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Sample records for region-specific protein abundance

  1. Region-specific protein misfolding cyclic amplification reproduces brain tropism of prion strains.

    Science.gov (United States)

    Privat, Nicolas; Levavasseur, Etienne; Yildirim, Serfildan; Hannaoui, Samia; Brandel, Jean-Philippe; Laplanche, Jean-Louis; Béringue, Vincent; Seilhean, Danielle; Haïk, Stéphane

    2017-10-06

    Human prion diseases such as Creutzfeldt-Jakob disease are transmissible brain proteinopathies, characterized by the accumulation of a misfolded isoform of the host cellular prion protein (PrP) in the brain. According to the prion model, prions are defined as proteinaceous infectious particles composed solely of this abnormal isoform of PrP (PrP Sc ). Even in the absence of genetic material, various prion strains can be propagated in experimental models. They can be distinguished by the pattern of disease they produce and especially by the localization of PrP Sc deposits within the brain and the spongiform lesions they induce. The mechanisms involved in this strain-specific targeting of distinct brain regions still are a fundamental, unresolved question in prion research. To address this question, we exploited a prion conversion in vitro assay, protein misfolding cyclic amplification (PMCA), by using experimental scrapie and human prion strains as seeds and specific brain regions from mice and humans as substrates. We show here that region-specific PMCA in part reproduces the specific brain targeting observed in experimental, acquired, and sporadic Creutzfeldt-Jakob diseases. Furthermore, we provide evidence that, in addition to cellular prion protein, other region- and species-specific molecular factors influence the strain-dependent prion conversion process. This important step toward understanding prion strain propagation in the human brain may impact research on the molecular factors involved in protein misfolding and the development of ultrasensitive methods for diagnosing prion disease. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Iron-Restricted Diet Affects Brain Ferritin Levels, Dopamine Metabolism and Cellular Prion Protein in a Region-Specific Manner

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    Jessica M. V. Pino

    2017-05-01

    disorders. Our findings show that nutritional iron deficiency produces these molecular alterations in a region-specific manner and provide new insight into the variety of molecular pathways that can lead to distinct neurological symptoms upon iron deficiency. Thus, adequate iron supplementation is essential for brain health and prevention of neurological diseases.

  3. 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.

  4. Cytoskeletal protein translation and expression in the rat brain are stressor-dependent and region-specific.

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    Petra Sántha

    Full Text Available Stress is an integral component of life that can sometimes cause a critical overload, depending on the qualitative and quantitative natures of the stressors. The involvement of actin, the predominant component of dendritic integrity, is a plausible candidate factor in stress-induced neuronal cytoskeletal changes. The major aim of this study was to compare the effects of three different stress conditions on the transcription and translation of actin-related cytoskeletal genes in the rat brain. Male Wistar rats were exposed to one or other of the frequently used models of physical stress, i.e. electric foot shock stress (EFSS, forced swimming stress (FSS, or psychosocial stress (PSS for periods of 3, 7, 14, or 21 days. The relative mRNA and protein expressions of β-actin, cofilin and mitogen-activated protein kinase 1 (MAPK-1 were determined by qRT- PCR and western blotting from hippocampus and frontal cortex samples. Stressor-specific alterations in both β-actin and cofilin expression levels were seen after stress. These alterations were most pronounced in response to EFSS, and exhibited a U-shaped time course. FSS led to a significant β-actin mRNA expression elevation in the hippocampus and the frontal cortex after 3 and 7 days, respectively, without any subsequent change. PSS did not cause any change in β-actin or cofilin mRNA or protein expression in the examined brain regions. EFSS, FSS and PSS had no effect on the expression of MAPK-1 mRNA at any tested time point. These findings indicate a very delicate, stress type-dependent regulation of neuronal cytoskeletal components in the rat hippocampus and frontal cortex.

  5. Protein abundance profiling of the Escherichia coli cytosol

    DEFF Research Database (Denmark)

    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 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...

  6. Region-specific differences in bioenergetic proteins and protein response to acute high fat diet in brains of low and high capacity runner rats.

    Science.gov (United States)

    Gan, Li; Ma, Delin; Li, Min; Yang, Fu-Chen; Rogers, Robert S; Wheatley, Joshua L; Koch, Lauren G; Britton, Steven L; Thyfault, John P; Geiger, Paige C; Stanford, John A

    2018-05-01

    Aerobic capacity is a strong predictor of mortality. Low capacity runner (LCR) rats exhibit reduced mitochondrial function in peripheral organs. A high fat diet (HFD) can worsen metabolic phenotype in LCR rats. Little is known about metabolic changes in the brains of these rats, however. This study examined protein markers of mitochondrial function and metabolism as a function of aerobic running capacity and an acute HFD in four brain regions: the striatum, hippocampus, hypothalamus, and substantia nigra. After 3 days HFD or chow diets, we measured peroxisome proliferator-activated receptor-γ coactivator 1α (PGC1-α), nuclear respiratory factors 1 (Nrf-1), mitochondrial transcription factor A (TFAM), and phosphorylated (activated) AMP-activated protein kinase (p-AMPK) protein levels in the four brain regions. LCR rats exhibited lower levels of mitochondrial proteins (PGC1-α, Nrf-1, TFAM), and greater p-AMPK, in striatum, but not in the other brain regions. Mitochondrial protein levels were greater in HFD LCR striatum, while p-AMPK was lower in this group. Markers of lower mitochondrial biogenesis and increased metabolic demand were limited to the LCR striatum, which nevertheless maintained the capacity to respond to an acute HFD challenge. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. Hunting for low abundant redox proteins in plant plasma membranes.

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    Lüthje, Sabine; Hopff, David; Schmitt, Anna; Meisrimler, Claudia-Nicole; Menckhoff, Ljiljana

    2009-04-13

    Nowadays electron transport (redox) systems in plasma membranes appear well established. Members of the flavocytochrome b family have been identified by their nucleotide acid sequences and characterized on the transcriptional level. For their gene products functions have been demonstrated in iron uptake and oxidative stress including biotic interactions, abiotic stress factors and plant development. In addition, NAD(P)H-dependent oxidoreductases and b-type cytochromes have been purified and characterized from plasma membranes. Several of these proteins seem to belong to the group of hypothetical or unknown proteins. Low abundance and the lack of amino acid sequence data for these proteins still hamper their functional analysis. Consequently, little is known about the physiological function and regulation of these enzymes. In recent years evidence has been presented for the existence of microdomains (so-called lipid rafts) in plasma membranes and their interaction with specific membrane proteins. The identification of redox systems in detergent insoluble membranes supports the idea that redox systems may have important functions in signal transduction, stress responses, cell wall metabolism, and transport processes. This review summarizes our present knowledge on plasma membrane redox proteins and discusses alternative strategies to investigate the function and regulation of these enzymes.

  8. Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis

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    Rom William N

    2005-08-01

    Full Text Available Abstract Background Cancer serum protein profiling by mass spectrometry has uncovered mass profiles that are potentially diagnostic for several common types of cancer. However, direct mass spectrometric profiling has a limited dynamic range and difficulties in providing the identification of the distinctive proteins. We hypothesized that distinctive profiles may result from the differential expression of relatively abundant serum proteins associated with the host response. Methods Eighty-four antibodies, targeting a wide range of serum proteins, were spotted onto nitrocellulose-coated microscope slides. The abundances of the corresponding proteins were measured in 80 serum samples, from 24 newly diagnosed subjects with lung cancer, 24 healthy controls, and 32 subjects with chronic obstructive pulmonary disease (COPD. Two-color rolling-circle amplification was used to measure protein abundance. Results Seven of the 84 antibodies gave a significant difference (p Conclusion Our results suggest that a distinctive serum protein profile involving abundant proteins may be observed in lung cancer patients relative to healthy subjects or patients with chronic disease and may have utility as part of strategies for detecting lung cancer.

  9. Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis

    International Nuclear Information System (INIS)

    Gao, Wei-Min; Haab, Brian B; Hanash, Samir M; Kuick, Rork; Orchekowski, Randal P; Misek, David E; Qiu, Ji; Greenberg, Alissa K; Rom, William N; Brenner, Dean E; Omenn, Gilbert S

    2005-01-01

    Cancer serum protein profiling by mass spectrometry has uncovered mass profiles that are potentially diagnostic for several common types of cancer. However, direct mass spectrometric profiling has a limited dynamic range and difficulties in providing the identification of the distinctive proteins. We hypothesized that distinctive profiles may result from the differential expression of relatively abundant serum proteins associated with the host response. Eighty-four antibodies, targeting a wide range of serum proteins, were spotted onto nitrocellulose-coated microscope slides. The abundances of the corresponding proteins were measured in 80 serum samples, from 24 newly diagnosed subjects with lung cancer, 24 healthy controls, and 32 subjects with chronic obstructive pulmonary disease (COPD). Two-color rolling-circle amplification was used to measure protein abundance. Seven of the 84 antibodies gave a significant difference (p < 0.01) for the lung cancer patients as compared to healthy controls, as well as compared to COPD patients. Proteins that exhibited higher abundances in the lung cancer samples relative to the control samples included C-reactive protein (CRP; a 13.3 fold increase), serum amyloid A (SAA; a 2.0 fold increase), mucin 1 and α-1-antitrypsin (1.4 fold increases). The increased expression levels of CRP and SAA were validated by Western blot analysis. Leave-one-out cross-validation was used to construct Diagonal Linear Discriminant Analysis (DLDA) classifiers. At a cutoff where all 56 of the non-tumor samples were correctly classified, 15/24 lung tumor patient sera were correctly classified. Our results suggest that a distinctive serum protein profile involving abundant proteins may be observed in lung cancer patients relative to healthy subjects or patients with chronic disease and may have utility as part of strategies for detecting lung cancer

  10. 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.

  11. Identification of stress responsive genes by studying specific relationships between mRNA and protein abundance.

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    Morimoto, Shimpei; Yahara, Koji

    2018-03-01

    Protein expression is regulated by the production and degradation of mRNAs and proteins but the specifics of their relationship are controversial. Although technological advances have enabled genome-wide and time-series surveys of mRNA and protein abundance, recent studies have shown paradoxical results, with most statistical analyses being limited to linear correlation, or analysis of variance applied separately to mRNA and protein datasets. Here, using recently analyzed genome-wide time-series data, we have developed a statistical analysis framework for identifying which types of genes or biological gene groups have significant correlation between mRNA and protein abundance after accounting for potential time delays. Our framework stratifies all genes in terms of the extent of time delay, conducts gene clustering in each stratum, and performs a non-parametric statistical test of the correlation between mRNA and protein abundance in a gene cluster. Consequently, we revealed stronger correlations than previously reported between mRNA and protein abundance in two metabolic pathways. Moreover, we identified a pair of stress responsive genes ( ADC17 and KIN1 ) that showed a highly similar time series of mRNA and protein abundance. Furthermore, we confirmed robustness of the analysis framework by applying it to another genome-wide time-series data and identifying a cytoskeleton-related gene cluster (keratin 18, keratin 17, and mitotic spindle positioning) that shows similar correlation. The significant correlation and highly similar changes of mRNA and protein abundance suggests a concerted role of these genes in cellular stress response, which we consider provides an answer to the question of the specific relationships between mRNA and protein in a cell. In addition, our framework for studying the relationship between mRNAs and proteins in a cell will provide a basis for studying specific relationships between mRNA and protein abundance after accounting for potential

  12. 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...... proteins are released and recovered in the eluate. We developed a series of distinct depletion protocols that proved useful for sample depletion and fractionation and facilitated targeted analysis of putative biomarkers such as IGF1-2, IBP2-7, ALS, KLK6-7, ISK5, and PLF4 by selected reaction monitoring...

  13. 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.

  14. 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.

  15. 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.

  16. Relative Abundance of Proteins in Blood Plasma Samples from Patients with Chronic Cerebral Ischemia.

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    Kaysheva, Anna L; Kopylov, Artur T; Ponomarenko, Elena A; Kiseleva, Olga I; Teryaeva, Nadezhda B; Potapov, Alexander A; Izotov, Alexander А; Morozov, Sergei G; Kudryavtseva, Valeria Yu; Archakov, Alexander I

    2018-03-01

    A comparative protein profile analysis of 17 blood plasma samples from patients with ischemia and 20 samples from healthy volunteers was carried out using ultra-high resolution mass spectrometry. The analysis of measurements was performed using the proteomics search engine OMSSA. Normalized spectrum abundance factor (NSAF) in the biological samples was assessed using SearchGUI. The findings of mass spectrometry analysis of the protein composition of blood plasma samples demonstrate that the depleted samples are quite similar in protein composition and relative abundance of proteins. By comparing them with the control samples, we have found a small group of 44 proteins characteristic of the blood plasma samples from patients with chronic cerebral ischemia. These proteins contribute to the processes of homeostasis maintenance, including innate immune response unfolding, the response of a body to stress, and contribution to the blood clotting cascade.

  17. Identification of stress responsive genes by studying specific relationships between mRNA and protein abundance

    Directory of Open Access Journals (Sweden)

    Shimpei Morimoto

    2018-03-01

    Full Text Available Protein expression is regulated by the production and degradation of mRNAs and proteins but the specifics of their relationship are controversial. Although technological advances have enabled genome-wide and time-series surveys of mRNA and protein abundance, recent studies have shown paradoxical results, with most statistical analyses being limited to linear correlation, or analysis of variance applied separately to mRNA and protein datasets. Here, using recently analyzed genome-wide time-series data, we have developed a statistical analysis framework for identifying which types of genes or biological gene groups have significant correlation between mRNA and protein abundance after accounting for potential time delays. Our framework stratifies all genes in terms of the extent of time delay, conducts gene clustering in each stratum, and performs a non-parametric statistical test of the correlation between mRNA and protein abundance in a gene cluster. Consequently, we revealed stronger correlations than previously reported between mRNA and protein abundance in two metabolic pathways. Moreover, we identified a pair of stress responsive genes (ADC17 and KIN1 that showed a highly similar time series of mRNA and protein abundance. Furthermore, we confirmed robustness of the analysis framework by applying it to another genome-wide time-series data and identifying a cytoskeleton-related gene cluster (keratin 18, keratin 17, and mitotic spindle positioning that shows similar correlation. The significant correlation and highly similar changes of mRNA and protein abundance suggests a concerted role of these genes in cellular stress response, which we consider provides an answer to the question of the specific relationships between mRNA and protein in a cell. In addition, our framework for studying the relationship between mRNAs and proteins in a cell will provide a basis for studying specific relationships between mRNA and protein abundance after

  18. 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/.

  19. Differential abundance of egg white proteins in laying hens treated with corticosterone.

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    Kim, Jimin; Choi, Yang-Ho

    2014-12-24

    Stressful environments can affect not only egg production and quality but also gene and protein abundance in the ovary and oviduct in laying hens. The oviductal magnum of laying hens is the organ responsible for the synthesis and secretion of egg white proteins. The objective of this study was to investigate the effects of dietary corticosterone as a stress model on the abundance of proteins in the egg white and of mRNA and proteins in the magnum in laying hens. After a 14-day acclimation, 40 laying hens were divided into two groups which were provided for the next 14 days with either control (Control) or corticosterone (Stress) diet containing at 30 mg/kg. Corticosterone treatment resulted in increased feed intake (P ≤ 0.05) and decreased egg production. Two-dimensional electrophoresis (2DE) with MALDI-TOF/TOF MS/MS using eggs obtained on days 0 and 5 revealed differential abundance of egg white proteins by Stress: transiently expressed in neural precursors (TENP), hemopexin (HPX), IgY-Fcυ3-4, and extracellular fatty acid-binding protein (Ex-FABP) were decreased while ovoinhibitor and ovalbumin-related protein X (OVAX) were increased on days 5 vs 0 (P ≤ 0.05). Expression of mRNAs and proteins was also significantly modulated in the magnum of hens in Stress on day 14 (P ≤ 0.05). In conclusion, the current study provides the first evidence showing that dietary corticosterone modulates protein abundance in the egg white in laying hens, and it suggests that environmental stress can differentially modify expression of egg white proteins in laying hens.

  20. 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......-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...

  1. Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly.

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    Aird, Steven D; Aggarwal, Shikha; Villar-Briones, Alejandro; Tin, Mandy Man-Ying; Terada, Kouki; Mikheyev, Alexander S

    2015-08-28

    While many studies have shown that extracellular proteins evolve rapidly, how selection acts on them remains poorly understood. We used snake venoms to understand the interaction between ecology, expression level, and evolutionary rate in secreted protein systems. Venomous snakes employ well-integrated systems of proteins and organic constituents to immobilize prey. Venoms are generally optimized to subdue preferred prey more effectively than non-prey, and many venom protein families manifest positive selection and rapid gene family diversification. Although previous studies have illuminated how individual venom protein families evolve, how selection acts on venoms as integrated systems, is unknown. Using next-generation transcriptome sequencing and mass spectrometry, we examined microevolution in two pitvipers, allopatrically separated for at least 1.6 million years, and their hybrids. Transcriptomes of parental species had generally similar compositions in regard to protein families, but for a given protein family, the homologs present and concentrations thereof sometimes differed dramatically. For instance, a phospholipase A2 transcript comprising 73.4 % of the Protobothrops elegans transcriptome, was barely present in the P. flavoviridis transcriptome (king cobra genome, suggesting that rapid evolution of abundant proteins may be generally true for snake venoms. Looking more broadly at Protobothrops, we show that rapid evolution of the most abundant components is due to positive selection, suggesting an interplay between abundance and adaptation. Given log-scale differences in toxin abundance, which are likely correlated with biosynthetic costs, we hypothesize that as a result of natural selection, snakes optimize return on energetic investment by producing more of venom proteins that increase their fitness. Natural selection then acts on the additive genetic variance of these components, in proportion to their contributions to overall fitness. Adaptive

  2. LDL receptor-related protein 1 regulates the abundance of diverse cell-signaling proteins in the plasma membrane proteome.

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    Gaultier, Alban; Simon, Gabriel; Niessen, Sherry; Dix, Melissa; Takimoto, Shinako; Cravatt, Benjamin F; Gonias, Steven L

    2010-12-03

    LDL receptor-related protein 1 (LRP1) is an endocytic receptor, reported to regulate the abundance of other receptors in the plasma membrane, including uPAR and tissue factor. The goal of this study was to identify novel plasma membrane proteins, involved in cell-signaling, that are regulated by LRP1. Membrane protein ectodomains were prepared from RAW 264.7 cells in which LRP1 was silenced and control cells using protease K. Peptides were identified by LC-MS/MS. By analysis of spectral counts, 31 transmembrane and secreted proteins were regulated in abundance at least 2-fold when LRP1 was silenced. Validation studies confirmed that semaphorin4D (Sema4D), plexin domain-containing protein-1 (Plxdc1), and neuropilin-1 were more abundant in the membranes of LRP1 gene-silenced cells. Regulation of Plxdc1 by LRP1 was confirmed in CHO cells, as a second model system. Plxdc1 coimmunoprecipitated with LRP1 from extracts of RAW 264.7 cells and mouse liver. Although Sema4D did not coimmunoprecipitate with LRP1, the cell-surface level of Sema4D was increased by RAP, which binds to LRP1 and inhibits binding of other ligands. These studies identify Plxdc1, Sema4D, and neuropilin-1 as novel LRP1-regulated cell-signaling proteins. Overall, LRP1 emerges as a generalized regulator of the plasma membrane proteome.

  3. Depleting high-abundant and enriching low-abundant proteins in human serum: An evaluation of sample preparation methods using magnetic nanoparticle, chemical depletion and immunoaffinity techniques.

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    de Jesus, Jemmyson Romário; da Silva Fernandes, Rafael; de Souza Pessôa, Gustavo; Raimundo, Ivo Milton; Arruda, Marco Aurélio Zezzi

    2017-08-01

    The efficiency of three different depletion methods to remove the most abundant proteins, enriching those human serum proteins with low abundance is checked to make more efficient the search and discovery of biomarkers. These methods utilize magnetic nanoparticles (MNPs), chemical reagents (sequential application of dithiothreitol and acetonitrile, DTT/ACN), and commercial apparatus based on immunoaffinity (ProteoMiner, PM). The comparison between methods shows significant removal of abundant protein, remaining in the supernatant at concentrations of 4.6±0.2, 3.6±0.1, and 3.3±0.2µgµL -1 (n=3) for MNPs, DTT/ACN and PM respectively, from a total protein content of 54µgµL -1 . Using GeLC-MS/MS analysis, MNPs depletion shows good efficiency in removing high molecular weight proteins (>80kDa). Due to the synergic effect between the reagents DTT and ACN, DTT/ACN-based depletion offers good performance in the depletion of thiol-rich proteins, such as albumin and transferrin (DTT action), as well as of high molecular weight proteins (ACN action). Furthermore, PM equalization confirms its efficiency in concentrating low-abundant proteins, decreasing the dynamic range of protein levels in human serum. Direct comparison between the treatments reveals 72 proteins identified when using MNP depletion (43 of them exclusively by this method), but only 20 proteins using DTT/ACN (seven exclusively by this method). Additionally, after PM treatment 30 proteins were identified, seven exclusively by this method. Thus, MNPs and DTT/ACN depletion can be simple, quick, cheap, and robust alternatives for immunochemistry-based protein depletion, providing a potential strategy in the search for disease biomarkers. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Identification of proteins of altered abundance in oil palm infected with Ganoderma boninense.

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    Al-Obaidi, Jameel R; Mohd-Yusuf, Yusmin; Razali, Nurhanani; Jayapalan, Jaime Jacqueline; Tey, Chin-Chong; Md-Noh, Normahnani; Junit, Sarni Mat; Othman, Rofina Yasmin; Hashim, Onn Haji

    2014-03-24

    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.

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

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    Al-Obaidi, Jameel R.; Mohd-Yusuf, Yusmin; Razali, Nurhanani; Jayapalan, Jaime Jacqueline; Tey, Chin-Chong; Md-Noh, Normahnani; Junit, Sarni Mat; Othman, Rofina Yasmin; Hashim, Onn Haji

    2014-01-01

    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. PMID:24663087

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-07-12

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

  8. 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. PMID:27453073

  9. Comparison of Depletion Strategies for the Enrichment of Low-Abundance Proteins in Urine.

    Science.gov (United States)

    Filip, Szymon; Vougas, Konstantinos; Zoidakis, Jerome; Latosinska, Agnieszka; Mullen, William; Spasovski, Goce; Mischak, Harald; Vlahou, Antonia; Jankowski, Joachim

    2015-01-01

    Proteome analysis of complex biological samples for biomarker identification remains challenging, among others due to the extended range of protein concentrations. High-abundance proteins like albumin or IgG of plasma and urine, may interfere with the detection of potential disease biomarkers. Currently, several options are available for the depletion of abundant proteins in plasma. However, the applicability of these methods in urine has not been thoroughly investigated. In this study, we compared different, commercially available immunodepletion and ion-exchange based approaches on urine samples from both healthy subjects and CKD patients, for their reproducibility and efficiency in protein depletion. A starting urine volume of 500 μL was used to simulate conditions of a multi-institutional biomarker discovery study. All depletion approaches showed satisfactory reproducibility (n=5) in protein identification as well as protein abundance. Comparison of the depletion efficiency between the unfractionated and fractionated samples and the different depletion strategies, showed efficient depletion in all cases, with the exception of the ion-exchange kit. The depletion efficiency was found slightly higher in normal than in CKD samples and normal samples yielded more protein identifications than CKD samples when using both initial as well as corresponding depleted fractions. Along these lines, decrease in the amount of albumin and other targets as applicable, following depletion, was observed. Nevertheless, these depletion strategies did not yield a higher number of identifications in neither the urine from normal nor CKD patients. Collectively, when analyzing urine in the context of CKD biomarker identification, no added value of depletion strategies can be observed and analysis of unfractionated starting urine appears to be preferable.

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

    Directory of Open Access Journals (Sweden)

    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.

  11. Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

    Science.gov (United States)

    Rocca, Jennifer D.; Hall, Edward K.; Lennon, Jay T.; Evans, Sarah E.; Waldrop, Mark P.; Cotner, James B.; Nemergut, Diana R.; Graham, Emily B.; Wallenstein, Matthew D.

    2015-01-01

    For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates. We identified 415 studies that quantified the abundance of genes or transcripts for enzymes involved in carbon or nitrogen cycling. However, in only 59 of these manuscripts did the authors report both gene or transcript abundance and rates of the appropriate process. We found that within studies there was a significant but weak positive relationship between gene abundance and the corresponding process. Correlations were not strengthened by accounting for habitat type, differences among genes or reaction products versus reactants, suggesting that other ecological and methodological factors may affect the strength of this relationship. Our findings highlight the need for fundamental research on the factors that control transcription, translation and enzyme function in natural systems to better link genomic and transcriptomic data to ecosystem processes.

  12. Effects of copper and tributyltin on stress protein abundance in the rotifer Brachionus plicatilis.

    Science.gov (United States)

    Cochrane, B J; Irby, R B; Snell, T W

    1991-01-01

    1. Exposure of the rotifer Brachionus plicatilis to elevated temperature resulted in the synthesis of a number of proteins, including a prominent one of 58,000 Da (SP58). 2. This protein is immunologically crossreactive with the 65,000 Da heat shock protein of the moth Heliothis virescens, which is a member of a highly conserved family of mitochondrial proteins. 3. Exposure of rotifers to sublethal doses of CuSO4 leads to a 4-5-fold increase in abundance of SP58, with maximum increase occurring at a dose that is approximately 5% of the LC50 for that compound. 4. A similar response was seen with tributyl tin (TBT). Kinetics of induction were sigmoidal, with induction occurring in the range of 20-30 micrograms/l. 5. No response was observed when rotifers were exposed to aluminum chloride, mercury chloride, pentachlorophenol, sodium arsenite, sodium azide, sodium dodecyl sulfate, or zinc chloride. 6. These results indicate that changes in stress protein abundance may prove useful as a biomarker of exposure to particular toxicants.

  13. Separomics applied to the proteomics and peptidomics of low-abundance proteins: Choice of methods and challenges - A review.

    Science.gov (United States)

    Baracat-Pereira, Maria Cristina; de Oliveira Barbosa, Meire; Magalhães, Marcos Jorge; Carrijo, Lanna Clicia; Games, Patrícia Dias; Almeida, Hebréia Oliveira; Sena Netto, José Fabiano; Pereira, Matheus Rodrigues; de Barros, Everaldo Gonçalves

    2012-06-01

    The enrichment and isolation of proteins are considered limiting steps in proteomic studies. Identification of proteins whose expression is transient, those that are of low-abundance, and of natural peptides not described in databases, is still a great challenge. Plant extracts are in general complex, and contaminants interfere with the identification of proteins involved in important physiological processes, such as plant defense against pathogens. This review discusses the challenges and strategies of separomics applied to the identification of low-abundance proteins and peptides in plants, especially in plants challenged by pathogens. Separomics is described as a group of methodological strategies for the separation of protein molecules for proteomics. Several tools have been used to remove highly abundant proteins from samples and also non-protein contaminants. The use of chromatographic techniques, the partition of the proteome into subproteomes, and an effort to isolate proteins in their native form have allowed the isolation and identification of rare proteins involved in different processes.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    Zhu, Yingying; Lin, Xisha; Li, He; Li, Yingqiu; Shi, Xuebin; Zhao, Fan; Xu, Xinglian; Li, Chunbao; Zhou, Guanghong

    2016-01-01

    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.

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

    Science.gov (United States)

    Zhu, Yingying; Lin, Xisha; Li, He; Li, Yingqiu; Shi, Xuebin; Zhao, Fan; Xu, Xinglian; Li, Chunbao; Zhou, Guanghong

    2016-01-01

    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. PMID:27042829

  17. Exoproteome analysis reveals higher abundance of proteins linked to alkaline stress in persistent Listeria monocytogenes strains.

    Science.gov (United States)

    Rychli, Kathrin; Grunert, Tom; Ciolacu, Luminita; Zaiser, Andreas; Razzazi-Fazeli, Ebrahim; Schmitz-Esser, Stephan; Ehling-Schulz, Monika; Wagner, Martin

    2016-02-02

    The foodborne pathogen Listeria monocytogenes, responsible for listeriosis a rare but severe infection disease, can survive in the food processing environment for month or even years. So-called persistent L. monocytogenes strains greatly increase the risk of (re)contamination of food products, and are therefore a great challenge for food safety. However, our understanding of the mechanism underlying persistence is still fragmented. In this study we compared the exoproteome of three persistent strains with the reference strain EGDe under mild stress conditions using 2D differential gel electrophoresis. Principal component analysis including all differentially abundant protein spots showed that the exoproteome of strain EGDe (sequence type (ST) 35) is distinct from that of the persistent strain R479a (ST8) and the two closely related ST121 strains 4423 and 6179. Phylogenetic analyses based on multilocus ST genes showed similar grouping of the strains. Comparing the exoproteome of strain EGDe and the three persistent strains resulted in identification of 22 differentially expressed protein spots corresponding to 16 proteins. Six proteins were significantly increased in the persistent L. monocytogenes exoproteomes, among them proteins involved in alkaline stress response (e.g. the membrane anchored lipoprotein Lmo2637 and the NADPH dehydrogenase NamA). In parallel the persistent strains showed increased survival under alkaline stress, which is often provided during cleaning and disinfection in the food processing environments. In addition, gene expression of the proteins linked to stress response (Lmo2637, NamA, Fhs and QoxA) was higher in the persistent strain not only at 37 °C but also at 10 °C. Invasion efficiency of EGDe was higher in intestinal epithelial Caco2 and macrophage-like THP1 cells compared to the persistent strains. Concurrently we found higher expression of proteins involved in virulence in EGDe e.g. the actin-assembly-inducing protein ActA and the

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

    Science.gov (United States)

    Wise, Michael J

    2003-10-29

    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. 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. 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, via a role in DNA-binding. In general, non-globular and

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

    Directory of Open Access Journals (Sweden)

    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

  20. Investigation of SnSPR1, a novel and abundant surface protein of Sarcocystis neurona merozoites.

    Science.gov (United States)

    Zhang, Deqing; Howe, Daniel K

    2008-04-15

    An expressed sequence tag (EST) sequencing project has produced over 15,000 partial cDNA sequences from the equine pathogen Sarcocystis neurona. While many of the sequences are clear homologues of previously characterized genes, a significant number of the S. neurona ESTs do not exhibit similarity to anything in the extensive sequence databases that have been generated. In an effort to characterize parasite proteins that are novel to S. neurona, a seemingly unique gene was selected for further investigation based on its abundant representation in the collection of ESTs and the predicted presence of a signal peptide and glycolipid anchor addition on the encoded protein. The gene was expressed in E. coli, and monospecific polyclonal antiserum against the recombinant protein was produced by immunization of a rabbit. Characterization of the native protein in S. neurona merozoites and schizonts revealed that it is a low molecular weight surface protein that is expressed throughout intracellular development of the parasite. The protein was designated Surface Protein 1 (SPR1) to reflect its display on the outer surface of merozoites and to distinguish it from the ubiquitous SAG/SRS surface antigens of the heteroxenous Coccidia. Interestingly, infection assays in the presence of the polyclonal antiserum suggested that SnSPR1 plays some role in attachment and/or invasion of host cells by S. neurona merozoites. The work described herein represents a general template for selecting and characterizing the various unidentified gene sequences that are plentiful in the EST databases for S. neurona and other apicomplexans. Furthermore, this study illustrates the value of investigating these novel sequences since it can offer new candidates for diagnostic or vaccine development while also providing greater insight into the biology of these parasites.

  1. Spatial Mapping of Protein Abundances in the Mouse Brain by Voxelation Integrated with High-Throughput Liquid Chromatography ? Mass Spectrometry

    International Nuclear Information System (INIS)

    Petyuk, Vladislav A.; Qian, Weijun; Chin, Mark H.; Wang, Haixing H.; Livesay, Eric A.; Monroe, Matthew E.; Adkins, Joshua N.; Jaitly, Navdeep; Anderson, David J.; Camp, David G.; Smith, Desmond J.; Smith, Richard D.

    2007-01-01

    Temporally and spatially resolved mapping of protein abundance patterns within the mammalian brain is of significant interest for understanding brain function and molecular etiologies of neurodegenerative diseases; however, such imaging efforts have been greatly challenged by complexity of the proteome, throughput and sensitivity of applied analytical methodologies, and accurate quantitation of protein abundances across the brain. Here, we describe a methodology for comprehensive spatial proteome mapping that addresses these challenges by employing voxelation integrated with automated microscale sample processing, high-throughput LC system coupled with high resolution Fourier transform ion cyclotron mass spectrometer and a ''universal'' stable isotope labeled reference sample approach for robust quantitation. We applied this methodology as a proof-of-concept trial for the analysis of protein distribution within a single coronal slice of a C57BL/6J mouse brain. For relative quantitation of the protein abundances across the slice, an 18O-isotopically labeled reference sample, derived from a whole control coronal slice from another mouse, was spiked into each voxel sample and stable isotopic intensity ratios were used to obtain measures of relative protein abundances. In total, we generated maps of protein abundance patterns for 1,028 proteins. The significant agreement of the protein distributions with previously reported data supports the validity of this methodology, which opens new opportunities for studying the spatial brain proteome and its dynamics during the course of disease progression and other important biological and associated health aspects in a discovery-driven fashion

  2. Protein degradation rate is the dominant mechanism accounting for the differences in protein abundance of basal p53 in a human breast and colorectal cancer cell line.

    Directory of Open Access Journals (Sweden)

    Eszter Lakatos

    Full Text Available We determine p53 protein abundances and cell to cell variation in two human cancer cell lines with single cell resolution, and show that the fractional width of the distributions is the same in both cases despite a large difference in average protein copy number. We developed a computational framework to identify dominant mechanisms controlling the variation of protein abundance in a simple model of gene expression from the summary statistics of single cell steady state protein expression distributions. Our results, based on single cell data analysed in a Bayesian framework, lends strong support to a model in which variation in the basal p53 protein abundance may be best explained by variations in the rate of p53 protein degradation. This is supported by measurements of the relative average levels of mRNA which are very similar despite large variation in the level of protein.

  3. Protein degradation rate is the dominant mechanism accounting for the differences in protein abundance of basal p53 in a human breast and colorectal cancer cell line.

    Science.gov (United States)

    Lakatos, Eszter; Salehi-Reyhani, Ali; Barclay, Michael; Stumpf, Michael P H; Klug, David R

    2017-01-01

    We determine p53 protein abundances and cell to cell variation in two human cancer cell lines with single cell resolution, and show that the fractional width of the distributions is the same in both cases despite a large difference in average protein copy number. We developed a computational framework to identify dominant mechanisms controlling the variation of protein abundance in a simple model of gene expression from the summary statistics of single cell steady state protein expression distributions. Our results, based on single cell data analysed in a Bayesian framework, lends strong support to a model in which variation in the basal p53 protein abundance may be best explained by variations in the rate of p53 protein degradation. This is supported by measurements of the relative average levels of mRNA which are very similar despite large variation in the level of protein.

  4. Chloroform-assisted phenol extraction improving proteome profiling of maize embryos through selective depletion of high-abundance storage proteins.

    Directory of Open Access Journals (Sweden)

    Erhui Xiong

    Full Text Available The presence of abundant storage proteins in plant embryos greatly impedes seed proteomics analysis. Vicilin (or globulin-1 is the most abundant storage protein in maize embryo. There is a need to deplete the vicilins from maize embryo extracts for enhanced proteomics analysis. We here reported a chloroform-assisted phenol extraction (CAPE method for vicilin depletion. By CAPE, maize embryo proteins were first extracted in an aqueous buffer, denatured by chloroform and then subjected to phenol extraction. We found that CAPE can effectively deplete the vicilins from maize embryo extract, allowing the detection of low-abundance proteins that were masked by vicilins in 2-DE gel. The novelty of CAPE is that it selectively depletes abundant storage proteins from embryo extracts of both monocot (maize and dicot (soybean and pea seeds, whereas other embryo proteins were not depleted. CAPE can significantly improve proteome profiling of embryos and extends the application of chloroform and phenol extraction in plant proteomics. In addition, the rationale behind CAPE depletion of abundant storage proteins was explored.

  5. Relative Abundance of Integral Plasma Membrane Proteins in Arabidopsis Leaf and Root Tissue Determined by Metabolic Labeling and Mass Spectrometry

    Science.gov (United States)

    Bernfur, Katja; Larsson, Olaf; Larsson, Christer; Gustavsson, Niklas

    2013-01-01

    Metabolic labeling of proteins with a stable isotope (15N) in intact Arabidopsis plants was used for accurate determination by mass spectrometry of differences in protein abundance between plasma membranes isolated from leaves and roots. In total, 703 proteins were identified, of which 188 were predicted to be integral membrane proteins. Major classes were transporters, receptors, proteins involved in membrane trafficking and cell wall-related proteins. Forty-one of the integral proteins, including nine of the 13 isoforms of the PIP (plasma membrane intrinsic protein) aquaporin subfamily, could be identified by peptides unique to these proteins, which made it possible to determine their relative abundance in leaf and root tissue. In addition, peptides shared between isoforms gave information on the proportions of these isoforms. A comparison between our data for protein levels and corresponding data for mRNA levels in the widely used database Genevestigator showed an agreement for only about two thirds of the proteins. By contrast, localization data available in the literature for 21 of the 41 proteins show a much better agreement with our data, in particular data based on immunostaining of proteins and GUS-staining of promoter activity. Thus, although mRNA levels may provide a useful approximation for protein levels, detection and quantification of isoform-specific peptides by proteomics should generate the most reliable data for the proteome. PMID:23990937

  6. Phospholipase D specific for the phosphatidylinositol anchor of cell-surface proteins is abundant in plasma

    International Nuclear Information System (INIS)

    Low, M.G.; Prasad, A.R.S.

    1988-01-01

    An enzyme activity capable of degrading the glycosyl-phosphatidylinositol membrane anchor of cell-surface proteins has previously been reported in a number of mammalian tissues. The experiments reported here demonstrate that this anchor-degrading activity is also abundant in mammalian plasma. The activity was inhibited by EGTA or 1,10-phenanthroline. It was capable of removing the anchor from alkaline phosphatase, 5'-nucleotidase, and variant surface glycoprotein but had little or no activity toward phosphatidylinositol or phosphatidylcholine. Phosphatidic acid was the only 3 H-labeled product when this enzyme hydrolyzed [ 3 H]myristate-labeled variant surface glycoprotein. It could be distinguished from the Ca 2 =-dependent inositol phospholipid-specific phospholipase C activity in several rat tissues on the basis of its molecular size and its sensitivity to 1,10-phenanthroline. The data therefore suggest that this activity is due to a phospholipase D with specificity for glycosylphosphatidylinositol structures. Although the precise physiological function of this anchor-specific phospholipase D remains to be determined, these findings indicate that it could play an important role in regulating the expression and release of cell-surface proteins in vivo

  7. Separomics applied to the proteomics and peptidomics of low-abundance proteins: choice of methods and challenges - a review

    Directory of Open Access Journals (Sweden)

    Maria Cristina Baracat-Pereira

    2012-01-01

    Full Text Available The enrichment and isolation of proteins are considered limiting steps in proteomic studies. Identification of proteins whose expression is transient, those that are of low-abundance, and of natural peptides not described in databases, is still a great challenge. Plant extracts are in general complex, and contaminants interfere with the identification of proteins involved in important physiological processes, such as plant defense against pathogens. This review discusses the challenges and strategies of separomics applied to the identification of low-abundance proteins and peptides in plants, especially in plants challenged by pathogens. Separomics is described as a group of methodological strategies for the separation of protein molecules for proteomics. Several tools have been used to remove highly abundant proteins from samples and also non-protein contaminants. The use of chromatographic techniques, the partition of the proteome into subproteomes, and an effort to isolate proteins in their native form have allowed the isolation and identification of rare proteins involved in different processes.

  8. Separomics applied to the proteomics and peptidomics of low-abundance proteins: Choice of methods and challenges – A review

    Science.gov (United States)

    Baracat-Pereira, Maria Cristina; de Oliveira Barbosa, Meire; Magalhães, Marcos Jorge; Carrijo, Lanna Clicia; Games, Patrícia Dias; Almeida, Hebréia Oliveira; Sena Netto, José Fabiano; Pereira, Matheus Rodrigues; de Barros, Everaldo Gonçalves

    2012-01-01

    The enrichment and isolation of proteins are considered limiting steps in proteomic studies. Identification of proteins whose expression is transient, those that are of low-abundance, and of natural peptides not described in databases, is still a great challenge. Plant extracts are in general complex, and contaminants interfere with the identification of proteins involved in important physiological processes, such as plant defense against pathogens. This review discusses the challenges and strategies of separomics applied to the identification of low-abundance proteins and peptides in plants, especially in plants challenged by pathogens. Separomics is described as a group of methodological strategies for the separation of protein molecules for proteomics. Several tools have been used to remove highly abundant proteins from samples and also non-protein contaminants. The use of chromatographic techniques, the partition of the proteome into subproteomes, and an effort to isolate proteins in their native form have allowed the isolation and identification of rare proteins involved in different processes. PMID:22802713

  9. Nitrogen 15 abundance in protein fractions of beans fertilized with (15NH4)2SO4

    International Nuclear Information System (INIS)

    Chaud, Saula Goulart; Oliveira, Admar Costa de; Trivelin, Paulo Cesar Ocheuze

    2002-01-01

    Studies evaluating the protein nutritive value of beans labelled with 15 N, using 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 Pirata 1) with 1.394 atoms % 15 N, 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 15 N, 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 L 1 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. (author)

  10. [Removal of high-abundance proteins in plasma of the obese by improved TCA/acetone precipitation method].

    Science.gov (United States)

    Wang, Jun; Feng, Liru; Yu, Wei; Xu, Jian; Yang, Hui; Liu, Xiaoli

    2013-09-01

    To develop an improved trichloroacetic acid (TCA)/acetone precipitation method for removal of high-abundance proteins in plasma of the obese. Volumes of TCA/acetone solution (1, 3, 4, 5, 6, 8, 10 and 20 times of the sample) and concentrations of TCA (10%, 30%, 50%, 60%, 70% TCA/acetone solution) have been investigated to optimize the conditions of sample preparation. SDS-PAGE were used to separate and tested proteins in the supernatant and sediment. The best concentration of the TCA/acetone solution was first determined by SDS-PAGE. The protein in precipitation from 10% TCA/acetone solution processing and the new determined concentration TCA/acetone solution processing were verified by 2-D-SDS-PAGE. And then the digested products of the protein in precipitation and supernatant by trypsin were analyzed by nano HPLC-Chip-MS/MS to verify which is the best concentration to process the plasma. The best volume of TCA/acetone is four times to sample, which less or more TCA/acetone would reduce the removal efficiency of high-abundance proteins. The concentration of TCA in acetone solution should be 60%, which may remove more high-abundance proteins in plasma than 10%, 30%, 50% TCA in acetone solution. If the TCA concentration is more than 60%, the reproducibility will be much poorer due to fast precipitation of proteins. The results of mass identification showed that human plasma prepared with 60% TCA/acetone (4 times sample volume) could be verified more low-abundance proteins than 10%. The most desirable conditions for removal of high-abundance proteins in plasma is 60% TCA/acetone (4 times sample volume), especially for the plasma of obesity.

  11. Looking deep inside: detection of low-abundance proteins in leaf extracts of Arabidopsis and phloem exudates of pumpkin.

    Science.gov (United States)

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

    2012-07-01

    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.

  12. High-throughput fractionation of human plasma for fast enrichment of low- and high-abundance proteins.

    Science.gov (United States)

    Breen, Lucas; Cao, Lulu; Eom, Kirsten; Srajer Gajdosik, Martina; Camara, Lila; Giacometti, Jasminka; Dupuy, Damian E; Josic, Djuro

    2012-05-01

    Fast, cost-effective and reproducible isolation of IgM from plasma is invaluable to the study of IgM and subsequent understanding of the human immune system. Additionally, vast amounts of information regarding human physiology and disease can be derived from analysis of the low abundance proteome of the plasma. In this study, methods were optimized for both the high-throughput isolation of IgM from human plasma, and the high-throughput isolation and fractionation of low abundance plasma proteins. To optimize the chromatographic isolation of IgM from human plasma, many variables were examined including chromatography resin, mobile phases, and order of chromatographic separations. Purification of IgM was achieved most successfully through isolation of immunoglobulin from human plasma using Protein A chromatography with a specific resin followed by subsequent fractionation using QA strong anion exchange chromatography. Through these optimization experiments, an additional method was established to prepare plasma for analysis of low abundance proteins. This method involved chromatographic depletion of high-abundance plasma proteins and reduction of plasma proteome complexity through further chromatographic fractionation. Purification of IgM was achieved with high purity as confirmed by SDS-PAGE and IgM-specific immunoblot. Isolation and fractionation of low abundance protein was also performed successfully, as confirmed by SDS-PAGE and mass spectrometry analysis followed by label-free quantitative spectral analysis. The level of purity of the isolated IgM allows for further IgM-specific analysis of plasma samples. The developed fractionation scheme can be used for high throughput screening of human plasma in order to identify low and high abundance proteins as potential prognostic and diagnostic disease biomarkers.

  13. Multiple marker abundance profiling

    DEFF Research Database (Denmark)

    Hooper, Cornelia M.; Stevens, Tim J.; Saukkonen, Anna

    2017-01-01

    proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment...

  14. Region-specific RNA m6A methylation represents a new layer of control in the gene regulatory network in the mouse brain.

    Science.gov (United States)

    Chang, Mengqi; Lv, Hongyi; Zhang, Weilong; Ma, Chunhui; He, Xue; Zhao, Shunli; Zhang, Zhi-Wei; Zeng, Yi-Xin; Song, Shuhui; Niu, Yamei; Tong, Wei-Min

    2017-09-01

    N 6 -methyladenosine (m 6 A) is the most abundant epitranscriptomic mark found on mRNA and has important roles in various physiological processes. Despite the relatively high m 6 A levels in the brain, its potential functions in the brain remain largely unexplored. We performed a transcriptome-wide methylation analysis using the mouse brain to depict its region-specific methylation profile. RNA methylation levels in mouse cerebellum are generally higher than those in the cerebral cortex. Heterogeneity of RNA methylation exists across different brain regions and different types of neural cells including the mRNAs to be methylated, their methylation levels and methylation site selection. Common and region-specific methylation have different preferences for methylation site selection and thereby different impacts on their biological functions. In addition, high methylation levels of fragile X mental retardation protein (FMRP) target mRNAs suggest that m 6 A methylation is likely to be used for selective recognition of target mRNAs by FMRP in the synapse. Overall, we provide a region-specific map of RNA m 6 A methylation and characterize the distinct features of specific and common methylation in mouse cerebellum and cerebral cortex. Our results imply that RNA m 6 A methylation is a newly identified element in the region-specific gene regulatory network in the mouse brain. © 2017 The Authors.

  15. Enrichment and identification of the most abundant zinc binding proteins in developing barley grains by Zinc-IMAC capture and nano LC-MS/MS

    DEFF Research Database (Denmark)

    Dionisio, Giuseppe; Uddin, Mohammad Nasir; Vincze, Eva

    2018-01-01

    exhibited zinc binding. In the aleurone/subaleurone, zinc affinity captured proteins were late abundant embryogenesis proteins, dehydrins, many isoforms of non-specific lipid transfer proteins, and alpha amylase trypsin inhibitor. Conclusions: We have shown evidence that abundant barley grain proteins have......Background: Zinc accumulates in the embryo, aleurone, and subaleurone layers at different amounts in cereal grains. Our hypothesis is that zinc could be stored bound, not only to low MW metabolites/proteins, but also to high MW proteins as well. Methods: In order to identify the most abundant zinc...

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

    Science.gov (United States)

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

    2014-04-01

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

  17. In vivo versus in vitro protein abundance analysis of Shigella dysenteriae type 1 reveals changes in the expression of proteins involved in virulence, stress and energy metabolism

    Directory of Open Access Journals (Sweden)

    Donohue-Rolfe Arthur

    2011-06-01

    Full Text Available Abstract Background Shigella dysenteriae serotype 1 (SD1 causes the most severe form of epidemic bacillary dysentery. Quantitative proteome profiling of Shigella dysenteriae serotype 1 (SD1 in vitro (derived from LB cell cultures and in vivo (derived from gnotobiotic piglets was performed by 2D-LC-MS/MS and APEX, a label-free computationally modified spectral counting methodology. Results Overall, 1761 proteins were quantitated at a 5% FDR (false discovery rate, including 1480 and 1505 from in vitro and in vivo samples, respectively. Identification of 350 cytoplasmic membrane and outer membrane (OM proteins (38% of in silico predicted SD1 membrane proteome contributed to the most extensive survey of the Shigella membrane proteome reported so far. Differential protein abundance analysis using statistical tests revealed that SD1 cells switched to an anaerobic energy metabolism under in vivo conditions, resulting in an increase in fermentative, propanoate, butanoate and nitrate metabolism. Abundance increases of transcription activators FNR and Nar supported the notion of a switch from aerobic to anaerobic respiration in the host gut environment. High in vivo abundances of proteins involved in acid resistance (GadB, AdiA and mixed acid fermentation (PflA/PflB indicated bacterial survival responses to acid stress, while increased abundance of oxidative stress proteins (YfiD/YfiF/SodB implied that defense mechanisms against oxygen radicals were mobilized. Proteins involved in peptidoglycan turnover (MurB were increased, while β-barrel OM proteins (OmpA, OM lipoproteins (NlpD, chaperones involved in OM protein folding pathways (YraP, NlpB and lipopolysaccharide biosynthesis (Imp were decreased, suggesting unexpected modulations of the outer membrane/peptidoglycan layers in vivo. Several virulence proteins of the Mxi-Spa type III secretion system and invasion plasmid antigens (Ipa proteins required for invasion of colonic epithelial cells, and release

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

    Directory of Open Access Journals (Sweden)

    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

  19. Triple SILAC quantitative proteomic analysis reveals differential abundance of cell signaling proteins between normal and lung cancer-derived exosomes.

    Science.gov (United States)

    Clark, David J; Fondrie, William E; Yang, Austin; Mao, Li

    2016-02-05

    Exosomes are 30-100 nm sized membrane vesicles released by cells into the extracellular space that mediate intercellular communication via transfer of proteins and other biological molecules. To better understand the role of these microvesicles in lung carcinogenesis, we employed a Triple SILAC quantitative proteomic strategy to examine the differential protein abundance between exosomes derived from an immortalized normal bronchial epithelial cell line and two non-small cell lung cancer (NSCLC) cell lines harboring distinct activating mutations in the cell signaling molecules: Kirsten rat sarcoma viral oncogene homolog (KRAS) or epidermal growth factor receptor (EGFR). In total, we were able to quantify 721 exosomal proteins derived from the three cell lines. Proteins associated with signal transduction, including EGFR, GRB2 and SRC, were enriched in NSCLC exosomes, and could actively regulate cell proliferation in recipient cells. This study's investigation of the NSCLC exosomal proteome has identified enriched protein cargo that can contribute to lung cancer progression, which may have potential clinical implications in biomarker development for patients with NSCLC. The high mortality associated with lung cancer is a result of late-stage diagnosis of the disease. Current screening techniques used for early detection of lung cancer lack the specificity for accurate diagnosis. Exosomes are nano-sized extracellular vesicles, and the increased abundance of select protein cargo in exosomes derived from cancer cells may be used for diagnostic purposes. In this paper, we applied quantitative proteomic analysis to elucidate abundance differences in exosomal protein cargo between two NSCLC cell lines with distinctive oncogene mutations and an immortalized normal bronchial epithelial cell line. This study revealed proteins associated with cell adhesion, the extracellular matrix, and a variety of signaling molecules were enriched in NSCLC exosomes. The present data reveals

  20. Brain region specific mitophagy capacity could contribute to selective neuronal vulnerability in Parkinson's disease

    Directory of Open Access Journals (Sweden)

    Zabel Claus

    2011-09-01

    Full Text Available Abstract Parkinson's disease (PD is histologically well defined by its characteristic degeneration of dopaminergic neurons in the substantia nigra pars compacta. Remarkably, divergent PD-related mutations can generate comparable brain region specific pathologies. This indicates that some intrinsic region-specificity respecting differential neuron vulnerability exists, which codetermines the disease progression. To gain insight into the pathomechanism of PD, we investigated protein expression and protein oxidation patterns of three different brain regions in a PD mouse model, the PINK1 knockout mice (PINK1-KO, in comparison to wild type control mice. The dysfunction of PINK1 presumably affects mitochondrial turnover by disturbing mitochondrial autophagic pathways. The three brain regions investigated are the midbrain, which is the location of substantia nigra; striatum, the major efferent region of substantia nigra; and cerebral cortex, which is more distal to PD pathology. In all three regions, mitochondrial proteins responsible for energy metabolism and membrane potential were significantly altered in the PINK1-KO mice, but with very different region specific accents in terms of up/down-regulations. This suggests that disturbed mitophagy presumably induced by PINK1 knockout has heterogeneous impacts on different brain regions. Specifically, the midbrain tissue seems to be most severely hit by defective mitochondrial turnover, whereas cortex and striatum could compensate for mitophagy nonfunction by feedback stimulation of other catabolic programs. In addition, cerebral cortex tissues showed the mildest level of protein oxidation in both PINK1-KO and wild type mice, indicating either a better oxidative protection or less reactive oxygen species (ROS pressure in this brain region. Ultra-structural histological examination in normal mouse brain revealed higher incidences of mitophagy vacuoles in cerebral cortex than in striatum and substantia

  1. The effect of colostrum intake on blood plasma proteome profile in newborn lambs: low abundance proteins

    DEFF Research Database (Denmark)

    Hernandez Castellano, Lorenzo E; de Almeida, André Martinho; Ventosa, Miguel

    2014-01-01

    Colostrum intake by newborn lambs plays a fundamental role in the perinatal period, ensuring lamb survival. In this study, blood plasma samples from two groups of newborn lambs (Colostrum group and Delayed Colostrum group) at 2 and 14 h after birth were treated to reduce the content of high abund...

