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Sample records for abundance n-glycosylated protein

  1. 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....

  2. In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins.

    Science.gov (United States)

    Fang, Pan; Wang, Xin-Jian; Xue, Yu; Liu, Ming-Qi; Zeng, Wen-Feng; Zhang, Yang; Zhang, Lei; Gao, Xing; Yan, Guo-Quan; Yao, Jun; Shen, Hua-Li; Yang, Peng-Yuan

    2016-06-21

    N-glycosylation is one of the most prominent and abundant posttranslational modifications of proteins. It is estimated that over 50% of mammalian proteins undergo glycosylation. However, the analysis of N-glycoproteins has been limited by the available analytical technology. In this study, we comprehensively mapped the N-glycosylation sites in the mouse brain proteome by combining complementary methods, which included seven protease treatments, four enrichment techniques and two fractionation strategies. Altogether, 13492 N-glycopeptides containing 8386 N-glycosylation sites on 3982 proteins were identified. After evaluating the performance of the above methods, we proposed a simple and efficient workflow for large-scale N-glycosylation site mapping. The optimized workflow yielded 80% of the initially identified N-glycosylation sites with considerably less effort. Analysis of the identified N-glycoproteins revealed that many of the mouse brain proteins are N-glycosylated, including those proteins in critical pathways for nervous system development and neurological disease. Additionally, several important biomarkers of various diseases were found to be N-glycosylated. These data confirm that N-glycosylation is important in both physiological and pathological processes in the brain, and provide useful details about numerous N-glycosylation sites in brain proteins.

  3. Distribution of N-glycosylation sequons in proteins: how apart are they?

    DEFF Research Database (Denmark)

    Rao, Shyama Prasad; Buus, Ole Thomsen; Wollenweber, Bernd

    2011-01-01

    of experimentally confirmed eukaryotic N-glycoproteins we analyzed the relative position and distribution of sequons. N-Glycosylation probability was found to be lower in the termini of protein sequences compared to the mid region. N-glycosylated sequons were found much farther from C terminus compared to the N......N-glycosylation is a common protein modification process, which affects a number of properties of proteins. Little is known about the distribution of N-glycosylation sequons, for example, the distance between glycosylated sites and their position in the protein primary sequence. Using a large set......-terminus of the protein sequence and this effect was more pronounced for NXS sequons. The distribution of sequons, modeled based on balls-in-boxes classical occupancy, showed a near-maximum probability. Considerable proportion of sequons was found within a distance of ten amino acids, indicating that the steric hindrance...

  4. N-Glycosylation of Carnosinase Influences Protein Secretion and Enzyme Activity Implications for Hyperglycemia

    NARCIS (Netherlands)

    Riedl, Eva; Koeppel, Hannes; Pfister, Frederick; Peters, Verena; Sauerhoefer, Sibylle; Sternik, Paula; Brinkkoetter, Paul; Zentgraf, Hanswalter; Navis, Gerjan; Henning, Robert H.; Van Den Born, Jacob; Bakker, Stephan J. L.; Janssen, Bart; van der Woude, Fokko J.; Yard, Benito A.

    OBJECTIVE-The (CTG)(n) polymorphism in the serum carnosinase (CN-1) gene affects CN-1 secretion Since CN-1 is heavily glycosylated and glycosylation might influence protein secretion as well, we tested the role of N-glycosylation for CN-1 secretion and enzyme activity. We also tested whether CN-1

  5. N-Glycosylation of Plant-produced Recombinant Proteins

    NARCIS (Netherlands)

    Bosch, H.J.; Castilho, A.; Loos, A.; Schots, A.; Steinkeller, H.

    2013-01-01

    Plants are gaining increasingly acceptance as a production platform for recombinant proteins. One reason for this is their ability to carry out posttranslational protein modifications in a similar if not identical way as mammalian cells. The capability of plants to carry out human-like complex

  6. Endoplasmic reticulum stress and N-glycosylation modulate expression of WFS1 protein

    International Nuclear Information System (INIS)

    Yamaguchi, Suguru; Ishihara, Hisamitsu; Tamura, Akira; Yamada, Takahiro; Takahashi, Rui; Takei, Daisuke; Katagiri, Hideki; Oka, Yoshitomo

    2004-01-01

    Mutations of the WFS1 gene are responsible for two hereditary diseases, Wolfram syndrome and low frequency sensorineural hearing loss. The WFS1 protein is a glycoprotein located in the endoplasmic reticulum (ER) membrane but its function is poorly understood. Herein we show WFS1 mRNA and protein levels in pancreatic islets to be increased with ER-stress inducers, thapsigargin and dithiothreitol. Another ER-stress inducer, the N-glycosylation inhibitor tunicamycin, also raised WFS1 mRNA but not protein levels. Site-directed mutagenesis showed both Asn-663 and Asn-748 to be N-glycosylated in mouse WFS1 protein. The glycosylation-defective WFS1 protein, in which Asn-663 and Asn-748 had been substituted with aspartate, exhibited an increased protein turnover rate. Consistent with this, the WFS1 protein was more rapidly degraded in the presence of tunicamycin. These data indicate that ER-stress and N-glycosylation play important roles in WFS1 expression and stability, and also suggest regulatory roles for this protein in ER-stress induced cell death

  7. Identification and characterization of N-glycosylated proteins using proteomics

    DEFF Research Database (Denmark)

    Selby, David S; Larsen, Martin R; Calvano, Cosima Damiana

    2008-01-01

    and analysis of glycoproteins and glycopeptides. Combinations of affinity-enrichment techniques, chemical and biochemical protocols, and advanced mass spectrometry facilitate detailed glycoprotein analysis in proteomics, from fundamental biological studies to biomarker discovery in biomedicine....... is a complex task and is currently achieved by mass spectrometry-based methods that enable identification of glycoproteins and localization, classification, and analysis of individual glycan structures on proteins. In this chapter we briefly introduce a range of analytical technologies for recovery...

  8. Evolutionary Pattern of N-Glycosylation Sequon Numbers  in Eukaryotic ABC Protein Superfamilies

    Directory of Open Access Journals (Sweden)

    R. Shyama Prasad Rao

    2010-02-01

    Full Text Available Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline which are the potential sites of asparagine (N linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins and their underlying causes have largely been unexplored. We computed the actual and probabilistic occurrence of NXS/T sequons in ABC protein superfamilies from eight diverse eukaryotic organisms. The ABC proteins contained significantly higher NXS/T sequon numbers compared to respective genome-wide average, but the sequon density was significantly lower owing to the increase in protein size and decrease in sequon specific amino acids. However, mammalian ABC proteins have significantly higher sequon density, and both serine and threonine containing sequons (NXS and NXT have been positively selected—against the recent findings of only threonine specific Darwinian selection of sequons in proteins. The occurrence of sequons was positively correlated with the frequency of sequon specific amino acids and negatively correlated with proline and the NPS/T sequences. Further, the NPS/T sequences were significantly higher than expected in plant ABC proteins which have the lowest number of NXS/T sequons. Accord- ingly, compared to overall proteins, N-glycosylation sequons in ABC protein superfamilies have a distinct pattern of occurrence, and the results are discussed in an evolutionary perspective.

  9. Engineer medium and feed for modulating N-glycosylation of recombinant protein production in CHO cell culture

    DEFF Research Database (Denmark)

    Fan, Yuzhou; Kildegaard, Helene Faustrup; Andersen, Mikael Rørdam

    2017-01-01

    Chinese hamster ovary (CHO) cells have become the primary expression system for the production of complex recombinant proteins due to their long-term success in industrial scale production and generating appropriate protein N-glycans similar to that of humans. Control and optimization of protein N......-glycosylation is crucial, as the structure of N-glycans can largely influence both biological and physicochemical properties of recombinant proteins. Protein N-glycosylation in CHO cell culture can be controlled and tuned by engineering medium, feed, culture process, as well as genetic elements of the cell...

  10. Engineer Medium and Feed for Modulating N-Glycosylation of Recombinant Protein Production in CHO Cell Culture.

    Science.gov (United States)

    Fan, Yuzhou; Kildegaard, Helene Faustrup; Andersen, Mikael Rørdam

    2017-01-01

    Chinese hamster ovary (CHO) cells have become the primary expression system for the production of complex recombinant proteins due to their long-term success in industrial scale production and generating appropriate protein N-glycans similar to that of humans. Control and optimization of protein N-glycosylation is crucial, as the structure of N-glycans can largely influence both biological and physicochemical properties of recombinant proteins. Protein N-glycosylation in CHO cell culture can be controlled and tuned by engineering medium, feed, culture process, as well as genetic elements of the cell. In this chapter, we will focus on how to carry out experiments for N-glycosylation modulation through medium and feed optimization. The workflow and typical methods involved in the experiment process will be presented.

  11. In-Depth N-Glycosylation Reveals Species-Specific Modifications and Functions of the Royal Jelly Protein from Western (Apis mellifera) and Eastern Honeybees (Apis cerana).

    Science.gov (United States)

    Feng, Mao; Fang, Yu; Han, Bin; Xu, Xiang; Fan, Pei; Hao, Yue; Qi, Yuping; Hu, Han; Huo, Xinmei; Meng, Lifeng; Wu, Bin; Li, Jianke

    2015-12-04

    Royal jelly (RJ), secreted by honeybee workers, plays diverse roles as nutrients and defense agents for honeybee biology and human health. Despite being reported to be glycoproteins, the glycosylation characterization and functionality of RJ proteins in different honeybee species are largely unknown. An in-depth N-glycoproteome analysis and functional assay of RJ produced by Apis mellifera lingustica (Aml) and Apis cerana cerana (Acc) were conducted. RJ produced by Aml yielded 80 nonredundant N-glycoproteins carrying 190 glycosites, of which 23 novel proteins harboring 35 glycosites were identified. For Acc, all 43 proteins glycosylated at 138 glycosites were reported for the first time. Proteins with distinct N-glycoproteomic characteristics in terms of glycoprotein species, number of N-glycosylated sites, glycosylation motif, abundance level of glycoproteins, and N-glycosites were observed in this two RJ samples. The fact that the low inhibitory efficiency of N-glycosylated major royal jelly protein 2 (MRJP2) against Paenibacillus larvae (P. larvae) and the absence of antibacterial related glycosylated apidaecin, hymenoptaecin, and peritrophic matrix in the Aml RJ compared to Acc reveal the mechanism for why the Aml larvae are susceptible to P. larvae, the causative agent of a fatal brood disease (American foulbrood, AFB). The observed antihypertension activity of N-glycosylated MRJP1 in two RJ samples and a stronger activity found in Acc than in Aml reveal that specific RJ protein and modification are potentially useful for the treatment of hypertensive disease for humans. Our data gain novel understanding that the western and eastern bees have evolved species-specific strategies of glycosylation to fine-tune protein activity for optimizing molecular function as nutrients and immune agents for the good of honeybee and influence on the health promoting activity for human as well. This serves as a valuable resource for the targeted probing of the biological

  12. Proteomics and pathway analysis of N-glycosylated mammary gland proteins in response to Escherichia coli mastitis in cattle.

    Science.gov (United States)

    Yang, Yongxin; Shen, Weijun; Zhao, Xiaowei; Zhao, Huiling; Huang, Dongwei; Cheng, Guanglong

    2014-06-01

    The aim of this study was to investigate the N-linked glycosylated protein profile of mammary tissue from healthy cows and cows with mastitis due to Escherichia coli, in order to understand the molecular mechanisms of the host response to mastitis. N-glycopeptides were enriched with a lectin mixture and identified through high-accuracy mass spectrometry. A total of 551 N-glycosylation sites, corresponding to 294 proteins, were identified in the mammary tissues of healthy cows; these glycoproteins were categorised into three functional groups and clustered into 11 specific pathways. A total of 511 N-glycosylation sites, corresponding to 283 glycosylated proteins, were detected in the mammary tissues of cows with E. coli mastitis. There were differences in N-glycosylation sites in 98 proteins in the mammary tissues of healthy cows and cows with mastitis due to E. coli. Most proteins with altered glycosylation were those involved in responses to stress, cell adhesion and the immune response, and were assigned to five specific pathways based on their gene ontology annotation. The results from this study show that the glycosylated protein profile in the mammary tissues of healthy and mastitic cows are different, and altered glycoproteins are associated with several pathways, including the lysosome and O-glycan biosynthesis pathways. Copyright © 2014. Published by Elsevier Ltd.

  13. Protein N-glycosylation in eukaryotic microalgae and its impact on the production of nuclear expressed biopharmaceuticals

    Directory of Open Access Journals (Sweden)

    Elodie eMathieu-Rivet

    2014-07-01

    Full Text Available Microalgae are currently used for the production of food compounds. Recently, few microalgae species have been investigated as potential biofactories for the production of biopharmaceuticals. Indeed in this context, microalgae are cheap, classified as Generally Recognized As Safe (GRAS organisms and can be grown easily. However, problems remain to be solved before any industrial production of microalgae-made biopharmaceuticals. Among them, post-translational modifications of the proteins need to be considered. Especially, N-glycosylation acquired by the secreted recombinant proteins is of major concern since most of the biopharmaceuticals are N-glycosylated and it is well recognized that glycosylation represent one of their critical quality attribute. Therefore, the evaluation of microalgae as alternative cell factory for biopharmaceutical productions thus requires to investigate their N-glycosylation capability in order to determine to what extend it differs from their human counterpart and to determine appropriate strategies for remodelling the microalgae glycosylation into human-compatible oligosaccharides. Here, we review the secreted recombinant proteins which have been successfully produced in microalgae. We also report on recent bioinformatics and biochemical data concerning the structure of glycans N-linked to proteins from various microalgae phyla and comment the consequences on the glycan engineering strategies that may be necessary to render those microalgae-made biopharmaceuticals compatible with human therapy.

  14. Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study.

    Science.gov (United States)

    Lee, Hui Sun; Qi, Yifei; Im, Wonpil

    2015-03-09

    N-linked glycosylation is one of the most important, chemically complex, and ubiquitous post-translational modifications in all eukaryotes. The N-glycans that are covalently linked to proteins are involved in numerous biological processes. There is considerable interest in developments of general approaches to predict the structural consequences of site-specific glycosylation and to understand how these effects can be exploited in protein design with advantageous properties. In this study, the impacts of N-glycans on protein structure and dynamics are systematically investigated using an integrated computational approach of the Protein Data Bank structure analysis and atomistic molecular dynamics simulations of glycosylated and deglycosylated proteins. Our study reveals that N-glycosylation does not induce significant changes in protein structure, but decreases protein dynamics, likely leading to an increase in protein stability. Overall, these results suggest not only a common role of glycosylation in proteins, but also a need for certain proteins to be properly glycosylated to gain their intrinsic dynamic properties.

  15. Revealing the mechanisms of protein disorder and N-glycosylation in CD44-hyaluronan binding using molecular simulation

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    Olgun eGuvench

    2015-06-01

    Full Text Available The extracellular N-terminal hyaluronan binding domain (HABD of CD44 is a small globular domain that confers hyaluronan (HA binding functionality to this large transmembrane glycoprotein. When recombinantly expressed by itself, HABD exists as a globular water-soluble protein that retains the capacity to bind HA. This has enabled atomic-resolution structural biology experiments that have revealed the structure of HABD and its binding mode with oligomeric HA. Such experiments have also pointed to an order-to-disorder transition in HABD that is associated with HA binding. However, it had remained unclear how this structural transition was involved in binding since it occurs in a region of HABD distant from the HA-binding site. Furthermore, HABD is known to be N-glycosylated, and such glycosylation can diminish HA binding when the associated N-glycans are capped with sialic acid residues. The intrinsic flexibility of disordered proteins and of N-glycans makes it difficult to apply experimental structural biology approaches to probe the molecular mechanisms of how the order-to-disorder transition and N-glycosylation can modulate HA binding by HABD. We review recent results from molecular dynamics simulations that provide atomic-resolution mechanistic understanding of such modulation to help bridge gaps between existing experimental binding and structural biology data. Findings from these simulations include: Tyr42 may function as a molecular switch that converts the HA binding site from a low affinity to a high affinity state; in the partially-disordered form of HABD, basic amino acids in the C-terminal region can gain sufficient mobility to form direct contacts with bound HA to further stabilize binding; and terminal sialic acids on covalently-attached N-glycans can form charge-paired hydrogen bonding interactions with basic amino acids that could otherwise bind to HA, thereby blocking HA binding to glycosylated CD44 HABD.

  16. N-glycosylation in sugarcane

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    Maia Ivan G.

    2001-01-01

    Full Text Available The N-linked glycosylation of secretory and membrane proteins is the most complex posttranslational modification known to occur in eukaryotic cells. It has been shown to play critical roles in modulating protein function. Although this important biological process has been extensively studied in mammals, much less is known about this biosynthetic pathway in plants. The enzymes involved in plant N-glycan biosynthesis and processing are still not well defined and the mechanism of their genetic regulation is almost completely unknown. In this paper we describe our first attempt to understand the N-linked glycosylation mechanism in a plant species by using the data generated by the Sugarcane Expressed Sequence Tag (SUCEST project. The SUCEST database was mined for sugarcane gene products potentially involved in the N-glycosylation pathway. This approach has led to the identification and functional assignment of 90 expressed sequence tag (EST clusters sharing significant sequence similarity with the enzymes involved in N-glycan biosynthesis and processing. The ESTs identified were also analyzed to establish their relative abundance.

