels for HDM allergy. PMID:27548813

  16. Abundant protein phosphorylation potentially regulates Arabidopsis anther development.

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    Ye, Juanying; Zhang, Zaibao; You, Chenjiang; Zhang, Xumin; Lu, Jianan; Ma, Hong

    2016-09-01

    As the male reproductive organ of flowering plants, the stamen consists of the anther and filament. Previous studies on stamen development mainly focused on single gene functions by genetic methods or gene expression changes using comparative transcriptomic approaches, especially in model plants such as Arabidopsis thaliana However, studies on Arabidopsis anther protein expression and post-translational modifications are still lacking. Here we report proteomic and phosphoproteomic studies on developing Arabidopsis anthers at stages 4-7 and 8-12. We identified 3908 high-confidence phosphorylation sites corresponding to 1637 phosphoproteins. Among the 1637 phosphoproteins, 493 were newly identified, with 952 phosphorylation sites. Phosphopeptide enrichment prior to LC-MS analysis facilitated the identification of low-abundance proteins and regulatory proteins, thereby increasing the coverage of proteomic analysis, and facilitated the analysis of more regulatory proteins. Thirty-nine serine and six threonine phosphorylation motifs were uncovered from the anther phosphoproteome and further analysis supports that phosphorylation of casein kinase II, mitogen-activated protein kinases, and 14-3-3 proteins is a key regulatory mechanism in anther development. Phosphorylated residues were preferentially located in variable protein regions among family members, but they were they were conserved across angiosperms in general. Moreover, phosphorylation might reduce activity of reactive oxygen species scavenging enzymes and hamper brassinosteroid signaling in early anther development. Most of the novel phosphoproteins showed tissue-specific expression in the anther according to previous microarray data. This study provides a community resource with information on the abundance and phosphorylation status of thousands of proteins in developing anthers, contributing to understanding post-translational regulatory mechanisms during anther development. PMID:27531888

  17. Regular Patterns for Proteome-Wide Distribution of Protein Abundance across Species

    OpenAIRE

    Fan Zhong; Dong Yang; Yunwei Hao; Chengzhao Lin; Ying Jiang; Wantao Ying; Songfeng Wu; Yunping Zhu; Siqi Liu; Pengyuan Yang; Xiaohong Qian; Fuchu He

    2012-01-01

    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 positi...

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    the application of pH-sensitive poly(N-isopropylacrylamide-acrylic acid) hydrogel particles for removal of abundant plasma proteins, prior to proteome analysis by MS. Protein depletion occurs by two separate mechanisms: (1) hydrogel particles incubated with low concentrations of plasma capture abundant proteins...... 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....

  19. LEAPdb: a database for the late embryogenesis abundant proteins

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    Jaspard Emmanuel

    2010-04-01

    Full Text Available Abstract Background Late Embryogenesis Abundant Proteins database (LEAPdb contains resource regarding LEAP from plants and other organisms. Although LEAP are grouped into several families, there is no general consensus on their definition and on their classification. They are associated with abiotic stress tolerance, but their actual function at the molecular level is still enigmatic. The scarcity of 3-D structures for LEAP remains a handicap for their structure-function relationships analysis. Finally, the growing body of published data about LEAP represents a great amount of information that needs to be compiled, organized and classified. Results LEAPdb gathers data about 8 LEAP sub-families defined by the PFAM, the Conserved Domain and the InterPro databases. Among its functionalities, LEAPdb provides a browse interface for retrieving information on the whole database. A search interface using various criteria such as sophisticated text expression, amino acids motifs and other useful parameters allows the retrieving of refined subset of entries. LEAPdb also offers sequence similarity search. Information is displayed in re-ordering tables facilitating the analysis of data. LEAP sequences can be downloaded in three formats. Finally, the user can submit his sequence(s. LEAPdb has been conceived as a user-friendly web-based database with multiple functions to search and describe the different LEAP families. It will likely be helpful for computational analyses of their structure - function relationships. Conclusions LEAPdb contains 769 non-redundant and curated entries, from 196 organisms. All LEAP sequences are full-length. LEAPdb is publicly available at http://forge.info.univ-angers.fr/~gh/Leadb/index.php.

  20. 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.

  1. Regular Patterns for Proteome-Wide Distribution of Protein Abundance across Species

    Science.gov (United States)

    Jiang, Ying; Ying, Wantao; Wu, Songfeng; Zhu, Yunping; Liu, Siqi; Yang, Pengyuan; Qian, Xiaohong; He, Fuchu

    2012-01-01

    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. PMID:22427835

  2. 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.

  3. In-depth analysis of low abundant proteins in bovine colostrum using different fractionation techniques

    DEFF Research Database (Denmark)

    Nissen, Asger; Bendixen, Emøke; Ingvartsen, Klaus Lønne;

    2012-01-01

    Bovine colostrum is well known for its large content of bioactive components and its importance for neonatal survival. Unfortunately, the colostrum proteome is complicated by a wide dynamic range, because of a few dominating proteins that hamper sensitivity and proteome coverage achieved on low...... abundant proteins. Moreover, the composition of colostrum is complex and the proteins are located within different physical fractions that make up the colostrum. To gain a more exhaustive picture of the bovine colostrum proteome and gather information on protein location, we performed an extensive pre......-speed centrifugation contributed most to detection of low abundant proteins. Hence, prefractionation of colostrum prior to 2D-LC-MS/MS analysis expanded our knowledge on the presence and location of low abundant proteins in bovine colostrum....

  4. 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. PMID:27322723

  5. 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.

  6. 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.

  7. In-depth analysis of low abundant proteins in bovine colostrum using different fractionation techniques.

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    Nissen, Asger; Bendixen, Emøke; Ingvartsen, Klaus Lønne; Røntved, Christine Maria

    2012-09-01

    Bovine colostrum is well known for its large content of bioactive components and its importance for neonatal survival. Unfortunately, the colostrum proteome is complicated by a wide dynamic range, because of a few dominating proteins that hamper sensitivity and proteome coverage achieved on low abundant proteins. Moreover, the composition of colostrum is complex and the proteins are located within different physical fractions that make up the colostrum. To gain a more exhaustive picture of the bovine colostrum proteome and gather information on protein location, we performed an extensive pre-analysis fractionation of colostrum prior to 2D-LC-MS/MS analysis. Physical and chemical properties of the proteins and colostrum were used alone or in combination for the separation of proteins. ELISA was used to quantify and verify the presence of proteins in colostrum. In total, 403 proteins were identified in the nonfractionated colostrum (NF) and seven fractions (F1-F7) using six different fractionation techniques. Fractionation contributed with 69 additional proteins in the fluid phase compared with NF. Different fractionation techniques each resulted in detection of unique subsets of proteins. Whey production by high-speed centrifugation contributed most to detection of low abundant proteins. Hence, prefractionation of colostrum prior to 2D-LC-MS/MS analysis expanded our knowledge on the presence and location of low abundant proteins in bovine colostrum. PMID:22848049

  8. Assessment of the natural variation of low abundant metabolic proteins in soybean seeds using proteomics

    Science.gov (United States)

    Using two-dimensional polyacrylamide gel electrophoresis and mass spectrometry, we investigated the distribution of the low abundant proteins that are involved in soybean seed development in four wild and twelve cultivated soybean genotypes. We found proteomic variation of these proteins within and...

  9. 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.

  10. 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.

  11. Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

    Science.gov (United States)

    He, Yi-Ming; Ma, Bin-Guang

    2016-05-01

    Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions.

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

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    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/.

  13. 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

    2016-01-01

    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. PMID:27405981

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

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    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

    2016-01-01

    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. PMID:27405981

  15. Purification and Characterization of Abundant Secreted Protein in Suspension-Cultured Pumpkin Cells 1

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    Esaka, Muneharu; Enoki, Keiko; Kouchi, Bonko; Sasaki, Takuji

    1990-01-01

    The abundant secreted protein with molecular weight of 32,000 was purified from the culture medium of suspension-cultured pumpkin (Cucurbita sp.) cells. Two steps, ammonium sulfate fractionation and Sepharose 6B column chromatography, were sufficient for purification to homogeneity. Antibodies against the pure protein were used to show that a protein of the same size is made by callus cells. There is considerable homology between the amino-terminal amino acid sequence of this secreted protein and chitinase isolated from tobacco (Nicotiana tabacum L.) or bean (Phaseolus vulgaris L.). Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:16667554

  16. Discrepancy between mRNA and protein abundance: Insight from information retrieval process in computers

    OpenAIRE

    Wang, Degeng

    2008-01-01

    Discrepancy between the abundance of cognate protein and RNA molecules is frequently observed. A theoretical understanding of this discrepancy remains elusive, and it is frequently described as surprises and/or technical difficulties in the literature. Protein and RNA represent different steps of the multi-stepped cellular genetic information flow process, in which they are dynamically produced and degraded. This paper explores a comparison with a similar process in computers - multi-step inf...

  17. Identification of Proteins of Altered Abundance in Oil Palm Infected with Ganoderma boninense

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    Jameel R. Al-Obaidi

    2014-03-01

    Full Text Available Basal stem rot is a common disease that affects oil palm, causing loss of yield and finally killing the trees. The disease, caused by fungus Ganoderma boninense, devastates thousands of hectares of oil palm plantings in Southeast Asia every year. In the present study, root proteins of healthy oil palm seedlings, and those infected with G. boninense, were analyzed by 2-dimensional gel electrophoresis (2-DE. When the 2-DE profiles were analyzed for proteins, which exhibit consistent significant change of abundance upon infection with G. boninense, 21 passed our screening criteria. Subsequent analyses by mass spectrometry and database search identified caffeoyl-CoA O-methyltransferase, caffeic acid O-methyltransferase, enolase, fructokinase, cysteine synthase, malate dehydrogenase, and ATP synthase as among proteins of which abundances were markedly altered.

  18. 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.

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

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    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. PMID:27453073

  20. 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.

  1. Influence of Acute High Glucose on Protein Abundance Changes in Murine Glomerular Mesangial Cells

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    Michelle T. Barati

    2016-01-01

    Full Text Available The effects of acute exposure to high glucose levels as experienced by glomerular mesangial cells in postprandial conditions and states such as in prediabetes were investigated using proteomic methods. Two-dimensional gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry methods were used to identify protein expression patterns in immortalized rat mesangial cells altered by 2 h high glucose (HG growth conditions as compared to isoosmotic/normal glucose control (NG⁎ conditions. Unique protein expression changes at 2 h HG treatment were measured for 51 protein spots. These proteins could be broadly grouped into two categories: (1 proteins involved in cell survival/cell signaling and (2 proteins involved in stress response. Immunoblot experiments for a protein belonging to both categories, prohibitin (PHB, supported a trend for increased total expression as well as significant increases in an acidic PHB isoform. Additional studies confirmed the regulation of proteasomal subunit alpha-type 2 and the endoplasmic reticulum chaperone and oxidoreductase PDI (protein disulfide isomerase, suggesting altered ER protein folding capacity and proteasomal function in response to acute HG. We conclude that short term high glucose induces subtle changes in protein abundances suggesting posttranslational modifications and regulation of pathways involved in proteostasis.

  2. 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.

  3. Identification of Late Embryogenesis Abundant (LEA Protein Putative Interactors Using Phage Display

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    Allan Bruce Downie

    2012-05-01

    Full Text Available Arabidopsis thaliana seeds without functional SEED MATURATION PROTEIN1 (SMP1, a boiling soluble protein predicted to be of intrinsic disorder, presumed to be a LATE EMBRYOGENESIS ABUNDANT (LEA family protein based on sequence homology, do not enter secondary dormancy after 3 days at 40 °C. We hypothesized that SMP1 may protect a heat labile protein involved in the promotion of secondary dormancy. Recombinant SMP1 and GmPM28, its soybean (Glycine max, LEA4 homologue, protected the labile GLUCOSE-6-PHOSPHATE DEHYROGENASE enzyme from heat stress, as did a known protectant, Bovine Serum Albumin, whether the LEA protein was in solution or attached to the bottom of microtiter plates. Maintenance of a biological function for both recombinant LEA proteins when immobilized encouraged a biopanning approach to screen for potential protein interactors. Phage display with two Arabidopsis seed, T7 phage, cDNA libraries, normalized for transcripts present in the mature, dehydrated, 12-, 24-, or 36-h imbibed seeds, were used in biopans against recombinant SMP1 and GmPM28. Phage titer increased considerably over four rounds of biopanning for both LEA proteins, but not for BSA, at both 25 and at 41 °C, regardless of the library used. The prevalence of multiple, independent clones encoding portions of specific proteins repeatedly retrieved from different libraries, temperatures and baits, provides evidence suggesting these LEA proteins are discriminating which proteins they protect, a novel finding. The identification of putative LEA-interacting proteins provides targets for reverse genetic approaches to further dissect the induction of secondary dormancy in seeds in response to heat stress.

  4. 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.

  5. Mature adipocyte proteome reveals differentially altered protein abundances between lean, overweight and morbidly obese human subjects.

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    Benabdelkamel, Hicham; Masood, Afshan; Almidani, Ghaith M; Alsadhan, Abdulmajeed A; Bassas, Abdulelah F; Duncan, Mark W; Alfadda, Assim A

    2015-02-01

    Overweight (OW) and obese individuals are considered to be graded parts of the scale having increasing weight as a common feature. They may not, however, be part of the same continuum and may differ metabolically. In this study we applied an untargeted proteomic approach to compare protein abundances in mature adipocytes derived from the subcutaneous adipose tissue of overweight and morbidly obese female subjects to those of lean age matched controls. Mature adipocytes were isolated from liposuction samples of abdominal subcutaneous adipose tissue collected from both lean (L; n = 7, 23.3 ± 0.4 kg/m(2); mean BMI ± SD), overweight (OW; n = 8, 27.9 ± 0.6 kg/m(2); mean BMI ± SD) and morbidly obese (MOB; n = 7, 44.8 ± 3.8 kg/m(2); mean BMI ± SD) individuals. Total protein extracts were then compared by two-dimensional difference in gel electrophoresis (2D DIGE). One hundred and ten differentially expressed protein spots (i.e., fitting the statistical criteria ANOVA test, p interaction; in contrast, in the MOB group the major interacting pathways are associated with lipid metabolism, small molecule biochemistry and cancer. The differences in abundance of the differentially regulated proteins were validated by immunoblotting. These findings provide insights into metabolic differences in OW and MOB individuals. PMID:25498962

  6. LEAping to conclusions: A computational reanalysis of late embryogenesis abundant proteins and their possible roles

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    Wise Michael J

    2003-10-01

    Full Text Available Abstract Background The late embryogenesis abundant (LEA proteins cover a number of loosely related groups of proteins, originally found in plants but now being found in non-plant species. Their precise function is unknown, though considerable evidence suggests that LEA proteins are involved in desiccation resistance. Using a number of statistically-based bioinformatics tools the classification of a large set of LEA proteins, covering all Groups, is reexamined together with some previous findings. Searches based on peptide composition return proteins with similar composition to different LEA Groups; keyword clustering is then applied to reveal keywords and phrases suggestive of the Groups' properties. Results Previous research has suggested that glycine is characteristic of LEA proteins, but it is only highly over-represented in Groups 1 and 2, while alanine, thought characteristic of Group 2, is over-represented in Group 3, 4 and 6 but under-represented in Groups 1 and 2. However, for LEA Groups 1 2 and 3 it is shown that glutamine is very significantly over-represented, while cysteine, phenylalanine, isoleucine, leucine and tryptophan are significantly under-represented. There is also evidence that the Group 4 LEA proteins are more appropriately redistributed to Group 2 and Group 3. Similarly, Group 5 is better found among the Group 3 LEA proteins. Conclusions There is evidence that Group 2 and Group 3 LEA proteins, though distinct, might be related. This relationship is also evident in the overlapping sets of keywords for the two Groups, emphasising alpha-helical structure and, at a larger scale, filaments, all of which fits well with experimental evidence that proteins from both Groups are natively unstructured, but become structured under stress conditions. The keywords support localisation of LEA proteins both in the nucleus and associated with the cytoskeleton, and a mode of action similar to chaperones, perhaps the cold shock chaperones

  7. 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.

  8. Ultrasensitive Detection of Low-Abundance Protein Biomarkers by Mass Spectrometry Signal Amplification Assay.

    Science.gov (United States)

    Du, Ruijun; Zhu, Lina; Gan, Jinrui; Wang, Yuning; Qiao, Liang; Liu, Baohong

    2016-07-01

    A mass spectrometry signal amplification method is developed for the ultrasensitive and selective detection of low-abundance protein biomarkers by utilizing tag molecules on gold nanoparticles (AuNPs). EpCAM and thrombin as model targets are captured by specific aptamers immobilized on the AuNPs. With laser desorption/ionization time-of-flight mass spectrometry (LDI-TOF MS), the mass tag molecules are detected to represent the protein biomarkers. Benefiting from the MS signal amplification, the assay can achieve a limit of detection of 100 aM. The method is further applied to detect thrombin in fetal bovine serum and EpCAM in cell lysates to demonstrate its selectivity and feasibility in complex biological samples. With the high sensitivity and specificity, the protocol shows great promise for providing a new route to single-cell analysis and early disease diagnosis. PMID:27253396

  9. LEA (Late Embryogenesis Abundant proteins and their encoding genes in Arabidopsis thaliana

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    Hincha Dirk K

    2008-03-01

    Full Text Available Abstract Background LEA (late embryogenesis abundant proteins have first been described about 25 years ago as accumulating late in plant seed development. They were later found in vegetative plant tissues following environmental stress and also in desiccation tolerant bacteria and invertebrates. Although they are widely assumed to play crucial roles in cellular dehydration tolerance, their physiological and biochemical functions are largely unknown. Results We present a genome-wide analysis of LEA proteins and their encoding genes in Arabidopsis thaliana. We identified 51 LEA protein encoding genes in the Arabidopsis genome that could be classified into nine distinct groups. Expression studies were performed on all genes at different developmental stages, in different plant organs and under different stress and hormone treatments using quantitative RT-PCR. We found evidence of expression for all 51 genes. There was only little overlap between genes expressed in vegetative tissues and in seeds and expression levels were generally higher in seeds. Most genes encoding LEA proteins had abscisic acid response (ABRE and/or low temperature response (LTRE elements in their promoters and many genes containing the respective promoter elements were induced by abscisic acid, cold or drought. We also found that 33% of all Arabidopsis LEA protein encoding genes are arranged in tandem repeats and that 43% are part of homeologous pairs. The majority of LEA proteins were predicted to be highly hydrophilic and natively unstructured, but some were predicted to be folded. Conclusion The analyses indicate a wide range of sequence diversity, intracellular localizations, and expression patterns. The high fraction of retained duplicate genes and the inferred functional diversification indicate that they confer an evolutionary advantage for an organism under varying stressful environmental conditions. This comprehensive analysis will be an important starting point for

  10. Online monitoring of immunoaffinity-based depletion of high-abundance blood proteins by UV spectrophotometry using enhanced green fluorescence protein and FITC-labeled human serum albumin

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    Yu Hyeong

    2010-12-01

    Full Text Available Abstract Background The removal of high-abundance proteins from plasma is an efficient approach to investigating flow-through proteins for biomarker discovery studies. Most depletion methods are based on multiple immunoaffinity methods available commercially including LC columns and spin columns. Despite its usefulness, high-abundance depletion has an intrinsic problem, the sponge effect, which should be assessed during depletion experiments. Concurrently, the yield of depletion of high-abundance proteins must be monitored during the use of the depletion column. To date, there is no reasonable technique for measuring the recovery of flow-through proteins after depletion and assessing the capacity for capture of high-abundance proteins. Results In this study, we developed a method of measuring recovery yields of a multiple affinity removal system column easily and rapidly using enhanced green fluorescence protein as an indicator of flow-through proteins. Also, we monitored the capture efficiency through depletion of a high-abundance protein, albumin labeled with fluorescein isothiocyanate. Conclusion This simple method can be applied easily to common high-abundance protein depletion methods, effectively reducing experimental variations in biomarker discovery studies.

  11. RECOMBINANT PROTEIN PRODUCTION OF ABUNDANT LARVAL TRANSCRIPT (ALT-2 IN ESCHERICHIA COLI

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    Kamran Ashraf

    2013-02-01

    Full Text Available Lymphatic filariasis is a major tropical disease caused by mosquito born nematodes Brugia malayi and Wuchereria bancrofti. Vaccine against filariasis must generate immunity to infective mosquito derived L3 stage. Two highly expressed genes designated abundant larval transcript-1 and -2 (alt-1 and alt-2. ALT-1 and ALT-2 represent closely related protein (79% it. Now, expression of this alt gene in E. coli BL21plysS for the production of vaccine is major challenge as no vaccine is available against this disease. Work was carried out to express this protein at laboratory scale bioreactor. At first optimization of different parameter like suitability of media, inducer concentration, induction time was done for getting maximum amount of recombinant protein. In shake flask studies, after induction (max cell density and max specific growth rate stage good expression of ALT-2 protein was found. However, at laboratory scale production done in bioreactor, expression level drastically decreased. Plasmid stability analysis was done in reactor and was found to be cause for decreased productivity. The stability was improved by increasing antibiotic concentration in the medium and also by pulsing antibiotic during induction. This led to better plasmid stability and increased expression levels in reactor similar to expression levels in shake flask studies.

  12. 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.

  13. 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

  14. 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

  15. Phylogenetic analysis of microalgae based on highly abundant proteins using mass spectrometry.

    Science.gov (United States)

    Lee, Hae-Won; Roh, Seong Woon; Cho, Kichul; Kim, Kil-Nam; Cha, In-Tae; Yim, Kyung June; Song, Hye Seon; Nam, Young-Do; Oda, Tatsuya; Chung, Young-Ho; Kim, Soo Jung; Choi, Jong-Soon; Kim, Daekyung

    2015-01-01

    The blooms of toxic phototrophic microorganisms, such as microalgae and cyanobacteria, which are typically found in freshwater and marine environments, are becoming more frequent and problematic in aquatic systems. Due to accumulation of toxic algae, harmful algal blooms (HABs) exert negative effects on aquatic systems. Therefore, rapid detection of harmful microalgae is important for monitoring the occurrence of HABs. Mass spectrometry-based methods have become sensitive, specific techniques for the identification and characterization of microorganisms. Matrix-assisted laser desorption/ionization (MALDI) with time-of-flight (TOF) mass spectrometry (MS) allows us to measure a unique molecular fingerprint of highly abundant proteins in a microorganism and has been used for the rapid, accurate identification of bacteria and fungi in clinical microbiology. Here, we tested the specificity of MALDI-TOF MS using microalgal strains (Heterocapsa, Alexandrium, Nannochloropsis, Chaetoceros, Chlorella, and Dunaliella spp.). Our research suggested that this method was comparable in terms of the rapid identification of microalgea to conventional methods based on genetic information and morphology. Thus, this efficient mass spectrometry-based technique may have applications in the rapid identification of harmful microorganisms from aquatic environmental samples. PMID:25476355

  16. 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

  17. 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.

  18. The ubiquitous distribution of late embryogenesis abundant proteins across cell compartments in Arabidopsis offers tailored protection against abiotic stress.

    Science.gov (United States)

    Candat, Adrien; Paszkiewicz, Gaël; Neveu, Martine; Gautier, Romain; Logan, David C; Avelange-Macherel, Marie-Hélène; Macherel, David

    2014-07-01

    Late embryogenesis abundant (LEA) proteins are hydrophilic, mostly intrinsically disordered proteins, which play major roles in desiccation tolerance. In Arabidopsis thaliana, 51 genes encoding LEA proteins clustered into nine families have been inventoried. To increase our understanding of the yet enigmatic functions of these gene families, we report the subcellular location of each protein. Experimental data highlight the limits of in silico predictions for analysis of subcellular localization. Thirty-six LEA proteins localized to the cytosol, with most being able to diffuse into the nucleus. Three proteins were exclusively localized in plastids or mitochondria, while two others were found dually targeted to these organelles. Targeting cleavage sites could be determined for five of these proteins. Three proteins were found to be endoplasmic reticulum (ER) residents, two were vacuolar, and two were secreted. A single protein was identified in pexophagosomes. While most LEA protein families have a unique subcellular localization, members of the LEA_4 family are widely distributed (cytosol, mitochondria, plastid, ER, and pexophagosome) but share the presence of the class A α-helix motif. They are thus expected to establish interactions with various cellular membranes under stress conditions. The broad subcellular distribution of LEA proteins highlights the requirement for each cellular compartment to be provided with protective mechanisms to cope with desiccation or cold stress. PMID:25005920

  19. 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

  20. MtPM25 is an atypical hydrophobic late embryogenesis-abundant protein that dissociates cold and desiccation-aggregated proteins

    NARCIS (Netherlands)

    Boucher, V.; Buitink, J.; Lin, X.; Boudet, J.; Hoekstra, F.A.; Hundertmark, M.; Renard, D.; Leprince, O.

    2010-01-01

    Late embryogenesis-abundant (LEA) proteins are one of the components involved in desiccation tolerance (DT) by maintaining cellular structures in the dry state. Among them, MtPM25, a member of the group 5 is specifically associated with DT in Medicago truncatula seeds. Its function is unknown and it

  1. 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.

  2. 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. PMID:14988443

  3. 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.

  4. Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

    OpenAIRE

    Yi-Ming He; Bin-Guang Ma

    2016-01-01

    Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophil...

  5. Development stage-specific proteomic profiling uncovers small, lineage specific proteins most abundant in the Aspergillus Fumigatus conidial proteome

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    Suh Moo-Jin

    2012-04-01

    Full Text Available Abstract Background The pathogenic mold Aspergillus fumigatus is the most frequent infectious cause of death in severely immunocompromised individuals such as leukemia and bone marrow transplant patients. Germination of inhaled conidia (asexual spores in the host is critical for the initiation of infection, but little is known about the underlying mechanisms of this process. Results To gain insights into early germination events and facilitate the identification of potential stage-specific biomarkers and vaccine candidates, we have used quantitative shotgun proteomics to elucidate patterns of protein abundance changes during early fungal development. Four different stages were examined: dormant conidia, isotropically expanding conidia, hyphae in which germ tube emergence has just begun, and pre-septation hyphae. To enrich for glycan-linked cell wall proteins we used an alkaline cell extraction method. Shotgun proteomic resulted in the identification of 375 unique gene products with high confidence, with no evidence for enrichment of cell wall-immobilized and secreted proteins. The most interesting discovery was the identification of 52 proteins enriched in dormant conidia including 28 proteins that have never been detected in the A. fumigatus conidial proteome such as signaling protein Pil1, chaperones BipA and calnexin, and transcription factor HapB. Additionally we found many small, Aspergillus specific proteins of unknown function including 17 hypothetical proteins. Thus, the most abundant protein, Grg1 (AFUA_5G14210, was also one of the smallest proteins detected in this study (M.W. 7,367. Among previously characterized proteins were melanin pigment and pseurotin A biosynthesis enzymes, histones H3 and H4.1, and other proteins involved in conidiation and response to oxidative or hypoxic stress. In contrast, expanding conidia, hyphae with early germ tubes, and pre-septation hyphae samples were enriched for proteins responsible for

  6. 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.

  7. 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.

  8. 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

  9. Comparison of amino acids physico-chemical properties and usage of late embryogenesis abundant proteins, hydrophilins and WHy domain.

    Science.gov (United States)

    Jaspard, Emmanuel; Hunault, Gilles

    2014-01-01

    Late Embryogenesis Abundant proteins (LEAPs) comprise several diverse protein families and are mostly involved in stress tolerance. Most of LEAPs are intrinsically disordered and thus poorly functionally characterized. LEAPs have been classified and a large number of their physico-chemical properties have been statistically analyzed. LEAPs were previously proposed to be a subset of a very wide family of proteins called hydrophilins, while a domain called WHy (Water stress and Hypersensitive response) was found in LEAP class 8 (according to our previous classification). Since little is known about hydrophilins and WHy domain, the cross-analysis of their amino acids physico-chemical properties and amino acids usage together with those of LEAPs helps to describe some of their structural features and to make hypothesis about their function. Physico-chemical properties of hydrophilins and WHy domain strongly suggest their role in dehydration tolerance, probably by interacting with water and small polar molecules. The computational analysis reveals that LEAP class 8 and hydrophilins are distinct protein families and that not all LEAPs are a protein subset of hydrophilins family as proposed earlier. Hydrophilins seem related to LEAP class 2 (also called dehydrins) and to Heat Shock Proteins 12 (HSP12). Hydrophilins are likely unstructured proteins while WHy domain is structured. LEAP class 2, hydrophilins and WHy domain are thus proposed to share a common physiological role by interacting with water or other polar/charged small molecules, hence contributing to dehydration tolerance. PMID:25296175

  10. Comparison of amino acids physico-chemical properties and usage of late embryogenesis abundant proteins, hydrophilins and WHy domain.

    Directory of Open Access Journals (Sweden)

    Emmanuel Jaspard

    Full Text Available Late Embryogenesis Abundant proteins (LEAPs comprise several diverse protein families and are mostly involved in stress tolerance. Most of LEAPs are intrinsically disordered and thus poorly functionally characterized. LEAPs have been classified and a large number of their physico-chemical properties have been statistically analyzed. LEAPs were previously proposed to be a subset of a very wide family of proteins called hydrophilins, while a domain called WHy (Water stress and Hypersensitive response was found in LEAP class 8 (according to our previous classification. Since little is known about hydrophilins and WHy domain, the cross-analysis of their amino acids physico-chemical properties and amino acids usage together with those of LEAPs helps to describe some of their structural features and to make hypothesis about their function. Physico-chemical properties of hydrophilins and WHy domain strongly suggest their role in dehydration tolerance, probably by interacting with water and small polar molecules. The computational analysis reveals that LEAP class 8 and hydrophilins are distinct protein families and that not all LEAPs are a protein subset of hydrophilins family as proposed earlier. Hydrophilins seem related to LEAP class 2 (also called dehydrins and to Heat Shock Proteins 12 (HSP12. Hydrophilins are likely unstructured proteins while WHy domain is structured. LEAP class 2, hydrophilins and WHy domain are thus proposed to share a common physiological role by interacting with water or other polar/charged small molecules, hence contributing to dehydration tolerance.

  11. 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.

  12. 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.

  13. Biochemical and structural characterization of an endoplasmic reticulum-localized late embryogenesis abundant (LEA) protein from the liverwort Marchantia polymorpha.