  2. 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.

  3. 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.

  4. Enrichment and Identification of the Most Abundant Zinc Binding Proteins in Developing Barley Grains by Zinc-IMAC Capture and Nano LC-MS/MS

    Directory of Open Access Journals (Sweden)

    Giuseppe Dionisio

    2018-01-01

    Full Text Available Background: Zinc accumulates in the embryo, aleurone, and subaleurone layers at different amounts in cereal grains. Our hypothesis is that zinc could be stored bound, not only to low MW metabolites/proteins, but also to high MW proteins as well. Methods: In order to identify the most abundant zinc binding proteins in different grain tissues, we microdissected barley grains into (1 seed coats; (2 aleurone/subaleurone; (3 embryo; and (4 endosperm. Initial screening for putative zinc binding proteins from the different tissue types was performed by fractionating proteins according to solubility (Osborne fractionation, and resolving those via Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE followed by polyvinylidene fluoride (PVDF membrane blotting and dithizone staining. Selected protein fractions were subjected to Zn2+-immobilized metal ion affinity chromatography, and the captured proteins were identified using nanoscale liquid chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS. Results: In the endosperm, the most abundant zinc binding proteins were the storage protein B-hordeins, gamma-, and D-hordeins, while in the embryo, 7S globulins storage proteins exhibited zinc binding. In the aleurone/subaleurone, zinc affinity captured proteins were late abundant embryogenesis proteins, dehydrins, many isoforms of non-specific lipid transfer proteins, and alpha amylase trypsin inhibitor. Conclusions: We have shown evidence that abundant barley grain proteins have been captured by Zn-IMAC, and their zinc binding properties in relationship to the possibility of zinc storage is discussed.

  5. Region-specific mechanical properties of the human patella tendon

    DEFF Research Database (Denmark)

    Haraldsson, B T; Aagaard, P; Krogsgaard, M

    2004-01-01

    The present study investigated the mechanical properties of tendon fascicles from the anterior and posterior human patellar tendon. Collagen fascicles from the anterior and posterior human patellar tendon in healthy young men (mean +/- SD, 29.0 +/- 4.6 yr, n = 6) were tested in a mechanical rig...... portion of the tendon, indicating region-specific material properties....

  6. Direct Correlation between Motile Behavior and Protein Abundance in Single Cells.

    Directory of Open Access Journals (Sweden)

    Yann S Dufour

    2016-09-01

    Full Text Available Understanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB at different levels, we quantitatively mapped motile phenotype (tumble bias to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-06-15

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

  8. Characterization of threonine side chain dynamics in an antifreeze protein using natural abundance 13C NMR spectroscopy

    International Nuclear Information System (INIS)

    Daley, Margaret E.; Sykes, Brian D.

    2004-01-01

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

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

    Science.gov (United States)

    Rashydov, Namik M; Hajduch, Martin

    2015-01-01

    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 http://www.chernobylproteomics.sav.sk.

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

    Directory of Open Access Journals (Sweden)

    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.

  11. Discovery and validation of protein abundance differences between follicular thyroid neoplasms.

    NARCIS (Netherlands)

    Netea-Maier, R.T.; Hunsucker, S.W.; Hoevenaars, B.M.; Helmke, S.M.; Slootweg, P.J.; Hermus, A.R.M.M.; Haugen, B.R.; Duncan, M.W.

    2008-01-01

    Distinguishing between benign follicular thyroid adenoma (FTA) and malignant follicular thyroid carcinoma (FTC) by cytologic features alone is not possible. Molecular markers may aid distinguishing FTA from FTC in patients with indeterminate cytology. The aim of this study is to define protein

  12. An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems.

    Science.gov (United States)

    Lu, Chuan; King, Ross D

    2009-08-15

    Distribution analysis is one of the most basic forms of statistical analysis. Thanks to improved analytical methods, accurate and extensive quantitative measurements can now be made of the mRNA, protein and metabolite from biological systems. Here, we report a large-scale analysis of the population abundance distributions of the transcriptomes, proteomes and metabolomes from varied biological systems. We compared the observed empirical distributions with a number of distributions: power law, lognormal, loglogistic, loggamma, right Pareto-lognormal (PLN) and double PLN (dPLN). The best-fit for mRNA, protein and metabolite population abundance distributions was found to be the dPLN. This distribution behaves like a lognormal distribution around the centre, and like a power law distribution in the tails. To better understand the cause of this observed distribution, we explored a simple stochastic model based on geometric Brownian motion. The distribution indicates that multiplicative effects are causally dominant in biological systems. We speculate that these effects arise from chemical reactions: the central-limit theorem then explains the central lognormal, and a number of possible mechanisms could explain the long tails: positive feedback, network topology, etc. Many of the components in the central lognormal parts of the empirical distributions are unidentified and/or have unknown function. This indicates that much more biology awaits discovery.

  13. A simple microfluidic platform to study age-dependent protein abundance and localization changes in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Margarita Cabrera

    2017-04-01

    Full Text Available The budding yeast Saccharomyces cerevisiae divides asymmetrically, with a smaller daughter cell emerging from its larger mother cell. While the daughter lineage is immortal, mother cells age with each cell division and have a finite lifespan. The replicative ageing of the yeast mother cell has been used as a model to study the ageing of mitotically active human cells. Several microfluidic platforms, which use fluid flow to selectively remove daughter cells, have recently been developed that can monitor cell physiology as mother cells age. However, these platforms are not trivial to set up and users often require many hours of training. In this study, we have developed a simple system, which combines a commercially available microfluidic platform (the CellASIC ONIX Microfluidic Platform and a genetic tool to prevent the proliferation of daughter cells (the Mother Enrichment Program, to monitor protein abundance and localization changes during approximately the first half of the yeast replicative lifespan. We validated our system by observing known age-dependent changes, such as decreased Sir2 abundance, and have identified a protein with a previously unknown age-dependent change in localization.

  14. Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton.

    Science.gov (United States)

    Magwanga, Richard Odongo; Lu, Pu; Kirungu, Joy Nyangasi; Lu, Hejun; Wang, Xingxing; Cai, Xiaoyan; Zhou, Zhongli; Zhang, Zhenmei; Salih, Haron; Wang, Kunbo; Liu, Fang

    2018-01-15

    Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein families have been carried out in other plants, but not in upland cotton. The main aim of this research work was to characterize the late embryogenesis abundant (LEA) protein families and to carry out gene expression analysis to determine their potential role in drought stress tolerance in upland cotton. Increased cotton production in the face of declining precipitation and availability of fresh water for agriculture use is the focus for breeders, cotton being the backbone of textile industries and a cash crop for many countries globally. In this work, a total of 242, 136 and 142 LEA genes were identified in G. hirsutum, G. arboreum and G. raimondii respectively. The identified genes were classified into eight groups based on their conserved domain and phylogenetic tree analysis. LEA 2 were the most abundant, this could be attributed to their hydrophobic character. Upland cotton LEA genes have fewer introns and are distributed in all chromosomes. Majority of the duplicated LEA genes were segmental. Syntenic analysis showed that greater percentages of LEA genes are conserved. Segmental gene duplication played a key role in the expansion of LEA genes. Sixty three miRNAs were found to target 89 genes, such as miR164, ghr-miR394 among others. Gene ontology analysis revealed that LEA genes are involved in desiccation and defense responses. Almost all the LEA genes in their promoters contained ABRE, MBS, W-Box and TAC-elements, functionally known to be involved in drought stress and other stress responses. Majority of the LEA genes were involved in secretory pathways. Expression profile analysis indicated that most of the LEA genes were highly expressed in drought tolerant cultivars Gossypium tomentosum as opposed to drought susceptible, G. hirsutum. The tolerant

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

    Directory of Open Access Journals (Sweden)

    Manuel Bauer

    2015-12-01

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

  16. EBV latent membrane protein 1 abundance correlates with patient age but not with metastatic behavior in north African nasopharyngeal carcinomas

    Directory of Open Access Journals (Sweden)

    Boudawara Tahia

    2005-04-01

    Full Text Available Abstract Background Undifferentiated nasopharyngeal carcinomas are rare in a majority of countries but they occur at a high incidence in South China and to a lesser extent in North Africa. They are constantly associated with the Epstein-Barr virus (EBV regardless of patient geographic origin. In North Africa, the distribution of NPC cases according to patient age is bi-modal with a large group of patients being around 50 years old (80% and a smaller group below 25 years old. We and others have previously shown that the juvenile form of NPC has distinct biological characteristics including a low amount of p53 and Bcl2 in the tumor tissue and a low level of anti-EBV IgG and IgA in the peripheral blood. Results To get more insight on potential oncogenic mechanisms specific of these two forms, LMP1 abundance was assessed in 82 NPC patients of both groups, using immuno-histochemistry and semi-quantitative evaluation of tissue staining. Serum levels of anti-EBV antibodies were simultaneously assessed. For LMP1 staining, we used the S12 antibody which has proven to be more sensitive than the common anti-LMP1 CS1-4 for analysis of tissue sections. In all NPC biopsies, at least a small fraction of cells was positively stained by S12. LMP1 abundance was strongly correlated to patient age, with higher amounts of the viral protein detected in specimens of the juvenile form. In contrast, LMP1 abundance was not correlated to the presence of lymph node or visceral metastases, nor to the risk of metastatic recurrence. It was also independent of the level of circulating anti-EBV antibodies. Conclusion The high amount of LMP1 recorded in tumors from young patients confirms that the juvenile form of NPC has specific features regarding not only cellular but also viral gene expression.

  17. Reporter-Based Synthetic Genetic Array Analysis: A Functional Genomics Approach for Investigating Transcript or Protein Abundance Using Fluorescent Proteins in Saccharomyces cerevisiae.

    Science.gov (United States)

    Göttert, Hendrikje; Mattiazzi Usaj, Mojca; Rosebrock, Adam P; Andrews, Brenda J

    2018-01-01

    Fluorescent reporter genes have long been used to quantify various cell features such as transcript and protein abundance. Here, we describe a method, reporter synthetic genetic array (R-SGA) analysis, which allows for the simultaneous quantification of any fluorescent protein readout in thousands of yeast strains using an automated pipeline. R-SGA combines a fluorescent reporter system with standard SGA analysis and can be used to examine any array-based strain collection available to the yeast community. This protocol describes the R-SGA methodology for screening different arrays of yeast mutants including the deletion collection, a collection of temperature-sensitive strains for the assessment of essential yeast genes and a collection of inducible overexpression strains. We also present an alternative pipeline for the analysis of R-SGA output strains using flow cytometry of cells in liquid culture. Data normalization for both pipelines is discussed.

  18. Age-and Brain Region-Specific Differences in Mitochondrial ...

    Science.gov (United States)

    Mitochondria are central regulators of energy homeostasis and play a pivotal role in mechanisms of cellular senescence. The objective of the present study was to evaluate mitochondrial bio­-energetic parameters in five brain regions [brainstem (BS), frontal cortex (FC), cerebellum (CER), striatum (STR), hippocampus (HIP)] of four diverse age groups [1 Month (young), 4 Month (adult), 12 Month (middle-aged), 24 Month (old age)] to understand age-related differences in selected brain regions and their contribution to age-related chemical sensitivity. Mitochondrial bioenergetics parameters and enzyme activity were measured under identical conditions across multiple age groups and brain regions in Brown Norway rats (n = 5). The results indicate age- and brain region-specific patterns in mitochondrial functional endpoints. For example, an age-specific decline in ATP synthesis (State 111 respiration) was observed in BS and HIP. Similarly, the maximal respiratory capacities (State V1 and V2) showed age-specific declines in all brain regions examined (young > adult > middle-aged > old age). Amongst all regions, HIP had the greatest change in mitochondrial bioenergetics, showing declines in the 4, 12 and 24 Month age groups. Activities of mitochondrial pyruvate dehydrogenase complex (PDHC) and electron transport chain (ETC) complexes I, II, and IV enzymes were also age- and brain-region specific. In general changes associated with age were more pronounced, with

  19. The Prader-Willi syndrome proteins MAGEL2 and necdin regulate leptin receptor cell surface abundance through ubiquitination pathways.

    Science.gov (United States)

    Wijesuriya, Tishani Methsala; De Ceuninck, Leentje; Masschaele, Delphine; Sanderson, Matthea R; Carias, Karin Vanessa; Tavernier, Jan; Wevrick, Rachel

    2017-11-01

    In Prader-Willi syndrome (PWS), obesity is caused by the disruption of appetite-controlling pathways in the brain. Two PWS candidate genes encode MAGEL2 and necdin, related melanoma antigen proteins that assemble into ubiquitination complexes. Mice lacking Magel2 are obese and lack leptin sensitivity in hypothalamic pro-opiomelanocortin neurons, suggesting dysregulation of leptin receptor (LepR) activity. Hypothalamus from Magel2-null mice had less LepR and altered levels of ubiquitin pathway proteins that regulate LepR processing (Rnf41, Usp8, and Stam1). MAGEL2 increased the cell surface abundance of LepR and decreased their degradation. LepR interacts with necdin, which interacts with MAGEL2, which complexes with RNF41 and USP8. Mutations in the MAGE homology domain of MAGEL2 suppress RNF41 stabilization and prevent the MAGEL2-mediated increase of cell surface LepR. Thus, MAGEL2 and necdin together control LepR sorting and degradation through a dynamic ubiquitin-dependent pathway. Loss of MAGEL2 and necdin may uncouple LepR from ubiquitination pathways, providing a cellular mechanism for obesity in PWS. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  20. Nitrogen 15 abundance in protein fractions of beans fertilized with ({sup 15}NH{sub 4}){sub 2}SO{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Chaud, Saula Goulart; Oliveira, Admar Costa de [Universidade Estadual de Campinas, SP (Brazil). Faculdade de Estudos Agricolas. Dept. de Planejamento Alimentar e Nutricao; Trivelin, Paulo Cesar Ocheuze [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil). Lab. de Isotopos Estaveis]. E-mail: admarco@fea.unicamp.br

    2002-12-01

    Studies evaluating the protein nutritive value of beans labelled with 15 N, using 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 Pirata 1) with 1.394 atoms % 15 N, resulted in the same abundance of the whole flour and of the protein fractions extracted from the beans with 0.5 mol L{sup -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 15 N, 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 L 1 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. (author)

  1. HEROD: a human ethnic and regional specific omics database.

    Science.gov (United States)

    Zeng, Xian; Tao, Lin; Zhang, Peng; Qin, Chu; Chen, Shangying; He, Weidong; Tan, Ying; Xia Liu, Hong; Yang, Sheng Yong; Chen, Zhe; Jiang, Yu Yang; Chen, Yu Zong

    2017-10-15

    Genetic and gene expression variations within and between populations and across geographical regions have substantial effects on the biological phenotypes, diseases, and therapeutic response. The development of precision medicines can be facilitated by the OMICS studies of the patients of specific ethnicity and geographic region. However, there is an inadequate facility for broadly and conveniently accessing the ethnic and regional specific OMICS data. Here, we introduced a new free database, HEROD, a human ethnic and regional specific OMICS database. Its first version contains the gene expression data of 53 070 patients of 169 diseases in seven ethnic populations from 193 cities/regions in 49 nations curated from the Gene Expression Omnibus (GEO), the ArrayExpress Archive of Functional Genomics Data (ArrayExpress), the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Geographic region information of curated patients was mainly manually extracted from referenced publications of each original study. These data can be accessed and downloaded via keyword search, World map search, and menu-bar search of disease name, the international classification of disease code, geographical region, location of sample collection, ethnic population, gender, age, sample source organ, patient type (patient or healthy), sample type (disease or normal tissue) and assay type on the web interface. The HEROD database is freely accessible at http://bidd2.nus.edu.sg/herod/index.php. The database and web interface are implemented in MySQL, PHP and HTML with all major browsers supported. phacyz@nus.edu.sg. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  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. Region-specific vulnerability to endoplasmic reticulum stress ...

    Indian Academy of Sciences (India)

    2013-11-06

    Nov 6, 2013 ... glucose-regulated protein (GRP) 78, a good marker of ER stress, were assessed by Western ..... calcium homeostasis is disturbed, because ATP is needed to ... lum stress and insulin signalling proteins in diabetes-induced.

  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

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

    Directory of Open Access Journals (Sweden)

    Caiqiu Gao

    2014-01-01

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

  6. 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.

  7. Evidence of educational inadequacies in region-specific musculoskeletal medicine.

    Science.gov (United States)

    Day, Charles S; Yeh, Albert C

    2008-10-01

    Recent studies suggest US medical schools are not effectively addressing musculoskeletal medicine in their curricula. We examined if there were specific areas of weakness by analyzing students' knowledge of and confidence in examining specific anatomic regions. A cross-sectional survey study of third- and fourth-year students at Harvard Medical School was conducted during the 2005 to 2006 academic year. One hundred sixty-two third-year students (88% response) and 87 fourth-year students (57% response) completed the Freedman and Bernstein cognitive mastery examination in musculoskeletal medicine and a survey eliciting their clinical confidence in examining the shoulder, elbow, hand, back, hip, knee, and foot on a one to five Likert scale. We specifically analyzed examination questions dealing with the upper extremity, lower extremity, back, and others, which included more systemic conditions such as arthritis, metabolic bone diseases, and cancer. Students failed to meet the established passing benchmark of 70% in all subgroups except for the others category. Confidence scores in performing a physical examination and in generating a differential diagnosis indicated students felt below adequate confidence (3.0 of 5) in five of the seven anatomic regions. Our study provides evidence that region-specific musculoskeletal medicine is a potential learning gap that may need to be addressed in the undergraduate musculoskeletal curriculum.

  8. Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

    Science.gov (United States)

    Chen, Wei-Hua; van Noort, Vera; Lluch-Senar, Maria; Hennrich, Marco L.; H. Wodke, Judith A.; Yus, Eva; Alibés, Andreu; Roma, Guglielmo; Mende, Daniel R.; Pesavento, Christina; Typas, Athanasios; Gavin, Anne-Claude; Serrano, Luis; Bork, Peer

    2016-01-01

    We developed a comprehensive resource for the genome-reduced bacterium Mycoplasma pneumoniae comprising 1748 consistently generated ‘-omics’ data sets, and used it to quantify the power of antisense non-coding RNAs (ncRNAs), lysine acetylation, and protein phosphorylation in predicting protein abundance (11%, 24% and 8%, respectively). These factors taken together are four times more predictive of the proteome abundance than of mRNA abundance. In bacteria, post-translational modifications (PTMs) and ncRNA transcription were both found to increase with decreasing genomic GC-content and genome size. Thus, the evolutionary forces constraining genome size and GC-content modify the relative contributions of the different regulatory layers to proteome homeostasis, and impact more genomic and genetic features than previously appreciated. Indeed, these scaling principles will enable us to develop more informed approaches when engineering minimal synthetic genomes. PMID:26773059

  9. Skeletal muscle protein synthesis and the abundance of the mRNA translation initiation repressor PDCD4 are inversely regulated by fasting and refeeding in rats.

    Science.gov (United States)

    Zargar, Sana; Moreira, Tracy S; Samimi-Seisan, Helena; Jeganathan, Senthure; Kakade, Dhanshri; Islam, Nushaba; Campbell, Jonathan; Adegoke, Olasunkanmi A J

    2011-06-01

    Optimal skeletal muscle mass is vital to human health, because defects in muscle protein metabolism underlie or exacerbate human diseases. The mammalian target of rapamycin complex 1 is critical in the regulation of mRNA translation and protein synthesis. These functions are mediated in part by the ribosomal protein S6 kinase 1 (S6K1) through mechanisms that are poorly understood. The tumor suppressor programmed cell death 4 (PDCD4) has been identified as a novel substrate of S6K1. Here, we examined 1) the expression of PDCD4 in skeletal muscle and 2) its regulation by feed deprivation (FD) and refeeding. Male rats (~100 g; n = 6) were subjected to FD for 48 h; some rats were refed for 2 h. FD suppressed muscle fractional rates of protein synthesis and Ser(67) phosphorylation of PDCD4 (-50%) but increased PDCD4 abundance (P muscle fractional rates of protein synthesis and reduced PDCD4 abundance relative to FD. Finally, when myoblasts were grown in amino acid- and serum-free medium, phenylalanine incorporation into proteins in cells depleted of PDCD4 more than doubled the values in cells with a normal level of PDCD4 (P skeletal muscle in parallel with the reduction of the abundance of this mRNA translation inhibitor.

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

    Science.gov (United States)

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

    2016-07-01

    The role of interleukin-1 (IL-1), a pro-inflammatory cytokine, in parturition is typically noted by changes in its concentrations. Studying the expression of its receptor family, IL-1 receptor (IL-1R) 1, IL-1R2, IL-1R accessory protein (IL-1RAcP), and its predominantly brain isoform, IL-1RAcPb, during late gestation in the uterus in the Long-Evans rat is another. We assessed changes in their mRNA and protein relative abundance in the uterus and compared IL-1RAcP and IL-1RAcPb mRNA abundance in uterus, cervix, ovaries, placenta, and whole blood of Long-Evans rats during late gestation or in RU486 and progesterone-treated dams using quantitative real-time PCR and western immunoblotting. IL-1R1, IL-1RAcP, and IL-1RAcPb mRNA abundance significantly increased in the uterus at delivery whereas IL-1R2 mRNA abundance significantly decreased. IL-1R1 protein increased at term and IL-1R2 protein decreased at term compared to nonpregnant uteri. IL1-RAcPb mRNA abundance was less than IL-1RAcP, but in the lower uterine segment it was the highest of all tissues examined. RU486 stimulated preterm delivery and an increase in IL-1R1 mRNA abundance whereas progesterone administration extended pregnancy and suppressed the increase in IL-1R1. These data suggest that changes in uterine sensitivity to IL-1 occur during late gestation and suggest another level of regulation for the control of delivery. The roles for IL-1RAcP and IL-1RAcPb need to be determined, but may relate to different intracellular signaling pathways. © 2016 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of the American Physiological Society and The Physiological Society.

  11. Brain noise is task dependent and region specific.

    Science.gov (United States)

    Misić, Bratislav; Mills, Travis; Taylor, Margot J; McIntosh, Anthony R

    2010-11-01

    The emerging organization of anatomical and functional connections during human brain development is thought to facilitate global integration of information. Recent empirical and computational studies have shown that this enhanced capacity for information processing enables a diversified dynamic repertoire that manifests in neural activity as irregularity and noise. However, transient functional networks unfold over multiple time, scales and the embedding of a particular region depends not only on development, but also on the manner in which sensory and cognitive systems are engaged. Here we show that noise is a facet of neural activity that is also sensitive to the task context and is highly region specific. Children (6-16 yr) and adults (20-41 yr) performed a one-back face recognition task with inverted and upright faces. Neuromagnetic activity was estimated at several hundred sources in the brain by applying a beamforming technique to the magnetoencephalogram (MEG). During development, neural activity became more variable across the whole brain, with most robust increases in medial parietal regions, such as the precuneus and posterior cingulate cortex. For young children and adults, activity evoked by upright faces was more variable and noisy compared with inverted faces, and this effect was reliable only in the right fusiform gyrus. These results are consistent with the notion that upright faces engender a variety of integrative neural computations, such as the relations among facial features and their holistic constitution. This study shows that transient changes in functional integration modulated by task demand are evident in the variability of regional neural activity.

  12. Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q-Exactive HF Mass Spectrometer.

    Science.gov (United States)

    Wei, Wei; Luo, Weijia; Wu, Feilin; Peng, Xuehui; Zhang, Yao; Zhang, Manli; Zhao, Yan; Su, Na; Qi, YingZi; Chen, Lingsheng; Zhang, Yangjun; Wen, Bo; He, Fuchu; Xu, Ping

    2016-11-04

    Since 2012, missing proteins (MPs) investigation has been one of the critical missions of Chromosome-Centric Human Proteome Project (C-HPP) through various biochemical strategies. On the basis of our previous testis MPs study, faster scanning and higher resolution mass-spectrometry-based proteomics might be conducive to MPs exploration, especially for low-abundance proteins. In this study, Q-Exactive HF (HF) was used to survey proteins from the same testis tissues separated by two separating methods (tricine- and glycine-SDS-PAGE), as previously described. A total of 8526 proteins were identified, of which more low-abundance proteins were uniquely detected in HF data but not in our previous LTQ Orbitrap Velos (Velos) reanalysis data. Further transcriptomics analysis showed that these uniquely identified proteins by HF also had lower expression at the mRNA level. Of the 81 total identified MPs, 74 and 39 proteins were listed as MPs in HF and Velos data sets, respectively. Among the above MPs, 47 proteins (43 neXtProt PE2 and 4 PE3) were ranked as confirmed MPs after verifying with the stringent spectra match and isobaric and single amino acid variants filtering. Functional investigation of these 47 MPs revealed that 11 MPs were testis-specific proteins and 7 MPs were involved in spermatogenesis process. Therefore, we concluded that higher scanning speed and resolution of HF might be factors for improving the low-abundance MP identification in future C-HPP studies. All mass-spectrometry data from this study have been deposited in the ProteomeXchange with identifier PXD004092.

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

    Directory of Open Access Journals (Sweden)

    Seong-Beom Ahn

    2014-06-01

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

  14. Highly efficient enrichment of low-abundance intact proteins by core-shell structured Fe3O4-chitosan@graphene composites.

    Science.gov (United States)

    Zhang, Peng; Fang, Xiaoni; Yan, Guoquan; Gao, Mingxia; Zhang, Xiangmin

    2017-11-01

    In proteomics research, the screening and monitoring of disease biomarkers is still a major challenge, mainly due to their low concentration in biological samples. However, the universal enrichment of intact proteins has not been further studied. In this work, we developed a Fe 3 O 4 -chitosan@graphene (Fe 3 O 4 -CS@G) core-shell composite to enrich low-abundance proteins from biological samples. Fe 3 O 4 -CS@G composite holds chitosan layer decorated Fe 3 O 4 core, which improves the hydrophilicity of materials greatly. Meanwhile, the graphene nanosheets shell formed via electrostatic assembly endows the composite with huge surface area (178m 2 /g). The good water dispersibility ensures the sufficient contact opportunities between graphene composites and proteins, and the large surface area provides enough adsorption sites for the enrichment of proteins. Using Fe 3 O 4 -CS@G, four standard proteins Cyt-c, BSA, Myo and OVA were enriched with better adsorption capacity and recovery rate, compared with previously reported magnetic graphene composites. Additionally, the mechanism of compared to" is corrected into "compared with". proteins adsorption on Fe 3 O 4 -CS@G was further studied, which indicates that hydrophobic and electrostatic interaction work together to facilitate the universal and efficient enrichment of proteins. Human plasma sample was employed to further evaluate the enrichment performance of Fe 3 O 4 -CS@G. Eventually, 123 proteins were identified from one of SAX fractions of human plasma, which is much better than commercial Sep-pak C18 enrichment column (39 proteins). All these outstanding performances suggest that Fe 3 O 4 -CS@G is an ideal platform for the enrichment of low-abundance intact proteins and thus holds great potential to facilitate the identification of biomarkers from biological samples in proteomics research. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Ion-Exchange Sample Displacement Chromatography as a Method for Fast and Simple Isolation of Low- and High-Abundance Proteins from Complex Biological Mixtures

    Directory of Open Access Journals (Sweden)

    Martina Srajer Gajdosik

    2014-01-01

    Full Text Available Sample displacement chromatography (SDC in reversed phase and ion-exchange modes was introduced at the end of 1980s. This chromatographic method was first used for preparative purification of synthetic peptides, and subsequently adapted for protein fractionation, mainly in anion-exchange mode. In the past few years, SDC has been successfully used for enrichment of low- and medium-abundance proteins from complex biological fluids on both monolithic and bulk chromatographic supports. If aqueous mobile phase is used with the application of mild chromatographic conditions, isolated proteins are not denatured and can also keep their biological activity. In this paper, the use of SDC in anion-exchange mode on a high-capacity chromatographic resin for separation of proteins from complex biological mixtures such as human plasma is demonstrated. By use of three and more columns coupled in series during sample application, and subsequent parallel elution of detached columns, additional separation of bound proteins was achieved. Highly enriched human serum albumin fraction and a number of physiologically active medium- and low-abundance proteins could be fractionated and detected by electrospray ionization tandem mass spectrometry (ESI-MS/MS and matrix assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS. The use of the aforementioned columns that can be sanitized with 1 M sodium hydroxide for further application of SDC in biotechnology and food technology was discussed.

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

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    Xiaolin Wu

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

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

    Directory of Open Access Journals (Sweden)

    Xiaolin eWu

    2015-01-01

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

  18. A combined blood based gene expression and plasma protein abundance signature for diagnosis of epithelial ovarian cancer - a study of the OVCAD consortium

    International Nuclear Information System (INIS)

    Pils, Dietmar; Sehouli, Jalid; Braicu, Ioana; Vergote, Ignace; Van Gorp, Toon; Mahner, Sven; Concin, Nicole; Speiser, Paul; Zeillinger, Robert; Tong, Dan; Hager, Gudrun; Obermayr, Eva; Aust, Stefanie; Heinze, Georg; Kohl, Maria; Schuster, Eva; Wolf, Andrea

    2013-01-01

    The immune system is a key player in fighting cancer. Thus, we sought to identify a molecular ‘immune response signature’ indicating the presence of epithelial ovarian cancer (EOC) and to combine this with a serum protein biomarker panel to increase the specificity and sensitivity for earlier detection of EOC. Comparing the expression of 32,000 genes in a leukocytes fraction from 44 EOC patients and 19 controls, three uncorrelated shrunken centroid models were selected, comprised of 7, 14, and 6 genes. A second selection step using RT-qPCR data and significance analysis of microarrays yielded 13 genes (AP2A1, B4GALT1, C1orf63, CCR2, CFP, DIS3, NEAT1, NOXA1, OSM, PAPOLG, PRIC285, ZNF419, and BC037918) which were finally used in 343 samples (90 healthy, six cystadenoma, eight low malignant potential tumor, 19 FIGO I/II, and 220 FIGO III/IV EOC patients). Using new 65 controls and 224 EOC patients (thereof 14 FIGO I/II) the abundances of six plasma proteins (MIF, prolactin, CA125, leptin, osteopondin, and IGF2) was determined and used in combination with the expression values from the 13 genes for diagnosis of EOC. Combined diagnostic models using either each five gene expression and plasma protein abundance values or 13 gene expression and six plasma protein abundance values can discriminate controls from patients with EOC with Receiver Operator Characteristics Area Under the Curve values of 0.998 and bootstrap .632+ validated classification errors of 3.1% and 2.8%, respectively. The sensitivities were 97.8% and 95.6%, respectively, at a set specificity of 99.6%. The combination of gene expression and plasma protein based blood derived biomarkers in one diagnostic model increases the sensitivity and the specificity significantly. Such a diagnostic test may allow earlier diagnosis of epithelial ovarian cancer

  19. Proteome-wide analysis of protein abundance and turnover remodelling during oncogenic transformation of human breast epithelial cells [version 1; referees: 2 approved, 1 approved with reservations

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    Tony Ly

    2018-05-01

    Full Text Available Background: Viral oncogenes and mutated proto-oncogenes are potent drivers of cancer malignancy. Downstream of the oncogenic trigger are alterations in protein properties that give rise to cellular transformation and the acquisition of malignant cellular phenotypes. Developments in mass spectrometry enable large-scale, multidimensional characterisation of proteomes. Such techniques could provide an unprecedented, unbiased view of how oncogene activation remodels a human cell proteome. Methods: Using quantitative MS-based proteomics and cellular assays, we analysed how transformation induced by activating v-Src kinase remodels the proteome and cellular phenotypes of breast epithelial (MCF10A cells. SILAC MS was used to comprehensively characterise the MCF10A proteome and to measure v-Src-induced changes in protein abundance across seven time-points (1-72 hrs. We used pulse-SILAC MS (Boisvert et al., 2012, to compare protein synthesis and turnover in control and transformed cells. Follow-on experiments employed a combination of cellular and functional assays to characterise the roles of selected Src-responsive proteins. Results: Src-induced transformation changed the expression and/or turnover levels of ~3% of proteins, affecting ~1.5% of the total protein molecules in the cell. Transformation increased the average rate of proteome turnover and disrupted protein homeostasis. We identify distinct classes of protein kinetics in response to Src activation. We demonstrate that members of the polycomb repressive complex 1 (PRC1 are important regulators of invasion and migration in MCF10A cells. Many Src-regulated proteins are present in low abundance and some are regulated post-transcriptionally. The signature of Src-responsive proteins is highly predictive of poor patient survival across multiple cancer types. Open access to search and interactively explore all these proteomic data is provided via the EPD database (www.peptracker.com/epd. Conclusions

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

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    Giulia Micallef

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

  1. 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...... 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......RNA expression of UT-B was not affected by dietary treatment, whereas mRNA expression of AQP3, 7, and 10 were greater in the high N compared with the low N fed cows. Using peptide-derived rabbit antibodies to cow AQP3, 7, and 8, immunoblotting revealed bands of approximately 27, 27, and 24 kDa in ruminal...

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    A gel-based method for a mass spectrometric site-specific glycoanalysis was developed using a recombinant glycoprotein expressed in two different cell lines. Hydrophilic interaction liquid chromatography at nanoscale level was used to enrich for glycopeptides prior to MS. The glycoprofiling...... glycoprofiling of a low abundance glycoprotein performed in an individual-specific manner allows for future studies of glycosylated biomarkers for person-specific detection of altered glycosylation and may thus allow early detection and monitoring of diseases....

  3. Increased uncoupling protein-2 mRNA abundance and glucocorticoid action in adipose tissue in the sheep fetus during late gestation is dependent on plasma cortisol and triiodothyronine

    Science.gov (United States)

    Gnanalingham, MG; Mostyn, A; Forhead, AJ; Fowden, AL; Symonds, ME; Stephenson, T

    2005-01-01

    The endocrine regulation of uncoupling protein-2 (UCP2), an inner mitochondrial protein, in fetal adipose tissue remains unclear. The present study aimed to determine if fetal plasma cortisol and triiodothyronine (T3) influenced the mRNA abundance of UCP2, glucocorticoid receptor (GR) and 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) and 2 (11βHSD2) in fetal adipose tissue in the sheep during late gestation. Perirenal–abdominal adipose tissue was sampled from ovine fetuses to which either cortisol (2–3 mg kg−1 day−1) or saline was infused for 5 days up to 127–130 days gestation, or near term fetuses (i.e. 142–145 days gestation) that were either adrenalectomised (AX) or remained intact. Fetal plasma cortisol and T3 concentrations were higher in the cortisol infused animals and lower in AX fetuses compared with their corresponding control group, and increased with gestational age. UCP2 and GR mRNA abundance were significantly lower in AX fetuses compared with age-matched controls, and increased with gestational age and by cortisol infusion. Glucocorticoid action in fetal adipose tissue was augmented by AX and suppressed by cortisol infusion, the latter also preventing the gestational increase in 11βHSD1 mRNA and decrease in 11βHSD2 mRNA. When all treatment groups were combined, both fetal plasma cortisol and T3 concentrations were positively correlated with UCP2, GR and 11βHSD2 mRNA abundance, but negatively correlated with 11βHSD1 mRNA abundance. In conclusion, plasma cortisol and T3 are both required for the late gestation rise in UCP2 mRNA and differentially regulate glucocorticoid action in fetal adipose tissue in the sheep during late gestation. PMID:15961419

  4. 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.

  5. Constrained Maximum Likelihood Estimation of Relative Abundances of Protein Conformation in a Heterogeneous Mixture from Small Angle X-Ray Scattering Intensity Measurements

    Science.gov (United States)

    Onuk, A. Emre; Akcakaya, Murat; Bardhan, Jaydeep P.; Erdogmus, Deniz; Brooks, Dana H.; Makowski, Lee

    2015-01-01

    In this paper, we describe a model for maximum likelihood estimation (MLE) of the relative abundances of different conformations of a protein in a heterogeneous mixture from small angle X-ray scattering (SAXS) intensities. To consider cases where the solution includes intermediate or unknown conformations, we develop a subset selection method based on k-means clustering and the Cramér-Rao bound on the mixture coefficient estimation error to find a sparse basis set that represents the space spanned by the measured SAXS intensities of the known conformations of a protein. Then, using the selected basis set and the assumptions on the model for the intensity measurements, we show that the MLE model can be expressed as a constrained convex optimization problem. Employing the adenylate kinase (ADK) protein and its known conformations as an example, and using Monte Carlo simulations, we demonstrate the performance of the proposed estimation scheme. Here, although we use 45 crystallographically determined experimental structures and we could generate many more using, for instance, molecular dynamics calculations, the clustering technique indicates that the data cannot support the determination of relative abundances for more than 5 conformations. The estimation of this maximum number of conformations is intrinsic to the methodology we have used here. PMID:26924916

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

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    Si Wu

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

  7. Identification of Besnoitia besnoiti proteins that showed differences in abundance between tachyzoite and bradyzoite stages by difference gel electrophoresis.

    Science.gov (United States)

    Fernández-García, Aurora; Alvarez-García, Gema; Marugán-Hernández, Virginia; García-Lunar, Paula; Aguado-Martínez, Adriana; Risco-Castillo, Verónica; Ortega-Mora, Luis M

    2013-07-01

    Bovine besnoitiosis is a chronic and debilitating disease, caused by the apicomplexan parasite Besnoitia besnoiti. Infection of cattle by B. besnoiti is governed by the tachyzoite stage, which is related to acute infection, and the bradyzoite stage gathered into macroscopic cysts located in subcutaneous tissue in the skin, mucosal membranes and sclera conjunctiva and related to persistence and chronic infection. However, the entire life cycle of this parasite and the molecular mechanisms underlying tachyzoite-to-bradyzoite conversion remain unknown. In this context, a different antigenic pattern has been observed between tachyzoite and bradyzoite extracts. Thus, to identify stage-specific proteins, a difference gel electrophoresis (DIGE) approach was used on tachyzoite and bradyzoite extracts followed by mass spectrometry (MS) analysis. A total of 130 and 132 spots were differentially expressed in bradyzoites and tachyzoites, respectively (average ratio ± 1.5, Presult, 5 up-regulated bradyzoite proteins (GAPDH, ENO1, LDH, SOD and RNA polymerase) and 5 up-regulated tachyzoite proteins (ENO2; LDH; ATP synthase; HSP70 and PDI) were identified. The present results set the basis for the identification of new proteins as drug targets. Moreover, the role of these proteins in tachyzoite-to-bradyzoite conversion and the role of the host cell environment should be a subject of further research.

  8. Circulating forms of immunoreactive parathyroid hormone-related protein for identifying patients with humoral hypercalcemia of malignancy. A comparative study with C-terminal (109-141)- and N-terminal (1-86)-region-specific PTHrP radioassay

    International Nuclear Information System (INIS)

    Suehiro, Mitsuko; Murakami, Minoru; Fukuchi, Minoru

    1994-01-01

    We evaluated the circulating forms of immunoreactive parathyroid hormone-related protein(PTHrP) in 115 healthy subjects and 122 patients with malignant diseases by using radioassay systems (RAS) specific for the C-terminal (109-141) fragment of PTHrP (C-RAS) and for the N-terminal(1-86) (N-RAS). PTHrP levels in healthy controls ranged from 1.5 to 38.2 (mean: 24.5) pmol/L with the C-RAS and from 0.9 to 2.5 (mean: 1.7) pmol/L with the N-RAS. The ratio of circulating N-terminal fragment (N) to C-terminal fragment (C) of PTHrP was calculated to be about 1 : 14.4 in the healthy subjects. Of the 122 patients with malignant diseases, 40 (32.8%) had circulating PTHrP levels undetectable with the N-RAS, but only 11 (9.0%) patients had levels undetectable with the C-RAS. Of the former 122 patients, 41 (33.6%) had high PTHrP as determined with the C-RAS, and 10 (8.2%) had high PTHrP as determined with the N-RAS. The former of these included only 8 (19.5%) humoral hypercalcemia malignancy(HHM) patients, while the latter included 8 (80.0%) HHM patients. The circulating N to C ratio was about 1 : 70.7 in the HHM patients. The N and C obtained with the different RASs showed a close correlation (r=0.86). The values also showed a close correlation with serum Ca; r=0.75 for C-RAS and r=0.81 for N-RAS. In addition, the correlation between the PTHrP reading obtained with the different RASs and serum Cr were: r=0.42 with C-RAS and r=0.26 with N-RAS. The circulating form of immunoreactive PTHrP fragments is therefore comprised mainly of PTHrP (109-141). In contrast, circulating concentrations of the PTHrP (1-86) fragment are very low, but detection of the PTHrP (1-86) fragment with the N-RAS is a more useful indicator of HHM with fewer false positive results and is less likely to be influenced by renal function than the detection of the PHPrP (109-141) fragment with C-RAS. (author)

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

    DEFF Research Database (Denmark)

    Lefort, Natalie; Glancy, Brian; Bowen, Benjamin

    2010-01-01

    the higher ROS production. Tandem mass spectrometry identified protein abundance differences per mitochondrial mass in insulin resistance, including lower abundance of complex I subunits and enzymes involved in the oxidation of branched-chain amino acids (BCAA) and fatty acids (e.g., carnitine...

  10. 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...

  11. Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: analysis of human plasma and cerebrospinal fluid.

    Science.gov (United States)

    Hyung, Seok-Won; Piehowski, Paul D; Moore, Ronald J; Orton, Daniel J; Schepmoes, Athena A; Clauss, Therese R; Chu, Rosalie K; Fillmore, Thomas L; Brewer, Heather; Liu, Tao; Zhao, Rui; Smith, Richard D

    2014-11-01

    Removal of highly abundant proteins in plasma is often carried out using immunoaffinity depletion to extend the dynamic range of measurements to lower abundance species. While commercial depletion columns are available for this purpose, they generally are not applicable to limited sample quantities (depletion media can be prohibitive for larger-scale studies. Modern LC-MS instrumentation provides the sensitivity necessary to scale-down depletion methods with minimal sacrifice to proteome coverage, which makes smaller volume depletion columns desirable for maximizing sample recovery when samples are limited, as well as for reducing the expense of large-scale studies. We characterized the performance of a 346 μL column volume microscale depletion system, using four different flow rates to determine the most effective depletion conditions for ∼6-μL injections of human plasma proteins and then evaluated depletion reproducibility at the optimum flow rate condition. Depletion of plasma using a commercial 10-mL depletion column served as the control. Results showed depletion efficiency of the microscale column increased as flow rate decreased, and that our microdepletion was reproducible. In an initial application, a 600-μL sample of human cerebrospinal fluid (CSF) pooled from multiple sclerosis patients was depleted and then analyzed using reversed phase liquid chromatography-mass spectrometry to demonstrate the utility of the system for this important biofluid where sample quantities are more commonly limited.

  12. Region-specific maturation of cerebral cortex in human fetal brain: diffusion tensor imaging and histology

    International Nuclear Information System (INIS)

    Trivedi, Richa; Gupta, Rakesh K.; Saksena, Sona; Husain, Nuzhat; Srivastava, Savita; Rathore, Ram K.S.; Sarma, Manoj K.; Malik, Gyanendra K.; Das, Vinita; Pradhan, Mandakini; Pandey, Chandra M.; Narayana, Ponnada A.

    2009-01-01

    In this study, diffusion tensor imaging (DTI) and glial fibrillary acidic protein (GFAP) immunohistochemical analysis in different cortical regions in fetal brains at different gestational age (GA) were performed. DTI was performed on 50 freshly aborted fetal brains with GA ranging from 12 to 42 weeks to compare age-related fractional anisotropy (FA) changes in different cerebral cortical regions that include frontal, parietal, occipital, and temporal lobes at the level of thalami. GFAP immunostaining was performed and the percentage of GFAP-positive areas was quantified. The cortical FA values in the frontal lobe peaked at around 26 weeks of GA, occipital and temporal lobes at around 20 weeks, and parietal lobe at around 23 weeks. A significant, but modest, positive correlation (r=0.31, p=0.02) was observed between cortical FA values and percentage area of GFAP expression in cortical region around the time period during which the migrational events are at its peak, i.e., GA ≤ 28 weeks for frontal cortical region and GA≤22 weeks for rest of the lobes. The DTI-derived FA quantification with its GFAP immunohistologic correlation in cortical regions of the various lobes of the cerebral hemispheres supports region-specific migrational and maturational events in human fetal brain. (orig.)

  13. Region-specific maturation of cerebral cortex in human fetal brain: diffusion tensor imaging and histology

    Energy Technology Data Exchange (ETDEWEB)

    Trivedi, Richa; Gupta, Rakesh K.; Saksena, Sona [Sanjay Gandhi Post Graduate Institute of Medical Sciences, Department of Radiodiagnosis, Lucknow, UP (India); Husain, Nuzhat; Srivastava, Savita [CSM Medical University, Department of Pathology, Lucknow (India); Rathore, Ram K.S.; Sarma, Manoj K. [Indian Institute of Technology, Department of Mathematics and Statistics, Kanpur (India); Malik, Gyanendra K. [CSM Medical University, Department of Pediatrics, Lucknow (India); Das, Vinita [CSM Medical University, Department of Obstetrics and Gynecology, Lucknow (India); Pradhan, Mandakini [Sanjay Gandhi Postgraduate Institute of Medical Sciences, Department of Medical Genetics, Lucknow (India); Pandey, Chandra M. [Sanjay Gandhi Postgraduate Institute of Medical Sciences, Department of Biostatistics, Lucknow (India); Narayana, Ponnada A. [University of Texas Medical School at Houston, Department of Diagnostic and Interventional Imaging, Houston, TX (United States)

    2009-09-15

    In this study, diffusion tensor imaging (DTI) and glial fibrillary acidic protein (GFAP) immunohistochemical analysis in different cortical regions in fetal brains at different gestational age (GA) were performed. DTI was performed on 50 freshly aborted fetal brains with GA ranging from 12 to 42 weeks to compare age-related fractional anisotropy (FA) changes in different cerebral cortical regions that include frontal, parietal, occipital, and temporal lobes at the level of thalami. GFAP immunostaining was performed and the percentage of GFAP-positive areas was quantified. The cortical FA values in the frontal lobe peaked at around 26 weeks of GA, occipital and temporal lobes at around 20 weeks, and parietal lobe at around 23 weeks. A significant, but modest, positive correlation (r=0.31, p=0.02) was observed between cortical FA values and percentage area of GFAP expression in cortical region around the time period during which the migrational events are at its peak, i.e., GA {<=} 28 weeks for frontal cortical region and GA{<=}22 weeks for rest of the lobes. The DTI-derived FA quantification with its GFAP immunohistologic correlation in cortical regions of the various lobes of the cerebral hemispheres supports region-specific migrational and maturational events in human fetal brain. (orig.)

  14. Region-specific proteolysis differentially regulates type 1 inositol 1,4,5-trisphosphate receptor activity.

    Science.gov (United States)

    Wang, Liwei; Wagner, Larry E; Alzayady, Kamil J; Yule, David I

    2017-07-14

    The inositol 1,4,5 trisphosphate receptor (IP 3 R) is an intracellular Ca 2+ release channel expressed predominately on the membranes of the endoplasmic reticulum. IP 3 R1 can be cleaved by caspase or calpain into at least two receptor fragments. However, the functional consequences of receptor fragmentation are poorly understood. Our previous work has demonstrated that IP 3 R1 channels, formed following either enzymatic fragmentation or expression of the corresponding complementary polypeptide chains, retain tetrameric architecture and are still activated by IP 3 binding despite the loss of peptide continuity. In this study, we demonstrate that region-specific receptor fragmentation modifies channel regulation. Specifically, the agonist-evoked temporal Ca 2+ release profile and protein kinase A modulation of Ca 2+ release are markedly altered. Moreover, we also demonstrate that activation of fragmented IP 3 R1 can result in a distinct functional outcome. Our work suggests that proteolysis of IP 3 R1 may represent a novel form of modulation of IP 3 R1 channel function and increases the repertoire of Ca 2+ signals achievable through this channel. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Olanzapine Reverses MK-801-Induced Cognitive Deficits and Region-Specific Alterations of NMDA Receptor Subunits

    Science.gov (United States)

    Liu, Xiao; Li, Jitao; Guo, Chunmei; Wang, Hongli; Sun, Yaxin; Wang, Han; Su, Yun-Ai; Li, Keqing; Si, Tianmei

    2018-01-01

    Cognitive dysfunction constitutes an essential component in schizophrenia for its early presence in the pathophysiology of the disease and close relatedness to life quality of patients. To develop effective treatment of cognitive deficits, it is important to understand their neurobiological causes and to identify potential therapeutic targets. In this study, adopting repeated MK-801 treatment as an animal model of schizophrenia, we investigated whether antipsychotic drugs, olanzapine and haloperidol, can reverse MK-801-induced cognitive deficits and how the reversal processes recruited proteins involved in glutamate neurotransmission in rat medial prefrontal cortex (mPFC) and hippocampus. We found that low-dose chronic MK-801 treatment impaired object-in-context recognition memory and reversal learning in the Morris water maze, leaving reference memory relatively unaffected, and that these cognitive deficits can be partially reversed by olanzapine, not haloperidol, treatment. At the molecular level, chronic MK-801 treatment resulted in the reduction of multiple N-methyl-D-aspartate (NMDA) receptor subunits in rat mPFC and olanzapine, not haloperidol, treatment restored the levels of GluN1 and phosphorylated GluN2B in this region. Taken together, MK-801-induced cognitive deficits may be associated with region-specific changes in NMDA receptor subunits and the reversal of specific NMDA receptor subunits may underlie the cognition-enhancing effects of olanzapine. PMID:29375333

  16. Hepatic nuclear sterol regulatory binding element protein 2 abundance is decreased and that of ABCG5 increased in male hamsters fed plant sterols.

    Science.gov (United States)

    Harding, Scott V; Rideout, Todd C; Jones, Peter J H

    2010-07-01

    The effect of dietary plant sterols on cholesterol homeostasis has been well characterized in the intestine, but how plant sterols affect lipid metabolism in other lipid-rich tissues is not known. Changes in hepatic cholesterol homeostasis in response to high dietary intakes of plant sterols were determined in male golden Syrian hamsters fed hypercholesterolemia-inducing diets with and without 2% plant sterols (wt:wt; Reducol, Forbes Meditech) for 28 d. Plasma and hepatic cholesterol concentrations, cholesterol biosynthesis and absorption, and changes in the expression of sterol response element binding protein 2 (SREBP2) and liver X receptor-beta (LXRbeta) and their target genes were measured. Plant sterol feeding reduced plasma total cholesterol, non-HDL cholesterol, and HDL cholesterol concentrations 43% (P 6-fold (P = 0.029) and >2-fold (P sterol-fed hamsters compared with controls. Plant sterol feeding also increased fractional cholesterol synthesis >2-fold (P sterol feeding increased hepatic protein expression of cytosolic (inactive) SREBP2, decreased nuclear (active) SREBP2, and tended to increase LXRbeta (P = 0.06) and ATP binding cassette transporter G5, indicating a differential modulation of the expression of proteins central to cholesterol metabolism. In conclusion, high-dose plant sterol feeding of hamsters changes hepatic protein abundance in favor of cholesterol excretion despite lower hepatic cholesterol concentrations and higher cholesterol fractional synthesis.