  17. Altered trafficking and unfolded protein response induction as a result of M3 muscarinic receptor impaired N-glycosylation.

    Science.gov (United States)

    Romero-Fernandez, Wilber; Borroto-Escuela, Dasiel O; Alea, Mileidys Perez; Garcia-Mesa, Yoelvis; Garriga, Pere

    2011-12-01

    The human M(3) muscarinic acetylcholine receptor is present in both the central and peripheral nervous system, and it is involved in the pathophysiology of several neurodegenerative and autoimmune diseases. We suggested a possible N-glycosylation map for the M(3) muscarinic receptor expressed in COS-7 cells. Here, we examined the role that N-linked glycans play in the folding and in the cell surface trafficking of this receptor. The five potential asparagine-linked glycosylation sites in the muscarinic receptor were mutated and transiently expressed in COS-7 cells. The elimination of N-glycan attachment sites did not affect the cellular expression levels of the receptor. However, proper receptor localization to the plasma membrane was affected as suggested by reduced [(3)H]-N-methylscopolamine binding. Confocal microscopy confirmed this observation and showed that the nonglycosylated receptor was primarily localized in the intracellular compartments. The mutant variant showed an increase in phosphorylation of the α-subunit of eukaryote initiation factor 2, and other well-known endoplasmic reticulum stress markers of the unfolded protein response pathway, which further supports the proposal of the improper intracellular accumulation of the nonglycosylated receptor. The receptor devoid of glycans showed more susceptibility to events that culminate in apoptosis reducing cell viability. Our findings suggest up-regulation of pro-apoptotic Bax protein, down-regulation of anti-apoptotic Bcl-2, and cleavage of caspase-3 effectors. Collectively, our data provide experimental evidence of the critical role that N-glycan chains play in determining muscarinic receptor distribution, localization, as well as cell integrity. © The Author 2011. Published by Oxford University Press. All rights reserved.

  18. A Crude 1-DNJ Extract from Home Made Bombyx Batryticatus Inhibits Diabetic Cardiomyopathy-Associated Fibrosis in db/db Mice and Reduces Protein N-Glycosylation Levels

    Directory of Open Access Journals (Sweden)

    Qing Zhao

    2018-06-01

    Full Text Available The traditional Chinese drug Bombyx Batryticatus (BB, which is also named the white stiff silkworm, has been widely used in Chinese clinics for thousands of years. It is famous for its antispasmodic and blood circulation-promoting effects. Cardiomyocyte hypertrophy, interstitial cell hyperplasia, and myocardial fibrosis are closely related to the N-glycosylation of key proteins. To examine the alterations of N-glycosylation that occur in diabetic myocardium during the early stage of the disease, and to clarify the therapeutic effect of 1-Deoxynojirimycin (1-DNJ extracted from BB, we used the db/db (diabetic mouse model and an approach based on hydrophilic chromatography solid-phase extraction integrated with an liquid Chromatograph Mass Spectrometer (LC-MS identification strategy to perform a site-specific N-glycosylation analysis of left ventricular cardiomyocyte proteins. Advanced glycation end products (AGEs, hydroxyproline, connective tissue growth factor (CTGF, and other serum biochemical indicators were measured with enzyme-linked immunosorbent assays (ELISA. In addition, the α-1,6-fucosylation of N-glycans was profiled with lens culinaris agglutinin (LCA lectin blots and fluorescein isothiocyanate (FITC-labelled lectin affinity histochemistry. The results indicated that 1-DNJ administration obviously downregulated myocardium protein N-glycosylation in db/db mice. The expression levels of serum indicators and fibrosis-related cytokines were reduced significantly by 1-DNJ in a dose-dependent manner. The glycan α-1,6-fucosylation level of the db/db mouse myocardium was elevated, and the intervention effect of 1-DNJ administration on N-glycan α-1,6-fucosylation was significant. To verify this result, the well-known transforming growth factor-β (TGF-β/Smad2/3 pathway was selected, and core α-1,6-fucosylated TGF-β receptor II (TGFR-βII was analysed semi-quantitatively with western blotting. The result supported the conclusions obtained

  19. Apical sorting of lysoGPI-anchored proteins occurs independent of association with detergent-resistant membranes but dependent on their N-glycosylation.

    Science.gov (United States)

    Castillon, Guillaume Alain; Michon, Laetitia; Watanabe, Reika

    2013-06-01

    Most glycosylphosphatidylinositol-anchored proteins (GPI-APs) are located at the apical surface of epithelial cells. The apical delivery of GPI-APs is believed to result from their association with lipid rafts. We find that overexpression of C-terminally tagged PGAP3 caused predominant production of lysoGPI-APs, an intermediate precursor in the GPI lipid remodeling process in Madin-Darby canine kidney cells. In these cells, produced lysoGPI-APs are not incorporated into detergent-resistant membranes (DRMs) but still are delivered apically, suggesting that GPI-AP association with DRMs is not necessary for apical targeting. In contrast, apical transport of both fully remodeled and lyso forms of GPI-APs is dependent on N-glycosylation, confirming a general role of N-glycans in apical protein transport. We also find that depletion of cholesterol causes apical-to-basolateral retargeting not only of fully remodeled GPI-APs, but also of lysoGPI-APs, as well as endogenous soluble and transmembrane proteins that would normally be targeted to the apical membrane. These findings confirm the essential role for cholesterol in the apical protein targeting and further demonstrate that the mechanism of cholesterol-dependent apical sorting is not related to DRM association of GPI-APs.

  20. Deciphering a pathway of Halobacterium salinarum N-glycosylation

    Science.gov (United States)

    Kandiba, Lina; Eichler, Jerry

    2015-01-01

    Genomic analysis points to N-glycosylation as being a common posttranslational modification in Archaea. To date, however, pathways of archaeal N-glycosylation have only been described for few species. With this in mind, the similarities of N-linked glycans decorating glycoproteins in the haloarchaea Haloferax volcanii and Halobacterium salinarum directed a series of bioinformatics, genetic, and biochemical experiments designed to describe that Hbt. salinarum pathway responsible for biogenesis of one of the two N-linked oligosaccharides described in this species. As in Hfx. volcanii, where agl (archaeal glycosylation) genes that encode proteins responsible for the assembly and attachment of a pentasaccharide to target protein Asn residues are clustered in the genome, Hbt. salinarum also contains a group of clustered homologous genes (VNG1048G-VNG1068G). Introduction of these Hbt. salinarum genes into Hfx. volcanii mutant strains deleted of the homologous sequence restored the lost activity. Moreover, transcription of the Hbt. salinarum genes in the native host, as well as in vitro biochemical confirmation of the predicted functions of several of the products of these genes provided further support for assignments made following bioinformatics and genetic experiments. Based on the results obtained in this study, the first description of an N-glycosylation pathway in Hbt. salinarum is offered. PMID:25461760

  1. Modulation of protein phosphorylation, N-glycosylation and Lys-acetylation in grape (Vitis vinifera) mesocarp and exocarp owing to Lobesia botrana infection

    DEFF Research Database (Denmark)

    Melo-Braga, Marcella N; Verano-Braga, Thiago; León, Ileana R

    2012-01-01

    Grapevine (Vitis vinifera) is an economically important fruit crop that is subject to many types of insect and pathogen attack. To better elucidate the plant response to Lobesia botrana pathogen infection, we initiated a global comparative proteomic study monitoring steady-state protein expressio...... resistance response protein 206. This study represents a substantial step toward the understanding of protein and PTMs-mediated plant-pathogen interaction shedding light on the mechanisms underlying the grape infection....

  2. Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood Samples

    DEFF Research Database (Denmark)

    Boersema, P.J.; Geiger, T.; Wiśniewski, J.R.

    2013-01-01

    Cells secrete a large number of proteins to communicate with their surroundings. Furthermore, plasma membrane proteins and intracellular proteins can be released into the extracellular space by regulated or non-regulated processes. Here, we profiled the supernatant of 11 cell lines....... In total, 1398 unique N-glycosylation sites were identified and quantified. Enriching for N-glycosylated peptides focused the analysis on classically secreted and membrane proteins. N-glycosylated secretome profiles correctly clustered the different cell lines to their respective cancer stage, suggesting...

  3. Role of N-glycosylation sites and CXC motifs in trafficking of Medicago trunculata Nod Factor Perception protein to the plasma membrane.

    NARCIS (Netherlands)

    Lefebvre, B.; Klaus-Heisen, D.; Pietraszewska-Bogiel, A.; Hervé, M.; Camut, S.; Auriac, M.C.; Gasciolli, V.; Nurisso, A.; Gadella, T.W.; Cullimore, J.

    2012-01-01

    The lysin motif receptor like kinase, NFP, is a key protein in the legume Medicago truncatula for the perception of lipochitooligosaccharidic Nod Factors, which are secreted bacterial signals essential for establishing the nitrogen-fixing legume-rhizobia symbiosis. Predicted structural and genetic

  4. N-glycosylation of Colorectal Cancer Tissues

    Science.gov (United States)

    Balog, Crina I. A.; Stavenhagen, Kathrin; Fung, Wesley L. J.; Koeleman, Carolien A.; McDonnell, Liam A.; Verhoeven, Aswin; Mesker, Wilma E.; Tollenaar, Rob A. E. M.; Deelder, André M.; Wuhrer, Manfred

    2012-01-01

    Colorectal cancer is the third most common cancer worldwide with an annual incidence of ∼1 million cases and an annual mortality rate of ∼655,000 individuals. There is an urgent need for identifying novel targets to develop more sensitive, reliable, and specific tests for early stage detection of colon cancer. Post-translational modifications are known to play an important role in cancer progression and immune surveillance of tumors. In the present study, we compared the N-glycan profiles from 13 colorectal cancer tumor tissues and corresponding control colon tissues. The N-glycans were enzymatically released, purified, and labeled with 2-aminobenzoic acid. Aliquots were profiled by hydrophilic interaction liquid chromatography (HILIC-HPLC) with fluorescence detection and by negative mode MALDI-TOF-MS. Using partial least squares discriminant analysis to investigate the N-glycosylation changes in colorectal cancer, an excellent separation and prediction ability were observed for both HILIC-HPLC and MALDI-TOF-MS data. For structure elucidation, information from positive mode ESI-ion trap-MS/MS and negative mode MALDI-TOF/TOF-MS was combined. Among the features with a high separation power, structures containing a bisecting GlcNAc were found to be decreased in the tumor, whereas sulfated glycans, paucimannosidic glycans, and glycans containing a sialylated Lewis type epitope were shown to be increased in tumor tissues. In addition, core-fucosylated high mannose N-glycans were detected in tumor samples. In conclusion, the combination of HILIC and MALDI-TOF-MS profiling of N-glycans with multivariate statistical analysis demonstrated its potential for identifying N-glycosylation changes in colorectal cancer tissues and provided new leads that might be used as candidate biomarkers. PMID:22573871

  5. N-Glycosylation of cholera toxin B subunit: serendipity for novel plant-made vaccines?

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    Nobuyuki eMatoba

    2015-12-01

    Full Text Available The non-toxic B subunit of cholera toxin (CTB has attracted considerable interests from vaccinologists due to strong mucosal immunomodulatory effects and potential utility as a vaccine scaffold for heterologous antigens. Along with other conventional protein expression systems, various plant species have been used as recombinant production hosts for CTB and its fusion proteins. However, it has recently become clear that the protein is N-glycosylated within the endoplasmic reticulum of plant cells – a eukaryotic post-translational modification that is not present in native CTB. While functionally active aglycosylated variants have been successfully engineered to circumvent potential safety and regulatory issues related to glycosylation, this modification may actually provide advantageous characteristics to the protein as a vaccine platform. Based on data from our recent studies, I discuss the unique features of N-glycosylated CTB produced in plants for the development of novel vaccines.

  6. Genes Involved in the Endoplasmic Reticulum N-Glycosylation Pathway of the Red Microalga Porphyridium sp.: A Bioinformatic Study

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    Oshrat Levy-Ontman

    2014-02-01

    Full Text Available N-glycosylation is one of the most important post-translational modifications that influence protein polymorphism, including protein structures and their functions. Although this important biological process has been extensively studied in mammals, only limited knowledge exists regarding glycosylation in algae. The current research is focused on the red microalga Porphyridium sp., which is a potentially valuable source for various applications, such as skin therapy, food, and pharmaceuticals. The enzymes involved in the biosynthesis and processing of N-glycans remain undefined in this species, and the mechanism(s of their genetic regulation is completely unknown. In this study, we describe our pioneering attempt to understand the endoplasmic reticulum N-Glycosylation pathway in Porphyridium sp., using a bioinformatic approach. Homology searches, based on sequence similarities with genes encoding proteins involved in the ER N-glycosylation pathway (including their conserved parts were conducted using the TBLASTN function on the algae DNA scaffold contigs database. This approach led to the identification of 24 encoded-genes implicated with the ER N-glycosylation pathway in Porphyridium sp. Homologs were found for almost all known N-glycosylation protein sequences in the ER pathway of Porphyridium sp.; thus, suggesting that the ER-pathway is conserved; as it is in other organisms (animals, plants, yeasts, etc..

  7. Differential dependence on N-glycosylation of anthrax toxin receptors CMG2 and TEM8.

    Directory of Open Access Journals (Sweden)

    Sarah Friebe

    Full Text Available ANTXR 1 and 2, also known as TEM8 and CMG2, are two type I membrane proteins, which have been extensively studied for their role as anthrax toxin receptors, but with a still elusive physiological function. Here we have analyzed the importance of N-glycosylation on folding, trafficking and ligand binding of these closely related proteins. We find that TEM8 has a stringent dependence on N-glycosylation. The presence of at least one glycan on each of its two extracellular domains, the vWA and Ig-like domains, is indeed necessary for efficient trafficking to the cell surface. In the absence of any N-linked glycans, TEM8 fails to fold correctly and is recognized by the ER quality control machinery. Expression of N-glycosylation mutants reveals that CMG2 is less vulnerable to sugar loss. The absence of N-linked glycans in one of the extracellular domains indeed has little impact on folding, trafficking or receptor function of the wild type protein expressed in tissue culture cells. N-glycans do, however, seem required in primary fibroblasts from human patients. Here, the presence of N-linked sugars increases the tolerance to mutations in cmg2 causing the rare genetic disease Hyaline Fibromatosis Syndrome. It thus appears that CMG2 glycosylation provides a buffer towards genetic variation by promoting folding of the protein in the ER lumen.

  8. N-Glycosylation of Lipocalin 2 Is Not Required for Secretion or Exosome Targeting

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    Erawan Borkham-Kamphorst

    2018-04-01

    Full Text Available Lipocalin 2 (LCN2 is a highly conserved secreted adipokine acting as a serum transport protein for small hydrophobic molecules such as fatty acids and steroids. In addition, LCN2 limits bacterial growth by sequestering iron-containing siderophores and further protects against intestinal inflammation and tumorigenesis associated with alterations in the microbiota. Human LCN2 contains one N-glycosylation site conserved in other species. It was postulated that this post-translational modification could facilitate protein folding, protects from proteolysis, is required for proper trafficking from the Golgi apparatus to the cell surface, and might be relevant for effective secretion. We here show that the homologous nucleoside antibiotic tunicamycin blocks N-linked glycosylation but not secretion of LCN2 in primary murine hepatocytes, derivatives thereof, human lung carcinoma cell line A549, and human prostate cancer cell line PC-3. Moreover, both the glycosylated and the non-glycosylated LCN2 variants are equally targeted to exosomes, demonstrating that this post-translational modification is not necessary for proper trafficking of LCN2 into these membranous extracellular vesicles. Furthermore, a hydrophobic cluster analysis revealed that the N-glycosylation site is embedded in a highly hydrophobic evolutionarily conserved surrounding. In sum, our data indicate that the N-glycosylation of LCN2 is not required for proper secretion and exosome cargo recruitment in different cell types, but might be relevant to increase overall solubility.

  9. N-glycosylation of the β2 adrenergic receptor regulates receptor function by modulating dimerization.

    Science.gov (United States)

    Li, Xiaona; Zhou, Mang; Huang, Wei; Yang, Huaiyu

    2017-07-01

    N-glycosylation is a common post-translational modification of G-protein-coupled receptors (GPCRs). However, it remains unknown how N-glycosylation affects GPCR signaling. β 2 adrenergic receptor (β 2 AR) has three N-glycosylation sites: Asn6, Asn15 at the N-terminus, and Asn187 at the second extracellular loop (ECL2). Here, we show that deletion of the N-glycan did not affect receptor expression and ligand binding. Deletion of the N-glycan at the N-terminus rather than Asn187 showed decreased effects on isoproterenol-promoted G-protein-dependent signaling, β-arrestin2 recruitment, and receptor internalization. Both N6Q and N15Q showed decreased receptor dimerization, while N187Q did not influence receptor dimerization. As decreased β 2 AR homodimer accompanied with reduced efficiency for receptor function, we proposed that the N-glycosylation of β 2 AR regulated receptor function by influencing receptor dimerization. To verify this hypothesis, we further paid attention to the residues at the dimerization interface. Studies of Lys60 and Glu338, two residues at the receptor dimerization interface, exhibited that the K60A/E338A showed decreased β 2 AR dimerization and its effects on receptor signaling were similar to N6Q and N15Q, which further supported the importance of receptor dimerization for receptor function. This work provides new insights into the relationship among glycosylation, dimerization, and function of GPCRs. Peptide-N-glycosidase F (PNGase F, EC 3.2.2.11); endo-β-N-acetylglucosaminidase A (Endo-A, EC 3.2.1.96). © 2017 Federation of European Biochemical Societies.