    Science.gov (United States)

    Hatanaka, Rie; Furuki, Takao; Shimizu, Tempei; Takezawa, Daisuke; Kikawada, Takahiro; Sakurai, Minoru; Sugawara, Yasutake

    2014-11-28

    Late embryogenesis abundant (LEA) proteins, which accumulate to high levels in seeds during late maturation, are associated with desiccation tolerance. A member of the LEA protein family was found in cultured cells of the liverwort Marchantia polymorpha; preculture treatment of these cells with 0.5M sucrose medium led to their acquisition of desiccation tolerance. We characterized this preculture-induced LEA protein, designated as MpLEA1. MpLEA1 is predominantly hydrophilic with a few hydrophobic residues that may represent its putative signal peptide. The protein also contains a putative endoplasmic reticulum (ER) retention sequence, HEEL, at the C-terminus. Microscopic observations indicated that GFP-fused MpLEA1 was mainly localized in the ER. The recombinant protein MpLEA1 is intrinsically disordered in solution. On drying, MpLEA1 shifted predominantly toward α-helices from random coils. Such changes in conformation are a typical feature of the group 3 LEA proteins. Recombinant MpLEA1 prevented the aggregation of α-casein during desiccation-rehydration events, suggesting that MpLEA1 exerts anti-aggregation activity against desiccation-sensitive proteins by functioning as a "molecular shield". Moreover, the anti-aggregation activity of MpLEA1 was ten times greater than that of BSA or insect LEA proteins, which are known to prevent aggregation on drying. Here, we show that an ER-localized LEA protein, MpLEA1, possesses biochemical and structural features specific to group 3 LEA proteins. PMID:25450698

  14. An odorant-binding protein is abundantly expressed in the nose and in the seminal fluid of the rabbit.

    Directory of Open Access Journals (Sweden)

    Rosa Mastrogiacomo

    Full Text Available We have purified an abundant lipocalin from the seminal fluid of the rabbit, which shows significant similarity with the sub-class of pheromone carriers "urinary" and "salivary" and presents an N-terminal sequence identical with that of an odorant-binding protein (rabOBP3 expressed in the nasal tissue of the same species. This protein is synthesised in the prostate and found in the seminal fluid, but not in sperm cells. The same protein is also expressed in the nasal epithelium of both sexes, but is completely absent in female reproductive organs. It presents four cysteines, among which two are arranged to form a disulphide bridge, and is glycosylated. This is the first report of an OBP identified at the protein level in the seminal fluid of a vertebrate species. The protein purified from seminal fluid is bound to some organic chemicals whose structure is currently under investigation. We reasonably speculate that, like urinary and salivary proteins reported in other species of mammals, this lipocalin performs a dual role, as carrier of semiochemicals in the seminal fluid and as detector of chemical signals in the nose.

  15. An odorant-binding protein is abundantly expressed in the nose and in the seminal fluid of the rabbit.

    Science.gov (United States)

    Mastrogiacomo, Rosa; D'Ambrosio, Chiara; Niccolini, Alberto; Serra, Andrea; Gazzano, Angelo; Scaloni, Andrea; Pelosi, Paolo

    2014-01-01

    We have purified an abundant lipocalin from the seminal fluid of the rabbit, which shows significant similarity with the sub-class of pheromone carriers "urinary" and "salivary" and presents an N-terminal sequence identical with that of an odorant-binding protein (rabOBP3) expressed in the nasal tissue of the same species. This protein is synthesised in the prostate and found in the seminal fluid, but not in sperm cells. The same protein is also expressed in the nasal epithelium of both sexes, but is completely absent in female reproductive organs. It presents four cysteines, among which two are arranged to form a disulphide bridge, and is glycosylated. This is the first report of an OBP identified at the protein level in the seminal fluid of a vertebrate species. The protein purified from seminal fluid is bound to some organic chemicals whose structure is currently under investigation. We reasonably speculate that, like urinary and salivary proteins reported in other species of mammals, this lipocalin performs a dual role, as carrier of semiochemicals in the seminal fluid and as detector of chemical signals in the nose. PMID:25391153

  16. Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 1. High abundance proteins, acute phase proteins and peptidomics.

    Science.gov (United States)

    Thomas, Funmilola Clara; Mullen, William; Tassi, Riccardo; Ramírez-Torres, Adela; Mudaliar, Manikhandan; McNeilly, Tom N; Zadoks, Ruth N; Burchmore, Richard; David Eckersall, P

    2016-08-16

    A peptidomic investigation of milk from an experimental model of Streptococcus uberis mastitis in dairy cows has incorporated a study of milk high abundance and acute phase (APP) proteins as well as analysis of low molecular weight peptide biomarkers. Intramammary infection (IMI) with S. uberis caused a shift in abundance from caseins, β-lactoglobulin and α-lactalbumin to albumin, lactoferrin and IgG with the increase in lactoferrin occurring last. The APP response of haptoglobin, mammary associated serum amyloid A3 and C-reactive protein occurred between 30-48 hours post challenge with peak concentrations of APPs at 72-96 hours post challenge and declined thereafter at a rate resembling the fall in bacterial count rather than the somatic cell count. A peptide biomarker panel for IMI based on capillary electrophoresis and mass spectrometry was developed. It comprised 77 identified peptides (IMI77) composed mainly of casein derived peptides but also including peptides of glycosylation dependent cell adhesion molecule and serum amyloid A. The panel had a biomarker classification score that increased from 36 hour to 81 hour post challenge, significantly differentiating infected from non-infected milk, thus suggesting potential as a peptide biomarker panel of bovine mastitis and specifically that of S. uberis origin. The use of omic technology has shown a multifactorial cross system reaction in high and low abundance proteins and their peptide derivatives with changes of over a thousand fold in analyte levels in response to S. uberis infection. PMID:27412456

  17. 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.

  18. Thousand and one ways to quantify and compare protein abundances in label-free bottom-up proteomics.

    Science.gov (United States)

    Blein-Nicolas, Mélisande; Zivy, Michel

    2016-08-01

    How to process and analyze MS data to quantify and statistically compare protein abundances in bottom-up proteomics has been an open debate for nearly fifteen years. Two main approaches are generally used: the first is based on spectral data generated during the process of identification (e.g. peptide counting, spectral counting), while the second makes use of extracted ion currents to quantify chromatographic peaks and infer protein abundances based on peptide quantification. These two approaches actually refer to multiple methods which have been developed during the last decade, but were submitted to deep evaluations only recently. In this paper, we compiled these different methods as exhaustively as possible. We also summarized the way they address the different problems raised by bottom-up protein quantification such as normalization, the presence of shared peptides, unequal peptide measurability and missing data. This article is part of a Special Issue entitled: Plant Proteomics- a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. PMID:26947242

  19. 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

  20. 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.

  1. 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.

  2. 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.

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

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    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

  4. Uses of Phage Display in Agriculture: Sequence Analysis and Comparative Modeling of Late Embryogenesis Abundant Client Proteins Suggest Protein-Nucleic Acid Binding Functionality

    Directory of Open Access Journals (Sweden)

    Rekha Kushwaha

    2013-01-01

    Full Text Available A group of intrinsically disordered, hydrophilic proteins—Late Embryogenesis Abundant (LEA proteins—has been linked to survival in plants and animals in periods of stress, putatively through safeguarding enzymatic function and prevention of aggregation in times of dehydration/heat. Yet despite decades of effort, the molecular-level mechanisms defining this protective function remain unknown. A recent effort to understand LEA functionality began with the unique application of phage display, wherein phage display and biopanning over recombinant Seed Maturation Protein homologs from Arabidopsis thaliana and Glycine max were used to retrieve client proteins at two different temperatures, with one intended to represent heat stress. From this previous study, we identified 21 client proteins for which clones were recovered, sometimes repeatedly. Here, we use sequence analysis and homology modeling of the client proteins to ascertain common sequence and structural properties that may contribute to binding affinity with the protective LEA protein. Our methods uncover what appears to be a predilection for protein-nucleic acid interactions among LEA client proteins, which is suggestive of subcellular residence. The results from this initial computational study will guide future efforts to uncover the protein protective mechanisms during heat stress, potentially leading to phage-display-directed evolution of synthetic LEA molecules.

  5. Functional characterization of the late embryogenesis abundant (LEA) protein gene family from Pinus tabuliformis (Pinaceae) in Escherichia coli.

    Science.gov (United States)

    Gao, Jie; Lan, Ting

    2016-01-01

    Late embryogenesis abundant (LEA) proteins are a large and highly diverse gene family present in a wide range of plant species. LEAs are proposed to play a role in various stress tolerance responses. Our study represents the first-ever survey of LEA proteins and their encoding genes in a widely distributed pine (Pinus tabuliformis) in China. Twenty-three LEA genes were identified from the P. tabuliformis belonging to seven groups. Proteins with repeated motifs are an important feature specific to LEA groups. Ten of 23 pine LEA genes were selectively expressed in specific tissues, and showed expression divergence within each group. In addition, we selected 13 genes representing each group and introduced theses genes into Escherichia coli to assess the protective function of PtaLEA under heat and salt stresses. Compared with control cells, the E. coli cells expressing PtaLEA fusion protein exhibited enhanced salt and heat resistance and viability, indicating the protein may play a protective role in cells under stress conditions. Furthermore, among these enhanced tolerance genes, a certain extent of function divergence appeared within a gene group as well as between gene groups, suggesting potential functional diversity of this gene family in conifers. PMID:26781930

  6. 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.

  7. Differences in abundances of cell-signalling proteins in blood reveal novel biomarkers for early detection of clinical Alzheimer's disease.

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    Mateus Rocha de Paula

    Full Text Available BACKGROUND: In November 2007 a study published in Nature Medicine proposed a simple test based on the abundance of 18 proteins in blood to predict the onset of clinical symptoms of Alzheimer's Disease (AD two to six years before these symptoms manifest. Later, another study, published in PLoS ONE, showed that only five proteins (IL-1, IL-3, EGF, TNF- and G-CSF have overall better prediction accuracy. These classifiers are based on the abundance of 120 proteins. Such values were standardised by a Z-score transformation, which means that their values are relative to the average of all others. METHODOLOGY: The original datasets from the Nature Medicine paper are further studied using methods from combinatorial optimisation and Information Theory. We expand the original dataset by also including all pair-wise differences of z-score values of the original dataset ("metafeatures". Using an exact algorithm to solve the resulting Feature Set problem, used to tackle the feature selection problem, we found signatures that contain either only features, metafeatures or both, and evaluated their predictive performance on the independent test set. CONCLUSIONS: It was possible to show that a specific pattern of cell signalling imbalance in blood plasma has valuable information to distinguish between NDC and AD samples. The obtained signatures were able to predict AD in patients that already had a Mild Cognitive Impairment (MCI with up to 84% of sensitivity, while maintaining also a strong prediction accuracy of 90% on a independent dataset with Non Demented Controls (NDC and AD samples. The novel biomarkers uncovered with this method now confirms ANG-2, IL-11, PDGF-BB, CCL15/MIP-1; and supports the joint measurement of other signalling proteins not previously discussed: GM-CSF, NT-3, IGFBP-2 and VEGF-B.

  8. Visualizing and Quantifying Intracellular Behavior and Abundance of the Core Circadian Clock Protein PERIOD2.

    Science.gov (United States)

    Smyllie, Nicola J; Pilorz, Violetta; Boyd, James; Meng, Qing-Jun; Saer, Ben; Chesham, Johanna E; Maywood, Elizabeth S; Krogager, Toke P; Spiller, David G; Boot-Handford, Raymond; White, Michael R H; Hastings, Michael H; Loudon, Andrew S I

    2016-07-25

    Transcriptional-translational feedback loops (TTFLs) are a conserved molecular motif of circadian clocks. The principal clock in mammals is the suprachiasmatic nucleus (SCN) of the hypothalamus. In SCN neurons, auto-regulatory feedback on core clock genes Period (Per) and Cryptochrome (Cry) following nuclear entry of their protein products is the basis of circadian oscillation [1, 2]. In Drosophila clock neurons, the movement of dPer into the nucleus is subject to a circadian gate that generates a delay in the TTFL, and this delay is thought to be critical for oscillation [3, 4]. Analysis of the Drosophila clock has strongly influenced models of the mammalian clock, and such models typically infer complex spatiotemporal, intracellular behaviors of mammalian clock proteins. There are, however, no direct measures of the intracellular behavior of endogenous circadian proteins to support this: dynamic analyses have been limited and often have no circadian dimension [5-7]. We therefore generated a knockin mouse expressing a fluorescent fusion of native PER2 protein (PER2::VENUS) for live imaging. PER2::VENUS recapitulates the circadian functions of wild-type PER2 and, importantly, the behavior of PER2::VENUS runs counter to the Drosophila model: it does not exhibit circadian gating of nuclear entry. Using fluorescent imaging of PER2::VENUS, we acquired the first measures of mobility, molecular concentration, and localization of an endogenous circadian protein in individual mammalian cells, and we showed how the mobility and nuclear translocation of PER2 are regulated by casein kinase. These results provide new qualitative and quantitative insights into the cellular mechanism of the mammalian circadian clock. PMID:27374340

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

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    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

  10. 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

  11. Disordered nucleiome: Abundance of intrinsic disorder in the DNA- and RNA-binding proteins in 1121 species from Eukaryota, Bacteria and Archaea.

    Science.gov (United States)

    Wang, Chen; Uversky, Vladimir N; Kurgan, Lukasz

    2016-05-01

    Intrinsically disordered proteins (IDPs) are abundant in various proteomes, where they play numerous important roles and complement biological activities of ordered proteins. Among functions assigned to IDPs are interactions with nucleic acids. However, often, such assignments are made based on the guilty-by-association principle. The validity of the extension of these correlations to all nucleic acid binding proteins has never been analyzed on a large scale across all domains of life. To fill this gap, we perform a comprehensive computational analysis of the abundance of intrinsic disorder and intrinsically disordered domains in nucleiomes (∼548 000 nucleic acid binding proteins) of 1121 species from Archaea, Bacteria and Eukaryota. Nucleiome is a whole complement of proteins involved in interactions with nucleic acids. We show that relative to other proteins in the corresponding proteomes, the DNA-binding proteins have significantly increased disorder content and are significantly enriched in disordered domains in Eukaryotes but not in Archaea and Bacteria. The RNA-binding proteins are significantly enriched in the disordered domains in Bacteria, Archaea and Eukaryota, while the overall abundance of disorder in these proteins is significantly increased in Bacteria, Archaea, animals and fungi. The high abundance of disorder in nucleiomes supports the notion that the nucleic acid binding proteins often require intrinsic disorder for their functions and regulation. PMID:27037624

  12. Immunological Characterization of Tristetraprolin as a Low Abundance, Inducible, Stable Cytosolic Protein*

    OpenAIRE

    Cao, Heping; Tuttle, Jane S.; Blackshear, Perry J.

    2004-01-01

    Tristetraprolin (TTP) is a zinc finger protein that can bind to AU-rich elements within certain mRNAs, resulting in deadenylation and destabilization of those mRNAs. Its physiological targets include the mRNAs encoding the cytokines tumor necrosis factor α (TNF) and granulocyte-macrophage colony-stimulating factor. TTP was originally identified on the basis of its massive but transient increase in mRNA levels following mitogen stimulation of fibroblasts. It has been difficult to reconcile thi...

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

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    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.

  14. 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.

  15. 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-tRNA(Leu) that evades the translational proofreading activities 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. PMID:24013929

  16. 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. PMID:25244376

  17. The abundant and essential HU proteins in Deinococcus deserti and Deinococcus radiodurans are translated from leaderless mRNA.

    Science.gov (United States)

    Bouthier de la Tour, Claire; Blanchard, Laurence; Dulermo, Rémi; Ludanyi, Monika; Devigne, Alice; Armengaud, Jean; Sommer, Suzanne; de Groot, Arjan

    2015-12-01

    HU proteins have an important architectural role in nucleoid organization in bacteria. Compared with HU of many bacteria, HU proteins from Deinococcus species possess an N-terminal lysine-rich extension similar to the eukaryotic histone H1 C-terminal domain involved in DNA compaction. The single HU gene in Deinococcus radiodurans, encoding DrHU, is required for nucleoid compaction and cell viability. Deinococcus deserti contains three expressed HU genes, encoding DdHU1, DdHU2 and DdHU3. Here, we show that either DdHU1 or DdHU2 is essential in D. deserti. DdHU1 and DdHU2, but not DdHU3, can substitute for DrHU in D. radiodurans, indicating that DdHU3 may have a non-essential function different from DdHU1, DdHU2 and DrHU. Interestingly, the highly abundant DrHU and DdHU1 proteins, and also the less expressed DdHU2, are translated in Deinococcus from leaderless mRNAs, which lack a 5'-untranslated region and, hence, the Shine-Dalgarno sequence. Unexpectedly, cloning the DrHU or DdHU1 gene under control of a strong promoter in an expression plasmid, which results in leadered transcripts, strongly reduced the DrHU and DdHU1 protein level in D. radiodurans compared with that obtained from the natural leaderless gene. We also show that the start codon position for DrHU and DdHU1 should be reannotated, resulting in proteins that are 15 and 4 aa residues shorter than initially reported. The expression level and start codon correction were crucial for functional characterization of HU in Deinococcus.

  18. A group 6 late embryogenesis abundant protein from common bean is a disordered protein with extended helical structure and oligomer-forming properties.

    Science.gov (United States)

    Rivera-Najera, Lucero Y; Saab-Rincón, Gloria; Battaglia, Marina; Amero, Carlos; Pulido, Nancy O; García-Hernández, Enrique; Solórzano, Rosa M; Reyes, José L; Covarrubias, Alejandra A

    2014-11-14

    Late embryogenesis-abundant proteins accumulate to high levels in dry seeds. Some of them also accumulate in response to water deficit in vegetative tissues, which leads to a remarkable association between their presence and low water availability conditions. A major sub-group of these proteins, also known as typical LEA proteins, shows high hydrophilicity and a high percentage of glycine and other small amino acid residues, distinctive physicochemical properties that predict a high content of structural disorder. Although all typical LEA proteins share these characteristics, seven groups can be distinguished by sequence similarity, indicating structural and functional diversity among them. Some of these groups have been extensively studied; however, others require a more detailed analysis to advance in their functional understanding. In this work, we report the structural characterization of a group 6 LEA protein from a common bean (Phaseolus vulgaris L.) (PvLEA6) by circular dichroism and nuclear magnetic resonance showing that it is a disordered protein in aqueous solution. Using the same techniques, we show that despite its unstructured nature, the addition of trifluoroethanol exhibited an intrinsic potential in this protein to gain helicity. This property was also promoted by high osmotic potentials or molecular crowding. Furthermore, we demonstrate that PvLEA6 protein is able to form soluble homo-oligomeric complexes that also show high levels of structural disorder. The association between PvLEA6 monomers to form dimers was shown to occur in plant cells by bimolecular fluorescence complementation, pointing to the in vivo functional relevance of this association. PMID:25271167

  19. Proteome profiling of the growth phases of Leishmania pifanoi promastigotes in axenic culture reveals differential abundance of immunostimulatory proteins.

    Science.gov (United States)

    Alcolea, Pedro J; Alonso, Ana; García-Tabares, Francisco; Mena, María del Carmen; Ciordia, Sergio; Larraga, Vicente

    2016-06-01

    Leishmaniasis is a term that encompasses a compendium of neglected tropical diseases caused by dimorphic and digenetic protozoan parasites from the genus Leishmania (Kinetoplastida: Trypanosomatidae). The clinical manifestations of neotropical cutaneous leishmaniasis (NCL) caused by Leishmania pifanoi and other species of the "Leishmania mexicana complex" mainly correspond to anergic diffuse cutaneous leishmaniasis (ADCL), which is the origin of considerable morbidity. Despite the outstanding advances in the characterization of the trypanosomatid genomes and proteomes, the biology of this species has been scarcely explored. However, the close relation of L. pifanoi to the sequenced species L. mexicana and others included in the "L. mexicana complex" allowed us to perform a two-dimension electrophoresis (2DE) approach to the promastigote proteome at the differential expression level. Protein identifications were performed by matrix-assisted laser desorption-ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF). This insight has revealed similarities and differences between L. pifanoi and other species responsible for cutaneous and visceral leishmaniasis. Interestingly, certain proteins that were previously described as immunostimulatory (elongation factor 1β, trypanothione peroxidase, heat shock protein 70, enolase, GDP-forming succinyl-CoA and aldehyde dehydrogenase) are more abundant in the final growth stages of promastigotes (late-logarithmic and/or stationary phase) in the case of L. pifanoi. PMID:26992294

  20. 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

  1. Engineering protein processing of the mammary gland to produce abundant hemophilia B therapy in milk.

    Science.gov (United States)

    Zhao, Jianguo; Xu, Weijie; Ross, Jason W; Walters, Eric M; Butler, Stephen P; Whyte, Jeff J; Kelso, Lindsey; Fatemi, Mostafa; Vanderslice, Nicholas C; Giroux, Keith; Spate, Lee D; Samuel, Melissa S; Murphy, Cliff N; Wells, Kevin D; Masiello, Nick C; Prather, Randall S; Velander, William H

    2015-01-01

    Both the low animal cell density of bioreactors and their ability to post-translationally process recombinant factor IX (rFIX) limit hemophilia B therapy to <20% of the world's population. We used transgenic pigs to make rFIX in milk at about 3,000-fold higher output than provided by industrial bioreactors. However, this resulted in incomplete γ-carboxylation and propeptide cleavage where both processes are transmembrane mediated. We then bioengineered the co-expression of truncated, soluble human furin (rFurin) with pro-rFIX at a favorable enzyme to substrate ratio. This resulted in the complete conversion of pro-rFIX to rFIX while yielding a normal lactation. Importantly, these high levels of propeptide processing by soluble rFurin did not preempt γ-carboxylation in the ER and therefore was compartmentalized to the Trans-Golgi Network (TGN) and also to milk. The Golgi specific engineering demonstrated here segues the ER targeted enhancement of γ-carboxylation needed to biomanufacture coagulation proteins like rFIX using transgenic livestock. PMID:26387706

  2. Looking Deep Inside: Detection of Low-Abundance Proteins in Leaf Extracts of Arabidopsis and Phloem Exudates of Pumpkin1[W

    Science.gov (United States)

    Fröhlich, Andreas; Gaupels, Frank; Sarioglu, Hakan; Holzmeister, Christian; Spannagl, Manuel; Durner, Jörg; Lindermayr, Christian

    2012-01-01

    The field of proteomics suffers from the immense complexity of even small proteomes and the enormous dynamic range of protein concentrations within a given sample. Most protein samples contain a few major proteins, which hamper in-depth proteomic analysis. In the human field, combinatorial hexapeptide ligand libraries (CPLL; such as ProteoMiner) have been used for reduction of the dynamic range of protein concentrations; however, this technique is not established in plant research. In this work, we present the application of CPLL to Arabidopsis (Arabidopsis thaliana) leaf proteins. One- and two-dimensional gel electrophoresis showed a decrease in high-abundance proteins and an enrichment of less abundant proteins in CPLL-treated samples. After optimization of the CPLL protocol, mass spectrometric analyses of leaf extracts led to the identification of 1,192 proteins in control samples and an additional 512 proteins after the application of CPLL. Upon leaf infection with virulent Pseudomonas syringae DC3000, CPLL beads were also used for investigating the bacterial infectome. In total, 312 bacterial proteins could be identified in infected Arabidopsis leaves. Furthermore, phloem exudates of pumpkin (Cucurbita maxima) were analyzed. CPLL prefractionation caused depletion of the major phloem proteins 1 and 2 and improved phloem proteomics, because 67 of 320 identified proteins were detectable only after CPLL treatment. In sum, our results demonstrate that CPLL beads are a time- and cost-effective tool for reducing major proteins, which often interfere with downstream analyses. The concomitant enrichment of less abundant proteins may facilitate a deeper insight into the plant proteome. PMID:22555880

  3. Integrated Proteomic and Glycoproteomic Analyses of Prostate Cancer Cells Reveal Glycoprotein Alteration in Protein Abundance and Glycosylation.

    Science.gov (United States)

    Shah, Punit; Wang, Xiangchun; Yang, Weiming; Toghi Eshghi, Shadi; Sun, Shisheng; Hoti, Naseruddin; Chen, Lijun; Yang, Shuang; Pasay, Jered; Rubin, Abby; Zhang, Hui

    2015-10-01

    Prostate cancer is the most common cancer among men in the U.S. and worldwide, and androgen-deprivation therapy remains the principal treatment for patients. Although a majority of patients initially respond to androgen-deprivation therapy, most will eventually develop castration resistance. An increased understanding of the mechanisms that underline the pathogenesis of castration resistance is therefore needed to develop novel therapeutics. LNCaP and PC3 prostate cancer cell lines are models for androgen-dependence and androgen-independence, respectively. Herein, we report the comparative analysis of these two prostate cancer cell lines using integrated global proteomics and glycoproteomics. Global proteome profiling of the cell lines using isobaric tags for relative and absolute quantitation (iTRAQ) labeling and two- dimensional (2D) liquid chromatography-tandem MS (LC-MS/MS) led to the quantification of 8063 proteins. To analyze the glycoproteins, glycosite-containing peptides were isolated from the same iTRAQ-labeled peptides from the cell lines using solid phase extraction followed by LC-MS/MS analysis. Among the 1810 unique N-linked glycosite-containing peptides from 653 identified N-glycoproteins, 176 glycoproteins were observed to be different between the two cell lines. A majority of the altered glycoproteins were also observed with changes in their global protein expression levels. However, alterations in 21 differentially expressed glycoproteins showed no change at the protein abundance level, indicating that the glycosylation site occupancy was different between the two cell lines. To determine the glycosylation heterogeneity at specific glycosylation sites, we further identified and quantified 1145 N-linked glycopeptides with attached glycans in the same iTRAQ-labeled samples. These intact glycopeptides contained 67 glycan compositions and showed increased fucosylation in PC3 cells in several of the examined glycosylation sites. The increase in

  4. 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

  5. Expression profiles of 12 late embryogenesis abundant protein genes from Tamarix hispida in response to abiotic stress.

    Science.gov (United States)

    Gao, Caiqiu; Liu, Yali; Wang, Chao; Zhang, Kaimin; Wang, Yucheng

    2014-01-01

    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. PMID:25133264

  6. Characterization of the Human Adipocyte Proteome and Reproducibility of Protein Abundance by One-dimensional Gel Electrophoresis and HPLC-ESI-MS/MS

    OpenAIRE

    Xie, Xitao; Yi, Zhengping; Bowen, Benjamin; Wolf, Cassandra; Flynn, Charles R; Sinha, Sandeep; Mandarino, Lawrence J.; Meyer, Christian

    2010-01-01

    Abnormalities in adipocytes play an important role in various conditions, including the metabolic syndrome, type 2 diabetes mellitus and cardiovascular disease, but little is known about alterations at the protein level. We therefore sought to 1) comprehensively characterize the human adipocyte proteome for the first time, and 2) demonstrate feasibility of measuring adipocyte protein abundances by one-dimensional SDS-PAGE and High Performance Liquid Chromatography -Electron Spray Ionization -...

  7. 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...

  8. 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.

  9. On the abundance of intrinsically disordered proteins in the human proteome and its relation to diseases: there is no enrichment

    OpenAIRE

    Deiana, Antonio; Giansanti, Andrea

    2014-01-01

    Intrinsically disordered proteins are fascinating the community of protein science since the last decade, at least. There is a well-established line of research that intends to reveal the crucial role played by intrinsically disordered proteins (IDPs) in the development of human diseases. The main argument is that IDPs are differentially more present in groups of disease-related proteins. In this note we compare the frequency of disorder in human proteins, both disease-related and not. The fr...

  10. 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.

  11. Research advance in late-embryogenesis-abundant proteins%植物晚期胚胎富集蛋白的研究进展

    Institute of Scientific and Technical Information of China (English)

    詹立平; 赵鑫; 邹学忠

    2007-01-01

    植物在非生物胁迫下会诱导多种蛋白的产生,其中LEA蛋白是逆境生理学研究的热点之一.本文主要介绍了植物LEA蛋白(Late-embryogenesis-abundant protein)的分类、结构与功能,lea基因的表达调控以及转基因的相关研究进展.

  12. 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.

  13. 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.

    Science.gov (United States)

    Wu, Xiaolin; Gong, Fangping; Yang, Le; Hu, Xiuli; Tai, Fuju; Wang, Wei

    2014-01-01

    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. PMID:25653661

  14. Preovulatory Aging In Vivo and In Vitro Affects Maturation Rates, Abundance of Selected Proteins, Histone Methylation Pattern and Spindle Integrity in Murine Oocytes.

    Science.gov (United States)

    Demond, Hannah; Trapphoff, Tom; Dankert, Deborah; Heiligentag, Martyna; Grümmer, Ruth; Horsthemke, Bernhard; Eichenlaub-Ritter, Ursula

    2016-01-01

    Delayed ovulation and delayed fertilization can lead to reduced developmental competence of the oocyte. In contrast to the consequences of postovulatory aging of the oocyte, hardly anything is known about the molecular processes occurring during oocyte maturation if ovulation is delayed (preovulatory aging). We investigated several aspects of oocyte maturation in two models of preovulatory aging: an in vitro follicle culture and an in vivo mouse model in which ovulation was postponed using the GnRH antagonist cetrorelix. Both models showed significantly reduced oocyte maturation rates after aging. Furthermore, in vitro preovulatory aging deregulated the protein abundance of the maternal effect genes Smarca4 and Nlrp5, decreased the levels of histone H3K9 trimethylation and caused major deterioration of chromosome alignment and spindle conformation. Protein abundance of YBX2, an important regulator of mRNA stability, storage and recruitment in the oocyte, was not affected by in vitro aging. In contrast, in vivo preovulatory aging led to reduction in Ybx2 transcript and YBX2 protein abundance. Taken together, preovulatory aging seems to affect various processes in the oocyte, which could explain the low maturation rates and the previously described failures in fertilization and embryonic development. PMID:27611906

  15. The Unstructured N-terminal Region of Arabidopsis Group 4 Late Embryogenesis Abundant (LEA) Proteins Is Required for Folding and for Chaperone-like Activity under Water Deficit.

    Science.gov (United States)

    Cuevas-Velazquez, Cesar L; Saab-Rincón, Gloria; Reyes, José Luis; Covarrubias, Alejandra A

    2016-05-13

    Late embryogenesis abundant (LEA) proteins are a conserved group of proteins widely distributed in the plant kingdom that participate in the tolerance to water deficit of different plant species. In silico analyses indicate that most LEA proteins are structurally disordered. The structural plasticity of these proteins opens the question of whether water deficit modulates their conformation and whether these possible changes are related to their function. In this work, we characterized the secondary structure of Arabidopsis group 4 LEA proteins. We found that they are disordered in aqueous solution, with high intrinsic potential to fold into α-helix. We demonstrate that complete dehydration is not required for these proteins to sample ordered structures because milder water deficit and macromolecular crowding induce high α-helix levels in vitro, suggesting that prevalent conditions under water deficit modulate their conformation. We also show that the N-terminal region, conserved across all group 4 LEA proteins, is necessary and sufficient for conformational transitions and that their protective function is confined to this region, suggesting that folding into α-helix is required for chaperone-like activity under water limitation. We propose that these proteins can exist as different conformers, favoring functional diversity, a moonlighting property arising from their structural dynamics. PMID:27006402

  16. 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. PMID:25990084

  17. 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.

  18. 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. PMID:24992539

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    Xiaoli Tang

    2016-01-01

    Full Text Available 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.

  1. 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. PMID:27123459

  2. Computational and statistical analyses of amino acid usage and physico-chemical properties of the twelve late embryogenesis abundant protein classes.