  17. Abundance in proteins expressed after functional electrical stimulation cycling or arm cycling ergometry training in persons with chronic spinal cord injury.

    Science.gov (United States)

    Gorgey, Ashraf S; Graham, Zachary A; Bauman, William A; Cardozo, Christopher; Gater, David R

    2017-07-01

    Longitudinal design. The study determined the effects of two forms of exercise training on the abundance of two proteins, (glucose transporter-4 [GLUT-4], adenosine monophosphate kinase [AMPK]) involved in glucose utilization and the transcriptional coactivator that regulates the genes involved in energy metabolism and mitochondrial biogenesis (peroxisome proliferator-activated receptor (PPAR) coactivator 1 alpha [PGC-1α]), in muscles in men with chronic motor-complete spinal cord injury (SCI). Clinical trial at a Medical Center. Nine men with chronic motor-complete SCI participated in functional electrical stimulation lower extremity cycling (FES-LEC; n = 4) or arm cycling ergometer (arm-cycling ergometer [ACE]; n = 5) 5 days/week for 16 weeks. Whole body composition was measured by dual energy X-ray absorptiometry. An intravenous glucose tolerance test was performed to measure glucose effectiveness (Sg) and insulin sensitivity (Si). Muscle biopsies of the right vastus lateralis (VL) and triceps muscles were collected one week prior to and post the exercise training intervention. Neither training intervention altered body composition or carbohydrate metabolism. GLUT-4 increased by 3.8 fold in the VL after FES training and increased 0.6 fold in the triceps after ACE training. PGC-1α increased by 2.3 fold in the VL after FES training and 3.8 fold in the triceps after ACE training. AMPK increased by 3.4 fold in the VL after FES training and in the triceps after ACE training. FES-LEC and ACE training were associated with greater protein expressions in the trained muscles by effectively influencing the abundance of GLUT-4, AMPK and PGC-1α. Thus, FES-LEC training of paralyzed muscle can modulate protein expression similar to that of trained and innervated muscle.

  18. Dimerization and DNA-binding of ASR1, a small hydrophilic protein abundant in plant tissues suffering from water loss

    International Nuclear Information System (INIS)

    Maskin, Laura; Frankel, Nicolas; Gudesblat, Gustavo; Demergasso, Maria J.; Pietrasanta, Lia I.; Iusem, Norberto D.

    2007-01-01

    The Asr gene family is present in Spermatophyta. Its members are generally activated under water stress. We present evidence that tomato ASR1, one of the proteins of the family, accumulates in seed during late stages of embryogenesis, a physiological process characterized by water loss. In vitro, electrophoretic assays show a homo-dimeric structure for ASR1 and highlight strong non-covalent interactions between monomers prone to self-assemble. Direct visualization of single molecules by atomic force microscopy (AFM) confirms that ASR1 forms homodimers and that uncovers both monomers and dimers bind double stranded DNA

  19. Regional specific groundwater arsenic levels and neuropsychological functioning: a cross-sectional study.

    Science.gov (United States)

    Edwards, Melissa; Johnson, Leigh; Mauer, Cortney; Barber, Robert; Hall, James; O'Bryant, Sid

    2014-01-01

    The purpose of the study was to examine the link between geographic information system (GIS)-estimated regional specific groundwater levels and neuropsychological functioning in a sample of individuals with and without cognitive impairment. This cross-sectional study design analyzed data from 1390 participants (733 Alzheimer's disease, 127 Mild Cognitive Impairment, and 530 with normal cognition) enrolled in the Texas Alzheimer's Research and Care Consortium. GISs analyses were used to estimate regional specific groundwater arsenic concentrations using the Environmental Systems Research Institute and arsenic concentrations from the Texas Water Development Board. In the full cohort, regional specific arsenic concentrations were positively associated with language abilities (p = 0.008), but associated with poorer verbal memory, immediate (p = 0.008), and delayed (p arsenic being related with cognition most prominently among mild cognitive impairment cases. Overall, estimated regional specific groundwater arsenic levels were negatively associated with neuropsychological performance.

  20. Protein covalent immobilization via its scarce thiol versus abundant amine groups: Effect on orientation, cell binding domain exposure and conformational lability.

    Science.gov (United States)

    Ba, O M; Hindie, M; Marmey, P; Gallet, O; Anselme, K; Ponche, A; Duncan, A C

    2015-10-01

    Quantity, orientation, conformation and covalent linkage of naturally cell adhesive proteins adsorbed or covalently linked to a surface, are known to influence the preservation of their subsequent long term cell adhesion properties and bioactivity. In the present work, we explore two different strategies for the covalent linking of plasma fibronectin (pFN) - used as a cell adhesive model protein, onto a polystyrene (PS) surface. One is aimed at tethering the protein to the surface in a semi-oriented fashion (via one of the 4 free thiol reactive groups on the protein) with a heterofunctional coupling agent (SSMPB method). The other aims to immobilize the protein in a more random fashion by reaction between the abundant pendant primary amine bearing amino acids of the pFN and activated carboxylic surface functions obtained after glutaric anhydride surface treatment (GA method). The overall goal will be to verify the hypothesis of a correlation between covalent immobilization of a model cell adhesive protein to a PS surface in a semi-oriented configuration (versus randomly oriented) with promotion of enhanced exposure of the protein's cell binding domain. This in turn would lead to enhanced cell adhesion. Ideally the goal is to elaborate substrates exhibiting a long term stable protein monolayer with preserved cell adhesive properties and bioactivity for biomaterial and/or cell adhesion commercial plate applications. However, the initial restrictive objective of this paper is to first quantitatively and qualitatively investigate the reversibly (merely adsorbed) versus covalently irreversibly bound protein to the surface after the immobilization procedure. Although immobilized surface amounts were similar (close to the monolayer range) for all immobilization approaches, covalent grafting showed improved retention and stronger "tethering" of the pFN protein to the surface (roughly 40%) after SDS rinsing compared to that for mere adsorption (0%) suggesting an added value

  1. Correlation Between Expression of Recombinant Proteins and Abundance of H3K4Me3 on the Enhancer of Human Cytomegalovirus Major Immediate-Early Promoter.

    Science.gov (United States)

    Soo, Benjamin P C; Tay, Julian; Ng, Shirelle; Ho, Steven C L; Yang, Yuansheng; Chao, Sheng-Hao

    2017-08-01

    Role of epigenetic regulation in the control of gene expression is well established. The impact of several epigenetic mechanisms, such as DNA methylation and histone acetylation, on recombinant protein production in mammalian cells has been investigated recently. Here we investigate the correlation between the selected epigenetic markers and five trastuzumab biosimilar-producing Chinese hamster ovary (CHO) cell lines in which the expression of trastuzumab is driven by human cytomegalovirus (HCMV) major immediate-early (MIE) promoter. We chose the producing clones in which transcription was the determinative step for the production of recombinant trastuzumab. We found that the abundance of trimethylation of histone 3 at lysine 4 (H3K4Me3) on the enhancer of HCMV MIE promoter correlated well with the relative titers of recombinant trastuzumab among the clones. Such close correlation was not observed between the recombinant protein and other epigenetic markers examined in our study. Our results demonstrate that the HCMV MIE enhancer-bound H3K4Me3 epigenetic marker may be used as the epigenetic indicator to predict the relative production of recombinant proteins between the producing CHO cell lines.

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

    Directory of Open Access Journals (Sweden)

    Yue Yang

    2011-01-01

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

  3. Complex and region-specific changes in astroglial markers in the aging brain.

    Science.gov (United States)

    Rodríguez, José J; Yeh, Chia-Yu; Terzieva, Slavica; Olabarria, Markel; Kulijewicz-Nawrot, Magdalena; Verkhratsky, Alexei

    2014-01-01

    Morphological aging of astrocytes was investigated in entorhinal cortex (EC), dentate gyrus (DG), and cornu ammonis 1 (CA1) regions of hippocampus of male SV129/C57BL6 mice of different age groups (3, 9, 18, and 24 months). Astroglial profiles were visualized by immunohistochemistry by using glial fibrillary acidic protein (GFAP), glutamine synthetase (GS), and s100β staining; these profiles were imaged using confocal or light microscopy for subsequent morphometric analysis. GFAP-positive profiles in the DG and the CA1 of the hippocampus showed progressive age-dependent hypertrophy, as indicated by an increase in surface, volume, and somata volume at 24 months of age compared with 3-month-old mice. In contrast with the hippocampal regions, aging induced a decrease in GFAP-positive astroglial profiles in the EC: the surface, volume, and cell body volume of astroglial cells at 24 months of age were decreased significantly compared with the 3-month group. The GS-positive astrocytes displayed smaller cellular surface areas at 24 months compared with 3-month-old animals in both areas of hippocampus, whereas GS-positive profiles remained unchanged in the EC of old mice. The morphometry of s100β-immunoreactive profiles revealed substantial increase in the EC, more moderate increase in the DG, and no changes in the CA1 area. Based on the morphological analysis of 3 astroglial markers, we conclude that astrocytes undergo a complex age-dependent remodeling in a brain region-specific manner. Copyright © 2014. Published by Elsevier Inc.

  4. 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...... born to mothers fed either a low-protein diet (LP), that is, 14% of metabolizable energy (ME) from protein (foetal low – FL), n = 16, or an adequate-protein (AP) diet, that is, 29% of ME from protein (foetal adequate – FA), n = 16) in the last 16.3 ± 1.8 days of pregnancy were used. The FL offspring...... had lower birth weight and lower relative abundance of fructose-1,6-bisphosphatase (Fru-1,6-P2ase) and pyruvate kinase mRNA in foetal hepatic tissue than FA kits. The mothers were fed a diet containing adequate protein until weaning. At weaning (7 weeks of age), half of the kits from each foetal...

  5. A comparison of pine and spruce in recovery from winter stress; changes in recovery kinetics, and the abundance and phosphorylation status of photosynthetic proteins during winter.

    Science.gov (United States)

    Merry, Ryan; Jerrard, Jacob; Frebault, Julia; Verhoeven, Amy

    2017-09-01

    During winter evergreens maintain a sustained form of thermal energy dissipation that results in reduced photochemical efficiency measured using the chlorophyll fluorescence parameter Fv/Fm. Eastern white pine (Pinus strobus L.) and white spruce [Picea glauca (Moench) Voss] have been shown to differ in their rate of recovery of Fv/Fm from winter stress. The goal of this study was to monitor changes in photosynthetic protein abundance and phosphorylation status during winter recovery that accompany these functional changes. An additional goal was to determine whether light-dependent changes in light harvesting complex II (LHCII) phosphorylation occur during winter conditions. We used a combination of field measurements and recovery experiments to monitor chlorophyll fluorescence and photosynthetic protein content and phosphorylation status. We found that pine recovered three times more slowly than spruce, and that the kinetics of recovery in spruce included a rapid and slow component, while in pine there was only a rapid component to recovery. Both species retained relatively high amounts of the light harvesting protein Lhcb5 (CP26) and the PsbS protein during winter, suggesting a role for these proteins in sustained thermal dissipation. Both species maintained high phosphorylation of LHCII and the D1 protein in darkness during winter. Pine and spruce differed in the kinetics of the dephosphorylation of LHCII and D1 upon warming, suggesting the rate of dephosphorylation of LHCII and D1 may be important in the rapid component of recovery from winter stress. Finally, we demonstrated that light-dependent changes in LHII phosphorylation do not continue to occur on subzero winter days and that needles are maintained in a phosphorylation pattern consistent with the high light conditions to which those needles are exposed. Our results suggest a role for retained phosphorylation of both LHCII and D1 in maintenance of the photosynthetic machinery in a winter conformation

  6. 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.

  7. 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. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  8. Induction of ketosis in rats fed low-carbohydrate, high-fat diets depends on the relative abundance of dietary fat and protein.

    Science.gov (United States)

    Bielohuby, Maximilian; Menhofer, Dominik; Kirchner, Henriette; Stoehr, Barbara J M; Müller, Timo D; Stock, Peggy; Hempel, Madlen; Stemmer, Kerstin; Pfluger, Paul T; Kienzle, Ellen; Christ, Bruno; Tschöp, Matthias H; Bidlingmaier, Martin

    2011-01-01

    Low-carbohydrate/high-fat diets (LC-HFDs) in rodent models have been implicated with both weight loss and as a therapeutic approach to treat neurological diseases. LC-HFDs are known to induce ketosis; however, systematic studies analyzing the impact of the macronutrient composition on ketosis induction and weight loss success are lacking. Male Wistar rats were pair-fed for 4 wk either a standard chow diet or one of three different LC-HFDs, which only differed in the relative abundance of fat and protein (percentages of fat/protein in dry matter: LC-75/10; LC-65/20; LC-55/30). We subsequently measured body composition by nuclear magnetic resonance (NMR), analyzed blood chemistry and urine acetone content, evaluated gene expression changes of key ketogenic and gluconeogenic genes, and measured energy expenditure (EE) and locomotor activity (LA) during the first 4 days and after 3 wk on the respective diets. Compared with chow, rats fed with LC-75/10, LC-65/20, and LC-55/30 gained significantly less body weight. Reductions in body weight were mainly due to lower lean body mass and paralleled by significantly increased fat mass. Levels of β-hydroxybutyate were significantly elevated feeding LC-75/10 and LC-65/20 but decreased in parallel to reductions in dietary fat. Acetone was about 16-fold higher with LC-75/10 only (P ketosis. LC-HFDs must be high in fat, but also low in protein contents to be clearly ketogenic. Independent of the macronutrient composition, LC-HFD-induced weight loss is not due to increased EE and LA.

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

    Science.gov (United States)

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

    2017-01-01

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

  10. The AP2 clathrin adaptor protein complex regulates the abundance of GLR-1 glutamate receptors in the ventral nerve cord of Caenorhabditis elegans.

    Science.gov (United States)

    Garafalo, Steven D; Luth, Eric S; Moss, Benjamin J; Monteiro, Michael I; Malkin, Emily; Juo, Peter

    2015-05-15

    Regulation of glutamate receptor (GluR) abundance at synapses by clathrin-mediated endocytosis can control synaptic strength and plasticity. We take advantage of viable, null mutations in subunits of the clathrin adaptor protein 2 (AP2) complex in Caenorhabditis elegans to characterize the in vivo role of AP2 in GluR trafficking. In contrast to our predictions for an endocytic adaptor, we found that levels of the GluR GLR-1 are decreased at synapses in the ventral nerve cord (VNC) of animals with mutations in the AP2 subunits APM-2/μ2, APA-2/α, or APS-2/σ2. Rescue experiments indicate that APM-2/μ2 functions in glr-1-expressing interneurons and the mature nervous system to promote GLR-1 levels in the VNC. Genetic analyses suggest that APM-2/μ2 acts upstream of GLR-1 endocytosis in the VNC. Consistent with this, GLR-1 accumulates in cell bodies of apm-2 mutants. However, GLR-1 does not appear to accumulate at the plasma membrane of the cell body as expected, but instead accumulates in intracellular compartments including Syntaxin-13- and RAB-14-labeled endosomes. This study reveals a novel role for the AP2 clathrin adaptor in promoting the abundance of GluRs at synapses in vivo, and implicates AP2 in the regulation of GluR trafficking at an early step in the secretory pathway. © 2015 Garafalo et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  11. Brain region-specific altered expression and association of mitochondria-related genes in autism.

    Science.gov (United States)

    Anitha, Ayyappan; Nakamura, Kazuhiko; Thanseem, Ismail; Yamada, Kazuo; Iwayama, Yoshimi; Toyota, Tomoko; Matsuzaki, Hideo; Miyachi, Taishi; Yamada, Satoru; Tsujii, Masatsugu; Tsuchiya, Kenji J; Matsumoto, Kaori; Iwata, Yasuhide; Suzuki, Katsuaki; Ichikawa, Hironobu; Sugiyama, Toshiro; Yoshikawa, Takeo; Mori, Norio

    2012-11-01

    Mitochondrial dysfunction (MtD) has been observed in approximately five percent of children with autism spectrum disorders (ASD). MtD could impair highly energy-dependent processes such as neurodevelopment, thereby contributing to autism. Most of the previous studies of MtD in autism have been restricted to the biomarkers of energy metabolism, while most of the genetic studies have been based on mutations in the mitochondrial DNA (mtDNA). Despite the mtDNA, most of the proteins essential for mitochondrial replication and function are encoded by the genomic DNA; so far, there have been very few studies of those genes. Therefore, we carried out a detailed study involving gene expression and genetic association studies of genes related to diverse mitochondrial functions. For gene expression analysis, postmortem brain tissues (anterior cingulate gyrus (ACG), motor cortex (MC) and thalamus (THL)) from autism patients (n=8) and controls (n=10) were obtained from the Autism Tissue Program (Princeton, NJ, USA). Quantitative real-time PCR arrays were used to quantify the expression of 84 genes related to diverse functions of mitochondria, including biogenesis, transport, translocation and apoptosis. We used the delta delta Ct (∆∆Ct) method for quantification of gene expression. DNA samples from 841 Caucasian and 188 Japanese families were used in the association study of genes selected from the gene expression analysis. FBAT was used to examine genetic association with autism. Several genes showed brain region-specific expression alterations in autism patients compared to controls. Metaxin 2 (MTX2), neurofilament, light polypeptide (NEFL) and solute carrier family 25, member 27 (SLC25A27) showed consistently reduced expression in the ACG, MC and THL of autism patients. NEFL (P = 0.038; Z-score 2.066) and SLC25A27 (P = 0.046; Z-score 1.990) showed genetic association with autism in Caucasian and Japanese samples, respectively. The expression of DNAJC19, DNM1L, LRPPRC

  12. Brain region-specific altered expression and association of mitochondria-related genes in autism

    Directory of Open Access Journals (Sweden)

    Anitha Ayyappan

    2012-11-01

    Full Text Available Abstract Background Mitochondrial dysfunction (MtD has been observed in approximately five percent of children with autism spectrum disorders (ASD. MtD could impair highly energy-dependent processes such as neurodevelopment, thereby contributing to autism. Most of the previous studies of MtD in autism have been restricted to the biomarkers of energy metabolism, while most of the genetic studies have been based on mutations in the mitochondrial DNA (mtDNA. Despite the mtDNA, most of the proteins essential for mitochondrial replication and function are encoded by the genomic DNA; so far, there have been very few studies of those genes. Therefore, we carried out a detailed study involving gene expression and genetic association studies of genes related to diverse mitochondrial functions. Methods For gene expression analysis, postmortem brain tissues (anterior cingulate gyrus (ACG, motor cortex (MC and thalamus (THL from autism patients (n=8 and controls (n=10 were obtained from the Autism Tissue Program (Princeton, NJ, USA. Quantitative real-time PCR arrays were used to quantify the expression of 84 genes related to diverse functions of mitochondria, including biogenesis, transport, translocation and apoptosis. We used the delta delta Ct (∆∆Ct method for quantification of gene expression. DNA samples from 841 Caucasian and 188 Japanese families were used in the association study of genes selected from the gene expression analysis. FBAT was used to examine genetic association with autism. Results Several genes showed brain region-specific expression alterations in autism patients compared to controls. Metaxin 2 (MTX2, neurofilament, light polypeptide (NEFL and solute carrier family 25, member 27 (SLC25A27 showed consistently reduced expression in the ACG, MC and THL of autism patients. NEFL (P = 0.038; Z-score 2.066 and SLC25A27 (P = 0.046; Z-score 1.990 showed genetic association with autism in Caucasian and Japanese samples, respectively. The

  13. Proof of region-specific multipotent progenitors in human breast epithelia

    DEFF Research Database (Denmark)

    Fridriksdottir, Agla J; Villadsen, René; Morsing, Mikkel

    2017-01-01

    in luminal progenitors to interrogate the differentiation repertoire of candidate stem cells in TDLUs. We show that stem-like activity in serial passage culture and in vivo breast morphogenesis relies on the preservation of a myoepithelial phenotype. By enrichment for region-specific progenitors, we identify...

  14. 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

  15. 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

  16. 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

    2010-10-01

    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. 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. NADH- and FADH(2)-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). 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.

  17. Region-specific involvement of BDNF secretion and synthesis in conditioned taste aversion memory formation.

    Science.gov (United States)

    Ma, Ling; Wang, Dong-Dong; Zhang, Tian-Yi; Yu, Hui; Wang, Yue; Huang, Shu-Hong; Lee, Francis S; Chen, Zhe-Yu

    2011-02-09

    Brain-derived neurotrophic factor (BDNF) and its receptor, tropomyosin-related kinase receptor B (TrkB), play a critical role in activity-dependent plasticity processes such as long-term potentiation, learning, and memory. It has been shown that BDNF exerts different or even opposite effects on behavior depending on the neural circuit. However, the detailed role of BDNF in memory process on the basis of its location has not been fully understood. Here, we aim to investigate the regional specific involvement of BDNF/TrkB in hippocampal-independent conditioned taste aversion (CTA) memory processes. We found region-specific changes in BDNF expression during CTA learning. CTA conditioning induced increased BDNF levels in the central nuclei of amygdala (CeA) and insular cortex, but not in the basolateral amygdala (BLA) and ventromedial prefrontal cortex. Interestingly, we found that the enhanced TrkB phosphorylation occurred at the time point before the increased BDNF expression, suggesting rapid induction of activity-dependent BDNF secretion by CTA learning. Moreover, targeted infusion of BDNF antibodies or BDNF antisense oligonucleotides revealed that activity-dependent BDNF secretion and synthesis in the CeA, but not the BLA, was respectively involved in the short- and long-term memory formation of CTA. Finally, we found that infusion of exogenous BDNF into the CeA could enhance CTA learning. These data suggest that region-specific BDNF release and synthesis temporally regulate different CTA memory phases through activation of TrkB receptors.

  18. Molecular Characterization of Aquaporin 1 and Aquaporin 3 from the Gills of the African Lungfish, Protopterus annectens, and Changes in Their Branchial mRNA Expression Levels and Protein Abundance during Three Phases of Aestivation.

    Science.gov (United States)

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

    2016-01-01

    African lungfishes can undergo long periods of aestivation on land during drought. During aestivation, lungfishes are confronted with desiccation and dehydration, and their gills become non-functional and covered with a thick layer of dried mucus. Aquaporins (Aqps) are a superfamily of integral membrane proteins which generally facilitate the permeation of water through plasma membranes. This study aimed to obtain the complete cDNA coding sequences of aqp1 and aqp3 from the gills of Protopterus annectens , and to determine their branchial mRNA and protein expression levels during the induction, maintenance and arousal phases of aestivation. Dendrogramic analyses of the deduced Aqp1 and Aqp3 amino acid sequences of P. annectens revealed their close relationships with those of Latimeria chalumnae and tetrapods. During the induction phase, there were significant decreases in the transcript levels of aqp1 and aqp3 in the gills of P. annectens , but the branchial Aqp1 and Aqp3 protein abundance remained unchanged. As changes in transcription might precede changes in translation, this could be regarded as an adaptive response to decrease the protein abundance of Aqp1 and Aqp3 in the subsequent maintenance phase of aestivation. As expected, the branchial transcript levels and protein abundance of aqp1 /Aqp1 and aqp3 /Aqp3 were significantly down-regulated during the maintenance phase, probably attributable to the shutdown of branchial functions and the cessation of volume regulation of branchial epithelial cells. Additionally, these changes could reduce the loss of water through branchial epithelial surfaces, supplementing the anti-desiccating property of the dried mucus. Upon arousal, it was essential for the lungfish to restore branchial functions. Indeed, the protein abundance of Aqp1 recovered partially, with complete recovery of mRNA expression level and protein abundance of Aqp3, in the gills of P. annectens after 3 days of arousal. These results provide insights

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

    Science.gov (United States)

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

  20. Emergence of differentially regulated pathways associated with the development of regional specificity in chicken skin.

    Science.gov (United States)

    Chang, Kai-Wei; Huang, Nancy A; Liu, I-Hsuan; Wang, Yi-Hui; Wu, Ping; Tseng, Yen-Tzu; Hughes, Michael W; Jiang, Ting Xin; Tsai, Mong-Hsun; Chen, Chien-Yu; Oyang, Yen-Jen; Lin, En-Chung; Chuong, Cheng-Ming; Lin, Shau-Ping

    2015-01-23

    Regional specificity allows different skin regions to exhibit different characteristics, enabling complementary functions to make effective use of the integumentary surface. Chickens exhibit a high degree of regional specificity in the skin and can serve as a good model for when and how these regional differences begin to emerge. We used developing feather and scale regions in embryonic chickens as a model to gauge the differences in their molecular pathways. We employed cosine similarity analysis to identify the differentially regulated and co-regulated genes. We applied low cell techniques for expression validation and chromatin immunoprecipitation (ChIP)-based enhancer identification to overcome limited cell availabilities from embryonic chicken skin. We identified a specific set of genes demonstrating a high correlation as being differentially expressed during feather and scale development and maturation. Some members of the WNT, TGF-beta/BMP, and Notch family known to be involved in feathering skin differentiation were found to be differentially regulated. Interestingly, we also found genes along calcium channel pathways that are differentially regulated. From the analysis of differentially regulated pathways, we used calcium signaling pathways as an example for further verification. Some voltage-gated calcium channel subunits, particularly CACNA1D, are expressed spatio-temporally in the skin epithelium. These calcium signaling pathway members may be involved in developmental decisions, morphogenesis, or epithelial maturation. We further characterized enhancers associated with histone modifications, including H3K4me1, H3K27ac, and H3K27me3, near calcium channel-related genes and identified signature intensive hotspots that may be correlated with certain voltage-gated calcium channel genes. We demonstrated the applicability of cosine similarity analysis for identifying novel regulatory pathways that are differentially regulated during development. Our study

  1. Region-specific reduction in brain volume in young adults with perinatal hypoxic-ischaemic encephalopathy.

    Science.gov (United States)

    Bregant, Tina; Rados, Milan; Vasung, Lana; Derganc, Metka; Evans, Alan C; Neubauer, David; Kostovic, Ivica

    2013-11-01

    A severe form of perinatal hypoxic-ischaemic encephalopathy (HIE) carries a high risk of perinatal death and severe neurological sequelae while in mild HIE only discrete cognitive disorders may occur. To compare total brain volumes and region-specific cortical measurements between young adults with mild-moderate perinatal HIE and a healthy control group of the same age. MR imaging was performed in a cohort of 14 young adults (9 males, 5 females) with a history of mild or moderate perinatal HIE. The control group consisted of healthy participants, matched with HIE group by age and gender. Volumetric analysis was done after the processing of MR images using a fully automated CIVET pipeline. We measured gyrification indexes, total brain volume, volume of grey and white matter, and of cerebrospinal fluid. We also measured volume, thickness and area of the cerebral cortex in the parietal, occipital, frontal, and temporal lobe, and of the isthmus cinguli, parahippocampal and cingulated gyrus, and insula. The HIE patient group showed smaller absolute volumetric data. Statistically significant (p right hemisphere, of cortical areas in the right temporal lobe and parahippocampal gyrus, of cortical volumes in the right temporal lobe and of cortical thickness in the right isthmus of the cingulate gyrus were found. Comparison between the healthy group and the HIE group of the same gender showed statistically significant changes in the male HIE patients, where a significant reduction was found in whole brain volume; left parietal, bilateral temporal, and right parahippocampal gyrus cortical areas; and bilateral temporal lobe cortical volume. Our analysis of total brain volumes and region-specific corticometric parameters suggests that mild-moderate forms of perinatal HIE lead to reductions in whole brain volumes. In the study reductions were most pronounced in temporal lobe and parahippocampal gyrus. Copyright © 2013 European Paediatric Neurology Society. All rights reserved.

  2. Identification of unknown protein complex members by radiolocalization and analysis of low-abundance complexes resolved using native polyacrylamide gel electrophoresis.

    Science.gov (United States)

    Bose, Mahuya; Adams, Brian P; Whittal, Randy M; Bose, Himangshu S

    2008-02-01

    Identification of unknown binding partners of a protein of interest can be a difficult process. Current strategies to determine protein binding partners result in a high amount of false-positives, requiring use of several different methods to confirm the accuracy of the apparent association. We have developed and utilized a method that is reliable and easily substantiated. Complexes are isolated from cell extract after exposure to the radiolabeled protein of interest, followed by resolution on a native polyacrylamide gel. Native conformations are preserved, allowing the complex members to maintain associations. By radiolabeling the protein of interest, the complex can be easily identified at detection levels below the threshold of Serva Blue, Coomassie, and silver stains. The visualized radioactive band is analyzed by MS to identify binding partners, which can be subsequently verified by antibody shift and immunoprecipitation of the complex. By using this method we have successfully identified binding partners of two proteins that reside in different locations of a cellular organelle.

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

    Directory of Open Access Journals (Sweden)

    González Mario

    2012-09-01

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

  4. Region-specific role for Pten in maintenance of epithelial phenotype and integrity

    Science.gov (United States)

    Flodby, Per; Sunohara, Mitsuhiro; Castillo, Dan R.; McConnell, Alicia M.; Krishnaveni, Manda S.; Banfalvi, Agnes; Li, Min; Stripp, Barry; Zhou, Beiyun; Crandall, Edward D.; Minoo, Parviz

    2017-01-01

    Previous studies have demonstrated resistance to naphthalene-induced injury in proximal airways of mice with lung epithelial-specific deletion of the tumor-suppressor gene Pten, attributed to increased proliferation of airway progenitors. We tested effects of Pten loss following bleomycin injury, a model typically used to study distal lung epithelial injury, in conditional PtenSFTPC-cre knockout mice. Pten-deficient airway epithelium exhibited marked hyperplasia, particularly in small bronchioles and at bronchoalveolar duct junctions, with reduced E-cadherin and β-catenin expression between cells toward the luminal aspect of the hyperplastic epithelium. Bronchiolar epithelial and alveolar epithelial type II (AT2) cells in PtenSFTPC-cre mice showed decreased expression of epithelial markers and increased expression of mesenchymal markers, suggesting at least partial epithelial-mesenchymal transition at baseline. Surprisingly, and in contrast to previous studies, mutant mice were exquisitely sensitive to bleomycin, manifesting rapid weight loss, respiratory distress, increased early mortality (by day 5), and reduced dynamic lung compliance. This was accompanied by sloughing of the hyperplastic airway epithelium with occlusion of small bronchioles by cellular debris, without evidence of increased parenchymal lung injury. Increased airway epithelial cell apoptosis due to loss of antioxidant defenses, reflected by decreased expression of superoxide dismutase 3, in combination with deficient intercellular adhesion, likely predisposed to airway sloughing in knockout mice. These findings demonstrate an important role for Pten in maintenance of airway epithelial phenotype integrity and indicate that responses to Pten deletion in respiratory epithelium following acute lung injury are highly context-dependent and region-specific. PMID:27864284

  5. Regional specificity in deltamethrin induced cytochrome P450 expression in rat brain

    International Nuclear Information System (INIS)

    Yadav, Sanjay; Johri, Ashu; Dhawan, Alok; Seth, Prahlad K.; Parmar, Devendra

    2006-01-01

    Oral administration of deltamethrin (5 mg/kg x 7 or 15 or 21 days) was found to produce a time-dependent increase in the mRNA expression of xenobiotic metabolizing cytochrome P450 1A1 (CYP1A1), 1A2 and CYP2B1, 2B2 isoenzymes in rat brain. RT-PCR studies further showed that increase in the mRNA expression of these CYP isoenzymes observed after 21 days of exposure was region specific. Hippocampus exhibited maximum increase in the mRNA expression of CYP1A1, which was followed by pons-medulla, cerebellum and hypothalamus. The mRNA expression of CYP2B1 also exhibited maximum increase in the hypothalamus and hippocampus followed by almost similar increase in midbrain and cerebellum. In contrast, mRNA expression of CYP1A2 and CYP2B2, the constitutive isoenzymes exhibited relatively higher increase in pons-medulla, cerebellum and frontal cortex. Immunoblotting studies carried out with polyclonal antibody raised against rat liver CYP1A1/1A2 or CYP2B1/2B2 isoenzymes also showed increase in immunoreactivity comigrating with CYP1A1/1A2 or 2B1/2B2 in the microsomal fractions isolated from hippocampus, hypothalamus and cerebellum of rat treated with deltamethrin. Though the exact relationship of the xenobiotic metabolizing CYPs with the physiological function of the brain is yet to be clearly understood, the increase in the mRNA expression of the CYPs in the brain regions that regulate specific brain functions affected by deltamethrin have further indicated that modulation of these CYPs could be associated with the various endogenous functions of the brain

  6. Region-specific changes in presynaptic agmatine and glutamate levels in the aged rat brain.

    Science.gov (United States)

    Jing, Y; Liu, P; Leitch, B

    2016-01-15

    During the normal aging process, the brain undergoes a range of biochemical and structural alterations, which may contribute to deterioration of sensory and cognitive functions. Age-related deficits are associated with altered efficacy of synaptic neurotransmission. Emerging evidence indicates that levels of agmatine, a putative neurotransmitter in the mammalian brain, are altered in a region-specific manner during the aging process. The gross tissue content of agmatine in the prefrontal cortex (PFC) of aged rat brains is decreased whereas levels in the temporal cortex (TE) are increased. However, it is not known whether these changes in gross tissue levels are also mirrored by changes in agmatine levels at synapses and thus could potentially contribute to altered synaptic function with age. In the present study, agmatine levels in presynaptic terminals in the PFC and TE regions (300 terminals/region) of young (3month; n=3) and aged (24month; n=3) brains of male Sprague-Dawley rats were compared using quantitative post-embedding immunogold electron-microscopy. Presynaptic levels of agmatine were significantly increased in the TE region (60%; pagmatine and glutamate were co-localized in the same synaptic terminals, and quantitative analyses revealed significantly reduced glutamate levels in agmatine-immunopositive synaptic terminals in both regions in aged rats compared to young animals. This study, for the first time, demonstrates differential effects of aging on agmatine and glutamate in the presynaptic terminals of PFC and TE. Future research is required to understand the functional significance of these changes and the underlying mechanisms. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

  7. High-fat diet-induced brain region-specific phenotypic spectrum of CNS resident microglia.

    Science.gov (United States)

    Baufeld, Caroline; Osterloh, Anja; Prokop, Stefan; Miller, Kelly R; Heppner, Frank L

    2016-09-01

    Diets high in fat (HFD) are known to cause an immune response in the periphery as well as the central nervous system. In peripheral adipose tissue, this immune response is primarily mediated by macrophages that are recruited to the tissue. Similarly, reactivity of microglia, the innate immune cells of the brain, has been shown to occur in the hypothalamus of mice fed a high-fat diet. To characterize the nature of the microglial response to diets high in fat in a temporal fashion, we studied the phenotypic spectrum of hypothalamic microglia of mice fed high-fat diet for 3 days and 8 weeks by assessing their tissue reaction and inflammatory signature. While we observed a significant increase in Iba1+ myeloid cells and a reaction of GFAP+ astrocytes in the hypothalamus after 8 weeks of HFD feeding, we found the hypothalamic myeloid cell reaction to be limited to endogenous microglia and not mediated by infiltrating myeloid cells. Moreover, obese humans were found to present with signs of hypothalamic gliosis and exacerbated microglia dystrophy, suggesting a targeted microglia response to diet in humans as well. Notably, the glial reaction occurring in the mouse hypothalamus was not accompanied by an increase in pro-inflammatory cytokines, but rather by an anti-inflammatory reaction. Gene expression analyses of isolated microglia not only confirmed this observation, but also revealed a downregulation of microglia genes important for sensing signals in the microenvironment. Finally, we demonstrate that long-term exposure of microglia to HFD in vivo does not impair the cell's ability to respond to additional stimuli, like lipopolysaccharide. Taken together, our findings support the notion that microglia react to diets high in fat in a region-specific manner in rodents as well as in humans; however, this response changes over time as it is not exclusively pro-inflammatory nor does exposure to HFD prime microglia in the hypothalamus.

  8. Regionally specific white matter disruptions of fornix and cingulum in schizophrenia.

    Directory of Open Access Journals (Sweden)

    Muhammad Farid Abdul-Rahman

    Full Text Available Limbic circuitry disruptions have been implicated in the psychopathology and cognitive deficits of schizophrenia, which may involve white matter disruptions of the major tracts of the limbic system, including the fornix and the cingulum. Our study aimed to investigate regionally specific abnormalities of the fornix and cingulum in schizophrenia using diffusion tensor imaging (DTI. We determined the fractional anisotropy (FA, radial diffusivity (RD, and axial diffusivity (AD profiles along the fornix and cingulum tracts using a fibertracking technique and a brain mapping algorithm, the large deformation diffeomorphic metric mapping (LDDMM, in the DTI scans of 33 patients with schizophrenia and 31 age-, gender-, and handedness-matched healthy controls. We found that patients with schizophrenia showed reduction in FA and increase in RD in bilateral fornix, and increase in RD in left anterior cingulum when compared to healthy controls. In addition, tract-based analysis revealed specific loci of these white matter differences in schizophrenia, that is, FA reductions and AD and RD increases occur in the region of the left fornix further from the hippocampus, FA reductions and RD increases occur in the rostral portion of the left anterior cingulum, and RD and AD increases occur in the anterior segment of the left middle cingulum. In patients with schizophrenia, decreased FA in the specific loci of the left fornix and increased AD in the right cingulum adjoining the hippocampus correlated with greater severity of psychotic symptoms. These findings support precise disruptions of limbic-cortical integrity in schizophrenia and disruption of these structural networks may contribute towards the neural basis underlying the syndrome of schizophrenia and clinical symptomatology.

  9. Oxytocin Reduces Cocaine Cued Fos Activation in a Regionally Specific Manner

    Science.gov (United States)

    Leong, Kah-Chung; Freeman, Linnea R; Berini, Carole R; Ghee, Shannon M; See, Ronald E

    2017-01-01

    Abstract Background Oxytocin may be a possible treatment for multiple neuropsychiatric disorders, including cocaine addiction. Little is known about the site-specific effects of oxytocin on various drug addiction-related brain regions. Furthermore, sexually dimorphic effects of oxytocin on neural function in the addiction circuit have not been established. Here, we studied Fos expression following cocaine-cued reinstatement in both male and female rats. Methods Male and female rats underwent self-administration, extinction, and reinstatement tests. On test days, rats were given oxytocin or vehicle, and lever pressing was measured in response to conditioned cocaine cues. Rats were perfused and Fos staining measured in the central amygdala, medial prefrontal cortex, nucleus accumbens core, and subthalamic nucleus. Fos/oxytocin double labeling occurred in the paraventricular nucleus of the hypothalamus. Results Rats reinstated to cocaine cues relative to extinction responding and oxytocin reduced cocaine seeking. Oxytocin combined with contingent cue presentations increased Fos+ oxytocin cell bodies within the paraventricular nucleus of the hypothalamus relative to vehicle. Fos expression robustly increased in the central amygdala following oxytocin administration. Oxytocin reversed cue-induced Fos expression in the medial prefrontal cortex, nucleus accumbens core, and subthalamic nucleus. Central oxytocin infusion also attenuated reinstated cocaine seeking. Conclusions Oxytocin decreased reinstated cocaine seeking, increased Fos activation in the paraventricular nucleus of the hypothalamus and central amygdala, but normalized cue-induced Fos activation in the medial prefrontal cortex, nucleus accumbens core, and subthalamic nucleus, thereby demonstrating regionally specific activation patterns. No sex differences were seen for the effects of oxytocin on cocaine seeking and Fos activation, indicating that oxytocin acts on similar central neural circuits critical to

  10. Chromosome region-specific libraries for human genome analysis. Final progress report, 1 March 1991--28 February 1994

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    Kao, F.T.

    1994-04-01

    The objectives of this grant proposal include (1) development of a chromosome microdissection and PCR-mediated microcloning technology, (2) application of this microtechnology to the construction of region-specific libraries for human genome analysis. During this grant period, the authors have successfully developed this microtechnology and have applied it to the construction of microdissection libraries for the following chromosome regions: a whole chromosome 21 (21E), 2 region-specific libraries for the long arm of chromosome 2, 2q35-q37 (2Q1) and 2q33-q35 (2Q2), and 4 region-specific libraries for the entire short arm of chromosome 2, 2p23-p25 (2P1), 2p21-p23 (2P2), 2p14-p16 (wP3) and 2p11-p13 (2P4). In addition, 20--40 unique sequence microclones have been isolated and characterized for genomic studies. These region-specific libraries and the single-copy microclones from the library have been used as valuable resources for (1) isolating microsatellite probes in linkage analysis to further refine the disease locus; (2) isolating corresponding clones with large inserts, e.g. YAC, BAC, P1, cosmid and phage, to facilitate construction of contigs for high resolution physical mapping; and (3) isolating region-specific cDNA clones for use as candidate genes. These libraries are being deposited in the American Type Culture Collection (ATCC) for general distribution.

  11. MP20, the second most abundant lens membrane protein and member of the tetraspanin superfamily, joins the list of ligands of galectin-3

    Directory of Open Access Journals (Sweden)

    Donaldson Paul J

    2001-08-01

    Full Text Available Abstract Background Although MP20 is the second most highly expressed membrane protein in the lens its function remains an enigma. Putative functions for MP20 have recently been inferred from its assignment to the tetraspanin superfamily of integral membrane proteins. Members of this family have been shown to be involved in cellular proliferation, differentiation, migration, and adhesion. In this study, we show that MP20 associates with galectin-3, a known adhesion modulator. Results MP20 and galectin-3 co-localized in selected areas of the lens fiber cell plasma membrane. Individually, these proteins purified with apparent molecular masses of 60 kDa and 22 kDa, respectively. A 104 kDa complex was formed in vitro upon mixing the purified proteins. A 102 kDa complex of MP20 and galectin-3 could also be isolated from detergent-solubilized native fiber cell membranes. Binding between MP20 and galectin-3 was disrupted by lactose suggesting the lectin site was involved in the interaction. Conclusions MP20 adds to a growing list of ligands of galectin-3 and appears to be the first representative of the tetraspanin superfamily identified to possess this specificity.

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

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    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.

  13. 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)

    Trott, G.; Pereira-Lima, J.F.S.; Leães, C.G.S.; Ferreira, N.P.; Barbosa-Coutinho, L.M.; Oliveira, M.C.

    2015-01-01

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

  14. Behavioral stress alters corticolimbic microglia in a sex- and brain region-specific manner.

    Science.gov (United States)

    Bollinger, Justin L; Collins, Kaitlyn E; Patel, Rushi; Wellman, Cara L

    2017-01-01

    Women are more susceptible to numerous stress-linked psychological disorders (e.g., depression) characterized by dysfunction of corticolimbic brain regions critical for emotion regulation and cognitive function. Although sparsely investigated, a number of studies indicate sex differences in stress effects on neuronal structure, function, and behaviors associated with these regions. We recently demonstrated a basal sex difference in- and differential effects of stress on- microglial activation in medial prefrontal cortex (mPFC). The resident immune cells of the brain, microglia are implicated in synaptic and dendritic plasticity, and cognitive-behavioral function. Here, we examined the effects of acute (3h/day, 1 day) and chronic (3h/day, 10 days) restraint stress on microglial density and morphology, as well as immune factor expression in orbitofrontal cortex (OFC), basolateral amygdala (BLA), and dorsal hippocampus (DHC) in male and female rats. Microglia were visualized, classified based on their morphology, and stereologically counted. Microglia-associated transcripts (CD40, iNOS, Arg1, CX3CL1, CX3CR1, CD200, and CD200R) were assessed in brain punches from each region. Expression of genes linked with cellular stress, neuroimmune state, and neuron-microglia communication varied between unstressed male and female rats in a region-specific manner. In OFC, chronic stress upregulated a wider variety of immune factors in females than in males. Acute stress increased microglia-associated transcripts in BLA in males, whereas chronic stress altered immune factor expression in BLA more broadly in females. In DHC, chronic stress increased immune factor expression in males but not females. Moreover, acute and chronic stress differentially affected microglial morphological activation state in male and female rats across all brain regions investigated. In males, chronic stress altered microglial activation in a pattern consistent with microglial involvement in stress

  15. Behavioral stress alters corticolimbic microglia in a sex- and brain region-specific manner

    Science.gov (United States)

    Bollinger, Justin L.; Collins, Kaitlyn E.; Patel, Rushi

    2017-01-01

    Women are more susceptible to numerous stress-linked psychological disorders (e.g., depression) characterized by dysfunction of corticolimbic brain regions critical for emotion regulation and cognitive function. Although sparsely investigated, a number of studies indicate sex differences in stress effects on neuronal structure, function, and behaviors associated with these regions. We recently demonstrated a basal sex difference in- and differential effects of stress on- microglial activation in medial prefrontal cortex (mPFC). The resident immune cells of the brain, microglia are implicated in synaptic and dendritic plasticity, and cognitive-behavioral function. Here, we examined the effects of acute (3h/day, 1 day) and chronic (3h/day, 10 days) restraint stress on microglial density and morphology, as well as immune factor expression in orbitofrontal cortex (OFC), basolateral amygdala (BLA), and dorsal hippocampus (DHC) in male and female rats. Microglia were visualized, classified based on their morphology, and stereologically counted. Microglia-associated transcripts (CD40, iNOS, Arg1, CX3CL1, CX3CR1, CD200, and CD200R) were assessed in brain punches from each region. Expression of genes linked with cellular stress, neuroimmune state, and neuron-microglia communication varied between unstressed male and female rats in a region-specific manner. In OFC, chronic stress upregulated a wider variety of immune factors in females than in males. Acute stress increased microglia-associated transcripts in BLA in males, whereas chronic stress altered immune factor expression in BLA more broadly in females. In DHC, chronic stress increased immune factor expression in males but not females. Moreover, acute and chronic stress differentially affected microglial morphological activation state in male and female rats across all brain regions investigated. In males, chronic stress altered microglial activation in a pattern consistent with microglial involvement in stress

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

    Science.gov (United States)

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

    2015-04-01

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

  17. Molecular characterization of three Rhesus glycoproteins from the gills of the African lungfish, Protopterus annectens, and effects of aestivation on their mRNA expression levels and protein abundance.

    Directory of Open Access Journals (Sweden)

    You R Chng

    Full Text Available African lungfishes are ammonotelic in water. They can aestivate for long periods on land during drought. During aestivation, the gills are covered with dried mucus and ammonia excretion ceases. In fishes, ammonia excretion through the gills involves Rhesus glycoproteins (RhGP/Rhgp. This study aimed to obtain the complete cDNA coding sequences of rhgp from the gills of Protopterus annectens, and to determine their branchial mRNA and protein expression levels during the induction, maintenance and arousal phases of aestivation. Three isoforms of rhgp (rhag, rhbg and rhcg were obtained in the gills of P. annectens. Their complete cDNA coding sequences ranged between 1311 and 1398 bp, coding for 436 to 465 amino acids with estimated molecular masses between 46.8 and 50.9 kDa. Dendrogramic analyses indicated that Rhag was grouped closer to fishes, while Rhbg and Rhcg were grouped closer to tetrapods. During the induction phase, the protein abundance of Rhag, but not its transcript level, was down-regulated in the gills, suggesting that there could be a decrease in the release of ammonia from the erythrocytes to the plasma. Furthermore, the branchial transcript levels of rhbg and rhcg decreased significantly, in preparation for the subsequent shutdown of gill functions. During the maintenance phase, the branchial expression levels of rhag/Rhag, rhbg/Rhbg and rhcg/Rhcg decreased significantly, indicating that their transcription and translation were down-regulated. This could be part of an overall mechanism to shut down branchial functions and save metabolic energy used for transcription and translation. It could also be regarded as an adaptive response to stop ammonia excretion. During the arousal phase, it is essential for the lungfish to regain the ability to excrete ammonia. Indeed, the protein abundance of Rhag, Rhbg and Rhcg recovered to the corresponding control levels after 1 day or 3 days of recovery from 6 months of aestivation.

  18. Region-Specific Involvement of Actin Rearrangement-Related Synaptic Structure Alterations in Conditioned Taste Aversion Memory

    Science.gov (United States)

    Bi, Ai-Ling; Wang, Yue; Li, Bo-Qin; Wang, Qian-Qian; Ma, Ling; Yu, Hui; Zhao, Ling; Chen, Zhe-Yu

    2010-01-01

    Actin rearrangement plays an essential role in learning and memory; however, the spatial and temporal regulation of actin dynamics in different phases of associative memory has not been fully understood. Here, using the conditioned taste aversion (CTA) paradigm, we investigated the region-specific involvement of actin rearrangement-related…

  19. Perturbations of Amino Acid Metabolism Associated with Glyphosate-Dependent Inhibition of Shikimic Acid Metabolism Affect Cellular Redox Homeostasis and Alter the Abundance of Proteins Involved in Photosynthesis and Photorespiration1[W][OA

    Science.gov (United States)

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

    2011-01-01

    The herbicide glyphosate inhibits the shikimate pathway of the synthesis of amino acids such as phenylalanine, tyrosine, and tryptophan. However, much uncertainty remains concerning precisely how glyphosate kills plants or affects cellular redox homeostasis and related processes in glyphosate-sensitive and glyphosate-resistant crop plants. To address this issue, we performed an integrated study of photosynthesis, leaf proteomes, amino acid profiles, and redox profiles in the glyphosate-sensitive soybean (Glycine max) genotype PAN809 and glyphosate-resistant Roundup Ready Soybean (RRS). RRS leaves accumulated much more glyphosate than the sensitive line but showed relatively few changes in amino acid metabolism. Photosynthesis was unaffected by glyphosate in RRS leaves, but decreased abundance of photosynthesis/photorespiratory pathway proteins was observed together with oxidation of major redox pools. While treatment of a sensitive genotype with glyphosate rapidly inhibited photosynthesis and triggered the appearance of a nitrogen-rich amino acid profile, there was no evidence of oxidation of the redox pools. There was, however, an increase in starvation-associated and defense proteins. We conclude that glyphosate-dependent inhibition of soybean leaf metabolism leads to the induction of defense proteins without sustained oxidation. Conversely, the accumulation of high levels of glyphosate in RRS enhances cellular oxidation, possibly through mechanisms involving stimulation of the photorespiratory pathway. PMID:21757634

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

    Science.gov (United States)

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

    2011-09-01

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

  1. Differential requirements for Gli2 and Gli3 in the regional specification of the mouse hypothalamus

    Directory of Open Access Journals (Sweden)

    Roberta eHaddad-Tóvolli

    2015-03-01

    Full Text Available Secreted protein Sonic hedgehog (Shh ventralizes the neural tube by modulating the crucial balance between activating and repressing functions (GliA, GliR of transcription factors Gli2 and Gli3. This balance—the Shh-Gli code—is species- and context-dependent and has been elucidated for the mouse spinal cord. The hypothalamus, a forebrain region regulating vital functions like homeostasis and hormone secretion, shows dynamic and intricate Shh expression as well as complex regional differentiation. Here we asked if particular combinations of Gli2 and Gli3 and of GliA and GliR functions contribute to the variety of hypothalamic regions, i.e. we wanted to clarify the hypothalamic version of the Shh-Gli code. Based on mouse mutant analysis, we show that: 1 hypothalamic regional heterogeneity is based in part on differentially stringent requirements for Gli2 or Gli3; 2 another source of diversity are differential requirements for Shh of neural vs non-neural origin; 3 Gli2 is indispensable for the specification of a medial progenitor domain generating several essential hypothalamic nuclei plus the pituitary and median eminence; 4 the suppression of Gli3R by neural and non-neural Shh is essential for hypothalamic specification. Finally, we have mapped our results on a recent model which considers the hypothalamus as a transverse region with alar and basal portions. Our data confirm the model and are explained by it.

  2. Probing region-specific microstructure of human cortical areas using high angular and spatial resolution diffusion MRI.

    Science.gov (United States)

    Aggarwal, Manisha; Nauen, David W; Troncoso, Juan C; Mori, Susumu

    2015-01-15

    Regional heterogeneity in cortical cyto- and myeloarchitecture forms the structural basis of mapping of cortical areas in the human brain. In this study, we investigate the potential of diffusion MRI to probe the microstructure of cortical gray matter and its region-specific heterogeneity across cortical areas in the fixed human brain. High angular resolution diffusion imaging (HARDI) data at an isotropic resolution of 92-μm and 30 diffusion-encoding directions were acquired using a 3D diffusion-weighted gradient-and-spin-echo sequence, from prefrontal (Brodmann area 9), primary motor (area 4), primary somatosensory (area 3b), and primary visual (area 17) cortical specimens (n=3 each) from three human subjects. Further, the diffusion MR findings in these cortical areas were compared with histological silver impregnation of the same specimens, in order to investigate the underlying architectonic features that constitute the microstructural basis of diffusion-driven contrasts in cortical gray matter. Our data reveal distinct and region-specific diffusion MR contrasts across the studied areas, allowing delineation of intracortical bands of tangential fibers in specific layers-layer I, layer VI, and the inner and outer bands of Baillarger. The findings of this work demonstrate unique sensitivity of diffusion MRI to differentiate region-specific cortical microstructure in the human brain, and will be useful for myeloarchitectonic mapping of cortical areas as well as to achieve an understanding of the basis of diffusion NMR contrasts in cortical gray matter. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Region-Specific Defects of Respiratory Capacities in the Ndufs4(KO Mouse Brain.