  10. Encoding asymmetry of the N-glycosylation motif facilitates glycoprotein evolution.

    Directory of Open Access Journals (Sweden)

    Ryan Williams

    Full Text Available Protein N-glycosylation is found in all domains of life and has a conserved role in glycoprotein folding and stability. In animals, glycoproteins transit through the Golgi where the N-glycans are trimmed and rebuilt with sequences that bind lectins, an innovation that greatly increases structural diversity and redundancy of glycoprotein-lectin interaction at the cell surface. Here we ask whether the natural tension between increasing diversity (glycan-protein interactions and site multiplicity (backup and status quo might be revealed by a phylogenic examination of glycoproteins and NXS/T(X ≠ P N-glycosylation sites. Site loss is more likely by mutation at Asn encoded by two adenosine (A-rich codons, while site gain is more probable by generating Ser or Thr downstream of an existing Asn. Thus mutations produce sites at novel positions more frequently than the reversal of recently lost sites, and therefore more paths though sequence space are made available to natural selection. An intra-species comparison of secretory and cytosolic proteins revealed a departure from equilibrium in sequences one-mutation-away from NXS/T and in (A content, indicating strong selective pressures and exploration of N-glycosylation positions during vertebrate evolution. Furthermore, secretory proteins have evolved at rates proportional to N-glycosylation site number, indicating adaptive interactions between the N-glycans and underlying protein. Given the topology of the genetic code, mutation of (A is more often nonsynonomous, and Lys, another target of many PTMs, is also encoded by two (A-rich codons. An examination of acetyl-Lys sites in proteins indicated similar evolutionary dynamics, consistent with asymmetry of the target and recognition portions of modified sites. Our results suggest that encoding asymmetry is an ancient mechanism of evolvability that increases diversity and experimentation with PTM site positions. Strong selective pressures on PTMs may have

  11. Tissue transglutaminase inhibits the TRPV5-dependent calcium transport in an N-glycosylation-dependent manner

    DEFF Research Database (Denmark)

    Boros, Sandor; Xi, Qi; Dimke, Henrik Anthony

    2011-01-01

    Tissue transglutaminase (tTG) is a multifunctional Ca(2+)-dependent enzyme, catalyzing protein crosslinking. The transient receptor potential vanilloid (TRPV) family of cation channels was recently shown to contribute to the regulation of TG activities in keratinocytes and hence skin barrier form......, these observations imply that tTG is a novel extracellular enzyme inhibiting the activity of TRPV5. The inhibition of TRPV5 occurs in an N-glycosylation-dependent manner, signifying a common final pathway by which distinct extracellular factors regulate channel activity....

  12. Detecting significant changes in protein abundance

    Directory of Open Access Journals (Sweden)

    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.

  13. N-Glycosylation of Human R-Spondin 1 Is Required for Efficient Secretion and Stability but Not for Its Heparin Binding Ability

    Directory of Open Access Journals (Sweden)

    Chiung-Fang Chang

    2016-06-01

    Full Text Available R-spondin 1 (Rspo1 plays an essential role in stem cell biology by potentiating Wnt signaling activity. Despite the fact that Rspo1 holds therapeutic potential for a number of diseases, its biogenesis is not fully elucidated. All Rspo proteins feature two amino-terminal furin-like repeats, which are responsible for Wnt signal potentiation, and a thrombospondin type 1 (TSR1 domain that can provide affinity towards heparan sulfate proteoglycans. Using chemical inhibitors, deglycosylase and site-directed mutagenesis, we found that human Rspo1 and Rspo3 are both N-glycosylated at N137, a site near the C-terminus of the furin repeat 2 domain, and Rspo2 is N-glycosylated at N160, a position near the N-terminus of TSR1 domain. Elimination of N-glycosylation at these sites affects their accumulation in media but have no effect on the ability towards heparin. Introduction of the N-glycosylation site to Rspo2 mutant at the position homologous to N137 in Rspo1 restored full glycosylation and rescued the accumulation defect of nonglycosylated Rspo2 mutant in media. Similar effect can be observed in the N137 Rspo1 or Rspo3 mutant engineered with Rspo2 N-glycosylation site. The results highlight the importance of N-glycosylation at these two positions in efficient folding and secretion of Rspo family. Finally, we further showed that human Rspo1 is subjected to endoplasmic reticulum (ER quality control in N-glycan-dependent manner. While N-glycan of Rspo1 plays a role in its intracellular stability, it had little effect on secreted Rspo1. Our findings provide evidence for the critical role of N-glycosylation in the biogenesis of Rspo1.

  14. Mass spectrometry characterization for N-glycosylation of immunoglobulin Y from hen egg yolk.

    Science.gov (United States)

    Sheng, Long; He, Zhenjiao; Liu, Yaping; Ma, Meihu; Cai, Zhaoxia

    2018-03-01

    Immunoglobulin Y (IgY) is a new therapeutic antibody that exists in hen egg yolk. It is a glycoprotein, not much is known about its N-glycan structures, site occupancy and site-specific N-glycosylation. In this study, purified protein from hen egg yolk was identified as IgY based on SDS-PAGE and MALDI-TOF/TOF MS. N-glycan was released from IgY using peptide-N4-(N-acetyl-beta-glucosaminyl) asparagine-amidase treatment, and the molecular weight of IgY was calculated using the difference between the molecular weight of IgY and deglycosylated IgY. Two potential N-Glycosylation sites (ASN 308 and ASN 409 ) were detected on IgY by nanoLC-ESI MS. Sugar chains were separated using normal phase liquid chromatography after fluorescence labeling, and 17 N-glycan structures were confirmed using ESI-MS. The sugar chain pattern contained high-mannose oligosaccharide, hybrid oligosaccharide and complex oligosaccharide. These results could lead to other important information regarding IgY glycosylation. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Defectively N-glycosylated and non-O-glycosylated aminopeptidase N (CD13) is normally expressed at the cell surface and has full enzymatic activity

    DEFF Research Database (Denmark)

    Norén, K; Hansen, Gert Helge; Clausen, H

    1997-01-01

    In order to study the effects of the absence of O-glycosylation and modifications of N-glycosylation on a class II membrane protein, pig and human aminopeptidase N (CD13) were stably expressed in the ldl(D) cell line. This cell line carries a UDP-Gal/UDP-GalNAc-epimerase deficiency which blocks...... the conversion of glucose into galactose derivatives. Thus it is possible in the ldl(D) cell line to selectively block O-glycosylation by the omission of N-acetylgalactoseamine from the culture medium and to alter N-glycosylation by the omission of galactose. In this way selectively altered glycosylated forms...

  16. Kex1 protease is involved in yeast cell death induced by defective N-glycosylation, acetic acid, and chronological aging.

    Science.gov (United States)

    Hauptmann, Peter; Lehle, Ludwig

    2008-07-04

    N-glycosylation in the endoplasmic reticulum is an essential protein modification and highly conserved in evolution from yeast to humans. The key step of this pathway is the transfer of the lipid-linked core oligosaccharide to the nascent polypeptide chain, catalyzed by the oligosaccharyltransferase complex. Temperature-sensitive oligosaccharyltransferase mutants of Saccharomyces cerevisiae at the restrictive temperature, such as wbp1-1, as well as wild-type cells in the presence of the N-glycosylation inhibitor tunicamycin display typical apoptotic phenotypes like nuclear condensation, DNA fragmentation, phosphatidylserine translocation, caspase-like activity, and reactive oxygen species accumulation. Since deletion of the yeast metacaspase YCA1 did not abrogate this death pathway, we postulated a different proteolytic process to be responsible. Here, we show that Kex1 protease is involved in the programmed cell death caused by defective N-glycosylation. Its disruption decreases caspase-like activity, production of reactive oxygen species, and fragmentation of mitochondria and, conversely, improves growth and survival of cells. Moreover, we demonstrate that Kex1 contributes also to the active cell death program induced by acetic acid stress or during chronological aging, suggesting that Kex1 plays a more general role in cellular suicide of yeast.

  17. N-glycosylation-negative catalase: a useful tool for exploring the role of hydrogen peroxide in the endoplasmic reticulum.

    Science.gov (United States)

    Lortz, S; Lenzen, S; Mehmeti, I

    2015-03-01

    Disulfide bond formation during protein folding of nascent proteins is associated with the generation of H2O2 in the endoplasmic reticulum (ER). Approaches to quantifying H2O2 directly within the ER failed because of the oxidative environment in the ER lumen, and ER-specific catalase expression to detoxify high H2O2 concentrations resulted in an inactive protein owing to N-glycosylation. Therefore, the N-glycosylation motifs at asparagine-244 and -439 of the human catalase protein were deleted by site-directed mutagenesis. The ER-targeted expression of these variants revealed that the deletion of the N-glycosylation motif only at asparagine-244 (N244) was associated with the maintenance of full enzymatic activity in the ER. Expression of catalase N244 in the ER (ER-Catalase N244) was ER-specific and protected the cells significantly against exogenously added H2O2. With the expression of ER-Catalase N244, a highly effective H2O2 inactivation within the ER was achieved for the first time. Catalase has a high H2O2-inactivation capacity without the need of reducing cofactors, which might interfere with the ER redox homeostasis, and is not involved in protein folding. With these characteristics ER-Catalase N244 is an ideal tool to explore the impact of ER-generated H2O2 on the generation of disulfide bonds or to study the induction of ER-stress pathways through protein folding overload and accumulation of H2O2. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Charge and Polarity Preferences for N-Glycosylation: A Genome-Wide In Silico Study and Its Implications Regarding Constitutive Proliferation and Adhesion of Carcinoma Cells.

    Science.gov (United States)

    Manwar Hussain, Muhammad Ramzan; Iqbal, Zeeshan; Qazi, Wajahat M; Hoessli, Daniel C

    2018-01-01

    The structural and functional diversity of the human proteome is mediated by N - and O- linked glycosylations that define the individual properties of extracellular and membrane-associated proteins. In this study, we utilized different computational tools to perform in silico based genome-wide mapping of 1,117 human proteins and unravel the contribution of both penultimate and vicinal amino acids for the asparagine-based, site-specific N -glycosylation. Our results correlate the non-canonical involvement of charge and polarity environment of classified amino acids (designated as L, O, A, P, and N groups) in the N -glycosylation process, as validated by NetNGlyc predictions, and 130 literature-reported human proteins. From our results, particular charge and polarity combinations of non-polar aliphatic, acidic, basic, and aromatic polar side chain environment of both penultimate and vicinal amino acids were found to promote the N -glycosylation process. However, the alteration in side-chain charge and polarity environment of genetic variants, particularly in the vicinity of Asn-containing epitope, may induce constitutive glycosylation (e.g., aberrant glycosylation at preferred and non-preferred sites) of membrane proteins causing constitutive proliferation and triggering epithelial-to-mesenchymal transition. The current genome-wide mapping of 1,117 proteins (2,909 asparagine residues) was used to explore charge- and polarity-based mechanistic constraints in N -glycosylation, and discuss alterations of the neoplastic phenotype that can be ascribed to N -glycosylation at preferred and non-preferred sites.

  19. Glycosylation of the N-terminal potential N-glycosylation sites in the human α1,3-fucosyltransferase V and -VI (hFucTV and -VI)

    DEFF Research Database (Denmark)

    Christensen, Lise Lotte; Bross, Peter Gerd; Ørntoft, Torben Falck

    2000-01-01

    Human alpha1,3-fucosyltransferase V and -VI (hFucTV and -VI) each contain four potential N-glycosylation sites (hFucTV: Asn60, Asn105, Asn167 and Asn198 and hFucTVI: Asn46, Asn91, Asn153 and Asn184). Glycosylation of the two N-terminal potential N-glycosylation sites (hFucTV: Asn60, Asn105 and h......FucTVI: Asn46 and Asn91) have never been studied in detail. In the present study, we have analysed the glycosylation of these potential N-glycosylation sites. Initially, we compared the molecular mass of hFucTV and -VI expressed in COS-7 cells treated with tunicamycin with the mass of the proteins...... in untreated cells. The difference in molecular mass between the proteins in treated and untreated cells corresponded to the presence of at least three N-linked glycans. We then made a series of mutants, in which the asparagine residues in the N-terminal potential N-glycosylation sites were replaced...

  20. 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...

  1. N-Glycosylation optimization of recombinant antibodies in CHO cell through process and metabolic engineering

    DEFF Research Database (Denmark)

    Fan, Yuzhou

    , analysis, control and optimization of N-glycosylation were thoroughly reviewed. In particular, how to control and optimize N-glycosylation in CHO cells was exclusively studied. The main focus of this PhD project is to find effective approaches of modulating N-glycosylation of CHO-derived recombinant...... galactose as feed additives, changing process parameters such as seeding density and cultivation duration are all demonstrated to be effective. The causal explanation of their impact on glycosylation can be various, including product, metabolism, proteome and physiology-associated mechanism. In the middle...... part of the thesis, both literature reviews and experimental applications were provided to demonstrate how to use omics data and implement systems biology to understand biological activities, especially N-glycosylation in CHO cells. In the last part of the thesis, the second strategy that apply genetic...

  2. N-Glycosylation instead of cholesterol mediates oligomerization and apical sorting of GPI-APs in FRT cells.

    Science.gov (United States)

    Imjeti, Naga Salaija; Lebreton, Stéphanie; Paladino, Simona; de la Fuente, Erwin; Gonzalez, Alfonso; Zurzolo, Chiara

    2011-12-01

    Sorting of glycosylphosphatidyl-inositol--anchored proteins (GPI-APs) in polarized epithelial cells is not fully understood. Oligomerization in the Golgi complex has emerged as the crucial event driving apical segregation of GPI-APs in two different kind of epithelial cells, Madin-Darby canine kidney (MDCK) and Fisher rat thyroid (FRT) cells, but whether the mechanism is conserved is unknown. In MDCK cells cholesterol promotes GPI-AP oligomerization, as well as apical sorting of GPI-APs. Here we show that FRT cells lack this cholesterol-driven oligomerization as apical sorting mechanism. In these cells both apical and basolateral GPI-APs display restricted diffusion in the Golgi likely due to a cholesterol-enriched membrane environment. It is striking that N-glycosylation is the critical event for oligomerization and apical sorting of GPI-APs in FRT cells but not in MDCK cells. Our data indicate that at least two mechanisms exist to determine oligomerization in the Golgi leading to apical sorting of GPI-APs. One depends on cholesterol, and the other depends on N-glycosylation and is insensitive to cholesterol addition or depletion.

  3. N-glycosylation by N-acetylglucosaminyltransferase V enhances the interaction of CD147/basigin with integrin β1 and promotes HCC metastasis.

    Science.gov (United States)

    Cui, Jian; Huang, Wan; Wu, Bo; Jin, Jin; Jing, Lin; Shi, Wen-Pu; Liu, Zhen-Yu; Yuan, Lin; Luo, Dan; Li, Ling; Chen, Zhi-Nan; Jiang, Jian-Li

    2018-05-01

    While the importance of protein N-glycosylation in cancer cell migration is well appreciated, the precise mechanisms by which N-acetylglucosaminyltransferase V (GnT-V) regulates cancer processes remain largely unknown. In the current study, we report that GnT-V-mediated N-glycosylation of CD147/basigin, a tumor-associated glycoprotein that carries β1,6-N-acetylglucosamine (β1,6-GlcNAc) glycans, is upregulated during TGF-β1-induced epithelial-to-mesenchymal transition (EMT), which correlates with tumor metastasis in patients with hepatocellular carcinoma (HCC). Interruption of β1,6-GlcNAc glycan modification of CD147/basigin decreased matrix metalloproteinase (MMP) expression in HCC cell lines and affected the interaction of CD147/basigin with integrin β1. These results reveal that β1,6-branched glycans modulate the biological function of CD147/basigin in HCC metastasis. Moreover, we showed that the PI3K/Akt pathway regulates GnT-V expression and that inhibition of GnT-V-mediated N-glycosylation suppressed PI3K signaling. In summary, β1,6-branched N-glycosylation affects the biological function of CD147/basigin and these findings provide a novel approach for the development of therapeutic strategies targeting metastasis. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

  4. Trends and approaches in N-Glycosylation engineering in Chinese hamster ovary cell culture

    DEFF Research Database (Denmark)

    Fan, Yuzhou; Kildegaard, Helene Faustrup; Andersen, Mikael Rørdam

    will summarize a group of recent strategies andapproaches and come up with case studies for N-glycosylation engineering in CHO cells and show several examples of relevantstudy cases from our research: 1) media and feed design, 2) culture process optimization, 3) substrate addition, 4) geneticengineering, 5...

  5. N-glycosylation increases the circulatory half-life of human growth hormone

    DEFF Research Database (Denmark)

    Flintegaard, Thomas V; Thygesen, Peter; Rahbek-Nielsen, Henrik

    2010-01-01

    Therapeutic use of recombinant GH typically involves daily sc injections. We examined the possibilities for prolonging the in vivo circulation of GH by introducing N-glycans. Human GH variants with a single potential N-glycosylation site (N-X-S/T) introduced by site-directed mutagenesis were expr...

  6. The C-terminal N-glycosylation sites of the human alpha1,3/4-fucosyltransferase III, -V, and -VI (hFucTIII, -V, adn -VI) are necessary for the expression of full enzyme activity.