    Directory of Open Access Journals (Sweden)

    Emmanuel Jaspard

    Full Text Available Late Embryogenesis Abundant Proteins (LEAPs are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168 and probably LEAP class 11 (PF04927 are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs.

  3. PHYSCOMITRELLA PATENS ARABINOGALACTAN PROTEINS CONTAIN ABUNDANT TERMINAL 3-O-METHYL-L-RHAMMOSYL RESIDUES NOT FOUND IN ANGIOSPERMS

    Science.gov (United States)

    A biochemical investigation of arabinogalactan proteins (AGPs) in Physcomitrella patens was undertaken with particular emphasis on the glycan chains. Following homogenization and differential centrifugation of moss gametophytes, AGPs were obtained by Arrive phenylglycoside-induced precipitation from...

  4. Protein abundance of urea transporters and aquaporin 2 change differently in nephrotic pair-fed vs. non-pair-fed rats

    OpenAIRE

    Bou Matar, Raed N.; Malik, Bela; Wang, Xiaonan H.; Martin, Christopher F; Eaton, Douglas C.; Sands, Jeff M.; Klein, Janet D.

    2012-01-01

    Salt and water retention is a hallmark of nephrotic syndrome (NS). In this study, we test for changes in the abundance of urea transporters, aquaporin 2 (AQP2), Na-K-2Cl cotransporter 2 (NKCC2), and Na-Cl cotransporter (NCC), in non-pair-fed and pair-fed nephrotic animals. Doxorubicin-injected male Sprague-Dawley rats (n = 10) were followed in metabolism cages. Urinary excretion of protein, sodium, and urea was measured periodically. Kidney inner medulla (IM), outer medulla, and cortex tissue...

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

    Science.gov (United States)

    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 kDa, 26 kDa, 33 kDa and 56 kDa have been identified as allergens. Re...

  6. RcLEA, a late embryogenesis abundant protein gene isolated from Rosa chinensis, confers tolerance to Escherichia coli and Arabidopsis thaliana and stabilizes enzyme activity under diverse stresses.

    Science.gov (United States)

    Zhang, Xuan; Lu, Songchong; Jiang, Changhua; Wang, Yaofeng; Lv, Bo; Shen, Jiabin; Ming, Feng

    2014-07-01

    The late embryogenesis abundant (LEA) protein family is a large protein family that is closely associated with resistance to abiotic stresses in many organisms, such as plants, bacteria and animals. In this study, we isolated a LEA gene, RcLEA, which was cytoplasm-localized, from Rosa chinensis. RcLEA was found to be induced by high temperature through RT-PCR. Overexpression of RcLEA in Escherichia coli improved its growth performance compared with the control under high temperature, low temperature, NaCl and oxidative stress conditions. RcLEA was also overexpressed in Arabidopsis thaliana. The transgenic Arabidopsis showed better growth after high and low temperature treatment and exhibited less peroxide according to 3, 3-diaminobenzidine staining. However, RcLEA did not improve the tolerance to NaCl or osmotic stress in Arabidopsis. In vitro analysis showed that RcLEA was able to prevent the freeze-thaw-induced inactivation or heat-induced aggregation of various substrates, such as lactate dehydrogenase and citrate synthase. It also protected the proteome of E. coli from denaturation when the proteins were heat-shocked or subjected to acidic conditions. Furthermore, bimolecular fluorescence complementation assays suggested that RcLEA proteins function in a complex manner by making the form of homodimers. PMID:24760474

  7. Abundant type III lipid transfer proteins in Arabidopsis tapetum are secreted to the locule and become a constituent of the pollen exine.

    Science.gov (United States)

    Huang, Ming-Der; Chen, Tung-Ling L; Huang, Anthony H C

    2013-11-01

    Lipid transfer proteins (LTPs) are small secretory proteins in plants with defined lipid-binding structures for possible lipid exocytosis. Special groups of LTPs unique to the anther tapetum are abundant, but their functions are unclear. We studied a special group of LTPs, type III LTPs, in Arabidopsis (Arabidopsis thaliana). Their transcripts were restricted to the anther tapetum, with levels peaking at the developmental stage of maximal pollen-wall exine synthesis. We constructed an LTP-Green Fluorescent Protein (LTP-GFP) plasmid, transformed it into wild-type plants, and monitored LTP-GFP in developing anthers with confocal laser scanning microscopy. LTP-GFP appeared in the tapetum and was secreted via the endoplasmic reticulum-trans-Golgi network machinery into the locule. It then moved to the microspore surface and remained as a component of exine. Immuno-transmission electron microscopy of native LTP in anthers confirmed the LTP-GFP observations. The in vivo association of LTP-GFP and exine in anthers was not observed with non-type III or structurally modified type III LTPs or in transformed exine-defective mutant plants. RNA interference knockdown of individual type III LTPs produced no observable mutant phenotypes. RNA interference knockdown of two type III LTPs produced microscopy-observable morphologic changes in the intine underneath the exine (presumably as a consequence of changes in the exine not observed by transmission electron microscopy) and pollen susceptible to dehydration damage. Overall, we reveal a novel transfer pathway of LTPs in which LTPs bound or nonbound to exine precursors are secreted from the tapetum to become microspore exine constituents; this pathway explains the need for plentiful LTPs to incorporate into the abundant exine. PMID:24096413

  8. The pepper late embryogenesis abundant protein CaLEA1 acts in regulating abscisic acid signaling, drought and salt stress response.

    Science.gov (United States)

    Lim, Chae Woo; Lim, Sohee; Baek, Woonhee; Lee, Sung Chul

    2015-08-01

    As sessile organisms, plants are constantly challenged by environmental stresses, including drought and high salinity. Among the various abiotic stresses, osmotic stress is one of the most important factors for growth and significantly reduces crop productivity in agriculture. Here, we report a function of the CaLEA1 protein in the defense responses of plants to osmotic stress. Our analyses showed that the CaLEA1 gene was strongly induced in pepper leaves exposed to drought and increased salinity. Furthermore, we determined that the CaLEA1 protein has a late embryogenesis abundant (LEA)_3 homolog domain highly conserved among other known group 5 LEA proteins and is localized in the processing body. We generated CaLEA1-silenced peppers and CaLEA1-overexpressing (OX) transgenic Arabidopsis plants to evaluate their responses to dehydration and high salinity. Virus-induced gene silencing of CaLEA1 in pepper plants conferred enhanced sensitivity to drought and salt stresses, which was accompanied by high levels of lipid peroxidation in dehydrated and NaCl-treated leaves. CaLEA1-OX plants exhibited enhanced sensitivity to abscisic acid (ABA) during seed germination and in the seedling stage; furthermore, these plants were more tolerant to drought and salt stress than the wild-type plants because of enhanced stomatal closure and increased expression of stress-responsive genes. Collectively, our data suggest that CaLEA1 positively regulates drought and salinity tolerance through ABA-mediated cell signaling. PMID:25302464

  9. Knockout of the abundant Trichomonas vaginalis hydrogenosomal membrane protein TvHMP23 increases hydrogenosome size but induces no compensatory up-regulation of paralogous copies.

    Science.gov (United States)

    Brás, Xavier Pereira; Zimorski, Verena; Bolte, Kathrin; Maier, Uwe-G; Martin, William F; Gould, Sven B

    2013-05-01

    The Trichomonas vaginalis genome encodes up to 60000 genes, many of which stem from genome duplication events. Paralogous copies thus accompany most T. vaginalis genes, a phenomenon that limits genetic manipulation. We characterized one of the parasite's most abundant hydrogenosomal membrane proteins, TvHMP23, which is phylogenetically distinct from canonical metabolite carriers, and which localizes to the inner hydrogenosomal membrane as shown through sub-organellar fractionation and protease protection assays. Knockout of Tvhmp23 through insertion of the selectable neomycin marker led to a size increase of hydrogenosomes, the first knockout-induced phenotypes reported for Trichomonas, but no growth impairment. The transcriptional response of its four paralogous copies then analyzed revealed that they are not up-regulated, and hence do not compensate for the Tvhmp23 knockout. PMID:23499435

  10. Stem-cell-abundant proteins Nanog, Nucleostemin and Musashi1 are highly expressed in malignant cervical epithelial cells

    International Nuclear Information System (INIS)

    Nanog, nucleostemin (NS) and musashi1 (Msi1) are proteins that are highly expressed in undifferentiated embryonic stem (ES) cells and have been shown to be essential in maintaining the pluripotency and regulating the proliferation and asymmetric division of ES cells and several nervous system tumor cells. The roles of Nanog, NS and Msi1 in development and progression of cervical carcinoma have, until now, not been well documented. In this study, expression of Nanog, NS and Msi1 was detected by immunohistochemistry analysis in 235 patients with various degrees of cervical epithelial lesions, including 49 with normal cervical epithelia, 31 with mild dysplasia (CIN I), 77 with moderate-severe dysplasia (CIN II-III) and 78 with squamous cervical carcinomas (SCCs). Associations with various clinical pathological prognostic variables were analyzed in 50 early-stage SCC patients. Nanog, NS and Msi1 expression levels were significantly higher in SCC patients compared with CIN patients, and were higher in CIN patients compared with those with normal cervical epithelia. Nanog expression levels showed significantly differences according to different tumor sizes (P < 0.05), whereas there were no differences in NS and Msi1 expression levels according to different clinical pathological parameters. Our findings indicate that Nanog, NS and Msi1 may be involved in carcinogenesis of the cervix and progression of cervical carcinoma

  11. Influence of pregnancy in mid-to-late gestation on circulating metabolites, visceral organ mass, and abundance of proteins relating to energy metabolism in mature beef cows.

    Science.gov (United States)

    Wood, K M; Awda, B J; Fitzsimmons, C; Miller, S P; McBride, B W; Swanson, K C

    2013-12-01

    In mid-to-late gestation, nutrient demand increases to meet the growth requirements of the conceptus and cows may alter metabolism in response to energy demands of pregnancy. By better understanding the metabolic role of pregnancy, there may be opportunities to better understand maintenance energy costs and improve overall feed efficiency. Eighteen mature Simmental/Angus crossbred cows, pregnant (PREG; n = 9) and nonpregnant (OPEN; n = 9), were used to investigate the effect of pregnancy on BW change, carcass traits, visceral organ mass, and circulating serum metabolites. Cows were blocked by day of expected parturition such that each block was slaughtered 4 to 5 wk before parturition. Cows were individually fed for ad libitum intake using Calan gates for 89 to 105 d. Cows were weighed, ultrasounded for rib (over the 12th and 13th rib) and rump fat, and a serum sample obtained at d 1, 56, and 3 to 5 d before slaughter. At slaughter, organs were removed, trimmed of fat, and weighed. Serum was analyzed for β-hydroxybutyrate (BHBA), NEFA, glucose, urea, total cholesterol, and triiodothyronine (T3). Tissue samples from liver, kidney, sternomandibularis muscle, ruminal papillae, pancreas, and small intestinal mucosa were collected at slaughter and snap frozen in liquid N. Western blots were conducted to quantify abundance of: proliferating cell nuclear antigen (PCNA), ATP synthase, ubiquitin, and Na(+)/K+ ATPase for all tissues; PPARγ, PPARγ coactivator 1α (PGC1-α), 5'-adenosine monophosphate-activated protein kinase (AMPK) and phosphorylated-AMPK (pAMPK) for liver, muscle, and rumen; phosphoenolpyruvate carboxykinase (PEPCK) for liver and kidney; and uncoupling protein 2 (UCP2) for liver. Data were analyzed using PROC MIXED in SAS as a replicated randomized complete block. Liver weights (actual, relative to BW, relative to HCW) were heavier (P ≤ 0.02) in OPEN. Rumen mass and kidney fat weight, both relative to BW, were also greater (P ≤ 0.04) in OPEN. On d 56

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

    Science.gov (United States)

    Liu, Yiling; Xie, Lixia; Liang, Xilong; Zhang, Shihong

    2015-01-01

    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. PMID:26569231

  13. 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. PMID:25200982

  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. 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.

  16. Late Embryogenesis Abundant (LEA Constitutes a Large and Diverse Family of Proteins Involved in Development and Abiotic Stress Responses in Sweet Orange (Citrus sinensis L. Osb..

    Directory of Open Access Journals (Sweden)

    Andresa Muniz Pedrosa

    Full Text Available Late Embryogenesis Abundant (LEA proteins are an ubiquitous group of polypeptides that were first described to accumulate during plant seed dehydration, at the later stages of embryogenesis. Since then they have also been recorded in vegetative plant tissues experiencing water limitation and in anhydrobiotic bacteria and invertebrates and, thereby, correlated with the acquisition of desiccation tolerance. This study provides the first comprehensive study about the LEA gene family in sweet orange (Citrus sinensis L. Osb., the most important and widely grown fruit crop around the world. A surprisingly high number (72 of genes encoding C. sinensis LEAs (CsLEAs were identified and classified into seven groups (LEA_1, LEA_2, LEA_3 and LEA_4, LEA_5, DEHYDRIN and SMP based on their predicted amino acid sequences and also on their phylogenetic relationships with the complete set of Arabidopsis thaliana LEA proteins (AtLEAs. Approximately 60% of the CsLEAs identified in this study belongs to the unusual LEA_2 group of more hydrophobic LEA proteins, while the other LEA groups contained a relatively small number of members typically hydrophilic. A correlation between gene structure and motif composition was observed within each LEA group. Investigation of their chromosomal localizations revealed that the CsLEAs were non-randomly distributed across all nine chromosomes and that 33% of all CsLEAs are segmentally or tandemly duplicated genes. Analysis of the upstream sequences required for transcription revealed the presence of various stress-responsive cis-acting regulatory elements in the promoter regions of CsLEAs, including ABRE, DRE/CRT, MYBS and LTRE. Expression analysis using both RNA-seq data and quantitative real-time RT-PCR (qPCR revealed that the CsLEA genes are widely expressed in various tissues, and that many genes containing the ABRE promoter sequence are induced by drought, salt and PEG. These results provide a useful reference for further

  17. Late Embryogenesis Abundant (LEA) Constitutes a Large and Diverse Family of Proteins Involved in Development and Abiotic Stress Responses in Sweet Orange (Citrus sinensis L. Osb.).

    Science.gov (United States)

    Pedrosa, Andresa Muniz; Martins, Cristina de Paula Santos; Gonçalves, Luana Pereira; Costa, Marcio Gilberto Cardoso

    2015-01-01

    Late Embryogenesis Abundant (LEA) proteins are an ubiquitous group of polypeptides that were first described to accumulate during plant seed dehydration, at the later stages of embryogenesis. Since then they have also been recorded in vegetative plant tissues experiencing water limitation and in anhydrobiotic bacteria and invertebrates and, thereby, correlated with the acquisition of desiccation tolerance. This study provides the first comprehensive study about the LEA gene family in sweet orange (Citrus sinensis L. Osb.), the most important and widely grown fruit crop around the world. A surprisingly high number (72) of genes encoding C. sinensis LEAs (CsLEAs) were identified and classified into seven groups (LEA_1, LEA_2, LEA_3 and LEA_4, LEA_5, DEHYDRIN and SMP) based on their predicted amino acid sequences and also on their phylogenetic relationships with the complete set of Arabidopsis thaliana LEA proteins (AtLEAs). Approximately 60% of the CsLEAs identified in this study belongs to the unusual LEA_2 group of more hydrophobic LEA proteins, while the other LEA groups contained a relatively small number of members typically hydrophilic. A correlation between gene structure and motif composition was observed within each LEA group. Investigation of their chromosomal localizations revealed that the CsLEAs were non-randomly distributed across all nine chromosomes and that 33% of all CsLEAs are segmentally or tandemly duplicated genes. Analysis of the upstream sequences required for transcription revealed the presence of various stress-responsive cis-acting regulatory elements in the promoter regions of CsLEAs, including ABRE, DRE/CRT, MYBS and LTRE. Expression analysis using both RNA-seq data and quantitative real-time RT-PCR (qPCR) revealed that the CsLEA genes are widely expressed in various tissues, and that many genes containing the ABRE promoter sequence are induced by drought, salt and PEG. These results provide a useful reference for further exploration of

  18. THE LOCAL EXPRESSION AND ABUNDANCE OF INSULIN-LIKE GROWTH FACTOR (IGF) BINDING PROTEINS IN SKELETAL MUSCLE ARE REGULATED BY AGE AND GENDER BUT NOT LOCAL IGF-I "IN VIVO"

    Science.gov (United States)

    We wished to determine whether sustained IGF-I production in skeletal muscle increases local IGF binding protein (IGFBP) abundance, thereby mitigating the long-term stimulation of muscle growth by IGF-I. Muscle growth of transgenic mice that overexpress IGF-I in muscle (SIS2) and of wild-type (Wt) m...

  19. 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

    Science.gov (United States)

    Lefort, Natalie; Glancy, Brian; Bowen, Benjamin; Willis, Wayne T.; Bailowitz, Zachary; De Filippis, Elena A.; Brophy, Colleen; Meyer, Christian; Højlund, Kurt; Yi, Zhengping; Mandarino, Lawrence J.

    2010-01-01

    OBJECTIVE The contribution of mitochondrial dysfunction to skeletal muscle insulin resistance remains elusive. Comparative proteomics are being applied to generate new hypotheses in human biology and were applied here to isolated mitochondria to identify novel changes in mitochondrial protein abundance present in insulin-resistant muscle. RESEARCH DESIGN AND METHODS Mitochondria were isolated from vastus lateralis muscle from lean and insulin-sensitive individuals and from obese and insulin-resistant individuals who were otherwise healthy. Respiration and reactive oxygen species (ROS) production rates were measured in vitro. Relative abundances of proteins detected by mass spectrometry were determined using a normalized spectral abundance factor method. RESULTS NADH- and FADH2-linked maximal respiration rates were similar between lean and obese individuals. Rates of pyruvate and palmitoyl-dl-carnitine (both including malate) ROS production were significantly higher in obesity. Mitochondria from obese individuals maintained higher (more negative) extramitochondrial ATP free energy at low metabolic flux, suggesting that stronger mitochondrial thermodynamic driving forces may underlie 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. PMID:20682693

  20. 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

    OpenAIRE

    Lefort, Natalie; Glancy, Brian; Bowen, Benjamin; Willis, Wayne T.; Bailowitz, Zachary; De Filippis, Elena A.; Brophy, Colleen; Meyer, Christian; Højlund, Kurt; Yi, Zhengping; Mandarino, Lawrence J.

    2010-01-01

    OBJECTIVE The contribution of mitochondrial dysfunction to skeletal muscle insulin resistance remains elusive. Comparative proteomics are being applied to generate new hypotheses in human biology and were applied here to isolated mitochondria to identify novel changes in mitochondrial protein abundance present in insulin-resistant muscle. RESEARCH DESIGN AND METHODS Mitochondria were isolated from vastus lateralis muscle from lean and insulin-sensitive individuals and from obese and insulin-r...

  1. Cloning and characterization of a potentially protective chitinase-like recombinant antigen from Wuchereria bancrofti.

    OpenAIRE

    N. Raghavan; Freedman, D O; Fitzgerald, P C; Unnasch, T R; Ottesen, E A; Nutman, T B

    1994-01-01

    While there is no direct evidence demonstrating the existence of protective immunity to Wuchereria bancrofti infection in humans, the presence of individuals, in populations in areas where infection is endemic, with no clinical evidence of past or current infection despite appreciable exposure to the infective larvae, suggests that protective immunity to filarial parasites may occur naturally. Earlier work indicated that such putatively immune individuals generated antibodies to a 43-kDa anti...

  2. 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.

  3. Comparative analysis of the heat stable proteome of radicles of Medicago truncatula seeds during germination identifies late embryogenesis abundant proteins associated with desiccation tolerance

    NARCIS (Netherlands)

    Boudet, J.; Buitink, J.; Hoekstra, F.A.; Rogniaux, H.; Larré, C.; Satour, P.; Leprince, O.

    2006-01-01

    A proteomic analysis was performed on the heat stable protein fraction of imbibed radicles of Medicago truncatula seeds to investigate whether proteins can be identified that are specifically linked to desiccation tolerance (DT). Radicles were compared before and after emergence (2.8 mm long) in ass

  4. 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.

  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

    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.

  7. 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

    and palmitoyl-DL-carnitine (both including malate) ROS production were significantly higher in obesity. Mitochondria from obese individuals maintained higher (more negative) extramitochondrial ATP free energy at low metabolic flux, suggesting that stronger mitochondrial thermodynamic driving forces may underlie...... 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......OBJECTIVE: The contribution of mitochondrial dysfunction to skeletal muscle insulin resistance remains elusive. Comparative proteomics are being applied to generate new hypotheses in human biology and were applied here to isolated mitochondria to identify novel changes in mitochondrial protein...

  8. Abundant immunohistochemical expression of dopamine D2 receptor and p53 protein in meningiomas: follow-up, relation to gender, age, tumor grade, and recurrence

    International Nuclear Information System (INIS)

    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 D2 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 D2 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 D2 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 D2 receptor observed in this study warrants further investigation of the therapeutic potential of dopamine agonists in the evolution of meningiomas

  9. Abundant immunohistochemical expression of dopamine D2 receptor and p53 protein in meningiomas: follow-up, relation to gender, age, tumor grade, and recurrence

    Directory of Open Access Journals (Sweden)

    G. Trott

    2015-05-01

    Full Text Available 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 D2 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 D2 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 D2 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 D2 receptor observed in this study warrants further investigation of the therapeutic potential of dopamine agonists in the evolution of meningiomas.

  10. 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.

  11. The local expression and abundance of insulin-like growth factor (IGF) binding proteins in skeletal muscle are regulated by age and gender but not local IGF-I in vivo.

    Science.gov (United States)

    Oliver, William T; Rosenberger, Judy; Lopez, Rusmely; Gomez, Adam; Cummings, Kathleen K; Fiorotto, Marta L

    2005-12-01

    We wished to determine whether sustained IGF-I production in skeletal muscle increases local IGF binding protein (IGFBP) abundance, thereby mitigating the long-term stimulation of muscle growth by IGF-I. Muscle growth of transgenic mice that overexpress IGF-I in muscle (SIS2) and of wild-type (Wt) mice was compared. At 3, 5, 10, and 20 wk of age, hind-limb muscle weights and IGFBP-3, -4, -5, and -6 mRNA and protein abundances were quantified. Additional mice were injected with IGF-I or LR3-IGF-I, and phosphorylation of the type 1 IGF receptor (IGF-1R) was compared. Muscle mass was 20% greater in SIS2 compared with Wt mice by 10 wk of age (P LR3-IGF-I stimulated IGF-1R phosphorylation to a greater extent than IGF-I at both 5 and 10 wk of age (P 0.21). Thus, variations in local IGF-I levels do not appear to regulate muscle IGFBP expression. The age- and gender-specific differences in muscle IGFBP expression are not sufficient to alter the response of the muscle to the IGFs but may impact the IGF-independent effects of these IGFBPs. PMID:16166219

  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. 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...

  14. Application of Natural Isotopic Abundance ¹H-¹³C- and ¹H-¹⁵N-Correlated Two-Dimensional NMR for Evaluation of the Structure of Protein Therapeutics.

    Science.gov (United States)

    Arbogast, Luke W; Brinson, Robert G; Marino, John P

    2016-01-01

    Methods for characterizing the higher-order structure of protein therapeutics are in great demand for establishing consistency in drug manufacturing, for detecting drug product variations resulting from modifications in the manufacturing process, and for comparing a biosimilar to an innovator reference product. In principle, solution NMR can provide a robust approach for characterization of the conformation(s) of protein therapeutics in formulation at atomic resolution. However, molecular weight limitations and the perceived need for stable isotope labeling have to date limited its practical applications in the biopharmaceutical industry. Advances in NMR magnet and console technologies, cryogenically cooled probes, and new rapid acquisition methodologies, particularly selective optimized flip-angle short transient pulse schemes and nonuniform sampling, have greatly ameliorated these limitations. Here, we describe experimental methods for the collection and analysis of 2D (1)H(N)-(15)N-amide- and (1)H-(13)C-methyl-correlated spectra applied to protein drug products at natural isotopic abundance, including representatives from the rapidly growing class of monoclonal antibody (mAb) therapeutics. Practical aspects of experimental setup and data acquisition for both standard and rapid acquisition NMR techniques are described. Furthermore, strategies for the statistical comparison of 2D (1)H(N)-(15)N-amide- and (1)H-(13)C-methyl-correlated spectra are detailed. PMID:26791974

  15. 植物胚胎发育晚期丰富蛋白1组的结构与功能%Structure and function of group 1 late embryogenesis abundant proteins

    Institute of Scientific and Technical Information of China (English)

    邹永东; 施丽沙; 刘国宝; 洪锐沙; 郑易之

    2008-01-01

    植物胚胎发育晚期丰富蛋白(late embryogenesis abundant proteins,LEA)是植物胚胎发生后期种子中大量积累的一类蛋白质.根据蛋白质的氨基酸基序和保守结构特点,LEA蛋白一般分为6组,其中第1组LEA蛋白(LEA1)含有高度保守的20氨基酸基序.LEA1蛋白在水溶液中主要呈无规则结构,具高亲水性和热稳定性,与植物抗逆功能密切相关.本文就LEA1蛋白的功能和结构等方面的研究做一综述.

  16. Enhanced Detection of Low-Abundance Host Cell Protein Impurities in High-Purity Monoclonal Antibodies Down to 1 ppm Using Ion Mobility Mass Spectrometry Coupled with Multidimensional Liquid Chromatography.

    Science.gov (United States)

    Doneanu, Catalin E; Anderson, Malcolm; Williams, Brad J; Lauber, Matthew A; Chakraborty, Asish; Chen, Weibin

    2015-10-20

    The enormous dynamic range of proteinaceous species present in protein biotherapeutics poses a significant challenge for current mass spectrometry (MS)-based methods to detect low-abundance HCP impurities. Previously, an HCP assay based on two-dimensional chromatographic separation (high pH/low pH) coupled to high-resolution quadrupole time-of-flight (QTOF) mass spectrometry and developed in the author's laboratory has been shown to achieve a detection limit of about 50 ppm (parts per milion) for the identification and quantification of HCPs present in monoclonal antibodies following Protein A purification.1 To improve the HCP detection limit we have explored the utility of several new analytical techniques for HCP analysis and thereby developed an improved liquid chromatography-mass spectrometry (LC-MS) methodology for enhanced detection of HCPs. The new method includes (1) the use of a new charge-surface-modified (CSH) C18 stationary phase to mitigate the challenges of column saturation, peak tailing, and distortion that are commonly observed in the HCP analysis; (2) the incorporation of traveling-wave ion mobility (TWIM) separation of coeluting peptide precursors, and (3) the improvement of fragmentation efficiency of low-abundance HCP peptides by correlating the collision energy used for precursor fragmentation with their mobility drift time. As a result of these improvements, the detection limit of the new methodology was greatly improved, and HCPs present at a concentration as low as 1 ppm (1 ng HCP/mg mAb) were successfully identified and quantified. The newly developed method was applied to analyze two high-purity mAbs (NIST mAb and Infliximab) expressed in a murine cell line. For both samples, low-abundance HCPs (down to 1 ppm) were confidently identified, and the identities of the HCPs were further confirmed by targeted MS/MS experiments. In addition, the performance of the assay was evaluated by an interlaboratory study in which three independent

  17. 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.

  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. 大豆Em(LEA1)蛋白保守结构域的结构和聚集特性%Structures and Assembly of Conserved Domains from Soybean Late Embryogenesis Abundant Protein Em

    Institute of Scientific and Technical Information of China (English)

    薛蓉; 邹永东; 郑易之; 吴亦洁; 李晓晶; 裴奉奎

    2012-01-01

    In this study, we investigated the structures and assembly of C domain of soybean late embryogenesis abundant (LEAI) protein EM(Em-C) and M domain of soybean LEAI protein EM (Em-2M) from the soybean LEAI protein Em in different environments using CD and NMR spectros-copy. In water and dimyristoylphosphatidyglycerol(DMPG) solution, both peptides were predominantly disordered. In 50% 2,2,2-trifluoroethanol(TFE) aqueous solution, Em-C had increasing folding and self-assembled as dimer, and the region including hydrophobic residues might form helical structure. Em-2M formed less ordered structure than Em-C and existed as monomer in 50% TFE aqueous solution. These results suggested that the change of environment might lead to variation of spatial structure and assembly behavior for the two peptides Em-C and Em-2M. The present study may provide an insight into the structural properties of Em protein in different environments and the roles of some important segments in Em protein.%采用圆二色谱(CD)和核磁共振波谱(NMR)方法研究了大豆Em(LEA1)蛋白保守基序Em-C和Em-2M多肽在不同环境中的结构及聚集行为.研究表明,在水和DMPG溶液中,两种多肽主要以无规结构形式存在.在50% TFE溶液中,Em-C多肽折叠结构增加,含疏水残基的部分区域可能形成α-螺旋结构,且分子以二聚体形式存在;而Em-2M则以单体形式存在,且有序结构较少.以上结果表明,环境变化可能导致两种多肽的空间结构和聚集行为改变,这有助于理解Em蛋白在不同环境中的结构特点,及其重要区域在全长蛋白中所起的作用.

  20. 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

    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...

  1. Cloning and Sequence Analysis of a Late Embryogenesis Abundant Protein Gene in Solanum torvum%野生茄托鲁巴姆 LEA 蛋白基因的克隆与序列分析

    Institute of Scientific and Technical Information of China (English)

    叶雪凌; 周宝利

    2013-01-01

      Solanum torvum,a wild species of eggplant,is highly resistant to Verticillium wilt.Therefore,it is the ideal material for studying the mechanism of resistance to Verticillium wilt in eggplant.Late embryogenesis abundant proteins (LEA proteins) are a group of stress-responsive proteins in higher plants that are induced by environmental stress.In this study,a up-regulated EST while infected by Verticillium wilt was used as a querying probe to blast the GenBank database.Based on the assembled homologous cDNA sequences ,a 490 bp cDNA was amplified and cloned by RT-PCR,designated StLEA1.The ORF of StLEA1 is 291 bp,coding a protein with 96 animo acids.The molecular weight of coding protein is 10.748 kDa and isoelectric point is 9.913.StLEA1 protein is a soluble protein with mul-tiple phosphorylation sites,conserve domain in Lea5,but without signal peptides .Quantitative RT-PCR analysis re-vealed that StLEA1 was up-regulated in roots while Solanum torvum was infected by Verticillium wilt.The result pro-vides the material for studying the resistance mechanism of wild eggplant to Verticillium wilt.%  野生茄托鲁巴姆高抗黄萎病,是研究茄子黄萎病抗性的理想试材。胚胎发育晚期丰富蛋白(LEA 蛋白)是植物在逆境条件下生成的一类应激蛋白。研究以1个受黄萎病菌诱导的托鲁巴姆 EST 为种子序列,结合电子克隆及RT-PCR 验证的策略,获得了 LEA 蛋白基因的全长 cDNA 序列,命名为 StLEA1。该基因的完整开放阅读框为291 bp,编码96个氨基酸,编码蛋白的分子量为10.748 kDa,等电点为9.913。经序列分析,StLEA1为水溶性蛋白,不存在信号肽,具有 LEA5家族的典型结构域和保守序列,预测含有多个磷酸化位点。表达分析表明,托鲁巴姆受黄萎病菌侵染后,StLEA1在根系中上调表达。为探讨野生茄托鲁巴姆抗黄萎病分子机制提供了素材。

  2. A stress-responsive late embryogenesis abundant protein 7 (CsLEA7) of tea [Camellia sinensis (L.) O. Kuntze] encodes for a chaperone that imparts tolerance to Escherichia coli against stresses.