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    Ernst-Bernhard Kayser

    Full Text Available Lack of NDUFS4, a subunit of mitochondrial complex I (NADH:ubiquinone oxidoreductase, causes Leigh syndrome (LS, a progressive encephalomyopathy. Knocking out Ndufs4, either systemically or in brain only, elicits LS in mice. In patients as well as in KO mice distinct regions of the brain degenerate while surrounding tissue survives despite systemic complex I dysfunction. For the understanding of disease etiology and ultimately for the development of rationale treatments for LS, it appears important to uncover the mechanisms that govern focal neurodegeneration.Here we used the Ndufs4(KO mouse to investigate whether regional and temporal differences in respiratory capacity of the brain could be correlated with neurodegeneration. In the KO the respiratory capacity of synaptosomes from the degeneration prone regions olfactory bulb, brainstem and cerebellum was significantly decreased. The difference was measurable even before the onset of neurological symptoms. Furthermore, neither compensating nor exacerbating changes in glycolytic capacity of the synaptosomes were found. By contrast, the KO retained near normal levels of synaptosomal respiration in the degeneration-resistant/resilient "rest" of the brain. We also investigated non-synaptic mitochondria. The KO expectedly had diminished capacity for oxidative phosphorylation (state 3 respiration with complex I dependent substrate combinations pyruvate/malate and glutamate/malate but surprisingly had normal activity with α-ketoglutarate/malate. No correlation between oxidative phosphorylation (pyruvate/malate driven state 3 respiration and neurodegeneration was found: Notably, state 3 remained constant in the KO while in controls it tended to increase with time leading to significant differences between the genotypes in older mice in both vulnerable and resilient brain regions. Neither regional ROS damage, measured as HNE-modified protein, nor regional complex I stability, assessed by blue native

  4. OXYGEN ABUNDANCES IN CEPHEIDS

    International Nuclear Information System (INIS)

    Luck, R. E.; Andrievsky, S. M.; Korotin, S. N.; Kovtyukh, V. V.

    2013-01-01

    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.

  5. Age- and region-specific imbalances of basal amino acids and monoamine metabolism in limbic regions of female Fmr1 knock-out mice.

    Science.gov (United States)

    Gruss, Michael; Braun, Katharina

    2004-07-01

    The Fragile X syndrome, a common form of mental retardation in humans, originates from the loss of expression of the Fragile X mental retardation gene leading to the absence of the encoded Fragile X mental retardation protein 1 (FMRP). A broad pattern of morphological and behavioral abnormalities is well described for affected humans as well as Fmr1 knock-out mice, a transgenic animal model for the human Fragile X syndrome. In the present study, we examined neurochemical differences between female Fmr1 knock-out and wildtype mice with particular focus on neurotransmission. Significant age- and region-specific differences of basal tissue neurotransmitter and metabolite levels measured by high performance liquid chromatography were found. Those differences were more numerous in juvenile animals (postnatal day (PND) 28-31) compared to adults (postnatal day 209-221). In juvenile female knock-out mice, especially aspartate and taurine were increased in cortical regions, striatum, cerebellum, and brainstem. Furthermore, compared to the wildtype animals, the juvenile knock-out mice displayed an increased level of neuronal inhibition in the hippocampus and brainstem reflected by decreased ratios of (aspartate + glutamate)/(taurine + GABA), as well as an increased dopamine (DA) turnover in cortical regions, striatum, and hippocampus. These results provide the first evidence that the lack of FMRP expression in female Fmr1 knock-out mice is accompanied by age-dependent, region-specific alterations in brain amino acids, and monoamine turnover, which might be related to the reported synaptical and behavioural alterations in these animals.

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

    Science.gov (United States)

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

    2012-04-01

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

  7. Orion A helium abundance

    International Nuclear Information System (INIS)

    Tsivilev, A.P.; Ershov, A.A.; Smirnov, G.T.; Sorochenko, R.L.

    1986-01-01

    The 22.4-GHz (H,He)66-alpha and 36.5-GHz (H,He)56-alpha radio recombination lines have been observed at several Jaffe-Pankonin positions in the central part of the Orion A source. The measured relative abundance of ionized helium increases with distance, averaging 11.6 percent at peripheral points. The observed behavior is interpreted by a blister-type model nebula, which implies that Orion A has a true He abundance of 12 percent, is moving with a radial velocity of 5 km/sec, and is expanding. 18 references

  8. SU-F-I-12: Region-Specific Dictionary Learning for Low-Dose X-Ray CT Reconstruction

    International Nuclear Information System (INIS)

    Xu, Q; Han, H; Xing, L

    2016-01-01

    Purpose: Dictionary learning based method has attracted more and more attentions in low-dose CT due to the superior performance on suppressing noise and preserving structural details. Considering the structures and noise vary from region to region in one imaging object, we propose a region-specific dictionary learning method to improve the low-dose CT reconstruction. Methods: A set of normal-dose images was used for dictionary learning. Segmentations were performed on these images, so that the training patch sets corresponding to different regions can be extracted out. After that, region-specific dictionaries were learned from these training sets. For the low-dose CT reconstruction, a conventional reconstruction, such as filtered back-projection (FBP), was performed firstly, and then segmentation was followed to segment the image into different regions. Sparsity constraints of each region based on its dictionary were used as regularization terms. The regularization parameters were selected adaptively according to different regions. A low-dose human thorax dataset was used to evaluate the proposed method. The single dictionary based method was performed for comparison. Results: Since the lung region is very different from the other part of thorax, two dictionaries corresponding to lung region and the rest part of thorax respectively were learned to better express the structural details and avoid artifacts. With only one dictionary some artifact appeared in the body region caused by the spot atoms corresponding to the structures in the lung region. And also some structure in the lung regions cannot be recovered well by only one dictionary. The quantitative indices of the result by the proposed method were also improved a little compared to the single dictionary based method. Conclusion: Region-specific dictionary can make the dictionary more adaptive to different region characteristics, which is much desirable for enhancing the performance of dictionary learning

  9. SU-F-I-12: Region-Specific Dictionary Learning for Low-Dose X-Ray CT Reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Q; Han, H; Xing, L [Stanford University School of Medicine, Stanford, CA (United States)

    2016-06-15

    Purpose: Dictionary learning based method has attracted more and more attentions in low-dose CT due to the superior performance on suppressing noise and preserving structural details. Considering the structures and noise vary from region to region in one imaging object, we propose a region-specific dictionary learning method to improve the low-dose CT reconstruction. Methods: A set of normal-dose images was used for dictionary learning. Segmentations were performed on these images, so that the training patch sets corresponding to different regions can be extracted out. After that, region-specific dictionaries were learned from these training sets. For the low-dose CT reconstruction, a conventional reconstruction, such as filtered back-projection (FBP), was performed firstly, and then segmentation was followed to segment the image into different regions. Sparsity constraints of each region based on its dictionary were used as regularization terms. The regularization parameters were selected adaptively according to different regions. A low-dose human thorax dataset was used to evaluate the proposed method. The single dictionary based method was performed for comparison. Results: Since the lung region is very different from the other part of thorax, two dictionaries corresponding to lung region and the rest part of thorax respectively were learned to better express the structural details and avoid artifacts. With only one dictionary some artifact appeared in the body region caused by the spot atoms corresponding to the structures in the lung region. And also some structure in the lung regions cannot be recovered well by only one dictionary. The quantitative indices of the result by the proposed method were also improved a little compared to the single dictionary based method. Conclusion: Region-specific dictionary can make the dictionary more adaptive to different region characteristics, which is much desirable for enhancing the performance of dictionary learning

  10. Abundance of adiponectin system and G-protein coupled receptor GPR109A mRNA in adipose tissue and liver of F2 offspring cows of Charolais × German Holstein crosses that differ in body fat accumulation.

    Science.gov (United States)

    Mielenz, M; Kuhla, B; Hammon, H M

    2013-01-01

    In addition to its role in energy storage, adipose tissue (AT) is an important endocrine organ and it secretes adipokines. The adipokine adiponectin improves insulin sensitivity by activation of its receptors AdipoR1 and AdipoR2. Lipolysis in AT is downregulated by the G-protein coupled receptor (GPR109A), which binds the endogenous ligand β-hydroxybutyrate (BHBA). Insulin sensitivity is reduced during the transition from late pregnancy to early lactation in dairy cattle and BHBA is increased postpartum, implying the involvement of the adiponectin system and GPR109A in this process. The aim of the current investigation was to study the effect of the genetic background of cows on the mRNA abundance of the adiponectin system, as well as GPR109A, in an F(2) population of 2 Charolais × German Holstein families. These families were deduced from full- and half-sibs sharing identical but reciprocal paternal and maternal Charolais grandfathers. The animals of the 2 families showed significant differences in fat accretion and milk secretion and were designated fat-type (high fat accretion but low milk production) and lean-type (low fat accretion but high milk production). The mRNA of the adiponectin system and GPR109A were quantified by real-time PCR in different fat depots (subcutaneous from back, mesenteric, kidney) and liver. The mRNA data were correlated with AT masses (intermuscular topside border fat, kidney, mesenteric, omental, total inner fat mass, total subcutaneous fat mass, and total fat mass) and blood parameters (glucose, nonesterified fatty acids, BHBA, urea, insulin, and glucagon). The abundance of adiponectin system mRNA was higher in discrete AT depots of fat-type cows [adiponectin mRNA in mesenteric fat (trend), AdipoR1 in kidney and mesenteric AT, and AdipoR2 in subcutaneous fat (trend)] than in lean-type cows. More GPR109A mRNA was found in kidney fat of the lean-type family than in that of the fat-type family. In liver, the abundance of AdipoR2 and

  11. Light exposure enhances urea absorption in the fluted giant clam, Tridacna squamosa, and up-regulates the protein abundance of a light-dependent urea active transporter, DUR3-like, in its ctenidium.

    Science.gov (United States)

    Chan, Christabel Y L; Hiong, Kum C; Boo, Mel V; Choo, Celine Y L; Wong, Wai P; Chew, Shit F; Ip, Yuen K

    2018-04-19

    Giant clams live in nutrient-poor reef waters of the Indo-Pacific and rely on symbiotic dinoflagellates ( Symbiodinium spp., also known as zooxanthellae) for nutrients. As the symbionts are nitrogen deficient, the host clam has to absorb exogenous nitrogen and supply it to them. This study aimed to demonstrate light-enhanced urea absorption in the fluted giant clam, Tridacna squamosa , and to clone and characterize the urea active transporter DUR3-like from its ctenidium (gill). The results indicate that T. squamosa absorbs exogenous urea, and the rate of urea uptake in the light was significantly higher than that in darkness. The DUR3-like coding sequence obtained from its ctenidium comprised 2346 bp, encoding a protein of 782 amino acids and 87.0 kDa. DUR3-like was expressed strongly in the ctenidium, outer mantle and kidney. Twelve hours of exposure to light had no significant effect on the transcript level of ctenidial DUR3-like However, between 3 and 12 h of light exposure, DUR3-like protein abundance increased progressively in the ctenidium, and became significantly greater than that in the control at 12 h. DUR3-like had an apical localization in the epithelia of the ctenidial filaments and tertiary water channels. Taken together, these results indicate that DUR3-like might participate in light-enhanced urea absorption in the ctenidium of T. squamosa When made available to the symbiotic zooxanthellae that are known to possess urease, the absorbed urea can be metabolized to NH 3 and CO 2 to support amino acid synthesis and photosynthesis, respectively, during insolation. © 2018. Published by The Company of Biologists Ltd.

  12. Stellar Oxygen Abundances

    Science.gov (United States)

    King, Jeremy

    1994-04-01

    This dissertation addresses several issues concerning stellar oxygen abundances. The 7774 {\\AA} O I triplet equivalent widths of Abia & Rebolo [1989, AJ, 347, 186] for metal-poor dwarfs are found to be systematically too high. I also argue that current effective temperatures used in halo star abundance studies may be ~150 K too low. New color-Teff relations are derived for metal-poor stars. Using the revised Teff values and improved equivalent widths for the 7774A O I triplet, the mean [O/Fe] ratio for a handful of halo stars is found to be +0.52 with no dependence on Teff or [Fe/H]. Possible cosmological implications of the hotter Teff scale are discussed along with additional evidence supporting the need for a higher temperature scale for metal-poor stars. Our Teff scale leads to a Spite Li plateau value of N(Li)=2.28 +/- 0.09. A conservative minimal primordial value of N(Li)=2.35 is inferred. If errors in the observations and models are considered, consistency with standard models of Big Bang nucleosynthesis is still achieved with this larger Li abundance. The revised Teff scale raises the observed B/Be ratio of HD 140283 from 10 to 12, making its value more comfortably consistent with the production of the observed B and Be by ordinary spallation. Our Teff values are found to be in good agreement with values predicted from both the Victoria and Yale isochrone color-Teff relations. Thus, it appears likely that no changes in globular cluster ages would result. Next, we examine the location of the break in the [O/Fe] versus [Fe/H] plane in a quantitative fashion. Analysis of a relatively homogeneous data set does not favor any unique break point in the range -1.7 /= -3), in agreement with the new results for halo dwarfs. We find that the gap in the observed [O/H] distribution, noted by Wheeler et al. [1989, ARAA, 27, 279], persists despite the addition of more O data and may betray the occurrence of a hiatus in star formation between the end of halo formation and

  13. Lithium-induced neuroprotection in stroke involves increased miR-124 expression, reduced RE1-silencing transcription factor abundance and decreased protein deubiquitination by GSK3β inhibition-independent pathways.

    Science.gov (United States)

    Doeppner, Thorsten R; Kaltwasser, Britta; Sanchez-Mendoza, Eduardo H; Caglayan, Ahmet B; Bähr, Mathias; Hermann, Dirk M

    2017-03-01

    Lithium promotes acute poststroke neuronal survival, which includes mechanisms that are not limited to GSK3β inhibition. However, whether lithium induces long-term neuroprotection and enhanced brain remodeling is unclear. Therefore, mice were exposed to transient middle cerebral artery occlusion and lithium (1 mg/kg bolus followed by 2 mg/kg/day over up to 7 days) was intraperitoneally administered starting 0-9 h after reperfusion onset. Delivery of lithium no later than 6 h reduced infarct volume on day 2 and decreased brain edema, leukocyte infiltration, and microglial activation, as shown by histochemistry and flow cytometry. Lithium-induced neuroprotection persisted throughout the observation period of 56 days and was associated with enhanced neurological recovery. Poststroke angioneurogenesis and axonal plasticity were also enhanced by lithium. On the molecular level, lithium increased miR-124 expression, reduced RE1-silencing transcription factor abundance, and decreased protein deubiquitination in cultivated cortical neurons exposed to oxygen-glucose deprivation and in brains of mice exposed to cerebral ischemia. Notably, this effect was not mimicked by pharmacological GSK3β inhibition. This study for the first time provides efficacy data for lithium in the postacute ischemic phase, reporting a novel mechanism of action, i.e. increased miR-124 expression facilitating REST degradation by which lithium promotes postischemic neuroplasticity and angiogenesis.

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

    Science.gov (United States)

    Nakasone, Kiyoshi; Nagahama, Yoshitaka; Okubo, Kataaki

    2013-02-01

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

  15. Improving cluster-based methods for investigating potential for insect pest species establishment: region-specific risk factors

    Directory of Open Access Journals (Sweden)

    Michael J. Watts

    2011-09-01

    Full Text Available Existing cluster-based methods for investigating insect species assemblages or profiles of a region to indicate the risk of new insect pest invasion have a major limitation in that they assign the same species risk factors to each region in a cluster. Clearly regions assigned to the same cluster have different degrees of similarity with respect to their species profile or assemblage. This study addresses this concern by applying weighting factors to the cluster elements used to calculate regional risk factors, thereby producing region-specific risk factors. Using a database of the global distribution of crop insect pest species, we found that we were able to produce highly differentiated region-specific risk factors for insect pests. We did this by weighting cluster elements by their Euclidean distance from the target region. Using this approach meant that risk weightings were derived that were more realistic, as they were specific to the pest profile or species assemblage of each region. This weighting method provides an improved tool for estimating the potential invasion risk posed by exotic species given that they have an opportunity to establish in a target region.

  16. Generation of Regionally Specific Neural Progenitor Cells (NPCs) and Neurons from Human Pluripotent Stem Cells (hPSCs).

    Science.gov (United States)

    Cutts, Josh; Brookhouser, Nicholas; Brafman, David A

    2016-01-01

    Neural progenitor cells (NPCs) derived from human pluripotent stem cells (hPSCs) are a multipotent cell population capable of long-term expansion and differentiation into a variety of neuronal subtypes. As such, NPCs have tremendous potential for disease modeling, drug screening, and regenerative medicine. Current methods for the generation of NPCs results in cell populations homogenous for pan-neural markers such as SOX1 and SOX2 but heterogeneous with respect to regional identity. In order to use NPCs and their neuronal derivatives to investigate mechanisms of neurological disorders and develop more physiologically relevant disease models, methods for generation of regionally specific NPCs and neurons are needed. Here, we describe a protocol in which exogenous manipulation of WNT signaling, through either activation or inhibition, during neural differentiation of hPSCs, promotes the formation of regionally homogenous NPCs and neuronal cultures. In addition, we provide methods to monitor and characterize the efficiency of hPSC differentiation to these regionally specific cell identities.

  17. Mapping to mouse chromosome 3 of the gene encoding latexin (Lxn) expressed in neocortical neurons in a region-specific manner

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Ming-hao; Uratani, Yoshihiko; Arimatsu, Yasuyoshi [Mitsubishi Kasei Institute of Life Sciences, Tokyo (Japan)

    1997-02-01

    Latexin was first found as a 29-kDa antigen expressed in a subset of neurons in infragranular layers of lateral, but not dorsal, neocortical areas in the rat using a monoclonal antibody PC3.1. It was found that the vast majority of latexin-expressing neurons in both layers V and VI within the lateral neocortex were generated concurrently at Embryonic Day 15, demonstrating a strict correlation between the molecular identity of neurons and the time of their generation. Since neurons expressing latexin are located in the restricted part of the neocortex, latexin has been used as a useful molecular marker to elucidate the mechanism underlying cortical regional specification. The latexin cDNA isolated from a cDNA library of the rat cerebral cortex encodes a protein composed of 223-amino-acid residues containing two potential Ca{sup 2+}/calmodulin-dependent protein kinase sites and one cGMP-dependent protein kinase phosphorylation site. The absence of any signal peptide or potential transmembrane domain is consistent with the apparent cytosolic localization of latexin in the rat brain. The transcripts of latexin were expressed in not only neutral but also nonneural tissues (e.g., lung, spleen, kidney, heart, and digestive tracts). Recently, it has been demonstrated that latexin purified from the rat brain has inhibitory activity against carboxypeptidase A1, carboxypeptidase A2, and mast cell carboxypeptidase A, with less carboxypeptidase B-inhibiting activity. The amino acid sequence deduced from the rat latexin cDNA has no strict homology to any sequences so far known. Genomic Southern blot analysis using a cDNA probe of rat latexin suggested that the gene encoding latexin in the rat has homologues in other mammalian species and in the chicken, but not in the nematode, fly, or frog. 9 refs., 1 fig.

  18. Ammonia abundances in comets

    Science.gov (United States)

    Wyckoff, S.; Tegler, S.; Engel, L.

    The emission band strengths of the NH2 bands of Comets Halley, Hartley-Good, Thiele, and Borrelly were measured to determine the NH2 column densities for the comets. Production rates obtained using the Haser and vectorial models are in agreement within the observational errors, suggesting that a simple two-step decay model may be used to approximate the NH2 distribution in a comet's coma. Ammonia-to-water abundance ratios from 0.01 to 0.4 percent were found for the four comets. The ratio in Comet Halley is found to be Q(NH3)/Q(H2O) = 0.002 + or - 0.001. No significant difference in the ammonia abundance was found before or after perihelion in Comet Halley.

  19. Compilation of solar abundance data

    International Nuclear Information System (INIS)

    Hauge, Oe.; Engvold, O.

    1977-01-01

    Interest in the previous compilations of solar abundance data by the same authors (ITA--31 and ITA--39) has led to this third, revised edition. Solar abundance data of 67 elements are tabulated and in addition upper limits for the abundances of 5 elements are listed. References are made to 167 papers. A recommended abundance value is given for each element. (JIW)

  20. Abundances in galaxies

    International Nuclear Information System (INIS)

    Pagel, B.E.J.

    1991-01-01

    Standard (or mildly inhomogeneous) Big Bang nucleosynthesis theory is well confirmed by abundance measurements of light elements up to 7 Li 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 9 Be 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.)

  1. Region-Specific Effect of the Decellularized Meniscus Extracellular Matrix on Mesenchymal Stem Cell-Based Meniscus Tissue Engineering.

    Science.gov (United States)

    Shimomura, Kazunori; Rothrauff, Benjamin B; Tuan, Rocky S

    2017-03-01

    The meniscus is the most commonly injured knee structure, and surgical repair is often ineffective. Tissue engineering-based repair or regeneration may provide a needed solution. Decellularized, tissue-derived extracellular matrices (ECMs) have received attention for their potential use as tissue-engineered scaffolds. In considering meniscus-derived ECMs (mECMs) for meniscus tissue engineering, it is noteworthy that the inner and outer regions of the meniscus have different structural and biochemical features, potentially directing the differentiation of cells toward region-specific phenotypes. To investigate the applicability of mECMs for meniscus tissue engineering by specifically comparing region-dependent effects of mECMs on 3-dimensional constructs seeded with human bone marrow mesenchymal stem cells (hBMSCs). Controlled laboratory study. Bovine menisci were divided into inner and outer halves and were minced, treated with Triton X-100 and DNase, and extracted with urea. Then, hBMSCs (1 × 10 6 cells/mL) were encapsulated in a photo-cross-linked 10% polyethylene glycol diacrylate scaffold containing mECMs (60 μg/mL) derived from either the inner or outer meniscus, with an ECM-free scaffold as a control. The cell-seeded constructs were cultured with chondrogenic medium containing recombinant human transforming growth factor β3 (TGF-β3) and were analyzed for expression of meniscus-associated genes as well as for the collagen (hydroxyproline) and glycosaminoglycan content as a function of time. Decellularization was verified by the absence of 4',6-diamidino-2-phenylindole (DAPI)-stained cell nuclei and a reduction in the DNA content. Quantitative real-time polymerase chain reaction showed that collagen type I expression was significantly higher in the outer mECM group than in the other groups, while collagen type II and aggrecan expression was highest in the inner mECM group. The collagen (hydroxyproline) content was highest in the outer mECM group, while the

  2. Premature Aging Phenotype in Mice Lacking High-Affinity Nicotinic Receptors: Region-Specific Changes in Layer V Pyramidal Cell Morphology.

    Science.gov (United States)

    Konsolaki, Eleni; Skaliora, Irini

    2015-08-01

    The mechanisms by which aging leads to alterations in brain structure and cognitive deficits are unclear. Α deficient cholinergic system has been implicated as one of the main factors that could confer a heightened vulnerability to the aging process, and mice lacking high-affinity nicotinic receptors (β2(-/-)) have been proposed as an animal model of accelerated cognitive aging. To date, however, age-related changes in neuronal microanatomy have not been studied in these mice. In the present study, we examine the neuronal structure of yellow fluorescent protein (YFP(+)) layer V neurons in 2 cytoarchitectonically distinct cortical regions in wild-type (WT) and β2(-/-) animals. We find that (1) substantial morphological differences exist between YFP(+) cells of the anterior cingulate cortex (ACC) and primary visual cortex (V1), in both genotypes; (2) in WT animals, ACC cells are more susceptible to aging compared with cells in V1; and (3) β2 deletion is associated with a regionally and temporally specific increase in vulnerability to aging. ACC cells exhibit a prematurely aged phenotype already at 4-6 months, whereas V1 cells are spared in adulthood but strongly affected in old animals. Collectively, our data reveal region-specific synergistic effects of aging and genotype and suggest distinct vulnerabilities in V1 and ACC neurons. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Interactive and individual effects of sensory potentiation and region-specific changes in excitability after spinal cord injury.

    Science.gov (United States)

    Hoffman, N; Parker, D

    2011-12-29

    While promoting regeneration across lesion sites is a main focus of research into spinal injury, changes also occur in the sublesion spinal cord and its sensory inputs. However, how these varied effects relate to recovery remains largely unknown. Here, we have examined changes in sensory inputs and region-specific changes in spinal cord excitability after spinal cord lesions in the lamprey, a model system for studying regeneration and functional recovery, and related the changes to the degree of locomotor recovery.Proprioceptive responses below lesion sites were potentiated and their rate of adaptation reduced 8-10 weeks after lesioning (i.e. when animals usually showed significant locomotor recovery). These effects were associated with changes in cellular properties that were consistent with an increase in proprioceptor excitability. However, the changes in proprioceptive inputs did not correlate with the degree of locomotor recovery. There were region-specific changes in spinal cord excitability below lesion sites. In isolation, these excitability changes also did not correlate with the degree of locomotor recovery, but in this case, there were significant interactions between the magnitude of stimulation-evoked responses across the lesion site (used to assess the extent of regeneration) and sublesion changes in excitability. These interactions differed in animals that recovered well or poorly, suggesting that the nature of this interaction influenced recovery. These results add to the evidence for diverse changes in the spinal cord after injury, and suggest that regenerated inputs and their interactions with sublesion networks influence the degree of functional recovery. Copyright © 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

  4. Region-specificity of GABAA receptor mediated effects on orientation and direction selectivity in cat visual cortical area 18.

    Science.gov (United States)

    Jirmann, Kay-Uwe; Pernberg, Joachim; Eysel, Ulf T

    2009-01-01

    The role of GABAergic inhibition in orientation and direction selectivity has been investigated with the GABA(A)-Blocker bicuculline in the cat visual cortex, and results indicated a region specific difference of functional contributions of GABAergic inhibition in areas 17 and 18. In area 17 inhibition appeared mainly involved in sculpturing orientation and direction tuning, while in area 18 inhibition seemed more closely associated with temporal receptive field properties. However, different types of stimuli were used to test areas 17 and 18 and further studies performed in area 17 suggested an important influence of the stimulus type (single light bars vs. moving gratings) on the evoked responses (transient vs. sustained) and inhibitory mechanisms (GABA(A) vs. GABA(B)) which in turn might be more decisive for the specific results than the cortical region. To insert the missing link in this chain of arguments it was necessary to study GABAergic inhibition in area 18 with moving light bars, which has not been done so far. Therefore, in the present study we investigated area 18 cells responding to oriented moving light bars with extracellular recordings and reversible microiontophoretic blockade of GABAergig inhibition with bicuculline methiodide. The majority of neurons was characterized by a pronounced orientation specificity and variable degrees of direction selectivity. GABA(A)ergic inhibition significantly influenced preferred orientation and preferred direction in area 18. During the action of bicuculline orientation tuning width increased and orientation and direction selectivity indices decreased. Our results obtained in area 18 with moving bar stimuli, although in the proportion of affected cells similar to those described in area 17, quantitatively matched the findings for direction and orientation specificity obtained with moving gratings in area 18. Accordingly, stimulus type is not decisive in area 18 and the GABA(A) dependent, inhibitory intracortical

  5. Anomalous behavior of tellurium abundances

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, B L

    1984-01-01

    The cosmic abundance of Te is larger than for any element with atomic number greater than 40, but it is one of the least abundant elements in the earth's lithosphere and it is one of the five elements never reported in sea water. On the other hand, it is the fourth most abundant element in the human body (after Fe, Zn and Rb), and is unusually abundant in human food. It is shown that the high abundance in human food combined with the low abundance in soil requires that it be picked up by plant roots very much more efficiently than any other trace element.

  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. A Comprehensive Analysis of Chromoplast Differentiation Reveals Complex Protein Changes Associated with Plastoglobule Biogenesis and Remodeling of Protein Systems in Sweet Orange Flesh1[OPEN

    Science.gov (United States)

    Wang, Lun; Deng, Xiuxin

    2015-01-01

    Globular and crystalloid chromoplasts were observed to be region specifically formed in sweet orange (Citrus sinensis) flesh and converted from amyloplasts during fruit maturation, which was associated with the composition of specific carotenoids and the expression of carotenogenic genes. Subsequent isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomic analyses of purified plastids from the flesh during chromoplast differentiation and senescence identified 1,386 putative plastid-localized proteins, 1,016 of which were quantified by spectral counting. The iTRAQ values reflecting the expression abundance of three identified proteins were validated by immunoblotting. Based on iTRAQ data, chromoplastogenesis appeared to be associated with three major protein expression patterns: (1) marked decrease in abundance of the proteins participating in the translation machinery through ribosome assembly; (2) increase in abundance of the proteins involved in terpenoid biosynthesis (including carotenoids), stress responses (redox, ascorbate, and glutathione), and development; and (3) maintenance of the proteins for signaling and DNA and RNA. Interestingly, a strong increase in abundance of several plastoglobule-localized proteins coincided with the formation of plastoglobules in the chromoplast. The proteomic data also showed that stable functioning of protein import, suppression of ribosome assembly, and accumulation of chromoplast proteases are correlated with the amyloplast-to-chromoplast transition; thus, these processes may play a collective role in chromoplast biogenesis and differentiation. By contrast, the chromoplast senescence process was inferred to be associated with significant increases in stress response and energy supply. In conclusion, this comprehensive proteomic study identified many potentially new plastid-localized proteins and provides insights into the potential developmental and molecular mechanisms underlying chromoplast

  8. The regulation of growth and metabolism of kidney stem cells with regional specificity using extracellular matrix derived from kidney.

    Science.gov (United States)

    O'Neill, John D; Freytes, Donald O; Anandappa, Annabelle J; Oliver, Juan A; Vunjak-Novakovic, Gordana V

    2013-12-01

    Native extracellular matrix (ECM) that is secreted and maintained by resident cells is of great interest for cell culture and cell delivery. We hypothesized that specialized bioengineered niches for stem cells can be established using ECM-derived scaffolding materials. Kidney was selected as a model system because of the high regional diversification of renal tissue matrix. By preparing the ECM from three specialized regions of the kidney (cortex, medulla, and papilla; whole kidney, heart, and bladder as controls) in three forms: (i) intact sheets of decellularized ECM, (ii) ECM hydrogels, and (iii) solubilized ECM, we investigated how the structure and composition of ECM affect the function of kidney stem cells (with mesenchymal stem cells, MSCs, as controls). All three forms of the ECM regulated KSC function, with differential structural and compositional effects. KSCs cultured on papilla ECM consistently displayed lower proliferation, higher metabolic activity, and differences in cell morphology, alignment, and structure formation as compared to KSCs on cortex and medulla ECM, effects not observed in corresponding MSC cultures. These data suggest that tissue- and region-specific ECM can provide an effective substrate for in vitro studies of therapeutic stem cells. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Region-specific associations between sex, social status, and oxytocin receptor density in the brains of eusocial rodents.

    Science.gov (United States)

    Mooney, S J; Coen, C W; Holmes, M M; Beery, A K

    2015-09-10

    Naturally occurring variations in neuropeptide receptor distributions in the brain contribute to numerous mammalian social behaviors. In naked mole-rats, which live in large social groups and exhibit remarkable reproductive skew, colony-related social behaviors vary with reproductive status. Here we examined whether variation in social status is associated with variations in the location and/or density of oxytocin binding in this species. Autoradiography was performed to assess forebrain oxytocin receptor (OTR) densities in breeding and non-breeding naked mole-rats of both sexes. Overall, males exhibited higher OTR binding in the medial amygdala in comparison to females. While there were no main effects of reproductive status in any region, a sex difference in OTR binding in the nucleus accumbens was mediated by status. Specifically, breeding males tended to have more OTR binding than breeding females in the nucleus accumbens, while no sex difference was observed in subordinates. These effects suggest that oxytocin may act in a sex- and region-specific way that corresponds to reproductive status and associated social behaviors. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

  10. Cognitive deficits in adult rats by lead intoxication are related with regional specific inhibition of cNOS.

    Science.gov (United States)

    García-Arenas, Guadalupe; Ramírez-Amaya, Victor; Balderas, Israela; Sandoval, Jimena; Escobar, Martha L; Ríos, Camilo; Bermúdez-Rattoni, Federico

    2004-02-04

    It is well known that lead can affect several cognitive abilities in developing animals. In this work, we investigate the effects of different sub-chronic lead doses (0, 65, 125, 250 and 500 ppm of lead acetate in their drinking water for 14 days) in the performance of male adult rats in a water maze, cue maze and inhibitory avoidance tasks. We found that the acquisition of these tasks was not affected by lead, however, the highest dosage of lead (500 ppm) impaired memory consolidation in spatial and inhibitory avoidance tasks, but not in cue maze task while the 250 ppm dose only affected retrieval of spatial memory. Additionally, hippocampal long-term potentiation (LTP) induction in the perforant path after exposing adult rats to different doses of lead was studied. LTP induction was affected in a dose-dependent manner, and treatments of 250 and 500 ppm completely blocked LTP. We investigated the effects of lead intoxication on the activity of constitutive nitric oxide synthase (cNOS) in different brain regions of adult animals. The activity of cNOS was significantly inhibited in the hippocampus and cerebellum but not in the frontal cortex and brain stem, although lead had accumulated in all brain regions. These results suggest that lead intoxication can impair memory in adult animals and this impairment might be related with region-specific effects on cNOS activity.

  11. Region-specific vulnerability to lipid peroxidation and evidence of neuronal mechanisms for polyunsaturated fatty acid biosynthesis in the healthy adult human central nervous system.

    Science.gov (United States)

    Naudí, Alba; Cabré, Rosanna; Dominguez-Gonzalez, Mayelin; Ayala, Victoria; Jové, Mariona; Mota-Martorell, Natalia; Piñol-Ripoll, Gerard; Gil-Villar, Maria Pilar; Rué, Montserrat; Portero-Otín, Manuel; Ferrer, Isidre; Pamplona, Reinald

    2017-05-01

    Lipids played a determinant role in the evolution of the brain. It is postulated that the morphological and functional diversity among neural cells of the human central nervous system (CNS) is projected and achieved through the expression of particular lipid profiles. The present study was designed to evaluate the differential vulnerability to oxidative stress mediated by lipids through a cross-regional comparative approach. To this end, we compared 12 different regions of CNS of healthy adult subjects, and the fatty acid profile and vulnerability to lipid peroxidation, were determined by gas chromatography (GC) and gas chromatography/mass spectrometry (GC/MS), respectively. In addition, different components involved in PUFA biosynthesis, as well as adaptive defense mechanisms against lipid peroxidation, were also measured by western blot and immunohistochemistry, respectively. We found that: i) four fatty acids (18.1n-9, 22:6n-3, 20:1n-9, and 18:0) are significant discriminators among CNS regions; ii) these differential fatty acid profiles generate a differential selective neural vulnerability (expressed by the peroxidizability index); iii) the cross-regional differences for the fatty acid profiles follow a caudal-cranial gradient which is directly related to changes in the biosynthesis pathways which can be ascribed to neuronal cells; and iv) the higher the peroxidizability index for a given human brain region, the lower concentration of the protein damage markers, likely supported by the presence of adaptive antioxidant mechanisms. In conclusion, our results suggest that there is a region-specific vulnerability to lipid peroxidation and offer evidence of neuronal mechanisms for polyunsaturated fatty acid biosynthesis in the human central nervous system. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Twilight of Abundance

    Science.gov (United States)

    Archibald, David

    2014-03-01

    Baby boomers enjoyed the most benign period in human history: fifty years of relative peace, cheap energy, plentiful grain supply, and a warming climate due to the highest solar activity for 8,000 years. The party is over - prepare for the twilight of abundance. David Archibald reveals the grim future the world faces on its current trajectory: massive fuel shortages, the bloodiest warfare in human history, a global starvation crisis, and a rapidly cooling planet. Archibald combines pioneering science with keen economic knowledge to predict the global disasters that could destroy civilization as we know it - disasters that are waiting just around the corner. But there's good news, too: We can have a good future if we prepare for it. Advanced, civilized countries can have a permanently high standard of living if they choose to invest in the technologies that will get them there. Archibald, a climate scientist as well as an inventor and a financial specialist, explains which scientific breakthroughs can save civilization in the coming crisis - if we can cut through the special interest opposition to these innovations and allow free markets to flourish.

  13. Using the longest significance run to estimate region-specific p-values in genetic association mapping studies

    Directory of Open Access Journals (Sweden)

    Yang Hsin-Chou

    2008-05-01

    Full Text Available Abstract Background Association testing is a powerful tool for identifying disease susceptibility genes underlying complex diseases. Technological advances have yielded a dramatic increase in the density of available genetic markers, necessitating an increase in the number of association tests required for the analysis of disease susceptibility genes. As such, multiple-tests corrections have become a critical issue. However the conventional statistical corrections on locus-specific multiple tests usually result in lower power as the number of markers increases. Alternatively, we propose here the application of the longest significant run (LSR method to estimate a region-specific p-value to provide an index for the most likely candidate region. Results An advantage of the LSR method relative to procedures based on genotypic data is that only p-value data are needed and hence can be applied extensively to different study designs. In this study the proposed LSR method was compared with commonly used methods such as Bonferroni's method and FDR controlling method. We found that while all methods provide good control over false positive rate, LSR has much better power and false discovery rate. In the authentic analysis on psoriasis and asthma disease data, the LSR method successfully identified important candidate regions and replicated the results of previous association studies. Conclusion The proposed LSR method provides an efficient exploratory tool for the analysis of sequences of dense genetic markers. Our results show that the LSR method has better power and lower false discovery rate comparing with the locus-specific multiple tests.

  14. Optogenetic fMRI and electrophysiological identification of region-specific connectivity between the cerebellar cortex and forebrain.

    Science.gov (United States)

    Choe, Katrina Y; Sanchez, Carlos F; Harris, Neil G; Otis, Thomas S; Mathews, Paul J

    2018-06-01

    Complex animal behavior is produced by dynamic interactions between discrete regions of the brain. As such, defining functional connections between brain regions is critical in gaining a full understanding of how the brain generates behavior. Evidence suggests that discrete regions of the cerebellar cortex functionally project to the forebrain, mediating long-range communication potentially important in motor and non-motor behaviors. However, the connectivity map remains largely incomplete owing to the challenge of driving both reliable and selective output from the cerebellar cortex, as well as the need for methods to detect region specific activation across the entire forebrain. Here we utilize a paired optogenetic and fMRI (ofMRI) approach to elucidate the downstream forebrain regions modulated by activating a region of the cerebellum that induces stereotypical, ipsilateral forelimb movements. We demonstrate with ofMRI, that activating this forelimb motor region of the cerebellar cortex results in functional activation of a variety of forebrain and midbrain areas of the brain, including the hippocampus and primary motor, retrosplenial and anterior cingulate cortices. We further validate these findings using optogenetic stimulation paired with multi-electrode array recordings and post-hoc staining for molecular markers of activated neurons (i.e. c-Fos). Together, these findings demonstrate that a single discrete region of the cerebellar cortex is capable of influencing motor output and the activity of a number of downstream forebrain as well as midbrain regions thought to be involved in different aspects of behavior. Copyright © 2018 Elsevier Inc. All rights reserved.

  15. Brain tissue- and region-specific abnormalities on volumetric MRI scans in 21 patients with Bardet-Biedl syndrome (BBS

    Directory of Open Access Journals (Sweden)

    Johnston Jennifer

    2011-07-01

    Full Text Available Abstract Background Bardet-Biedl syndrome (BBS is a heterogeneous human disorder inherited in an autosomal recessive pattern, and characterized by the primary findings of obesity, polydactyly, hypogonadism, and learning and behavioural problems. BBS mouse models have a neuroanatomical phenotype consisting of third and lateral ventriculomegaly, thinning of the cerebral cortex, and reduction in the size of the corpus striatum and hippocampus. These abnormalities raise the question of whether humans with BBS have a characteristic morphologic brain phenotype. Further, although behavioral, developmental, neurological and motor defects have been noted in patients with BBS, to date, there are limited reports of brain findings in BBS. The present study represents the largest systematic evaluation for the presence of structural brain malformations and/or progressive changes, which may contribute to these functional problems. Methods A case-control study of 21 patients, most aged 13-35 years, except for 2 patients aged 4 and 8 years, who were diagnosed with BBS by clinical criteria and genetic analysis of known BBS genes, and were evaluated by qualitative and volumetric brain MRI scans. Healthy controls were matched 3:1 by age, sex and race. Statistical analysis was performed using SAS language with SAS STAT procedures. Results All 21 patients with BBS were found to have statistically significant region- and tissue-specific patterns of brain abnormalities. There was 1 normal intracranial volume; 2 reduced white matter in all regions of the brain, but most in the occipital region; 3 preserved gray matter volume, with increased cerebral cortex volume in only the occipital lobe; 4 reduced gray matter in the subcortical regions of the brain, including the caudate, putamen and thalamus, but not in the cerebellum; and 5 increased cerebrospinal fluid volume. Conclusions There are distinct and characteristic abnormalities in tissue- and region- specific volumes

  16. Brain Region-Specific Effects of cGMP-Dependent Kinase II Knockout on AMPA Receptor Trafficking and Animal Behavior

    Science.gov (United States)

    Kim, Seonil; Pick, Joseph E.; Abera, Sinedu; Khatri, Latika; Ferreira, Danielle D. P.; Sathler, Matheus F.; Morison, Sage L.; Hofmann, Franz; Ziff, Edward B.

    2016-01-01

    Phosphorylation of GluA1, a subunit of AMPA receptors (AMPARs), is critical for AMPAR synaptic trafficking and control of synaptic transmission. cGMP-dependent protein kinase II (cGKII) mediates this phosphorylation, and cGKII knockout (KO) affects GluA1 phosphorylation and alters animal behavior. Notably, GluA1 phosphorylation in the KO…

  17. Energy abundance and economic progress

    International Nuclear Information System (INIS)

    Schurr, S.H.

    1983-01-01

    A discussion is presented on the benefits of energy abundance and on the links between energy supply, economic growth and human welfare in the United States. It is argued that the restoration of energy abundance with dependable sources of supply should be a major national objective. (U.K.)

  18. Abundances in the Galactic bulge

    Energy Technology Data Exchange (ETDEWEB)

    Barbuy, B; Alves-Brito, A [Universidade de Sao Paulo, IAG, Rua do Matao 1226, Sao Paulo 05508-900 (Brazil); Ortolani, S; Zoccali, M [Dipartimento di Astronomia, Universita di Padova, Vicolo dell' Osservatorio 2, I-35122 Padova (Italy); Hill, V; Gomez, A [Observatoire de Paris-Meudon, 92195 Meudon Cedex (France); Melendez, J [Centro de AstrofIsica da Universidade de Porto, Rua das Estrelas, 4150-762 Porto (Portugal); Asplund, M [Max Planck Institute for Astrophysics, Postfach 1317, 85741 Garching (Germany); Bica, E [Departamento de Astronomia, Universidade Federal do Rio Grande do Sul, CP 15051, Porto Alegre 91501-970 (Brazil); Renzini, A [Osservatorio Astronomico di Padova, Vicolo dell' Osservatorio 5, I-35122 Padova (Italy); Minniti, D [Department of Astronomy and Astrophysics, Universidad Catolica de Chile, Casilla 306, Santiago 22 (Chile)], E-mail: barbuy@astro.iag.usp.br

    2008-12-15

    The metallicity distribution and abundance ratios of the Galactic bulge are reviewed. Issues raised by recent work of different groups, in particular the high metallicity end, the overabundance of {alpha}-elements in the bulge relative to the thick disc and the measurement of giants versus dwarfs, are discussed. Abundances in the old moderately metal-poor bulge globular clusters are described.

  19. Trp53 deficient mice predisposed to preterm birth display region-specific lipid alterations at the embryo implantation site

    Energy Technology Data Exchange (ETDEWEB)

    Lanekoff, Ingela; Cha, Jeeyeon; Kyle, Jennifer E.; Dey, Sudhansu K.; Laskin, Julia; Burnum-Johnson, Kristin E.

    2016-09-13

    Here we demonstrate that conditional deletion of mouse uterine Trp53 (p53d/d), molecularly linked to mTORC1 activation and causally linked to premature uterine senescence and preterm birth, results in aberrant lipid signatures within the heterogeneous cell types of embryo implantation sites on day 8 of pregnancy. In situ nanospray desorption electrospray ionization mass spectrometry imaging (nano-DESI MSI) was used to characterize the molecular speciation of free fatty acids, monoacylglycerols, unmodified and oxidized phosphatidylcholine (PC/Ox-PC), and diacylglycerol (DG) species within implantation sites of p53d/d mice and floxed littermates. Implantation sites from p53d/d mice exhibited distinct spatially resolved changes demonstrating accumulation of DG species, depletion of Ox-PC species, and increase in species with more unsaturated acyl chains, including arachidonic and docosahexaenoic acid. Understanding abnormal changes in the abundance and localization of individual lipid species early in the progression to premature birth is important for discovering novel targets for treatments and diagnosis.

  20. Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX

    NARCIS (Netherlands)

    Abbeele, van den P.; Grootaert, C.; Marzorati, M.; Possemiers, S.; Verstraete, W.; Gérard, P.; Rabot, S.; Bruneau, A.; Aidy, El S.F.; Derrien, M.M.N.; Zoetendal, E.G.; Kleerebezem, M.; Smidt, H.; Wiele, van der T.

    2010-01-01

    Dynamic, multicompartment in vitro gastrointestinal simulators are often used to monitor gut microbial dynamics and activity. These reactors need to harbor a microbial community that is stable upon inoculation, colon region specific, and relevant to in vivo conditions. Together with the

  1. Oxygen abundances in halo stars

    Science.gov (United States)

    Bessell, Michael S.; Sutherland, Ralph S.; Ruan, Kui

    1991-12-01

    The present study determines the oxygen abundance for a sample of metal-poor G dwarfs by analysis of OH lines between 3080 and 3200 A and the permitted high-excitation far-red O I triple. The oxygen abundances determined from the low-excitation OH lines are up to 0.55 dex lower than those measured from the high-excitation O I lines. The abundances for the far-red O I triplet lines agree with those rederived from Abia and Rebolo (1989), and the abundances from the OH lines in dwarfs and giants are in agreement with the rederived O abundances of Barbuy (1988) and others from the forbidden resonance O I line. Because the chi = 0.1.7 eV OH lines are formed in the same layers as the majority of Fe, Ti, and other neutral metal lines used for abundance analyses, it is argued that the OH lines and the forbidden O I line yield the true oxygen abundances relative to the metals.

  2. 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

    interferon-induced proteins, were not detected in the master MRC-5 images. The identity of 36 of the transformation-sensitive proteins whose levels are up or down regulated by two times or more was determined and additional information can be transferred from the master transformed human epithelial amnion......, 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...

  3. Spectral unmixing: estimating partial abundances

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2009-01-01

    Full Text Available techniques is complicated when considering very similar spectral signatures. Iron-bearing oxide/hydroxide/sulfate minerals have similar spectral signatures. The study focuses on how could estimates of abundances of spectrally similar iron-bearing oxide...

  4. Ammonia abundances in four comets

    International Nuclear Information System (INIS)

    Wickoff, S.; Tegler, S.C.; Engel, L.

    1991-01-01

    NH2 emission band strengths were measured in four comets and the NH2 column densities were determined in order to measure the ammonia content of the comets. The mean ammonia/water abundance ratio derived for the four comets is found to be 0.13 + or - 0.06 percent, with no significant variation among the comets. The uniformity of this abundance attests to a remarkable degree of chemical homogeneity over large scales in the comet-forming region of the primordial solar nebula, and contrasts with the CO abundance variations found previously in comets. The N2 and NH3 abundances indicate a condensation temperature in the range 20-160 K, consistent with virtually all comet formation hypotheses. 64 refs

  5. Magellanic Clouds Cepheids: Thorium Abundances

    Directory of Open Access Journals (Sweden)

    Yeuncheol Jeong

    2018-03-01

    Full Text Available The analysis of the high-resolution spectra of 31 Magellanic Clouds Cepheid variables enabled the identification of thorium lines. The abundances of thorium were found with spectrum synthesis method. The calculated thorium abundances exhibit correlations with the abundances of other chemical elements and atmospheric parameters of the program stars. These correlations are similar for both Clouds. The correlations of iron abundances of thorium, europium, neodymium, and yttrium relative to the pulsational periods are different in the Large Magellanic Cloud (LMC and the Small Magellanic Cloud (SMC, namely the correlations are negative for LMC and positive or close to zero for SMC. One of the possible explanations can be the higher activity of nucleosynthesis in SMC with respect to LMC in the recent several hundred million years.

  6. NEFSC Survey Indices of Abundance

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Northeast Fisheries Survey Bottom trawl survey indices of abundance such as stratified mean number per tow or mean weight per tow by species stock. Includes indices...

  7. Nuclear Overhauser Enhancement imaging of glioblastoma at 7 Tesla: region specific correlation with apparent diffusion coefficient and histology.

    Science.gov (United States)

    Paech, Daniel; Burth, Sina; Windschuh, Johannes; Meissner, Jan-Eric; Zaiss, Moritz; Eidel, Oliver; Kickingereder, Philipp; Nowosielski, Martha; Wiestler, Benedikt; Sahm, Felix; Floca, Ralf Omar; Neumann, Jan-Oliver; Wick, Wolfgang; Heiland, Sabine; Bendszus, Martin; Schlemmer, Heinz-Peter; Ladd, Mark Edward; Bachert, Peter; Radbruch, Alexander

    2015-01-01

    To explore the correlation between Nuclear Overhauser Enhancement (NOE)-mediated signals and tumor cellularity in glioblastoma utilizing the apparent diffusion coefficient (ADC) and cell density from histologic specimens. NOE is one type of chemical exchange saturation transfer (CEST) that originates from mobile macromolecules such as proteins and might be associated with tumor cellularity via altered protein synthesis in proliferating cells. For 15 patients with newly diagnosed glioblastoma, NOE-mediated CEST-contrast was acquired at 7 Tesla (asymmetric magnetization transfer ratio (MTRasym) at 3.3ppm, B1 = 0.7 μT). Contrast enhanced T1 (CE-T1), T2 and diffusion-weighted MRI (DWI) were acquired at 3 Tesla and coregistered. The T2 edema and the CE-T1 tumor were segmented. ADC and MTRasym values within both regions of interest were correlated voxelwise yielding the correlation coefficient rSpearman (rSp). In three patients who underwent stereotactic biopsy, cell density of 12 specimens per patient was correlated with corresponding MTRasym and ADC values of the biopsy site. Eight of 15 patients showed a weak or moderate positive correlation of MTRasym and ADC within the T2 edema (0.16≤rSp≤0.53, pcorrelations were statistically insignificant (p>0.05, n = 4) or yielded rSp≈0 (pcorrelation between MTRasym and ADC was found in CE-T1 tumor (-0.310.05, n = 6). The biopsy-analysis within CE-T1 tumor revealed a strong positive correlation between tumor cellularity and MTRasym values in two of the three patients (rSppatient3 = 0.69 and rSppatient15 = 0.87, pcorrelation of ADC and cellularity was heterogeneous (rSppatient3 = 0.545 (p = 0.067), rSppatient4 = -0.021 (p = 0.948), rSppatient15 = -0.755 (p = 0.005)). NOE-imaging is a new contrast promising insight into pathophysiologic processes in glioblastoma regarding cell density and protein content, setting itself apart from DWI. Future studies might be based on the assumption that NOE-mediated CEST visualizes

  8. Introduction to protein blotting.

    Science.gov (United States)

    Kurien, Biji T; Scofield, R Hal

    2009-01-01

    Protein blotting is a powerful and important procedure for the immunodetection of proteins following electrophoresis, particularly proteins that are of low abundance. Since the inception of the protocol for protein transfer from an electrophoresed gel to a membrane in 1979, protein blotting has evolved greatly. The scientific community is now confronted with a variety of ways and means to carry out this transfer.