    Science.gov (United States)

    Christensen, L L; Jensen, U B; Bross, P; Orntoft, T F

    2000-09-01

    The alpha1,3/4-fucosyltransferases are involved in the synthesis of fucosylated cell surface glycoconjugates. Human alpha1,3/4-fucosyltransferase III, -V, and -VI (hFucTIII, -V, and -VI) contain two conserved C-terminal N-glycosylation sites (hFucTIII: Asn154 and Asn185; hFucTV: Asn167 and Asn198; and hFucTVI: Asn153 and Asn184). In the present study, we have analyzed the functional role of these potential N-glycosylation sites, laying the main emphasis on the sites in hFucTIII. Tunicamycin treatment completely abolished hFucTIII enzyme activity while castanospermine treatment diminished hFucTIII enzyme activity to approximately 40% of the activity of the native enzyme. To further analyze the role of the conserved N-glycosylation sites in hFucTIII, -V, and -VI, we made a series of mutant genomic DNAs in which the asparagine residues in the potential C-terminal N-glycosylation sites were replaced by glutamine. Subsequently, the hFucTIII, -V, and -VI wild type and the mutants were expressed in COS-7 cells. All the mutants exhibited lower enzyme activity than the wild type and elimination of individual sites had different effects on the activity. The mutations did not affect the protein level of the mutants in the cells, but reduced the molecular mass as predicted. Kinetic analysis of hFucTIII revealed that lack of glycosylation at Asn185 did not change the Km values for the oligosaccharide acceptor and the nucleotide sugar donor. The present study demonstrates that hFucTIII, -V, and -VI require N-glycosylation at the two conserved C-terminal N-glycosylation sites for expression of full enzyme activity.

  7. [Conformation analysis of the N-glycosylation site Asn-X-Thr/Ser in glycoproteins].

    Science.gov (United States)

    Avanov, A Ia; Lipkind, G M

    1990-03-01

    Theoretical conformational analysis of oligopeptides CH3CO-Asn-X-Thr-NHCH3 (X = Gly, Ala, Pro), modelling N-glycosylation site, and their glycosylated derivatives CH3CO-(GlcNAc beta 1-4GlcNAc beta 1) Asn-X-Thr-NHCH3 has been carried out. Active conformations of the site are found, corresponding to structural prerequisities of N-glycosylation: Asn residue's position in beta-turn and hydrogen bond formation between side chains of Asn and Thr/Ser residues. In this case the L conformation of the central residue X is most probable. Since Pro residue does not possess this conformation, sequences with X = Pro are not glycosylated. It is shown that glycosylation of the above-mentioned sites is accompanied by reorientation of the Asn residue's side chains.

  8. Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation

    Directory of Open Access Journals (Sweden)

    Dall’Olio Giovanni

    2012-06-01

    Full Text Available Abstract Background Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment and innate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Results Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection are frequent on genes that are known to be at bifurcation points, and that are identified as being in key position by a network-level analysis such as MGAT3 and GCS1. Conclusions These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  11. 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

  12. 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

  13. N-Glycosylation analysis of yeast Carboxypeptidase Y reveals the ultimate removal of phosphate from glycans at Asn368.

    Science.gov (United States)

    B S, Gnanesh Kumar; Surolia, Avadhesha

    2017-05-01

    Carboxypeptidase Y from Saccharomyces cerivisiae was characterized for its site specific N-glycosylation through mass spectrometry. The N-glycopeptides were derived using non specific proteases and are analysed directly on liquid chromatography coupled to ion trap mass spectrometer in tandem mode. The evaluation of glycan fragment ions and the Y 1 ions (peptide+HexNAc) +n revealed the glycan sequence and the corresponding site of attachment. We observed the microheterogeneity in N-glycans such as Man 11-15 GlcNAc 2 at Asn 13 , Man 8-12 GlcNAc 2 at Asn 87 , Man 9-14 GlcNAc 2 at Asn 168 and phosphorylated Man 12-17 GlcNAc 2 as well as Man 11-16 GlcNAc 2 at Asn 368 . The presence of N-glycans with Man <18 GlcNAc 2 indicated that in vacuoles the steady release of mannose/phospho mannose residues from glycans occurs initially at Asn 13 or Asn 168 followed by at Asn 368 . However, glycans at Asn 87 which comprises Man 8-12 residues as reported earlier remain intact suggesting its inaccessibility for a similar processing. This in turn indicates the interaction of the glycan at Asn 87 with the polypeptide chain implicating it in the folding of the protein. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Mechanistic understanding of N-glycosylation in Ebola virus glycoprotein maturation and function.

    Science.gov (United States)

    Wang, Bin; Wang, Yujie; Frabutt, Dylan A; Zhang, Xihe; Yao, Xiaoyu; Hu, Dan; Zhang, Zhuo; Liu, Chaonan; Zheng, Shimin; Xiang, Shi-Hua; Zheng, Yong-Hui

    2017-04-07

    The Ebola virus (EBOV) trimeric envelope glycoprotein (GP) precursors are cleaved into the receptor-binding GP 1 and the fusion-mediating GP 2 subunits and incorporated into virions to initiate infection. GP 1 and GP 2 form heterodimers that have 15 or two N -glycosylation sites (NGSs), respectively. Here we investigated the mechanism of how N -glycosylation contributes to GP expression, maturation, and function. As reported before, we found that, although GP 1 NGSs are not critical, the two GP 2 NGSs, Asn 563 and Asn 618 , are essential for GP function. Further analysis uncovered that Asn 563 and Asn 618 regulate GP processing, demannosylation, oligomerization, and conformation. Consequently, these two NGSs are required for GP incorporation into EBOV-like particles and HIV type 1 (HIV-1) pseudovirions and determine viral transduction efficiency. Using CRISPR/Cas9 technology, we knocked out the two classical endoplasmic reticulum chaperones calnexin (CNX) and/or calreticulin (CRT) and found that both CNX and CRT increase GP expression. Nevertheless, NGSs are not required for the GP interaction with CNX or CRT. Together, we conclude that, although Asn 563 and Asn 618 are not required for EBOV GP expression, they synergistically regulate its maturation, which determines its functionality. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. The impact of N-glycosylation on conformation and stability of immunoglobulin Y from egg yolk.

    Science.gov (United States)

    Sheng, Long; He, Zhenjiao; Chen, Jiahui; Liu, Yaofa; Ma, Meihu; Cai, Zhaoxia

    2017-03-01

    Immunoglobulin Y (IgY) is a new therapeutic antibody, and its applications in industry are very broad. To provide insight into the effects of N-glycosylation on IgY, its conformation and stability were studied. In this research, IgY was extracted from egg yolk and then digested by peptide-N4-(N-acetyl-beta-glucosaminyl) asparagine-amidase. SDS-PAGE and infrared absorption spectrum showed that carbohydrates were distinctly reduced after enzymolysis. The circular dichroism spectrum indicated that the IgY molecule became more flexible and disordered after removal of N-glycan. The fluorescence intensity revealed that Trp residues were buried in a more hydrophobic environment after disposal of N-glycan. Storage stability decreased with the removal of oligosaccharide chains based on size-exclusion chromatography analysis. Deglycosylated IgY exhibited less resistance to guanidine hydrochloride-induced unfolding. After deglycosylation, IgY was more sensitive to pepsin. Therefore, N-glycosylation played an important role in the maintenance of the structure and stability of IgY. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Viral Restriction Activity of Feline BST2 Is Independent of Its N-Glycosylation and Induction of NF-κB Activation.

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    Weiran Wang

    Full Text Available BST2 (CD317, tetherin, HM1.24 is an interferon-inducible transmembrane protein which can directly inhibit the release of enveloped virus particles from infected cells, and its anti-viral activity is reported to be related to the specific topological arrangement of its four structural domains. The N-terminal cytoplasmic tail of feline BST2 (fBST2 is characterized by a shorter N-terminal region compared to those of other known homologs. In this study, we investigated the functional impact of modifying the cytoplasmic tail region of fBST2 and its molecular mechanism. The fBST2 protein with the addition of a peptide at the N-terminus retained anti-release activity against human immunodeficiency virus type-1 and pseudovirus based on feline immunodeficiency virus at a weaker level compared with the wild-type fBST2. However, the fBST2 protein with addition of a peptide internally in the ectodomain proximal to the GPI anchor still retained its anti-viral activity well. Notably, the N-glycosylation state and the cell surface level of the N-terminally modified variants were unlike those of the wild-type protein, while no difference was observed in their intracellular localizations. However, in contrast to human BST2, the wild-type fBST2 did not show the ability to activate NF-κB. Consistent with previous reports, our findings showed that adding a peptide in the cytoplasmic tail region of fBST2 may influence its anti-viral activity. The shorter N-terminal cytoplasmic region of fBST2 compared with human BST2 did not apparently affect its anti-viral activity, which is independent of its N-glycosylation and ability to activate NF-κB.

  17. N-glycosylation of colorectal cancer tissues: a liquid chromatography and mass spectrometry-based investigation.

    Science.gov (United States)

    Balog, Crina I A; Stavenhagen, Kathrin; Fung, Wesley L J; Koeleman, Carolien A; McDonnell, Liam A; Verhoeven, Aswin; Mesker, Wilma E; Tollenaar, Rob A E M; Deelder, André M; Wuhrer, Manfred

    2012-09-01

    Colorectal cancer is the third most common cancer worldwide with an annual incidence of ~1 million cases and an annual mortality rate of ~655,000 individuals. There is an urgent need for identifying novel targets to develop more sensitive, reliable, and specific tests for early stage detection of colon cancer. Post-translational modifications are known to play an important role in cancer progression and immune surveillance of tumors. In the present study, we compared the N-glycan profiles from 13 colorectal cancer tumor tissues and corresponding control colon tissues. The N-glycans were enzymatically released, purified, and labeled with 2-aminobenzoic acid. Aliquots were profiled by hydrophilic interaction liquid chromatography (HILIC-HPLC) with fluorescence detection and by negative mode MALDI-TOF-MS. Using partial least squares discriminant analysis to investigate the N-glycosylation changes in colorectal cancer, an excellent separation and prediction ability were observed for both HILIC-HPLC and MALDI-TOF-MS data. For structure elucidation, information from positive mode ESI-ion trap-MS/MS and negative mode MALDI-TOF/TOF-MS was combined. Among the features with a high separation power, structures containing a bisecting GlcNAc were found to be decreased in the tumor, whereas sulfated glycans, paucimannosidic glycans, and glycans containing a sialylated Lewis type epitope were shown to be increased in tumor tissues. In addition, core-fucosylated high mannose N-glycans were detected in tumor samples. In conclusion, the combination of HILIC and MALDI-TOF-MS profiling of N-glycans with multivariate statistical analysis demonstrated its potential for identifying N-glycosylation changes in colorectal cancer tissues and provided new leads that might be used as candidate biomarkers.

  18. Purification, cloning, characterization, and N-glycosylation analysis of a novel β-fructosidase from Aspergillus oryzae FS4 synthesizing levan- and neolevan-type fructooligosaccharides.

    Directory of Open Access Journals (Sweden)

    Li Xu

    Full Text Available β-Fructosidases are a widespread group of enzymes that catalyze the hydrolysis of terminal fructosyl units from various substrates. These enzymes also exhibit transglycosylation activity when they function with high concentrations of sucrose, which is used to synthesize fructooligosaccharides (FOS in the food industry. A β-fructosidase (BfrA with high transglycosylation activity was purified from Aspergillus oryzae FS4 as a monomeric glycoprotein. Compared with the most extensively studied Aspergillus spp. fructosidases that synthesize inulin-type β-(2-1-linked FOS, BfrA has unique transfructosylating property of synthesizing levan- and neolevan-type β-(2-6-linked FOS. The coding sequence (bfrAFS4, 1.86 kb of BfrA was amplified and expressed in Escherichia coli and Pichia pastoris. Both native and recombinant proteins showed transfructosylation and hydrolyzation activities with broad substrate specificity. These proteins could hydrolyze the following linkages: Glc α-1, 2-β Fru; Glc α-1, 3-α Fru; and Glc α-1, 5-β Fru. Compared with the unglycosylated E. coli-expressed BfrA (E.BfrA, the N-glycosylated native (N.BfrA and the P. pastoris-expressed BfrA (P.BfrA were highly stable at a wide pH range (pH 4 to 11, and significantly more thermostable at temperatures up to 50°C with a maximum activity at 55°C. Using sucrose as substrate, the Km and kcat values for total activity were 37.19±5.28 mM and 1.0016±0.039×104 s-1 for N.BfrA. Moreover, 10 of 13 putative N-glycosylation sites were glycosylated on N.BfrA, and N-glycosylation was essential for enzyme thermal stability and optima activity. Thus, BfrA has demonstrated as a well-characterized A. oryzae fructosidase with unique transfructosylating capability of synthesizing levan- and neolevan-type FOS.

  19. Structure-function analysis of the human sialyltransferase ST3Gal I - Role of N-glycosylation and a novel conserved sialylmotif

    DEFF Research Database (Denmark)

    Jeanneau, C.; Chazalet, V.; Auge, C.

    2004-01-01

    of these residues and of the conserved residues of motif VS (HX4E) was assessed using as a template the human ST3Gal I. Mutational analysis showed that residues His(299) and Tyr(300) of the new motif, and His(316) of the VS motif, are essential for activity since their substitution by alanine yielded inactive...... showed that none of the mutants tested had any significant effect in nucleotide donor binding. Instead the mutant proteins were affected in their binding to the acceptor and/or demonstrated lower catalytic efficiency. Although the human ST3Gal I has four N-glycan attachment sites in its catalytic domain...... that are potentially glycosylated, none of them was shown to be necessary for enzyme activity. However, N-glycosylation appears to contribute to the proper folding and trafficking of the enzyme....

  20. Topological studies of hSVCT1, the human sodium-dependent vitamin C transporter and the influence of N-glycosylation on its intracellular targeting

    Energy Technology Data Exchange (ETDEWEB)

    Velho, Albertina M. [Department of Biosciences University of Kent, CT2 7NJ (United Kingdom); Jarvis, Simon M., E-mail: S.M.Jarvis@westminster.ac.uk [Department of Biosciences University of Kent, CT2 7NJ (United Kingdom); University of Westminster, School of Biosciences, London W1W 6UW (United Kingdom)

    2009-08-01

    The Na{sup +}-dependent transporters, hSVCT1 and hSVCT2, were assessed in COS-1 cells for their membrane topology. Antibodies to N- and C-termini of hSVCT1 and C-terminus of hSVCT2 identified positive immunofluorescence only after permeabilisation, suggesting these regions are intracellular. PNGase F treatment confirmed that WT hSVCT1 ({approx} 70-100 kDa) is glycosylated and site-directed mutagenesis of the three putative N-glycosylation sites, Asn138, Asn144, Asn230, demonstrated that mutants N138Q and N144Q were glycosylated ({approx} 68-90 kDa) with only 31-65% of WT L-ascorbic acid (AA) uptake while the glycosylation profile of N230Q remained unaltered ({approx} 98% of WT activity). However, the N138Q/N144Q double mutant displayed barely detectable membrane expression at {approx} 65 kDa, no apparent glycosylation and minimal AA uptake (< 10%) with no discernible improvement in expression or activity when cultured at 28 {sup o}C or 37 {sup o}C. Marker protein immunocytochemistry with N138Q/N144Q identified intracellular aggregates with hSVCT1 localised at the nuclear membrane but absent at the plasma membrane thus implicating its role as a possible intracellular transporter and suggesting N-glycosylation is required for hSVCT1 membrane targeting. Also, Lys242 on the same putative hydrophilic loop as Asn230 after biotinylation was inaccessible from the extracellular side when analysed by MALDI-TOF MS. A new hSVCT1 secondary structure model supporting these findings is proposed.

  1. 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.

  2. Study of ethanol-induced Golgi disorganization reveals the potential mechanism of alcohol-impaired N-glycosylation

    Science.gov (United States)

    Casey, Carol A.; Bhat, Ganapati; Holzapfel, Melissa S.; Petrosyan, Armen

    2016-01-01

    Background It is known that ethanol (EtOH) and its metabolites have a negative effect on protein glycosylation. The fragmentation of the Golgi apparatus induced by alteration of the structure of largest Golgi matrix protein, giantin, is the major consequence of damaging effects of EtOH-metabolism on the Golgi, however, the link between this and abnormal glycosylation remains unknown. Because previously we have shown that Golgi morphology dictates glycosylation, we examined the effect EtOH administration has on function of Golgi residential enzymes involved in N-glycosylation. Methods HepG2 cells transfected with mouse ADH1 (VA-13 cells) were treated with 35 mM ethanol for 72 h. Male Wistar rats were pair-fed Lieber-DeCarli diets for 5 to 8 weeks. Characterization of Golgi-associated mannosyl (α-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase (MGAT1), α-1,2-mannosidase (Man-I) and α-mannosidase II (Man-II) were performed in VA-13 cells and rat hepatocytes followed by 3D Structured Illumination Microscopy (SIM). Results First, we detected that EtOH administration results in the loss of sialylated N-glycans on asialoglycoprotein receptor, however the high mannose-type N-glycans are increased. Further analysis by 3D SIM microscopy revealed that EtOH treatment despite Golgi disorganization does not change cis-Golgi localization for Man-I, but does induce medial-to-cis relocation of MGAT1 and Man-II. Using different approaches, including electron microscopy, we revealed that EtOH treatment results in dysfunction of Arf1 GTPase followed by a deficiency in COPI vesicles at the Golgi. Silencing beta-COP or expression of GDP-bound mutant Arf1(T31N) mimics the EtOH effect on retaining MGAT1 and Man-II at the cis-Golgi, suggesting that (a) EtOH specifically blocks activation of Arf1, and (b) EtOH alters the proper localization of Golgi enzymes through impairment of COPI. Importantly, the level of MGAT1 was reduced, because likely MGAT1, contrary to Man-I and Man

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

    Science.gov (United States)

    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

  4. 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...