    Science.gov (United States)

    Paul, Asosii; Singh, Sewa; Sharma, Shweta; Kumar, Sanjay

    2014-11-01

    The present study characterized CsLEA7, a group 7 late embryogenesis abundant (LEA) gene, from tea [Camellia sinensis (L.) O. Kuntze]. The gene had an open reading frame of 462 base pairs encoding 153 amino acids with calculated molecular weight of 16.63 kDa and an isoelectric point (pI) of 4.93. Analysis revealed CsLEA7 to be an intrinsically ordered protein consisting of nine β-strands and two α-helices. CsLEA7 expressed ubiquitously in all the tissues analyzed with highest level of transcripts in mature leaf as compared to in flower bud, younger leaves, stem and fruit. Expression was the least in root tissue. CsLEA7 exhibited up-regulation in response to low temperature, polyethylene glycol-8000, sodium chloride and hydrogen peroxide in tea. Analysis of the promoter of CsLEA7 revealed a core promoter element and distinct cis-acting regulatory elements regulating gene expression under abiotic stresses. CsLEA7 exhibited chaperonic activity as evinced by protection to malate dehydrogenase against heat denaturation assay. Recombinant Escherichia coli cells producing CsLEA7 exhibited improved tolerance against diverse cues: polyethylene glycol-8000, sodium chloride, hydrogen peroxide and low temperature signifying its role in imparting stress tolerance. PMID:25052187

  3. 第三组胚胎晚期丰富蛋白lea3基因研究概述%Research advance in the group three of late-embryogenesis-abundant proteins and genes

    Institute of Scientific and Technical Information of China (English)

    汤晓倩; 于丽霞; 武晓璐; 鄢波

    2010-01-01

    晚期胚胎富集蛋白(late embryogenesis abundant protein,LEA蛋白)是在高等植物胚胎发育晚期大量积累的一类蛋白,根据其结构特点LEA蛋白一般分为6组,其中第3组LEA蛋白(LEA3)含有11个氨基酸串联重复的基元序列,可以形成α-螺旋结构,能在干旱胁迫的环境中保护生物大分子,减轻水份胁迫对植物造成的伤害,与植物抗逆性密切相关.该文就lea3基因及其蛋白的结构、功能、基因表达和应用等进行简要的综述,并对lea3基因及其蛋白今后的研究方向和应用前景进行了展望.

  4. Abundances in galaxies

    International Nuclear Information System (INIS)

    Standard (or mildly inhomogeneous) Big Bang nucleosynthesis theory is well confirmed by abundance measurements of light elements up to 7Li and the resulting upper limit to the number of neutrino families confirmed in accelerator experiments. Extreme inhomogeneous models with a closure density in form of baryons seem to be ruled out and there is no evidence for a cosmic 'floor' to 9Be or heavier elements predicted in some versions of those models. Galaxies show a correlation between luminous mass and abundance of carbon and heavier elements, usually attributed to escape of hot gas from shallow potential wells. Uncertainties include the role of dark matter and biparametric behaviour of ellipticals. Spirals have radial gradients which may arise from a variety of causes. In our own Galaxy one can distinguish three stellar populations - disk, halo and bulge - characterised by differing metallicity distribution functions. Differential abundance effects are found among different elements in stars as a function of metallicity and presumably age, notably in the ratio of oxygen and α-particle elements to iron. These may eventually be exploitable to set a time scale for the formation of the halo, bulge and disk. (orig.)

  5. Interstellar Atomic Abundances

    CERN Document Server

    Jenkins, E B

    2003-01-01

    A broad array of interstellar absorption features that appear in the ultraviolet spectra of bright sources allows us to measure the abundances and ionization states of many important heavy elements that exist as free atoms in the interstellar medium. By comparing these abundances with reference values in the Sun, we find that some elements have abundances relative to hydrogen that are approximately consistent with their respective solar values, while others are depleted by factors that range from a few up to around 1000. These depletions are caused by the atoms condensing into solid form onto dust grains. Their strengths are governed by the volatility of compounds that are produced, together with the densities and velocities of the gas clouds. We may characterize the depletion trends in terms of a limited set of parameters; ones derived here are based on measurements of 15 elements toward 144 stars with known values of N(H I) and N(H2). In turn, these parameters may be applied to studies of the production, de...

  6. Abundance, Excess, Waste

    Directory of Open Access Journals (Sweden)

    Rox De Luca

    2016-02-01

    Her recent work focuses on the concepts of abundance, excess and waste. These concerns translate directly into vibrant and colourful garlands that she constructs from discarded plastics collected on Bondi Beach where she lives. The process of collecting is fastidious, as is the process of sorting and grading the plastics by colour and size. This initial gathering and sorting process is followed by threading the components onto strings of wire. When completed, these assemblages stand in stark contrast to the ease of disposability associated with the materials that arrive on the shoreline as evidence of our collective human neglect and destruction of the environment around us. The contrast is heightened by the fact that the constructed garlands embody the paradoxical beauty of our plastic waste byproducts, while also evoking the ways by which those byproducts similarly accumulate in randomly assorted patterns across the oceans and beaches of the planet.

  7. Transgenic Cotton with Late Embryogenesis Abundant Protein (LEA) Gene and its Drought Tolerance%转晚期胚胎发生丰富蛋白(LEA)基因棉花及抗旱性分析

    Institute of Scientific and Technical Information of China (English)

    裴金玲; 杨红兰; 李春平; 张大伟; 李小双; 蔡明; 张道远

    2012-01-01

    本研究将紫杆柽柳(Tamarix and rossowii Litv)晚期胚胎发生丰富蛋白(LEA DQ663481)基因导入新疆早熟棉新陆早18号,通过冬季海南加代、夏季新疆继代的方法获得T3代转基因棉花株系.从40株大田卡那霉素检测阳性植株中,经过PCR筛选证明3株为阳性的转化株.在室内条件下,对转化株幼苗进行水培实验,并用12% (w/v) PEG-6000处理12h模拟干旱胁迫.结果显示,干旱胁迫之后,转LEA基因棉花基因表达量显著增加;丙二醛生成量显著降低;游离脯氨酸、可溶性糖、可溶性蛋白的生成量显著增加;棉花表型分析也证明了转LEA基因棉花抗旱性有提高.培养45d后,转LEA基因棉花的生物量高于非转基因棉花.本研究结果表明,在干旱胁迫条件下,转LEA基因棉花表现出了优良的生长和生理优势,显示出转LEA基因棉花能提高棉花的抗旱能力.%The open reading frames of Late Embryogenesis Abundant Protein (LEA DQ663481) Gene, from Tamarix and rossowii Litv, were introduced into the Xinjiang early-maturing cotton, Xinluzaol8. T3 transgenic cotton plants were obtained through generation-adding in Hainan during winter and subculture in Xinjiang during summer from 40 plants with kanamycin positive resistance in the field, three individual positive transgenic cotton plants were obtained through PCR identification. These growing cotton shoots were cultured in room by hydroponic system and had been treated by 12% (w/v) PEG-6000 for 12 hours to simulate drought stress. Real-time quantitative RT-PCR analysis indicates the expression of LEA gene is higher in transgenic plants than in non-transgenic ones after that treatment. The contents of proline, soluble proteins and soluble sugar are also significantly higher in transgenic plants under drought stress. On the contrary, the malonyldiadehyde (MDA) content is significantly lower. The phenotypes of transgenic plants also indicate that LEA gene enhance their drought

  8. 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.

  9. 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.

  10. Solar System Abundances of the Elements

    CERN Document Server

    Lodders, Katharina

    2010-01-01

    Representative abundances of the chemical elements for use as a solar abundance standard in astronomical and planetary studies are summarized. Updated abundance tables for solar system abundances based on meteorites and photospheric measurements are presented.

  11. 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.

  12. 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

    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......, this comprehensive database will outline an integrated picture of the expression levels and properties of the thousands of protein components of organelles, pathways and cytoskeletal systems that may be directly or indirectly involved in properties associated with the transformed state. Udgivelsesdato: 1990-Dec...

  13. 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...

  14. Solar and stellar photospheric abundances

    Science.gov (United States)

    Allende Prieto, Carlos

    2016-07-01

    The determination of photospheric abundances in late-type stars from spectroscopic observations is a well-established field, built on solid theoretical foundations. Improving those foundations to refine the accuracy of the inferred abundances has proven challenging, but progress has been made. In parallel, developments on instrumentation, chiefly regarding multi-object spectroscopy, have been spectacular, and a number of projects are collecting large numbers of observations for stars across the Milky Way and nearby galaxies, promising important advances in our understanding of galaxy formation and evolution. After providing a brief description of the basic physics and input data involved in the analysis of stellar spectra, a review is made of the analysis steps, and the available tools to cope with large observational efforts. The paper closes with a quick overview of relevant ongoing and planned spectroscopic surveys, and highlights of recent research on photospheric abundances.

  15. Surface abundances of OC supergiants

    CERN Document Server

    Martins, F; Bouret, J -C; Barba, R; Howarth, I

    2016-01-01

    Some O and B stars show unusually strong or weak lines of carbon and/or nitrogen. These objects are classified as OBN or OBC stars. It has recently been shown that nitrogen enrichment and carbon depletion are the most likely explanations for the existence of the ON class. We investigate OC stars (all being supergiants) to check that surface abundances are responsible for the observed anomalous line strengths. We perform a spectroscopic analysis of three OC supergiants using atmosphere models. A fourth star was previously studied by us. Our sample thus comprises all OC stars known to date in the Galaxy. We determine the stellar parameters and He, C, N, and O surface abundances. We show that all stars have effective temperatures and surface gravities fully consistent with morphologically normal O supergiants. However, OC stars show little, if any, nitrogen enrichment and carbon surface abundances consistent with the initial composition. OC supergiants are thus barely chemically evolved, unlike morphologically n...

  16. Solar and Stellar Photospheric Abundances

    CERN Document Server

    Prieto, Carlos Allende

    2016-01-01

    The determination of photospheric abundances in late-type stars from spectroscopic observations is a well-established field, built on solid theoretical foundations. Improving those foundations to refine the accuracy of the inferred abundances has proven challenging, but progress has been made. In parallel, developments on instrumentation, chiefly regarding multi-object spectroscopy, have been spectacular, and a number of projects are collecting large numbers of observations for stars across the Milky Way and nearby galaxies, promising important advances in our understanding of galaxy formation and evolution. After providing a brief description of the basic physics and input data involved in the analysis of stellar spectra, a review is made of the analysis steps, and the available tools to cope with large observational efforts. The paper closes with a quick overview of relevant ongoing and planned spectroscopic surveys, and highlights of recent research on photospheric abundances.

  17. 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.

  18. Increased abundance of the adaptor protein containing pleckstrin homology domain, phosphotyrosine binding domain and leucine zipper motif (APPL1) in patients with obesity and type 2 diabetes: evidence for altered adiponectin signalling

    OpenAIRE

    Holmes, R.M.; Yi, Z; De Filippis, E.; Berria, R.; S. Shahani; P. Sathyanarayana; Sherman, V.; K. Fujiwara; Meyer, C.; Christ-Roberts, C.; Hwang, H; Finlayson, J.; Dong, L. Q.; Mandarino, L. J.; Bajaj, M.

    2011-01-01

    Aims/hypothesis The adiponectin signalling pathway is largely unknown, but recently the adaptor protein containing pleckstrin homology domain, phosphotyrosine binding domain and leucine zipper motif (APPL1), has been shown to interact directly with adiponectin receptor (ADIPOR)1. APPL1 is present in C2C12 myoblasts and mouse skeletal muscle, but its presence in human skeletal muscle has not been investigated. Methods Samples from type 2 diabetic, and lean and non-diabetic obese participants w...

  19. 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

    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......-DE analysis (P meat samples in the present study. These include proteins related to control of flux through the tricarboxylate cycle [2...

  20. Functions of late embryogenesis abundant proteins in desiccation-tolerance of organisms: a review%胚胎晚期富集蛋白与生物的干旱胁迫耐受性

    Institute of Scientific and Technical Information of China (English)

    刘昀; 刘国宝; 李冉辉; 邹永东; 郑易之

    2010-01-01

    胚胎晚期富集蛋白(Late embryogenesis abundant,LEA)是参与生物体抵抗干旱胁迫的一类重要蛋白.LEA蛋白可分为7组.大多数LEA蛋白具有亲水性及热稳定性.LEA蛋白在水溶液中通常为无折叠状态,但脱水胁迫可诱导其转变为α-螺旋.近年来关于LEA蛋白的研究取得了较多进展.研究结果表明LEA蛋白可定位于细胞内的多种细胞器中,且LEA蛋白可能具有多重保护作用,如保护蛋白质及酶活性、或保护细胞的膜结构、或具有抗氧化作用、结合离子或保护DNA等.以下主要介绍了LEA蛋白的功能、二级结构及保护作用机制.

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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

  7. Abundances in stars with exoplanets

    OpenAIRE

    Israelian, Garik

    2003-01-01

    Extensive spectroscopic studies of stars with and without planets have concluded that stars hosting planets are significantly more metal-rich than those without planets. More subtle trends of different chemical elements begin to appear as the number of detected extrasolar planetary systems continues to grow. I review our current knowledge concerning the observed abundance trends of various chemical elements in stars with exoplanets and their possible implications.

  8. Oxygen Gas Phase Abundance Revisited

    CERN Document Server

    André, M K; Howk, J C; Ferlet, R; Désert, J M; Hébrard, G; Lacour, S; Lecavelier-des-Etangs, A; Vidal-Madjar, A; Moos, H W

    2003-01-01

    We present new measurements of the interstellar gas-phase oxygen abundance along the sight lines towards 19 early-type galactic stars at an average distance of 2.6 kpc. We derive O {\\small I} column densities from {\\it HST}/STIS observations of the weak 1355 \\AA intersystem transition. We derive total hydrogen column densities [N(H {\\small I})+2N(H$_2$)] using {\\it HST}/STIS observations of \\lya and {\\it FUSE} observations of molecular hydrogen. The molecular hydrogen content of these sight lines ranges from f(H$_2$) = 2N(H$_2$)/[N(H {\\small I})+2N(H$_2$)] = 0.03 to 0.47. The average $$ of 6.3$\\times10^{21}$ cm$^{-2}$ mag$^{-1}$ with a standard deviation of 15% is consistent with previous surveys. The mean oxygen abundance along these sight lines, which probe a wide range of galactic environments in the distant ISM, is 10$^6$ \\oh = $408 \\pm 13$ (1 $\\sigma$ in the mean). %$({\\rm O/H})_{gas} = 408 \\pm 14$(1 $\\sigma$). We see no evidence for decreasing gas-phase oxygen abundance with increasing molecular hydroge...

  9. Planetary nebulae abundances and stellar evolution

    OpenAIRE

    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 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...

  10. 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...

  11. 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...

  12. Solar System chemical abundances corrected for systematics

    OpenAIRE

    Gonzalez, Guillermo

    2014-01-01

    The relative chemical abundances between CI meteorites and the solar photosphere exhibit a significant trend with condensation temperature. A trend with condensation temperature is also seen when the solar photospheric abundances are compared to those of nearby solar twins. We use both these trends to determine the alteration of the elemental abundances of the meteorties and the photosphere by fractionation and calculate a new set of primordial Solar System abundances.

  13. 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 ...

  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. Abundance of Hepatic Transporters in Caucasians: A Meta-Analysis.

    Science.gov (United States)

    Burt, Howard J; Riedmaier, Arian Emami; Harwood, Matthew D; Crewe, H Kim; Gill, Katherine L; Neuhoff, Sibylle

    2016-10-01

    This study aimed to derive quantitative abundance values for key hepatic transporters suitable for in vitro-in vivo extrapolation within a physiologically based pharmacokinetic modeling framework. A meta-analysis was performed whereby data on abundance measurements, sample preparation methods, and donor demography were collated from the literature. To define values for a healthy Caucasian population, a subdatabase was created whereby exclusion criteria were applied to remove samples from non-Caucasian individuals, those with underlying disease, or those with subcellular fractions other than crude membrane. Where a clinically relevant active genotype was known, only samples from individuals with an extensive transporter phenotype were included. Authors were contacted directly when additional information was required. After removing duplicated samples, the weighted mean, geometric mean, standard deviation, coefficient of variation, and between-study homogeneity of transporter abundances were determined. From the complete database containing 24 transporters, suitable abundance data were available for 11 hepatic transporters from nine studies after exclusion criteria were applied. Organic anion transporting polypeptides OATP1B1 and OATP1B3 showed the highest population abundance in healthy adult Caucasians. For several transporters, the variability in abundance was reduced significantly once the exclusion criteria were applied. The highest variability was observed for OATP1B3 > OATP1B1 > multidrug resistance protein 2 > multidrug resistance gene 1. No relationship was found between transporter expression and donor age. To our knowledge, this study provides the first in-depth analysis of current quantitative abundance data for a wide range of hepatic transporters, with the aim of using these data for in vitro-in vivo extrapolation, and highlights the significance of investigating the background of tissue(s) used in quantitative transporter proteomic studies. Similar

  16. Surface abundances of ON stars

    Science.gov (United States)

    Martins, F.; Simón-Díaz, S.; Palacios, A.; Howarth, I.; Georgy, C.; Walborn, N. R.; Bouret, J.-C.; Barbá, R.

    2015-06-01

    Context. Massive stars burn hydrogen through the CNO cycle during most of their evolution. When mixing is efficient or when mass transfer in binary systems occurs, chemically processed material is observed at the surface of O and B stars. Aims: ON stars show stronger lines of nitrogen than morphologically normal counterparts. Whether this corresponds to the presence of material processed through the CNO cycle is not known. Our goal is to answer this question. Methods: We performed a spectroscopic analysis of a sample of ON stars with atmosphere models. We determined the fundamental parameters as well as the He, C, N, and O surface abundances. We also measured the projected rotational velocities. We compared the properties of the ON stars to those of normal O stars. Results: We show that ON stars are usually rich in helium. 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 cannot account for the extreme enrichment observed among ON main sequence stars. Some ON stars are members of binary systems, but others are single stars as indicated by stable radial velocities. Mass transfer is therefore not a simple explanation for the observed chemical properties. Conclusions: We conclude that ON stars show extreme chemical enrichment at their surface, consistent with nucleosynthesis through the CNO cycle. Its origin is not clear at present. Based on observations obtained 1) at the Anglo-Australian Telescope; 2) at the Canada-France-Hawaii Telescope (CFHT), which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l'Univers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii; 3) at the ESO/La Silla Observatory under programs 081.D-2008, 083.D-0589, 086.D-0997; 4) the Nordic Optical Telescope, operated on the island of La

  17. Significant biases affecting abundance determinations

    Science.gov (United States)

    Wesson, Roger

    2015-08-01

    I have developed two highly efficient codes to automate analyses of emission line nebulae. The tools place particular emphasis on the propagation of uncertainties. The first tool, ALFA, uses a genetic algorithm to rapidly optimise the parameters of gaussian fits to line profiles. It can fit emission line spectra of arbitrary resolution, wavelength range and depth, with no user input at all. It is well suited to highly multiplexed spectroscopy such as that now being carried out with instruments such as MUSE at the VLT. The second tool, NEAT, carries out a full analysis of emission line fluxes, robustly propagating uncertainties using a Monte Carlo technique.Using these tools, I have found that considerable biases can be introduced into abundance determinations if the uncertainty distribution of emission lines is not well characterised. For weak lines, normally distributed uncertainties are generally assumed, though it is incorrect to do so, and significant biases can result. I discuss observational evidence of these biases. The two new codes contain routines to correctly characterise the probability distributions, giving more reliable results in analyses of emission line nebulae.

  18. 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/...

  19. Hydrocarbon Reserves: Abundance or Scarcity

    International Nuclear Information System (INIS)

    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 impact on the growth

  20. 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

  1. Stellar abundances of beryllium and CUBES

    CERN Document Server

    Smiljanic, R

    2014-01-01

    Stellar abundances of beryllium are useful in different areas of astrophysics, including studies of the Galactic chemical evolution, of stellar evolution, and of the formation of globular clusters. Determining Be abundances in stars is, however, a challenging endeavor. The two Be II resonance lines useful for abundance analyses are in the near UV, a region strongly affected by atmospheric extinction. CUBES is a new spectrograph planned for the VLT that will be more sensitive than current instruments in the near UV spectral region. It will allow the observation of fainter stars, expanding the number of targets where Be abundances can be determined. Here, a brief review of stellar abundances of Be is presented together with a discussion of science cases for CUBES. In particular, preliminary simulations of CUBES spectra are presented, highlighting its possible impact in investigations of Be abundances of extremely metal-poor stars and of stars in globular clusters.

  2. 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...

  3. Monitoring Butterfly Abundance: Beyond Pollard Walks

    OpenAIRE

    Pellet, Jérôme; Bried, Jason T.; Parietti, David; Gander, Antoine; Heer, Patrick O.; Cherix, Daniel; Arlettaz, Raphaël

    2012-01-01

    Most butterfly monitoring protocols rely on counts along transects (Pollard walks) to generate species abundance indices and track population trends. It is still too often ignored that a population count results from two processes: the biological process (true abundance) and the statistical process (our ability to properly quantify abundance). Because individual detectability tends to vary in space (e.g., among sites) and time (e.g., among years), it remains unclear whether index counts truly...

  4. 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

  5. Abundance of introduced species at home predicts abundance away in herbaceous communities

    Science.gov (United States)

    Firn, Jennifer; Moore, Joslin L.; MacDougall, Andrew S.; Borer, Elizabeth T.; Seabloom, Eric W.; HilleRisLambers, Janneke; Harpole, W. Stanley; Cleland, Elsa E.; Brown, Cynthia S.; Knops, Johannes M.H.; Prober, Suzanne M.; Pyke, David A.; Farrell, Kelly A.; Bakker, John D.; O'Halloran, Lydia R.; Adler, Peter B.; Collins, Scott L.; D'Antonio, Carla M.; Crawley, Michael J.; Wolkovich, Elizabeth M.; La Pierre, Kimberly J.; Melbourne, Brett A.; Hautier, Yann; Morgan, John W.; Leakey, Andrew D.B.; Kay, Adam; McCulley, Rebecca; Davies, Kendi F.; Stevens, Carly J.; Chu, Cheng-Jin; Holl, Karen D.; Klein, Julia A.; Fay, Phillip A.; Hagenah, Nicole; Kirkman, Kevin P.; Buckley, Yvonne M.

    2011-01-01

    Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced vs. native communities, because ecological or evolutionary-based shifts in populations underlie invasion success. Here, data for 26 herbaceous species at 39 sites, within eight countries, revealed that species abundances were similar at native (home) and introduced (away) sites - grass species were generally abundant home and away, while forbs were low in abundance, but more abundant at home. Sites with six or more of these species had similar community abundance hierarchies, suggesting that suites of introduced species are assembling similarly on different continents. Overall, we found that substantial changes to populations are not necessarily a pre-condition for invasion success and that increases in species abundance are unusual. Instead, abundance at home predicts abundance away, a potentially useful additional criterion for biosecurity programmes.

  6. Application of Fluorescence Spectroscopy in Studying the Protective Function of 11-Amino Acid Motif of Group3 Late Embryogenesis Abundant Protein%应用荧光光谱法研究植物LEA3蛋白11-氨基酸基序的保护功能

    Institute of Scientific and Technical Information of China (English)

    刘昀; 邓银霞; 张玉芹; 徐宏; 郑易之

    2011-01-01

    胚胎晚期富集蛋白(late embryogenesis abundant,LEA)是增强生物抵抗干旱、低温和盐渍等多种胁迫的重要功能蛋白,但其保护机理仍不清楚.本文利用紫外光谱法证实,含多拷贝11-氨基酸基序的多肽(如PM2D和PM2E)可较好的保护经冻融的乳酸脱氢酶(LDH)活性.进一步通过荧光光谱法证实,含多拷贝11-氨基酸基序的多肽可通过多位点协同结合模式,稳定LDH酶的结构.而含低拷贝11-氨基酸基序的多肽(如PM2F和PM2G)与LDH酶只有一种结合位点,二者的结合强度较弱,因而不能表现出对LDH酶活性的保护作用.此外,含多拷贝11-氨基酸的多肽与海藻糖在保护LDH酶活性上存在协同作用,且二者有着不同的保护机理.%Late embryogenesis abundant protein (LEA) can enhance the tolerance of organisms under drought, low-temperature and other stress conditions. However, their protection mechanisms are still unclear. In the present paper, the peptides consisting of multi-copies of 11-amino acid motif, such as PM2D and PM2E are proved to protect the activity of the lactate dehydrogenase (LDH) from freeze-thaw by using ultroviolet spectrometry. Furthermore, the fluorescence spectroscopic results show that the peptide consisting of multi-copies of 11-amino acid can stabilize the structure of LDH through synergy and multi-sites binding. However, the peptides consisting of less copies of 11-amino acid, such as PM2F and PM2G bind to LDH through one site,and the binding is weak. They thus can not protect the activity of LDH. In addition, the peptides consisted of multi-copies of 11-amino acid protect LDH by acting with trehalose synergically, and the protection mechanisms of LEA and trehalose on LDH are different.

  7. 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. PMID:27429769

  8. Taking species abundance distributions beyond individuals

    NARCIS (Netherlands)

    Morlon, Helene; White, Ethan P.; Etienne, Rampal S.; Green, Jessica L.; Ostling, Annette; Alonso, David; Enquist, Brian J.; He, Fangliang; Hurlbert, Allen; Magurran, Anne E.; Maurer, Brian A.; McGill, Brian J.; Olff, Han; Storch, David; Zillio, Tommaso; Chave, Jérôme

    2009-01-01

    The species abundance distribution (SAD) is one of the few universal patterns in ecology. Research on this fundamental distribution has primarily focused on the study of numerical counts, irrespective of the traits of individuals. Here we show that considering a set of Generalized Species Abundance

  9. 沙冬青胚胎晚期发生丰富蛋白基因序列及表达特性分析%Sequence analysis and expression pattern of AmLEA14 encoding a late embryogenesis abundant protein in Ammopiptanthus mongolicus

    Institute of Scientific and Technical Information of China (English)

    师静; 刘美芹; 史军娜; 赵晓鑫; 卢存福; 尹伟伦

    2012-01-01

    For a better understanding of stress responses of desert plant Ammopiptanthus mongolicus,we reported molecular characterization and expression analysis of AmLEA14 gene from the EST data of cold-and drought-stressed A.mongolicus.Sequence analysis showed that the overall length of gene AmLEA14 was 579 bp,and the cDNA of AmLEA14 contained a 459 bp ORF encoding a polypeptide of 152 amio acids with a calculated molecular mass of 16.6 kDa and a theoretical pI of 4.9.Sequence and structural analysis showed that AmLEA14 protein was a member of late embryogenesis abundant protein class 4.Phylogenetic analysis indicated that AmLEA14 protein was most closely related to soybean LEA14 protein (P46519.1).Real-time quantitative PCR analysis showed that AmLEA14 was constitutively expressed,up-regulated by cold,drought stressed,and specifically accumulated at the late stage of cold treatment.Otherwise,AmLEA14 was down-regulated by heat stress.The combined results indicate that AmLEA14 protein plays some role in abiotic stress responses,mainly in cold tolerant mechanism,and is valuable for future abiotic stress researches in A.mongolicus.%从沙冬青叶片EST文库中获得了胚胎晚期发生丰富蛋白(LEA)基因cDNA全长序列,命名为AmLEA14。序列分析表明该基因全长579bp,含有一个459bp编码152个氨基酸的开放阅读框,推测编码的蛋白质分子质量为16.6ku。二级结构预测显示此编码蛋白属于第4类LEA蛋白。系统发生分析表明,此编码蛋白与大豆LEA14蛋白(P46519.1)的亲缘关系最近。荧光定量PCR结果显示,AmLEA14的表达量在低温、干旱、盐胁迫条件下升高,但是主要在低温胁迫后期富集。推测AmLEA14基因可能在沙冬青抵御低温、干旱、盐胁迫中发挥作用,主要是参与沙冬青的低温防御机制。

  10. Solar Energetic Particles: Sampling Coronal Abundances

    Science.gov (United States)

    Reames, Donald V.

    1998-05-01

    In the large solar energetic particle (SEP) events, coronal mass ejections (CMEs) drive shock waves out through the corona that accelerate elements of the ambient material to MeV energies in a fairly democratic, temperature-independent manner. These events provide the most complete source of information on element abundances in the corona. Relative abundances of 22 elements from H through Zn display the well-known dependence on the first ionization potential (FIP) that distinguishes coronal and photospheric material. For most elements, the main abundance variations depend upon the gyrofrequency, and hence on the charge-to-mass ratio, Q/A, of the ion. Abundance variations in the dominant species, H and He, are not Q/A dependent, presumably because of non-linear wave-particle interactions of H and He during acceleration. Impulsive flares provide a different sample of material that confirms the Ne:Mg:Si and He/C abundances in the corona.

  11. Silicon abundances in population I giants

    Science.gov (United States)

    Boehm-Vitense, Erika

    1992-01-01

    Silicon to carbon abundance ratios for population I giants were determined from emission lines originating in the transition layers between stellar chromospheres and coronae. For effective temperatures larger than 6200 K we find a group of stars with increased silicon to carbon but normal nitrogen to carbon abundance ratios. These stars are presumably descendents from Ap stars with increased surface silicon to carbon abundance ratios. For G stars this anomaly disappears as is to be expected due to the increased depth of the convection zone and therefore deeper mixing which dilutes the surface overabundances. The disappearance of the abundance anomalies proves that the anomalous abundances observed for the F giants are indeed only a surface phenomenon. It also proves that the same holds for their progenitors, the Ap and Am stars, as has been generally believed. Unexplained is the increased silicon to carbon abundance ratio observed for several stars cooler than 5100 L. RS CVn and related stars do not show this increased abundance ratio. There are also some giants which appear to be enriched in carbon, perhaps due to a helium flash with some mixing if the star is a clump star.

  12. 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.

  13. 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).

  14. 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] $=-0.48 \\pm 0.02$.

  15. 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...

  16. 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...

  17. 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...