  9. Genetic Ablation of Type III Adenylyl Cyclase Exerts Region-Specific Effects on Cilia Architecture in the Mouse Nose.

    Directory of Open Access Journals (Sweden)

    Rosemary C Challis

    Full Text Available We recently reported that olfactory sensory neurons in the dorsal zone of the mouse olfactory epithelium exhibit drastic location-dependent differences in cilia length. Furthermore, genetic ablation of type III adenylyl cyclase (ACIII, a key olfactory signaling protein and ubiquitous marker for primary cilia, disrupts the cilia length pattern and results in considerably shorter cilia, independent of odor-induced activity. Given the significant impact of ACIII on cilia length in the dorsal zone, we sought to further investigate the relationship between cilia length and ACIII level in various regions throughout the mouse olfactory epithelium. We employed whole-mount immunohistochemical staining to examine olfactory cilia morphology in phosphodiesterase (PDE 1C-/-;PDE4A-/- (simplified as PDEs-/- hereafter and ACIII-/- mice in which ACIII levels are reduced and ablated, respectively. As expected, PDEs-/- animals exhibit dramatically shorter cilia in the dorsal zone (i.e., where the cilia pattern is found, similar to our previous observation in ACIII-/- mice. Remarkably, in a region not included in our previous study, ACIII-/- animals (but not PDEs-/- mice have dramatically elongated, comet-shaped cilia, as opposed to characteristic star-shaped olfactory cilia. Here, we reveal that genetic ablation of ACIII has drastic, location-dependent effects on cilia architecture in the mouse nose. These results add a new dimension to our current understanding of olfactory cilia structure and regional organization of the olfactory epithelium. Together, these findings have significant implications for both cilia and sensory biology.

  10. Imaging mass spectrometry in papillary thyroid carcinoma for the identification and validation of biomarker proteins.

    Science.gov (United States)

    Min, Kyueng-Whan; Bang, Joo-Young; Kim, Kwang Pyo; Kim, Wan-Seop; Lee, Sang Hwa; Shanta, Selina Rahman; Lee, Jeong Hwa; Hong, Ji Hye; Lim, So Dug; Yoo, Young-Bum; Na, Chan-Hyun

    2014-07-01

    Direct tissue imaging mass spectrometry (IMS) by matrix-assisted laser desorption ionization and time-of-flight (MALDI-TOF) mass spectrometry has become increasingly important in biology and medicine, because this technology can detect the relative abundance and spatial distribution of interesting proteins in tissues. Five thyroid cancer samples, along with normal tissue, were sliced and transferred onto conductive glass slides. After laser scanning by MALDI-TOF equipped with a smart beam laser, images were created for individual masses and proteins were classified at 200-µm spatial resolution. Based on the spatial distribution, region-specific proteins on a tumor lesion could be identified by protein extraction from tumor tissue and analysis using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Using all the spectral data at each spot, various intensities of a specific peak were detected in the tumor and normal regions of the thyroid. Differences in the molecular weights of expressed proteins between tumor and normal regions were analyzed using unsupervised and supervised clustering. To verify the presence of discovered proteins through IMS, we identified ribosomal protein P2, which is specific for cancer. We have demonstrated the feasibility of IMS as a useful tool for the analysis of tissue sections, and identified the tumor-specific protein ribosomal protein P2.

  11. 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.

  12. Nitrogen abundance in Comet Halley

    International Nuclear Information System (INIS)

    Wyckoff, S.; Tegler, S.C.; Engel, L.

    1991-01-01

    Data on the nitrogen-containing compounds that observed spectroscopically in the coma of Comet Halley are summarized, and the elemental abundance of nitrogen in the Comet Halley nucleus is derived. It is found that 90 percent of elemental nitrogen is in the dust fraction of the coma, while in the gas fraction, most of the nitrogen is contained in NH3 and CN. The elemental nitrogen abundance in the ice component of the nucleus was found to be deficient by a factor of about 75, relative to the solar photosphere, indicating that the chemical partitioning of N2 into NH3 and other nitrogen compounds during the evolution of the solar nebula cannot account completely for the low abundance ratio N2/NH3 = 0.1, observed in the comet. It is suggested that the low N2/NH3 ratio in Comet Halley may be explained simply by physical fractionation and/or thermal diffusion. 88 refs

  13. Abundances in field dwarf stars. II. Carbon and nitrogen abundances

    Energy Technology Data Exchange (ETDEWEB)

    Laird, J.B.

    1985-02-15

    Intermediate-dispersion spectra of 116 field dwarf stars, plus 10 faint field giants and 3 Hyades dwarfs, have been used to derive carbon and nitrogen abundances relative to iron. The program sample includes both disk and halo stars, spanning a range in (Fe/H) of +0.50 to -2.45. Synthetic spectra of CH and NH bands have been used to determine carbon and nitrogen abundances. The C/Fe ratio is solar over the range of metallicity studied, with an estimated intrinsic scatter of 0.10 dex. Down to (Fe/H)roughly-equal-1.8, below which the nitrogen abundance could not be measured, the N/Fe ratio is also constant for the majority of stars, indicating that nitrogen production is largely primary. Four halo stars are found to be enhanced in nitrogen relative to iron, by factors between 5 and 50, although their carbon abundances appear to be normal. These results are discussed in connection with the chemical evolution of the Galaxy and the sites of C, N, and Fe nucleosynthesis. The results require that C, N, and Fe be produced in stars of similar mass. Our current understanding of N production, then, implies that most Type I supernovae have intermediate-mass progenitors. The nitrogen in the N-enhanced halo stars is very probably primordial, indicating that the interstellar medium at early epochs contained substantial inhomogeneities.

  14. Abundances in field dwarf stars. II. Carbon and nitrogen abundances

    International Nuclear Information System (INIS)

    Laird, J.B.

    1985-01-01

    Intermediate-dispersion spectra of 116 field dwarf stars, plus 10 faint field giants and 3 Hyades dwarfs, have been used to derive carbon and nitrogen abundances relative to iron. The program sample includes both disk and halo stars, spanning a range in [Fe/H] of +0.50 to -2.45. Synthetic spectra of CH and NH bands have been used to determine carbon and nitrogen abundances. The C/Fe ratio is solar over the range of metallicity studied, with an estimated intrinsic scatter of 0.10 dex. Down to [Fe/H]roughly-equal-1.8, below which the nitrogen abundance could not be measured, the N/Fe ratio is also constant for the majority of stars, indicating that nitrogen production is largely primary. Four halo stars are found to be enhanced in nitrogen relative to iron, by factors between 5 and 50, although their carbon abundances appear to be normal. These results are discussed in connection with the chemical evolution of the Galaxy and the sites of C, N, and Fe nucleosynthesis. The results require that C, N, and Fe be produced in stars of similar mass. Our current understanding of N production, then, implies that most Type I supernovae have intermediate-mass progenitors. The nitrogen in the N-enhanced halo stars is very probably primordial, indicating that the interstellar medium at early epochs contained substantial inhomogeneities

  15. Brain region-specific expression of MeCP2 isoforms correlates with DNA methylation within Mecp2 regulatory elements.

    Directory of Open Access Journals (Sweden)

    Carl O Olson

    Full Text Available MeCP2 is a critical epigenetic regulator in brain and its abnormal expression or compromised function leads to a spectrum of neurological disorders including Rett Syndrome and autism. Altered expression of the two MeCP2 isoforms, MeCP2E1 and MeCP2E2 has been implicated in neurological complications. However, expression, regulation and functions of the two isoforms are largely uncharacterized. Previously, we showed the role of MeCP2E1 in neuronal maturation and reported MeCP2E1 as the major protein isoform in the adult mouse brain, embryonic neurons and astrocytes. Recently, we showed that DNA methylation at the regulatory elements (REs within the Mecp2 promoter and intron 1 impact the expression of Mecp2 isoforms in differentiating neural stem cells. This current study is aimed for a comparative analysis of temporal, regional and cell type-specific expression of MeCP2 isoforms in the developing and adult mouse brain. MeCP2E2 displayed a later expression onset than MeCP2E1 during mouse brain development. In the adult female and male brain hippocampus, both MeCP2 isoforms were detected in neurons, astrocytes and oligodendrocytes. Furthermore, MeCP2E1 expression was relatively uniform in different brain regions (olfactory bulb, striatum, cortex, hippocampus, thalamus, brainstem and cerebellum, whereas MeCP2E2 showed differential enrichment in these brain regions. Both MeCP2 isoforms showed relatively similar distribution in these brain regions, except for cerebellum. Lastly, a preferential correlation was observed between DNA methylation at specific CpG dinucleotides within the REs and Mecp2 isoform-specific expression in these brain regions. Taken together, we show that MeCP2 isoforms display differential expression patterns during brain development and in adult mouse brain regions. DNA methylation patterns at the Mecp2 REs may impact this differential expression of Mecp2/MeCP2 isoforms in brain regions. Our results significantly contribute

  16. CHLORINE ABUNDANCES IN COOL STARS

    Energy Technology Data Exchange (ETDEWEB)

    Maas, Z. G.; Pilachowski, C. A. [Indiana University Bloomington, Astronomy Department, Swain West 319, 727 East Third Street, Bloomington, IN 47405-7105 (United States); Hinkle, K., E-mail: zmaas@indiana.edu, E-mail: cpilacho@indiana.edu, E-mail: hinkle@noao.edu [National Optical Astronomy Observatory, P.O. Box 26732, Tucson, AZ 85726 (United States)

    2016-12-01

    Chlorine abundances are reported in 15 evolved giants and 1 M dwarf in the solar neighborhood. The Cl abundance was measured using the vibration-rotation 1-0 P8 line of H{sup 35}Cl at 3.69851 μ m. The high-resolution L -band spectra were observed using the Phoenix infrared spectrometer on the Kitt Peak Mayall 4 m telescope. The average [{sup 35}Cl/Fe] abundance in stars with −0.72 < [Fe/H] < 0.20 is [{sup 35}Cl/Fe] = (−0.10 ± 0.15) dex. The mean difference between the [{sup 35}Cl/Fe] ratios measured in our stars and chemical evolution model values is (0.16 ± 0.15) dex. The [{sup 35}Cl/Ca] ratio has an offset of ∼0.35 dex above model predictions, suggesting that chemical evolution models are underproducing 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 H ii regions. In one star where both H{sup 35}Cl and H{sup 37}Cl could be measured, a {sup 35}Cl/{sup 37}Cl isotope ratio of 2.2 ± 0.4 was found, consistent with values found in the Galactic ISM and predicted chemical evolution models.

  17. Chinook Abundance - Point Features [ds180

    Data.gov (United States)

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

  18. Steelhead Abundance - Linear Features [ds185

    Data.gov (United States)

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

  19. Steelhead Abundance - Point Features [ds184

    Data.gov (United States)

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

  20. Coho Abundance - Linear Features [ds183

    Data.gov (United States)

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

  1. Coho Abundance - Point Features [ds182

    Data.gov (United States)

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

  2. Abundance estimation and conservation biology

    Science.gov (United States)

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

    2004-01-01

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

  3. 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

  4. A role for tight junction-associated MARVEL proteins in larval sea lamprey (Petromyzon marinus) osmoregulation.

    Science.gov (United States)

    Kolosov, Dennis; Bui, Phuong; Donini, Andrew; Wilkie, Mike P; Kelly, Scott P

    2017-10-15

    This study reports on tight junction-associated MARVEL proteins of larval sea lamprey ( Petromyzon marinus ) and their potential role in ammocoete osmoregulation. Two occludin isoforms (designated Ocln and Ocln-a) and a tricellulin (Tric) were identified. Transcripts encoding ocln , ocln-a and tric were broadly expressed in larval lamprey, with the greatest abundance of ocln in the gut, liver and kidney, ocln-a in the gill and skin, and tric in the kidney. Ocln and Ocln-a resolved as ∼63 kDa and ∼35 kDa MW proteins, respectively, while Tric resolved as a ∼50 kDa protein. Ocln immunolocalized to the gill vasculature and in gill mucous cells while Ocln-a localized to the gill pouch and gill epithelium. Both Ocln and Ocln-a localized in the nephron, the epidermis and the luminal side of the gut. In branchial tissue, Tric exhibited punctate localization, consistent with its presence at regions of tricellular contact. Following ion-poor water (IPW) acclimation of ammocoetes, serum [Na + ] and [Cl - ] decreased, but not [Ca 2+ ], and carcass moisture content increased. In association, Ocln abundance increased in the skin and kidney, but reduced in the gill of IPW-acclimated ammocoetes while Ocln-a abundance reduced in the kidney only. Tric abundance increased in the gill. Region-specific alterations in ocln , ocln-a and tric mRNA abundance were also observed in the gut. Data support a role for Ocln, Ocln-a and Tric in the osmoregulatory strategies of a basal vertebrate. © 2017. Published by The Company of Biologists Ltd.

  5. Region-specific connectivity in patients with periventricular nodular heterotopia and epilepsy: A study combining diffusion tensor imaging and functional MRI.

    Science.gov (United States)

    Liu, Wenyu; An, Dongmei; Tong, Xin; Niu, Running; Gong, Qiyong; Zhou, Dong

    2017-10-01

    Periventricular nodular heterotopia (PNH) is an important cause of chronic epilepsy. The purpose of this study was to evaluate region-specific connectivity in PNH patients with epilepsy and assess correlation between connectivity strength and clinical factors including duration and prognosis. Diffusion tensor imaging (DTI) and resting state functional MRI (fMRI) were performed in 28 subjects (mean age 27.4years; range 9-56years). The structural connectivity of fiber bundles passing through the manually-selected segmented nodules and other brain regions were analyzed by tractography. Cortical lobes showing functional correlations to nodules were also determined. For all heterotopic gray matter nodules, including at least one in each subject, the most frequent segments to which nodular heterotopia showed structural (132/151) and functional (146/151) connectivity were discrete regions of the ipsilateral overlying cortex. Agreement between diffusion tensor tractography and functional connectivity analyses was conserved in 81% of all nodules (122/151). In patients with longer duration or refractory epilepsy, the connectivity was significantly stronger, particularly to the frontal and temporal lobes (P<0.05). Nodules in PNH were structurally and functionally connected to the cortex. The extent is stronger in patients with longstanding or intractable epilepsy. These findings suggest the region-specific interactions may help better evaluate prognosis and seek medical or surgical interventions of PNH-related epilepsy. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein-Friesian breeding program from 1986 to 2015.

    Science.gov (United States)

    Doekes, Harmen P; Veerkamp, Roel F; Bijma, Piter; Hiemstra, Sipke J; Windig, Jack J

    2018-04-11

    In recent decades, Holstein-Friesian (HF) selection schemes have undergone profound changes, including the introduction of optimal contribution selection (OCS; around 2000), a major shift in breeding goal composition (around 2000) and the implementation of genomic selection (GS; around 2010). These changes are expected to have influenced genetic diversity trends. Our aim was to evaluate genome-wide and region-specific diversity in HF artificial insemination (AI) bulls in the Dutch-Flemish breeding program from 1986 to 2015. Pedigree and genotype data (~ 75.5 k) of 6280 AI-bulls were used to estimate rates of genome-wide inbreeding and kinship and corresponding effective population sizes. Region-specific inbreeding trends were evaluated using regions of homozygosity (ROH). Changes in observed allele frequencies were compared to those expected under pure drift to identify putative regions under selection. We also investigated the direction of changes in allele frequency over time. Effective population size estimates for the 1986-2015 period ranged from 69 to 102. Two major breakpoints were observed in genome-wide inbreeding and kinship trends. Around 2000, inbreeding and kinship levels temporarily dropped. From 2010 onwards, they steeply increased, with pedigree-based, ROH-based and marker-based inbreeding rates as high as 1.8, 2.1 and 2.8% per generation, respectively. Accumulation of inbreeding varied substantially across the genome. A considerable fraction of markers showed changes in allele frequency that were greater than expected under pure drift. Putative selected regions harboured many quantitative trait loci (QTL) associated to a wide range of traits. In consecutive 5-year periods, allele frequencies changed more often in the same direction than in opposite directions, except when comparing the 1996-2000 and 2001-2005 periods. Genome-wide and region-specific diversity trends reflect major changes in the Dutch-Flemish HF breeding program. Introduction of

  7. Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX.

    Science.gov (United States)

    Van den Abbeele, Pieter; Grootaert, Charlotte; Marzorati, Massimo; Possemiers, Sam; Verstraete, Willy; Gérard, Philippe; Rabot, Sylvie; Bruneau, Aurélia; El Aidy, Sahar; Derrien, Muriel; Zoetendal, Erwin; Kleerebezem, Michiel; Smidt, Hauke; Van de Wiele, Tom

    2010-08-01

    Dynamic, multicompartment in vitro gastrointestinal simulators are often used to monitor gut microbial dynamics and activity. These reactors need to harbor a microbial community that is stable upon inoculation, colon region specific, and relevant to in vivo conditions. Together with the reproducibility of the colonization process, these criteria are often overlooked when the modulatory properties from different treatments are compared. We therefore investigated the microbial colonization process in two identical simulators of the human intestinal microbial ecosystem (SHIME), simultaneously inoculated with the same human fecal microbiota with a high-resolution phylogenetic microarray: the human intestinal tract chip (HITChip). Following inoculation of the in vitro colon compartments, microbial community composition reached steady state after 2 weeks, whereas 3 weeks were required to reach functional stability. This dynamic colonization process was reproducible in both SHIME units and resulted in highly diverse microbial communities which were colon region specific, with the proximal regions harboring saccharolytic microbes (e.g., Bacteroides spp. and Eubacterium spp.) and the distal regions harboring mucin-degrading microbes (e.g., Akkermansia spp.). Importantly, the shift from an in vivo to an in vitro environment resulted in an increased Bacteroidetes/Firmicutes ratio, whereas Clostridium cluster IX (propionate producers) was enriched compared to clusters IV and XIVa (butyrate producers). This was supported by proportionally higher in vitro propionate concentrations. In conclusion, high-resolution analysis of in vitro-cultured gut microbiota offers new insight on the microbial colonization process and indicates the importance of digestive parameters that may be crucial in the development of new in vitro models.

  8. Collaborative Research and Support of Fitzsimmons Army Medical Center DWH Research Program Projects. The Effects of Region-Specific Resistance Exercises on Bone Mass in Premenopausal Military Women, Protocol 8

    National Research Council Canada - National Science Library

    Hayes, Robert

    1995-01-01

    .... The purpose of this study is to determine if peak bone mass can be improved after age 20, the age at which peak bone mass is usually reached, and to compare the effects of region-specific resistance...

  9. 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.

  10. Vertebral heights and ratios are not only race-specific, but also gender- and region-specific: establishment of reference values for mainland Chinese.

    Science.gov (United States)

    Ning, Lei; Song, Li-Jiang; Fan, Shun-Wu; Zhao, Xing; Chen, Yi-Lei; Li, Zhao-Zhi; Hu, Zi-Ang

    2017-10-11

    This study established gender-specific reference values in mainland Chinese (MC) and is important for quantitative morphometry for diagnosis and epidemiological study of osteoporotic vertebral compressive fracture. Comparisons of reference values among different racial populations are then performed to demonstrate the MC-specific characteristic. Osteoporotic vertebral compressive fracture (OVCF) is a common complication of osteoporosis in the elder population. Clinical diagnosis and epidemiological study of OVCF often employ quantitative morphometry, which relies heavily on the comparison of patients' vertebral parameters to existing reference values derived from the normal population. Thus, reference values are crucial in clinical diagnosis. To our knowledge, this is the first study to establish reference values of the mainland Chinese (MC) for quantitative morphometry. Vertebral heights including anterior (Ha), middle (Hm), posterior (Hp) heights, and predicted posterior height (pp) from T4 to L5 were obtained; and ratios of Ha/Hp, Hm/Hp and Hp/pp. were calculated from 585 MC (both female and male) for establishing reference values and subsequent comparisons with other studies. Vertebral heights increased progressively from T4 to L3 but then decreased in L4 and L5. Both genders showed similar ratios of vertebral dimensions, but male vertebrae were statistically larger than those of female (P values for MC. Our results also indicated the necessity of establishing reference values that are not only race- and gender-specific, but also population- or region-specific for accurate quantitative morphometric assessment of OVCF.

  11. Regional specific binding of [11C]RO 15 1788 to central type benzodiazepine receptors in human brain: quantitative evaluation by PET

    International Nuclear Information System (INIS)

    Pappata, S.; Samson, Y.; Chavoix, C.; Prenant, C.; Maziere, M.; Baron, J.C.

    1988-01-01

    The central type benzodiazepine receptors were studied in 17 healthy human subjects with 11 C-RO 15 1788 and positron emission tomography (PET). The brain regional distribution of the tracer in eight control studies performed after injection of trace doses of 11 C-RO 15 1788 was consistent with that of benzodiazepine receptors. Saturation studies with co-injected cold RO 15 1788 in the remaining subjects showed a dose-dependent decrease of brain radiotracer until full inhibition of specific binding was achieved with doses above 0.1 mg/kg (four studies). Based on the results, a simple method to estimate the specifically bound 11 C-RO 15 1788 regionally in a single PET study is proposed, using the data from the full-saturation studies as a stable estimate of the nondisplaceable radioligand concentration. Using this method, it was found that quasiequilibrium between the estimated specifically bound and nondisplaceable components was achieved at times equal to or longer than 20 min after tracer administration. The validity of this method was partly supported by further results, showing a good agreement between the regional specific binding so calculated and postmortem data of receptor density

  12. 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 impact on the growth

  13. Hydrocarbon Reserves: Abundance or Scarcity

    International Nuclear Information System (INIS)

    2005-01-01

    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 impact on the growth

  14. 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

  15. The ascorbate peroxidase APX1 is a direct target of a zinc finger transcription factor ZFP36 and a late embryogenesis abundant protein OsLEA5 interacts with ZFP36 to co-regulate OsAPX1 in seed germination in rice.

    Science.gov (United States)

    Huang, Liping; Jia, Jing; Zhao, Xixi; Zhang, MengYao; Huang, Xingxiu; E Ji; Ni, Lan; Jiang, Mingyi

    2018-01-01

    Seed germination is a vital developmental process. Abscisic acid (ABA) is an essential repressor of seed germination, while ROS (reactive oxygen species) also plays a vital role in regulating seed germination. ABA could inhibit the production of ROS in seed germination, but the mechanism of ABA reduced ROS production in seed germination was hitherto unknown. Here, by ChIP (chromatin immunoprecipitation)-seq, we found that ZFP36, a rice zinc finger transcription factor, could directly bind to the promoter of OsAPX1, coding an ascorbate peroxidase (APX) which has the most affinity for H 2 O 2 (substrate; a type of ROS), and act as a transcriptional activator of OsAPX1 promoter. Moreover, ZFP36 could interact with a late embryogenesis abundant protein OsLEA5 to co-regulate the promoter activity of OsAPX1. The seed germination is highly inhibited in ZFP36 overexpression plants under ABA treatment, while an RNA interference (RNAi) mutant of OsLEA5 rice seeds were less sensitive to ABA, and exogenous ASC (ascorbate acid) could alleviate the inhibition induced by ABA. Thus, our conclusion is that OsAPX1 is a direct target of ZFP36 and OsLEA5 could interact with ZFP36 to co-regulate ABA-inhibited seed germination by controlling the expression of OsAPX1. Copyright © 2017. Published by Elsevier Inc.

  16. Region-specific expression and hormonal regulation of the first exon variants of rat prolactin receptor mRNA in rat brain and anterior pituitary gland.

    Science.gov (United States)

    Nogami, H; Hoshino, R; Ogasawara, K; Miyamoto, S; Hisano, S

    2007-08-01

    Recent studies have revealed the occurrence of five first exon variants of the rat prolactin receptor mRNA, suggesting that multiple promoters direct prolactin receptor transcription in response to different regulatory factors. In the present study, regional expression of these first exon variants, as well as two prolactin receptor subtypes generated by alternative splicing, was examined in the brains and anterior pituitary glands of female rats. Expression of the long-form was detected in the choroid plexus, hypothalamus, hippocampus, cerebral cortex and anterior pituitary gland, whereas the short form was detected only in the choroid plexus. E1-3 mRNA, a first exon variant, was detected in the choroid plexus, hypothalamus, and anterior pituitary gland, whereas E1-4 was detected only in the choroid plexus. Other variants were not detectable by the polymerase chain reaction protocol employed in this study. Ovariectomy increased the short form in the choroid plexus and the E1-3 expression in the choroid plexus and pituitary gland, but changes in the long-form and E1-4 expression were minimal. Replacement of oestrogens and prolactin suggest that oestrogens down-regulate E1-3 expression in the choroid plexus and pituitary gland, and that the negative effect of oestrogen is mediated by prolactin in the pituitary gland. The present results revealed the region-specific promoter usage in prolactin receptor mRNA transcription, as well as the involvement of oestrogens in the regulation of E1-3 mRNA expression in the brain and pituitary gland.

  17. Rapid generation of sub-type, region-specific neurons and neural networks from human pluripotent stem cell-derived neurospheres

    Directory of Open Access Journals (Sweden)

    Aynun N. Begum

    2015-11-01

    Full Text Available Stem cell-based neuronal differentiation has provided a unique opportunity for disease modeling and regenerative medicine. Neurospheres are the most commonly used neuroprogenitors for neuronal differentiation, but they often clump in culture, which has always represented a challenge for neurodifferentiation. In this study, we report a novel method and defined culture conditions for generating sub-type or region-specific neurons from human embryonic and induced pluripotent stem cells derived neurosphere without any genetic manipulation. Round and bright-edged neurospheres were generated in a supplemented knockout serum replacement medium (SKSRM with 10% CO2, which doubled the expression of the NESTIN, PAX6 and FOXG1 genes compared with those cultured with 5% CO2. Furthermore, an additional step (AdSTEP was introduced to fragment the neurospheres and facilitate the formation of a neuroepithelial-type monolayer that we termed the “neurosphederm”. The large neural tube-type rosette (NTTR structure formed from the neurosphederm, and the NTTR expressed higher levels of the PAX6, SOX2 and NESTIN genes compared with the neuroectoderm-derived neuroprogenitors. Different layers of cortical, pyramidal, GABAergic, glutamatergic, cholinergic neurons appeared within 27 days using the neurosphederm, which is a shorter period than in traditional neurodifferentiation-protocols (42–60 days. With additional supplements and timeline dopaminergic and Purkinje neurons were also generated in culture too. Furthermore, our in vivo results indicated that the fragmented neurospheres facilitated significantly better neurogenesis in severe combined immunodeficiency (SCID mouse brains compared with the non-fragmented neurospheres. Therefore, this neurosphere-based neurodifferentiation protocol is a valuable tool for studies of neurodifferentiation, neuronal transplantation and high throughput screening assays.

  18. Confocal Microscopy and Image Analysis Indicates a Region-Specific Relation between Active Caspases and Cytoplasm in Ejaculated and Epididymal Sperm

    Science.gov (United States)

    García Vazquez, Susana; Aragón Martínez, Andrés; Flores-Alonso, Juan Carlos

    2012-01-01

    Previously, it was suggested a relation between the presence of apoptosis markers with cytoplasm in mammalian sperm. In this work, flow cytometry, confocal microscopy and image analysis were used to analyze the relationship between active caspase-3 and -7 and intracellular esterases expression in ejaculated or epididymal ram sperm. Sperm obtained from ejaculates from the caput, corpus, or cauda of the epididymis were treated with an inhibitor of active caspase-3 and -7 and a marker of cytoplasmic esterases. Additionally, ejaculated sperm were incubated for one, two, or three hours before evaluation for active caspases. Sperm subpopulations positive for active caspases and/or intracellular esterases were detected by flow cytometry and confocal microscopy; however, image analysis of confocal images showed that the correlation between active caspases and cytoplasmic esterases in sperm is region-specific. Lower values of Spearman correlation coefficients were found when whole sperm or head sperm was analyzed; however, a high correlation was observed for midpiece sperm. Incubation of sperm for two or three hours promoted the autoactivation of caspases. It has been suggested that the presence of apoptotic markers in sperm are related with a process of abortive apoptosis and with errors during spermiogenesis. Our results permit us suggest that the origin of the relationship between active caspases and cytoplasmic esterases is due to differentiation errors occurring during spermiogenesis because the percentages of sperm with active caspases are not different in the caput, corpus, or cauda of the epididymis. In this study we demonstrate that existing sperm subpopulations can express active caspases and intracellular esterases and that the correlation between these molecules is high in midpiece sperm. PMID:22530029

  19. 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.

  20. Abundance Tomography of Type Ia Supernovae

    International Nuclear Information System (INIS)

    Stehle, M.; Mazzali, P.A.; Hillebrandt, W.

    2005-01-01

    An analysis of early time spectra of Type Ia Supernovae is presented. A new method to derive a detailed abundance distribution of the SN ejecta through comparison with synthetic spectra, called 'Abundance Tomography' is introduced and applied to the normal SN Ia 2002bo. Conclusions regarding the explosion mechanism are drawn

  1. Diversity, composition and abundance of macroinvertebrates ...

    African Journals Online (AJOL)

    user

    these genera were found at all sampling stations as shown in Table 2. Out of the orders sampled, Hemiptera, Pulmonata and. Coleoptera had the highest number of genera with 5, 4 and 4, respectively. In terms of relative abundance, dipterans and Pulmonata were the most abundant while. Hydracarina (water mites) were ...

  2. Resource Abundance and Resource Dependence in China

    NARCIS (Netherlands)

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

    2010-01-01

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

  3. Determinants of distribution, abundance and reproductive success ...

    African Journals Online (AJOL)

    ... while local vegetation structure determines the abundance of locally established populations. The abundance of trees affects nest site availability and breeding success, based on observations at two oases. Blackbird nests were usually situated on pomegranate trees and olive trees. The Common Blackbird is a successful ...

  4. Diversity and abundance of ammonia-oxidizing

    NARCIS (Netherlands)

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

    2013-01-01

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

  5. Amino acid metabolism conflicts with protein diversity

    OpenAIRE

    Krick, Teresa; Shub, David A.; Verstraete, Nina; Ferreiro, Diego U.; Alonso, Leonardo G.; Shub, Michael; Sanchez, Ignacio E.

    2014-01-01

    The 20 protein-coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins. On the other hand, a diverse set of protein sequences is necessary to build functional proteomes. Here, we present a simple model for a cost-diversity trade-off postulating that n...

  6. Stellar pulsation and the abundance of helium

    International Nuclear Information System (INIS)

    Schmidt, E.G.

    1978-01-01

    It has been suggested that the appearance of nonvariable stars within the Cepheid strip could be explained by a range in the helium abundance of Population I stars. In order to study this possibility, spectra were obtained of the main-sequence B stars in the galactic cluster NGC 129, which contains a nonvariable Cepheid-strip star, and M25, which contains a relatively hot Cepheid. Unfortunately, several of the stars in these clusters turn out to be helium-weak stars. In NGC 129 two stars which appear normal give a normal abundance, while in M25 all of the observed stars have abnormally low abundances. The significance of the low abundance in M25 is not clear. The abundance in NGC 129 is not low enough to support the above suggestion. 4 figures, 2 tables

  7. Influence of Coronal Abundance Variations

    Science.gov (United States)

    Scargle, Jeffrey D. (Technical Monitor); Kashyap, Vinay

    2005-01-01

    The PI of this project was Jeff Scargle of NASA/Ames. Co-I's were Alma Connors of Eureka Scientific/Wellesley, and myself. Part of the work was subcontracted to Eureka Scientific via SAO, with Vinay Kashyap as PI. This project was originally assigned grant number NCC2-1206, and was later changed to NCC2-1350 for administrative reasons. The goal of the project was to obtain, derive, and develop statistical and data analysis tools that would be of use in the analyses of high-resolution, high-sensitivity data that are becoming available with new instruments. This is envisioned as a cross-disciplinary effort with a number of "collaborators" including some at SA0 (Aneta Siemiginowska, Peter Freeman) and at the Harvard Statistics department (David van Dyk, Rostislav Protassov, Xiao-li Meng, Epaminondas Sourlas, et al). We have developed a new tool to reliably measure the metallicities of thermal plasma. It is unfeasible to obtain high-resolution grating spectra for most stars, and one must make the best possible determination based on lower-resolution, CCD-type spectra. It has been noticed that most analyses of such spectra have resulted in measured metallicities that were significantly lower than when compared with analyses of high- resolution grating data where available (see, e.g., Brickhouse et al., 2000, ApJ 530,387). Such results have led to the proposal of the existence of so-called Metal Abundance Deficient, or "MAD" stars (e.g., Drake, J.J., 1996, Cool Stars 9, ASP Conf.Ser. 109, 203). We however find that much of these analyses may be systematically underestimating the metallicities, and using a newly developed method to correctly treat the low-counts regime at the high-energy tail of the stellar spectra (van Dyk et al. 2001, ApJ 548,224), have found that the metallicities of these stars are generally comparable to their photospheric values. The results were reported at the AAS (Sourlas, Yu, van Dyk, Kashyap, and Drake, 2000, BAAS 196, v32, #54.02), and at the

  8. Biomarkers of Exposure to Toxic Substances. Volume 2: Genomics: Unique Patterns of Differential Gene Expression and Pathway Perturbation Resulting from Exposure to Nephrotoxins with Regional Specific Toxicity

    Science.gov (United States)

    2009-05-01

    producing cells in TGF-beta 1-induced renal interstitial fibrosis,” Histochemistry and Cell Biology., 119, 4, Apr 2003 pp. 267-80. Chen X, Abair TD ...protein l53 (predicted) 1367559_at ferritin light chain 1 1367589_at aconitase 2, mitochondrial 1367591_at peroxiredoxin 3 1367609_at macrophage

  9. Interstellar Abundances Toward X Per, Revisited

    Science.gov (United States)

    Valencic, Lynne A.; Smith, Randall K.

    2014-01-01

    The nearby X-ray binary X Per (HD 24534) provides a useful beacon with which to measure elemental abundances in the local ISM. We examine absorption features of 0, Mg, and Si along this line of sight using spectra from the Chandra Observatory's LETG/ ACIS-S and XMM-Newton's RGS instruments. In general, we find that the abundances and their ratios are similar to those of young F and G stars and the most recent solar values. We compare our results with abundances required by dust grain models.

  10. Abundance variations in solar active regions

    Science.gov (United States)

    Strong, K. T.; Lemen, J. R.; Linford, G. A.

    1991-01-01

    The diversity in the published values of coronal abundances is unsettling, especially as the range of results seems to be beyond the quoted uncertainties. Measurements of the relative abundance of iron and neon derived from soft X-ray spectra of active regions are presented. From a data base of over 200 spectra taken by the Solar Maximum Mission Flat Crystal Spectrometer, it is found that the relative abundance can vary by as much as a factor of about 7 and can change on timescales of less than 1 h.

  11. Abundance and distribution of the highly iterated palindrome 1 (HIP1) among prokaryotes

    OpenAIRE

    Delaye, Luis; Moya, Andrés

    2011-01-01

    We have studied the abundance and phylogenetic distribution of the Highly Iterated Palindrome 1 (HIP1) among sequenced prokaryotic genomes. We show that an overrepresentation of HIP1 is exclusive of some lineages of cyanobacteria, and that this abundance was gained only once during evolution and was subsequently lost in the lineage leading to marine pico-cyanobacteria. We show that among cyanobacterial protein sequences with annotated Pfam domains, only OpcA (glucose 6-phosphate dehydrogenase...

  12. Abundance analyses of thirty cool carbon stars

    International Nuclear Information System (INIS)

    Utsumi, Kazuhiko

    1985-01-01

    The results were previously obtained by use of the absolute gf-values and the cosmic abundance as a standard. These gf-values were found to contain large systematic errors, and as a result, the solar photospheric abundances were revised. Our previous results, therefore, must be revised by using new gf-values, and abundance analyses are extended for as many carbon stars as possible. In conclusion, in normal cool carbon stars heavy metals are overabundant by factors of 10 - 100 and rare-earth elements are overabundant by a factor of about 10, and in J-type cool carbon stars, C 12 /C 13 ratio is smaller, C 2 and CN bands and Li 6708 are stronger than in normal cool carbon stars, and the abundances of s-process elements with respect to Fe are nearly normal. (Mori, K.)

  13. Palaeoceanographic implications of abundance and mean ...

    Indian Academy of Sciences (India)

    Temporal variation in abundance and mean proloculus diameter of the benthic foraminiferal species. Epistominella ... sediments, ice cores, tree rings, corals, etc. are used. ..... Deep-sea foraminifera in the South Atlantic Ocean: Eco- logy and ...

  14. Chinook Abundance - Linear Features [ds181

    Data.gov (United States)

    California Natural Resource Agency — 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...

  15. 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...

  16. Abundance estimation of spectrally similar minerals

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2009-07-01

    Full Text Available This paper evaluates a spectral unmixing method for estimating the partial abundance of spectrally similar minerals in complex mixtures. The method requires formulation of a linear function of individual spectra of individual minerals. The first...

  17. Heavy element abundances of Nova Cygni 1975

    International Nuclear Information System (INIS)

    Ferland, G.J.; Shields, G.A.

    1978-01-01

    McDonald observations of the nebular phase of the outburst of Nova Cygni 1975 are analyzed to measure the abundances of several heavy elements. A new analytical procedure is used to derive the electron density and temperature from the emission line intensities of [O III], [Ne III], and He I observed between days 40 and 120. These physical conditions are used to derive the abundances. We find that Fe has approximately a solar abundance, whereas C, N, O, and Ne are enhanced by factors approx.20 to 100. The enhanced abundance of neon was theoretically unexpected.The derived physical conditions and line intensities are compared with predictions of an equilibrium photoionization model. The model successfully predicts the intensities of He I, [O III], and [Ne III]; but it underestimates the strength of [Ne V] and [Fe VII], which may originate in a mechanically heated ''subcoronal'' line region

  18. Good abundances from bad spectra - I. Techniques

    Science.gov (United States)

    Jones, J. Bryn; Gilmore, Gerard; Wyse, Rosemary F. G.

    1996-01-01

    Stellar spectra derived from multiple-object fibre-fed spectroscopic radial-velocity surveys, of the type feasible with, among other examples, AUTOFIB, 2dF, HYDRA, NESSIE, and the Sloan survey, differ significantly from those traditionally used for determination of stellar abundances. The spectra tend to be of moderate resolution (around 1A) and signal-to-noise ratio (around 10-20 per resolution element), and cannot usually have reliable continuum shapes determined over wavelength ranges in excess of a few tens of Angstroms. None the less, with care and a calibration of stellar effective temperature from photometry, independent of the spectroscopy, reliable iron abundances can be derived. We have developed techniques to extract true iron abundances and surface gravities from low-signal-to-noise ratio, intermediate-resolution spectra of G-type stars in the 4000-5000A wavelength region. Spectroscopic indices sensitive to iron abundance and gravity are defined from a set of narrow (few-several A wide) wavelength intervals. The indices are calibrated theoretically using synthetic spectra. Given adequate data and a photometrically determined effective temperature, one can derive estimates of the stellar iron abundance and surface gravity. We have also defined a single abundance indicator for the analysis of very low-signal-to-noise ratio spectra; with the further assumption of a value for the stellar surface gravity, this is able to provide useful iron abundance information from spectra having signal-to-noise ratios as low as 10 (1-A elements). 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 a separate paper (Jones, Wyse & Gilmore). The technique provides precise iron abundances, with zero-point correct to ~0.1 dex, and is reliable, with typical uncertainties being <~0.2 dex. A derivation of the in situ thick disc metallicity

  19. Chemical Abundances in SFG and DLA

    OpenAIRE

    Schulte-Ladbeck, Regina E.; König, Brigitte; Cherinka, Brian

    2005-01-01

    We investigate the chemical abundances of local star-forming galaxies which cause Damped Lyman Alpha lines. A metallicity versus redshift diagram is constructed, on which the chemical abundances of low-redshift star-forming galaxy populations are compared with those of high-redshift Damped Lyman Alpha systems. We disucss two types of experiments on individual star-forming galaxies. In the first, the Damped Lyman Alpha line is created against an internal ultraviolet light source generated by a...

  20. Composition and abundance of tree regeneration

    Science.gov (United States)

    Todd F. Hutchinson; Elaine Kennedy Sutherland; Charles T. Scott

    2003-01-01

    The composition and abundance of tree seedlings and saplings in the four study areas in southern Ohio were related to soil moisture via a GIS-derived integrated moisture index and to soil texture and fertility. For seedlings, the total abundance of small stems (less than 30 cm tall) was significantly greater on xeric plots (81,987/ha) than on intermediate (54,531/ha)...

  1. Abundance of lithium in Pleiades F stars

    International Nuclear Information System (INIS)

    Pilachowski, C.A.; Booth, J.; Hobbs, L.M.

    1987-01-01

    The abundance of lithium has been determined for 18 stars in the Pleiades cluster with spectral types from A7V to G0V. The pronounced dip in the lithium abundance among the mid-F stars which has been reported for other, older star clusters is not present in the Pleiades. The removal of lithium from the surfaces of middle-F dwarfs therefore occurs principally after about 100 Myr on the main sequence. 25 references

  2. TEA: A CODE CALCULATING THERMOCHEMICAL EQUILIBRIUM ABUNDANCES

    Energy Technology Data Exchange (ETDEWEB)

    Blecic, Jasmina; Harrington, Joseph; Bowman, M. Oliver, E-mail: jasmina@physics.ucf.edu [Planetary Sciences Group, Department of Physics, University of Central Florida, Orlando, FL 32816-2385 (United States)

    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 and Sharp, the free thermochemical equilibrium code Chemical Equilibrium with Applications (CEA), and the example given by Burrows and 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.

  3. TEA: A CODE CALCULATING THERMOCHEMICAL EQUILIBRIUM ABUNDANCES

    International Nuclear Information System (INIS)

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

    2016-01-01

    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. 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 and Sharp, the free thermochemical equilibrium code Chemical Equilibrium with Applications (CEA), and the example given by Burrows and 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.

  4. Clustering in the stellar abundance space

    Science.gov (United States)

    Boesso, R.; Rocha-Pinto, H. J.

    2018-03-01

    We have studied the chemical enrichment history of the interstellar medium through an analysis of the n-dimensional stellar abundance space. This work is a non-parametric analysis of the stellar chemical abundance space. The main goal is to study the stars from their organization within this abundance space. Within this space, we seek to find clusters (in a statistical sense), that is, stars likely to share similar chemo-evolutionary history, using two methods: the hierarchical clustering and the principal component analysis. We analysed some selected abundance surveys available in the literature. For each sample, we labelled the group of stars according to its average abundance curve. In all samples, we identify the existence of a main enrichment pattern of the stars, which we call chemical enrichment flow. This flow is set by the structured and well-defined mean rate at which the abundances of the interstellar medium increase, resulting from the mixture of the material ejected from the stars and stellar mass-loss and interstellar medium gas. One of the main results of our analysis is the identification of subgroups of stars with peculiar chemistry. These stars are situated in regions outside of the enrichment flow in the abundance space. These peculiar stars show a mismatch in the enrichment rate of a few elements, such as Mg, Si, Sc and V, when compared to the mean enrichment rate of the other elements of the same stars. We believe that the existence of these groups of stars with peculiar chemistry may be related to the accretion of planetary material on to stellar surfaces or may be due to production of the same chemical element by different nucleosynthetic sites.

  5. Cytoplasm-predominant Pten associates with increased region-specific brain tyrosine hydroxylase and dopamine D2 receptors in mouse model with autistic traits.

    Science.gov (United States)

    He, Xin; Thacker, Stetson; Romigh, Todd; Yu, Qi; Frazier, Thomas W; Eng, Charis

    2015-01-01

    Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders characterized by impairment in social communication/interaction and inflexible/repetitive behavior. Several lines of evidence support genetic factors as a predominant cause of ASD. Among those autism susceptibility genes that have been identified, the PTEN tumor suppressor gene, initially identified as predisposing to Cowden heritable cancer syndrome, was found to be mutated in a subset of ASD patients with extreme macrocephaly. However, the ASD-relevant molecular mechanism mediating the effect of PTEN mutations remains elusive. We developed a Pten knock-in murine model to study the effects of Pten germline mutations, specifically altering subcellular localization, in ASD. Proteins were isolated from the hemispheres of the male littermates, and Western blots were performed to determine protein expression levels of tyrosine hydroxylase (TH). Immunohistochemical stains were carried out to validate the localization of TH and dopamine D2 receptors (D2R). PC12 cells ectopically expressing either wild-type or missense mutant PTEN were then compared for the differences in TH expression. Mice carrying Pten mutations have high TH and D2R in the striatum and prefrontal cortex. They also have increased phosphorylation of cAMP response element-binding protein (CREB) and TH. Mechanistically, PTEN downregulates TH production in PC12 cells via inhibiting the phosphoinositide 3-kinase (PI3K)/CREB signaling pathway, while PTEN reduces TH phosphorylation via suppressing MAPK pathway. Unlike wild-type PTEN but similar to the mouse knock-in mutant Pten, three naturally occurring missense mutations of PTEN that we previously identified in ASD patients, H93R, F241S, and D252G, were not able to suppress TH when overexpressed in PC12 cells. In addition, two other PTEN missense mutations, C124S (pan phosphatase dead) and G129E (lipid phosphatase dead), failed to suppress TH when ectopically expressed in PC12 cells

  6. Bracken: estimating species abundance in metagenomics data

    Directory of Open Access Journals (Sweden)

    Jennifer Lu

    2017-01-01

    Full Text Available Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.

  7. Abundance of sea kraits correlates with precipitation.

    Directory of Open Access Journals (Sweden)

    Harvey B Lillywhite

    Full Text Available Recent studies have shown that sea kraits (Laticauda spp.--amphibious sea snakes--dehydrate without a source of fresh water, drink only fresh water or very dilute brackish water, and have a spatial distribution of abundance that correlates with freshwater sites in Taiwan. The spatial distribution correlates with sites where there is a source of fresh water in addition to local precipitation. Here we report six years of longitudinal data on the abundance of sea kraits related to precipitation at sites where these snakes are normally abundant in the coastal waters of Lanyu (Orchid Island, Taiwan. The number of observed sea kraits varies from year-to-year and correlates positively with previous 6-mo cumulative rainfall, which serves as an inverse index of drought. Grouped data for snake counts indicate that mean abundance in wet years is nearly 3-fold greater than in dry years, and this difference is significant. These data corroborate previous findings and suggest that freshwater dependence influences the abundance or activity of sea kraits on both spatial and temporal scales. The increasing evidence for freshwater dependence in these and other marine species have important implications for the possible impact of climate change on sea snake distributions.

  8. Seismological measurement of solar helium abundance

    International Nuclear Information System (INIS)

    Vorontsov, S.V.; Pamyatnykh, A.A.

    1991-01-01

    The internal structure and evolution of the Sun depends on its chemical composition, particularly the helium abundance. In addition, the helium abundance in the solar envelope is thought to represent the protosolar value, making it a datum of cosmological significance. Spectroscopic measurements of the helium abundance are uncertain, and the most reliable estimates until now have come from the calibration of solar evolutionary models. The frequencies of solar acoustic oscillations are sensitive, however, to the behaviour of the speed of sound in the Sun's helium ionization zone, which allows a helioseismological determination of the helium abundance. Sound-speed inversion of helioseismological data can be used for this purpose, but precise frequency measurements of high-degree oscillation modes are needed. Here we describe a new approach based on an analysis of the phase shift of acoustic waves of intermediate-degree modes. From the accurate intermediate-mode data now available, we obtain a helium mass fraction Y=0.25±0.01 in the solar convection zone, significantly smaller than the value Y=0.27-0.29 predicted by recent solar evolutionary models. The discrepancy indicates either that initial helium abundance was reduced in the envelope by downward diffusion or that the protosolar value was lower than currently accepted. (author)

  9. Deuterium abundance, from ultraviolet to visible

    International Nuclear Information System (INIS)

    Hebrard, Guillaume

    2000-01-01

    In the frame of the standard Big Bang model, the primordial abundance of deuterium is the most sensitive to the baryonic density of the Universe. It was synthesized only during the primordial nucleosynthesis few minutes after the Big Bang and no other standard mechanism is able to produce any further significant amount. On the contrary, since deuterium is burned up within stars, its abundance D/H decreases along cosmic evolution. Thus, D/H measurements constrain Big Bang and galactic chemical evolution models. There are three samples of deuterium abundances: primordial, proto-solar and interstellar. Each of them is representative of a given epoch, respectively about 15 Gyrs past, 4.5 Gyrs past and present epoch. Although the evolution of the deuterium abundance seems to be qualitatively understood, the measurements show some dispersion. Present thesis works are linked to deuterium interstellar abundance measurements. Such measurements are classically obtained from spectroscopic observations of the hydrogen and deuterium Lyman series in absorption in the ultraviolet spectral range, using space observatories. Results presented here were obtained with the Hubble Space Telescope and FUSE, which has recently been launched. Simultaneously, a new way to observe deuterium has been proposed, in the visible spectral range from ground-based telescopes. This has led to the first detections and the identification of the deuterium Balmer series, in emission in HII regions, using CFHT and VLT telescopes. (author) [fr

  10. Subdwarf ultraviolet excesses and metal abundances

    International Nuclear Information System (INIS)

    Carney, B.W.

    1979-01-01

    The relation between stellar ultraviolet excesses and abundances is reexamined with the aid of new data, and an investigation is made of the accuracy of previous abundance analyses. A high-resolution echellogram of the subdwarf HD 201891 is analyzed to illustrate some of the problems. Generally, the earliest and latest analytical techniques yield consistent results for dwarfs. New UBV data yield normalized ultraviolet excesses, delta (U-B)/sub 0.6/, which are compared to abundances to produce a graphical relation that may be used to estimate [Fe/H] to +- 0.2 dex, given UBV colors accurate to +- 0.01 mag. The relation suggests a possible discontinuity between the halo and old-disk stars

  11. INTERSTELLAR ABUNDANCES TOWARD X Per, REVISITED

    International Nuclear Information System (INIS)

    Valencic, Lynne A.; Smith, Randall K.

    2013-01-01

    The nearby X-ray binary X Per (HD 24534) provides a useful beacon with which to examine dust grain types and measure elemental abundances in the local interstellar medium (ISM). The absorption features of O, Fe, Mg, and Si along this line of sight were measured using spectra from the Chandra X-Ray Observatory's LETG/ACIS-S and XMM-Newton's RGS instruments, and the Spex software package. The spectra were fit with dust analogs measured in the laboratory. The O, Mg, and Si abundances were compared to those from standard references, and the O abundance was compared to that along lines of sight toward other X-ray binaries. The results are as follows. First, it was found that a combination of MgSiO 3 (enstatite) and Mg 1.6 Fe 0.4 SiO 4 (olivine) provided the best fit to the O K edge, with N(MgSiO 3 )/N(Mg 1.6 Fe 0.4 SiO 4 ) = 3.4. Second, the Fe L edge could be fit with models that included metallic iron, but it was not well described by the laboratory spectra currently available. Third, the total abundances of O, Mg, and Si were in very good agreement with that of recently re-analyzed B stars, suggesting that they are good indicators of abundances in the local ISM, and the depletions were also in agreement with expected values for the diffuse ISM. Finally, the O abundances found from X-ray binary absorption spectra show a similar correlation with Galactocentric distances as seen in other objects.

  12. Barium and iron abundances in red giants

    International Nuclear Information System (INIS)

    Fernandez-Villacanas, J.L.; Rego, M.; Cornide, M.

    1990-01-01

    An intermediate-dispersion abundance analysis has been carried out on a sample of 21 barium and 14 comparison stars. The excess of barium over iron has been used as the most representative indicator of peculiarity. These excesses are higher in the peculiar stars than in the nonpeculiar stars. Particularly interesting is the case of HD 67447, included in the comparison stars, with an excess Ba/Fe abundance = 1.61, probably a new barium star. A trend indicating a possible anticorrelation between barium overabundance and metallicity favors the suggestion that the barium strong group is older than the barium weak one. 36 refs

  13. Bacterial community profiles in low microbial abundance sponges

    KAUST Repository

    Giles, Emily; Kamke, Janine; Moitinho-Silva, Lucas; Taylor, Michael W.; Hentschel, Ute T E; Ravasi, Timothy; Schmitt, Susanne

    2012-01-01

    It has long been recognized that sponges differ in the abundance of associated microorganisms, and they are therefore termed either 'low microbial abundance' (LMA) or 'high microbial abundance' (HMA) sponges. Many previous studies concentrated

  14. Abundances in planetary nebulae near the galactic centre .1. Abundance determinations

    NARCIS (Netherlands)

    Ratag, MA; Pottasch, [No Value; Dennefeld, M; Menzies, J

    1997-01-01

    Abundance determinations of about 110 planetary nebulae, which are likely to be in the Galactic Bulge are presented. Plasma diagnostics have been performed by making use of the available forbidden line ratios combined with radio continuum measurements. Chemical abundances of He, O, N, Ne, S, Ar, and

  15. Correlation between some environmental variables and abundance ...

    African Journals Online (AJOL)

    Correlation between some environmental variables and abundance of Almophrya mediovacuolata (Ciliophora: Anoplophryidae) endocommensal ciliate of an ... The survey primarily involved soil samples collection from the same spots of EW collection and preparation for physico-chemical analysis; evaluation in situ of the ...