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

    Directory of Open Access Journals (Sweden)

    Rajesh S.

    2008-10-01

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

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

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    Ayami Yamaguchi

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

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

    Directory of Open Access Journals (Sweden)

    Nie Jing

    2011-05-01

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

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

    Science.gov (United States)

    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.

  9. 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

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

    Science.gov (United States)

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

    2015-11-01

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

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

    Science.gov (United States)

    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.

  12. Preventing E-cadherin aberrant N-glycosylation at Asn-554 improves its critical function in gastric cancer

    Science.gov (United States)

    Carvalho, S; Catarino, TA; Dias, AM; Kato, M; Almeida, A; Hessling, B; Figueiredo, J; Gärtner, F; Sanches, JM; Ruppert, T; Miyoshi, E; Pierce, M; Carneiro, F; Kolarich, D; Seruca, R; Yamaguchi, Y; Taniguchi, N; Reis, CA; Pinho, SS

    2016-01-01

    E-cadherin is a central molecule in the process of gastric carcinogenesis and its posttranslational modifications by N-glycosylation have been described to induce a deleterious effect on cell adhesion associated with tumor cell invasion. However, the role that site-specific glycosylation of E-cadherin has in its defective function in gastric cancer cells needs to be determined. Using transgenic mice models and human clinical samples, we demonstrated that N-acetylglucosaminyltransferase V (GnT-V)-mediated glycosylation causes an abnormal pattern of E-cadherin expression in the gastric mucosa. In vitro models further indicated that, among the four potential N-glycosylation sites of E-cadherin, Asn-554 is the key site that is selectively modified with β1,6 GlcNAc-branched N-glycans catalyzed by GnT-V. This aberrant glycan modification on this specific asparagine site of E-cadherin was demonstrated to affect its critical functions in gastric cancer cells by affecting E-cadherin cellular localization, cis-dimer formation, molecular assembly and stability of the adherens junctions and cell–cell aggregation, which was further observed in human gastric carcinomas. Interestingly, manipulating this site-specific glycosylation, by preventing Asn-554 from receiving the deleterious branched structures, either by a mutation or by silencing GnT-V, resulted in a protective effect on E-cadherin, precluding its functional dysregulation and contributing to tumor suppression. PMID:26189796

  13. 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...

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  16. 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.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  19. 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.

  20. Identification of N-glycosylation in prolyl endoprotease from Aspergillus niger and evaluation of the enzyme for its possible application in proteomics.

    Science.gov (United States)

    Sebela, Marek; Rehulka, Pavel; Kábrt, Jaromír; Rehulková, Helena; Ozdian, Tomás; Raus, Martin; Franc, Vojtech; Chmelík, Josef

    2009-11-01

    An acidic prolyl endoprotease from Aspergillus niger was isolated from the commercial product Brewers Clarex to evaluate its possible application in proteomics. The chromatographic purification yielded a single protein band in sodium dodecyl sulfate polyacrylamide gel electrophoresis providing an apparent molecular mass of 63 kDa and a broad peak (m/z 58,061) in linear matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) indicating the glycoprotein nature of the enzyme. Indeed, a colorimetric assessment with phenol and sulfuric acid showed the presence of neutral sugars (9% of weight). The subsequent treatment with N-glycosidase F released a variety of high-mannose type N-glycans, which were successfully detected using MALDI-TOF MS. MALDI-TOF/TOF tandem MS analysis of glycopeptides from a tryptic digest of prolyl endoprotease unraveled the identity of the N-glycosylation site in the primary structure. The data obtained also show that the enzyme is present in its processed form, i.e. without putative signal and propeptide parts. Spectrophotometric measurements demonstrated optimal activity at pH 4.0-4.5 and also high thermostability for the cleavage at the C-terminal part of proline residues. In-solution digestion of standard proteins (12-200 kDa) allowed to evaluate the cleavage specificity. The enzyme acts upon proline and alanine residues, but there is an additional minor cleavage at some other residues like Gly, Leu, Arg, Ser and Tyr. The digestion of a honeybee peptide comprising six proline residues (apidaecin 1A) led to the detection of specific peptides terminated by proline as it was confirmed by MALDI postsource decay analysis. Copyright 2009 John Wiley & Sons, Ltd.

  1. N-Glycosylation Improves the Pepsin Resistance of Histidine Acid Phosphatase Phytases by Enhancing Their Stability at Acidic pHs and Reducing Pepsin's Accessibility to Its Cleavage Sites

    Science.gov (United States)

    Niu, Canfang; Luo, Huiying; Shi, Pengjun; Huang, Huoqing; Wang, Yaru; Yang, Peilong

    2015-01-01

    N-Glycosylation can modulate enzyme structure and function. In this study, we identified two pepsin-resistant histidine acid phosphatase (HAP) phytases from Yersinia kristensenii (YkAPPA) and Yersinia rohdei (YrAPPA), each having an N-glycosylation motif, and one pepsin-sensitive HAP phytase from Yersinia enterocolitica (YeAPPA) that lacked an N-glycosylation site. Site-directed mutagenesis was employed to construct mutants by altering the N-glycosylation status of each enzyme, and the mutant and wild-type enzymes were expressed in Pichia pastoris for biochemical characterization. Compared with those of the N-glycosylation site deletion mutants and N-deglycosylated enzymes, all N-glycosylated counterparts exhibited enhanced pepsin resistance. Introduction of the N-glycosylation site into YeAPPA as YkAPPA and YrAPPA conferred pepsin resistance, shifted the pH optimum (0.5 and 1.5 pH units downward, respectively) and improved stability at acidic pH (83.2 and 98.8% residual activities at pH 2.0 for 1 h). Replacing the pepsin cleavage sites L197 and L396 in the immediate vicinity of the N-glycosylation motifs of YkAPPA and YrAPPA with V promoted their resistance to pepsin digestion when produced in Escherichia coli but had no effect on the pepsin resistance of N-glycosylated enzymes produced in P. pastoris. Thus, N-glycosylation may improve pepsin resistance by enhancing the stability at acidic pH and reducing pepsin's accessibility to peptic cleavage sites. This study provides a strategy, namely, the manipulation of N-glycosylation, for improvement of phytase properties for use in animal feed. PMID:26637601

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. N-glycosylation and disulfide bonding affects GPRC6A receptor expression, function, and dimerization

    DEFF Research Database (Denmark)

    Nørskov-Lauritsen, Lenea; Jørgensen, Stine; Bräuner-Osborne, Hans

    2015-01-01

    Investigation of post-translational modifications of receptor proteins is important for our understanding of receptor pharmacology and disease physiology. However, our knowledge about post-translational modifications of class C G protein-coupled receptors and how these modifications regulate expr...... covalently linked dimers through cysteine disulfide linkage in the extracellular amino-terminal domain and here we show that GPRC6A indeed is a homodimer and that a disulfide bridge between the C131 residues is formed....

  8. The C-terminal N-glycosylation sites of the human α1,3/4-fucosyltransferase III, -V and -VI (hFucTIII, -V and -VI) are necessary for the expression of full enzyme activity

    DEFF Research Database (Denmark)

    Christensen, Lise Lotte; Jensen, Uffe Birk; Bross, Peter Gerd

    2000-01-01

    FucTIII enzyme activity to approximately 40% of the activity of the native enzyme. To further analyze the role of the conserved N-glycosylation sites in hFucTIII, -V, and -VI, we made a series of mutant genomic DNAs in which the asparagine residues in the potential C-terminal N-glycosylation sites were replaced...

  9. 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.

  10. Calreticulin discriminates the proximal region at the N-glycosylation site of Glc1Man9GlcNAc2 ligand

    Energy Technology Data Exchange (ETDEWEB)

    Hirano, Makoto; Adachi, Yuka [Department of Materials and Life Science, Seikei University, 3-3-1 Kichijoji-kita, Musashino, Tokyo 180-8633 (Japan); Ito, Yukishige [Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); ERATO, Japan Science and Technology Agency, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Totani, Kiichiro, E-mail: ktotani@st.seikei.ac.jp [Department of Materials and Life Science, Seikei University, 3-3-1 Kichijoji-kita, Musashino, Tokyo 180-8633 (Japan)

    2015-10-23

    Calreticulin (CRT) is well known as a lectin-like chaperone that recognizes Glc1Man9GlcNAc2 (G1M9)-glycoproteins in the endoplasmic reticulum (ER). However, whether CRT can directly interact with the aglycone moiety (protein portion) of the glycoprotein remains controversial. To improve our understanding of CRT interactions, structure-defined G1M9-derivatives with different aglycones (–OH, –Gly–NH{sub 2}, and –Gly–Glu–{sup t}Bu) were used as CRT ligands, and their interactions with recombinant CRT were analyzed using thermal shift analysis. The results showed that CRT binds strongly to a G1M9-ligand in the order –Gly–Glu–{sup t}Bu > –Gly–NH{sub 2} > –OH, which is the same as that of the reglucosylation of Man9GlcNAc2 (M9)-derivatives by the folding sensor enzyme UGGT (UDP-glucose: glycoprotein glucosyltransferase). Our results indicate that, similar to UGGT, CRT discriminates the proximal region at the N-glycosylation site, suggesting a similar mechanism mediating the recognition of aglycone moieties in the ER glycoprotein quality control system. - Highlights: • Glc1Man9GlcNAc2 (G1M9) ligands with different aglycones were chemically prepared. • Calreticulin (CRT) discriminates the aglycone of Glc1Man9GlcNAc2 (G1M9) ligand. • CRT binds with G1M9 ligands in a similar manner to folding sensor enzyme.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. Model-based analysis of N-glycosylation in Chinese hamster ovary cells

    DEFF Research Database (Denmark)

    Krambeck, Frederick J.; Bennun, Sandra V; Andersen, Mikael Rørdam

    2017-01-01

    The Chinese hamster ovary (CHO) cell is the gold standard for manufacturing of glycosylated recombinant proteins for production of biotherapeutics. The similarity of its glycosylation patterns to the human versions enable the products of this cell line favorable pharmacokinetic properties and lower...

  16. 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

  17. Importance of N-Glycosylation on CD147 for Its Biological Functions

    Science.gov (United States)

    Bai, Yang; Huang, Wan; Ma, Li-Tian; Jiang, Jian-Li; Chen, Zhi-Nan

    2014-01-01

    Glycosylation of glycoproteins is one of many molecular changes that accompany malignant transformation. Post-translational modifications of proteins are closely associated with the adhesion, invasion, and metastasis of tumor cells. CD147, a tumor-associated antigen that is highly expressed on the cell surface of various tumors, is a potential target for cancer diagnosis and therapy. A significant biochemical property of CD147 is its high level of glycosylation. Studies on the structure and function of CD147 glycosylation provide valuable clues to the development of targeted therapies for cancer. Here, we review current understanding of the glycosylation characteristics of CD147 and the glycosyltransferases involved in the biosynthesis of CD147 N-glycans. Finally, we discuss proteins regulating CD147 glycosylation and the biological functions of CD147 glycosylation. PMID:24739808

  18. Importance of N-Glycosylation on CD147 for Its Biological Functions

    Directory of Open Access Journals (Sweden)

    Yang Bai

    2014-04-01

    Full Text Available Glycosylation of glycoproteins is one of many molecular changes that accompany malignant transformation. Post-translational modifications of proteins are closely associated with the adhesion, invasion, and metastasis of tumor cells. CD147, a tumor-associated antigen that is highly expressed on the cell surface of various tumors, is a potential target for cancer diagnosis and therapy. A significant biochemical property of CD147 is its high level of glycosylation. Studies on the structure and function of CD147 glycosylation provide valuable clues to the development of targeted therapies for cancer. Here, we review current understanding of the glycosylation characteristics of CD147 and the glycosyltransferases involved in the biosynthesis of CD147 N-glycans. Finally, we discuss proteins regulating CD147 glycosylation and the biological functions of CD147 glycosylation.

  19. Cloning and expression of N-glycosylation-related glucosidase from Glaciozyma antarctica

    Science.gov (United States)

    Yajit, Noor Liana Mat; Kamaruddin, Shazilah; Hashim, Noor Haza Fazlin; Bakar, Farah Diba Abu; Murad, Abd. Munir Abd.; Mahadi, Nor Muhammad; Mackeen, Mukram Mohamed

    2016-11-01

    The need for functional oligosaccharides in various field is ever growing. The enzymatic approach for synthesis of oligosaccharides is advantageous over traditional chemical synthesis because of the regio- and stereo- selectivity that can be achieved without the need for protection chemistry. In this study, the α-glucosidase I protein sequence from Saccharomyces cerevisiae (UniProt database) was compared using Basic Local Alignment Search Tool (BLAST) with Glaciozyma antarctica genome database. Results showed 33% identity and an E-value of 1 × 10-125 for α-glucosidase I. The gene was amplified, cloned into the pPICZα C vector and used to transform Pichia pastoris X-33 cells. Soluble expression of α-Glucosidase I (˜91 kDa) was achieved at 28 °C with 1.0 % of methanol.

  20. 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

  1. 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

  2. Rapid chemical de-N-glycosylation and derivatization for liquid chromatography of immunoglobulin N-linked glycans.

    Directory of Open Access Journals (Sweden)

    Akihiko Kameyama

    Full Text Available Glycan analysis may result in exploitation of glycan biomarkers and evaluation of heterogeneity of glycosylation of biopharmaceuticals. For N-linked glycan analysis, we investigated alkaline hydrolysis of the asparagine glycosyl carboxamide of glycoproteins as a deglycosylation reaction. By adding hydroxylamine into alkaline de-N-glycosylation, we suppressed the degradation of released glycans and obtained a mixture of oximes, free glycans, and glycosylamines. The reaction was completed within 1 h, and the mixture containing oximes was easily tagged with 2-aminobenzamide by reductive amination. Here, we demonstrated N-linked glycan analysis using this method for a monoclonal antibody, and examined whether this method could liberate glycans without degradation from apo-transferrin containing NeuAc and NeuGc and horseradish peroxidase containing Fuc α1-3 GlcNAc at the reducing end. Furthermore, we compared glycan recoveries between conventional enzymatic glycan release and this method. Increasing the reaction temperature and reaction duration led to degradation, whereas decreasing these parameters resulted in lower release. Considering this balance, we proposed to carry out the reaction at 80°C for 1 h for asialo glycoproteins from mammals and at 50°C for 1 h for sialoglycoproteins.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. N-glycosylated catalytic unit meets O-glycosylated propeptide: complex protein architecture in a fungal hexosaminidase

    Czech Academy of Sciences Publication Activity Database

    Plíhal, Ondřej; Sklenář, Jan; Kmoníčková, J.; Man, Petr; Pompach, Petr; Havlíček, Vladimír; Křen, Vladimír; Bezouška, Karel

    2004-01-01

    Roč. 32, č. 5 (2004), s. 764-765 ISSN 0300-5127 R&D Projects: GA ČR GA203/04/1045 Institutional research plan: CEZ:AV0Z5020903 Keywords : asperillus oryzoe * glycosyl hydrolase * preproprotein Subject RIV: EE - Microbiology, Virology Impact factor: 2.267, year: 2004

  9. Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins.

    Science.gov (United States)

    Irani, Zahra Azimzadeh; Kerkhoven, Eduard J; Shojaosadati, Seyed Abbas; Nielsen, Jens

    2016-05-01

    Pichia pastoris is used for commercial production of human therapeutic proteins, and genome-scale models of P. pastoris metabolism have been generated in the past to study the metabolism and associated protein production by this yeast. A major challenge with clinical usage of recombinant proteins produced by P. pastoris is the difference in N-glycosylation of proteins produced by humans and this yeast. However, through metabolic engineering, a P. pastoris strain capable of producing humanized N-glycosylated proteins was constructed. The current genome-scale models of P. pastoris do not address native nor humanized N-glycosylation, and we therefore developed ihGlycopastoris, an extension to the iLC915 model with both native and humanized N-glycosylation for recombinant protein production, but also an estimation of N-glycosylation of P. pastoris native proteins. This new model gives a better prediction of protein yield, demonstrates the effect of the different types of N-glycosylation of protein yield, and can be used to predict potential targets for strain improvement. The model represents a step towards a more complete description of protein production in P. pastoris, which is required for using these models to understand and optimize protein production processes. © 2015 Wiley Periodicals, Inc.

  10. 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

  11. N-Glycosylation of an IgG antibody secreted by Nicotiana tabacum BY-2 cells can be modulated through co-expression of human β-1,4-galactosyltransferase.

    Science.gov (United States)

    Navarre, Catherine; Smargiasso, Nicolas; Duvivier, Laurent; Nader, Joseph; Far, Johann; De Pauw, Edwin; Boutry, Marc

    2017-06-01

    Nicotiana tabacum BY-2 suspension cells have several advantages that make them suitable for the production of full-size monoclonal antibodies which can be purified directly from the culture medium. Carbohydrate characterization of an antibody (Lo-BM2) expressed in N. tabacum BY-2 cells showed that the purified Lo-BM2 displays N-glycan homogeneity with a high proportion (>70%) of the complex GnGnXF glycoform. The stable co-expression of a human β-1,4-galactosyltransferase targeted to different Golgi sub-compartments altered Lo-BM2N-glycosylation and resulted in the production of an antibody that exhibited either hybrid structures containing a low abundance of the plant epitopes (α-1,3-fucose and β-1,2-xylose), or a large amount of galactose-extended N-glycan structures. These results demonstrate the suitability of stable N-glycoengineered N. tabacum BY-2 cell lines for the production of human-like antibodies.