  18. Testing Relationships between Energy and Vertebrate Abundance

    International Nuclear Information System (INIS)

    Understanding what drives variation in the abundance of organisms is fundamental to evolutionary ecology and wildlife management. Yet despite its importance, there is still great uncertainty about the main factors influencing variation in vertebrate abundance across taxa. We believe valuable knowledge and increased predictive power could be gained by taking into account both the intrinsic factors of species and the extrinsic factors related to environmental surroundings in the commonly cited RQ model, which provides a simple conceptual framework valid at both the interspecific and the intraspecific scales. Approaches comparing studies undertaken at different spatial and taxonomic scales could be key to our ability to better predict abundance, and thanks to the increased availability of population size data, global geographic datasets, and improved comparative methods, there might be unprecedented opportunities to (1) gain a greater understanding of vertebrate abundance patterns and (2) test existing theories on free-ranging animals.

  19. Primordial Deuterium Abundance and Cosmic Baryon Density

    OpenAIRE

    Hogan, Craig J.

    1994-01-01

    The comparison of cosmic abundances of the light elements with the density of baryonic stars and gas in the universe today provides a critical test of big bang theory and a powerful probe of the nature of dark matter. A new technique allows determination of cosmic deuterium abundances in quasar absorption clouds at large redshift, allowing a new test of big bang homogeneity in diverse, very distant systems. The first results of these studies are summarized, along with their implications. The ...

  20. Estimating whale abundance using sparse hydrophone arrays

    OpenAIRE

    Harris, Danielle Veronica

    2012-01-01

    Passive acoustic monitoring has been used to investigate many aspects of marine mammal ecology, although methods to estimate absolute abundance and density using acoustic data have only been developed in recent years. The instrument configuration in an acoustic survey determines which abundance estimation methods can be used. Sparsely distributed arrays of instruments are useful because wide geographic areas can be covered. However, instrument spacing in sparse arrays is such that the same...

  1. 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.

  2. Spatial scaling of species abundance distributions

    OpenAIRE

    Borda-de-Água, Luís; Borges, Paulo A. V.; Hubbell, Stephen P.; Pereira, Henrique M

    2012-01-01

    Copyright © 2012 The Authors. Ecography © 2012 Nordic Society Oikos. Species abundance distributions are an essential tool in describing the biodiversity of ecological communities. We now know that their shape changes as a function of the size of area sampled. Here we analyze the scaling properties of species abundance distributions by using the moments of the logarithmically transformed number of individuals. We find that the moments as a function of area size are well fitted by power law...

  3. How selection structures species abundance distributions

    OpenAIRE

    Magurran, A.E; Henderson, P. A.

    2012-01-01

    How do species divide resources to produce the characteristic species abundance distributions seen in nature? One way to resolve this problem is to examine how the biomass (or capacity) of the spatial guilds that combine to produce an abundance distribution is allocated among species. Here we argue that selection on body size varies across guilds occupying spatially distinct habitats. Using an exceptionally well-characterized estuarine fish community, we show that biomass is concentrated in l...

  4. 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...

  5. 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.

  6. 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.

  7. Report on carbon and nitrogen abundance studies

    Science.gov (United States)

    Boehm-Vitense, Erika

    1991-01-01

    The aim of the proposal was to determine the nitrogen to carbon abundance ratios from transition layer lines in stars with different T(sub eff) and luminosities. The equations which give the surface emission line fluxes and the measured ratio of the NV to CIV emission line fluxes are presented and explained. The abundance results are compared with those of photospheric abundance studies for stars in common with the photospheric investigations. The results show that the analyses are at least as accurate as the photospheric determinations. These studies can be extended to F and early G stars for which photospheric abundance determinations for giants are hard to do because molecular bands become too weak. The abundance determination in the context of stellar evolution is addressed. The N/C abundance ratio increases steeply at the point of evolution for which the convection zone reaches deepest. Looking at the evolution of the rotation velocities v sin i, a steep decrease in v sin i is related to the increasing depth of the convection zone. It is concluded that the decrease in v sin i for T(sub eff) less than or approximately = 5800 K is most probably due to the rearrangement of the angular momentum in the stars due to deep convective mixing. It appears that the convection zone is rotating with nearly depth independent angular momentum. Other research results and ongoing projects are discussed.

  8. 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...

  9. Clonal growth and plant species abundance

    Science.gov (United States)

    Herben, Tomáš; Nováková, Zuzana; Klimešová, Jitka

    2014-01-01

    Background and Aims Both regional and local plant abundances are driven by species' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf–height–seed) traits and by actual performance in the botanical garden. Methods Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area – height – seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates. Key Results After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level. Conclusions Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially

  10. Molecular cloning and expression analysis of a late embryogenesis abundant protein gene (SmLEA2) from Salvia miltiorrhiza%丹参晚期胚胎富集蛋白基因的克隆及表达模式分析

    Institute of Scientific and Technical Information of China (English)

    武玉翠; 葛茜; 周宏骏; 晋鑫鑫; 王喆之

    2015-01-01

    目的 克隆丹参晚期胚胎富集蛋白(late embryogenesis abundant protein,LEA)基因,并进行生物信息学和表达模式分析.方法 对丹参转录组数据库进行BLAST同源性比对,发现一条新的与LEA基因家族同源性较高的序列,命名为SmLEA2,GenBank登录号为HQ676610.进一步利用PCR和RT-PCR技术从丹参gDNA以及cDNA水平克隆得到了SmLEA2基因全长.采用软件分析蛋白质结构性质和系统进化关系.利用实时荧光定量PCR的方法对不同部位、不同发育时期以及不同处理丹参的SmLEA2表达量进行检测.结果 获得SmLEA2 gDNA长1 961 bp,由1个外显子和1个内含子组成,并且内含子位于ATG的上游;开放阅读框长为960 bp,共编码319个氨基酸.生物信息学分析显示,SmLEA2是存在于细胞质中的亲水蛋白,无跨膜结构域和信号肽,其相对分子质量为35 340,等电点为4.77.该基因在丹参的根、茎、叶中均有表达,并且在茎中的表达量最高.随着花的成熟和种子的发育,该基因表达量逐渐升高,并且该基因的表达受茉莉酸甲酯(MeJA)以及脱落酸(ABA)的诱导作用影响.结论 克隆得到的丹参SmLEA2可能参与种子发育过程,并在丹参防御反应中发挥作用.

  11. Na+/K+-ATPase α-subunit (nkaα isoforms and their mRNA expression levels, overall Nkaα protein abundance, and kinetic properties of Nka in the skeletal muscle and three electric organs of the electric eel, Electrophorus electricus.

    Directory of Open Access Journals (Sweden)

    Biyun Ching

    Full Text Available This study aimed to obtain the coding cDNA sequences of Na+/K+-ATPase α (nkaα isoforms from, and to quantify their mRNA expression in, the skeletal muscle (SM, the main electric organ (EO, the Hunter's EO and the Sach's EO of the electric eel, Electrophorus electricus. Four nkaα isoforms (nkaα1c1, nkaα1c2, nkaα2 and nkaα3 were obtained from the SM and the EOs of E. electricus. Based on mRNA expression levels, the major nkaα expressed in the SM and the three EOs of juvenile and adult E. electricus were nkaα1c1 and nkaα2, respectively. Molecular characterization of the deduced Nkaα1c1 and Nkaα2 sequences indicates that they probably have different affinities to Na+ and K+. Western blotting demonstrated that the protein abundance of Nkaα was barely detectable in the SM, but strongly detected in the main and Hunter's EOs and weakly in the Sach's EO of juvenile and adult E. electricus. These results corroborate the fact that the main EO and Hunter's EO have high densities of Na+ channels and produce high voltage discharges while the Sach's EO produces low voltage discharges. More importantly, there were significant differences in kinetic properties of Nka among the three EOs of juvenile E. electricus. The highest and lowest Vmax of Nka were detected in the main EO and the Sach's EO, respectively, with the Hunter's EO having a Vmax value intermediate between the two, indicating that the metabolic costs of EO discharge could be the highest in the main EO. Furthermore, the Nka from the main EO had the lowest Km (or highest affinity for Na+ and K+ among the three EOs, suggesting that the Nka of the main EO was more effective than those of the other two EOs in maintaining intracellular Na+ and K+ homeostasis and in clearing extracellular K+ after EO discharge.

  12. Linking species abundance distributions in numerical abundance and biomass through simple assumptions about community structure

    OpenAIRE

    Henderson, Peter A.; Magurran, Anne E

    2010-01-01

    Species abundance distributions (SADs) are widely used as a tool for summarizing ecological communities but may have different shapes, depending on the currency used to measure species importance. We develop a simple plotting method that links SADs in the alternative currencies of numerical abundance and biomass and is underpinned by testable predictions about how organisms occupy physical space. When log numerical abundance is plotted against log biomass, the species lie within an approximat...

  13. Potential environmental functions of widespread, abundant, uncultured marine archaea

    Science.gov (United States)

    Lloyd, K. G.; Schreiber, L.; Petersen, D. G.; Schramm, A.; Jorgensen, B.

    2012-12-01

    The vast majority of marine subsurface microorganisms are uncultivated, and therefore have unknown metabolisms. Much of the prokaryotes present in the marine subsurface are archaea, and, in turn, much of the archaea fall into the Miscellaneous Crenarchaeotal Group. These organisms are widely distributed globally and are phylogenetically diverse, comprising 17 distinct subgroups, defined by 16S rRNA genes (Kubo et al. 2012). The subgroups do not seem to have any well-defined environmental distribution (i.e., they are all present in different types of marine and terrestrial environments). However, the abundance of sequences from a certain environment type differs among subgroups, and may provide clues to their role in these environments. We sequenced the genome of a single cell of MCG extracted directly from marine sediments. Although coverage was low (~30%), the data quality was high. Conserved genes show that MCG is deeply branching within the newly named "Thaumarchaeota", and contains a complete pathway for the degradation or extracellular proteins. A further search through metagenomic data shows that this process may be widespread in marine sediments. We hypothesize that MCG archaea may be important in anaerobic protein decomposition in marine sediments. Reference Kubo et al., 2012. Archaea of the Miscellaneous Crenarchaeotal Group (MCG) are abundant, diverse, and widespread in marine sediments. ISME Journal, in press, doi:10.1038/ismej.2012.37.

  14. 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...

  15. 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...

  16. Good abundances from bad spectra; 1, techniques

    CERN Document Server

    Bryn, J; Wyse, R F G; Gilmore, Gerard; Wyse, Rosemary F G

    1995-01-01

    We have developed techniques to extract true iron abundances and surface gravities from spectra of the type provided by the multiple-object fibre-fed spectroscopic radial-velocity surveys underway with 2dF, HYDRA, NESSIE, and the forthcoming Sloan survey. Our method is optimised for low S/N, intermediate resolution blue spectra of G stars. Spectroscopic indices sensitive to iron abundance and gravity are defined from a set of narrow (few Angstrom) wavelength intervals, and calibrated using synthetic spectra. We have also defined a single abundance indicator which is able to provide useful iron abundance information from spectra having S/N ratios as low as 10 per Angstrom. The theoretical basis and calibration using synthetic spectra are described in this paper. The empirical calibration of these techniques by application to observational data is described in Jones, Wyse and Gilmore (PASP July 1995). The technique provides precise iron abundances, with zero-point correct to \\sim 0.1 dex, and is reliable, with ...

  17. Why is Trichodesmium abundant in the Kuroshio?

    Science.gov (United States)

    Shiozaki, T.; Takeda, S.; Itoh, S.; Kodama, T.; Liu, X.; Hashihama, F.; Furuya, K.

    2015-12-01

    The genus Trichodesmium is recognized as an abundant and major diazotroph in the Kuroshio, but the reason for this remains unclear. The present study investigated the abundance of Trichodesmium spp. and nitrogen fixation together with concentrations of dissolved iron and phosphate in the Kuroshio and its marginal seas. We performed the observations near the Miyako Islands, which form part of the Ryukyu Islands, situated along the Kuroshio, since our satellite analysis suggested that material transport could occur from the islands to the Kuroshio. Trichodesmium spp. bloomed (> 20 000 filaments L-1) near the Miyako Islands, abundance was high in the Kuroshio and the Kuroshio bifurcation region of the East China Sea, but was low in the Philippine Sea. The abundance of Trichodesmium spp. was significantly correlated with the total nitrogen fixation activity. The surface concentrations of dissolved iron (0.19-0.89 nM) and phosphate (differences in Trichodesmium spp. abundance and nitrogen fixation. Numerical particle-tracking experiments simulated the transportation of water around the Ryukyu Islands to the Kuroshio. Our results indicate that Trichodesmium growing around the Ryukyu Islands could be advected into the Kuroshio.

  18. Abundances of Molecular Species in Barnard 68

    CERN Document Server

    Francesco, J D; Welch, W J; Bergin, E A; Francesco, James Di; Hogerheijde, Michiel R.; Welch, William J.; Bergin, Edwin A.

    2002-01-01

    Abundances for 5 molecules (C18O, CS, NH3, H2CO, and C3H2) and 1 molecular ion (N2H+) and upper limits for the abundances of 1 molecule (13CO) and 1 molecular ion (HCO+) are derived for gas within the Bok globule Barnard 68 (B68). The abundances were determined using our own BIMA millimeter interferometer data and single-dish data gathered from the literature, in conjunction with a Monte Carlo radiative transfer model. Since B68 is the only starless core to have its density structure strongly constrained via extinction mapping, a major uncertainty has been removed from these determinations. All abundances for B68 are lower than those derived for translucent and cold dense clouds, but perhaps only significantly for N2H+, NH3, and C3H2. Depletion of CS toward the extinction peak of B68 is hinted at by the large offset between the extinction peak and the position of maximum CS line brightness. Abundances derived here for C18O and N2H+ are consistent with other, recently determined values at positions observed in...

  19. 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.

  20. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications.

    Science.gov (United States)

    Gu, W; Crawford, E D; O'Donovan, B D; Wilson, M R; Chow, E D; Retallack, H; DeRisi, J L

    2016-01-01

    Next-generation sequencing has generated a need for a broadly applicable method to remove unwanted high-abundance species prior to sequencing. We introduce DASH (Depletion of Abundant Sequences by Hybridization). Sequencing libraries are 'DASHed' with recombinant Cas9 protein complexed with a library of guide RNAs targeting unwanted species for cleavage, thus preventing them from consuming sequencing space. We demonstrate a more than 99 % reduction of mitochondrial rRNA in HeLa cells, and enrichment of pathogen sequences in patient samples. We also demonstrate an application of DASH in cancer. This simple method can be adapted for any sample type and increases sequencing yield without additional cost. PMID:26944702

  1. Simulation of arthropod abundance from plant composition

    Directory of Open Access Journals (Sweden)

    WenJun Zhang

    2011-04-01

    Full Text Available The relationship between arthropod abundance and plant composition is extremely complex. It is very hard to develop a mechanistic model to describe the relationship. This study aimed to simulate arthropod abundance from plant composition on grassland using an artificial neural network developed by the author, and to compare simulation performances between the neural network and conventional models. The results revealed that there were complex interactions between plants and arthropods, and the arthropod abundance on grassland was significantly determined of plant families and their cover-degrees rather than plant species and their cover-degrees. Neural network exhibited a better simulation performance than multivariate regression and response surface model. Cross validation indicated that prediction performance of neural network was also superior to these models. It was concluded that neural network is an effective tool to model arthropod abundance from plant composition on grassland. A moderate dimensionality for input space may be determined to produce a reasonably trained neural network. Such procedures for dimensionality reduction as PCE, etc., were suggested being used in the data treatment in neural network modeling. A high dimensionality for input space and a few samples in the input set would result in the deficient learning of neural network. Randomization procedure for sample submission would help to eliminate the sequence correlation but may result in a worse performance in simulation and prediction. It was suggested that randomization procedure could be used to the sample submission for these situations with a lot of samples and a lower dimensionality.

  2. North Sea Elasmobranchs: distribution, abundance and biodiversity

    NARCIS (Netherlands)

    Daan, N.; Heessen, H.J.L.; Hofstede, ter R.

    2005-01-01

    Based on data from various international and national surveys, an overview is given of the fine-scale distribution (resolution of 20¿longitude * 10¿ latitude; ¿ 10*10 nm) and trends in abundance of elasmobranch species reported from the North Sea. Presence-absence maps are produced based on 4 survey

  3. The Galactic Thick Disk Stellar Abundances

    CERN Document Server

    Prochaska, J X; Carney, B W; McWilliam, A; Wolfe, A M; Prochaska, Jason X.; Naumov, Sergei O.; Carney, Bruce W.; William, Andrew Mc; Wolfe, Arthur M.

    2000-01-01

    We present first results from a program to measure the chemical abundances of a large (N>30) sample of thick disk stars with the principal goal of investigating the formation history of the Galactic thick disk. Our analysis confirms previous studies of O and Mg in the thick disk stars which reported enhancements in excess of the thin disk population. Furthermore, the observations of Si, Ca, Ti, Mn, Co, V, Zn, Al, and Eu all argue that the thick disk population has a distinct chemical history from the thin disk. With the exception of V and Co, the thick disk abundance patterns match or tend towards the values observed for halo stars with [Fe/H]~-1. This suggests that the thick disk stars had a chemical enrichment history similar to the metal-rich halo stars. With the possible exception of Si, the thick disk abundance patterns are in excellent agreement with the chemical abundances observed in the metal-poor bulge stars suggesting the two populations formed from the same gas reservoir at a common epoch. We disc...

  4. Nitrous Oxide Production by Abundant Benthic Macrofauna

    DEFF Research Database (Denmark)

    Stief, Peter; Schramm, Andreas

    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...

  5. The Abundance of Large Arcs From CLASH

    Science.gov (United States)

    Xu, Bingxiao; Postman, Marc; Meneghetti, Massimo; Coe, Dan A.; Clash Team

    2015-01-01

    We have developed an automated arc-finding algorithm to perform a rigorous comparison of the observed and simulated abundance of large lensed background galaxies (a.k.a arcs). We use images from the CLASH program to derive our observed arc abundance. Simulated CLASH images are created by performing ray tracing through mock clusters generated by the N-body simulation calibrated tool -- MOKA, and N-body/hydrodynamic simulations -- MUSIC, over the same mass and redshift range as the CLASH X-ray selected sample. We derive a lensing efficiency of 15 ± 3 arcs per cluster for the X-ray selected CLASH sample and 4 ± 2 arcs per cluster for the simulated sample. The marginally significant difference (3.0 σ) between the results for the observations and the simulations can be explained by the systematically smaller area with magnification larger than 3 (by a factor of ˜4) in both MOKA and MUSIC mass models relative to those derived from the CLASH data. Accounting for this difference brings the observed and simulated arc statistics into full agreement. We find that the source redshift distribution does not have big impact on the arc abundance but the arc abundance is very sensitive to the concentration of the dark matter halos. Our results suggest that the solution to the "arc statistics problem" lies primarily in matching the cluster dark matter distribution.

  6. Will Abundant Natural Gas Solve Climate Change?

    Science.gov (United States)

    McJeon, H. C.; Edmonds, J.; Bauer, N.; Leon, C.; Fisher, B.; Flannery, B.; Hilaire, J.; Krey, V.; Marangoni, G.; Mi, R.; Riahi, K.; Rogner, H.; Tavoni, M.

    2015-12-01

    The rapid deployment of hydraulic fracturing and horizontal drilling technologies enabled the production of previously uneconomic shale gas resources in North America. Global deployment of these advanced gas production technologies could bring large influx of economically competitive unconventional gas resources to the energy system. It has been hoped that abundant natural gas substituting for coal could reduce carbon dioxide (CO2) emissions, which in turn could reduce climate forcing. Other researchers countered that the non-CO2 greenhouse gas (GHG) emissions associated with shale gas production make its lifecycle emissions higher than those of coal. In this study, we employ five state-of-the-art integrated assessment models (IAMs) of energy-economy-climate systems to assess the full impact of abundant gas on climate change. The models show large additional natural gas consumption up to +170% by 2050. The impact on CO2 emissions, however, is found to be much smaller (from -2% to +11%), and a majority of the models reported a small increase in climate forcing (from -0.3% to +7%) associated with the increased use of abundant gas. Our results show that while globally abundant gas may substantially change the future energy market equilibrium, it will not significantly mitigate climate change on its own in the absence of climate policies.

  7. Abundance of Terrestrial Planets by Microlensing

    OpenAIRE

    Yock, Philip

    2000-01-01

    Terrestrial planets may be detected using the gravitational microlensing technique. This was demonstrated in the high magnification event MACHO-98-BLG-35. Observing strategies aimed at measuring the abundance of terrestrial planets are discussed, using both existing telescopes and planned telescopes.

  8. 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...

  9. Chemical abundances and kinematics of barium stars

    Science.gov (United States)

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

    2016-07-01

    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 scaleheight, radial velocities, abundances of the Na, Al, α-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 MOOG. We found that the metallicities, the temperatures and the surface gravities for barium stars cannot be represented by a single Gaussian distribution. The abundances of α-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 heavy-element abundance pattern as given by the ratio [s/Fe], we found that the barium stars present several degrees of enrichment. We also obtained the [hs/ls] ratio by measuring the photospheric abundances of the Ba-peak and the Zr-peak elements. Our results indicated that the [s/Fe] and the [hs/ls] ratios are strongly anticorrelated with the metallicity. Our kinematical analysis showed that 90 per cent of the barium stars belong to the thin disc population. Based on their luminosities, none of the barium stars are luminous enough to be an asymptotic giant branch star, nor to become self-enriched in the s-process elements. Finally, we determined that the barium stars also follow an age-metallicity relation.

  10. 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

  11. Chemical abundance analysis of 19 barium stars

    Science.gov (United States)

    Yang, Guo-Chao; Liang, Yan-Chun; Spite, Monique; Chen, Yu-Qin; Zhao, Gang; Zhang, Bo; Liu, Guo-Qing; Liu, Yu-Juan; Liu, Nian; Deng, Li-Cai; Spite, Francois; Hill, Vanessa; Zhang, Cai-Xia

    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 Teff, surface gravities log g, metallicity [Fe/H] and microturbulence velocity ξt) and equivalent widths of stellar absorption lines. These samples of Ba stars are giants as indicated by atmospheric parameters, metallicities and kinematic analysis about UVW velocity. Chemical abundances of 17 elements were obtained for these Ba stars. Their Na, Al, α- and iron-peak elements (O, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Ni) are similar to the solar abundances. Our samples of Ba stars show obvious overabundances of neutron-capture (n-capture) process elements relative to the Sun. Their median abundances of [Ba/Fe], [La/Fe] and [Eu/Fe] are 0.54, 0.65 and 0.40, respectively. The Y I and Zr I abundances are lower than Ba, La and Eu, but higher than the α- and iron-peak elements for the strong Ba stars and similar to the iron-peak elements for the mild stars. There exists a positive correlation between Ba intensity and [Ba/Fe]. For the n-capture elements (Y, Zr, Ba, La), there is an anti-correlation between their [X/Fe] and [Fe/H]. We identify nine of our sample stars as strong Ba stars with [Ba/Fe] >0.6 where seven of them have Ba intensity Ba=2-5, one has Ba=1.5 and another one has Ba=1.0. The remaining ten stars are classified as mild Ba stars with 0.17<[Ba/Fe] <0.54.

  12. Recent advances of protein microarrays

    OpenAIRE

    Hultschig, Claus; Kreutzberger, Jürgen; Seitz, Harald; Konthur, Zoltán; Büssow, Konrad; Lehrach, Hans

    2006-01-01

    Technological innovations and novel applications have greatly advanced the field of protein microarrays. Over the past two years, different types of protein microarrays have been used for serum profiling, protein abundance determinations, and identification of proteins that bind DNA or small compounds. However, considerable development is still required to ensure common quality standards and to establish large content repertoires. Here, we summarize applications available to date and discuss ...

  13. Relative abundance determinations in extremely metal poor giants. II. Transition probabilities and the abundance determinations

    International Nuclear Information System (INIS)

    The abundances of Fe and other elements are determined for a star of intermediate metallicity and for nine extremely metal poor stars, including two members of the globular cluster M92 and CD -38 deg 245. The accuracy of the transition probabilities for Fe I and other elements is evaluated. The distribution of the abundances of other elements with respect to Fe is the same for most of the cases studied. Manganese is the only element that shows a different relative abundance in an extremely metal poor star. 120 refs

  14. 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.

  15. 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.

  16. Attenuation of species abundance distributions by sampling.

    Science.gov (United States)

    Shimadzu, Hideyasu; Darnell, Ross

    2015-04-01

    Quantifying biodiversity aspects such as species presence/ absence, richness and abundance is an important challenge to answer scientific and resource management questions. In practice, biodiversity can only be assessed from biological material taken by surveys, a difficult task given limited time and resources. A type of random sampling, or often called sub-sampling, is a commonly used technique to reduce the amount of time and effort for investigating large quantities of biological samples. However, it is not immediately clear how (sub-)sampling affects the estimate of biodiversity aspects from a quantitative perspective. This paper specifies the effect of (sub-)sampling as attenuation of the species abundance distribution (SAD), and articulates how the sampling bias is induced to the SAD by random sampling. The framework presented also reveals some confusion in previous theoretical studies. PMID:26064626

  17. 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...

  18. Abundances in the diffuse interstellar medium

    International Nuclear Information System (INIS)

    The wealth of interstellar absorption line data obtained with the Copernicus and IUE satellites has opened up a new era in studies of the interstellar gas. It is now well established that certain elements, generally those with high condensation temperatures, are substantially under-abundant in the gas-phase relative to total solar or cosmic abundances. This depletion of elements is due to the existence of solid material in the form of dust grains in the interstellar medium. Surprisingly, however, recent surveys indicate that even volatile elements such as Zn and S are significantly depleted in many sight lines. Developments in this field which have been made possible by the large base of UV interstellar absorption line data built up over recent years are reviewed and the implications of the results for our understanding of the physical processes governing depletion are discussed. (author)

  19. 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 ...

  20. 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. PMID:26601249

  1. Elemental abundances and classification of CEMP stars

    CERN Document Server

    Allen, Dinah M; Rossi, Silvia; Beers, Tim C; Tsangarides, Stelios A

    2012-01-01

    We present a detailed study of Carbon-Enhanced Metal-Poor (CEMP) stars, based on high-resolution spectroscopic observations of a sample of 18 stars. The stellar spectra for this sample were obtained at the 4.2m William Herschel Telescope (WHT) in 2001 and 2002, using the Utrecht Echelle Spectrograph (UES), at a resolving power R ~52000 and S/N ~ 40, covering the wavelength range lambda-lambda 3700-5700 A. The atmospheric parameters determined for this sample indicate temperatures ranging from 4750 C to 7100 K, log g from 1.5 to 4.3, and metallicities -3.0 <= [Fe/H] <= -1.7. Elemental abundances for C, Na, Mg, Sc, Ti, Cr, Cu, Zn, Sr, Y, Zr, Ba, La, Ce, Nd, Sm, Eu, Gd, Dy are determined. Abundances for an additional 109 stars were taken from the literature and combined with the data of our sample. The literature sample reveals a lack of reliable abundance estimates for species that might be associated with the r-process elements for about 67% of CEMP stars, preventing a complete understanding of this clas...

  2. 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...

  3. 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...

  4. 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...

  5. How selection structures species abundance distributions

    Science.gov (United States)

    Magurran, Anne E.; Henderson, Peter A.

    2012-01-01

    How do species divide resources to produce the characteristic species abundance distributions seen in nature? One way to resolve this problem is to examine how the biomass (or capacity) of the spatial guilds that combine to produce an abundance distribution is allocated among species. Here we argue that selection on body size varies across guilds occupying spatially distinct habitats. Using an exceptionally well-characterized estuarine fish community, we show that biomass is concentrated in large bodied species in guilds where habitat structure provides protection from predators, but not in those guilds associated with open habitats and where safety in numbers is a mechanism for reducing predation risk. We further demonstrate that while there is temporal turnover in the abundances and identities of species that comprise these guilds, guild rank order is conserved across our 30-year time series. These results demonstrate that ecological communities are not randomly assembled but can be decomposed into guilds where capacity is predictably allocated among species. PMID:22787020

  6. 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...

  7. Aerial survey estimates of fallow deer abundance

    Science.gov (United States)

    Gogan, Peter J.; Gates, Natalie B.; Lubow, Bruce C.; Pettit, Suzanne

    2012-01-01

    Reliable estimates of the distribution and abundance of an ungulate species is essential prior to establishing and implementing a management program. We used ground surveys to determine distribution and ground and aerial surveys and individually marked deer to estimate the abundance of fallow deer (Dama dama) in north-coastal California. Fallow deer had limited distribution and heterogeneous densities. Estimated post-rut densities across 4 annual surveys ranged from a low of 1.4 (SE=0.2) deer/km2 to a high of 3.3 (se=0.5) deer/km2 in a low density stratum and from 49.0 (SE=8.3) deer/km2 to 111.6 deer/km2 in a high density stratum. Sightability was positively influenced by the presence of white color-phase deer in a group and group size, and varied between airial and ground-based observers and by density strata. Our findings underscore the utility of double-observer surveys and aerial surveys with individually marked deer, both incorporating covariates to model sightability, to estimate deer abundance.

  8. CH abundance gradient in TMC-1

    CERN Document Server

    Suutarinen, Aleksi; Harju, Jorma; Heikkilä, Arto; Hotzel, Stephan; Juvela, Mika; Millar, Tom J; Walsh, Catherina; Wouterloot, Jan Gerard Amos

    2011-01-01

    We observed the 9-cm Lambda-doubling lines of CH along the dense filament of TMC-1. The CH column densities were compared with the total H2 column densities derived using the 2MASS NIR data and previously published SCUBA maps and with OH column densities derived using previous observations with Effelsberg. We also modelled the chemical evolution of TMC-1 adopting physical conditions typical of dark clouds using the UMIST Database for Astrochemistry gas-phase reaction network to aid the interpretation of the observed OH/CH abundance ratios. The CH column density has a clear peak in the vicinity of the cyanopolyyne maximum of TMC-1. The fractional CH abundance relative to H2 increases steadily from the northwestern end of the filament where it lies around 1.0e-8, to the southeast where it reaches a value of 2.0e-8. The OH and CH column densities are well correlated, and we obtained OH/CH abundance ratios of ~ 16 - 20. These values are clearly larger than what has been measured recently in diffuse interstellar g...

  9. Galactic abundance gradients from Cepheids : On the iron abundance gradient around 10-12 kpc

    OpenAIRE

    Lemasle, B.; Francois, P.; Piersimoni, A.; Pedicelli, S.; Bono, G.; Laney, C. D.; Primas, F.; Romaniello, M.

    2008-01-01

    Context: Classical Cepheids can be adopted to trace the chemical evolution of the Galactic disk since their distances can be estimated with very high accuracy. Aims: Homogeneous iron abundance measurements for 33 Galactic Cepheids located in the outer disk together with accurate distance determinations based on near-infrared photometry are adopted to constrain the Galactic iron gradient beyond 10 kpc. Methods: Iron abundances were determined using high resolution Cepheid spectra collected wit...

  10. 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

  11. Patterns of food abundance for breeding waterbirds in the san luis valley of Colorado

    Science.gov (United States)

    Gammonley, J.H.; Laubhan, M.K.