  16. Abundances and morphology in planetary nebulae

    NARCIS (Netherlands)

    Pottasch, [No Value; Kastner, JH; Soker, N; Rappaport, SA

    2000-01-01

    The abundances of 16 well studied have been determined. New ISO measurements have been combined with optical and ultraviolet data from the literature, in an attempt to obtain accurate values. Only He, O, C, N, Ne, Ar, and S are considered. High values of N/O are sometimes, but not always, found in

  17. Securing abundance : The politics of energy security

    NARCIS (Netherlands)

    Kester, Johannes

    2016-01-01

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

  18. Photoelectric absorption cross sections with variable abundances

    Science.gov (United States)

    Balucinska-Church, Monika; Mccammon, Dan

    1992-01-01

    Polynomial fit coefficients have been obtained for the energy dependences of the photoelectric absorption cross sections of 17 astrophysically important elements. These results allow the calculation of X-ray absorption in the energy range 0.03-10 keV in material with noncosmic abundances.

  19. Estimating the relationship between abundance and distribution

    DEFF Research Database (Denmark)

    Rindorf, Anna; Lewy, Peter

    2012-01-01

    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...

  20. Quasar Elemental Abundances at High Redshifts

    DEFF Research Database (Denmark)

    Dietrich, M.; Hamann, F.; Shields, J. C.

    2003-01-01

    the framework of the most recent photoionization models to estimate the metallicity of the gas associated with the high-z quasars. Standard photoionization parameters and the assumption of secondary nitrogen enrichment indicate an average abundance of Z/Z_sol = 4 to 5 in the line emitting gas. Assuming a time...

  1. Cosmological evolution of the nitrogen abundance

    Science.gov (United States)

    Vangioni, Elisabeth; Dvorkin, Irina; Olive, Keith A.; Dubois, Yohan; Molaro, Paolo; Petitjean, Patrick; Silk, Joe; Kimm, Taysun

    2018-06-01

    The abundance of nitrogen in the interstellar medium is a powerful probe of star formation processes over cosmological time-scales. Since nitrogen can be produced both in massive and intermediate-mass stars with metallicity-dependent yields, its evolution is challenging to model, as evidenced by the differences between theoretical predictions and observations. In this work, we attempt to identify the sources of these discrepancies using a cosmic evolution model. To further complicate matters, there is considerable dispersion in the abundances from observations of damped Lyα absorbers (DLAs) at z ˜ 2-3. We study the evolution of nitrogen with a detailed cosmic chemical evolution model and find good agreement with these observations, including the relative abundances of (N/O) and (N/Si). We find that the principal contribution of nitrogen comes from intermediate-mass stars, with the exception of systems with the lowest N/H, where nitrogen production might possibly be dominated by massive stars. This last result could be strengthened if stellar rotation which is important at low metallicity can produce significant amounts of nitrogen. Moreover, these systems likely reside in host galaxies with stellar masses below 108.5 M⊙. We also study the origin of the observed dispersion in nitrogen abundances using the cosmological hydrodynamical simulations Horizon-AGN. We conclude that this dispersion can originate from two effects: difference in the masses of the DLA host galaxies, and difference in their position inside the galaxy.

  2. Species identification, distribution and abundance of Gerreidae ...

    African Journals Online (AJOL)

    the distribution and abundance of Gerres in estuaries wa'S collected from July 1978 to ..... the channel area between the W.L.R. and the mouth (not the tidal basin) during ..... overwhelming importance in the kelp beds of Britain. Recently Blaber ...

  3. Abundances in planetary nebulae : Including ISO results

    NARCIS (Netherlands)

    Pottasch, [No Value; Beintema, DA; Sales, JB; Feibelman, WA; Kwok, S; Dopita, M; Sutherland, R

    2003-01-01

    The far infrared nebular spectrum provides a valuable complement to the observed lines in other spectral regions. There are several reasons for this, the most important being the large increase in the number of ions observed, and the fact that the abundances found from these lines are relatively

  4. Distribution And Seasonal Abundance Of Anopheline Mosquito ...

    African Journals Online (AJOL)

    The essence of this study was to identify Anopheles mosquito species in Nguru, Yobe State and to determine their distribution and relative abundance in the months of the year. Insecticide and aspirator were used to collect mosqutoes in human dwellngs and preserved in 2% formalin for identcation using dissectng ...

  5. Abundance Ratios in Dwarf Elliptical Galaxies

    NARCIS (Netherlands)

    Sen, Seyda; Peletier, Reynier F.; Toloba, Elisa; Mentz, Jaco J.

    The aim of this study is to determine abundance ratios and star formation histories (SFH) of dwarf ellipticals in the nearby Virgo cluster. We perform a stellar population analysis of 39 dEs and study them using index-index and scaling relations. We find an unusual behaviour where [Na/Fe] is

  6. Abundance, composition and distribution of simple sequence ...

    Indian Academy of Sciences (India)

    δ∗(W-29, W-70) = 1.25; δ∗(W-93, W-70 = 0.75)) even though they originate from different geographical regions. We can, therefore, infer that the WSSV sequences are closely related by ancestry. Table 3. Dinucleotide relative abundance in the ...

  7. 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.

  8. Abundance and guild structure of grasshoppers (Orthoptera ...

    African Journals Online (AJOL)

    1995-01-18

    Jan 18, 1995 ... April, 1994, we compared the abundance and guild structure .... was placed in a functional group on the basis of taxonomic ... hypothesis that they would be unaffected by changes in the ..... spatial separation from the heavily grazed area. the lightly ..... found to increase (Morris 1967, 1969, 1979; Morris &.

  9. Clonal growth and plant species abundance.

    Science.gov (United States)

    Herben, Tomáš; Nováková, Zuzana; Klimešová, Jitka

    2014-08-01

    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. 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. 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. 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 underlying clonal growth effects on abundance. Garden

  10. Abundances in very metal-poor stars

    Science.gov (United States)

    Johnson, Jennifer Anne

    We measured the abundances of 35 elements in 22 field red giants and a red giant in the globular cluster M92. We found the [Zn/Fe] ratio increases with decreasing [Fe/H], reaching ~0.3 at [Fe/H] = -3.0. While this is a larger [Zn/Fe] than found by previous investigators, it is not sufficient to account for the [Zn/Fe] observed in the damped Lyα systems. We test different models for the production of the s-process elements by comparing our [Y/Zr] values, which have been produced by the r- process, to predictions of what the s-process does not produce. We find that the models of Arlandini et al. (1999), which calculate s-process production in a model AGB star, agree the best. We then look at the r-process abundances across a wide range in mass. The [Y/Ba] values for most of our stars cluster around -0.30, but there are three outliers with [Y/Ba] values up to 1 dex higher. Thus the heavy element abundances do not show the same pattern from Z = 39 to Z = 56. However, our abundances ratios from Pd (Z = 46) to Yb (Z = 70) are consistent with a scaled solar system r- process pattern, arguing that at least the heavy r- process elements are made in a universal pattern. If we assume that this same pattern hold through thorium, we can determine the ages of our stars from the present abundance of radioactive thorium and an initial thorium abundance based on the abundance of stable heavy elements. Our results for five stars are consistent with those stars being the same age. Our mean age is 10.8 +/- 2 Gyr. However that result depends critically on the assumed Th/stable ratio, which we adopt from models of the r-process. For an average age of 15 Gyrs, the initial Th/Eu ratio we would need is 0.590. Finally, the [element/Fe] ratios for elements in the iron group and lower do not show any dispersion, unlike for the r- process elements such as Y and Ba. Therefore the individual contributions of supernovae have been erased for the lighter elements.

  11. Identification and Characterization of the Most Abundant Cellulases in Stylet Secretions from Globodera rostochiensis

    NARCIS (Netherlands)

    Rehman, S.; Butterbach, P.B.E.; Popeijus, H.E.; Overmars, H.A.; Davis, E.L.; Jones, J.T.; Goverse, A.; Bakker, J.; Smant, G.

    2009-01-01

    Plant-parasitic cyst nematodes secrete cell wall modifying proteins during their invasion of host plants. In this study, we used a monoclonal antibody to immunopurify and to sequence the N terminus of the most abundant cellulases in stylet secretions of preparasitic juveniles of Globodera

  12. A biogeographical perspective on species abundance distributions

    DEFF Research Database (Denmark)

    Matthews, Thomas J.; Borges, Paulo A. V.; de Azevedo, Eduardo Brito

    2017-01-01

    It has become increasingly recognized that multiple processes can generate similar shapes of species abundance distributions (SADs), with the result that the fit of a given SAD model cannot unambiguously provide evidence in support of a given theory or model. An alternative approach to comparing...... the fit of different SAD models to data from a single site is to collect abundance data from a variety of sites, and then build models to analyse how different SAD properties (e.g. form, skewness) vary with different predictor variables. Such a biogeographical approach to SAD research is potentially very...... revealing, yet there has been a general lack of interest in SADs in the biogeographical literature. In this Perspective, we address this issue by highlighting findings of recent analyses of SADs that we consider to be of intrinsic biogeographical interest. We use arthropod data drawn from the Azorean...

  13. Nitrous Oxide Production by Abundant Benthic Macrofauna

    DEFF Research Database (Denmark)

    Stief, Peter; Schramm, Andreas

    of the short-term metabolic induction of gut denitrification is the preferential production of nitrous oxide rather than dinitrogen. On a large scale, gut denitrification in, for instance, Chironomus plumosus larvae can increase the overall nitrous oxide emission of lake sediment by a factor of eight. We...... screened more than 20 macrofauna species for nitrous oxide production and identified filter-feeders and deposit-feeders that occur ubiquitously and at high abundance (e.g., chironomids, ephemeropterans, snails, and mussels) as the most important emitters of nitrous oxide. In contrast, predatory species...... 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...

  14. Abundances in the diffuse interstellar medium

    International Nuclear Information System (INIS)

    Harris, A.W.

    1988-04-01

    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)

  15. Chemical element abundance in K giant atmospheres

    International Nuclear Information System (INIS)

    Komarov, N.S.; Shcherbak, A.N.

    1980-01-01

    With the help of modified method of differential curves of growth studied are physical parameters of atmospheres of giant stars of KO111 spectral class of the NGC 752, M25 and UMa cluster. Observations have been made on reflector of Crimea astrophysical observatory of Academy of Sciences of the USSR in the period from February to May, 1978. Spectograms are obtained for the wave length range from 5000-5500 A. It is shown that the change of chemical content in the wide range in heavy element composition does not influence the star atmosphere structUre. It follows from the results of the investigation that the abundance of chemical elements in stars of various scattered clusters, is the same in the range of errors of measurements and is similar to the abundance of chemical elements in the Sun atmosphere

  16. Attenuation of species abundance distributions by sampling

    Science.gov (United States)

    Shimadzu, Hideyasu; Darnell, Ross

    2015-01-01

    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. Integral Field Spectroscopy Surveys: Oxygen Abundance Gradients

    Science.gov (United States)

    Sánchez, S. F.; Sánchez-Menguiano, L.

    2017-07-01

    We present here the recent results on our understanding of oxygen abundance gradients derived using Integral Field Spectroscopic surveys. In particular we analyzed more than 2124 datacubes corresponding to individual objects observed by the CALIFA (˜ 734 objects) and the public data by MaNGA (˜ 1390 objects), deriving the oxygen abundance gradient for each galaxy. We confirm previous results that indicate that the shape of this gradient is very similar for all galaxies with masses above 109.5M⊙, presenting in average a very similar slope of ˜ -0.04 dex within 0.5-2.0 re, with a possible drop in the inner regions (r109.5M⊙) the gradient seems to be flatter than for more massive ones. All these results agree with an inside-out growth of massive galaxies and indicate that low mass ones may still be growing in an outside in phase.

  18. Photometric metal abundances for twenty clusters

    International Nuclear Information System (INIS)

    Jennens, P.A.; Helfer, H.L.

    1975-01-01

    Metal abundances, colour excesses and distance moduli have been determined for individual giant stars, using UBViyz photometry, in NGC 188, 559, 752, 1245, 1342, 1907, 1912, 2099, 5139 (ω cen), 5316, 5617, 5822, 5823, 6067, IC 4651, 6819, 6940, 7142, 7261 and 7789. All six clusters with ages 3 to 8x10 9 yr have metal abundances agreeing with one another; their average value of [Fe/H]=-0.24+-0.05, agrees with the average found for the bright K-giants near the Sun. All six clusters are at least 140pc from the galactic plane. For the younger clusters less than approximately 10 9 yr old, one-third are metal deficient. The very young cluster, NGC 559, is probably very metal weak. (author)

  19. Investigation of plutonium abundance and age analysis

    Energy Technology Data Exchange (ETDEWEB)

    Huailong, Wu; Jian, Gong; Fanhua, Hao [China Academy of Engineering Physics, Mianyang (China). Inst. of Nuclear Physics and Chemistry

    2007-06-15

    Based on spectra analysis software, all of the plutonium material peak counts are analyzed. Relatively efficiency calibration is done by the non-coupling peaks of {sup 239}Pu. By using the known isotopes half life and yield, the coupling peaks counts are allocated by non-coupling peaks, consequently the atom ratios of each isotope are gotten. The formula between atom ratio and abundance or age is deduced by plutonium material isotopes decay characteristic. And so the abundance and age of plutonium material is gotten. After some re- peat measurements for a plutonium equipment are completed, a comparison between our analysis results and PC-FRAM and the owner's reference results are done. (authors)

  20. Big-Bang nucleosynthesis and lithium abundance

    International Nuclear Information System (INIS)

    Singh, Vinay; Lahiri, Joydev; Bhowmick, Debasis; Basu, D.N.

    2017-01-01

    The predictions of the standard big-bang nucleosynthesis (BBN) theory depend on the astrophysical nuclear reaction rates and on additional three parameters, the number of flavours of light neutrinos, the neutron lifetime and the baryon-to-photon ratio in the uni- verse. The effect of the modification of thirty-five reaction rates on light element abundance yields in BBN was investigated earlier by us. In the present work we have replaced the neutron lifetime, baryon-to-photon ratio by the most recent values and further modified 3 He( 4 He,γ) 7 Be reaction rate which is used directly for estimating the formation of 7 Li as a result of β + decay by the most recent equation. We find that these modifications reduce the calculated abundance of 7 Li by ∼ 12%

  1. A global database of ant species abundances

    Czech Academy of Sciences Publication Activity Database

    Gibb, H.; Dunn, R. R.; Sanders, N. J.; Grossman, B. F.; Photakis, M.; Abril, S.; Agosti, D.; Andersen, A. N.; Angulo, E.; Armbrecht, I.; Arnan, X.; Baccaro, F. B.; Bishop, T. R.; Boulay, R.; Brühl, C.; Castracani, C.; Cerdá, X.; Del Toro, I.; Delsinne, T.; Diaz, M.; Donoso, D. A.; Ellison, A. M.; Enríquez, M. L.; Fayle, Tom Maurice; Feener, D. H.; Fisher, B. L.; Fisher, R. N.; Fitzpatrick, M. C.; Gómez, C.; Gotelli, N. J.; Gove, A.; Grasso, D. A.; Groc, S.; Guenard, B.; Gunawardene, N.; Heterick, B.; Hoffmann, B.; Janda, Milan; Jenkins, C.; Kaspari, M.; Klimeš, Petr; Lach, L.; Laeger, T.; Lattke, J.; Leponce, M.; Lessard, J.-P.; Longino, J.; Lucky, A.; Luke, S. H.; Majer, J.; McGlynn, T. P.; Menke, S.; Mezger, D.; Mori, A.; Moses, Jimmy; Munyai, T. C.; Pacheco, R.; Paknia, O.; Pearce-Duvet, J.; Pfeiffer, M.; Philpott, S. M.; Resasco, J.; Retana, J.; Silva, R. R.; Sorger, M. D.; Souza, J.; Suarez, A.; Tista, M.; Vasconcelos, H. L.; Vonshak, M.; Weisser, M. D.; Yates, M.; Parr, C. L.

    2017-01-01

    Roč. 98, č. 3 (2017), s. 883-884 ISSN 0012-9658 R&D Projects: GA ČR GB14-36098G; GA ČR GAP505/12/2467; GA ČR GPP505/12/P875 Institutional support: RVO:60077344 Keywords : abundance * ants * database Subject RIV: EH - Ecology, Behaviour OBOR OECD: Ecology Impact factor: 4.809, year: 2016 http://onlinelibrary.wiley.com/doi/10.1002/ecy.1682/abstract

  2. Uranium abundance in some sudanese phosphate ores

    International Nuclear Information System (INIS)

    Adam, A.A.; Eltayeb, M.A.H.

    2009-01-01

    This work was carried out mainly to analysis of some Sudanese phosphate ores, for their uranium abundance and total phosphorus content measured as P 2 O 5 %. For this purpose, 30 samples of two types of phosphate ore from Eastern Nuba Mountains, in Sudan namely, Kurun and Uro areas were examined. In addition, the relationship between uranium and major, and trace elements were obtained, also, the natural radioactivity of the phosphate samples was measured, in order to characterize and differentiate between the two types of phosphate ores. The uranium abundance in Uro phosphate with 20.3% P 2 O 5 is five time higher than in Kurun phosphate with 26.7% P 2 O 5 . The average of uranium content was found to be 56.6 and 310 mg/kg for Kurun and Uro phosphate ore, respectively. The main elements in Kurun and Uro phosphate ore are silicon, aluminum, and phosphorus, while the most abundant trace elements in these two ores are titanium, strontium and barium. Pearson correlation coefficient revealed that uranium in Kurun phosphate shows strong positive correlation with P 2 O 5 , and its distribution is essentially controlled by the variations of P2O5 concentration, whereas uranium in Uro phosphate shows strong positive correlation with strontium, and its distribution is controlled by the variations of Sr concentration. Uranium behaves in different ways in Kurun phosphate and in Uro phosphate. Uro phosphate shows higher concentrations of all the estimated radionuclides than Kurun phosphate. According to the obtained results, it can be concluded that Uro phosphate is consider as secondary uranium source, and is more suitable for uranium recovery, because it has high uranium abundance and low P 2 O 5 %, than Kurun phosphate. (authors) [es

  3. Liquidity Hoarding and Inefficient Abundant Funding

    OpenAIRE

    Enisse Kharroubi

    2015-01-01

    This paper studies banks’ choice between building liquidity buffers and raising funding ex post to deal with reinvestment shocks. We uncover the possibility of an inefficient liquidity squeeze equilibrium when ex post funding is abundant. In the model, banks typically build larger liquidity buffers when they expect funding to be expensive. However, when banks hold larger liquidity buffers, pledgeable income is larger and they hence can raise more funding, which in the aggregate raises the fun...

  4. Abundance of boron in Vega and Sirius

    International Nuclear Information System (INIS)

    Praderie, F.; Boesgaard, A.M.; Milliard, B.; Pitois, M.L.

    1977-01-01

    High-resolution (0.05 A) observations of the region of the B II resonance line (1362 A) have been made of Vega (AO V) and Sirius (Al V) with the Copernicus satellite. A strong B II feature is present in Vega, but only a weak line, due primarily to V III, is present is Sirius. An upper limit of B/H -12 is derived for Sirius from line-profile fitting. A local thermodynamic equilibrium (LTE) synthesis of the B II blend in Vega results in an abundance ratio B/H=1 x 10 -10 . Calculations of the effects of non--LTE on the line profile show that the LTE abundance would not be increased by more than 50% (B.H=1.5 x 10 -10 ) to account for departures from LTE. The B content of Vega probably represents the cosmic B abundance. The B deficiency in Sirius could result from interaction with the white-dwarf companion at an earlier stage in its evolution or from diffusion processes in the Sirius atmosphere.Difficult observations at 0.10 A resolution of subordinate lines from multiplet (3) of B II at 1624 A show that those lines are not present in Sirius; but the identification of B in Vega appears to be confirmed by the presence of weak lines at 1624 A in this star

  5. 2015-2016 Palila abundance estimates

    Science.gov (United States)

    Camp, Richard J.; Brinck, Kevin W.; Banko, Paul C.

    2016-01-01

    The palila (Loxioides bailleui) population was surveyed annually during 1998−2016 on Mauna Kea Volcano to determine abundance, population trend, and spatial distribution. In the latest surveys, the 2015 population was estimated at 852−1,406 birds (point estimate: 1,116) and the 2016 population was estimated at 1,494−2,385 (point estimate: 1,934). Similar numbers of palila were detected during the first and subsequent counts within each year during 2012−2016; the proportion of the total annual detections in each count ranged from 46% to 56%; and there was no difference in the detection probability due to count sequence. Furthermore, conducting repeat counts improved the abundance estimates by reducing the width of the confidence intervals between 9% and 32% annually. This suggests that multiple counts do not affect bird or observer behavior and can be continued in the future to improve the precision of abundance estimates. Five palila were detected on supplemental survey stations in the Ka‘ohe restoration area, outside the core survey area but still within Palila Critical Habitat (one in 2015 and four in 2016), suggesting that palila are present in habitat that is recovering from cattle grazing on the southwest slope. The average rate of decline during 1998−2016 was 150 birds per year. Over the 18-year monitoring period, the estimated rate of change equated to a 58% decline in the population.

  6. Absolute isotopic abundances of Ti in meteorites

    International Nuclear Information System (INIS)

    Niederer, F.R.; Papanastassiou, D.A.; Wasserburg, G.J.

    1985-01-01

    The absolute isotope abundance of Ti has been determined in Ca-Al-rich inclusions from the Allende and Leoville meteorites and in samples of whole meteorites. The absolute Ti isotope abundances differ by a significant mass dependent isotope fractionation transformation from the previously reported abundances, which were normalized for fractionation using 46 Ti/ 48 Ti. Therefore, the absolute compositions define distinct nucleosynthetic components from those previously identified or reflect the existence of significant mass dependent isotope fractionation in nature. We provide a general formalism for determining the possible isotope compositions of the exotic Ti from the measured composition, for different values of isotope fractionation in nature and for different mixing ratios of the exotic and normal components. The absolute Ti and Ca isotopic compositions still support the correlation of 50 Ti and 48 Ca effects in the FUN inclusions and imply contributions from neutron-rich equilibrium or quasi-equilibrium nucleosynthesis. The present identification of endemic effects at 46 Ti, for the absolute composition, implies a shortfall of an explosive-oxygen component or reflects significant isotope fractionation. Additional nucleosynthetic components are required by 47 Ti and 49 Ti effects. Components are also defined in which 48 Ti is enhanced. Results are given and discussed. (author)

  7. The shape of terrestrial abundance distributions

    Science.gov (United States)

    Alroy, John

    2015-01-01

    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

  8. Elemental abundances of solar sibling candidates

    International Nuclear Information System (INIS)

    Ramírez, I.; Lambert, D. L.; Endl, M.; Cochran, W. D.; MacQueen, P. J.; Bajkova, A. T.; Bobylev, V. V.; Roederer, I. U.; 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, HD 162826, satisfies both chemical and dynamical conditions for being a sibling of the Sun. Measurements of rare-element abundances for this star further confirm its solar composition, with the only possible exception of Sm. Analysis of long-term high-precision radial velocity data rules out the presence of hot Jupiters and confirms that this star is not in a binary system. We find that chemical tagging does not necessarily benefit from studying as many elements as possible but instead from identifying and carefully measuring the abundances of those elements that show large star-to-star scatter at a given metallicity. Future searches employing data products from ongoing massive astrometric and spectroscopic surveys can be optimized by acknowledging this fact.

  9. THE CORONAL ABUNDANCE ANOMALIES OF M DWARFS

    Energy Technology Data Exchange (ETDEWEB)

    Wood, Brian E.; Laming, J. Martin [Naval Research Laboratory, Space Science Division, Washington, DC 20375 (United States); Karovska, Margarita, E-mail: brian.wood@nrl.navy.mil [Smithsonian Astrophysical Observatory, 60 Garden St., Cambridge, MA 02138 (United States)

    2012-07-01

    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 toward modeling the inverse FIP phenomenon in M dwarfs, building on past work that has demonstrated that MHD waves coursing through coronal loops can lead to a ponderomotive force that fractionates elements in a manner consistent with the FIP effect. We demonstrate that in certain circumstances this model can also lead to an inverse FIP effect, pointing the way to more detailed modeling of M dwarf coronal abundances in the future.

  10. The Coronal Abundance Anomalies of M Dwarfs

    Science.gov (United States)

    Wood, Brian E.; Laming, J. Martin; Karovska, Margarita

    2012-07-01

    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 toward modeling the inverse FIP phenomenon in M dwarfs, building on past work that has demonstrated that MHD waves coursing through coronal loops can lead to a ponderomotive force that fractionates elements in a manner consistent with the FIP effect. We demonstrate that in certain circumstances this model can also lead to an inverse FIP effect, pointing the way to more detailed modeling of M dwarf coronal abundances in the future.

  11. THE CORONAL ABUNDANCE ANOMALIES OF M DWARFS

    International Nuclear Information System (INIS)

    Wood, Brian E.; Laming, J. Martin; 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 toward modeling the inverse FIP phenomenon in M dwarfs, building on past work that has demonstrated that MHD waves coursing through coronal loops can lead to a ponderomotive force that fractionates elements in a manner consistent with the FIP effect. We demonstrate that in certain circumstances this model can also lead to an inverse FIP effect, pointing the way to more detailed modeling of M dwarf coronal abundances in the future.

  12. The primordial helium abundance from updated emissivities

    International Nuclear Information System (INIS)

    Aver, Erik; Olive, Keith A.; Skillman, Evan D.; Porter, R.L.

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

  13. A global database of ant species abundances

    Science.gov (United States)

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

    2017-01-01

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

  14. 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

  15. An 8/15-channel Tx/Rx head neck RF coil combination with region-specific B1 + shimming for whole-brain MRI focused on the cerebellum at 7T.

    Science.gov (United States)

    Pfaffenrot, Viktor; Brunheim, Sascha; Rietsch, Stefan H G; Koopmans, Peter J; Ernst, Thomas M; Kraff, Oliver; Orzada, Stephan; Quick, Harald H

    2018-02-09

    To design and evaluate an 8/15-channel transmit/receive (Tx/Rx) head-neck RF coil combination with region-specific B1+ shimming for whole-brain MRI with focus on improved functional MRI of the cerebellum at 7 T. An 8-channel transceiver RF head coil was combined with a 7-channel receive-only array. The noise parameters and acceleration capabilities of this 8Tx/15Rx coil setup were compared with a commercially available 1Tx/32Rx RF head coil. Region-specific 8-channel B1+ shimming was applied when using the 8Tx/15Rx RF coil. To evaluate the capability for functional MRI of the cerebellum, temporal SNR and statistical nonparametric maps for finger-tapping experiments with 14 healthy subjects were derived by applying a variable slice thickness gradient-echo echo-planar functional MRI sequence. The 8Tx/15Rx setup had a lower maximum noise correlation between channels, but higher average correlations compared with the 1Tx/32Rx coil. Both RF coils exhibited identical g-factors in the cerebellum with R = 3 acceleration. The enlarged FOV of the 8Tx/15Rx coil in combination with region-specific B1+ shimming increased homogeneity of the transmission field and temporal SNR in caudal cerebellar regions. Temporal SNR losses in cranial parts were reduced, resulting in more highly significant voxels in the caudally activated areas and identical patterns in the cranial cerebellar parts during a finger-tapping task. Compared with the 1Tx/32Rx RF coil, the presented 8Tx/15Rx RF coil combination successfully improves functional MRI of the human cerebellum at 7 T while maintaining whole-brain coverage. A clear temporal SNR gain in caudal cerebellar regions is shown. © 2018 International Society for Magnetic Resonance in Medicine.

  16. Bringing abundance into environmental politics: Constructing a Zionist network of water abundance, immigration, and colonization.

    Science.gov (United States)

    Alatout, Samer

    2009-06-01

    For more than five decades, resource scarcity has been the lead story in debates over environmental politics. More importantly, and whenever environmental politics implies conflict, resource scarcity is constructed as the culprit. Abundance of resources, if at all visited in the literature, holds less importance. Resource abundance is seen, at best, as the other side of scarcity--maybe the successful conclusion of multiple interventions that may turn scarcity into abundance. This paper reinstates abundance as a politico-environmental category in its own right. Rather than relegating abundance to a second-order environmental actor that matters only on occasion, this paper foregrounds it as a crucial element in modern environmental politics. On the substantive level, and using insights from science and technology studies, especially a slightly modified actor-network framework, I describe the emergence and consolidation of a Zionist network of abundance, immigration, and colonization in Palestine between 1918 and 1948. The essential argument here is that water abundance was constructed as fact, and became a political rallying point around which a techno-political network emerged that included a great number of elements. To name just a few, the following were enrolled in the service of such a network: geologists, geophysicists, Zionist settlement experts, Zionist organizations, political and technical categories of all sorts, Palestinians as the negated others, Palestinian revolts in search of political rights, the British Mandate authorities, the hydrological system of Palestine, and the absorptive capacity of Palestine, among others. The point was to successfully articulate these disparate elements into a network that seeks opening Palestine for Jewish immigration, redefining Palestinian geography and history through Judeo-Christian Biblical narratives, and, in the process, de-legitimizing political Palestinian presence in historic Palestine.

  17. 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

  18. Abundance ratios in dwarf elliptical galaxies

    Science.gov (United States)

    Şen, Ş.; Peletier, R. F.; Boselli, A.; den Brok, M.; Falcón-Barroso, J.; Hensler, G.; Janz, J.; Laurikainen, E.; Lisker, T.; Mentz, J. J.; Paudel, S.; Salo, H.; Sybilska, A.; Toloba, E.; van de Ven, G.; Vazdekis, A.; Yesilyaprak, C.

    2018-04-01

    We determine abundance ratios of 37 dwarf ellipticals (dEs) in the nearby Virgo cluster. This sample is representative of the early-type population of galaxies in the absolute magnitude range -19.0 originate from late-type dwarfs or small spirals. Na-yields appear to be very metal-dependent, in agreement with studies of giant ellipticals, probably due to the large dependence on the neutron-excess in stars. We conclude that dEs have undergone a considerable amount of chemical evolution, they are therefore not uniformly old, but have extended SFH, similar to many of the Local Group galaxies.

  19. New Normal in Russian Economy: Regional Specificity

    Directory of Open Access Journals (Sweden)

    Yakov Petrovich Silin

    2016-09-01

    Full Text Available The main objective of the article is to study the concepts of “New Normal”, “New Industrialization” and the questions of formation and development of the productions of the fifth and sixth technological modes in the regional economic area. Substantive expansion of “New Normal” concept was argued, it became popular during the global financial and economic crisis of 2008. The logic of transformation to a “New Normal” is true not only for the world economy, individual countries and regions, but also for the Sverdlovsk region. The scientific hypothesis of the article consists in the identifying the characteristics of “New Normal” at the regional level and showing the possible directions of transformation from a «New Normal” situation using the concept of new industrialization for the regional economy. The main features of “New Normal” in the region were identified and analyzed. There are, for example, the slow growth of industrial production, the reducing of the investment climate, the low dynamics of metal prices. It is proved that the realization of the concept of new industrialization in the region can become the most attractive answer to the challenges of «New Normal». The need for the integration of the processes of new industrialization with the formation and development of the productions of the fifth and sixth technological waves is proved. The article is focused on the possibility of the transformation of the Sverdlovsk region in the region of the technological breakthrough of the 21st century. It is demonstrated that during 15–20 years, the priority will be the development of the productions of the fifth and sixth technological waves that will be based on the high-tech production of military-industrial complex, nuclear energy as well as nanotechnology and nanomaterials. It is proved that at this time, the model of innovative development of the region may be realized. It is able to lead the regional economy out of the labyrinth of “New Normal” and to move it to a new growth path.

  20. The galaxy clustering crisis in abundance matching

    Science.gov (United States)

    Campbell, Duncan; van den Bosch, Frank C.; Padmanabhan, Nikhil; Mao, Yao-Yuan; Zentner, Andrew R.; Lange, Johannes U.; Jiang, Fangzhou; Villarreal, Antonio

    2018-06-01

    Galaxy clustering on small scales is significantly underpredicted by sub-halo abundance matching (SHAM) models that populate (sub-)haloes with galaxies based on peak halo mass, Mpeak. SHAM models based on the peak maximum circular velocity, Vpeak, have had much better success. The primary reason for Mpeak-based models fail is the relatively low abundance of satellite galaxies produced in these models compared to those based on Vpeak. Despite success in predicting clustering, a simple Vpeak-based SHAM model results in predictions for galaxy growth that are at odds with observations. We evaluate three possible remedies that could `save' mass-based SHAM: (1) SHAM models require a significant population of `orphan' galaxies as a result of artificial disruption/merging of sub-haloes in modern high-resolution dark matter simulations; (2) satellites must grow significantly after their accretion; and (3) stellar mass is significantly affected by halo assembly history. No solution is entirely satisfactory. However, regardless of the particulars, we show that popular SHAM models based on Mpeak cannot be complete physical models as presented. Either Vpeak truly is a better predictor of stellar mass at z ˜ 0 and it remains to be seen how the correlation between stellar mass and Vpeak comes about, or SHAM models are missing vital component(s) that significantly affect galaxy clustering.

  1. 3He Abundances in Planetary Nebulae

    Science.gov (United States)

    Guzman-Ramirez, Lizette

    2017-10-01

    Determination of the 3He isotope is important to many fields of astrophysics, including stellar evolution, chemical evolution, and cosmology. The isotope is produced in stars which evolve through the planetary nebula phase. Planetary nebulae are the final evolutionary phase of low- and intermediate-mass stars, where the extensive mass lost by the star on the asymptotic giant branch is ionised by the emerging white dwarf. This ejecta quickly disperses and merges with the surrounding ISM. 3He abundances in planetary nebulae have been derived from the hyperfine transition of the ionised 3He, 3He+, at the radio rest frequency 8.665 GHz. 3He abundances in PNe can help test models of the chemical evolution of the Galaxy. Many hours have been put into trying to detect this line, using telescopes like the Effelsberg 100m dish of the Max Planck Institute for Radio Astronomy, the National Radio Astronomy Observatory (NRAO) 140-foot telescope, the NRAO Very Large Array, the Arecibo antenna, the Green Bank Telescope, and only just recently, the Deep Space Station 63 antenna from the Madrid Deep Space Communications Complex.

  2. Parameters and abundances in luminous stars

    International Nuclear Information System (INIS)

    Earle Luck, R.

    2014-01-01

    Parameters and abundances for 451 stars of spectral types F, G, and K of luminosity classes I and II have been derived. Absolute magnitudes and E(B – V) have been derived for the warmer stars in order to investigate the galactic abundance gradient. The value found here: d[Fe/H]/dR ∼ –0.06 dex kpc –1 , agrees well with previous determinations. Stellar evolution indicators have also been investigated with the derived C/O ratios indicating that standard CN processing has been operating. Perhaps the most surprising result found in these supposedly relatively young intermediate-mass stars is that both [O/Fe] and [C/Fe] show a correlation with [Fe/H] much the same as found in older populations. While the stars were selected based on luminosity class, there does exist a significant [Fe/H] range in the sample. The likely explanation of this is that there is a significant range in age in the sample; that is, some of the sample are low-mass red-giant stars with types that place them within the selection criteria.

  3. Optical region elemental abundance analyses of B and A stars

    International Nuclear Information System (INIS)

    Adelman, S.J.

    1984-01-01

    Abundance analyses using optical region data and fully line blanketed model atmospheres have been performed for six moderately sharplined middle to late B-type stars. The derived abundances have values similar to those of the Sun. (author)

  4. Abundance determinations in HII regions and planetary nebulae

    OpenAIRE

    Stasinska, Grazyna

    2002-01-01

    The methods of abundance determinations in HII regions and planetary nebulae are described, with emphasis on the underlying assumptions and inherent problems. Recent results on abundances in Galactic HII regions and in Galactic and extragalactic Planetary Nebulae are reviewed.

  5. DAWN GRAND MAP VESTA HYDROGEN ABUNDANCE V1.0

    Data.gov (United States)

    National Aeronautics and Space Administration — A global map of the abundance of hydrogen in micrograms/g within the regolith of asteroid 4 Vesta is provided for two-degree equal-angle pixels. Hydrogen abundances...

  6. Relation between grade and abundance of manganese nodules

    Digital Repository Service at National Institute of Oceanography (India)

    Sudhakar, M.

    Data from more than 1000 locations in the Central Indian Ocean Basin (CIOB) where both bulk nodule chemistry and abundance were determined and utilized to study the relationship between grade and abundance of manganese nodule deposits. Grade...

  7. Relative Abundance of Adult Mosquitoes in University of Abuja Main ...

    African Journals Online (AJOL)

    Relative Abundance of Adult Mosquitoes in University of Abuja Main ... relative abundance of adult mosquitoes in four selected sites in University of Abuja ... These results indicated that vectors of mosquito-borne diseases are breeding in the ...

  8. Tungsten abundances in some volcanic rocks

    International Nuclear Information System (INIS)

    Helsen, J.N.; Shaw, D.M.; Crocket, J.H.

    1978-01-01

    A radiochemical N.A.A. method was used to obtain new values on W distribution in some 125 volcanic rocks, mainly basalts and andesites, from different petrotectonic environments. These W data are below previously reported abundances. New median values in various types of rocks are suggested (ppm W). Basalts: ocean floor, 0.15; ocean islands subalkaline, 0.28; ocean islands alkaline, 0.60; island arc, 0.19; continental margin, 0.40; continental subalkaline, 0.30; continental alkaline, 1.35. Andesites: island arc, 0.23; continental margin, 1.05. Median values for all 91 basalts and all 20 andesites are 0.36 and 0.29 ppm respectively. (author)

  9. 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.

  10. Elemental abundance analyses with coadded DAO spectrograms: Pt. 5

    International Nuclear Information System (INIS)

    Adelman, S.J.

    1988-01-01

    Elemental abundance analyses of three mercury-manganese stars were performed in a manner consistent with previous analyses of this series. A few correlations are found between the derived abundances and with the effective temperature in accordance with the expectations of radiative diffusion explanations of the derived abundances. The helium abundances are smaller than the value required to sustain the superficial helium convection zone in the atmospheres of these stars. (author)

  11. Cosmological implications of light element abundances: theory.

    Science.gov (United States)

    Schramm, D N

    1993-06-01

    Primordial nucleosynthesis provides (with the microwave background radiation) one of the two quantitative experimental tests of the hot Big Bang cosmological model (versus alternative explanations for the observed Hubble expansion). The standard homogeneous-isotropic calculation fits the light element abundances ranging from 1H at 76% and 4He at 24% by mass through 2H and 3He at parts in 105 down to 7Li at parts in 1010. It is also noted how the recent Large Electron Positron Collider (and Stanford Linear Collider) results on the number of neutrinos (Nnu) are a positive laboratory test of this standard Big Bang scenario. The possible alternate scenario of quark-hadron-induced inhomogeneities is also discussed. It is shown that when this alternative scenario is made to fit the observed abundances accurately, the resulting conclusions on the baryonic density relative to the critical density (Omegab) remain approximately the same as in the standard homogeneous case, thus adding to the robustness of the standard model and the conclusion that Omegab approximately 0.06. This latter point is the driving force behind the need for nonbaryonic dark matter (assuming total density Omegatotal = 1) and the need for dark baryonic matter, since the density of visible matter Omegavisible < Omegab. The recent Population II B and Be observations are also discussed and shown to be a consequence of cosmic ray spallation processes rather than primordial nucleosynthesis. The light elements and Nnu successfully probe the cosmological model at times as early as 1 sec and a temperature (T) of approximately 10(10) K (approximately 1 MeV). Thus, they provided the first quantitative arguments that led to the connections of cosmology to nuclear and particle physics.

  12. Use of abundance of one species as a surrogate for abundance of others

    Science.gov (United States)

    Samuel A. Cushman; Kevin S. McKelvey; Barry R. Noon; Kevin McGarigal

    2010-01-01

    Indicator species concepts have a long history in conservation biology. Arguments in favor of these approaches generally stress expediency and assume efficacy. We tested the premise that the abundance patterns of one species can be used to infer those of other species. Our data consisted of 72,495 bird observations on 55 species across 1046 plots distributed across 30...

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

    Science.gov (United States)

    J. Firn; J.L. Moore; A.S. MacDougall; E.T. Borer; E.W. Seabloom; J. HilleRisLambers; S. Harpole; E.E. Cleland; C.S. Brown; J.M.H. Knops; S.M. Prober; D.A. Pyke; K.A. Farrell; J.D. Bakker; L.R. O’Halloran; P.B. Adler; S.L. Collins; C.M. D’Antonio; M.J. Crawley; E.M. Wolkovich; K.J. La Pierre; B.A. Melbourne; Y. Hautier; J.W. Morgan; A.D.B. Leakey; A.D. Kay; R.L. McCulley; K.F. Davies; C.J. Stevens; C.J. Chu

    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...

  14. 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.

  15. Composition, Abundance and Distribution of Brachyuran Larvae in ...

    African Journals Online (AJOL)

    ... Ocypodidae, Grapsidae and Xanthidae. Abundance of brachyuran larvae was significantly positively correlated with total zooplankton abundance (r2 = 0.8) and salinity (r2 = 0.71). Keywords: Brachyuran larvae, abundance, composition, Mida creek, Kenya West Indian Ocean Journal of Marine Science Vol. 3 (2) 2004: pp.

  16. Protein oxidation and peroxidation

    DEFF Research Database (Denmark)

    Davies, Michael Jonathan

    2016-01-01

    Proteins are major targets for radicals and two-electron oxidants in biological systems due to their abundance and high rate constants for reaction. With highly reactive radicals damage occurs at multiple side-chain and backbone sites. Less reactive species show greater selectivity with regard...... to the residues targeted and their spatial location. Modification can result in increased side-chain hydrophilicity, side-chain and backbone fragmentation, aggregation via covalent cross-linking or hydrophobic interactions, protein unfolding and altered conformation, altered interactions with biological partners...... and modified turnover. In the presence of O2, high yields of peroxyl radicals and peroxides (protein peroxidation) are formed; the latter account for up to 70% of the initial oxidant flux. Protein peroxides can oxidize both proteins and other targets. One-electron reduction results in additional radicals...

  17. Aldosterone-mineralocorticoid receptor promotes urine prostasin through glomerular barrier injury and not tissue abundance

    DEFF Research Database (Denmark)

    Stolzenburg Oxlund, Christina; Kurt, B.; Schwarzensteiner, I.

    2015-01-01

    with placebo or the mineralocorticoid antagonist spironolactone. Western immunoblotting of creatinine-normalized urine samples was performed from placebo and spironolactone treated patients with and without albuminuria. Tissue prostasin was measured in membranes from human nephrectomy recieving either ACE......-i/ANGII or no antihypertensive treatment prior to operation. Urine and tissue prostasin was measured in puromycin-induced nephrotic syndrome rats. Results: Plasma prostasin concentration increased significantly with spironolactone but was not changed with placebo. Urine prostasin concentration was below detection limit....... Puromycin-induced nephrotic syndrome in rats was associated with significant increase in u-prostasin while kidney tissue prostasin protein abundance was not changed. Prostasin protein abundance was similar in membranes from human nephrectomy homogenate from patients treated preoperatively with ACE...

  18. Challenges of transferring models of fish abundance between coral reefs.

    Science.gov (United States)

    Sequeira, Ana M M; Mellin, Camille; Lozano-Montes, Hector M; Meeuwig, Jessica J; Vanderklift, Mathew A; Haywood, Michael D E; Babcock, Russell C; Caley, M Julian

    2018-01-01

    Reliable abundance estimates for species are fundamental in ecology, fisheries, and conservation. Consequently, predictive models able to provide reliable estimates for un- or poorly-surveyed locations would prove a valuable tool for management. Based on commonly used environmental and physical predictors, we developed predictive models of total fish abundance and of abundance by fish family for ten representative taxonomic families for the Great Barrier Reef (GBR) using multiple temporal scenarios. We then tested if models developed for the GBR (reference system) could predict fish abundances at Ningaloo Reef (NR; target system), i.e., if these GBR models could be successfully transferred to NR. Models of abundance by fish family resulted in improved performance (e.g., 44.1% fish abundance (9% fish species richness from the GBR to NR, transferability for these fish abundance models was poor. When compared with observations of fish abundance collected in NR, our transferability results had low validation scores ( R 2   0.05). High spatio-temporal variability of patterns in fish abundance at the family and population levels in both reef systems likely affected the transferability of these models. Inclusion of additional predictors with potential direct effects on abundance, such as local fishing effort or topographic complexity, may improve transferability of fish abundance models. However, observations of these local-scale predictors are often not available, and might thereby hinder studies on model transferability and its usefulness for conservation planning and management.

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

    Science.gov (United States)

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

    2014-06-01

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

  20. Beryllium abundances in Hg-Mn stars

    International Nuclear Information System (INIS)

    Boesgaard, A.M.; Heacox, W.D.; Wolff, S.C.; Borsenberger, J.; Praderie, F.

    1982-01-01

    The Hg-Mn stars show anomalous line strengths of many chemical elements including Be. We have observed the Be ii resonance doublet at lambdalambda 3130, 3131 at 6.7 A mm -1 in 43 Hg-Mn stars and 10 normal stars in the same temperature range with the coude spectrograph of the 2.24 m University of Hawaii telescope at Mauna Kea. Measured equivalent widths of the two lines and/or the blend of the doublet have been compared with predictions from (1) LTE model atmospheres and (2) non-LTE line formation on non-LTE model atmospheres. (For strong Be ii lines, the LTE calculations result in more Be by factors of 2 to 4 than do the non-LTE calculations.) Overabundances of factors of 20--2 x 10 4 relative to solar have been found for 75% of the Hg-Mn stars. The 25% with little or no Be are typically among the cooler Hg-Mn stars, but for the stars with Be excesses, there is only marginal evidence for a correlationi of the size of the overabundance and temperature. It is suggested that diffusion driven by radiation pressure is responsible for the observed Be abundance anomalies

  1. Ecotype diversification of an abundant Roseobacter lineage.

    Science.gov (United States)

    Sun, Ying; Zhang, Yao; Hollibaugh, James T; Luo, Haiwei

    2017-04-01

    The Roseobacter DC5-80-3 cluster (also known as the RCA clade) is among the most abundant bacterial lineages in temperate and polar oceans. Previous studies revealed two phylotypes within this cluster that are distinctly distributed in the Antarctic and other ocean provinces. Here, we report a nearly complete genome co-assembly of three closely related single cells co-occurring in the Antarctic, and compare it to the available genomes of the other phylotype from ocean regions where iron is more accessible but phosphorus and nitrogen are less. The Antarctic phylotype exclusively contains an operon structure consisting of a dicitrate transporter fecBCDE and an upstream regulator likely for iron uptake, whereas the other phylotype consistently carry a high-affinity phosphate pst transporter and the phoB-phoR regulatory system, a high-affinity ammonium amtB transporter, urea and taurine utilization systems. Moreover, the Antarctic phylotype uses proteorhodopsin to acquire light, whereas the other uses bacteriochlorophyll-a and the sulfur-oxidizing sox cluster for energy acquisition. This is potentially an iron-saving strategy for the Antarctic phylotype because only the latter two pathways have iron-requiring cytochromes. Therefore, the two DC5-80-3 phylotypes, while diverging by only 1.1% in their 16S rRNA genes, have evolved systematic differences in metabolism to support their distinct ecologies. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  2. Radiogenic lead-208 abundance 88.34 %

    International Nuclear Information System (INIS)

    Seneda, Jose A.; Abrao, Alcidio; Dias, Mauro S.; Kakazu, Mauricio H.; Salvador, Vera L.R.; Queiroz, Carlos A.S.; Rocha, Soraya M.R. da; Sato, Key

    2009-01-01

    Brazil has a long tradition in thorium technology, from the monazite ores mining until the production of the nuclear grade thorium compounds. Early in 1969 the Institute of Energy and Nuclear Research (IPEN) designed a project for a pilot plant installation to purify the thorium compounds, based on the solvent extraction technique. Thorium compounds used came from monazite's industrialization. During the course of the operation of this plant, a crude sludge were formed containing thorium not extracted and the whole rare earths, plus minor impurities like sodium, titanium, zirconium, hafnium, iron, silicon, phosphate and the thorium daughters were accumulated. Included is the radiogenic lead-208. This sludge, hereafter named 'RETOTER', was treated with hydrochloric acid and the lead was separated and recovered by anion exchange technology. The lead-208 was analyzed by mass spectrometry (HR-ICPMS) technique. The lead-208 abundance measure was 88.34%, this allowed the calculation of the thermal neutron capture cross section of σ 0 γ = 14,6 +/- 0.7 mb, considerably lower than the σ 0 γ = 174.2 +/- 0.7 mb value of the natural lead. (author)

  3. Pregalactic helium abundance and abundance gradients across our galaxy from planetary nebulae

    Energy Technology Data Exchange (ETDEWEB)

    D' Odorico, S; Peimbert, M [Universidad Nacional Autonoma de Mexico, Mexico City. Instituto de Astronomia; Sabbadin, F [Padua Univ. (Italy). Istituto di Astronomia

    1976-03-01

    From the observations of planetary nebulae by Peimbert and Torres-Peimbert we have studied the radial gradients across our galaxy of the helium, oxygen and nitrogen abundance relative to hydrogen. The increase of the oxygen to hydrogen abundance ratio from a radial distance to the galactic center of 14 to 8 kpc is about a factor of 3 while that of the nitrogen to hydrogen ratio is about twice as large. By adopting oxygen as representative of the heavy elements it is found that the helium enrichment is coupled to the heavy metal enrichment by ..delta..Y/..delta..Zapproximately2.9 in close agreement with the value derived from H II regions. The pregalactic N(He)/N(H) value derived from planetary nebulae is 0.073+-0.008 also in agreement with the value derived from H II regions.

  4. Carbon and oxygen abundances of field RR Lyrae stars. I. Carbon abundances

    International Nuclear Information System (INIS)

    Butler, D.; Manduca, A.; Deming, D.; Bell, R.A.

    1982-01-01

    From an analysis of KPNO 4-m echelle plates and simultaneous uvbyβ photometry, we have determined carbon abundances and carbon-to-iron ratios for a large number of field RR Lyrae stars having [Fe/H]> or approx. =-1.2. It is found that these field RR Lyrae stars: stars which are known to be in an advanced evolutionary state: have carbon-to-iron ratios which are similar to those of unevolved stars

  5. Multifactorial Understanding of Ion Abundance in Tandem Mass Spectrometry Experiments.

    Science.gov (United States)

    Fazal, Zeeshan; Southey, Bruce R; Sweedler, Jonathan V; Rodriguez-Zas, Sandra L

    2013-01-29

    In a bottom-up shotgun approach, the proteins of a mixture are enzymatically digested, separated, and analyzed via tandem mass spectrometry. The mass spectra relating fragment ion intensities (abundance) to the mass-to-charge are used to deduce the amino acid sequence and identify the peptides and proteins. The variables that influence intensity were characterized using a multi-factorial mixed-effects model, a ten-fold cross-validation, and stepwise feature selection on 6,352,528 fragment ions from 61,543 peptide ions. Intensity was higher in fragment ions that did not have neutral mass loss relative to any mass loss or that had a +1 charge state. Peptide ions classified for proton mobility as non-mobile had lowest intensity of all mobility levels. Higher basic residue (arginine, lysine or histidine) counts in the peptide ion and low counts in the fragment ion were associated with lower fragment ion intensities. Higher counts of proline in peptide and fragment ions were associated with lower intensities. These results are consistent with the mobile proton theory. Opposite trends between peptide and fragment ion counts and intensity may be due to the different impact of factor under consideration at different stages of the MS/MS experiment or to the different distribution of observations across peptide and fragment ion levels. Presence of basic residues at all three positions next to the fragmentation site was associated with lower fragment ion intensity. The presence of proline proximal to the fragmentation site enhanced fragmentation and had the opposite trend when located distant from the site. A positive association between fragment ion intensity and presence of sulfur residues (cysteine and methionine) on the vicinity of the fragmentation site was identified. These results highlight the multi-factorial nature of fragment ion intensity and could improve the algorithms for peptide identification and the simulation in tandem mass spectrometry experiments.