  12. 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

  13. 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.

  14. 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

  15. 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)

  16. [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.

  17. 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.

  18. 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.

  19. 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...

  20. 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...

  1. 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.

  2. 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

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

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    Suh Moo-Jin

    2012-04-01

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

  4. 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

  5. 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...

  6. 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.

  7. 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.

  8. 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.

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

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    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.

  10. 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.

  11. 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

  12. 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.

  13. Structure of the dimeric N-glycosylated form of fungal β-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies

    Directory of Open Access Journals (Sweden)

    Sklenář Jan

    2007-05-01

    Full Text Available Abstract Background Fungal β-N-acetylhexosaminidases catalyze the hydrolysis of chitobiose into its constituent monosaccharides. These enzymes are physiologically important during the life cycle of the fungus for the formation of septa, germ tubes and fruit-bodies. Crystal structures are known for two monomeric bacterial enzymes and the dimeric human lysosomal β-N-acetylhexosaminidase. The fungal β-N-acetylhexosaminidases are robust enzymes commonly used in chemoenzymatic syntheses of oligosaccharides. The enzyme from Aspergillus oryzae was purified and its sequence was determined. Results The complete primary structure of the fungal β-N-acetylhexosaminidase from Aspergillus oryzae CCF1066 was used to construct molecular models of the catalytic subunit of the enzyme, the enzyme dimer, and the N-glycosylated dimer. Experimental data were obtained from infrared and Raman spectroscopy, and biochemical studies of the native and deglycosylated enzyme, and are in good agreement with the models. Enzyme deglycosylated under native conditions displays identical kinetic parameters but is significantly less stable in acidic conditions, consistent with model predictions. The molecular model of the deglycosylated enzyme was solvated and a molecular dynamics simulation was run over 20 ns. The molecular model is able to bind the natural substrate – chitobiose with a stable value of binding energy during the molecular dynamics simulation. Conclusion Whereas the intracellular bacterial β-N-acetylhexosaminidases are monomeric, the extracellular secreted enzymes of fungi and humans occur as dimers. Dimerization of the fungal β-N-acetylhexosaminidase appears to be a reversible process that is strictly pH dependent. Oligosaccharide moieties may also participate in the dimerization process that might represent a unique feature of the exclusively extracellular enzymes. Deglycosylation had only limited effect on enzyme activity, but it significantly affected

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

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    Mateus Rocha de Paula

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

  15. 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

  16. 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.

  17. 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.

  18. Differences in N-glycosylation of recombinant human coagulation factor VII derived from BHK, CHO, and HEK293 cells.

    Science.gov (United States)

    Böhm, Ernst; Seyfried, Birgit K; Dockal, Michael; Graninger, Michael; Hasslacher, Meinhard; Neurath, Marianne; Konetschny, Christian; Matthiessen, Peter; Mitterer, Artur; Scheiflinger, Friedrich

    2015-09-18

    BACKGROUND & Recombinant factor VII (rFVII), the precursor molecule for recombinant activated FVII (rFVIIa), is, due to its need for complex post translational modifications, produced in mammalian cells. To evaluate the suitability of a human cell line in order to produce rFVII with post-translational modifications as close as possible to pdFVII, we compared the biochemical properties of rFVII synthesized in human embryonic kidney-derived (HEK)293 cells (HEK293rFVII) with those of rFVII expressed in Chinese hamster ovary (CHO, CHOrFVII) and baby hamster kidney (BHK, BHKrFVII) cells, and also with those of plasma derived FVII (pdFVII), using various analytical methods. rFVII was purified from selected production clones derived from BHK, CHO, and HEK293 cells after stable transfection, and rFVII isolates were analyzed for protein activity, impurities and post-translational modifications. RESULTS & The analytical results showed no apparent gross differences between the various FVII proteins, except in their N-linked glycosylation pattern. Most N-glycans found on rFVII produced in HEK293 cells were not detected on rFVII from CHO and BHK cells, or, somewhat unexpectedly, on pdFVII; all other protein features were similar. HEK293rFVII glycans were mainly characterized by a higher structural variety and a lower degree of terminal sialylation, and a high amount of terminal N-acetyl galactosamines (GalNAc). All HEK293rFVII oligosaccharides contained one or more fucoses (Fuc), as well as hybrid and high mannose (Man) structures. From all rFVII isolates investigated, CHOrFVII contained the highest degree of sialylation and no terminal GalNAc, and CHO cells were therefore assumed to be the best option for the production of rFVII.

  19. 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

  20. Identification of Residues Important for the Activity of Haloferax volcanii AglD, a Component of the Archaeal N-Glycosylation Pathway

    Directory of Open Access Journals (Sweden)

    Lina Kaminski

    2010-01-01

    Full Text Available In Haloferax volcanii, AglD adds the final hexose to the N-linked pentasaccharide decorating the S-layer glycoprotein. Not knowing the natural substrate of the glycosyltransferase, together with the challenge of designing assays compatible with hypersalinity, has frustrated efforts at biochemical characterization of AglD activity. To circumvent these obstacles, an in vivo assay designed to identify amino acid residues important for AglD activity is described. In the assay, restoration of AglD function in an Hfx. volcanii aglD deletion strain transformed to express plasmid-encoded versions of AglD, generated through site-directed mutagenesis at positions encoding residues conserved in archaeal homologues of AglD, is reflected in the behavior of a readily detectable reporter of N-glycosylation. As such Asp110 and Asp112 were designated as elements of the DXD motif of AglD, a motif that interacts with metal cations associated with nucleotide-activated sugar donors, while Asp201 was predicted to be the catalytic base of the enzyme.

  1. Identification of residues important for the activity of Haloferax volcanii AglD, a component of the archaeal N-glycosylation pathway.

    Science.gov (United States)

    Kaminski, Lina; Eichler, Jerry

    2010-05-06

    In Haloferax volcanii, AglD adds the final hexose to the N-linked pentasaccharide decorating the S-layer glycoprotein. Not knowing the natural substrate of the glycosyltransferase, together with the challenge of designing assays compatible with hypersalinity, has frustrated efforts at biochemical characterization of AglD activity. To circumvent these obstacles, an in vivo assay designed to identify amino acid residues important for AglD activity is described. In the assay, restoration of AglD function in an Hfx. volcanii aglD deletion strain transformed to express plasmid-encoded versions of AglD, generated through site-directed mutagenesis at positions encoding residues conserved in archaeal homologues of AglD, is reflected in the behavior of a readily detectable reporter of N-glycosylation. As such Asp110 and Asp112 were designated as elements of the DXD motif of AglD, a motif that interacts with metal cations associated with nucleotide-activated sugar donors, while Asp201 was predicted to be the catalytic base of the enzyme.

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

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    Manuel Bauer

    2015-12-01

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

  3. GlcNAc-1-P-transferase–tunicamycin complex structure reveals basis for inhibition of N-glycosylation

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Jiho; Mashalidis, Ellene H.; Kuk, Alvin C. Y.; Yamamoto, Kazuki; Kaeser, Benjamin; Ichikawa, Satoshi; Lee, Seok-Yong

    2018-02-19

    N-linked glycosylation is a predominant post-translational modification of protein in eukaryotes, and its dysregulation is the etiology of several human disorders. The enzyme UDP-N-acetylglucosamine:dolichyl-phosphate N-acetylglucosaminephosphotransferase (GlcNAc-1-P-transferase or GPT) catalyzes the first and committed step of N-linked glycosylation in the endoplasmic reticulum membrane, and it is the target of the natural product tunicamycin. Tunicamycin has potent antibacterial activity, inhibiting the bacterial cell wall synthesis enzyme MraY, but its usefulness as an antibiotic is limited by off-target inhibition of human GPT. Our understanding of how tunicamycin inhibits N-linked glycosylation and efforts to selectively target MraY are hampered by a lack of structural information. Here we present crystal structures of human GPT in complex with tunicamycin. In conclusion, structural and functional analyses reveal the difference between GPT and MraY in their mechanisms of inhibition by tunicamycin. We demonstrate that this difference could be exploited to design MraY-specific inhibitors as potential antibiotics.

  4. 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.

  5. Isolation, N-glycosylations and Function of a Hyaluronidase-Like Enzyme from the Venom of the Spider Cupiennius salei.

    Directory of Open Access Journals (Sweden)

    Olivier Biner

    Full Text Available Hyaluronidases are important venom components acting as spreading factor of toxic compounds. In several studies this spreading effect was tested on vertebrate tissue. However, data about the spreading activity on invertebrates, the main prey organisms of spiders, are lacking. Here, a hyaluronidase-like enzyme was isolated from the venom of the spider Cupiennius salei. The amino acid sequence of the enzyme was determined by cDNA analysis of the venom gland transcriptome and confirmed by protein analysis. Two complex N-linked glycans akin to honey bee hyaluronidase glycosylations, were identified by tandem mass spectrometry. A C-terminal EGF-like domain was identified in spider hyaluronidase using InterPro. The spider hyaluronidase-like enzyme showed maximal activity at acidic pH, between 40-60°C, and 0.2 M KCl. Divalent ions did not enhance HA degradation activity, indicating that they are not recruited for catalysis.Besides hyaluronan, the enzyme degrades chondroitin sulfate A, whereas heparan sulfate and dermatan sulfate are not affected. The end products of hyaluronan degradation are tetramers, whereas chondroitin sulfate A is mainly degraded to hexamers. Identification of terminal N-acetylglucosamine or N-acetylgalactosamine at the reducing end of the oligomers identified the enzyme as an endo-β-N-acetyl-D-hexosaminidase hydrolase. The spreading effect of the hyaluronidase-like enzyme on invertebrate tissue was studied by coinjection of the enzyme with the Cupiennius salei main neurotoxin CsTx-1 into Drosophila flies. The enzyme significantly enhances the neurotoxic activity of CsTx-1. Comparative substrate degradation tests with hyaluronan, chondroitin sulfate A, dermatan sulfate, and heparan sulfate with venoms from 39 spider species from 21 families identified some spider families (Atypidae, Eresidae, Araneidae and Nephilidae without activity of hyaluronidase-like enzymes. This is interpreted as a loss of this enzyme and fits quite well

  6. Isolation, N-glycosylations and Function of a Hyaluronidase-Like Enzyme from the Venom of the Spider Cupiennius salei

    Science.gov (United States)

    Trachsel, Christian; Moser, Aline; Kopp, Lukas; Langenegger, Nicolas; Kämpfer, Urs; von Ballmoos, Christoph; Nentwig, Wolfgang; Schürch, Stefan; Schaller, Johann

    2015-01-01

    Structure of Cupiennius salei venom hyaluronidase Hyaluronidases are important venom components acting as spreading factor of toxic compounds. In several studies this spreading effect was tested on vertebrate tissue. However, data about the spreading activity on invertebrates, the main prey organisms of spiders, are lacking. Here, a hyaluronidase-like enzyme was isolated from the venom of the spider Cupiennius salei. The amino acid sequence of the enzyme was determined by cDNA analysis of the venom gland transcriptome and confirmed by protein analysis. Two complex N-linked glycans akin to honey bee hyaluronidase glycosylations, were identified by tandem mass spectrometry. A C-terminal EGF-like domain was identified in spider hyaluronidase using InterPro. The spider hyaluronidase-like enzyme showed maximal activity at acidic pH, between 40–60°C, and 0.2 M KCl. Divalent ions did not enhance HA degradation activity, indicating that they are not recruited for catalysis. Function of venom hyaluronidases Besides hyaluronan, the enzyme degrades chondroitin sulfate A, whereas heparan sulfate and dermatan sulfate are not affected. The end products of hyaluronan degradation are tetramers, whereas chondroitin sulfate A is mainly degraded to hexamers. Identification of terminal N-acetylglucosamine or N-acetylgalactosamine at the reducing end of the oligomers identified the enzyme as an endo-β-N-acetyl-D-hexosaminidase hydrolase. The spreading effect of the hyaluronidase-like enzyme on invertebrate tissue was studied by coinjection of the enzyme with the Cupiennius salei main neurotoxin CsTx-1 into Drosophila flies. The enzyme significantly enhances the neurotoxic activity of CsTx-1. Comparative substrate degradation tests with hyaluronan, chondroitin sulfate A, dermatan sulfate, and heparan sulfate with venoms from 39 spider species from 21 families identified some spider families (Atypidae, Eresidae, Araneidae and Nephilidae) without activity of hyaluronidase-like enzymes

  7. 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.

  8. Processing, fusogenicity, virion incorporation and CXCR4-binding activity of a feline immunodeficiency virus envelope glycoprotein lacking the two conserved N-glycosylation sites at the C-terminus of the V3 domain.

    Science.gov (United States)

    González, Silvia A; Affranchino, José L

    2016-07-01

    The process of feline immunodeficiency virus (FIV) entry into its target cells is initiated by the association of the surface (SU) subunit of the viral envelope glycoprotein (Env) with the cellular receptors CD134 and CXCR4. This event is followed by the fusion of the viral and cellular membranes, which is mediated by the transmembrane (TM) subunit of Env. We and others have previously demonstrated that the V3 domain of the SU subunit of Env is essential for CXCR4 binding. Of note, there are two contiguous and highly conserved potential N-glycosylation sites ((418)NST(420) and (422)NLT(424)) located at the C-terminal side of the V3 domain. We therefore decided to study the relevance for Env functions of these N-glycosylation motifs and found that disruption of both of them by introducing the N418Q/N422Q double amino acid substitution drastically impairs Env processing into the SU and TM subunits. Moreover, the simultaneous mutation of these N-glycosylation sites prevents Env incorporation into virions and Env-mediated cell-to-cell fusion. Notably, a recombinant soluble version of the SU glycoprotein carrying the double amino acid replacement N418Q/N422Q at the V3 C-terminal side binds to CXCR4 with an efficiency similar to that of wild-type SU.

  9. 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.

  10. 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)

  11. 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

  12. Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins

    DEFF Research Database (Denmark)

    Irani, Zahra Azimzadeh; Kerkhoven, Eduard J.; Shojaosadati, Seyed Abbas

    2016-01-01

    prediction of protein yield, demonstrates the effect of the different types of N-glycosylation of protein yield, and can be used to predict potential targets for strain improvement. The model represents a step towards a more complete description of protein production in P. pastoris, which is required...... for using these models to understand and optimize protein production processes....

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. A new strategy for identification of N-glycosylated proteins and unambiguous assignment of their glycosylation sites using HILIC enrichment and partial deglycosylation

    DEFF Research Database (Denmark)

    Hägglund, Per; Bunkenborg, Jakob; Elortza, Felix

    2004-01-01

    remains linked to the asparagine residue. The removal of the major part of the glycan simplifies the MS/MS fragment ion spectra of glycopeptides, while the remaining GlcNAc residue enables unambiguous assignment of the glycosylation site together with the amino acid sequence. We first tested our approach...

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Influence of culture medium supplementation of tobacco NT1 cell suspension cultures on the N-glycosylation of human secreted alkaline phosphatase.

    Science.gov (United States)

    Becerra-Arteaga, Alejandro; Shuler, Michael L

    2007-08-15

    We report for the first time that culture conditions, specifically culture medium supplementation with nucleotide-sugar precursors, can alter significantly the N-linked glycosylation of a recombinant protein in plant cell culture. Human secreted alkaline phosphatase produced in tobacco NT1 cell suspension cultures was used as a model system. Plant cell cultures were supplemented with ammonia (30 mM), galactose (1 mM) and glucosamine (10 mM) to improve the extent of N-linked glycosylation. The highest levels of cell density and active extracellular SEAP in supplemented cultures were on average 260 g/L and 0.21 U/mL, respectively, compared to 340 g/L and 0.4 U/mL in unsupplemented cultures. The glycosylation profile of SEAP produced in supplemented cultures was determined via electrospray ionization mass spectrometry with precursor ion scanning and compared to that of SEAP produced in unsupplemented cultures. In supplemented and unsupplemented cultures, two biantennary complex-type structures terminated with one or two N-acetylglucosamines and one paucimannosidic glycan structure comprised about 85% of the SEAP glycan pool. These three structures contained plant-specific xylose and fucose residues and their relative abundances were affected by each supplement. High mannose structures (6-9 mannose residues) accounted for the remaining 15% glycans in all cases. The highest proportion (approximately 66%) of a single complex-type biantennary glycan structure terminated in both antennae by N- acetylglucosamine was obtained with glucosamine supplementation versus only 6% in unsupplemented medium. This structure is amenable for in vitro modification to yield a more human-like glycan and could serve as a route to plant cell culture produced therapeutic glycoproteins. (c) 2007 Wiley Periodicals, Inc.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

    Directory of Open Access Journals (Sweden)

    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

  9. 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.

  10. 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...

  11. 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

  12. 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.

  13. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  15. 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.

  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

    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...

  17. 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...

  18. 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.

  19. 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.