    2002-01-01

    We measured the amount and distribution of macroinvertebrates and seeds in four wetland habitats (short emergent, seasonal open water, semipermanent/permanent open water, and saltgrass [Distichlis spicata]) used by breeding ducks and shorebirds at a wetland complex in the San Luis Valley, Colorado, USA. Density of macroinvertebrates did not differ among habitats or sampling periods (P = 0.45), but dry mass, crude protein, and gross energy production were greater (P < 0.05) in short emergent than in other habitats. These differences were largely due to the greater dry mass of gastropods in short emergent than in other habitats. Total seed density, dry mass, crude protein, and gross energy differed among habitats and periods with interaction effects (P <0.01). Although seed abundance varied among habitats and sampling periods, abundance was greatest in short emergent during all sampling periods. Breeding waterbirds consumed a variety of macroinvertebrates and seeds on the study area. Patterns of abundance among habitats of macroinvertebrates and seeds consumed by six waterbird species were not consistent with patterns of foraging habitat use by most ducks and shorebirds at this wetland complex. Our results indicate that estimates of food or nutrient abundance are useful in assessing the functional role of broad habitat types, but factors other than food abundance also influence avian selection of wetland foraging habitats. ?? 2002, The Society of Wetland Scientists.

  12. 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

  13. Abundance anomalies in tidal disruption events

    Science.gov (United States)

    Kochanek, C. S.

    2016-05-01

    The ˜10 per cent of tidal disruption events (TDEs) due to stars more massive than M* ≳ M⊙ 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 per cent 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 with M* ≳ M⊙ 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 ˜1-2 M⊙ stars disrupted on the main sequence. Like helium, portions of the debris will show still larger changes in C and N, and the anomalies decline as the star leaves the main sequence. The enhanced [N/C] abundance ratio of these TDEs provides the first natural explanation for the rare, nitrogen-rich quasars and may also explain the strong nitrogen emission seen in ultraviolet spectra of ASASSN-14li.

  14. Abundance and diversity of marine microbial eukaryotes

    OpenAIRE

    Pernice, Massimo Ciro

    2014-01-01

    [EN]Microeukaryotes are important ecological players in any kind of ecosystem, most notably in the ocean, and it is therefore essential to collect information about their abundance and diversity. To achieve this general goal this thesis was structured in two parts. The first part represents an effort to define our “diversity unit” from studies based on the well-known cloning and Sanger sequencing approach. Basically, we wanted to establish a solid baseline for the second part of the thesis. W...

  15. Abundance Anomalies In Tidal Disruption Events

    OpenAIRE

    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 ...

  16. North Sea Elasmobranchs: distribution, abundance and biodiversity

    OpenAIRE

    Daan, N.; Heessen, H.J.L.; Hofstede, ter, AHM Arthur

    2005-01-01

    Based on data from various international and national surveys, an overview is given of the fine-scale distribution (resolution of 20¿longitude * 10¿ latitude; ¿ 10*10 nm) and trends in abundance of elasmobranch species reported from the North Sea. Presence-absence maps are produced based on 4 surveys, which help to delineate distribution limits of the less common species, while maps in terms of catch rates (International Bottom Trawl Survey data only) are given for the seven most common shark...

  17. Estimating the relationship between abundance and distribution

    DEFF Research Database (Denmark)

    Rindorf, Anna; Lewy, Peter

    2012-01-01

    provide unbiased estimates of the relationship when estimated from count data. The indices investigated include the proportion of empty samples, the proportion of structurally empty samples, Lloyds index of patchiness, measures derived from Lorenz curves (such as D95 and the Gini index), and measures...... 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...

  18. Neon and Oxygen Abundances and Abundance Ratio in the Solar Corona

    Science.gov (United States)

    Landi, E.; Testa, P.

    2015-02-01

    In this work we determine the Ne/O abundance ratio from Solar and Heliospheric Observatory (SOHO)/Solar Ultraviolet Measurement of Emitted Radiation (SUMER) off-disk observations of quiescent streamers over the 1996-2008 period. We find that the Ne/O ratio is approximately constant over solar cycle 23 from 1996 to 2005, at a value of 0.099 ± 0.017 this value is lower than the transition region determinations from the quiet Sun used to infer the neon photospheric abundance from the oxygen photospheric abundance. Also, the Ne/O ratio we determined from SUMER is in excellent agreement with in situ determinations from ACE/SWICS. In 2005-2008, the Ne/O abundance ratio increased with time and reached 0.25 ± 0.05, following the same trend found in the slowest wind analyzed by ACE/SWICS. Further, we measure the absolute abundance in the corona for both oxygen and neon from the data set of 1996 November 22, obtaining A o = 8.99 ± 0.04 and A Ne = 7.92 ± 0.03, and we find that both elements are affected by the first ionization potential (FIP) effect, with oxygen being enhanced by a factor of 1.4-2.1 over its photospheric abundance, and neon being changed by a factor of 0.75-1.20. We conclude that the Ne/O ratio is not constant in the solar atmosphere, both in time and at different heights, and that it cannot be reliably used to infer the neon abundance in the photosphere. Also, we argue that the FIP effect was less effective during the minimum of solar cycle 24, and that the Ne/O = 0.25 ± 0.05 value measured at that time is closer to the true photospheric value, leading to a neon photospheric abundance larger than assumed by ≈40%. We discuss the implications of these results for the solar abundance problem, for the FIP effect, and for the identification of the source regions of the solar wind.

  19. 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...

  20. 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.

  1. Element Abundances through the Cosmic Ages

    CERN Document Server

    Pettini, M

    2003-01-01

    The horizon for studies of element abundances has expanded dramatically in the last ten years. Once the domain of astronomers concerned chiefly with stars and nearby galaxies, this field has now become a key component of observational cosmology, as technological advances have made it possible to measure the abundances of several chemical elements in a variety of environments at redshifts up to z = 4, when the universe was in its infancy. In this series of lectures I summarise current knowledge on the chemical make-up of distant galaxies observed directly in their starlight, and of interstellar and intergalactic gas seen in absorption against the spectra of bright background sources. The picture which is emerging is one where the universe at z = 3 already included many of the constituents of today's galaxies-even at these early times we see evidence for Population I and II stars, while the `smoking gun' for Population III objects may be hidden in the chemical composition of the lowest density regions of the in...

  2. 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...

  3. 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.

  4. Fluorine Abundances in the Milky Way Bulge

    CERN Document Server

    Cunha, K; Gibson, B K

    2008-01-01

    Fluorine (19F) abundances are derived in a sample of 6 bulge red giants in Baade's Window. These giants span a factor of 10 in metallicity and this is the first study to define the behavior of 19F with metallicity in the bulge. The bulge results show an increase in F/O with increasing oxygen. This trend overlaps what is found in the disk at comparable metallicities, with the most oxygen-rich bulge target extending the disk trend. The increase in F/O in the disk arises from 19F synthesis in both asymptotic giant branch (AGB) stars and metal-rich Wolf-Rayet (WR) stars through stellar winds. The lack of an s-process enhancement in the most fluorine-rich bulge giant in this study, suggests that WR stars represented a larger contribution than AGB stars to 19F production in the bulge when compared to the disk. If this result for fluorine is combined with the previously published overall decline in the O/Mg abundance ratios in metal-rich bulge stars, it suggests that WR winds played a role in shaping chemical evolut...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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 ...

  10. The Coronal Abundance Anomalies of M Dwarfs

    CERN Document Server

    Wood, Brian E; Karovska, Margarita

    2012-01-01

    We analyze Chandra X-ray spectra of the M0 V+M0 V binary GJ 338. As quantified by X-ray surface flux, these are the most inactive M dwarfs ever observed with X-ray grating spectroscopy. We focus on measuring coronal abundances, in particular searching for evidence of abundance anomalies related to First Ionization Potential (FIP). In the solar corona and wind, low FIP elements are overabundant, which is the so-called "FIP effect." For other stars, particularly very active ones, an "inverse FIP effect" is often observed, with low FIP elements being underabundant. For both members of the GJ 338 binary, we find evidence for a modest inverse FIP effect, consistent with expectations from a previously reported correlation between spectral type and FIP bias. This amounts to strong evidence that all M dwarfs should exhibit the inverse FIP effect phenomenon, not just the active ones. We take the first step towards modeling the inverse FIP phenomenon in M dwarfs, building on past work that has demonstrated that MHD wav...

  11. 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.

  12. TEA: A Code for Calculating Thermochemical Equilibrium Abundances

    OpenAIRE

    Blecic, Jasmina; Harrington, Joseph; 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 o...

  13. Halo abundances within the cosmic web

    Science.gov (United States)

    Alonso, D.; Eardley, E.; Peacock, J. A.

    2015-03-01

    We investigate the dependence of the mass function of dark-matter haloes on their environment within the cosmic web of large-scale structure. A dependence of the halo mass function on large-scale mean density is a standard element of cosmological theory, allowing mass-dependent biasing to be understood via the peak-background split. On the assumption of a Gaussian density field, this analysis can be extended to ask how the mass function depends on the geometrical environment: clusters, filaments, sheets and voids, as classified via the tidal tensor (the Hessian matrix of the gravitational potential). In linear theory, the problem can be solved exactly, and the result is attractively simple: the conditional mass function has no explicit dependence on the local tidal field, and is a function only of the local density on the filtering scale used to define the tidal tensor. There is nevertheless a strong implicit predicted dependence on geometrical environment, because the local density couples statistically to the derivatives of the potential. We compute the predictions of this model and study the limits of their validity by comparing them to results deduced empirically from N-body simulations. We have verified that, to a good approximation, the abundance of haloes in different environments depends only on their densities, and not on their tidal structure. In this sense we find relative differences between halo abundances in different environments with the same density which are smaller than ˜13 per cent. Furthermore, for sufficiently large filtering scales, the agreement with the theoretical prediction is good, although there are important deviations from the Gaussian prediction at small, non-linear scales. We discuss how to obtain improved predictions in this regime, using the `effective-universe' approach.

  14. Abundant thorium as an alternative nuclear fuel

    International Nuclear Information System (INIS)

    It has long been known that thorium-232 is a fertile radioactive material that can produce energy in nuclear reactors for conversion to electricity. Thorium-232 is well suited to a variety of reactor types including molten fluoride salt designs, heavy water CANDU configurations, and helium-cooled TRISO-fueled systems. Among contentious commercial nuclear power issues are the questions of what to do with long-lived radioactive waste and how to minimize weapon proliferation dangers. The substitution of thorium for uranium as fuel in nuclear reactors has significant potential for minimizing both problems. Thorium is three times more abundant in nature than uranium. Whereas uranium has to be imported, there is enough thorium in the United States alone to provide adequate grid power for many centuries. A well-designed thorium reactor could produce electricity less expensively than a next-generation coal-fired plant or a current-generation uranium-fueled nuclear reactor. Importantly, thorium reactors produce substantially less long-lived radioactive waste than uranium reactors. Thorium-fueled reactors with molten salt configurations and very high temperature thorium-based TRISO-fueled reactors are both recommended for priority Generation IV funding in the 2030 time frame. - Highlights: • Thorium is an abundant nuclear fuel that is well suited to three advanced reactor configurations. • Important thorium reactor configurations include molten salt, CANDU, and TRISO systems. • Thorium has important nuclear waste disposal advantages relative to pressurized water reactors. • Thorium as a nuclear fuel has important advantages relative to weapon non-proliferation

  15. 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 ...

  16. Natural proteins: Sources, isolation, characterization and applications

    OpenAIRE

    Nehete, Jitendra Y.; Bhambar, Rajendra S.; Minal R Narkhede; Gawali, Sonali R.

    2013-01-01

    Worldwide, plant protein contributes substantially as a food resource because it contains essential amino acids for meeting human physiological requirements. However, many versatile plant proteins are used as medicinal agents as they are produced by using molecular tools of biotechnology. Proteins can be obtained from plants, animals and microorganism cells. The abundant economical proteins can be obtained from plant seeds. These natural proteins are obtained by isolation procedures depending...

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. YKL-40: a novel marker shared by chronic inflammation and oncogenic transformation

    DEFF Research Database (Denmark)

    Roslind, Anne; Johansen, Julia S

    2009-01-01

    YKL-40, a member of 'mammalian chitinase-like proteins', is secreted by macrophages, neutrophils, chondrocytes, endothelial-, vascular smooth muscle-, and cancer cells. High serum YKL-40 is a biomarker of poor prognosis in patients with cancer, inflammation and increased tissue remodelling. High ...

  2. 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...

  3. Microfibrillar-associated protein 4 modulates airway smooth muscle cell phenotype in experimental asthma

    DEFF Research Database (Denmark)

    Pilecki, Bartosz; Schlosser, Anders; Wulf-Johansson, Helle;

    2015-01-01

    BACKGROUND: Recently, several proteins of the extracellular matrix have been characterised as active contributors to allergic airway disease. Microfibrillar-associated protein 4 (MFAP4) is an extracellular matrix protein abundant in the lung, whose biological functions remain poorly understood...

  4. Abundance Profiles in Low-Mass Galaxies

    CERN Document Server

    Kobulnicky, H A

    1997-01-01

    The nitrogen and oxygen abundances in the warm ionized gas of low-mass, metal-poor galaxies appear surprisingly homogeneous considering the prevalence of large HII regions, which contain hundreds of massive stars. Of the six galaxies with extensive optical spectroscopy, only the largest and most metal-rich, the LMC, shows evidence for a chemical gradient akin to those commonly seen in spirals. Furthermore, no significant localized chemical fluctuations are found in the vicinity of young star clusters, despite large expected chemical yields of massive stars. An ad-hoc fine-tuning of the release, dispersal and mixing rates could give rise to the observed homogeneity, but a more probable explanation is that fresh ejecta reside in a hard-to-observe hot or cold phase. In any case, the observations indicate that heavy elements which have already mixed with the warm interstellar medium are homogeneously dispersed. Mixing of fresh ejecta with the surrounding warm ISM apparently requires longer than the lifetimes of t...

  5. 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...

  6. Non-Additive Effects of Genotypic Diversity Increase Floral Abundance and Abundance of Floral Visitors

    OpenAIRE

    Mark A Genung; Jean-Philippe Lessard; Claire B Brown; Bunn, Windy A.; Cregger, Melissa A.; W M Nicholas Reynolds; Emmi Felker-Quinn; Stevenson, Mary L.; Hartley, Amanda S.; Gregory M. Crutsinger; Schweitzer, Jennifer A.; Bailey, Joseph K.

    2010-01-01

    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 dist...

  7. Abundance models improve spatial and temporal prioritization of conservation resources.

    Science.gov (United States)

    Johnston, Alison; Fink, Daniel; Reynolds, Mark D; Hochachka, Wesley M; Sullivan, Brian L; Bruns, Nicholas E; Hallstein, Eric; Merrifield, Matt S; Matsumoto, Sandi; Kelling, Steve

    2015-10-01

    Conservation prioritization requires knowledge about organism distribution and density. This information is often inferred from models that estimate the probability of species occurrence rather than from models that estimate species abundance, because abundance data are harder to obtain and model. However, occurrence and abundance may not display similar patterns and therefore development of robust, scalable, abundance models is critical to ensuring that scarce conservation resources are applied where they can have the greatest benefits. Motivated by a dynamic land conservation program, we develop and assess a general method for modeling relative abundance using citizen science monitoring data. Weekly estimates of relative abundance and occurrence were compared for prioritizing times and locations of conservation actions for migratory waterbird species in California, USA. We found that abundance estimates consistently provided better rankings of observed counts than occurrence estimates. Additionally, the relationship between abundance and occurrence was nonlinear and varied by species and season. Across species, locations prioritized by occurrence models had only 10-58% overlap with locations prioritized by abundance models, highlighting that occurrence models will not typically identify the locations of highest abundance that are vital for conservation of populations. PMID:26591443

  8. 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.

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

    Science.gov (United States)

    Reames, Donald V.

    2016-07-01

    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.

  10. Reanalysis of the interstellar CH abundance

    International Nuclear Information System (INIS)

    A detailed investigation of the term structure of the X2II, A2Δ, B2Σ-, and C2Σ+ systems of CH is presented, as well as a discussion of a number of errors that have been found with respect to the historical analysis of the interstellar CH abundance. The primary cause for these errors is the neglect of the Λ doubling of the ground state. The effects of including this splitting are the following: (1) the oscillator strength doubles for each line arising from the ground state of the B-X and C-X electronic systems; (2) the 4300, 3886, and 3143 A lines each consist of a blend of two lines separated by 1.43, 1.28, and 2.17 km s-1, respectively; (3) the line at 3886 A arises solely from the upper half of the Λ doublet, and the lines at 3890 and 3878 A arise from the lower half of the Λ doublet; (4) the line at 3143 A arises solely from the lower half of the Λ doublet, and the lines at 3146 and 3137 A arise from the upper half of the Λ doublet; (5) the excitation temperature (a measure of the relative level population) of the ground-state Λ doublet has been calculated for the interstellar CH along the line of sight toward four stars (zeta Per, zeta Oph, X Per, and chi Oph) using published equivalent withs. The excitation temperature appears to be less than zero toward X Per and zeta Per, indicating that the population of the ground-state Λ doublet is inverted. The level populations along other lines of sight are known to be inverted from observations of the radio CH lines; this is the first detection of a radio maser by optical methods

  11. Testing spherical evolution for modelling void abundances

    Science.gov (United States)

    Achitouv, Ixandra; Neyrinck, Mark; Paranjape, Aseem

    2015-08-01

    We compare analytical predictions of void volume functions to those measured from N-body simulations, detecting voids with the ZOBOV void finder. We push to very small, non-linear voids, below few Mpc radius, by considering the unsampled dark matter density field. We also study the case where voids are identified using haloes. We develop analytical formula for the void abundance of both the excursion set approach and the peaks formalism. These formulas are valid for random walks smoothed with a top-hat filter in real space, with a large class of realistic barrier models. We test the extent to which the spherical evolution approximation, which forms the basis of the analytical predictions, models the highly aspherical voids that occur in the cosmic web, and are found by a watershed-based algorithm such as ZOBOV. We show that the volume function returned by ZOBOV is quite sensitive to the choice of treatment of subvoids, a fact that has not been appreciated previously. For reasonable choices of subvoid exclusion, we find that the Lagrangian density δv of the ZOBOV voids - which is predicted to be a constant δv ≈ -2.7 in the spherical evolution model - is different from the predicted value, showing substantial scatter and scale dependence. This result applies to voids identified at z = 0 with effective radius between 1 and 10 h-1 Mpc. Our analytical approximations are flexible enough to give a good description of the resulting volume function; however, this happens for choices of parameter values that are different from those suggested by the spherical evolution assumption. We conclude that analytical models for voids must move away from the spherical approximation in order to be applied successfully to observations, and we discuss some possible ways forward.

  12. Nitrogen abundances in damped Lyalpha absorbers

    Science.gov (United States)

    Zafar, T.; Centurión, M.; Molaro, P.; Péroux, C.; D'Odorico, V.; Vladilo, G.

    Nitrogen is thought to have both primary and secondary origins depending on whether the seed carbon and oxygen are produced by the star itself (primary) or already present in the interstellar medium (secondary) from which star forms. Damped Lyalpha (DLA) and sub-DLA systems with typical metallicities of -3.0≲ Z/Z⊙ ≲ -0.5 are excellent tools to study nitrogen production. We made a search for nitrogen in the European Southern Observatory (ESO) Ultraviolet Visual Echelle Spectrograph (UVES) advanced data products (EUADP) database. In the EUADP database, we find 10 new measurements and 9 upper limits of nitrogen. We further compiled DLA/sub-DLA data from the literature with estimates available of nitrogen and alpha -elements. This yields a total of 98 systems, i.e. the largest nitrogen abundance sample investigated so far. In agreement with previous studies, we indeed find a bimodal [N/alpha ] behaviour: three-quarter systems show a mean value of [N/alpha ] =-0.87 with a scatter of 0.21 dex and one-quarter shows ratios clustered at [N/alpha ] = -1.43 with a lower dispersion of 0.13 dex. The high [N/alpha ] group is consistent with the blue compact dwarves and dwarf irregular galaxies, suggesting primary nitrogen production. The low [N/alpha ] group is the lowest ever observed in any astrophysical site and probably provides an evidence of the primary production by fast rotating massive stars in young sites. Moreover, we find a transition between the two [N/alpha ] groups around [N/H] ≃-2.5. The transition is not abrupt and there are a few systems lying in the transition region. Additional observations of DLAs/sub-DLAs below [N/H] <-2.5 would provide more clues.

  13. Not just who, but how many: the importance of partner abundance in reef coral symbioses

    Directory of Open Access Journals (Sweden)

    Ross eCunning

    2014-08-01

    Full Text Available The performance and function of reef corals depends on the genetic identity of their symbiotic algal partners, with some symbionts providing greater benefits (e.g., photosynthate, thermotolerance than others. However, these interaction outcomes may also depend on partner abundance, with certain total numbers of symbionts providing greater net benefit under certain conditions. We suggest that symbiont abundance is a fundamental aspect of the dynamic interface between reef corals and the abiotic environment that ultimately determines the benefits, costs, and functional responses of these symbioses. This density-dependent framework suggests that corals may regulate the size of their symbiont pool to match microhabitat-specific optima, which may contribute to the high spatiotemporal variability in symbiont abundance observed within and among colonies and reefs. Differences in symbiont standing stock may subsequently explain variation in energetics, growth, reproduction, and stress susceptibility, and may mediate the impacts of environmental change on these outcomes. However, the importance of symbiont abundance has received relatively little recognition, possibly because commonly used metrics based on surface area (e.g., symbiont cells cm-2 may be only weakly linked to biological phenomena and are difficult to compare across studies. We suggest that normalizing symbionts to biological host parameters such as units of protein or numbers of host cells will more clearly elucidate the functional role of symbiont abundance in reef coral symbioses. In this article, we aim to generate testable hypotheses regarding the importance of symbiont abundance by first discussing different metrics and their potential links to symbiosis performance and breakdown, and then describing how natural variability and dynamics of symbiont communities may help explain ecological patterns on coral reefs and predict responses to environmental change.

  14. Evolution of dispersion in the cosmic deuterium abundance

    Science.gov (United States)

    Dvorkin, Irina; Vangioni, Elisabeth; Silk, Joseph; Petitjean, Patrick; Olive, Keith A.

    2016-05-01

    Deuterium is created during big bang nucleosynthesis, and, in contrast to the other light stable nuclei, can only be destroyed thereafter by fusion in stellar interiors. In this Letter, we study the cosmic evolution of the deuterium abundance in the interstellar medium (ISM) 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 a tight correlation between deuterium and metal abundances which could be used to measure the primordial deuterium abundance.

  15. 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...

  16. 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.

  17. 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 ...

  18. Restricted-access material-based high-molecular-weight protein depletion coupled on-line with namo-liquid chromatography-mass spectrometry for proteomics applications

    NARCIS (Netherlands)

    Rieux, Laurent; Bischoff, Rainer; Verpoorte, Elisabeth; Niederlander, Harm A. G.

    2007-01-01

    Proteomics samples often contain both abundant proteins and low-level proteins and peptides. Highly abundant proteins can mask and/or bind those of lower abundance and thereby hinder their analysis. In particular, we were concerned with samples containing large amounts of albumin (up to 4.0 mu M). I

  19. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... the vegetarian proteins, whether they have carbohydrate. Best Protein Choices The best choices are: Plant-based proteins ...

  20. Lipid-transfer proteins.

    Science.gov (United States)

    Ng, Tzi Bun; Cheung, Randy Chi Fai; Wong, Jack Ho; Ye, Xiujuan

    2012-01-01

    Lipid-transfer proteins (LTPs) are basic proteins found in abundance in higher plants. LTPs play lots of roles in plants such as participation in cutin formation, embryogenesis, defense reactions against phytopathogens, symbiosis, and the adaptation of plants to various environmental conditions. In addition, LTPs from field mustard and Chinese daffodil exhibit antiproliferative activity against human cancer cells. LTPs from chili pepper and coffee manifest inhibitory activity against fungi pathogenic to humans such as Candida species. The intent of this article is to review LTPs in the plant kingdom. PMID:23193591

  1. Radial molecular abundances and gas cooling in starless cores

    OpenAIRE

    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 c...

  2. Abundance and Diversity of Viruses in Six Delaware Soils

    OpenAIRE

    Williamson, Kurt E.; Radosevich, Mark; Wommack, K. Eric

    2005-01-01

    The importance of viruses in marine microbial ecology has been established over the past decade. Specifically, viruses influence bacterial abundance and community composition through lysis and alter bacterial genetic diversity through transduction and lysogenic conversion. By contrast, the abundance and distribution of viruses in soils are almost completely unknown. This study describes the abundance and diversity of autochthonous viruses in six Delaware soils: two agricultural soils, two coa...

  3. Cross-Scale Interactions and the Distribution-Abundance Relationship

    OpenAIRE

    Werner, Earl E.; Davis, Christopher J.; Skelly, David K.; Relyea, Rick A.; Benard, Michael F.; McCauley, Shannon J.

    2014-01-01

    Positive interspecific relationships between local abundance and extent of regional distribution are among the most ubiquitous patterns in ecology. Although multiple hypotheses have been proposed, the mechanisms underlying distribution-abundance (d-a) relationships remain poorly understood. We examined the intra- and interspecific distribution-abundance relationships for a metacommunity of 13 amphibian species sampled for 15 consecutive years. Mean density of larvae in occupied ponds was posi...

  4. A Data-intensive Assessment of the Species Abundance Distribution

    OpenAIRE

    Baldridge, Elita

    2013-01-01

    The hollow curve species abundance distribution describes the pattern of large numbers of rare species and a small number of common species in a community. The species abundance distribution is one of the most ubiquitous patterns in nature and many models have been proposed to explain the mechanisms that generate this pattern. While there have been numerous comparisons of species abundance distribution models, most of these comparisons only use a small subset of available models, focus on a s...

  5. Occupancy, spatial variance, and the abundance of species

    OpenAIRE

    He, F.; Gaston, K J

    2003-01-01

    A notable and consistent ecological observation known for a long time is that spatial variance in the abundance of a species increases with its mean abundance and that this relationship typically conforms well to a simple power law (Taylor 1961). Indeed, such models can be used at a spectrum of spatial scales to describe spatial variance in the abundance of a single species at different times or in different regions and of different species across the same set of areas (Tayl...

  6. Ecological niche structure and rangewide abundance patterns of species

    OpenAIRE

    Martínez-Meyer, Enrique; Díaz-Porras, Daniel; Peterson, A. Townsend; Yáñez-Arenas, Carlos

    2013-01-01

    Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the ecological nic...

  7. Positive Interspecific Relationship between Temporal Occurrence and Abundance in Insects

    OpenAIRE

    Scrosati, Ricardo A; Ruth D Patten; Lauff, Randolph F.

    2011-01-01

    One of the most studied macroecological patterns is the interspecific abundance-occupancy relationship, which relates species distribution and abundance across space. Interspecific relationships between temporal distribution and abundance, however, remain largely unexplored. Using data for a natural assemblage of tabanid flies measured daily during spring and summer in Nova Scotia, we found that temporal occurrence (proportion of sampling dates in which a species occurred in an experimental t...

  8. Modelling occurrence and abundance of species when detection is imperfect

    Science.gov (United States)

    Royle, J. Andrew; Nichols, J.D.; Kery, M.

    2005-01-01

    Relationships between species abundance and occupancy are of considerable interest in metapopulation biology and in macroecology. Such relationships may be described concisely using probability models that characterize variation in abundance of a species. However, estimation of the parameters of these models in most ecological problems is impaired by imperfect detection. When organisms are detected imperfectly, observed counts are biased estimates of true abundance, and this induces bias in stated occupancy or occurrence probability. In this paper we consider a class of models that enable estimation of abundance/occupancy relationships from counts of organisms that result from surveys in which detection is imperfect. Under such models, parameter estimation and inference are based on conventional likelihood methods. We provide an application of these models to geographically extensive breeding bird survey data in which alternative models of abundance are considered that include factors that influence variation in abundance and detectability. Using these models, we produce estimates of abundance and occupancy maps that honor important sources of spatial variation in avian abundance and provide clearly interpretable characterizations of abundance and occupancy adjusted for imperfect detection.

  9. 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.

  10. Parent Stars of Extrasolar Planets. IX. Lithium Abundances

    OpenAIRE

    Gonzalez, Guillermo

    2008-01-01

    We compare the Li abundances of a sample of stars with planets discovered with the Doppler method to a sample of stars without detected planets. We prepared the samples by combining the Li abundances reported in several recent studies in a consistent way. Our results confirm recent claims that the Li abundances of stars with planets are smaller than those of stars without planets near the solar temperature. We also find that the vsini and $R^{'}_{\\rm HK}$ anomalies correlate with the Li abund...

  11. Abundances of the heavy elements in the Magellanic Clouds. I. Metal abundances of F-type supergiants

    International Nuclear Information System (INIS)

    Metal abundances of eight F-type supergiants in each of the Magellanic Clouds were determined using the results of high-resolution spectroscopy analysis of these stars, together with new Stromgren uvby and Cousins (1980) BVRI photometry. It was found that the mean Fe abundance (Fe/H) for the SMC is -0.65 + or - 0.2 dex, and the mean Fe abundance for the LMC is -0.30 + or - 0.2 dex. The abundances of stars in both the SMC and LMC appear relatively uniform, and the abundances of the elements relative to Fe are very similar in both Magellanic Clouds and in Canopus (the carbon-to-iron abundances are the same for all three). It was also found that Nd and Sm are overabundant in both clouds, supporting the trends found by Spite et al. (1988) for the three SMC stars they studied. 140 refs

  12. 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.

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

    Science.gov (United States)

    Huhe; Borjigin, Shinchilelt; Buhebaoyin; Wu, Yanpei; Li, Minquan; Cheng, Yunxiang

    2016-01-01

    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 bacteria that mediate the nitrogen cycle in recently abandoned croplands. PMID:27140199

  14. 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...

  15. Spatio-temporal abundance and dispersal of Culicoides

    DEFF Research Database (Denmark)

    Kirkeby, Carsten

    . These models need to have proper input regarding the abundance and behavior of the vectors. If no vectors are present in an area, the disease will not spread. Thus the vector abundance is a very important factor for models of vector-borne diseases. This PhD project investigates different key factors important...

  16. 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

  17. A protocol for sampling vascular epiphyte richness and abundance

    NARCIS (Netherlands)

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

    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

  18. The end of abundance. Economic solutions to water scarcity

    NARCIS (Netherlands)

    Zetland, D.J.

    2011-01-01

    In a past of abundance, we had clean water to meet our demands for showers, pools, farms and rivers. Our laws and customs did not need to regulate or ration demand. Over time, our demand has grown, and scarcity has replaced abundance. We don't have as much clean water as we want. We can respond to t

  19. The implicit assumption of symmetry and the species abundance distribution

    NARCIS (Netherlands)

    Alonso, David; Ostling, Annette; Etienne, Rampal S.