  6. The Open Cluster Chemical Abundances and Mapping (OCCAM) Survey: Galactic Neutron CaptureAbundance Gradients

    Science.gov (United States)

    O'Connell, Julia; Frinchaboy, Peter M.; Shetrone, Matthew D.; Melendez, Matthew; Cunha, Katia; Majewski, Steven R.; Zasowski, Gail; APOGEE Team

    2017-06-01

    The evolution of elements, as a function or age, throughout the Milky Way disk provides a key constraint for galaxy evolution models. In an effort to provide these constraints, we have conducted an investigation into the r- and s- process elemental abundances for a large sample of open clusters as part of an optical follow-up to the SDSS-III/APOGEE-1 survey. Stars were identified as cluster members by the Open Cluster Chemical Abundance & Mapping (OCCAM) survey, which culls member candidates by radial velocity, metallicity and proper motion from the observed APOGEE sample. To obtain data for neutron capture elements in these clusters, we conducted a long-term observing campaign covering three years (2013-2016) using the McDonald Observatory Otto Struve 2.1-m telescope and Sandiford Cass Echelle Spectrograph (R ~ 60,000). We present Galactic neutron capture abundance gradients using 30+ clusters, within 6 kpc of the Sun, covering a range of ages from ~80 Myr to ~10 Gyr .

  7. Coordinating structural and functional synapse development: postsynaptic p21-activated kinase independently specifies glutamate receptor abundance and postsynaptic morphology.

    Science.gov (United States)

    Albin, Stephanie D; Davis, Graeme W

    2004-08-04

    Here, we show that postsynaptic p21-activated kinase (Pak) signaling diverges into two genetically separable pathways at the Drosophila neuromuscular junction. One pathway controls glutamate receptor abundance. Pak signaling within this pathway is specified by a required interaction with the adaptor protein Dreadlocks (Dock). We demonstrate that Dock is localized to the synapse via an Src homology 2-mediated protein interaction. Dock is not necessary for Pak localization but is necessary to restrict Pak signaling to control glutamate receptor abundance. A second genetically separable function of Pak kinase signaling controls muscle membrane specialization through the regulation of synaptic Discs-large. In this pathway, Dock is dispensable. We present a model in which divergent Pak signaling is able to coordinate two different features of postsynaptic maturation, receptor abundance, and muscle membrane specialization.

  8. Fluorine Abundances in AGB Carbon Stars: New Results?

    Science.gov (United States)

    Abia, C.; de Laverny, P.; Recio-Blanco, A.; Domínguez, I.; Cristallo, S.; Straniero, O.

    2009-09-01

    A recent reanalysis of the fluorine abundance in three Galactic Asymptotic Giant Branch (AGB) carbon stars (TX Psc, AQ Sgr and R Scl) by Abia et al. (2009) results in estimates of fluorine abundances systematically lower by ~0.8 dex on average, with respect to the sole previous estimates by Jorissen, Smith & Lambert (1992). The new F abundances are in better agreement with the predictions of full-network stellar models of low-mass (<3 Msolar) AGB stars.

  9. Modelling tick abundance using machine learning techniques and satellite imagery

    DEFF Research Database (Denmark)

    Kjær, Lene Jung; Korslund, L.; Kjelland, V.

    satellite images to run Boosted Regression Tree machine learning algorithms to predict overall distribution (presence/absence of ticks) and relative tick abundance of nymphs and larvae in southern Scandinavia. For nymphs, the predicted abundance had a positive correlation with observed abundance...... the predicted distribution of larvae was mostly even throughout Denmark, it was primarily around the coastlines in Norway and Sweden. Abundance was fairly low overall except in some fragmented patches corresponding to forested habitats in the region. Machine learning techniques allow us to predict for larger...... the collected ticks for pathogens and using the same machine learning techniques to develop prevalence maps of the ScandTick region....

  10. Origin of Stellar Abundances in the early Galaxy

    International Nuclear Information System (INIS)

    Montes, F.; Beers, T. C.; Cowan, J.; Elliot, T.; Schatz, H.; Farouqi, K.; Gallino, R.; Heil, M.; Kratz, K.-L.; Pfeiffer, B.; Pignatari, M.

    2007-01-01

    Observations of metal-poor stars in the last decade have revealed an abundance pattern that have recently been explained as the result of two nucleosynthesis processes, a strong r-process that creates most of the Z≥56 and some 38≤Z≤47 abundances and a light element primary process (LEPP) responsible for creating the remaining 38≤Z≤47 abundances and some small contribution to heavier elements. We review some of the current literature on the LEPP and show a derived abundance pattern as a function of mass number

  11. 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.

  12. 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 nitrogen cycle in recently abandoned croplands.

  13. Stellar oxygen abundances. I - A resolution to the 7774 A O I abundance discrepancy

    Science.gov (United States)

    King, Jeremy R.

    1993-09-01

    We investigate the discrepancy between O/Fe abundance ratios of metal-poor stars derived from the 7774 A O I triplet and O/Fe ratios determined from other oxygen lines. We propose a possible resolution to this discrepancy which also eliminates the correlation of O/Fe and T(eff) found in a recent 7774 A O I analysis. The equivalent widths of Abia & Rebolo (1989) are found to be systematically too high by 25 percent. Arguments are presented that current temperature estimates for halo stars are 150-200 K too low. Using the guidance of both model atmospheres and other empirical color-T(eff) relations, we construct new color temperature relations for metal-poor stars. These relations are tied to the temperature scale of Saxner & Hammarback (1985) for metal-rich stars. We use (b-y) and (V-K) indices to redetermine values of T(eff) for a handful of halo stars. (B-V)-T(eff) relations which do not take into account the effects of metallicity are found to be inadequate. Revised O/Fe ratios are determined using the new temperature scale. The mean abundance ratio of the reanalyzed halo dwarfs is about +0.52. There is no trend of O/Fe with Fe/H or T(eff).

  14. Spatio-temporal Variations of Abundance, Biomass, and ...

    African Journals Online (AJOL)

    The spatio-seasonal variations of Pseudodiaptomus hessei abundance, biomass and reproductive parameters were investigated in the Grand-Lahou lagoon at five stations during the dry and wet (or rainy) seasons from September 2005 to August 2006. In all sampling stations, abundance and biomass of P. hessei in the dry ...

  15. Elemental abundances in the Galactic bulge from microlensed dwarf stars

    NARCIS (Netherlands)

    Bensby, T.; Feltzing, S.; Johnson, J.A.; Gould, A.; Sana, H.; Gal-Yam, A.; Asplund, M.; Lucatello, S.; Melendez, J.; Udalski, A.; Kubas, D.; James, G.; Adén, D.; Simmerer, J.

    2010-01-01

    We present elemental abundances of 13 microlensed dwarf and subgiant stars in the Galactic bulge, which constitute the largest sample to date. We show that these stars span the full range of metallicity from Fe/H= −0.8 to +0.4, and that they follow well-defined abundance trends, coincident with

  16. Optical region elemental abundance analyses of B and A stars

    International Nuclear Information System (INIS)

    Adelman, S.J.; Young, J.M.; Baldwin, H.E.

    1984-01-01

    Abundance analyses using optical region data and fully line blanketed model atmospheres have been performed for two sharp-lined hot Am stars o Pegasi and σ Aquarii and for the sharp-lined marginally peculiar A star v Cancri. The derived abundances exhibit definite anomalies compared with those of normal B-type stars and the Sun. (author)

  17. LITHIUM ABUNDANCES OF EXTREMELY METAL-POOR TURNOFF STARS

    International Nuclear Information System (INIS)

    Aoki, Wako; Inoue, Susumu; Barklem, Paul S.; Beers, Timothy C.; Christlieb, Norbert; Perez, Ana E. GarcIa; Norris, John E.; Carollo, Daniela

    2009-01-01

    We have determined Li abundances for eleven metal-poor turnoff stars, among which eight have [Fe/H] <-3, based on LTE analyses of high-resolution spectra obtained with the High Dispersion Spectrograph on the Subaru Telescope. The Li abundances for four of these eight stars are determined for the first time by this study. Effective temperatures are determined by a profile analysis of Hα and Hβ. While seven stars have Li abundances as high as the Spite Plateau value, the remaining four objects with [Fe/H] <-3 have A(Li) =log (Li/H)+ 12 ∼< 2.0, confirming the existence of extremely metal-poor (EMP) turnoff stars having low Li abundances, as reported by previous work. The average of the Li abundances for stars with [Fe/H]<-3 is lower by 0.2 dex than that of the stars with higher metallicity. No clear constraint on the metallicity dependence or scatter of the Li abundances is derived from our measurements for the stars with [Fe/H]<-3. Correlations of the Li abundance with effective temperatures, with abundances of Na, Mg, and Sr, and with the kinematical properties are investigated, but no clear correlation is seen in the EMP star sample.

  18. Mechanisms driving postfire abundance of a generalist mammal

    Science.gov (United States)

    R. Zwolak; D. E. Pearson; Y. K. Ortega; E. E. Crone

    2012-01-01

    Changes in vertebrate abundance following disturbance are commonly attributed to shifts in food resources or predation pressure, but underlying mechanisms have rarely been tested. We examined four hypotheses for the commonly reported increase in abundance of deer mouse (Peromyscus maniculatus (Wagner, 1845)) following forest fires: source-sink dynamics, decreased...

  19. Spatial and temporal patterns of phytoplankton abundance and ...

    African Journals Online (AJOL)

    Bacillariophyta was the most abundant group (48.17% of total phytoplankton) and was uniformly distributed in all waters, followed by Cyanobacteria (33.33%), which decreased with distance offshore. Chlorophyta, the third highest in abundance (15.5%), increased with distance offshore. A total of 92 phytoplankton species ...

  20. The Paradox of Water Abundance in Mato Grosso, Brazil

    Directory of Open Access Journals (Sweden)

    Christopher Schulz

    2017-10-01

    Full Text Available While much effort has gone into studying the causes and consequences of water scarcity, the concept of water abundance has received considerably less attention in academic literature. Here, we aim to address this gap by providing a case study on the perceptions and political implications of water abundance in the Brazilian state of Mato Grosso. Combining a political ecology perspective on contemporary water governance (empirically based on stakeholder interviews with members of the state’s water sector with an overview of the environmental history of this hydrosocial territory, we argue, first, that water abundance has become a foundational element of Mato Grosso’s identity, situated in the wider context of natural resource abundance more generally and second, that water abundance today is a contested concept witnessing discursive struggles around its political implications and meaning. More specifically, there is a clash between the dominant conceptualisation of water abundance as a foundation for rich economic, ecological, social, and cultural values and benefits, often espoused by members of the political and economic elite, e.g., for marketing purposes, and a more critical but less widespread conceptualisation of water abundance as a source of carelessness, lack of awareness, and poor water governance, typically put forth by more informed technical staff of the public sector and civil society activists. By providing a distinct treatment and discussion of the concept of water abundance, our research has relevance for other water-rich regions beyond the immediate regional context.

  1. Abundance of birds in Fukushima as judged from Chernobyl

    International Nuclear Information System (INIS)

    Møller, Anders Pape; Hagiwara, Atsushi; Matsui, Shin; Kasahara, Satoe; Kawatsu, Kencho; Nishiumi, Isao; Suzuki, Hiroyuki; Ueda, Keisuke; Mousseau, Timothy A.

    2012-01-01

    The effects of radiation on abundance of common birds in Fukushima can be assessed from the effects of radiation in Chernobyl. Abundance of birds was negatively related to radiation, with a significant difference between Fukushima and Chernobyl. Analysis of 14 species common to the two areas revealed a negative effect of radiation on abundance, differing between areas and species. The relationship between abundance and radiation was more strongly negative in Fukushima than in Chernobyl for the same 14 species, demonstrating a negative consequence of radiation for birds immediately after the accident on 11 March 2011 during the main breeding season in March–July, when individuals work close to their maximum sustainable level. - Highlights: ► Abundance of birds was negatively related to radiation in Chernobyl and Fukushima. ► Effects of radiation on abundance differed between Chernobyl and Fukushima and among species. ► For 14 species common to the two areas the effects of radiation on abundance were stronger in Fukushima than in Chernobyl. - The negative effect of radiation on abundance of birds in Fukushima exceeded that for the same species in Chernobyl.

  2. Abundances of neon, sulfur, and argon in planetary nebulae

    International Nuclear Information System (INIS)

    Beck, S.C.; Lacy, J.H.; Townes, C.H.; Geballe, T.R.; Baas, F.

    1981-01-01

    Infrared observations of [Ne II], [S IV], and [Ar III] are used with optical observations to discuss the abundances of Ne, S, and Ar in 18 planetary nebulae. In addition, infrared observations of 18 other nebulae are presented. The derived abundances of S and Ar are each slightly enhanced relative to previous studies

  3. Probing AGB nucleosynthesis via accurate Planetary Nebula abundances

    NARCIS (Netherlands)

    Marigo, P; Bernard-Salas, J; Pottasch, S. R.; Tielens, A. G. G. M.; Wesselius, P. R.

    2003-01-01

    The elemental abundances of ten planetary nebulae, derived with high accuracy including ISO and IUE spectra, are analysed with the aid of synthetic evolutionary models for the TP-AGB phase. The accuracy on the observed abundances is essential in order to make a reliable comparison with the models.

  4. 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

  5. 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

  6. Inferring recent historic abundance from current genetic diversity

    NARCIS (Netherlands)

    Palsboll, Per J.; Peery, M. Zachariah; Olsen, Morten T.; Beissinger, Steven R.; Berube, Martine

    Recent historic abundance is an elusive parameter of great importance for conserving endangered species and understanding the pre-anthropogenic state of the biosphere. The number of studies that have used population genetic theory to estimate recent historic abundance from contemporary levels of

  7. Influence of summer biogeography on wood warbler stopover abundance

    Science.gov (United States)

    Jeffrey F. Kelly; Rob Smith; Deborah M. Finch; Frank R. Moore; Wang Yong

    1999-01-01

    We evaluated the effect of summer biogeography of migrant wood warblers (Parulidae) on their stopover abundance. To characterize abundance patterns, we used mist-net capture data from spring and fall migration in the Middle Rio Grande Valley, New Mexico, spring migration on the Gulf Coast of Louisiana, and fall migration on the Gulf Coast of Alabama. To describe the...

  8. Abundances and Habitat Sensitivities of Some River Fishes in ...

    African Journals Online (AJOL)

    Freshwater fishes from a diverse array of 11 families, some dominated by marine species and others containing only a few species, were collected by electrofishing from 84 locations on small rivers in central Thailand and their abundances related to habitat characteristics. Abundances were largest for Channa gachua, ...

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

    NARCIS (Netherlands)

    Alonso, D.; Ostling, A.; Etienne, R.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

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

    NARCIS (Netherlands)

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

    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

  11. 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.

  12. Chemical abundances of globular clusters in NGC 5128 (Centaurus A)

    Science.gov (United States)

    Hernandez, Svea; Larsen, Søren; Trager, Scott; Kaper, Lex; Groot, Paul

    2018-06-01

    We perform a detailed abundance analysis on integrated-light spectra of 20 globular clusters (GCs) in the early-type galaxy NGC 5128 (Centaurus A). The GCs were observed with X-Shooter on the Very Large Telescope (VLT). The cluster sample spans a metallicity range of -1.92 poor GCs in NGC 5128 is genuine, it could hint at a chemical enrichment history different than that experienced by the MW. We also measure Na abundances in 9 out of 20 GCs. We find evidence for intracluster abundance variations in six of these clusters where we see enhanced [Na/Fe] > +0.25 dex. We obtain the first abundance measurements of Cr, Mn, and Ni for a sample of the GC population in NGC 5128 and find consistency with the overall trends observed in the MW, with a slight enhancement (<0.1 dex) in the Fe-peak abundances measured in the NGC 5128.

  13. Repeated administration of phytocannabinoid Δ(9)-THC or synthetic cannabinoids JWH-018 and JWH-073 induces tolerance to hypothermia but not locomotor suppression in mice, and reduces CB1 receptor expression and function in a brain region-specific manner.

    Science.gov (United States)

    Tai, S; Hyatt, W S; Gu, C; Franks, L N; Vasiljevik, T; Brents, L K; Prather, P L; Fantegrossi, W E

    2015-12-01

    These studies probed the relationship between intrinsic efficacy and tolerance/cross-tolerance between ∆(9)-THC and synthetic cannabinoid drugs of abuse (SCBs) by examining in vivo effects and cellular changes concomitant with their repeated administration in mice. Dose-effect relationships for hypothermic effects were determined in order to confirm that SCBs JWH-018 and JWH-073 are higher efficacy agonists than ∆(9)-THC in mice. Separate groups of mice were treated with saline, sub-maximal hypothermic doses of JWH-018 or JWH-073 (3.0mg/kg or 10.0mg/kg, respectively) or a maximally hypothermic dose of 30.0mg/kg ∆(9)-THC once per day for 5 consecutive days while core temperature and locomotor activity were monitored via biotelemetry. Repeated administration of all drugs resulted in tolerance to hypothermic effects, but not locomotor effects, and this tolerance was still evident 14 days after the last drug administration. Further studies treated mice with 30.0mg/kg ∆(9)-THC once per day for 4 days, then tested with SCBs on day 5. Mice with a ∆(9)-THC history were cross-tolerant to both SCBs, and this cross-tolerance also persisted 14 days after testing. Select brain regions from chronically treated mice were examined for changes in CB1 receptor expression and function. Expression and function of hypothalamic CB1Rs were reduced in mice receiving chronic drugs, but cortical CB1R expression and function were not altered. Collectively, these data demonstrate that repeated ∆(9)-THC, JWH-018 and JWH-073 can induce long-lasting tolerance to some in vivo effects, which is likely mediated by region-specific downregulation and desensitization of CB1Rs. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Age- and Brain Region-Specific Changes of Glucose Metabolic Disorder, Learning, and Memory Dysfunction in Early Alzheimer’s Disease Assessed in APP/PS1 Transgenic Mice Using 18F-FDG-PET

    Directory of Open Access Journals (Sweden)

    Xue-Yuan Li

    2016-10-01

    Full Text Available Alzheimer’s disease (AD is a leading cause of dementia worldwide, associated with cognitive deficits and brain glucose metabolic alteration. However, the associations of glucose metabolic changes with cognitive dysfunction are less detailed. Here, we examined the brains of APP/presenilin 1 (PS1 transgenic (Tg mice aged 2, 3.5, 5 and 8 months using 18F-labed fluorodeoxyglucose (18F-FDG microPET to assess age- and brain region-specific changes of glucose metabolism. FDG uptake was calculated as a relative standardized uptake value (SUVr. Morris water maze (MWM was used to evaluate learning and memory dysfunction. We showed a glucose utilization increase in multiple brain regions of Tg mice at 2 and 3.5 months but not at 5 and 8 months. Comparisons of SUVrs within brains showed higher glucose utilization than controls in the entorhinal cortex, hippocampus, and frontal cortex of Tg mice at 2 and 3.5 months but in the thalamus and striatum at 3.5, 5 and 8 months. By comparing SUVrs in the entorhinal cortex and hippocampus, Tg mice were distinguished from controls at 2 and 3.5 months. In MWM, Tg mice aged 2 months shared a similar performance to the controls (prodromal-AD. By contrast, Tg mice failed training tests at 3.5 months but failed all MWM tests at 5 and 8 months, suggestive of partial or complete cognitive deficits (symptomatic-AD. Correlation analyses showed that hippocampal SUVrs were significantly correlated with MWM parameters in the symptomatic-AD stage. These data suggest that glucose metabolic disorder occurs before onset of AD signs in APP/PS1 mice with the entorhinal cortex and hippocampus affected first, and that regional FDG uptake increase can be an early biomarker for AD. Furthermore, hippocampal FDG uptake is a possible indicator for progression of Alzheimer’s cognition after cognitive decline, at least in animals.

  15. Age- and Brain Region-Specific Changes of Glucose Metabolic Disorder, Learning, and Memory Dysfunction in Early Alzheimer's Disease Assessed in APP/PS1 Transgenic Mice Using 18F-FDG-PET.

    Science.gov (United States)

    Li, Xue-Yuan; Men, Wei-Wei; Zhu, Hua; Lei, Jian-Feng; Zuo, Fu-Xing; Wang, Zhan-Jing; Zhu, Zhao-Hui; Bao, Xin-Jie; Wang, Ren-Zhi

    2016-10-18

    Alzheimer's disease (AD) is a leading cause of dementia worldwide, associated with cognitive deficits and brain glucose metabolic alteration. However, the associations of glucose metabolic changes with cognitive dysfunction are less detailed. Here, we examined the brains of APP/presenilin 1 (PS1) transgenic (Tg) mice aged 2, 3.5, 5 and 8 months using 18 F-labed fluorodeoxyglucose ( 18 F-FDG) microPET to assess age- and brain region-specific changes of glucose metabolism. FDG uptake was calculated as a relative standardized uptake value (SUVr). Morris water maze (MWM) was used to evaluate learning and memory dysfunction. We showed a glucose utilization increase in multiple brain regions of Tg mice at 2 and 3.5 months but not at 5 and 8 months. Comparisons of SUVrs within brains showed higher glucose utilization than controls in the entorhinal cortex, hippocampus, and frontal cortex of Tg mice at 2 and 3.5 months but in the thalamus and striatum at 3.5, 5 and 8 months. By comparing SUVrs in the entorhinal cortex and hippocampus, Tg mice were distinguished from controls at 2 and 3.5 months. In MWM, Tg mice aged 2 months shared a similar performance to the controls (prodromal-AD). By contrast, Tg mice failed training tests at 3.5 months but failed all MWM tests at 5 and 8 months, suggestive of partial or complete cognitive deficits (symptomatic-AD). Correlation analyses showed that hippocampal SUVrs were significantly correlated with MWM parameters in the symptomatic-AD stage. These data suggest that glucose metabolic disorder occurs before onset of AD signs in APP/PS1 mice with the entorhinal cortex and hippocampus affected first, and that regional FDG uptake increase can be an early biomarker for AD. Furthermore, hippocampal FDG uptake is a possible indicator for progression of Alzheimer's cognition after cognitive decline, at least in animals.

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

    Science.gov (United States)

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

    2015-02-01

    To fully understand skeletal muscle at the cellular level, it is essential to evaluate single muscle fibers. Accordingly, the major goals of this study were to determine if there are fiber type-related differences in single fibers from rat skeletal muscle for: 1) contraction-stimulated glucose uptake and/or 2) the abundance of GLUT4 and other metabolically relevant proteins. Paired epitrochlearis muscles isolated from Wistar rats were either electrically stimulated to contract (E-Stim) or remained resting (No E-Stim). Single fibers isolated from muscles incubated with 2-deoxy-d-[(3)H]glucose (2-DG) were used to determine fiber type [myosin heavy chain (MHC) isoform protein expression], 2-DG uptake, and abundance of metabolically relevant proteins, including the GLUT4 glucose transporter. E-Stim, relative to No E-Stim, fibers had greater (P contraction-stimulated glucose uptake. Copyright © 2015 the American Physiological Society.

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

    Science.gov (United States)

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

    2016-03-01

    Uterine leiomyoma are a common benign pelvic tumors composed of modified smooth muscle cells and a large amount of extracellular matrix (ECM). The proteoglycan composition of the leiomyoma ECM is thought to affect pathophysiology of the disease. To test this hypothesis, we examined the abundance (by immunoblotting) and expression (by quantitative real-time polymerase chain reaction) of the proteoglycans biglycan, decorin, and versican in leiomyoma and normal myometrium and determined whether expression is affected by steroid hormones and menstrual phase. Leiomyoma and normal myometrium were collected from women (n = 17) undergoing hysterectomy or myomectomy. In vitro studies were performed on immortalized leiomyoma (UtLM) and normal myometrial (hTERT-HM) cells with and without exposure to estradiol and progesterone. In leiomyoma tissue, abundance of decorin messenger RNA (mRNA) and protein were 2.6-fold and 1.4-fold lower, respectively, compared with normal myometrium. Abundance of versican mRNA was not different between matched samples, whereas versican protein was increased 1.8-fold in leiomyoma compared with myometrium. Decorin mRNA was 2.4-fold lower in secretory phase leiomyoma compared with proliferative phase tissue. In UtLM cells, progesterone decreased the abundance of decorin mRNA by 1.3-fold. Lower decorin expression in leiomyoma compared with myometrium may contribute to disease growth and progression. As decorin inhibits the activity of specific growth factors, its reduced level in the leiomyoma cell microenvironment may promote cell proliferation and ECM deposition. Our data suggest that decorin expression in leiomyoma is inhibited by progesterone, which may be a mechanism by which the ovarian steroids affect leiomyoma growth and disease progression. © The Author(s) 2015.

  18. A Metastable Equilibrium Model for the Relative Abundances of Microbial Phyla in a Hot Spring

    Science.gov (United States)

    Dick, Jeffrey M.; Shock, Everett L.

    2013-01-01

    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 depend on both the

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. Understanding and reducing statistical uncertainties in nebular abundance determinations

    Science.gov (United States)

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

    2012-06-01

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

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

    Science.gov (United States)

    Longino, John T; Branstetter, Michael G; Colwell, Robert K

    2014-01-01

    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.

  5. 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.

  6. Geographical factors of the abundance of flora in Russian cities

    Science.gov (United States)

    Veselkin, D. V.; Tretyakova, A. S.; Senator, S. A.; Saksonov, S. V.; Mukhin, V. A.; Rozenberg, G. S.

    2017-09-01

    An analysis of data on the species abundance of flora in 89 cities (urban flora) of the Russian Federation facilitated determination of its main factors. It has been revealed that the factors determining the abundance of native and alien components of urban flora vary. The city area and population number are the main factors of the total number of species and of the abundance of native species in urban flora. The diversity and participation of alien species increase in parallel with. the urbanization rate, anthropogenic transformation of the regions, and the age of cities and are in adverse correlation with the climate severity.

  7. Dust formation in a galaxy with primitive abundances.

    Science.gov (United States)

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

    2009-01-16

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

  8. 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

    -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...... and no hatching groups for any of the selected genes at 0, 2.5, and 5 HPF. However, at 30 HPF the hatch group showed significantly higher abundance of cpt1a, cpt1b, β-tubulin, phb2, and pigf5 transcripts than the no hatch group. Therefore, these results indicate that up-regulation of the transcription...

  9. Region-specific roles of the prelimbic cortex, the dorsal CA1, the ventral DG and ventral CA1 of the hippocampus in the fear return evoked by a sub-conditioning procedure in rats.

    Science.gov (United States)

    Fu, Juan; Xing, Xiaoli; Han, Mengfi; Xu, Na; Piao, Chengji; Zhang, Yue; Zheng, Xigeng

    2016-02-01

    The return of learned fear is an important issue in anxiety disorder research since an analogous process may contribute to long-term fear maintenance or clinical relapse. A number of studies demonstrate that mPFC and hippocampus are important in the modulation of post-extinction re-expression of fear memory. However, the region-specific role of these structures in the fear return evoked by a sub-threshold conditioning (SC) is not known. In the present experiments, we first examined specific roles of the prelimbic cortex (PL), the dorsal hippocampus (DH, the dorsal CA1 area in particular), the ventral hippocampus (the ventral dentate gyrus (vDG) and the ventral CA1 area in particular) in this fear return process. Then we examined the role of connections between PL and vCA1 with this behavioral approach. Rats were subjected to five tone-shock pairings (1.0-mA shock) to induce conditioned fear (freezing), followed by three fear extinction sessions (25 tone-alone trials each session). After a post-test for extinction memory, some rats were retrained with the SC procedure to reinstate tone-evoked freezing. Rat groups were injected with low doses of the GABAA agonist muscimol to selectively inactivate PL, DH, vDG, or vCA1 120 min before the fear return test. A disconnection paradigm with ipsilateral or contralateral muscimol injection of the PL and the vCA1 was used to examine the role of this pathway in the fear return. We found that transient inactivation of these areas significantly impaired fear return (freezing): inactivation of the prelimbic cortex blocked SC-evoked fear return in particular but did not influence fear expression in general; inactivation of the DH area impaired fear return, but had no effect on the extinction retrieval process; both ventral DG and ventral CA1 are required for the return of extinguished fear whereas only ventral DG is required for the extinction retrieval. These findings suggest that PL, DH, vDG, and vCA1 all contribute to the fear

  10. A role of peripheral myelin protein 2 in lipid homeostasis of myelinating Schwann cells

    NARCIS (Netherlands)

    Zenker, J.; Stettner, M.; Ruskamo, S.; Domenech-Estevez, E.; Baloui, H.; Medard, J.J.; Verheijen, M.H.G.; Brouwers, J.F.; Kursula, P.; Kieseier, B.C.; Chrast, R.

    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

  11. 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|info:eu-repo/dai/nl/173812694; Kursula, Petri; kieseier, bernd; Chrast, Roman

    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

  12. Why abundant tropical tree species are phylogenetically old.

    Science.gov (United States)

    Wang, Shaopeng; Chen, Anping; Fang, Jingyun; Pacala, Stephen W

    2013-10-01

    Neutral models of species diversity predict patterns of abundance for communities in which all individuals are ecologically equivalent. These models were originally developed for Panamanian trees and successfully reproduce observed distributions of abundance. Neutral models also make macroevolutionary predictions that have rarely been evaluated or tested. Here we show that neutral models predict a humped or flat relationship between species age and population size. In contrast, ages and abundances of tree species in the Panamanian Canal watershed are found to be positively correlated, which falsifies the models. Speciation rates vary among phylogenetic lineages and are partially heritable from mother to daughter species. Variable speciation rates in an otherwise neutral model lead to a demographic advantage for species with low speciation rate. This demographic advantage results in a positive correlation between species age and abundance, as found in the Panamanian tropical forest community.

  13. Abundance, recruitment and residency of two sparids in an ...

    African Journals Online (AJOL)

    Abundance, recruitment and residency of two sparids in an intermittently open estuary in South Africa. ... Abstract. The recruitment of distinct year-class cohorts in two sparid species, Rhabdosargus holubi and ... AJOL African Journals Online.

  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......,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts...... in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies. Udgivelsesdato: 2005-Jun...

  15. Abundance-range size relationships in stream vegetation in Denmark

    DEFF Research Database (Denmark)

    Riis, Tenna; Sand-Jensen, Kaj

    2002-01-01

    thecultivated lowlands of Denmark, we examined the overall relationship betweenlocal abundance and geographical range size of the vascular flora. We found asignificant positive relationship for all species at all stream localities andan even stronger relationship for ecologically similar species...

  16. Changes in abundance of the northern Benguela sardine stock ...

    African Journals Online (AJOL)

    Changes in abundance of the northern Benguela sardine stock during the decade ... with comments on the relative importance of fishing and the environment. ... Survey-based recruitment indices suggest that the changes in the 1990s were ...

  17. Factors influencing long-term and seasonal waterbird abundance ...

    African Journals Online (AJOL)

    ... influence waterbird communities include rainfall quantity and distribution, waterbird movement, breeding and moulting; anthropogenic drivers include activities such as fishing and agriculture. Results suggest that seasonal variations in resource availability influenced the waterbird community composition and abundance, ...

  18. 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...

  19. types and abundance of arthropod fauna in relation to physico ...

    African Journals Online (AJOL)

    DJFLEX

    TYPES AND ABUNDANCE OF ARTHROPOD FAUNA IN RELATION ... The occurrence of arthropods associated with the bottom sediment of Warri River was investigated, and samples were collected ..... to analysis of the vegetation on Danish.

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

    International Nuclear Information System (INIS)

    Rautenstrauch, K.R.; O'Farrell, T.P.

    1993-01-01

    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

  1. Composition, distribution and abundance of ichthyoplankton in the ...

    African Journals Online (AJOL)

    1989-06-29

    Jun 29, 1989 ... The species composition, distribution and seasonal abundance of ichthyoplankton in the Sundays River estuary was ... The importance of southern African estuaries as nursery areas for juvenile ... 1990,25(3) the mid-channel.

  2. Origin of the solar system s-process abundances

    International Nuclear Information System (INIS)

    Malaney, R.A.; Boothroyd, A.I.

    1987-01-01

    In the search for the origin of the solar system s-process abundances much attention has been focused on the intershell zones of thermally pulsing asymptotic giant branch (AGB) stars. It has recently been suggested that, relative to the poor fits obtained from intermediate-mass AGB models, low-mass AGB models may result in much better fits to the observed solar system abundances. This suggestion was motivated by the high intershell base temperatures indicated by recent low-mass AGB calculations. Using new data, presented for the peak intershell base temperature in such stars, the s-process enhancements occurring in the intershell zones of low-mass AGB stars are calculated. A nonsolar distribution of s-process abundances is reported for all realistic AGB models studied. Other possible astrophysical sites for the origin of the solar system s-process abundances are discussed. 35 references

  3. Distribution, abundance and ecology of the sponge Spheciospongia ...

    African Journals Online (AJOL)

    Western Indian Ocean Journal of Marine Science ... Journal Home > Vol 12, No 1 (2013) > ... Distribution, abundance and ecology of the sponge Spheciospongia vagabunda (Phylum: Porifera, Class: Demospongiae) in a shallow lagoon of ...

  4. A SOLAR SPECTROSCOPIC ABSOLUTE ABUNDANCE OF ARGON FROM RESIK

    International Nuclear Information System (INIS)

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

    2010-01-01

    Observations of He-like and H-like Ar (Ar XVII and Ar XVIII) lines at 3.949 A and 3.733 A, respectively, with the RESIK X-ray spectrometer on the CORONAS-F spacecraft, together with temperatures and emission measures from the two channels of GOES, have been analyzed to obtain the abundance of Ar in flare plasmas in the solar corona. The line fluxes per unit emission measure show a temperature dependence like that predicted from theory and lead to spectroscopically determined values for the absolute Ar abundance, A(Ar) = 6.44 ± 0.07 (Ar XVII) and 6.49 ± 0.16 (Ar XVIII), which are in agreement to within uncertainties. The weighted mean is 6.45 ± 0.06, which is between two recent compilations of the solar Ar abundance and suggests that the photospheric and coronal abundances of Ar are very similar.

  5. BOND: A quantum of solace for nebular abundance determinations

    Science.gov (United States)

    Vale Asari, N.; Stasińska, G.; Morisset, C.; Cid Fernandes, R.

    2017-11-01

    The abundances of chemical elements other than hydrogen and helium in a galaxy are the fossil record of its star formation history. Empirical relations such as mass-metallicity relation are thus seen as guides for studies on the history and chemical evolution of galaxies. Those relations usually rely on nebular metallicities measured with strong-line methods, which assume that H II regions are a one- (or at most two-) parameter family where the oxygen abundance is the driving quantity. Nature is however much more complex than that, and metallicities from strong lines may be strongly biased. We have developed the method BOND (Bayesian Oxygen and Nitrogen abundance Determinations) to simultaneously derive oxygen and nitrogen abundances in giant H II regions by comparing strong and semi-strong observed emission lines to a carefully-defined, finely-meshed grid of photoionization models. Our code and results are public and available at http://bond.ufsc.br.

  6. Methanotrophic abundance and community fingerprint in pine and ...

    African Journals Online (AJOL)

    methanotrophs) is important to assess the microbial oxidation of the greenhouse gas methane (CH4) in soil under different land uses. Soil samples were collected from two plantation plots of pine and tea in southern China. Methanotrophic abundance ...

  7. Effect of Spent Lubricating Oil on the Composition and Abundance ...

    African Journals Online (AJOL)

    Journal of Applied Sciences and Environmental Management ... The Modified Berlese-Tullgren Funnel method was used for the extraction of soil arthropod fauna. ... Soil arthropod taxa and abundance were significantly lower (u(2) = 51, ...

  8. The distribution, abundance, and habitat preference of lovebirds ...

    African Journals Online (AJOL)

    SARAH

    2014-04-30

    Apr 30, 2014 ... Key words: Abundance, micro-habitat, preference, riparian, vegetation .... human interference and more food resources availability. In the month of May, June .... force birds to feed on areas of less quality because survival rate ...

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

    International Nuclear Information System (INIS)

    Westphal, Andrew J.

    2000-01-01

    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

  10. The Open Cluster Chemical Abundances and Mapping (OCCAM) Survey: Detailed Age and Abundance Gradients using DR12

    Science.gov (United States)

    Frinchaboy, Peter M.; Thompson, Benjamin A.; O'Connell, Julia; Meyer, Brianne; Donor, John; Majewski, Steven R.; Holtzman, Jon A.; Zasowski, Gail; Beers, Timothy C.; Beaton, Rachael; Cunha, Katia M. L.; Hearty, Fred; Nidever, David L.; Schiavon, Ricardo P.; Smith, Verne V.; Hayden, Michael R.

    2015-01-01

    We present detailed abundance results for Galactic open clusters as part of the Open Cluster Chemical Abundances and Mapping (OCCAM) Survey, which is based primarily on data from the Sloan Digital Sky Survey/ Apache Point Observatory Galactic Evolution Experiment. Using 100 open clusters from the uniformly observed complete SDSS-III/APOGEE-1 DR12 dataset, we present age and multi-element abundance gradients for the disk of the Milky Way.This work is supported by an NSF AAG grant AST-1311835.

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

    International Nuclear Information System (INIS)

    Holden, N.E.

    1989-01-01

    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

  12. Dynamical explanation for the high water abundance detected in Orion

    International Nuclear Information System (INIS)

    Elitzur, M.

    1979-01-01

    Shock wave chemistry is suggested as the likely explanation for the high water abundance which has been recently detected in Orion by Phyllips et al. The existence of such a shock and its inferred properties are in agreement with other observations of Orion such as the broad velocity feature and H 2 vibration emission. Shock waves are proposed as the likely explanation for high water abundances observed in other sources such as the strong H 2 O masers

  13. The variation of interstellar element abundances with hydrogen density

    International Nuclear Information System (INIS)

    Keenan, F.P.; Hibbert, A.; Dufton, P.L.; Murray, M.J.

    1986-01-01

    The variation of the interstellar nitrogen, oxygen and magnesium abundances with mean line-of-sight hydrogen density is analysed in terms of a two-component model, which consists of warm, low-density neutral gas and cold clouds. In all cases the gas-phase abundances have been deduced using reliable oscillator strengths specifically calculated for this purpose. Depletions in the warm and cold gas, are derived from non-linear least-squares fits to the data. (author)

  14. Incorporating breeding abundance into spatial assignments on continuous surfaces.

    Science.gov (United States)

    Rushing, Clark S; Marra, Peter P; Studds, Colin E

    2017-06-01

    Determining the geographic connections between breeding and nonbreeding populations, termed migratory connectivity, is critical to advancing our understanding of the ecology and conservation of migratory species. Assignment models based on stable isotopes historically have been an important tool for studying migratory connectivity of small-bodied species, but the low resolution of these assignments has generated interest into combining isotopes with other sources in information. Abundance is one of the most appealing data sources to include in isotope-based assignments, but there are currently no statistical methods or guidelines for optimizing the contribution of stable isotopes and abundance for inferring migratory connectivity. Using known-origin stable-hydrogen isotope samples of six Neotropical migratory bird species, we rigorously assessed the performance of assignment models that differentially weight the contribution of the isotope and abundance data. For two species with adequate sample sizes, we used Pareto optimality to determine the set of models that simultaneously minimized both assignment error rate and assignment area. We then assessed the ability of the top models from these two species to improve assignments of the remaining four species compared to assignments based on isotopes alone. We show that the increased precision of models that include abundance is often offset by a large increase in assignment error. However, models that optimally weigh the abundance data relative to the isotope data can result in higher precision and, in some cases, lower error than models based on isotopes alone. The top models, however, depended on the distribution of relative breeding abundance, with patchier distributions requiring stronger downweighting of abundance, and we present general guidelines for future studies. These results confirm that breeding abundance can be an important source of information for studies investigating broad-scale movements of

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

    DEFF Research Database (Denmark)

    Wietz, Matthias; Gram, Lone; Jørgensen, Bo

    2010-01-01

    relative abundance 37%, average absolute abundance 3.7×105 cells mL-1) including SAR11 (30%/3×105), Gammaproteobacteria (14%/1.2×105), and Bacteroidetes (12%/1.3×105) globally dominated the bacterioplankton. The SAR86 clade (4.6%/4.1×104) and Actinobacteria (4.5%/4×104) were detected ubiquitously, whereas...

  16. Protein phosphorylation systems in postmortem human brain

    International Nuclear Information System (INIS)

    Walaas, S.I.; Perdahl-Wallace, E.; Winblad, B.; Greengard, P.

    1989-01-01

    Protein phosphorylation systems regulated by cyclic adenosine 3',5'-monophosphate (cyclic AMP), or calcium in conjunction with calmodulin or phospholipid/diacylglycerol, have been studied by phosphorylation in vitro of particulate and soluble fractions from human postmortem brain samples. One-dimensional or two-dimensional gel electrophoretic protein separations were used for analysis. Protein phosphorylation catalyzed by cyclic AMP-dependent protein kinase was found to be highly active in both particulate and soluble preparations throughout the human CNS, with groups of both widely distributed and region-specific substrates being observed in different brain nuclei. Dopamine-innervated parts of the basal ganglia and cerebral cortex contained the phosphoproteins previously observed in rodent basal ganglia. In contrast, calcium/phospholipid-dependent and calcium/calmodulin-dependent protein phosphorylation systems were less prominent in human postmortem brain than in rodent brain, and only a few widely distributed substrates for these protein kinases were found. Protein staining indicated that postmortem proteolysis, particularly of high-molecular-mass proteins, was prominent in deeply located, subcortical regions in the human brain. Our results indicate that it is feasible to use human postmortem brain samples, when obtained under carefully controlled conditions, for qualitative studies on brain protein phosphorylation. Such studies should be of value in studies on human neurological and/or psychiatric disorders

  17. Nuclear abundances and evolution of the interstellar medium

    International Nuclear Information System (INIS)

    Wannier, P.G.

    1980-01-01

    Observations of molecular and elemental abundances in the interstellar medium (ISM) are reviewed, with special attention given to isotope ratios. The derivation of molecular isotope abundances for the ISM is discussed, along with H and C fractionation. Millimeter- and centimeter-wave spectra of giant clouds are examined with respect to isotope abundances of C, O, N, Si, S, and D. Evidence for the current enrichment of the ISM by mass loss from evolved stars is considered, together with chemical abundance gradients in H II regions and planetary nebulae. Cosmic-ray observations pertaining to abundances in the ISM are summarized, with emphasis on available results for Ne, Mg, Si, Fe, and Ni. The observations reviewed are shown to support arguments in favor of: (1) the cosmological production of D and He-3 (2) the production of the CNO elements by hydrostatic hydrogen burning (3) the nucleosynthesis of Ne, Mg, Si, S, Fe, and Ni as a result of He burning (4) solar abundances of interstellar S, Fe, and Ni and (5) a direct association between observed inhomogeneities in the ISM and mass loss from evolved stellar objects

  18. Pathogenic Streptomyces spp. abundance affected by potato cultivars.

    Science.gov (United States)

    Nahar, Kamrun; Goyer, Claudia; Zebarth, Bernie J; Burton, David L; Whitney, Sean

    2018-04-16

    Potato cultivars vary in their tolerance to common scab (CS), however how they affect CS-causing Streptomyces spp. populations over time is poorly understood. This study investigated the effects of potato cultivar on pathogenic Streptomyces spp. abundance, measured using quantitative PCR, in three spatial locations in a CS-infested field: 1) soil close to the plant (SCP); 2) rhizosphere (RS); and 3) geocaulosphere (GS) soils. Two tolerant (Gold Rush, Hindenburg) and two susceptible cultivars (Green Mountain, Agria) were tested. The abundance of pathogenic Streptomyces spp. significantly increased in late August compared with other dates in RS of susceptible cultivars in both years. Abundance of pathogenic Streptomyces spp., when averaged over locations and time, was significantly greater in susceptible cultivars compared with tolerant cultivars in 2014. Principal coordinates analysis showed that SCP and RS soil properties (pH, organic carbon and nitrogen concentrations) explained 68% and 76% of total variation in Streptomyces spp. abundance among cultivars in 2013, respectively, suggesting that cultivars influenced CS pathogen growth conditions. The results suggested that the genetic background of potato cultivars influenced the abundance of pathogenic Streptomyces spp., with 5 to 6 times more abundant Streptomyces spp. in RS of susceptible cultivars compared with tolerant cultivars, which would result in substantially more inoculum left in the field after harvest.  .

  19. CHROMOSPHERIC MODELS AND THE OXYGEN ABUNDANCE IN GIANT STARS

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-04-10

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

  20. DIRECT EVALUATION OF THE HELIUM ABUNDANCES IN OMEGA CENTAURI

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-08-20

    A direct measure of the helium abundances from the near-infrared transition of He I at 1.08 {mu}m is obtained for two nearly identical red giant stars in the globular cluster Omega Centauri. One star exhibits the He I line; the line is weak or absent in the other star. Detailed non-local thermal equilibrium semi-empirical models including expansion in spherical geometry are developed to match the chromospheric H{alpha}, H{beta}, and Ca II K lines, in order to predict the helium profile and derive a helium abundance. The red giant spectra suggest a helium abundance of Y {<=} 0.22 (LEID 54064) and Y = 0.39-0.44 (LEID 54084) corresponding to a difference in the abundance {Delta}Y {>=} 0.17. Helium is enhanced in the giant star (LEID 54084) that also contains enhanced aluminum and magnesium. This direct evaluation of the helium abundances gives observational support to the theoretical conjecture that multiple populations harbor enhanced helium in addition to light elements that are products of high-temperature hydrogen burning. We demonstrate that the 1.08 {mu}m He I line can yield a helium abundance in cool stars when constraints on the semi-empirical chromospheric model are provided by other spectroscopic features.

  1. DETERMINING THE INITIAL HELIUM ABUNDANCE OF THE SUN

    International Nuclear Information System (INIS)

    Serenelli, Aldo M.; Basu, Sarbani

    2010-01-01

    We determine the dependence of the initial helium abundance and the present-day helium abundance in the convective envelope of solar models (Y ini and Y surf , respectively) on the parameters that are used to construct the models. We do so by using reference standard solar models (SSMs) to compute the power-law coefficients of the dependence of Y ini and Y surf on the input parameters. We use these dependencies to determine the correlation between Y ini and Y surf and use this correlation to eliminate uncertainties in Y ini from all solar model input parameters except the microscopic diffusion rate. We find an expression for Y ini that depends only on Y surf and the diffusion rate. By adopting the helioseismic determination of solar surface helium abundance, Y surf sun = 0.2485 ± 0.0035, and an uncertainty of 20% for the diffusion rate, we find that the initial solar helium abundance, Y ini sun , is 0.278 ± 0.006 independently of the reference SSMs (and particularly on the adopted solar abundances) used in the derivation of the correlation between Y ini and Y surf . When non-SSMs with extra mixing are used, then we derive Y ini sun = 0.273 ± 0.006. In both cases, the derived Y ini sun value is higher than that directly derived from solar model calibrations when the low-metallicity solar abundances (e.g., by Asplund et al.) are adopted in the models.

  2. 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

    2015-01-01

    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. PMID:25290506

  3. SULFUR ABUNDANCES IN THE ORION ASSOCIATION B STARS

    International Nuclear Information System (INIS)

    Daflon, Simone; Cunha, Katia; De la Reza, Ramiro; Holtzman, Jon; Chiappini, Cristina

    2009-01-01

    Sulfur abundances are derived for a sample of 10 B main-sequence star members of the Orion association. The analysis is based on LTE plane-parallel model atmospheres and non-LTE line formation theory by means of a self-consistent spectrum synthesis analysis of lines from two ionization states of sulfur, S II and S III. The observations are high-resolution spectra obtained with the ARCES spectrograph at the Apache Point Observatory. The abundance distribution obtained for the Orion targets is homogeneous within the expected errors in the analysis: A(S) = 7.15 ± 0.05. This average abundance result is in agreement with the recommended solar value (both from modeling of the photospheres in one-dimensional and three-dimensional, and meteorites) and indicates that little, if any, chemical evolution of sulfur has taken place in the last ∼4.5 billion years. The sulfur abundances of the young stars in Orion are found to agree well with results for the Orion Nebulae, and place strong constraints on the amount of sulfur depletion onto grains as being very modest or nonexistent. The sulfur abundances for Orion are consistent with other measurements at a similar galactocentric radius: combined with previous results for other OB-type stars produce a relatively shallow sulfur abundance gradient with a slope of -0.037 ± 0.012 dex kpc -1 .

  4. Abundance and genetic diversity of microbial polygalacturonase and pectate lyase in the sheep rumen ecosystem.

    Directory of Open Access Journals (Sweden)

    Peng Yuan

    Full Text Available Efficient degradation of pectin in the rumen is necessary for plant-based feed utilization. The objective of this study was to characterize the diversity, abundance, and functions of pectinases from microorganisms in the sheep rumen.A total of 103 unique fragments of polygalacturonase (PF00295 and pectate lyase (PF00544 and PF09492 genes were retrieved from microbial DNA in the rumen of a Small Tail Han sheep, and 66% of the sequences of these fragments had low identities (<65% with known sequences. Phylogenetic tree building separated the PF00295, PF00544, and PF09492 sequences into five, three, and three clades, respectively. Cellulolytic and noncellulolytic Butyrivibrio, Prevotella, and Fibrobacter species were the major sources of the pectinases. The two most abundant pectate lyase genes were cloned, and their protein products, expressed in Escherichia coli, were characterized. Both enzymes probably act extracellularly as their nucleotide sequences contained signal sequences, and they had optimal activities at the ruminal physiological temperature and complementary pH-dependent activity profiles.This study reveals the specificity, diversity, and abundance of pectinases in the rumen ecosystem and provides two additional ruminal pectinases for potential industrial use under physiological conditions.

  5. A hybrid approach to protein differential expression in mass spectrometry-based proteomics

    KAUST Repository

    Wang, X.; Anderson, G. A.; Smith, R. D.; Dabney, A. R.

    2012-01-01

    MOTIVATION: Quantitative mass spectrometry-based proteomics involves statistical inference on protein abundance, based on the intensities of each protein's associated spectral peaks. However, typical MS-based proteomics datasets have substantial

  6. Mass spectrometric identification of isoforms of PR proteins in xylem sap of fungus-infected tomato

    NARCIS (Netherlands)

    Rep, Martijn; Dekker, Henk L.; Vossen, Jack H.; de Boer, Albert D.; Houterman, Petra M.; Speijer, Dave; Back, Jaap W.; de Koster, Chris G.; Cornelissen, Ben J. C.

    2002-01-01

    The protein content of tomato (Lycopersicon esculentum) xylem sap was found to change dramatically upon infection with the vascular wilt fungus Fusarium oxysporum. Peptide mass fingerprinting and mass spectrometric sequencing were used to identify the most abundant proteins appearing during

  7. Inferring invasive species abundance using removal data from management actions

    Science.gov (United States)

    Davis, Amy J.; Hooten, Mevin B.; Miller, Ryan S.; Farnsworth, Matthew L.; Lewis, Jesse S.; Moxcey, Michael; Pepin, Kim M.