  20. Diagnostic accuracy of urinary prostate protein glycosylation profiling in prostatitis diagnosis.

    Science.gov (United States)

    Vermassen, Tijl; Van Praet, Charles; Poelaert, Filip; Lumen, Nicolaas; Decaestecker, Karel; Hoebeke, Piet; Van Belle, Simon; Rottey, Sylvie; Delanghe, Joris

    2015-01-01

    Although prostatitis is a common male urinary tract infection, clinical diagnosis of prostatitis is difficult. The developmental mechanism of prostatitis is not yet unraveled which led to the elaboration of various biomarkers. As changes in asparagine-linked-(N-)-glycosylation were observed between healthy volunteers (HV), patients with benign prostate hyperplasia and prostate cancer patients, a difference could exist in biochemical parameters and urinary N-glycosylation between HV and prostatitis patients. We therefore investigated if prostatic protein glycosylation could improve the diagnosis of prostatitis. Differences in serum and urine biochemical markers and in total urine N-glycosylation profile of prostatic proteins were determined between HV (N=66) and prostatitis patients (N=36). Additionally, diagnostic accuracy of significant biochemical markers and changes in N-glycosylation was assessed. Urinary white blood cell (WBC) count enabled discrimination of HV from prostatitis patients (Pprostatitis patients from HV (Pprostatitis patients compared to HV (Pprostatitis. Further research is required to unravel the developmental course of prostatic inflammation.

  1. 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.

  2. 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

  3. 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

  4. Characterization of the carbohydrate components of Taenia solium oncosphere proteins and their role in the antigenicity.

    Science.gov (United States)

    Arana, Yanina; Verastegui, Manuela; Tuero, Iskra; Grandjean, Louis; Garcia, Hector H; Gilman, Robert H

    2013-10-01

    This study examines the carbohydrate composition of Taenia solium whole oncosphere antigens (WOAs), in order to improve the understanding of the antigenicity of the T. solium. Better knowledge of oncosphere antigens is crucial to accurately diagnose previous exposure to T. solium eggs and thus predict the development of neurocysticercosis. A set of seven lectins conjugates with wide carbohydrate specificity were used on parasite fixations and somatic extracts. Lectin fluorescence revealed that D-mannose, D-glucose, D-galactose and N-acetyl-D-galactosamine residues were the most abundant constituents of carbohydrate chains on the surface of T. solium oncosphere. Lectin blotting showed that posttranslational modification with N-glycosylation was abundant while little evidence of O-linked carbohydrates was observed. Chemical oxidation and enzymatic deglycosylation in situ were performed to investigate the immunoreactivity of the carbohydrate moieties. Linearizing or removing the carbohydrate moieties from the protein backbones did not diminish the immunoreactivity of these antigens, suggesting that a substantial part of the host immune response against T. solium oncosphere is directed against the peptide epitopes on the parasite antigens. Finally, using carbohydrate probes, we demonstrated for the first time that the presence of several lectins on the surface of the oncosphere was specific to carbohydrates found in intestinal mucus, suggesting a possible role in initial attachment of the parasite to host cells.

  5. 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.

  6. 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

  7. Physical stability comparisons of IgG1-Fc variants: effects of N-glycosylation site occupancy and Asp/Gln residues at site Asn 297.

    Science.gov (United States)

    Alsenaidy, Mohammad A; Okbazghi, Solomon Z; Kim, Jae Hyun; Joshi, Sangeeta B; Middaugh, C Russell; Tolbert, Thomas J; Volkin, David B

    2014-06-01

    The structural integrity and conformational stability of various IgG1-Fc proteins produced from the yeast Pichia pastoris with different glycosylation site occupancy (di-, mono-, and nonglycosylated) were determined. In addition, the physical stability profiles of three different forms of nonglycosylated Fc molecules (varying amino-acid residues at site 297 in the CH 2 domain due to the point mutations and enzymatic digestion of the Fc glycoforms) were also examined. The physical stability of these IgG1-Fc glycoproteins was examined as a function of pH and temperature by high-throughput biophysical analysis using multiple techniques combined with data visualization tools (three index empirical phase diagrams and radar charts). Across the pH range of 4.0-6.0, the di- and monoglycosylated forms of the IgG1-Fc showed the highest and lowest levels of physical stability, respectively, with the nonglycosylated forms showing intermediate stability depending on solution pH. In the aglycosylated Fc proteins, the introduction of Asp (D) residues at site 297 (QQ vs. DN vs. DD forms) resulted in more subtle changes in structural integrity and physical stability depending on solution pH. The utility of evaluating the conformational stability profile differences between the various IgG1-Fc glycoproteins is discussed in the context of analytical comparability studies. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

  8. 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...

  9. 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

  10. 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.

  11. 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.

  12. The interaction between the first transmembrane domain and the thumb of ASIC1a is critical for its N-glycosylation and trafficking.

    Directory of Open Access Journals (Sweden)

    Lan Jing

    Full Text Available Acid-sensing ion channel-1a (ASIC1a, the primary proton receptor in the brain, contributes to multiple diseases including stroke, epilepsy and multiple sclerosis. Thus, a better understanding of its biogenesis will provide important insights into the regulation of ASIC1a in diseases. Interestingly, ASIC1a contains a large, yet well organized ectodomain, which suggests the hypothesis that correct formation of domain-domain interactions at the extracellular side is a key regulatory step for ASIC1a maturation and trafficking. We tested this hypothesis here by focusing on the interaction between the first transmembrane domain (TM1 and the thumb of ASIC1a, an interaction known to be critical in channel gating. We mutated Tyr71 and Trp287, two key residues involved in the TM1-thumb interaction in mouse ASIC1a, and found that both Y71G and W287G decreased synaptic targeting and surface expression of ASIC1a. These defects were likely due to altered folding; both mutants showed increased resistance to tryptic cleavage, suggesting a change in conformation. Moreover, both mutants lacked the maturation of N-linked glycans through mid to late Golgi. These data suggest that disrupting the interaction between TM1 and thumb alters ASIC1a folding, impedes its glycosylation and reduces its trafficking. Moreover, reducing the culture temperature, an approach commonly used to facilitate protein folding, increased ASIC1a glycosylation, surface expression, current density and slowed the rate of desensitization. These results suggest that correct folding of extracellular ectodomain plays a critical role in ASIC1a biogenesis and function.

  13. N-glycosylation profile of undifferentiated and adipogenically differentiated human bone marrow mesenchymal stem cells: towards a next generation of stem cell markers.

    Science.gov (United States)

    Hamouda, Houda; Ullah, Mujib; Berger, Markus; Sittinger, Michael; Tauber, Rudolf; Ringe, Jochen; Blanchard, Véronique

    2013-12-01

    Mesenchymal stem cells (MSCs) are multipotent cells that are easy to isolate and expand, develop into several tissues, including fat, migrate to diseased organs, have immunosuppressive properties and secrete regenerative factors. This makes MSCs ideal for regenerative medicine. For application and regulatory purposes, knowledge of (bio)markers characterizing MSCs and their development stages is of paramount importance. The cell surface is coated with glycans that possess lineage-specific nature, which makes glycans to be promising candidate markers. In the context of soft tissue generation, we aimed to identify glycans that could be markers for MSCs and their adipogenically differentiated progeny. MSCs were isolated from human bone marrow, adipogenically stimulated for 15 days and adipogenesis was verified by staining the lipid droplets and quantitative real time polymerase chain reaction of the marker genes peroxisome proliferator-activated receptor gamma (PPARG) and fatty acid binding protein-4 (FABP4). Using matrix-assisted laser desorption-ionization-time of flight mass spectrometry combined with exoglycosidase digestions, we report for the first time the N-glycome of MSCs during adipogenic differentiation. We were able to detect more than 100 different N-glycans, including high-mannose, hybrid, and complex N-glycans, as well as poly-N-acetyllactosamine chains. Adipogenesis was accompanied by an increased amount of biantennary fucosylated structures, decreased amount of fucosylated, afucosylated tri- and tetraantennary structures and increased sialylation. N-glycans H6N5F1 and H7N6F1 were significantly overexpressed in undifferentiated MSCs while H3N4F1 and H5N4F3 were upregulated in adipogenically differentiated MSCs. These glycan structures are promising candidate markers to detect and distinguish MSCs and their adipogenic progeny.

  14. 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.

  15. 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).

  16. The glycosylation status of the murine hepatitis coronavirus M protein affects the interferogenic capacity of the virus in vitro and its ability to replicate in the liver but not the brain

    International Nuclear Information System (INIS)

    Haan, Cornelis A.M. de; Wit, Marel de; Kuo, Lili; Montalto-Morrison, Cynthia; Haagmans, Bart L.; Weiss, Susan R.; Masters, Paul S.; Rottier, Peter J.M.

    2003-01-01

    The coronavirus M protein, the most abundant coronaviral envelope component, is invariably glycosylated, which provides the virion with a diffuse, hydrophilic cover on its outer surface. Remarkably, while the group 1 and group 3 coronaviruses all have M proteins with N-linked sugars, the M proteins of the group 2 coronaviruses [e.g., mouse hepatitis virus (MHV)] are O-glycosylated. The conservation of the N- and O-glycosylation motifs suggests that each of these types of carbohydrate modifications is beneficial to their respective virus. Since glycosylation of the M protein is not required for virus assembly, the oligosaccharides are likely to be involved in the virus-host interaction. In order to investigate the role of the M protein glycosylation in the host, two genetically modified MHVs were generated by using targeted RNA recombination. The recombinant viruses carried M proteins that were either N-glycosylated or not glycosylated at all, and these were compared with the parental, O-glycosylated, virus. The M protein glycosylation state did not influence the tissue culture growth characteristics of the recombinant viruses. However, it affected their interferogenic capacity as measured using fixed, virus-infected cells. Viruses containing M proteins with N-linked sugars induced type I interferons to higher levels than viruses carrying M proteins with O-linked sugars. MHV with unglycosylated M proteins appeared to be a poor interferon inducer. In mice, the recombinant viruses differed in their ability to replicate in the liver, but not in the brain, whereas their in vivo interferogenic capacity did not appear to be affected by their glycosylation status. Strikingly, their abilities to replicate in the liver correlated with their in vitro interferogenic capacity. This apparent correlation might be explained by the functioning of lectins, such as the mannose receptor, which are abundantly expressed in the liver but also play a role in the induction of interferon

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

    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

  18. 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

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

    Science.gov (United States)

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

    2010-10-01

    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.

  20. Human Plasma N-glycosylation as Analyzed by Matrix-Assisted Laser Desorption/Ionization-Fourier Transform Ion Cyclotron Resonance-MS Associates with Markers of Inflammation and Metabolic Health*

    Science.gov (United States)

    Reiding, Karli R.; Ruhaak, L. Renee; Uh, Hae-Won; el Bouhaddani, Said; van den Akker, Erik B.; Plomp, Rosina; McDonnell, Liam A.; Houwing-Duistermaat, Jeanine J.; Slagboom, P. Eline; Beekman, Marian; Wuhrer, Manfred

    2017-01-01

    Glycosylation is an abundant co- and post-translational protein modification of importance to protein processing and activity. Although not template-defined, glycosylation does reflect the biological state of an organism and is a high-potential biomarker for disease and patient stratification. However, to interpret a complex but informative sample like the total plasma N-glycome, it is important to establish its baseline association with plasma protein levels and systemic processes. Thus far, large-scale studies (n >200) of the total plasma N-glycome have been performed with methods of chromatographic and electrophoretic separation, which, although being informative, are limited in resolving the structural complexity of plasma N-glycans. MS has the opportunity to contribute additional information on, among others, antennarity, sialylation, and the identity of high-mannose type species. Here, we have used matrix-assisted laser desorption/ionization (MALDI)-Fourier transform ion cyclotron resonance (FTICR)-MS to study the total plasma N-glycome of 2144 healthy middle-aged individuals from the Leiden Longevity Study, to allow association analysis with markers of metabolic health and inflammation. To achieve this, N-glycans were enzymatically released from their protein backbones, labeled at the reducing end with 2-aminobenzoic acid, and following purification analyzed by negative ion mode intermediate pressure MALDI-FTICR-MS. In doing so, we achieved the relative quantification of 61 glycan compositions, ranging from Hex4HexNAc2 to Hex7HexNAc6dHex1Neu5Ac4, as well as that of 39 glycosylation traits derived thereof. Next to confirming known associations of glycosylation with age and sex by MALDI-FTICR-MS, we report novel associations with C-reactive protein (CRP), interleukin 6 (IL-6), body mass index (BMI), leptin, adiponectin, HDL cholesterol, triglycerides (TG), insulin, gamma-glutamyl transferase (GGT), alanine aminotransferase (ALT), and smoking. Overall, the

  1. Human Plasma N-glycosylation as Analyzed by Matrix-Assisted Laser Desorption/Ionization-Fourier Transform Ion Cyclotron Resonance-MS Associates with Markers of Inflammation and Metabolic Health.

    Science.gov (United States)

    Reiding, Karli R; Ruhaak, L Renee; Uh, Hae-Won; El Bouhaddani, Said; van den Akker, Erik B; Plomp, Rosina; McDonnell, Liam A; Houwing-Duistermaat, Jeanine J; Slagboom, P Eline; Beekman, Marian; Wuhrer, Manfred

    2017-02-01

    Glycosylation is an abundant co- and post-translational protein modification of importance to protein processing and activity. Although not template-defined, glycosylation does reflect the biological state of an organism and is a high-potential biomarker for disease and patient stratification. However, to interpret a complex but informative sample like the total plasma N-glycome, it is important to establish its baseline association with plasma protein levels and systemic processes. Thus far, large-scale studies (n >200) of the total plasma N-glycome have been performed with methods of chromatographic and electrophoretic separation, which, although being informative, are limited in resolving the structural complexity of plasma N-glycans. MS has the opportunity to contribute additional information on, among others, antennarity, sialylation, and the identity of high-mannose type species.Here, we have used matrix-assisted laser desorption/ionization (MALDI)-Fourier transform ion cyclotron resonance (FTICR)-MS to study the total plasma N-glycome of 2144 healthy middle-aged individuals from the Leiden Longevity Study, to allow association analysis with markers of metabolic health and inflammation. To achieve this, N-glycans were enzymatically released from their protein backbones, labeled at the reducing end with 2-aminobenzoic acid, and following purification analyzed by negative ion mode intermediate pressure MALDI-FTICR-MS. In doing so, we achieved the relative quantification of 61 glycan compositions, ranging from Hex 4 HexNAc 2 to Hex 7 HexNAc 6 dHex 1 Neu5Ac 4 , as well as that of 39 glycosylation traits derived thereof. Next to confirming known associations of glycosylation with age and sex by MALDI-FTICR-MS, we report novel associations with C-reactive protein (CRP), interleukin 6 (IL-6), body mass index (BMI), leptin, adiponectin, HDL cholesterol, triglycerides (TG), insulin, gamma-glutamyl transferase (GGT), alanine aminotransferase (ALT), and smoking. Overall

  2. A two-step recognition of signal sequences determines the translocation efficiency of proteins.

    OpenAIRE

    Belin, D; Bost, S; Vassalli, J D; Strub, K

    1996-01-01

    The cytosolic and secreted, N-glycosylated, forms of plasminogen activator inhibitor-2 (PAI-2) are generated by facultative translocation. To study the molecular events that result in the bi-topological distribution of proteins, we determined in vitro the capacities of several signal sequences to bind the signal recognition particle (SRP) during targeting, and to promote vectorial transport of murine PAI-2 (mPAI-2). Interestingly, the six signal sequences we compared (mPAI-2 and three mutated...

  3. 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

  4. Trafficking and processing of bacterial proteins by mammalian cells: Insights from chondroitinase ABC.

    Science.gov (United States)

    Muir, Elizabeth; Raza, Mansoor; Ellis, Clare; Burnside, Emily; Love, Fiona; Heller, Simon; Elliot, Matthew; Daniell, Esther; Dasgupta, Debayan; Alves, Nuno; Day, Priscilla; Fawcett, James; Keynes, Roger

    2017-01-01

    There is very little reported in the literature about the relationship between modifications of bacterial proteins and their secretion by mammalian cells that synthesize them. We previously reported that the secretion of the bacterial enzyme Chondroitinase ABC by mammalian cells requires the strategic removal of at least three N-glycosylation sites. The aim of this study was to determine if it is possible to enhance the efficacy of the enzyme as a treatment for spinal cord injury by increasing the quantity of enzyme secreted or by altering its cellular location. To determine if the efficiency of enzyme secretion could be further increased, cells were transfected with constructs encoding the gene for chondroitinase ABC modified for expression by mammalian cells; these contained additional modifications of strategic N-glycosylation sites or alternative signal sequences to direct secretion of the enzyme from the cells. We show that while removal of certain specific N-glycosylation sites enhances enzyme secretion, N-glycosylation of at least two other sites, N-856 and N-773, is essential for both production and secretion of active enzyme. Furthermore, we find that the signal sequence directing secretion also influences the quantity of enzyme secreted, and that this varies widely amongst the cell types tested. Last, we find that replacing the 3'UTR on the cDNA encoding Chondroitinase ABC with that of β-actin is sufficient to target the enzyme to the neuronal growth cone when transfected into neurons. This also enhances neurite outgrowth on an inhibitory substrate. Some intracellular trafficking pathways are adversely affected by cryptic signals present in the bacterial gene sequence, whilst unexpectedly others are required for efficient secretion of the enzyme. Furthermore, targeting chondroitinase to the neuronal growth cone promotes its ability to increase neurite outgrowth on an inhibitory substrate. These findings are timely in view of the renewed prospects for

  5. 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...