    2008-01-01

    Species abundance distributions (SADs) have played a historical role in the development of community ecology. They summarize information about the number and the relative abundance of the species encountered in a sample from a given community. For years ecologists have developed theory to characteri

  20. 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.

  1. 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.......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 have...... attained unequivocal support. Accordingly, the positive association in distribution-abundance relationships is generally considered to be due to a combination of these proposed mechanisms acting in concert. In this review, we suggest that much of the disparity between these hypotheses stems from...

  2. Carbon and nitrogen abundances determined from transition layer lines

    Science.gov (United States)

    Boehm-Vitense, Erika; Mena-Werth, Jose

    1992-01-01

    The possibility of determining relative carbon, nitrogen, and silicon abundances from the emission-line fluxes in the lower transition layers between stellar chromospheres and coronae is explored. Observations for main-sequence and luminosity class IV stars with presumably solar element abundances show that for the lower transition layers Em = BT sup -gamma. For a given carbon abundance the constants gamma and B in this relation can be determined from the C II and C IV emission-line fluxes. From the N V and S IV lines, the abundances of these elements relative to carbon can be determined from their surface emission-line fluxes. Ratios of N/C abundances determined in this way for some giants and supergiants agree within the limits of errors with those determined from molecular bands. For giants, an increase in the ratio of N/C at B-V of about 0.8 is found, as expected theoretically.

  3. 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.

  4. 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.

  5. 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

  6. Carbon and nitrogen abundance variations in globular cluster red giants

    Science.gov (United States)

    Martell, Sarah L.

    2008-06-01

    This dissertation describes investigations into two of the persistent questions of elemental abundances in Galactic globular clusters: the phenomenon of deep mixing, observed through the progressive depletion of surface carbon abundance as stars evolve along the red giant branch, and abundance bimodality, a phenomenon observed only in globular clusters, in which a subset of stars in a given globular cluster have a distinctive pattern of elemental enhancements and depletions relative to the Solar pattern. The first chapter gives an introduction to the history of globular cluster abundance studies, with particular focus on low-resolution spectroscopy. For both deep mixing and abundance bimodality, the leading theoretical models and the data which support and challenge them are laid out. Each section ends with a description of presently-unanswered questions; these are the motivation for the various projects contained in this dissertation. The second chapter describes the use of molecular handstrengths for determining elemental abundances from low-resolution spectra, and introduces a new CH bandstrength index that is designed to be sensitive to carbon abundance and insensitive to nitrogen abundance in Pop. II red giants over a wide range of metallicity. Various CH indices defined elsewhere in the literature are also discussed, and are shown to have comparable accuracy to the new index only over a limited range of stellar properties. Carbon abundances determined using the new CH index are compared to literature abundances for a few stars, and general concordance with published abundances is found. The third chapter contains a large-scale application of the new CH index: a survey of present-day carbon abundances and calculated carbon depletion rates in bright red giants belonging to eleven Galactic globular clusters spanning the full metallicity range of halo globular clusters. Targets were selected with similar evolutionary states, were observed with one instrument on

  7. 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.

  8. 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

  9. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    . The biophysical and structural investigations of PPIs consequently demand hybrid approaches, implementing orthogonal methods and strategies for global data analysis. Currently, impressive developments in hardware and software within several methodologies define a new era for the biostructural community. Data can......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...

  10. Seasonal Abundance of Aphids and Aphidophagous Insects in Pecan

    Directory of Open Access Journals (Sweden)

    Ghulam Abbas

    2012-12-01

    Full Text Available Seasonal occurrence of aphids and aphidophagous insects was monitored for six years (2006–2011 from full leaf expansion in May to leaf fall in October in “Desirable” variety pecan trees that were not treated with insecticides. Aphid outbreaks occurred two times per season, once in the spring and again in the late summer. Yellow pecan and blackmargined aphids exceeded the recommended treatment thresholds one time and black pecan aphids exceeded the recommended treatment levels three times over the six seasons. Increases in aphidophagous insect abundance coincided with aphid outbreaks in five of the six seasons. Among aphidophagous insects Harmonia axyridis and Olla v-nigrum were frequently collected in both the tree canopy and at the ground level, whereas, Coccinella septempunctata, Hippodamia convergens were rarely found in the tree canopy and commonly found at the ground level. Green lacewing abundance was higher in the ground level than in the tree canopy. Brown lacewings were more abundant in the tree canopy than at the ground level. Dolichopodid and syrphid fly abundance, at the ground level increased during peak aphid abundance in the tree canopy. Application of an aqueous solution of fermenting molasses to the pecan foliage during an aphid outbreak significantly increased the abundance of ladybeetles and lacewings and significantly reduced the abundance of yellow pecan, blackmargined and black pecan aphids.

  11. Seasonal Abundance of Aphids and Aphidophagous Insects in Pecan.

    Science.gov (United States)

    Dutcher, James D; Karar, Haider; Abbas, Ghulam

    2012-01-01

    Seasonal occurrence of aphids and aphidophagous insects was monitored for six years (2006-2011) from full leaf expansion in May to leaf fall in October in "Desirable" variety pecan trees that were not treated with insecticides. Aphid outbreaks occurred two times per season, once in the spring and again in the late summer. Yellow pecan and blackmargined aphids exceeded the recommended treatment thresholds one time and black pecan aphids exceeded the recommended treatment levels three times over the six seasons. Increases in aphidophagous insect abundance coincided with aphid outbreaks in five of the six seasons. Among aphidophagous insects Harmonia axyridis and Olla v-nigrum were frequently collected in both the tree canopy and at the ground level, whereas, Coccinella septempunctata, Hippodamia convergens were rarely found in the tree canopy and commonly found at the ground level. Green lacewing abundance was higher in the ground level than in the tree canopy. Brown lacewings were more abundant in the tree canopy than at the ground level. Dolichopodid and syrphid fly abundance, at the ground level increased during peak aphid abundance in the tree canopy. Application of an aqueous solution of fermenting molasses to the pecan foliage during an aphid outbreak significantly increased the abundance of ladybeetles and lacewings and significantly reduced the abundance of yellow pecan, blackmargined and black pecan aphids. PMID:26466738

  12. 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.

  13. 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.

  14. Metal abundance range in the Draco dwarf galaxy

    International Nuclear Information System (INIS)

    The multichannel scanner of the Hale telescope was used to measure the spectral flux distributions of 23 red giants in the Draco system over the range lambda lambda 3240 to 7620. The memberships of these stars in Draco were checked by use of the spectral scans, and for 17 of them the observations are of sufficient quality that estimates of metal abundance can be made. The scans of the Draco stars resemble in every way the scans of red giants in globular clusters. Large differences are seen among the scans of the Draco stars, which are due to a range in Fe/H. The distribution over metal abundance was found from the abundance estimates; its half-width corresponds to an abundance range of a factor of 2.7. The mean metal abundance [Fe/H] = -1.86 +- 0.09, which is larger than the abundance of M92. This result does not support the previous claims that Draco is more metal poor than the most metal-deficient globular clusters. The implications of these results for the interpetations of Draco's color--magnitude diagram and variable star population are discussed. The chemical evolution of Draco was modeled with simple models that assume mass loss and prompt initial enrichment. These models provide adequate fits to the observed abundance distribution, and suggest that the proto-Draco was initially approx. 100 times more massive than Draco is today. 10 figures, 2 tables

  15. 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 ...

  16. Abundance analysis of the outer halo globular cluster Palomar 14

    CERN Document Server

    Caliskan, S; Grebel, K E

    2011-01-01

    We determine the elemental abundances of nine red giant stars belonging to Palomar 14 (Pal 14). Pal 14 is an outer halo globular cluster (GC) at a distance of \\sim 70 kpc. Our abundance analysis is based on high-resolution spectra and one-dimensional stellar model atmospheres.We derived the abundances for the iron peak elements Sc, V, Cr, Mn, Co, Ni, the {\\alpha}-elements O, Mg, Si, Ca, Ti, the light odd element Na, and the neutron-capture elements Y, Zr, Ba, La, Ce, Nd, Eu, Dy, and Cu. Our data do not permit us to investigate light element (i.e., O to Mg) abundance variations. The neutron-capture elements show an r-process signature. We compare our measurements with the abundance ratios of inner and other outer halo GCs, halo field stars, GCs of recognized extragalactic origin, and stars in dwarf spheroidal galaxies (dSphs). The abundance pattern of Pal 14 is almost identical to those of Pal 3 and Pal 4, the next distant members of the outer halo GC population after Pal 14. The abundance pattern of Pal 14 is...

  17. 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.

  18. Geographical Range and Local Abundance of Tree Species in China

    Science.gov (United States)

    Ren, Haibao; Condit, Richard; Chen, Bin; Mi, Xiangcheng; Cao, Min; Ye, Wanhui; Hao, Zhanqing; Ma, Keping

    2013-01-01

    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 km2, and >90% of 651 species had ranges >105 km2. 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. PMID:24130772

  19. Model reduction for stochastic chemical systems with abundant species

    Science.gov (United States)

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-01

    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.

  20. Relative nuclei abundance inside the International Space Station

    Science.gov (United States)

    Larsson, Oscar

    2012-07-01

    The Sileye3/Alteino experiment was first operational on-board the International Space Station, ISS, 27 April 2002. From 2006 through 2009 it was activated for long duration measurements of relative particle abundance as part of the ESA ALTCRISS project. Measuring the relative abundance of different nuclei species inside the ISS gives important clues as to how the known cosmic ray spectrum outside the space station changes when traversing the hull, i.e. giving indications as to how the hadronic interactions in the hull gives rise to changes in the expected radiation environment for the astronauts, which is of great interest for risk assessments for future long duration deep space missions. In our work the relative abundance for nuclei species with energies above ≃ 60 MeV/n and 5 ≤ Z ≤ 26 are presented for different places and detector orientations inside the ISS, also with and without shielding of the detector. What can be seen when comparing with the relative abundance of nuclei in the cosmic rays, is a significant difference in abundance for odd Z nuclei, whereas even numbered are in better agreement. Odd Z nuclei are much more abundant inside the ISS. This is an update from our previous report with increased statistics and with relative abundance on more nuclei.

  1. 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.

  2. Label-free quantitative proteomics for the extremely thermophilic bacterium Caldicellulosiruptor obsidiansis reveal distinct abundance patterns upon growth on cellobiose, crystalline cellulose, and switchgrass.

    Science.gov (United States)

    Lochner, Adriane; Giannone, Richard J; Keller, Martin; Antranikian, Garabed; Graham, David E; Hettich, Robert L

    2011-12-01

    Mass spectrometric analysis of Caldicellulosiruptor obsidiansis cultures grown on four different carbon sources identified 65% of the cells' predicted proteins in cell lysates and supernatants. Biological and technical replication together with sophisticated statistical analysis were used to reliably quantify protein abundances and their changes as a function of carbon source. Extracellular, multifunctional glycosidases were significantly more abundant on cellobiose than on the crystalline cellulose substrates Avicel and filter paper, indicating either disaccharide induction or constitutive protein expression. Highly abundant flagellar, chemotaxis, and pilus proteins were detected during growth on insoluble substrates, suggesting motility or specific substrate attachment. The highly abundant extracellular binding protein COB47_0549 together with the COB47_1616 ATPase might comprise the primary ABC-transport system for cellooligosaccharides, while COB47_0096 and COB47_0097 could facilitate monosaccharide uptake. Oligosaccharide degradation can occur either via extracellular hydrolysis by a GH1 β-glycosidase or by intracellular phosphorolysis using two GH94 enzymes. When C. obsidiansis was grown on switchgrass, the abundance of hemicellulases (including GH3, GH5, GH51, and GH67 enzymes) and certain sugar transporters increased significantly. Cultivation on biomass also caused a concerted increase in cytosolic enzymes for xylose and arabinose fermentation.

  3. Carbon abundances and isotope ratios in 70 bright M giants

    International Nuclear Information System (INIS)

    Approximate carbon abundances and 12C/13C isotope ratios are obtained for 70 M giant stars from intermediate-resolution spectrophotometry of the CO bands near 2.3 μm. A low mean carbon abundance ([C/H]=-0.64±0.29) is obtained, suggesting that standard mixing is insufficient to explain atmospheric abundances in M giants. HR 8795 appears to be exceptionally carbon deficient, and is worthy of further study as a possible weak G-band star descendant. (author)

  4. Carbon abundances and isotope ratios in 70 bright M giants

    Energy Technology Data Exchange (ETDEWEB)

    Lazaro, C. (Inst. de Astrofisica de Canarias, Tenerife (Spain)); Lynas-Gray, A.E. (University Coll., London (UK). Dept. of Physics and Astronomy); Clegg, R.E.S. (Royal Greenwich Observatory, Cambridge (UK)); Mountain, C.M.; Zadrozny, A. (Imperial Coll. of Science and Technology, London (UK))

    1991-03-01

    Approximate carbon abundances and {sup 12}C/{sup 13}C isotope ratios are obtained for 70 M giant stars from intermediate-resolution spectrophotometry of the CO bands near 2.3 {mu}m. A low mean carbon abundance ((C/H)=-0.64+-0.29) is obtained, suggesting that standard mixing is insufficient to explain atmospheric abundances in M giants. HR 8795 appears to be exceptionally carbon deficient, and is worthy of further study as a possible weak G-band star descendant. (author).

  5. 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.

  6. Bacterioplankton abundance and production in Indian Ocean Regions

    Digital Repository Service at National Institute of Oceanography (India)

    Ramaiah, N.; Fernandes, V.; Rodrigues, V.V.; Paul, J.T.; Gauns, M.

    ]. These studies highlight that both bacterioplank- ton abundance and production within different regions of the IO vary seasonally. These studies are useful to note that the bacterial abundance and production are low during north- east monsoon (NEM) (December... for elucidating pelagic food-web dynamics in different regions of the IO. In view of this, a comparative account of abundance and productivity of the Hbac between seasons, regions, and depths (upper 120 m) of the IO is pro- vided in this chapter. 2. STUDY AREA...

  7. Nitrogen and oxygen abundances in the Local Universe

    OpenAIRE

    Vincenzo, Fiorenzo; Belfiore, Francesco; MAIOLINO, Roberto; Matteucci, Francesca; Ventura, Paolo

    2016-01-01

    We present chemical evolution models aimed at reproducing the observed (N/O) vs. (O/H) abundance pattern of star forming galaxies in the Local Universe. We derive gas-phase abundances from SDSS spectroscopy and a complementary sample of low-metallicity dwarf galaxies, making use of a consistent set of abundance calibrations. This collection of data clearly confirms the existence of a plateau in the (N/O) ratio at very low metallicity, followed by an increase of this ratio up to high values as...

  8. A Photometric Method for estimating CNO Abundances in Globular Clusters

    CERN Document Server

    Peat, David; Peat, David; Butler, Raymond

    2002-01-01

    Stromgren indices v and b are combined with broad-band index I, and a new index p, the short wavelength half of the v band, to estimate CN 4215A molecular absorption in a sample of stars in M22. The results have been used to estimate carbon and nitrogen abundances and suggest groups of stars within this cluster, each with a characteristic nitrogen abundance, but with a range of carbon abundances. The results suggest the possibility of stars consisting of material which has undergone CNO recycling two or three times. The method can be subsequently used for other globular clusters.

  9. Ecological niche structure and rangewide abundance patterns of species

    Science.gov (United States)

    Martínez-Meyer, Enrique; Díaz-Porras, Daniel; Peterson, A. Townsend; Yáñez-Arenas, Carlos

    2013-01-01

    Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the ecological niche). We demonstrate consistent negative abundance–ecological distance relationships across all 11 species analysed (turtles to wolves), and that relationships in environmental space are consistently stronger than relationships in geographical space. PMID:23134784

  10. Galactic abundances as a relic neutrino detection scheme

    DEFF Research Database (Denmark)

    Riis, Anna Sejersen; Thomas Zinner, Nikolaj; Hannestad, Steen

    2011-01-01

    to see the effect of NCB processes as a slightly eschewed abundance ratio of selected beta-decaying nuclei. First, the candidates must be chosen so that both the mother and daughter nuclei have a lifetime comparable to that of the Milky Way or the signal could be easily washed out by additional decays...... for 187-Re and 138-La and find that one needs abundance measurements with 24 digit precision in order to detect the effect of relic neutrinos. Or alternatively an enhancement of of the relic neutrino density by a factor of $10^{15}$ to produce an effect within the current abundance measurement precision....

  11. Applications of Yeast Surface Display for Protein Engineering.

    Science.gov (United States)

    Cherf, Gerald M; Cochran, Jennifer R

    2015-01-01

    The method of displaying recombinant proteins on the surface of Saccharomyces cerevisiae via genetic fusion to an abundant cell wall protein, a technology known as yeast surface display, or simply, yeast display, has become a valuable protein engineering tool for a broad spectrum of biotechnology and biomedical applications. This review focuses on the use of yeast display for engineering protein affinity, stability, and enzymatic activity. Strategies and examples for each protein engineering goal are discussed. Additional applications of yeast display are also briefly presented, including protein epitope mapping, identification of protein-protein interactions, and uses of displayed proteins in industry and medicine. PMID:26060074

  12. Functional challenge affects aquaporin mRNA abundance in mouse blastocysts

    DEFF Research Database (Denmark)

    Offenberg, Hanne Kjær; Thomsen, Preben Dybdahl

    2005-01-01

    The aquaporins (AQPs) are a family of channel proteins that facilitate diffusion of water across cell membranes. Three members of the AQP family have been detected in the mouse blastocyst: AQP 3 and 8 are located in the basolateral domain and AQP 9 predominantly in the apical domain of the tropho...... in vivo developed blastocysts. We found that in vitro culture resulted in lower levels of AQP 8, 9, and 11 compared to in vivo development. These experiments show that mouse embryos are capable of regulating AQP mRNA abundances in response to environmental alterations....

  13. Abundance of specific mRNA transcripts impacts hatching success in European eel, Anguilla anguilla L

    DEFF Research Database (Denmark)

    Rozenfeld, Christoffer; Butts, Ian A.E.; Tomkiewicz, Jonna;

    2016-01-01

    MaternalmRNA governs earlyembryonic development in fish and variation in abundance of maternal transcripts may contribute to variation in embryonic survival and hatch success in European eel, Anguilla anguilla. Previous studies have shown that quantities of the maternal gene products β......-tubulin, insulin-like growth factor 2 (igf2), nucleoplasmin (npm2), prohibitin 2 (phb2), phosphatidylinositol glycan biosynthesis class F protein 5 (pigf5), and carnitine O-palmitoyltransferase liver isoform-like 1 (cpt1) are associated with embryonic developmental competence in other teleosts. Here, the relations...... these genes in European eel after the mid-blastula transition, may be needed to sustain embryonic development and hatching success...

  14. Interstrain Variation in Amylase Gene Copy Number and mRNA Abundance in Three Mouse Tissues

    OpenAIRE

    Meisler, Miriam H.; Antonucci, Tammy K.; Treisman, Laurelee O.; Gumucio, Deborah L.; Samuelson, Linda C.

    1986-01-01

    Amylase expression in strain YBR differs in several respects from the standard mouse phenotype. The synthesis of salivary amylase is elevated twofold in YBR mice and the synthesis of pancreatic amylase is reduced to one-half the normal rate. We have compared the concentrations of amylase mRNA in the parotid, liver and pancreas of YBR mice with those in strains A/J and C3H. We observed differences in amylase mRNA abundance which can account for the levels of amylase protein synthesis in the pa...

  15. 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....

  16. Impact of stochastic gas motions on galaxy cluster abundance profiles

    CERN Document Server

    Rebusco, P; Böhringer, H; Forman, W

    2005-01-01

    The impact of stochastic gas motions on the metal distribution in cluster core is evaluated. Peaked abundance profiles are a characteristic feature of clusters with cool cores and abundance peaks are likely associated with the brightest cluster galaxies (BCGs) which dwell in cluster cores. The width of the abundance peaks is however significantly broader than the BCG light distribution, suggesting that some gas motions are transporting metals originating from within the BCG. Assuming that this process can be treated as diffusive and using the brightest X-ray cluster A426 (Perseus) as an example, we estimate that a diffusion coefficient of the order of $2 10^{29} {\\rm cm^2 s^{-1}}$ is needed to explain the width of the observed abundance profiles. Much lower (higher) diffusion coefficients would result in too peaked (too shallow) profiles. Such diffusion could be produced by stochastic gas motions and our analysis provides constraints on the product of their characteristic velocity and their spatial coherence ...

  17. Trek and ECCO: Abundance measurements of ultraheavy galactic cosmic rays

    International Nuclear Information System (INIS)

    Using the Trek detector, we have measured the abundances of the heaviest elements (with Z>70) in the galactic cosmic rays with sufficient charge resolution to resolve the even-Z elements. We find that the abundance of Pb compared to Pt is ∼3 times lower than the value expected from the most widely-held class of models of the origin of galactic cosmic ray nuclei, that is, origination in a partially ionized medium with solar-like composition. The low abundance of Pb is, however, consistent with the interstellar gas and dust model of Meyer, Drury and Ellison, and with a source enriched in r-process material, proposed by Binns et al. A high-resolution, high-statistics measurement of the abundances of the individual actinides would distinguish between these models. This is the goal of ECCO, the Extremely Heavy Cosmic-ray Composition Observer, which we plan to deploy on the International Space Station

  18. The Helium abundance problem and non-minimally coupled quintessence

    OpenAIRE

    Chen, Xuelei

    2000-01-01

    There is a tension between observed Helium abundance and the prediction of the standard Big Bang Nucleosynthesis. We show that non-minimally quintessence model may help to reduce this tension between theory and observation.

  19. 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...

  20. 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...

  1. Abundance of bacterial and diatom fouling on various surfaces

    Digital Repository Service at National Institute of Oceanography (India)

    PrabhaDevi

    Abundance of bacterial and diatom fouling on aluminium, fibreglass and stainless steel were studied from Dona Paula waters of the Zuari Estuary. Both these forms were reversibly attached in large numbers to surfaces during the initial 24 hr...

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

    International Nuclear Information System (INIS)

    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

  3. 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).

  4. 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...

  5. 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...

  6. 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

  7. Method for measuring the heavy stripped ion abundances of plasma

    International Nuclear Information System (INIS)

    A description is given of a system which uses a velocity filter and an energy filter in tandem to analyze the abundances and energy spreads of highly stripped ions. The system can also serve as a plasma diagnostic. (Auth.)

  8. Seabird abundance and behavior on Cape Peirce, Alaska, 1985

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report covers the seabird abundance and behavior on Cape Peirce on Togiak National Wildlife Refuge. Methods and results are discussed. Species covered include...

  9. Investigating Detailed Abundance Patterns in the Hyades Cluster

    Science.gov (United States)

    Williams, Drake; Schuler, Simon C.

    2016-01-01

    We have derived the paramters and abundances of up to 17 elements for seven stars within the Hyades open star cluster, through an analysis of high-resolution, high signal-to-noise ratio spectra obtained via the Harlan J. Smith 2.7 m telescope and the 2dcoude cross-dispersed echelle spectrometer at the McDonald Observatory. Four of the stars are solar-type dwarves while three giants were also analyzed to better calculate an overall metallicity of the entire cluster. In addition, we investigated whether there are differences in various stellar abundance trends across the open cluster. Here we present the results of our abundance analysis and stellar parameter derivations of the seven stars and discuss the implications of stellar abundance patterns across star clusters. We acknowledge support provided by grant NNX12AD19G to S.C.S. from the National Aeronautics and Space Administration as part of the Kepler Participating Scientist Program.

  10. Urban Warming Drives Insect Pest Abundance on Street Trees

    OpenAIRE

    Meineke, Emily K.; Robert R Dunn; Sexton, Joseph O.; Frank, Steven D.

    2013-01-01

    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 c...

  11. Regularity underlies erratic population abundances in marine ecosystems

    OpenAIRE

    Sun, Jie; Cornelius, Sean P.; Janssen, John; Gray, Kimberly A.; Motter, Adilson E.

    2015-01-01

    The abundance of a species' population in an ecosystem is rarely stationary, often exhibiting large fluctuations over time. Using historical data on marine species, we show that the year-to-year fluctuations of population growth rate obey a well-defined double-exponential (Laplace) distribution. This striking regularity allows us to devise a stochastic model despite seemingly irregular variations in population abundances. The model identifies the effect of reduced growth at low population den...

  12. 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.

  13. 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.

  14. An Extension of the Abundancy Index to Certain Quadratic Rings

    OpenAIRE

    Defant, Colin

    2015-01-01

    We begin by introducing an extension of the traditional abundancy index to imaginary quadratic rings with unique factorization. After showing that many of the properties of the traditional abundancy index continue to hold in our extended form, we investigate what we call $n$-powerfully solitary numbers in these rings. This definition serves to extend the concept of solitary numbers, which have been defined and studied in the integers. We end with some open questions and a conjecture.

  15. 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.

  16. Zooplankton composition and abundance in Mida Creek, Kenya

    OpenAIRE

    Osore, M.K.W.; Mwaluma, J.M.; FIERS, F; Daro, M.H.

    2004-01-01

    In order to determine the resident assemblages of zooplankton in Mida Creek, Kenya, a survey was conducted from May 1996 to Apr. 1997 for which we studied their seasonal composition, abundance, and distribution. Twenty-seven major zooplankton taxa were identified. The order Copepoda was the most abundant taxon dominated mainly by the genera Acartia, Paracalanus, Labidocera, Temora, Centropages, and Calanopia. Other common zooplankton taxa included the Medusae, Ctenophora, Brachyura larvae, an...

  17. 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.

  18. Ruthenium and hafnium abundances in giant and dwarf barium stars

    CERN Document Server

    Allen, D M

    2007-01-01

    We present abundances for Ru and Hf, compare them to abundances of other heavy elements, and discuss the problems found in determining Ru and Hf abundances with laboratory gf-values in the spectra of barium stars. We determined Ru and Hf abundances in a sample of giant and dwarf barium stars, by the spectral synthesis of two RuI (4080.574A and 4757.856A) and two HfII (4080.437A and 4093.155A) transitions. The stellar spectra were observed with FEROS/ESO, and the stellar atmospheric parameters lie in the range 4300 < Teff/K < 6500, -1.2 < [Fe/H] <= 0 and 1.4 <= log g < 4.6. The HfII 4080A and the RuI 4758A observed transitions result in a unreasonably high solar abundance, given certain known uncertainties, when fitted with laboratory gf-values. For these two transitions we determined empirical gf-values by fitting the observed line profiles of the spectra of the Sun and Arcturus. For the sample stars, this procedure resulted in a good agreement of Ru and Hf abundances given by the two availa...

  19. 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...

  20. 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.

  1. 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.

  2. The Solar Flare Sulphur Abundance from RESIK Observations

    CERN Document Server

    Sylwester, J; Phillips, K J H; Kuznetsov, V D

    2012-01-01

    The RESIK instrument on {\\em CORONAS-F} spacecraft observed several sulphur X-ray lines in three of its four channels covering the wavelength range 3.8-6.1 \\AA\\ during solar flares. The fluxes are analyzed to give the sulphur abundance. Data are chosen for when the instrument parameters were optimized. The measured fluxes of the \\ion{S}{15} $1s^2-1s4p$ ($w4$) line at 4.089 \\AA\\ gives $A({\\rm S}) = 7.16 \\pm 0.17$ (abundances on a logarithmic scale with $A({\\rm H}) = 12$) which we consider to be the most reliable. Estimates from other lines range from 7.13 to 7.24. The preferred S abundance estimate is very close to recent photospheric abundance estimates and to quiet-Sun solar wind and meteoritic abundances. This implies no fractionation of sulphur by processes tending to enhance the coronal abundance from the photospheric that depend on the first ionization potential (FIP), or that sulphur, though its FIP has an intermediate value of 10.36 eV, acts like a "high-FIP" element.

  3. 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.

  4. 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.

  5. 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

  6. Cassette Series Designed for Live-Cell Imaging of Proteins and High Resolution Techniques in Yeast

    OpenAIRE

    Young, Carissa L.; Raden, David L.; Caplan, Jeffrey; Czymmek, Kirk; Robinson, Anne S.

    2012-01-01

    During the past decade, it has become clear that protein function and regulation are highly dependent upon intracellular localization. Although fluorescent protein variants are ubiquitously used to monitor protein dynamics, localization, and abundance; fluorescent light microscopy techniques often lack the resolution to explore protein heterogeneity and cellular ultrastructure. Several approaches have been developed to identify, characterize, and monitor the spatial localization of proteins a...

  7. HEAT SHOCK PROTEINS IN DIABETES AND WOUND HEALING

    OpenAIRE

    Atalay, Mustafa; Oksala, Niku; Lappalainen, Jani; David E Laaksonen; Sen, Chandan K.; Roy, Sashwati

    2009-01-01

    The heat shock proteins (HSPs), originally identified as heat-inducible gene products, are a highly conserved family of proteins that respond to a wide variety of stress. Although HSPs are among the most abundant intracellular proteins, they are expressed at low levels under normal physiological conditions, and show marked induction in response to various stressors. HSPs function primarily as molecular chaperones, facilitating the folding of other cellular proteins, preventing protein aggrega...

  8. Applications of yeast surface display for protein engineering

    OpenAIRE

    Cherf, Gerald M.; Cochran, Jennifer R.

    2015-01-01

    The method of displaying recombinant proteins on the surface of Saccharomyces cerevisiae via genetic fusion to an abundant cell wall protein, a technology known as yeast surface display, or simply, yeast display, has become a valuable protein engineering tool for a broad spectrum of biotechnology and biomedical applications. This review focuses on the use of yeast display for engineering protein affinity, stability, and enzymatic activity. Strategies and examples for each protein engineering ...

  9. 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.

  10. Temperature-induced transitions in disordered proteins probed by NMR spectroscopy

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Poulsen, Flemming Martin; Kragelund, Birthe Brandt

    2012-01-01

    Intrinsically disordered proteins are abundant in nature and perform many important physiological functions. Multidimensional NMR spectroscopy has been crucial for the understanding of the conformational properties of disordered proteins and is increasingly used to probe their conformational ense...

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

    Science.gov (United States)

    Meineke, Emily K; Dunn, Robert R; Sexton, Joseph O; Frank, Steven D

    2013-01-01

    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. PMID:23544087

  12. 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., III; 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

  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. Is abundance a species attribute? An example with haematophagous ectoparasites.

    Science.gov (United States)

    Krasnov, Boris R; Shenbrot, Georgy I; Khokhlova, Irina S; Poulin, Robert

    2006-11-01

    Population density is a fundamental property of a species and yet it varies among populations of the same species. The variation comes from the interplay between intrinsic features of a species that tend to produce repeatable density values across all populations of the same species and extrinsic environmental factors that differ among localities and thus tend to produce spatial variation in density. Is inter-population variation in density too large for density to be considered a true species character? We addressed this question using data on abundance (number of parasites per individual host, i.e. equivalent to density) of fleas ectoparasitic on small mammals. The data included samples of 548 flea populations, representing 145 flea species and obtained from 48 different geographical regions. Abundances of the same flea species on the same host species, but in different regions, were more similar to each other than expected by chance, and varied significantly among flea species, with 46% of the variation among samples accounted by differences between flea species. Thus, estimates of abundance are repeatable within the same flea species. The same repeatability was also observed, but to a lesser extent, across flea genera, tribes and subfamilies. Independently of the identity of the flea species, abundance values recorded on the same host species, or in the same geographical region, also showed significant statistical repeatability, though not nearly as strong as that associated with abundance values from the same flea species. There were also no strong indications that regional differences in abiotic variables were an important determinant of variation in abundance of a given flea species on a given host species. Abundance thus appears to be a true species trait in fleas, although it varies somewhat within bounds set by species-specific life history traits. PMID:16896773

  15. 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.