    2016-01-01

    Evaluation of the progress of management programs for invasive species is crucial for demonstrating impacts to stakeholders and strategic planning of resource allocation. Estimates of abundance before and after management activities can serve as a useful metric of population management programs. However, many methods of estimating population size are too labor intensive and costly to implement, posing restrictive levels of burden on operational programs. Removal models are a reliable method for estimating abundance before and after management using data from the removal activities exclusively, thus requiring no work in addition to management. We developed a Bayesian hierarchical model to estimate abundance from removal data accounting for varying levels of effort, and used simulations to assess the conditions under which reliable population estimates are obtained. We applied this model to estimate site-specific abundance of an invasive species, feral swine (Sus scrofa), using removal data from aerial gunning in 59 site/time-frame combinations (480–19,600 acres) throughout Oklahoma and Texas, USA. Simulations showed that abundance estimates were generally accurate when effective removal rates (removal rate accounting for total effort) were above 0.40. However, when abundances were small (<50) the effective removal rate needed to accurately estimates abundances was considerably higher (0.70). Based on our post-validation method, 78% of our site/time frame estimates were accurate. To use this modeling framework it is important to have multiple removals (more than three) within a time frame during which demographic changes are minimized (i.e., a closed population; ≤3 months for feral swine). Our results show that the probability of accurately estimating abundance from this model improves with increased sampling effort (8+ flight hours across the 3-month window is best) and increased removal rate. Based on the inverse relationship between inaccurate abundances and

  8. Inferring invasive species abundance using removal data from management actions.

    Science.gov (United States)

    Davis, Amy J; Hooten, Mevin B; Miller, Ryan S; Farnsworth, Matthew L; Lewis, Jesse; Moxcey, Michael; Pepin, Kim M

    2016-10-01

    Evaluation of the progress of management programs for invasive species is crucial for demonstrating impacts to stakeholders and strategic planning of resource allocation. Estimates of abundance before and after management activities can serve as a useful metric of population management programs. However, many methods of estimating population size are too labor intensive and costly to implement, posing restrictive levels of burden on operational programs. Removal models are a reliable method for estimating abundance before and after management using data from the removal activities exclusively, thus requiring no work in addition to management. We developed a Bayesian hierarchical model to estimate abundance from removal data accounting for varying levels of effort, and used simulations to assess the conditions under which reliable population estimates are obtained. We applied this model to estimate site-specific abundance of an invasive species, feral swine (Sus scrofa), using removal data from aerial gunning in 59 site/time-frame combinations (480-19,600 acres) throughout Oklahoma and Texas, USA. Simulations showed that abundance estimates were generally accurate when effective removal rates (removal rate accounting for total effort) were above 0.40. However, when abundances were small (removal rate needed to accurately estimates abundances was considerably higher (0.70). Based on our post-validation method, 78% of our site/time frame estimates were accurate. To use this modeling framework it is important to have multiple removals (more than three) within a time frame during which demographic changes are minimized (i.e., a closed population; ≤3 months for feral swine). Our results show that the probability of accurately estimating abundance from this model improves with increased sampling effort (8+ flight hours across the 3-month window is best) and increased removal rate. Based on the inverse relationship between inaccurate abundances and inaccurate removal

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

    International Nuclear Information System (INIS)

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

    2014-01-01

    We present radial velocities, equivalent widths, model atmosphere parameters, and abundances or upper limits for 53 species of 48 elements derived from high resolution optical spectroscopy of 313 metal-poor stars. A majority of these stars were selected from the metal-poor candidates of the HK Survey of Beers, Preston, and Shectman. We derive detailed abundances for 61% of these stars for the first time. Spectra were obtained during a 10 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. 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.

  11. The shape of oxygen abundance profiles explored with MUSE

    Science.gov (United States)

    Sánchez, S. F.; Sánchez-Menguiano, L.; Pérez, I.

    2017-11-01

    We characterise the oxygen abundance radial distribution of a sample of 102 spiral galaxies observed with VLT/MUSE using the O3N2 calibrator. The high spatial resolution of the data allows us to detect 14345 HII regions with the same image quality as with photometric data, avoiding any dilution effect. We develop a new methodology to automatically fit the abundance radial profiles, finding that 55 galaxies of the sample exhibit a single negative gradient. The remaining 47 galaxies also display, as well as this negative trend, either an inner drop in the abundances (21), an outer flattening (10) or both (16), which suggests that these features are a common property of disc galaxies. The presence and depth of the inner drop depends on the stellar mass of the galaxies with the most massive systems presenting the deepest abundance drops, while there is no such dependence for the outer flattening. We find that the inner drop appears always around 0.5 r_e, while the position of the outer flattening varies over a wide range of galactocentric distances. Regarding the main negative gradient, we find a characteristic slope of α_{O/H} = - 0.10±0.03 dex/r_e. This slope is independent of the presence of bars and the density of the environment. However, when inner drops or outer flattenings are detected, slightly steeper gradients are observed. This suggests that radial motions might play an important role in shaping the abundance profiles. We define a new normalisation scale (r_{O/H}) for the radial profiles based on the characteristic abundance gradient, with which all the galaxies show a similar position for the inner drop (˜0.5 r_{O/H}) and the outer flattening (˜1.5 r_{O/H}).Finally, we find no significant dependence of the dispersion around the negative gradient with any galaxy property, with values compatible with the uncertainties of the derived abundances.

  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.; 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. 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.

  14. Hepatic NADlevels and NAMPT abundance are unaffected during prolonged high-fat diet consumption in C57BL/6JBomTac mice

    DEFF Research Database (Denmark)

    Dall, Morten; Penke, Melanie; Sulek, Karolina

    2018-01-01

    +have been reported to be dependent on age and body composition. The aim of the present study was to identify time course-dependent changes in hepatic NAD content and NAD+salvage capacity in mice challenged with a high-fat diet (HFD). We fed 7-week-old C57BL/6JBomTac male mice either regular chow or a 60...... regardless of diet. NAMPT protein abundance did not change with age or diet. HFD consumption caused a severe decrease in protein lysine malonylation after six weeks, which persisted throughout the experiment. This decrease was not associated with changes in SIRT5 abundance. In conclusion, hepatic NAD...

  15. Embryogenic competence acquisition in sugarcane callus is associated with differential H+ pump abundance and activity.

    Science.gov (United States)

    Passamani, Lucas Z; Bertolazi, Amanda A; Ramos, Alessandro C; Santa-Catarina, Claudete; Thelen, Jay J; Silveira, Vanildo

    2018-06-22

    Somatic embryogenesis is an important biological process in several plant species, including sugarcane. Proteomics approaches have shown that H + pumps are differentially regulated during somatic embryogenesis; however, the relationship between H + flux and embryogenic competence is still unclear. This work aimed to elucidate the association between extracellular H + flux and somatic embryo maturation in sugarcane. We performed a microsomal proteomics analysis and analyzed changes in extracellular H + flux and H + pump (P-H + -ATPase, V-H + -ATPase and H + -PPase) activity in embryogenic and non-embryogenic callus. A total of 657 proteins were identified, 16 of which were H + pumps. We observed that P-H + -ATPase and H + -PPase were more abundant in embryogenic callus. Compared with non-embryogenic callus, embryogenic callus showed higher H + influx, especially on maturation day 14, as well as higher H+ pump activity (mainly P-H+-ATPase and H+-PPase activity). H+-PPase appears to be the major H + pump in embryogenic callus during somatic embryo formation, functioning in both vacuole acidification and PPi homeostasis. These results provide evidence for an association between higher H + pump protein abundance and, consequently, higher H + flux and embryogenic competence acquisition in the callus of sugarcane, allowing for optimization of the somatic embryo conversion process by modulating the activities of these H + pumps.

  16. ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq.

    Science.gov (United States)

    Kucukural, Alper; Özadam, Hakan; Singh, Guramrit; Moore, Melissa J; Cenik, Can

    2013-10-01

    Unlike DNA, RNA abundances can vary over several orders of magnitude. Thus, identification of RNA-protein binding sites from high-throughput sequencing data presents unique challenges. Although peak identification in ChIP-Seq data has been extensively explored, there are few bioinformatics tools tailored for peak calling on analogous datasets for RNA-binding proteins. Here we describe ASPeak (abundance sensitive peak detection algorithm), an implementation of an algorithm that we previously applied to detect peaks in exon junction complex RNA immunoprecipitation in tandem experiments. Our peak detection algorithm yields stringent and robust target sets enabling sensitive motif finding and downstream functional analyses. ASPeak is implemented in Perl as a complete pipeline that takes bedGraph files as input. ASPeak implementation is freely available at https://sourceforge.net/projects/as-peak under the GNU General Public License. ASPeak can be run on a personal computer, yet is designed to be easily parallelizable. ASPeak can also run on high performance computing clusters providing efficient speedup. The documentation and user manual can be obtained from http://master.dl.sourceforge.net/project/as-peak/manual.pdf.

  17. 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.

  18. 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

  19. Ecological interactions and the distribution, abundance, and diversity of sponges.

    Science.gov (United States)

    Wulff, Janie

    2012-01-01

    Although abiotic factors may be important first-order filters dictating which sponge species can thrive at a particular site, ecological interactions can play substantial roles influencing distribution and abundance, and thus diversity. Ecological interactions can modify the influences of abiotic factors both by further constraining distribution and abundance due to competitive or predatory interactions and by expanding habitat distribution or abundance due to beneficial interactions that ameliorate otherwise limiting circumstances. It is likely that the importance of ecological interactions has been greatly underestimated because they tend to only be revealed by experiments and time-series observations in the field. Experiments have revealed opportunistic predation to be a primary enforcer of sponge distribution boundaries that coincide with habitat boundaries in several systems. Within habitats, by contrast, dramatic effects of predators on sponge populations seem to occur primarily in cases of unusually high recruitment rates or unusually low mortality rates for the predators, which are often specialists on the sponge species affected. Competitive interactions have been demonstrated to diminish populations or exclude sponge species from a habitat in only a few cases. Cases in which competitive interactions have appeared obvious have often turned out to be neutral or even beneficial interactions when observed over time. Especially striking in this regard are sponge-sponge interactions in dense sponge-dominated communities, which may promote the continued coexistence of all participating species. Mutualistic symbioses of sponges with other animals, plants, or macroalgae have been demonstrated to increase abundance, habitat distribution, and diversity of all participants. Symbiotic microbes can enhance sponge distribution and abundance but also render their hosts more vulnerable to environmental changes. And while photosynthetic symbionts can boost growth and

  20. Normalization and microbial differential abundance strategies depend upon data characteristics.

    Science.gov (United States)

    Weiss, Sophie; Xu, Zhenjiang Zech; Peddada, Shyamal; Amir, Amnon; Bittinger, Kyle; Gonzalez, Antonio; Lozupone, Catherine; Zaneveld, Jesse R; Vázquez-Baeza, Yoshiki; Birmingham, Amanda; Hyde, Embriette R; Knight, Rob

    2017-03-03

    Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data contains many zeros. Although we are typically interested in comparing relative abundance of taxa in the ecosystem of two or more groups, we can only measure the taxon relative abundance in specimens obtained from the ecosystems. Because the comparison of taxon relative abundance in the specimen is not equivalent to the comparison of taxon relative abundance in the ecosystems, this presents a special challenge. Second, because the relative abundance of taxa in the specimen (as well as in the ecosystem) sum to 1, these are compositional data. Because the compositional data are constrained by the simplex (sum to 1) and are not unconstrained in the Euclidean space, many standard methods of analysis are not applicable. Here, we evaluate how these challenges impact the performance of existing normalization methods and differential abundance analyses. Effects on normalization: Most normalization methods enable successful clustering of samples according to biological origin when the groups differ substantially in their overall microbial composition. Rarefying more clearly clusters samples according to biological origin than other normalization techniques do for ordination metrics based on presence or absence. Alternate normalization measures are potentially vulnerable to artifacts due to library size. Effects on differential abundance testing: We build on a previous work to evaluate seven proposed statistical methods using rarefied as well as raw data. Our simulation studies suggest that the false discovery rates of many differential abundance-testing methods are not increased by rarefying itself, although of course rarefying results in a loss of sensitivity due to elimination of a portion of available data. For groups with large (~10×) differences in the average

  1. 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

  2. ABUNDANCES IN THE LOCAL REGION. I. G AND K GIANTS

    Energy Technology Data Exchange (ETDEWEB)

    Luck, R. Earle, E-mail: rel2@case.edu [Department of Astronomy, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106-7215 (United States)

    2015-09-15

    Parameters and abundances for 1133 stars of spectral types F, G, and K of luminosity class III have been derived. In terms of stellar parameters, the primary point of interest is the disagreement between gravities derived with masses determined from isochrones, and gravities determined from an ionization balance. This is not a new result per se, but the size of this sample emphasizes the severity of the problem. A variety of arguments led to the selection of the ionization-balance gravity as the working value. The derived abundances indicate that the giants in the solar region have Sun-like total abundances and abundance ratios. Stellar evolution indicators have also been investigated with the Li abundances and the [C/Fe] and C/O ratios, indicating that standard processing has been operating in these stars. The more salient result for stellar evolution is that the [C/Fe] data across the red-giant clump indicates the presence of mass-dependent mixing in accord with standard stellar evolution predictions.

  3. Book review: A new view on the species abundance distribution

    Science.gov (United States)

    DeAngelis, Donald L.

    2018-01-01

    The sampled relative abundances of species of a taxonomic group, whether birds, trees, or moths, in a natural community at a particular place vary in a way that suggests a consistent underlying pattern, referred to as the species abundance distribution (SAD). Preston [1] conjectured that the numbers of species, plotted as a histogram of logarithmic abundance classes called octaves, seemed to fit a lognormal distribution; that is, the histograms look like normal distributions, although truncated on the left-hand, or low-species-abundance, end. Although other specific curves for the SAD have been proposed in the literature, Preston’s lognormal distribution is widely cited in textbooks and has stimulated attempts at explanation. An important aspect of Preston’s lognormal distribution is the ‘veil line’, a vertical line drawn exactly at the point of the left-hand truncation in the distribution, to the left of which would be species missing from the sample. Dewdney rejects the lognormal conjecture. Instead, starting with the long-recognized fact that the number of species sampled from a community, when plotted as histograms against population abundance, resembles an inverted J, he presents a mathematical description of an alternative that he calls the ‘J distribution’, a hyperbolic density function truncated at both ends. When multiplied by species richness, R, it becomes the SAD of the sample.

  4. Determination of lunar ilmenite abundances from remotely sensed data

    Science.gov (United States)

    Larson, Stephen M.; Johnson, Jeffrey R.; Singer, Robert B.

    1991-01-01

    The mineral ilmenite (FeTiO3) was found in abundance in lunar mare soils returned during the Apollo project. Lunar ilmenite often contains greater than 50 weight-percent titanium dioxide (TiO2), and is a primary potential resource for oxygen and other raw materials to supply future lunar bases. Chemical and spectroscopic analysis of the returned lunar soils produced an empirical function that relates the spectral reflectance ratio at 400 and 560 nm to the weight percent abundance of TiO2. This allowed mapping of the lunar TiO2 distribution using telescopic vidicon multispectral imaging from the ground; however, the time variant photometric response of the vidicon detectors produced abundance uncertainties of at least 2 to 5 percent. Since that time, solid-state charge-coupled device (CCD) detector technology capable of much improved photometric response has become available. An investigation of the lunar TiO2 distribution was carried out utilizing groundbased telescopic CCD multispectral imagery and spectroscopy. The work was approached in phases to develop optimum technique based upon initial results. The goal is to achieve the best possible TiO2 abundance maps from the ground as a precursor to lunar orbiter and robotic sample return missions, and to produce a better idea of the peak abundances of TiO2 for benefaction studies. These phases and the results are summarized.

  5. The invasive ant, Solenopsis invicta, reduces herpetofauna richness and abundance

    Science.gov (United States)

    Allen, Craig R.; Birge, Hannah E.; Slater, J.; Wiggers, E.

    2017-01-01

    Amphibians and reptiles are declining globally. One potential cause of this decline includes impacts resulting from co-occurrence with non-native red imported fire ant, Solenopsis invicta. Although a growing body of anecdotal and observational evidence from laboratory experiments supports this hypothesis, there remains a lack of field scale manipulations testing the effect of fire ants on reptile and amphibian communities. We addressed this gap by measuring reptile and amphibian (“herpetofauna”) community response to successful fire ant reductions over the course of 2 years following hydramethylnon application to five 100–200 ha plots in southeastern coastal South Carolina. By assessing changes in relative abundance and species richness of herpetofauna in response to fire ant reductions, we were able to assess whether some species were particularly vulnerable to fire ant presence, and whether this sensitivity manifested at the community level. We found that herpetofauna abundance and species richness responded positively to fire ant reductions. Our results document that even moderate populations of red imported fire ants decrease both the abundance and diversity of herpetofauna. Given global herpetofauna population declines and continued spread of fire ants, there is urgency to understand the impacts of fire ants beyond anecdotal and singles species studies. Our results provides the first community level investigation addressing these dynamics, by manipulating fire ant abundance to reveal a response in herpetofauna species abundance and richness.

  6. 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.

  7. Carbon and oxygen abundances across the Hertzsprung gap

    Energy Technology Data Exchange (ETDEWEB)

    Adamczak, Jens; Lambert, David L., E-mail: adamczak@astro.as.utexas.edu, E-mail: dll@astro.as.utexas.edu [McDonald Observatory, The University of Texas, Austin, TX 78712 (United States)

    2014-08-10

    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 M{sub ☉} 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 T{sub eff} < 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 Hertzsprung gap could be found before the homogenization of their atmospheres by the first dredge-up.

  8. Carbon and oxygen abundances across the Hertzsprung gap

    International Nuclear Information System (INIS)

    Adamczak, Jens; Lambert, David L.

    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 M ☉ 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 T eff < 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 Hertzsprung gap could be found before the homogenization of their atmospheres by the first dredge-up.

  9. Barcoded pyrosequencing analysis of the microbial community in a simulator of the human gastrointestinal tract showed a colon region-specific microbiota modulation for two plant-derived polysaccharide blends.

    Science.gov (United States)

    Marzorati, Massimo; Maignien, Lois; Verhelst, An; Luta, Gabriela; Sinnott, Robert; Kerckhof, Frederiek Maarten; Boon, Nico; Van de Wiele, Tom; Possemiers, Sam

    2013-02-01

    The combination of a Simulator of the Human Intestinal Microbial Ecosystem with ad hoc molecular techniques (i.e. pyrosequencing, denaturing gradient gel electrophoresis and quantitative PCR) allowed an evaluation of the extent to which two plant polysaccharide supplements could modify a complex gut microbial community. The presence of Aloe vera gel powder and algae extract in product B as compared to the standard blend (product A) improved its fermentation along the entire simulated colon. The potential extended effect of product B in the simulated distal colon, as compared to product A, was confirmed by: (i) the separate clustering of the samples before and after the treatment in the phylogenetic-based dendrogram and OTU-based PCoA plot only for product B; (ii) a higher richness estimator (+33 vs. -36 % of product A); and (iii) a higher dynamic parameter (21 vs. 13 %). These data show that the combination of well designed in vitro simulators with barcoded pyrosequencing is a powerful tool for characterizing changes occurring in the gut microbiota following a treatment. However, for the quantification of low-abundance species-of interest because of their relationship to potential positive health effects (i.e. bifidobacteria or lactobacilli)-conventional molecular ecological approaches, such as PCR-DGGE and qPCR, still remain a very useful complementary tool.

  10. Life Stage-specific Proteomes of Legionella pneumophila Reveal a Highly Differential Abundance of Virulence-associated Dot/Icm effectors*

    Science.gov (United States)

    Aurass, Philipp; Gerlach, Thomas; Becher, Dörte; Voigt, Birgit; Karste, Susanne; Bernhardt, Jörg; Riedel, Katharina; Hecker, Michael; Flieger, Antje

    2016-01-01

    Major differences in the transcriptional program underlying the phenotypic switch between exponential and post-exponential growth of Legionella pneumophila were formerly described characterizing important alterations in infection capacity. Additionally, a third state is known where the bacteria transform in a viable but nonculturable state under stress, such as starvation. We here describe phase-related proteomic changes in exponential phase (E), postexponential phase (PE) bacteria, and unculturable microcosms (UNC) containing viable but nonculturable state cells, and identify phase-specific proteins. We present data on different bacterial subproteomes of E and PE, such as soluble whole cell proteins, outer membrane-associated proteins, and extracellular proteins. In total, 1368 different proteins were identified, 922 were quantified and 397 showed differential abundance in E/PE. The quantified subproteomes of soluble whole cell proteins, outer membrane-associated proteins, and extracellular proteins; 841, 55, and 77 proteins, respectively, were visualized in Voronoi treemaps. 95 proteins were quantified exclusively in E, such as cell division proteins MreC, FtsN, FtsA, and ZipA; 33 exclusively in PE, such as motility-related proteins of flagellum biogenesis FlgE, FlgK, and FliA; and 9 exclusively in unculturable microcosms soluble whole cell proteins, such as hypothetical, as well as transport/binding-, and metabolism-related proteins. A high frequency of differentially abundant or phase-exclusive proteins was observed among the 91 quantified effectors of the major virulence-associated protein secretion system Dot/Icm (> 60%). 24 were E-exclusive, such as LepA/B, YlfA, MavG, Lpg2271, and 13 were PE-exclusive, such as RalF, VipD, Lem10. The growth phase-related specific abundance of a subset of Dot/Icm virulence effectors was confirmed by means of Western blotting. We therefore conclude that many effectors are predominantly abundant at either E or PE which suggests

  11. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Cosmological abundance of the QCD axion coupled to hidden photons

    Science.gov (United States)

    Kitajima, Naoya; Sekiguchi, Toyokazu; Takahashi, Fuminobu

    2018-06-01

    We study the cosmological evolution of the QCD axion coupled to hidden photons. For a moderately strong coupling, the motion of the axion field leads to an explosive production of hidden photons by tachyonic instability. We use lattice simulations to evaluate the cosmological abundance of the QCD axion. In doing so, we incorporate the backreaction of the produced hidden photons on the axion dynamics, which becomes significant in the non-linear regime. We find that the axion abundance is suppressed by at most O (102) for the decay constant fa =1016GeV, compared to the case without the coupling. For a sufficiently large coupling, the motion of the QCD axion becomes strongly damped, and as a result, the axion abundance is enhanced. Our results show that the cosmological upper bound on the axion decay constant can be relaxed by a few hundred for a certain range of the coupling to hidden photons.

  13. FLUORINE ABUNDANCES IN GALACTIC ASYMPTOTIC GIANT BRANCH STARS

    International Nuclear Information System (INIS)

    Abia, C.; Cristallo, S.; DomInguez, I.; Cunha, K.; Hinkle, K.; Smith, V. V.; De Laverny, P.; Recio-Blanco, A.; Eriksson, K.; Wahlin, R.; Gialanella, L.; Imbriani, G.; Straniero, O.

    2010-01-01

    An analysis of the fluorine abundance in Galactic asymptotic giant branch (AGB) carbon stars (24 N-type, 5 SC-type, and 5 J-type) is presented. This study uses the state-of-the-art carbon-rich atmosphere models and improved atomic and molecular line lists in the 2.3 μm region. Significantly lower F abundances are obtained in comparison to previous studies in the literature. This difference is mainly due to molecular blends. In the case of carbon stars of SC-type, differences in the model atmospheres are also relevant. The new F enhancements are now in agreement with the most recent theoretical nucleosynthesis models in low-mass AGB stars, solving the long-standing problem of F in Galactic AGB stars. Nevertheless, some SC-type carbon stars still show larger F abundances than predicted by stellar models. The possibility that these stars are of larger mass is briefly discussed.

  14. Stellar photospheric abundances as a probe of discs and planets

    Science.gov (United States)

    Jermyn, Adam S.; Kama, Mihkel

    2018-06-01

    Protoplanetary discs, debris discs, and disrupted or evaporating planets can all feed accretion on to stars. The photospheric abundances of such stars may then reveal the composition of the accreted material. This is especially likely in B to mid-F type stars, which have radiative envelopes and hence less bulk-photosphere mixing. We present a theoretical framework (CAM), considering diffusion, rotation, and other stellar mixing mechanisms to describe how the accreted material interacts with the bulk of the star. This allows the abundance pattern of the circumstellar material to be calculated from measured stellar abundances and parameters (vrot, Teff). We discuss the λ Boötis phenomenon and the application of CAM on stars hosting protoplanetary discs (HD 100546, HD 163296), debris discs (HD 141569, HD 21997), and evaporating planets (HD 195689/KELT-9).

  15. Primordial helium abundance determination using sulphur as metallicity tracer

    Science.gov (United States)

    Fernández, Vital; Terlevich, Elena; Díaz, Angeles I.; Terlevich, Roberto; Rosales-Ortega, F. F.

    2018-05-01

    The primordial helium abundance YP is calculated using sulphur as metallicity tracer in the classical methodology (with YP as an extrapolation of Y to zero metals). The calculated value, YP, S = 0.244 ± 0.006, is in good agreement with the estimate from the Planck experiment, as well as, determinations in the literature using oxygen as the metallicity tracer. The chemical analysis includes the sustraction of the nebular continuum and of the stellar continuum computed from simple stellar population synthesis grids. The S+2 content is measured from the near infrared [SIII]λλ9069Å, 9532Å lines, while an ICF(S3 +) is proposed based on the Ar3 +/Ar2 + fraction. Finally, we apply a multivariable linear regression using simultaneously oxygen, nitrogen and sulphur abundances for the same sample to determine the primordial helium abundance resulting in YP - O, N, S = 0.245 ± 0.007.

  16. Elemental abundances of intermediate-age open cluster NGC 3680

    Science.gov (United States)

    Mitschang, A. W.; De Silva, G. M.; Zucker, D. B.

    2012-06-01

    We present a new abundance analysis of the intermediate-age Galactic open cluster NGC 3680, based on high-resolution, high signal-to-noise ratio 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 anticorrelation 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 asymptotic giant branch nucleosynthesis models, suggesting that the r process played a significant role in the generation of both La and Nd in this cluster.

  17. Abundance of carbon and magnesium in the Orion nebula

    International Nuclear Information System (INIS)

    Perinotto, M.; Patriarchi, P.

    1980-01-01

    The Orion nebula has been observed in two positions with IUE (International Ultraviolet Explorer) in the low-resolution mode (approx.7 A) and in the spectral range 1150--3200 A. Emission lines of C II], C III], [O II], and He I have been measured and used to determine what is probably the first reliable abundance of carbon in H II regions. The logarithmic total abundance of carbon is found to be 8.4 close to the solar value. In contrast with the situation in the planetary nebula of similar excitation, IC 418, where the resonance Mg II lambda2800 line is observed to be relatively strong, in the Orion nebula the lambda2800 line is not detectable. an upper limit for the magnesium abundance of the order of 10 times smaller than in the Sun is suggested

  18. Effect of nuclear reaction rates on primordial abundances

    International Nuclear Information System (INIS)

    Mishra, Abhishek; Basu, D.N.

    2011-01-01

    The theoretical predictions of the primordial abundances of elements in the big-bang nucleosynthesis (BBN) are dominated by uncertainties in the input nuclear reaction rates. The effect of modifying these reaction rates on light element abundance yields in BBN by replacing the thirty-five reaction rates out of the existing eighty-eight has been investigated. Also the study have been taken of these yields as functions of evolution time or temperature. Here it has been found that using these new reaction rates results in only a little increase in helium mass fraction over that obtained previously in BBN calculations. This allows insights into the role of the nuclear reaction rates in the setting of the neutron-to-proton ratio during the BBN epoch. We observe that most of these nuclear reactions have minimal effect on the standard BBN abundance yields of 6 Li and 7 Li

  19. SILICON AND OXYGEN ABUNDANCES IN PLANET-HOST STARS

    International Nuclear Information System (INIS)

    Brugamyer, Erik; Dodson-Robinson, Sarah E.; Cochran, William D.; Sneden, Christopher

    2011-01-01

    The positive correlation between planet detection rate and host star iron abundance lends strong support to the core accretion theory of planet formation. However, iron is not the most significant mass contributor to the cores of giant planets. Since giant planet cores are thought to grow from silicate grains with icy mantles, the likelihood of gas giant formation should depend heavily on the oxygen and silicon abundance of the planet formation environment. Here we compare the silicon and oxygen abundances of a set of 76 planet hosts and a control sample of 80 metal-rich stars without any known giant planets. Our new, independent analysis was conducted using high resolution, high signal-to-noise data obtained at McDonald Observatory. Because we do not wish to simply reproduce the known planet-metallicity correlation, we have devised a statistical method for matching the underlying [Fe/H] distributions of our two sets of stars. We find a 99% probability that planet detection rate depends on the silicon abundance of the host star, over and above the observed planet-metallicity correlation. We do not detect any such correlation for oxygen. Our results would thus seem to suggest that grain nucleation, rather than subsequent icy mantle growth, is the important limiting factor in forming giant planets via core accretion. Based on our results and interpretation, we predict that planet detection should correlate with host star abundance for refractory elements responsible for grain nucleation and that no such trends should exist for the most abundant volatile elements responsible for icy mantle growth.

  20. One Percent Determination of the Primordial Deuterium Abundance

    Science.gov (United States)

    Cooke, Ryan J.; Pettini, Max; Steidel, Charles C.

    2018-03-01

    We report a reanalysis of a near-pristine absorption system, located at a redshift {z}abs}=2.52564 toward the quasar Q1243+307, based on the combination of archival and new data obtained with the HIRES echelle spectrograph on the Keck telescope. This absorption system, which has an oxygen abundance [O/H] = ‑2.769 ± 0.028 (≃1/600 of the solar abundance), is among the lowest metallicity systems currently known where a precise measurement of the deuterium abundance is afforded. Our detailed analysis of this system concludes, on the basis of eight D I absorption lines, that the deuterium abundance of this gas cloud is {log}}10({{D}}/{{H}})=-4.622+/- 0.015, which is in very good agreement with the results previously reported by Kirkman et al., but with an improvement on the precision of this single measurement by a factor of ∼3.5. Combining this new estimate with our previous sample of six high precision and homogeneously analyzed D/H measurements, we deduce that the primordial deuterium abundance is {log}}10{({{D}}/{{H}})}{{P}}=-4.5974+/- 0.0052 or, expressed as a linear quantity, {10}5{({{D}}/{{H}})}{{P}}=2.527+/- 0.030; this value corresponds to a one percent determination of the primordial deuterium abundance. Combining our result with a big bang nucleosynthesis (BBN) calculation that uses the latest nuclear physics input, we find that the baryon density derived from BBN agrees to within 2σ of the latest results from the Planck cosmic microwave background data. Based on observations collected at the W.M. Keck Observatory which is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W.M. Keck Foundation.

  1. Mangroves Enhance Reef Fish Abundance at the Caribbean Regional Scale.

    Science.gov (United States)

    Serafy, Joseph E; Shideler, Geoffrey S; Araújo, Rafael J; Nagelkerken, Ivan

    2015-01-01

    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.e., the Wider

  2. LITERATURE SURVEY ON ISOTOPIC ABUNDANCE RATIO MEASUREMENTS - 2001-2005

    International Nuclear Information System (INIS)

    HOLDEN, N.E.

    2005-01-01

    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

  3. A COMPARISON OF STELLAR ELEMENTAL ABUNDANCE TECHNIQUES AND MEASUREMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Hinkel, Natalie R.; Young, Patrick A.; Pagano, Michael D.; Desch, Steven J.; Anbar, Ariel D. [School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287 (United States); Adibekyan, Vardan; Mena, Elisa Delgado; Sousa, Sergio G.; Santos, Nuno C. [Instituto de Astrofísica e Ciências do Espaço, Universidade do Porto, CAUP, Rua das Estrelas, 4150-762 Porto (Portugal); Blanco-Cuaresma, Sergi [Observatoire de Genève, Université de Genève, CH-1290 Versoix (Switzerland); Carlberg, Joleen K. [NASA Goddard Space Flight Center, Code 667, Greenbelt MD 20771 (United States); Liu, Fan [Research School of Astronomy and Astrophysics, Australian National University, Cotter Road, Weston Creek, ACT 2611 (Australia); Nordlander, Thomas; Korn, Andreas; Gruyters, Pieter; Heiter, Ulrike [Department of Physics and Astronomy, Uppsala University, Box 516, 75120 Uppsala (Sweden); Jofré, Paula [Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA (United Kingdom); Soubiran, Caroline, E-mail: natalie.hinkel@gmail.com [CNRS/Univ. Bordeaux, LAB, UMR 5804, F-33270, Floirac (France)

    2016-09-01

    Stellar elemental abundances are important for understanding the fundamental properties of a star or stellar group, such as age and evolutionary history, as well as the composition of an orbiting planet. However, as abundance measurement techniques have progressed, there has been little standardization between individual methods and their comparisons. As a result, different stellar abundance procedures determine measurements that vary beyond the quoted error for the same elements within the same stars. The purpose of this paper is to better understand the systematic variations between methods and offer recommendations for producing more accurate results in the future. We invited a number of participants from around the world (Australia, Portugal, Sweden, Switzerland, and the United States) to calculate 10 element abundances (C, O, Na, Mg, Al, Si, Fe, Ni, Ba, and Eu) using the same stellar spectra for four stars (HD 361, HD 10700, HD 121504, and HD 202206). Each group produced measurements for each star using (1) their own autonomous techniques, (2) standardized stellar parameters, (3) a standardized line list, and (4) both standardized parameters and a line list. We present the resulting stellar parameters, absolute abundances, and a metric of data similarity that quantifies the homogeneity of the data. We conclude that standardization of some kind, particularly stellar parameters, improves the consistency between methods. However, because results did not converge as more free parameters were standardized, it is clear there are inherent issues within the techniques that need to be reconciled. Therefore, we encourage more conversation and transparency within the community such that stellar abundance determinations can be reproducible as well as accurate and precise.

  4. 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

  5. The abundance threshold for plague as a critical percolation phenomenon

    DEFF Research Database (Denmark)

    Davis, S; Trapman, P; Leirs, H

    2008-01-01

    . However, no natural examples have been reported. The central question of interest in percolation theory 4 , the possibility of an infinite connected cluster, corresponds in infectious disease to a positive probability of an epidemic. Archived records of plague (infection with Yersinia pestis....... Abundance thresholds are the theoretical basis for attempts to manage infectious disease by reducing the abundance of susceptibles, including vaccination and the culling of wildlife 6, 7, 8 . This first natural example of a percolation threshold in a disease system invites a re-appraisal of other invasion...

  6. Dark matter relic abundance and light sterile neutrinos

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Yi-Lei [Center for High Energy Physics,Peking University, Beijing 100871 (China); Zhu, Shou-hua [Center for High Energy Physics,Peking University, Beijing 100871 (China); Institute of Theoretical Physics & State Key Laboratory of Nuclear Physics and Technology,Peking University, Beijing 100871 (China); Collaborative Innovation Center of Quantum Matter,Beijing 100871 (China)

    2017-01-09

    In this paper, we calculate the relic abundance of the dark matter particles when they can annihilate into sterile neutrinos with the mass ≲100 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 a case, if the Yukawa coupling y{sub N} between the Higgs and the sterile neutrino is small, this process gives rise to a larger Ω{sub DM}h{sup 2} so we need a larger coupling between the dark matter and the sterile neutrino for a correct relic abundance.

  7. Instruction manual for ORNL tandem high abundance sensitivity mass spectrometer

    International Nuclear Information System (INIS)

    Smith, D.H.; McKown, H.S.; Chrisite, W.H.; Walker, R.L.; Carter, J.A.

    1976-06-01

    This manual describes the physical characteristics of the tandem mass spectrometer built by Oak Ridge National Laboratory for the International Atomic Energy Agency. Specific requirements met include ability to run small samples, high abundance sensitivity, good precision and accuracy, and adequate sample throughput. The instrument is capable of running uranium samples as small as 10 -12 g and has an abundance sensitivity in excess of 10 6 . Precision and accuracy are enhanced by a special sweep control circuit. Sample throughput is 6 to 12 samples per day. Operating instructions are also given

  8. Dependence of the Rossby number on helium and metal abundances

    International Nuclear Information System (INIS)

    Rucinski, S.M.; Vandenberg, D.A.

    1990-01-01

    Convective turnover times, tau, are calculated for solar-type stars of the zero-age main-sequence models of VandenBerg and Poll (1989) with helium abundances = 0.22, 0.27, and 0.32 and metal abundances = 0.0169, 0.024, and 0.03. Emphasis is given to the possible dependence of turnover times on the chemical composition of a star. It is found that deviations in log tau from a mean dependence on the (B-V) color are less than + or - 0.1. Thus, the predicted shape of the log tau vs. (B-V) relation is quite robust. 15 refs

  9. Energetic-particle abundances in impulsive solar flares

    Science.gov (United States)

    Reames, D. V.; Cane, H. V.; Von Rosenvinge, T. T.

    1990-01-01

    The abundances of elements and of He-3 in 90 solar electron events have been examined. It is found that the events fall into two distinct groups based upon their F/C ratio. Events in the F-rich group frequently have high He-3/He-4 ratios and are associated with type III and type V radio bursts in the parent flare. The F-poor events are associated with type IV bursts. These results on individual events support the conclusions of earlier work done with daily-averaged abundances.

  10. 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...

  11. Rare earth element abundances and distribution patterns in plant materials

    International Nuclear Information System (INIS)

    Aidid, S.B.

    1994-01-01

    Eight out of the fourteen rare earth elements were estimated from the leaves of Pelthophorum pterocarpum, the leaves and roots of Impatiens balsamina, and the soils from four sampling sites by instrumental neutron activation analysis. The chondrite normalized rare earth element abundances and distribution patterns in the plant materials were found to be significantly correlated to the abundances of the rare earth elements occurring in the soils. The extent of accumulation of the rare earth elements in some plant materials was also governed by the age of the plants and the plant organs. (author) 16 refs.; 4 figs.; 3 tabs

  12. Suppressing the QCD axion abundance by hidden monopoles

    International Nuclear Information System (INIS)

    Kawasaki, Masahiro

    2015-11-01

    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 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.

  13. 4He abundances: Optical versus radio recombination line measurements

    Science.gov (United States)

    Balser, Dana S.; Rood, Robert T.; Bania, T. M.

    2010-04-01

    Accurate measurements of the 4He/H abundance ratio are important in constraining Big Bang nucleosynthesis, models of stellar and Galactic evolution, and H ii region physics. We discuss observations of radio recombination lines using the Green Bank Telescope toward a small sample of H ii regions and planetary nebulae. We report 4He/H abundance ratio differences as high as 15-20% between optical and ratio data that are difficult to reconcile. Using the H ii regions S206 and M17 we determine 4He production in the Galaxy to be dY/dZ = 1.71 ± 0.86.

  14. 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.

  15. Abundance of intrinsic structural disorder in the histone H1 subtypes.

    Science.gov (United States)

    Kowalski, Andrzej

    2015-12-01

    The intrinsically disordered proteins consist of partially structured regions linked to the unstructured stretches, which consequently form the transient and dynamic conformational ensembles. They undergo disorder to order transition upon binding their partners. Intrinsic disorder is attributed to histones H1, perceived as assemblers of chromatin structure and the regulators of DNA and proteins activity. In this work, the comparison of intrinsic disorder abundance in the histone H1 subtypes was performed both by the analysis of their amino acid composition and by the prediction of disordered stretches, as well as by identifying molecular recognition features (MoRFs) and ANCHOR protein binding regions (APBR) that are responsible for recognition and binding. Both human and model organisms-animals, plants, fungi and protists-have H1 histone subtypes with the properties typical of disordered state. They possess a significantly higher content of hydrophilic and charged amino acid residues, arranged in the long regions, covering over half of the whole amino acid residues in chain. Almost complete disorder corresponds to histone H1 terminal domains, including MoRFs and ANCHOR. Those motifs were also identified in a more ordered histone H1 globular domain. Compared to the control (globular and fibrous) proteins, H1 histones demonstrate the increased folding rate and a higher proportion of low-complexity segments. The results of this work indicate that intrinsic disorder is an inherent structural property of histone H1 subtypes and it is essential for establishing a protein conformation which defines functional outcomes affecting on DNA- and/or partner protein-dependent cell processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. 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.

  17. Abundance and diversity of wild mammals along a hydrologic ...

    African Journals Online (AJOL)

    This study was conducted in the Eastern Usangu wetland in Mbeya and Iringa regions to examine the composition, abundance and diversity of mammals along a hydrological gradient. Data were collected in two seasons using distance sampling method along transects and a handheld GPS to locate positions. Statistical ...

  18. The solar iron abundance: not the last word

    NARCIS (Netherlands)

    Kostik, R.I.; Shchukina, N.G.; Rutten, R.J.

    1995-01-01

    Determinations of the solar iron abundance have converged to the meteoritic value with the Fe II studies of Holweger et al. (1990), Biémont et al. (1991) and Hannaford et al. (1992) and the Fe i results of Holweger et al. (1991). However, the latter authors pointed out that Blackwell et al. (1984)

  19. "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…

  20. Estimates of cetacean abundance in European Atlantic waters in summer

    OpenAIRE

    Hammond, P.S. (Phil) et al. (incl. Santos, M.B. (Maria Begoña)

    2017-01-01

    This report summarises design-based estimates of abundance for those cetacean species for which sufficient data were obtained during SCANS-III: harbour porpoise, bottlenose dolphin, Risso’s dolphin, white-beaked dolphin, white-sided dolphin, common dolphin, striped dolphin, pilot whale, all beaked whale species combined, sperm whale, minke whale and fin whale.

  1. Pex35 is a regulator of peroxisome abundance

    DEFF Research Database (Denmark)

    Yofe, Ido; Soliman, Kareem; Chuartzman, Silvia G

    2017-01-01

    Peroxisomes are cellular organelles with vital functions in lipid, amino acid, and redox metabolism. The cellular formation and dynamics of peroxisomes are governed by PEX genes, however, the regulation of peroxisome abundance is yet poorly understood. Here we use a high-content microscopy screen...

  2. Carbon Abundances in Starburst Galaxies of the Local Universe

    International Nuclear Information System (INIS)

    Peña-Guerrero, María A.; Leitherer, Claus; Mink, Selma de; Wofford, Aida; Kewley, Lisa

    2017-01-01

    The cosmological origin of carbon, the fourth most abundant element in the universe, is not well known and a matter of heavy debate. We investigate the behavior of C/O to O/H in order to constrain the production mechanism of carbon. We measured emission-line intensities in the spectral range from 1600 to 10000 Å on Space Telescope Imaging Spectrograph (STIS) long-slit spectra of 18 starburst galaxies in the local universe. We determined chemical abundances through traditional nebular analysis, and we used a Markov Chain Monte Carlo method to determine where our carbon and oxygen abundances lie in the parameter space. We conclude that our C and O abundance measurements are sensible. We analyzed the behavior of our sample in the [C/O] versus [O/H] diagram with respect to other objects such as DLAs, neutral ISM measurements, and disk and halo stars, finding that each type of object seems to be located in a specific region of the diagram. Our sample shows a steeper C/O versus O/H slope with respect to other samples, suggesting that massive stars contribute more to the production of C than N at higher metallicities, only for objects where massive stars are numerous; otherwise, intermediate-mass stars dominate the C and N production.

  3. Chemical Abundance Analysis of Moving Group W11450 (Latham 1)

    Science.gov (United States)

    O'Connell, Julia E.; Martens, Kylee; Frinchaboy, Peter M.

    2016-12-01

    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 ˜ 60,000), high-signal-to-noise ratio ( ˜ 100) spectra obtained with the Otto Struve 2.1 m telescope and the Sandiford Echelle Spectrograph at McDonald Observatory. The large star-to-star scatter in metallicity, -0.55 ≤ [Fe/H] ≤slant 0.06 dex (σ = 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 and W11450, are possible wide binaries. The candidate wide binary pair show similar chemical abundance patterns with not only iron but with other elements analyzed in this study, suggesting the proposed connection between these two stars may be real.

  4. H II region in NGC 6744: Spectrophotometry and chemical abundances

    International Nuclear Information System (INIS)

    Talent, D.L.

    1982-01-01

    Spectrophotometry of emission lines in the lambdalambda3700--6800 spectral range is presented for An H II region in an outer arm of NGC6744, a southern hemisphere galaxy of type SAB(r)bc II. The electron temperature, derived from the [O III] lines and assuming N/sub e/ = 100 cm -3 , was found to be 9,630 +- 450 K. Ionic abundances, derived in the usual fashion from the measured line strengths, were corrected to total relative number abundances by application of the standard ionization correction factor (ICF) scheme and by comparison to models. The derived abundances, relative to log Hequivalent12.00, are log He = 10.96 +- 0.06, log N = 7.34 +- 0.26, log O log O = 8.44 +- 0.10, log Ne = 7.80 +- 0.16, and log S = 6.75 +- 0.28. The NGC 6744 H II region abundances, and various ratios, are compared to similar data for H II regions in the SMC, LMC, and the Perseus arm of the Galaxy,. From the comparison it is suggested that the histories of nucleosynthesis in the outer regions of NGC 6744 and the Galaxy could have been quite similar

  5. Relic abundance of mass-varying cold dark matter particles

    International Nuclear Information System (INIS)

    Rosenfeld, Rogerio

    2005-01-01

    In models of coupled dark energy and dark matter the mass of the dark matter particle depends on the cosmological evolution of the dark energy field. In this Letter we exemplify in a simple model the effects of this mass variation on the relic abundance of cold dark matter

  6. Observing giant panda habitat and forage abundance from space

    NARCIS (Netherlands)

    Wang, T.

    2009-01-01

    Giant pandas are obligate bamboo grazers. The bamboos favoured by giant
    pandas are typical forest understorey plants. Therefore, the availability and
    abundance of understorey bamboo is a key factor in determining the quantity
    and quality of giant panda food resources. However,

  7. Intertidal barnacles are not uniformly abundant around the coast of ...

    African Journals Online (AJOL)

    spamer

    Intertidal barnacles are significantly more abundant on the south than on the west ... California Coastal Commission, 3111 Camino del Rio North, Suite 200, San ..... factors that are likely to affect adult growth and sur- .... north-west coast of the U.S.A. (e.g. Dayton 1971, .... SHANNON, L. V. 1985 — The Benguela ecosystem.

  8. APOGEE Chemical Abundances of the Sagittarius Dwarf Galaxy

    International Nuclear Information System (INIS)

    Hasselquist, Sten; Holtzman, Jon; Shetrone, Matthew; Smith, Verne; Nidever, David L.; McWilliam, Andrew; Fernández-Trincado, J. G.; Tang, Baitian; Beers, Timothy C.; Majewski, Steven R.; Anguiano, Borja; Tissera, Patricia B.; Alvar, Emma Fernández; Carigi, Leticia; Delgado Inglada, Gloria; Allende Prieto, Carlos; Battaglia, Giuseppina; García-Hernández, D. A.; Almeida, Andres; Frinchaboy, Peter

    2017-01-01

    The Apache Point Observatory Galactic Evolution Experiment provides the opportunity of measuring elemental abundances for C, N, O, Na, Mg, Al, Si, P, K, Ca, V, Cr, Mn, Fe, Co, and Ni in vast numbers of stars. We analyze thechemical-abundance patterns of these elements for 158 red giant stars belonging to the Sagittarius dwarf galaxy (Sgr). This is the largest sample of Sgr stars with detailed chemical abundances, and it is the first time that C, N, P, K, V, Cr, Co, and Ni have been studied at high resolution in this galaxy. We find that the Sgr stars with [Fe/H] ≳ −0.8 are deficient in all elemental abundance ratios (expressed as [X/Fe]) relative to the Milky Way, suggesting that the Sgr stars observed today were formed from gas that was less enriched by Type II SNe than stars formed in the Milky Way. By examining the relative deficiencies of the hydrostatic (O, Na, Mg, and Al) and explosive (Si, P, K, and Mn) elements, our analysis supports the argument that previous generations of Sgr stars were formed with a top-light initial mass function, one lacking the most massive stars that would normally pollute the interstellar medium with the hydrostatic elements. We use a simple chemical-evolution model, flexCE, to further support our claim and conclude that recent stellar generations of Fornax and the Large Magellanic Cloud could also have formed according to a top-light initial mass function.

  9. Terrestrial aurora: astrophysical laboratory for anomalous abundances in stellar systems

    Directory of Open Access Journals (Sweden)

    I. Roth

    2014-02-01

    Full Text Available The unique magnetic structure of the terrestrial aurora as a conduit of information between the ionosphere and magnetosphere can be utilized as a laboratory for physical processes at similar magnetic configurations and applied to various evolutionary phases of the solar (stellar system. The most spectacular heliospheric abundance enhancement involves the 3He isotope and selective heavy elements in impulsive solar flares. In situ observations of electromagnetic waves on active aurora are extrapolated to flaring corona in an analysis of solar acceleration processes of 3He, the only element that may resonate strongly with the waves, as well as heavy ions with specific charge-to-mass ratios, which may resonate weaker via their higher gyroharmonics. These results are applied to two observed anomalous astrophysical abundances: (1 enhanced abundance of 3He and possibly 13C in the late stellar evolutionary stages of planetary nebulae; and (2 enhanced abundance of the observed fossil element 26Mg in meteorites as a decay product of radioactive 26Al isotope due to interaction with the flare-energized 3He in the early solar system.

  10. Fish larval composition, abundance and seasonality in a southern ...

    African Journals Online (AJOL)

    abundance was relatively low (38 larvae 100 m-3 ), possibly as a result of the extremely low phytoplankton productivity and poor ... hoveelheid visplankton is laag (38 larwes 100 m-3), heelwaarskynlik as gevolg van die baie lae fitoplankton- opbrengs en lae ..... depressed ichthyoplankton food resources. According to.

  11. 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)

  12. Land use determinants of small mammals abundance and ...

    African Journals Online (AJOL)

    The objective of this study was to determine the relationship between land use types and practices and small mammal abundance and distribution. A field survey was used to collect data in three landscapes differing in plague incidences. Data collection was done both in the wet season (April-June 2012) and dry season ...

  13. 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.

  14. Mars atmospheric water vapor abundance: 1996-1997

    Science.gov (United States)

    Sprague, A. L.; Hunten, D. M.; Doose, L. R.; Hill, R. E.

    2003-05-01

    Measurements of martian atmospheric water vapor made throughout Ls = 18.0°-146.4° (October 3, 1996-July 12, 1997) show changes in Mars humidity on hourly, daily, and seasonal time scales. Because our observing program during the 1996-1997 Mars apparition did not include concomitant measurement of nearby CO 2 bands, high northern latitude data were corrected for dust and aerosol extinction assuming an optical depth of 0.8, consistent with ground-based and HST imaging of northern dust storms. All other measurements with airmass greater than 3.5 were corrected using a total optical depth of 0.5. Three dominant results from this data set are as follows: (1) pre- and post-opposition measurements made with the slit crossing many hours of local time on Mars' Earth-facing disk show a distinct diurnal pattern with highest abundances around and slightly after noon with low abundances in the late afternoon, (2) measurements of water vapor over the Mars Pathfinder landing site (Carl Sagan Memorial Station) on July 12, 1997, found 21 ppt μm in the spatial sector centered near 19° latitude, 36° longitude while abundances around the site varied from as low as 6 to as high as 28 ppt μm, and (3) water vapor abundance is patchy on hourly and daily time scales but follows the usual seasonal trends.

  15. Fish species composition, diversity and abundance of the lower New ...

    African Journals Online (AJOL)

    A thirteen-week investigation to determine the fish species composition, diversity and abundance of the Lower New Calabar River, in Rivers State, aimed at providing information on the fish stock and their status for documentation, knowledge improvement, and development of conservation and management strategies was ...

  16. Fishery characteristics and abundance estimates of the mangrove ...

    African Journals Online (AJOL)

    The mud crab Scylla serrata is lightly exploited along the East African seaboard. This study reports on fishing practices and gives preliminary estimates of abundance and size structures of the mud crab populations in Utende, Chole Island and Juani Island, Tanzania, and west of Quirimba and Ibo Island, Moçambique.

  17. Transcriptional profiling of cells sorted by RNA abundance

    NARCIS (Netherlands)

    Klemm, Sandy; Semrau, Stefan; Wiebrands, Kay; Mooijman, Dylan; Faddah, Dina A; Jaenisch, Rudolf; van Oudenaarden, Alexander

    We have developed a quantitative technique for sorting cells on the basis of endogenous RNA abundance, with a molecular resolution of 10-20 transcripts. We demonstrate efficient and unbiased RNA extraction from transcriptionally sorted cells and report a high-fidelity transcriptome measurement of

  18. Distribution and abundance of the Southern Fulmar Fulmarus glacialoides

    NARCIS (Netherlands)

    Creuwels, J.C.S.; Poncet, S.; Hodum, P.J.; Franeker, van J.A.

    2007-01-01

    We reviewed published and unpublished literature to establish the status of the breeding distribution and abundance of Southern Fulmars Fulmarus glacialoides. The species breeds widely throughout the Antarctic and on peri-Antarctic islands. From breeding population data collated from 73 of these

  19. Distribution and abundance of the Southern Fulmar Fulmarus glacialoides

    NARCIS (Netherlands)

    Creuwels, Jeroen C. S.; Poncet, Sally; Hodum, Peter J.; van Franeker, Jan A.

    We reviewed published and unpublished literature to establish the status of the breeding distribution and abundance of Southern Fulmars Fulmarus glacialoides. The species breeds widely throughout the Antarctic and on peri-Antarctic islands. From breeding population data collated from 73 of these

  20. Copepod composition, abundance and diversity in Makupa Creek ...

    African Journals Online (AJOL)

    Evenness (J) was, however, relatively constant (0.67 to 0.84) during the entire sampling period. These results point to suppressed copepod diversity and abundance in Makupa Creek, and possible reasons for this, which may include environmental degradation caused by pollution, are presented. Western Indian Ocean ...