  16. 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.

  17. 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. PMID:22187521

  18. 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.

  19. 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.

  20. 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

  1. [Effects of sewage discharge on abundance and biomass of meiofauna].

    Science.gov (United States)

    Huang, De-Ming; Liu, Xiao-Shou; Lin, Ming-Xian; Chen, Huai-Pu; Wei, Lian-Ming; Huang, Xin; Zhang, Zhi-Nan

    2014-10-01

    In order to elucidate the effects of sewage discharge on abundance and biomass of meio- fauna, a seasonal survey was carried out on meiofauna at stations with different distances to a sewage outlet in the middle intertidal zone of No. 1 bathing beach in Huiquan Bay, Qingdao in spring (April), summer (August), autumn (October) and winter (December), 2011. The results showed that the annual average meiofaunal abundance was (1859.9 ± 705.1) ind · 10 cm(-2), with higher values of (2444.9 ± 1220.5) ind · 10 cm(-2) at Station S2 (20 m to the sewage outlet) and (2492.2 ± 1839.9) ind · 10 cm(-2) at Station S3 (40 m to the sewage outlet), while the lowest value of (327.9 ± 183.2) ind · 10 cm(-2) was observed at Station S1 (0 m to the sewage outlet) in terms of horizontal distribution. The annual average biomass was (1513.4 ± 372.7) μg · 10 cm(-2). Meiofaunal abundance and biomass varied seasonally with the highest values in spring and the lowest values in summer. A total of 11 meiofaunal groups were identified, including nematodes, copepods, polychaetes, oligochaetes, tardigrades, halacaroideans, planarians, ostracods, isopods, crustacean nauplii and others. Free-living marine nematodes were the dominant group constituting 83. 1% of the total abundance, followed by benthic copepods, accounting for 12. 8% of the total abundance. In terms of vertical distribution, most of the meiofauna concentrated in the top 0-2 cm, and the meiofauna abundance decreased with increasing the sediment depth. Meiofauna was also noted to migrate deeper into the sediment in the winter. Pearson correlation analysis showed that meiofaunal abundance and biomass had highly significant negative correlations with sediment median particle diameter and organic matter content. In addition, tourism-induced activities affected meiofaunal abundance and distribution. A comparison with historical data from similar studies was carried out, and the applicability of the ratio of abundance of nematodes

  2. 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.

  3. 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.

  4. 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. PMID:26140532

  5. Analysis and modeling of scale-invariance in plankton abundance

    CERN Document Server

    Pelletier, J D

    1996-01-01

    The power spectrum, $S$, of horizontal transects of plankton abundance are often observed to have a power-law dependence on wavenumber, $k$, with exponent close to $-2$: $S(k)\\propto k^{-2}$ over a wide range of scales. I present power spectral analyses of aircraft lidar measurements of phytoplankton abundance from scales of 1 to 100 km. A power spectrum $S(k)\\propto k^{-2}$ is obtained. As a model for this observation, I consider a stochastic growth equation where the rate of change of plankton abundance is determined by turbulent mixing, modeled as a diffusion process in two dimensions, and exponential growth with a stochastically variable net growth rate representing a fluctuating environment. The model predicts a lognormal distribution of abundance and a power spectrum of horizontal transects $S(k)\\propto k^{-1.8}$, close to the observed spectrum. The model equation predicts that the power spectrum of variations in abundance in time at a point in space is $S(f)\\propto f^{-1.5}$ (where $f$ is the frequency...

  6. 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...

  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. 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.

  9. 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 ...

  10. 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...

  11. 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) ...

  12. 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.

  13. 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.

  14. Elemental abundances variations in plume and interplume regions

    Science.gov (United States)

    Guennou, Chloé; Savin, Daniel; Hahn, Michael

    2016-07-01

    Plumes are relatively bright, narrow structures in coronal holes that extend along open magnetic field lines far out into the corona. Extensive coronal measurements show abundances anomalies in the solar corona, in which elements with a low first ionization potential (FIP) Remote sensing spectroscopic measurements show that interplume regions have a photospheric composition. In contrast, the elemental composition of plume material is still unclear, previous spectroscopic measurements have reached contradictory results as to whether the elemental abundances in plumes are the same as or different from interplume regions. In this work, we measured the FIP bias, i.e. the ratio of coronal to photospheric abundances, in both interplumes and plumes using Hinode/Extreme Ultraviolet Imaging Spectrometer (EIS) data. Using spectral line intensities and Differential Emission Measure analysis, we assess the chemical composition of plumes and interplumes over an ~24 hour period in March, 2007. We find that some plumes do show different elemental abundances relative to interplumes. Moreover, the abundance anomaly in plumes is time dependent. If previous studies observed plumes at different stages in their evolution, this time dependence may explain the lack of consistency among previous results. Our work on plume and interplume elemental composition may also enable in situ measurements to answer the longstanding question of whether plumes contribute to the fast solar wind, which originates from coronal holes.

  15. 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.

  16. Beryllium abundances in stars with planets:Extending the sample

    CERN Document Server

    Gálvez-Ortiz, M C; Hernández, J I González; Israelian, G; Santos, N C; Rebolo, R; Ecuvillon, A

    2011-01-01

    Context: Chemical abundances of light elements as beryllium in planet-host stars allow us to study the planet formation scenarios and/or investigate possible surface pollution processes. Aims: We present here an extension of previous beryllium abundance studies. The complete sample consists of 70 stars hosting planets and 30 stars without known planetary companions. The aim of this paper is to further assess the trends found in previous studies with less number of objects. This will provide more information on the processes of depletion and mixing of light elements in the interior of late type stars, and will provide possible explanations for the abundance differences between stars that host planets and "single" stars. Methods: Using high resolution UVES spectra, we measure beryllium abundances of 26 stars that host planets and 1 "single" star mainly using the \\lambda 3131.065 A Be II line, by fitting synthetic spectra to the observational data. We also compile beryllium abundance measurements of 44 stars hos...

  17. 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...

  18. Effect of disjunct size distributions on foraminiferal species abundance determinations

    Energy Technology Data Exchange (ETDEWEB)

    Martin, R.E.; Liddell, W.D.

    1988-02-01

    Studies of foraminiferal distribution and abundance have typically employed a procedure (standard method) that entails counting approximately 300 specimens from a size range greater than some specified minimum (commonly 63 or 125 ..mu..m). This method fails to take into account that foraminifera may be found only within certain size fractions, either because of species specific size ranges or taphonomic processes (sorting, transport, abrasion). Use of a modified counting procedure (sieve method) takes into account foraminiferal size distributions. The sieve method uses counts of up to 300 specimens in each sand-size fraction (0.125-0.25, 0.25-0.5, 0.5-1, 1-2 mm) of each sample. Counts are then totaled for each sample (up to 1200 specimens per site) and used in determination of species abundances for each site. The sieve method has been of considerable utility in recognition of a foraminiferal bathymetric zonation preserved in sediment assemblages from fringing reef environments at Discovery Bay, north Jamaica. Well-documented reef zones (based on corals and physiography) are clearly defined in Q-mode cluster analysis (UPGMA) of species abundances determined using the sieve method. In contrast, individual fore reef zones are not recognized in cluster analysis of foraminiferal species abundances based on the standard method, nor by cluster analysis of species abundances within individual size fractions.

  19. 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

  20. 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.

  1. 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

  2. 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...

  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. Resolving microbial membership using Abundance and Variability In Taxonomy ('AVIT ).

    Science.gov (United States)

    Chakrabarti, Anirikh; Siddharth, Jay; Lauber, Christian L; Membrez, Mathieu; Betrisey, Bertrand; Loyer, Carole; Chou, Chieh Jason; Pataky, Zoltan; Golay, Alain; Parkinson, Scott J

    2016-01-01

    Development of NGS has revolutionized the analysis in microbial ecology contributing to our deeper understanding of microbiota in health and disease. However, the quality, quantity and confidence of summarized taxonomic abundances are in need of further scrutiny due to sample dependent and independent effects. In this article we introduce 'AVIT (Abundance and Variability In Taxonomy), an unbiased method to enrich for assigned members of microbial communities. As opposed to using a priori thresholds, 'AVIT uses inherent abundance and variability of taxa in a dataset to determine the inclusion or rejection of each taxa for further downstream analysis. Using in-vitro and in-vivo studies, we benchmarked performance and parameterized 'AVIT to establish a framework for investigating the dynamic range of microbial community membership in clinically relevant scenarios. PMID:27530237

  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. Ammonia abundance in the coma of Halley's Comet

    International Nuclear Information System (INIS)

    Consideration is given to recent work by Allen et al. (1987) which suggests that the value of the ratio of the abundance of the atomic masses 19 to 18 observed in situ in the inner coma of Comet Halley is incompatible with a pure H2O nucleus and requires an NH3 abundance of 1-2 percent. The present authors discuss possible ways of explaining the radial profile of r = 19/18, which deemphasizes the presence of NH3. It is shown that the observed value of the 19/18 mass ratio in the inner coma does not necessarily imply the existence of a significant abundance of NH3. An elevated UV flux, for which there is circumstantial evidence, could produce the same effect. 21 references

  7. 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...

  8. 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...

  9. 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 ...

  10. The abundant world: Paul Feyerabend's metaphysics of science.

    Science.gov (United States)

    Brown, Matthew J

    2016-06-01

    The goal of this paper is to provide an interpretation of Feyerabend's metaphysics of science as found in late works like Conquest of Abundance and Tyranny of Science. Feyerabend's late metaphysics consists of an attempt to criticize and provide a systematic alternative to traditional scientific realism, a package of views he sometimes referred to as "scientific materialism." Scientific materialism is objectionable not only on metaphysical grounds, nor because it provides a poor ground for understanding science, but because it implies problematic claims about the epistemic and cultural authority of science, claims incompatible with situating science properly in democratic societies. I show how Feyerabend's metaphysical view, which I call "the abundant world" or "abundant realism," constitute a sophisticated and challenging form of ontological pluralism that makes interesting connections with contemporary philosophy of science and issues of the political and policy role of science in a democratic society. PMID:27269274

  11. Revised element abundances for WC-type central stars

    CERN Document Server

    Todt, H; Hamann, W -R

    2007-01-01

    According to previous spectral analyses of Wolf-Rayet type central stars, late [WC] subtypes show systematically higher carbon-to-helium abundance ratios than early [WC] subtypes. If this were true, it would rule out that these stars form an evolutionary sequence. However, due to the different parameter domains and diagnostic lines, one might suspect systematic errors being the source of this discrepancy. In an ongoing project we are therefore checking the [WC] analyses by means of the last generation of non-LTE models for expanding stellar atmospheres which account for line-blanketing and wind clumping. So far, the abundance discrepancy is not resolved. Further element abundances (H, N, Fe) are determined and compared with evolutionary predictions.

  12. Diversity is maintained by seasonal variation in species abundance

    Science.gov (United States)

    2013-01-01

    Background Some of the most marked temporal fluctuations in species abundances are linked to seasons. In theory, multispecies assemblages can persist if species use shared resources at different times, thereby minimizing interspecific competition. However, there is scant empirical evidence supporting these predictions and, to the best of our knowledge, seasonal variation has never been explored in the context of fluctuation-mediated coexistence. Results Using an exceptionally well-documented estuarine fish assemblage, sampled monthly for over 30 years, we show that temporal shifts in species abundances underpin species coexistence. Species fall into distinct seasonal groups, within which spatial resource use is more heterogeneous than would be expected by chance at those times when competition for food is most intense. We also detect seasonal variation in the richness and evenness of the community, again linked to shifts in resource availability. Conclusions These results reveal that spatiotemporal shifts in community composition minimize competitive interactions and help stabilize total abundance. PMID:24007204

  13. 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...

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. The Iron Abundance of IOTA Herculis From Ultraviolet Iron Lines

    Science.gov (United States)

    Grigsby, J.; Mulliss, C.; Baer, G.

    1995-03-01

    We have obtained (Adelman 1992, 1993, private comunication) coadded, high-resolution IUE spectra of Iota Herculis (B3 IV) in both short wavelength (SWP) and long wavelength (LWP) regions. The spectra span the ultraviolet spectrum from 110 - 300 nm and have a SNR of roughly 30 -50; they are described in Adelman et. al. (1993, ApJ 419, 276). Abundance indicators were 54 lines of Fe II and 26 lines of Fe III whose atomic parameters have been measured in the laboratory. LTE synthetic spectra for comparison with observations were produced with the Kurucz model atmosphere and spectral synthesis codes ATLAS9/SYNTHE (Kurucz 1979, ApJS 40,1; Kurucz and Avrett 1981, SAO Special Report 391). Model parameters were chosen from the literature: effective temperature = 17500 K, log g =3.75, v sin i= 11 km/s, and turbulent velocity = 0 km/s. (Peters and Polidan 1985, in IAU Symposium 111, ed. D. S. Hayes et al. (Dordrecht: Reidel), 417). We determined the equivalent widths of the chosen lines by fitting gaussian profiles to the lines and by measuring the equivalent widths of the gaussians. We derived abundances by fitting a straight line to a plot of observed equivalent widths vs. synthetic equivalent widths; we adjusted the iron abundance of the models until a slope of unity was achieved. The abundances derived from the different ionization stages are in agreement: Fe II lines indicate an iron abundance that is 34 +15/-10% the solar value([Fe/H]=-0.47 +0.16-0.15dex), while from Fe III lines we obtain 34 +/- 10% ([Fe/H]=-0.47 +0.11/-0.15 dex). A search of the literature suggests that no previous investigations of this star's iron abundance have found agreement between the different ionization stages. We thank Saul Adelman for his generous assistance, and the Faculty Research Fund Board of Wittenberg University for support of this research.

  20. OsLEA1a, a New Em-Like Protein of Cereal Plants

    NARCIS (Netherlands)

    Shih, M.D.; Huang, L.T.; Wei, F.J.; Wu, M.T.; Hoekstra, F.A.; Hsing, Y.I.C.

    2010-01-01

    Proteins abundant in seeds during the late stages of development, late embryogenesis abundant (LEA) proteins, are associated with desiccation tolerance. More than 100 of the group I LEA genes, also termed Em genes, have been identified from plants, bacteria and animals. The wide distribution indicat

  1. 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.

  2. 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.

  3. HD 209621: Abundances of neutron-capture elements

    OpenAIRE

    Goswami, Aruna; Aoki, Wako

    2010-01-01

    High resolution spectra obtained from the Subaru Telescope High Dispersion Spectrograph have been used to update the stellar atmospheric parameters and metallicity of the star HD 209621. We have derived a metallicity of [Fe/H] = -1.93 for this star, and have found a large enhancement of carbon and of heavy elements, with respect to iron. Updates on the elemental abundances of four s-process elements (Y, Ce, Pr, Nd) along with the first estimates of abundances for a number of other heavy eleme...

  4. 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.

  5. 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.

  6. 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.

  7. 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...

  8. How Does Abundant Display Space Support Data Analysis?

    DEFF Research Database (Denmark)

    Knudsen, Søren

    This thesis explores information visualizations on large, high-resolution touch displays for analysis of massive amounts of data. The ever increasing rate at which data is collected about everything from peoples’ health, over organisations expenditures, to scientific experiments, necessitates new...... data analysis techniques. Information visualizations on large, high-resolution touch displays is a promising answer to these needs, and provide abundant display space for people to make sense of data. However, little is known about how to tailor interactive visualizations to abundant display space or...

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

    OpenAIRE

    Martínez de la Puente, Josué; Merino, Santiago; Tomás, Gustavo; Morales, Judith; Lobato, Elisa; Talavera, Salvador; Sarto i Monteys, V.

    2009-01-01

    Mechanisms affecting patterns of vector distribution among host individuals may influence the population and evol- utionary 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, ...

  10. Bulk eutectic Cu–Ag alloys with abundant twin boundaries

    International Nuclear Information System (INIS)

    Abundant growth twin boundaries are found and characterized in two bulk eutectic Cu–Ag alloys that can be obtained conveniently. The statistical electron backscattering diffraction results show that both hetero-twin and cube-on-cube orientation relationships coexist in the eutectic Cu–Ag alloy. The tensile strength of the eutectic alloy increases with a decrease in the layer thickness of the Cu/Ag phase. This study provides a potential way to produce bulk eutectic Cu–Ag alloy with abundant twin boundaries that offers a combination of high strength and high ductility.

  11. Species abundance patterns : the problem of testing stochastic models

    OpenAIRE

    Bersier, Louis-Félix; Sugihara, George

    2009-01-01

    1. Tokeshi (1990) proposed a goodness-of-fit test to distinguish among a general class of stochastic species abundance models using field data. This test is a good first step, but it is impaired by some shortcomings: there is no adjustment for the number of species (the rejection rate increases with the number of species in a data set); the variance of the generated abundance distributions are not taken into account (data sets with higher variance than a model are not rejected). 2. We pro...

  12. 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.

  13. Cellulose synthase interacting protein: A new factor in cellulose synthesis

    OpenAIRE

    Gu, Ying; Somerville, Chris

    2010-01-01

    Cellulose is the most abundant biopolymer on earth. The great abundance of cellulose places it at the forefront as a primary source of biomass for renewable biofuels. However, the knowledge of how plant cells make cellulose remains very rudimentary. Cellulose microfibrils are synthesized at the plasma membrane by hexameric protein complexes, also known as cellulose synthase complexes. The only known components of cellulose synthase complexes are cellulose synthase (CESA) proteins until the re...

  14. DISTINCTIVE LOCALIZATION OF GROUP 3 LATE EMBRYOGENESIS ABUNDANT SYNTHESIZING CELLS DURING BRINE SHRIMP DEVELOPMENT.

    Science.gov (United States)

    Kim, Bo Yong; Song, Hwa Young; Kim, Mi Young; Lee, Bong Hee; Kim, Kyung Joo; Jo, Kyung Jin; Kim, Suhng Wook; Lee, Seung Gwan; Lee, Boo Hyung

    2015-07-01

    Despite numerous studies on late embryogenesis abundant (LEA) proteins, their functions, roles, and localizations during developmental stages in arthropods remain unknown. LEA proteins protect crucial proteins against osmotic stress during the development and growth of various organisms. Thus, in this study, fluorescence in situ hybridization was used to determine the crucial regions protected against osmotic stress as well as the distinctive localization of group 3 (G3) LEA(+) cells during brine shrimp development. Several cell types were found to synthesize G3 LEA RNA, including neurons, muscular cells, APH-1(+) cells, and renal cells. The G3 LEA(+) neuronal cell bodies outside of the mushroom body projected their axonal bundles to the central body, but those inside the mushroom body projected their axonal bundles toward the deutocerebrum without innervating the central body. The cell bodies inside the mushroom body received axons of the G3 LEA(+) sensory cells at the medial ventral cup of the nauplius eye. Several glands were found to synthesize G3 LEA RNA during the nauplius stages of brine shrimp, including the sinus, antennal I and II, salt, and three ectodermal glands. This study provides the first demonstration of the formation of G3 LEA(+) sinus glands at the emergence stages of brine shrimp. These results suggest that G3 LEA protein is synthesized in several cell types. In particular, specific glands play crucial roles during the emergence and nauplius stages of brine shrimp. PMID:25781424

  15. 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.

  16. 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

  17. Abundances of 30 elements in 23 metal-poor stars

    CERN Document Server

    Johnson, J A

    2002-01-01

    We report the abundances of 30 elements in 23 metal-poor ([Fe/H] 0.10 dex, the relative abundances, especially between closely allied atoms such as the rare earth group, often show only small (<0.03 dex) changes. We found that some strong lines of FeI, MnI and CrI consistently gave lower abundances by ~0.2 dex, a number larger than the quoted errors in the gf values. After considering a model with depth-dependent microturbulent velocity and a model with hotter temperatures in the upper layers, we conclude that the latter did a better job of resolving the problem and agreeing with observational evidence for the structure of stars. The error analysis includes the effects of correlation of Teff, log g, and microturbulent velocity errors, which is crucial for certain element ratios, such as [Mg/Fe]. The abundances presented here are being analyzed and discussed in a separate series of papers.

  18. "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…

  19. Abundance analysis of s-process enhanced barium stars

    Science.gov (United States)

    Mahanta, Upakul; Karinkuzhi, Drisya; Goswami, Aruna; Duorah, Kalpana

    2016-08-01

    Detailed chemical composition studies of stars with enhanced abundances of neutron-capture elements can provide observational constraints for neutron-capture nucleosynthesis studies and clues for understanding their contribution to the Galactic chemical enrichment. We present abundance results from high-resolution spectral analyses of a sample of four chemically peculiar stars characterized by s-process enhancement. High-Resolution spectra (R ˜42000) of these objects spanning a wavelength range from 4000 to 6800 Å, are taken from the ELODIE archive. We have estimated the stellar atmospheric parameters, the effective temperature Teff, the surface gravity log g, and metallicity [Fe/H] from local thermodynamic equilibrium analysis using model atmospheres. We report estimates of elemental abundances for several neutron-capture elements, Sr, Y, Zr, Ba, La, Ce, Pr, Nd, Sm, Eu and Dy. While HD 49641 and HD 58368 show [Ba/Fe] ≥ 1.16 the other two objects HD 119650 and HD 191010 are found to be mild barium stars with [Ba/Fe] ˜ 0.4. The derived abundances of the elements are interpreted on the basis of existing theories for understanding their origin and evolution.

  20. Big Bang Nucleosynthesis and the Observed Abundances of Light Elements

    OpenAIRE

    Hogan, Craig J.

    1996-01-01

    The predictions of Standard Big Bang Nucleosynthesis are summarized and compared with observations of abundances of helium in HII regions, deuterium in quasar absorbers, deuterium and helium-3 in the Galaxy, and lithium in metal-poor stars. It is concluded that the prospects are good for a precise test of the theory.

  1. Invasive lionfish reduce native fish abundance on a regional scale.

    Science.gov (United States)

    Ballew, Nicholas G; Bacheler, Nathan M; Kellison, G Todd; Schueller, Amy M

    2016-01-01

    Invasive lionfish pose an unprecedented threat to biodiversity and fisheries throughout Atlantic waters off of the southeastern United States, the Caribbean, and the Gulf of Mexico. Here, we employ a spatially replicated Before-After-Control-Impact analysis with temporal pairing to quantify for the first time the impact of the lionfish invasion on native fish abundance across a broad regional scale and over the entire duration of the lionfish invasion (1990-2014). Our results suggest that 1) lionfish-impacted areas off of the southeastern United States are most prevalent off-shore near the continental shelf-break but are also common near-shore and 2) in impacted areas, lionfish have reduced tomtate (a native forage fish) abundance by 45% since the invasion began. Tomtate served as a model native fish species in our analysis, and as such, it is likely that the lionfish invasion has had similar impacts on other species, some of which may be of economic importance. Barring the development of a control strategy that reverses the lionfish invasion, the abundance of lionfish in the Atlantic, Caribbean, and Gulf of Mexico will likely remain at or above current levels. Consequently, the effect of lionfish on native fish abundance will likely continue for the foreseeable future. PMID:27578096

  2. 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.

  3. Elemental Abundance Survey of The Galactic Thick Disk

    CERN Document Server

    Reddy, B E; Allende-Prieto, C; Reddy, Bacham E.; Lambert, David L.; Prieto, Carlos Allende

    2006-01-01

    [Abridged abstract] We have performed an abundance analysis for 176 F- and G- dwarfs of the Galactic thick disk component. Using accurate radial velocities combined with $Hipparcos$ astrometry, kinematics (U, V, and W) and Galactic orbital parameters were computed. We estimate the probability for a star to belong to the thin disk, the thick disk or the halo. Abundances of C, O, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Y, Ba, Ce, Nd, and Eu have been obtained. The abundances for thick disk stars are compared with those for thin disk members from Reddy et al. (2003). The ratios of $\\alpha$-elements (O, Mg, Si, Ca and Ti) to iron for thick disk disk stars show a clear enhancement compared to thin disk members in the range $-0.3 <$ [Fe/H] $ < -1.2$. There are also other elements -- Al, Sc, V, Co, and possibly Zn -- which show enhanced ratios to iron in the thick disk relative to the thin disk. The abundances of Na, Cr, Mn, Ni, and Cu (relative to Fe) are very similar for thin and thick dis...

  4. Generating potassium abundance variations in the Solar Nebula

    Science.gov (United States)

    Hubbard, Alexander

    2016-08-01

    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 41K to 39K 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 mid-plane and settled out of the evaporated potassium. While orbital time-scales are at odds with laboratory chondrule cooling rate estimates, any other model for the origin for the potassium abundance variation has to wrestle with the severe logistical difficulty of generating a plethora of correlated reservoirs which varied strongly in their potassium abundances, but not in their potassium isotope ratios.

  5. 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...

  6. 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.

  7. 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)

  8. 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

  9. Pastoral del Nino: Bringing the Abundant Life to Paraguayan Children

    Science.gov (United States)

    Austin, Ann Berghout; Aquino, Cyle; Burro, Elizabeth

    2007-01-01

    Pastoral del Nino is transforming children's lives in rural Paraguay. Part of Pastoral Social (Catholic Social Services), Pastoral del Nino's primary focus is to bring "vida en abundancia" (the abundant life) to families by ensuring that mothers survive childbirth and children reach their first birthdays. In addition, the organization promotes…

  10. Boom in boarfish abundance: insight from otolith analysis

    DEFF Research Database (Denmark)

    Coad, Julie Olivia; Hüssy, Karin

    2012-01-01

    The boarfish Capros aper is a pelagic shoaling species widely distributed along the Northeast Atlantic continental shelf. In recent years, this species has experienced a dramatic boom in abundance in the Bay of Biscay and Celtic Sea. This study aims at resolving the mechanisms responsible for thi...

  11. 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.

  12. 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...

  13. 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 ...

  14. Light element abundances, galactic evolution, and the universal baryon density

    International Nuclear Information System (INIS)

    The present mean universal mean baryon density, rho/sub b/, is of particular interest because, in Friedmann cosmologies with no cosmological constant, it is this quantity together with the Hubble constant, H/sub o/, which determines the spatial curvature of the universe, i.e., whether it is open or closed. The most stringent upper limit to rho/sub b/ so far established comes from the present deuterium abundance. This paper proposes an alternative method to evaluate the range of permissible values of rho/sub b/. The method considers the abundance of both D and 7Li. By utilizing the abundance ratio of 7Li to D, the difficulty associated with the astration process can be essentially canceled from the problem. Further, this method is slightly more sensitive to rho/sub b/ than the method which uses the D abundance alone. The ratio of 7Li to D mass fractions is plotted as a function of the present baryon density for a background temperature of 2.80K. Results are tabulated; they indicate that rho/sub b/ is too small to close the universe by a factor of the order of 5. 1 figure, 1 table

  15. 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.

  16. Cross-scale interactions and the distribution-abundance relationship.

    Science.gov (United States)

    Werner, Earl E; Davis, Christopher J; Skelly, David K; Relyea, Rick A; Benard, Michael F; McCauley, Shannon J

    2014-01-01

    Positive interspecific relationships between local abundance and extent of regional distribution are among the most ubiquitous patterns in ecology. Although multiple hypotheses have been proposed, the mechanisms underlying distribution-abundance (d-a) relationships remain poorly understood. We examined the intra- and interspecific distribution-abundance relationships for a metacommunity of 13 amphibian species sampled for 15 consecutive years. Mean density of larvae in occupied ponds was positively related to number of ponds occupied by species; employing the fraction of ponds uniquely available to each species this same relationship sharply decelerates. The latter relationship suggested that more abundant species inhabited most available habitats annually, whereas rarer species were dispersal limited. We inferred the mechanisms responsible for this pattern based on the dynamics of one species, Pseudacris triseriata, which transitioned between a rare, narrowly distributed species to a common, widely distributed species and then back again. Both transitions were presaged by marked changes in mean local densities driven by climatic effects on habitat quality. We identified threshold densities separating these population regime shifts that differed with landscape configuration. Our data suggest that these transitions were caused by strong cross-scale interactions between local resource/niche processes and larger scale metapopulation processes. The patterns we observed have relevance for understanding the mechanisms of interspecific d-a relationships and critical thresholds associated with habitat fragmentation. PMID:24875899

  17. 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...

  18. Variation of the subhalo abundance in dark matter halos

    CERN Document Server

    Ishiyama, Tomoaki; Makino, Junichiro

    2008-01-01

    We analyzed the statistics of subhalo abundance of galaxy-sized and giant-galaxy-sized halos formed in a high-resolution cosmological simulation of a 46.5Mpc cube with the uniform mass resolution of $10^6 M_{\\odot}$. We analyzed all halos with mass more than $1.5 \\times 10^{12}M_{\\odot}$ formed in this simulation box. The total number of halos was 125. We found that the subhalo abundance, measured by the number of subhalos with maximum rotation velocity larger than 10% of that of the parent halo, shows large halo-to-halo variations. The results of recent ultra-high-resolution runs fall within the variation of our samples. We found that the concentration parameter and the radius at the moment of the maximum expansion shows fairly tight correlation with the subhalo abundance. This correlation suggests that the variation of the subhalo abundance is at least partly due to the difference in the formation history. Halos formed earlier have smaller number of subhalos at present.

  19. Invasive lionfish reduce native fish abundance on a regional scale

    Science.gov (United States)

    Ballew, Nicholas G.; Bacheler, Nathan M.; Kellison, G. Todd; Schueller, Amy M.

    2016-01-01

    Invasive lionfish pose an unprecedented threat to biodiversity and fisheries throughout Atlantic waters off of the southeastern United States, the Caribbean, and the Gulf of Mexico. Here, we employ a spatially replicated Before-After-Control-Impact analysis with temporal pairing to quantify for the first time the impact of the lionfish invasion on native fish abundance across a broad regional scale and over the entire duration of the lionfish invasion (1990–2014). Our results suggest that 1) lionfish-impacted areas off of the southeastern United States are most prevalent off-shore near the continental shelf-break but are also common near-shore and 2) in impacted areas, lionfish have reduced tomtate (a native forage fish) abundance by 45% since the invasion began. Tomtate served as a model native fish species in our analysis, and as such, it is likely that the lionfish invasion has had similar impacts on other species, some of which may be of economic importance. Barring the development of a control strategy that reverses the lionfish invasion, the abundance of lionfish in the Atlantic, Caribbean, and Gulf of Mexico will likely remain at or above current levels. Consequently, the effect of lionfish on native fish abundance will likely continue for the foreseeable future. PMID:27578096

  20. 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.