  6. 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.

  7. 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.

  8. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-03

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

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. Direct analysis of site-specific N-glycopeptides of serological proteins in dried blood spot samples.

    Science.gov (United States)

    Choi, Na Young; Hwang, Heeyoun; Ji, Eun Sun; Park, Gun Wook; Lee, Ju Yeon; Lee, Hyun Kyoung; Kim, Jin Young; Yoo, Jong Shin

    2017-08-01

    Dried blood spot (DBS) samples have a number of advantages, especially with respect to ease of collection, transportation, and storage and to reduce biohazard risk. N-glycosylation is a major post-translational modification of proteins in human blood that is related to a variety of biological functions, including metastasis, cell-cell interactions, inflammation, and immunization. Here, we directly analyzed tryptic N-glycopeptides from glycoproteins in DBS samples using liquid chromatography-tandem mass spectrometry (LC-MS/MS) without centrifugation of blood samples, depletion of major proteins, desalting of tryptic peptides, and enrichment of N-glycopeptides. Using this simple method, we identified a total of 41 site-specific N-glycopeptides from 16 glycoproteins in the DBS samples, from immunoglobulin gamma 1 (IgG-1, 10 mg/mL) down to complement component C7 (50 μg/mL). Of these, 32 N-glycopeptides from 14 glycoproteins were consistently quantified over 180 days stored at room temperature. The major abundant glycoproteins in the DBS samples were IgG-1 and IgG-2, which contain nine asialo-fucosylated complex types of 16 different N-glycopeptide isoforms. Sialo-non-fucosylated complex types were primarily detected in the other glycoproteins such as alpha-1-acid glycoprotein 1, 2, alpha-1-antitypsin, alpha-2-macroglobulin, haptoglobin, hemopexin, Ig alpha 1, 2 chain C region, kininogen-1, prothrombin, and serotransferrin. We first report the characterization of site-specific N-glycoproteins in DBS samples by LC-MS/MS with minimal sample preparation.

  16. 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.

  17. Trans-species Engineering of Glycosylated Therapeutic Proteins

    DEFF Research Database (Denmark)

    Yang, Zhang

    important to address. Whenever glycosylation has been found to be an important PTM for function or bioactivity, human therapeutics have generally been produced in mammalian Chinese hamster ovary (CHO) cell line. Oglycosylation is one of the most complex regulated PTMs of proteins but also one of the least...... understood. Currently, mammalian cells are required for human O-glycosylation. Increasing efforts have been devoted to engineering non-mammalian cells for production of recombinant proteins with “human-like” glycosylation. Substantial success has been achieved with designed N-glycosylation in both lower......Recombinant expression of therapeutic proteins is one of the major tasks in modern biomedicine. One of the most important factors with respect to therapeutic use in human is posttranslational modifications (PTMs) of the recombinant proteins, of which protein glycosylation is by far the most...

  18. 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

  19. Plant cell wall proteomics: mass spectrometry data, a trove for research on protein structure/function relationships.

    Science.gov (United States)

    Albenne, Cécile; Canut, Hervé; Boudart, Georges; Zhang, Yu; San Clemente, Hélène; Pont-Lezica, Rafael; Jamet, Elisabeth

    2009-09-01

    Proteomics allows the large-scale study of protein expression either in whole organisms or in purified organelles. In particular, mass spectrometry (MS) analysis of gel-separated proteins produces data not only for protein identification, but for protein structure, location, and processing as well. An in-depth analysis was performed on MS data from etiolated hypocotyl cell wall proteomics of Arabidopsis thaliana. These analyses show that highly homologous members of multigene families can be differentiated. Two lectins presenting 93% amino acid identity were identified using peptide mass fingerprinting. Although the identification of structural proteins such as extensins or hydroxyproline/proline-rich proteins (H/PRPs) is arduous, different types of MS spectra were exploited to identify and characterize an H/PRP. Maturation events in a couple of cell wall proteins (CWPs) were analyzed using site mapping. N-glycosylation of CWPs as well as the hydroxylation or oxidation of amino acids were also explored, adding information to improve our understanding of CWP structure/function relationships. A bioinformatic tool was developed to locate by means of MS the N-terminus of mature secreted proteins and N-glycosylation.

  20. 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

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. Unusual glycosylation of proteins: Beyond the universal sequon and other amino acids.

    Science.gov (United States)

    Dutta, Devawati; Mandal, Chhabinath; Mandal, Chitra

    2017-12-01

    Glycosylation of proteins is the most common, multifaceted co- and post-translational modification responsible for many biological processes and cellular functions. Significant alterations and aberrations of these processes are related to various pathological conditions, and often turn out to be disease biomarkers. Conventional N-glycosylation occurs through the recognition of the consensus sequon, asparagine (Asn)-X-serine (Ser)/threonine (Thr), where X is any amino acid except for proline, with N-acetylglucosamine (GlcNAc) as the first glycosidic linkage. Usually, O-glycosylation adds a glycan to the hydroxyl group of Ser or Thr beginning with N-acetylgalactosamine (GalNAc). Protein glycosylation is further governed by additional diversifications in sequon and structure, which are yet to be fully explored. This review mainly focuses on the occurrence of N-glycosylation in non-consensus motifs, where Ser/Thr at the +2 position is substituted by other amino acids. Additionally, N-glycosylation is also observed in other amide/amine group-containing amino acids. Similarly, O-glycosylation occurs at hydroxyl group-containing amino acids other than serine/threonine. The neighbouring amino acids and local structural features around the potential glycosylation site also play a significant role in determining the extent of glycosylation. All of these phenomena that yield glycosylation at the atypical sites are reported in a variety of biological systems, including different pathological conditions. Therefore, the discovery of more novel sequence patterns for N- and O-glycosylation may help in understanding the functions of complex biological processes and cellular functions. Taken together, all these information provided in this review would be helpful for the biological readers. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Effects of Fe and Mn deficiencies on the protein profiles of tomato (Solanum lycopersicum) xylem sap as revealed by shotgun analyses.

    Science.gov (United States)

    Ceballos-Laita, Laura; Gutierrez-Carbonell, Elain; Takahashi, Daisuke; Abadía, Anunciación; Uemura, Matsuo; Abadía, Javier; López-Millán, Ana Flor

    2018-01-06

    The aim of this work was to study the effects of Fe and Mn deficiencies on the xylem sap proteome of tomato using a shotgun proteomic approach, with the final goal of elucidating plant response mechanisms to these stresses. This approach yielded 643 proteins reliably identified and quantified with 70% of them predicted as secretory. Iron and Mn deficiencies caused statistically significant and biologically relevant abundance changes in 119 and 118 xylem sap proteins, respectively. In both deficiencies, metabolic pathways most affected were protein metabolism, stress/oxidoreductases and cell wall modifications. First, results suggest that Fe deficiency elicited more stress responses than Mn deficiency, based on the changes in oxidative and proteolytic enzymes. Second, both nutrient deficiencies affect the secondary cell wall metabolism, with changes in Fe deficiency occurring via peroxidase activity, and in Mn deficiency involving peroxidase, Cu-oxidase and fasciclin-like arabinogalactan proteins. Third, the primary cell wall metabolism was affected by both nutrient deficiencies, with changes following opposite directions as judged from the abundances of several glycoside-hydrolases with endo-glycolytic activities and pectin esterases. Fourth, signaling pathways via xylem involving CLE and/or lipids as well as changes in phosphorylation and N-glycosylation also play a role in the responses to these stresses. Biological significance In spite of being essential for the delivery of nutrients to the shoots, our knowledge of xylem responses to nutrient deficiencies is very limited. The present work applies a shotgun proteomic approach to unravel the effects of Fe and Mn deficiencies on the xylem sap proteome. Overall, Fe deficiency seems to elicit more stress in the xylem sap proteome than Mn deficiency, based on the changes measured in proteolytic and oxido-reductase proteins, whereas both nutrients exert modifications in the composition of the primary and secondary

  8. Trafficking and processing of bacterial proteins by mammalian cells: Insights from chondroitinase ABC.

    Directory of Open Access Journals (Sweden)

    Elizabeth Muir

    Full Text Available There is very little reported in the literature about the relationship between modifications of bacterial proteins and their secretion by mammalian cells that synthesize them. We previously reported that the secretion of the bacterial enzyme Chondroitinase ABC by mammalian cells requires the strategic removal of at least three N-glycosylation sites. The aim of this study was to determine if it is possible to enhance the efficacy of the enzyme as a treatment for spinal cord injury by increasing the quantity of enzyme secreted or by altering its cellular location.To determine if the efficiency of enzyme secretion could be further increased, cells were transfected with constructs encoding the gene for chondroitinase ABC modified for expression by mammalian cells; these contained additional modifications of strategic N-glycosylation sites or alternative signal sequences to direct secretion of the enzyme from the cells. We show that while removal of certain specific N-glycosylation sites enhances enzyme secretion, N-glycosylation of at least two other sites, N-856 and N-773, is essential for both production and secretion of active enzyme. Furthermore, we find that the signal sequence directing secretion also influences the quantity of enzyme secreted, and that this varies widely amongst the cell types tested. Last, we find that replacing the 3'UTR on the cDNA encoding Chondroitinase ABC with that of β-actin is sufficient to target the enzyme to the neuronal growth cone when transfected into neurons. This also enhances neurite outgrowth on an inhibitory substrate.Some intracellular trafficking pathways are adversely affected by cryptic signals present in the bacterial gene sequence, whilst unexpectedly others are required for efficient secretion of the enzyme. Furthermore, targeting chondroitinase to the neuronal growth cone promotes its ability to increase neurite outgrowth on an inhibitory substrate. These findings are timely in view of the renewed

  9. 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.

  10. 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)

  11. 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.)

  12. Trafficking of endoplasmic reticulum-retained recombinant proteins is unpredictable in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Thomas eDe Meyer

    2014-09-01

    Full Text Available A wide variety of recombinant proteins has been produced in the dicot model plant, Arabidopsis thaliana. Many of these proteins are targeted for secretion by means of an N terminal endoplasmic reticulum (ER signal peptide. In addition, they can also be designed for ER retention by adding a C terminal H/KDEL-tag. Despite extensive knowledge of the protein trafficking pathways, the final protein destination, especially of such H/KDEL-tagged recombinant proteins, is unpredictable. In this respect, glycoproteins are ideal study objects. Microscopy experiments reveal their deposition pattern and characterization of their N-glycans aids in elucidating the trafficking. Here, we combine microscopy and N glycosylation data generated in Arabidopsis leaves and seeds, and highlight the lack of a decent understanding of heterologous protein trafficking.

  13. 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.

  14. Capillary electrophoresis in the N-glycosylation analysis of biopharmaceuticals

    Czech Academy of Sciences Publication Activity Database

    Guttman, András

    2013-01-01

    Roč. 48, JUL-AUG (2013), s. 132-143 ISSN 0165-9936 Institutional support: RVO:68081715 Keywords : automated workflow * biopharmaceuticals * capillary electrophoresis Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 6.612, year: 2013

  15. 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.

  16. The Asia 2 specific signal peptide region and other domains in fusion protein genes characterized Asia 1 and Asia 2 canine distemper viruses

    Science.gov (United States)

    Sultan, Serageldeen; Charoenvisal, Nataya; Lan, Nguyen Thi; Yamaguchi, Ryoji; Maeda, Ken; Kai, Kazushige

    2009-01-01

    Background Although the presence of Asia 2 group of canine distemper virus (CDV) was known by the sequencing and phylogenetic analysis of hemagglutinin (H) gene, the fusion (F) protein gene sequence of Asia 2 group had not been identified. So, the sequence analysis of F gene was carried out to elucidate the genotypic varaitons among Asian isolates. Results The phylogenetic analysis of F and H gene sequences from fourteen CDV isolates obtained from diseased dogs in Japan and Thailand indicated that the F genes had a new initiation codon and extra 27 nucleotides upstream of the usual open reading frame (ORF) and the F proteins had extra 9 amino acids at the N-terminal position only in Asia 2 isolates. On the contrary, the Asia 1 isolates had three extra putative N-glycosylation sites (two sites in the signal peptide region and one site in the F1 region) except for two strains of Th12 and Ac96I (two sites in signal peptide region) adding to four putative N-glycosylation sites that were conserved among all Asian isolates and Onderstepoort strain. In addition to this difference in N-glycosylation sites, the signal peptide region had a great diversity between Asia 1 and Asia 2 isolates. Also, characteristic amino acids were detected for some strains. Conclusion Asia 2 isolates were distinguished from other CDV lineages by the extra 27 nucleotide sequence. The signal peptide region of F gene gives a remarkable differentiation between Asia 1 and Asia 2 isolates. Strains Th12 and Ac96I were differentiated from other Asia 1 strains by the F protein glycosylation sites. PMID:19807927

  17. 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.

  18. Gibberellic Acid-Induced Aleurone Layers Responding to Heat Shock or Tunicamycin Provide Insight into the N-Glycoproteome, Protein Secretion, and Endoplasmic Reticulum Stress

    DEFF Research Database (Denmark)

    Barba Espin, Gregorio; Dedvisitsakul, Plaipol; Hägglund, Per

    2014-01-01

    respond to gibberellic acid by secreting an array of proteins and provide a unique system for the analysis of plant protein secretion. Perturbation of protein secretion in gibberellic acid-induced aleurone layers by two independent mechanisms, heat shock and tunicamycin treatment, demonstrated overlapping...... and secretion, such as calreticulin, protein disulfide isomerase, proteasome subunits, and isopentenyl diphosphate isomerase. Sixteen heat shock proteins in 29 spots showed diverse responses to the treatments, with only a minority increasing in response to heat shock. The majority, all of which were small heat...... shock proteins, decreased in heat-shocked aleurone layers. Additionally, glycopeptide enrichment and N-glycosylation analysis identified 73 glycosylation sites in 65 aleurone layer proteins, with 53 of the glycoproteins found in extracellular fractions and 36 found in intracellular fractions...

  19. Glycosylation is essential for translocation of carp retinol-binding protein across the endoplasmic reticulum membrane

    International Nuclear Information System (INIS)

    Devirgiliis, Chiara; Gaetani, Sancia; Apreda, Marianna; Bellovino, Diana

    2005-01-01

    Retinoid transport is well characterized in many vertebrates, while it is still largely unexplored in fish. To study the transport and utilization of vitamin A in these organisms, we have isolated from a carp liver cDNA library retinol-binding protein, its plasma carrier. The primary structure of carp retinol-binding protein is very conserved, but presents unique features compared to those of the correspondent proteins isolated and characterized so far in other species: it has an uncleavable signal peptide and two N-glycosylation sites in the NH 2 -terminal region of the protein that are glycosylated in vivo. In this paper, we have investigated the function of the carbohydrate chains, by constructing three mutants deprived of the first, the second or both carbohydrates. The results of transient transfection of wild type and mutant retinol-binding protein in Cos cells followed by Western blotting and immunofluorescence analysis have shown that the absence of both carbohydrate moieties blocks secretion, while the presence of one carbohydrate group leads to an inefficient secretion. Experiments of carp RBP mRNA in vitro translation in a reticulocyte cell-free system in the presence of microsomes have demonstrated that N-glycosylation is necessary for efficient translocation across the endoplasmic reticulum membranes. Moreover, when Cos cells were transiently transfected with wild type and mutant retinol-binding protein (aa 1-67)-green fluorescent protein fusion constructs and semi-permeabilized with streptolysin O, immunofluorescence analysis with anti-green fluorescent protein antibody revealed that the double mutant is exposed to the cytosol, thus confirming the importance of glycan moieties in the translocation process

  20. Albizia lebbeck Seed Coat Proteins Bind to Chitin and Act as a Defense against Cowpea Weevil Callosobruchus maculatus.

    Science.gov (United States)

    Silva, Nadia C M; De Sá, Leonardo F R; Oliveira, Eduardo A G; Costa, Monique N; Ferreira, Andre T S; Perales, Jonas; Fernandes, Kátia V S; Xavier-Filho, Jose; Oliveira, Antonia E A

    2016-05-11

    The seed coat is an external tissue that participates in defense against insects. In some nonhost seeds, including Albizia lebbeck, the insect Callosobruchus maculatus dies during seed coat penetration. We investigated the toxicity of A. lebbeck seed coat proteins to C. maculatus. A chitin-binding protein fraction was isolated from seed coat, and mass spectrometry showed similarity to a C1 cysteine protease. By ELM program an N-glycosylation interaction motif was identified in this protein, and by molecular docking the potential to interact with N-acetylglucosamine (NAG) was shown. The chitin-binding protein fraction was toxic to C. maculatus and was present in larval midgut and feces but not able to hydrolyze larval gut proteins. It did not interfere, though, with the intestinal cell permeability. These results indicate that the toxicity mechanism of this seed coat fraction may be related to its binding to chitin, present in the larvae gut, disturbing nutrient absorption.

  1. 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.)

  2. 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.

  3. Small scale affinity purification and high sensitivity reversed phase nanoLC-MS N-glycan characterization of mAbs and fusion proteins.

    Science.gov (United States)

    Higel, Fabian; Seidl, Andreas; Demelbauer, Uwe; Sörgel, Fritz; Frieß, Wolfgang

    2014-01-01

    N-glycosylation is a complex post-translational modification with potential effects on the efficacy and safety of therapeutic proteins and known influence on the effector function of biopharmaceutical monoclonal antibodies (mAbs). Comprehensive characterization of N-glycosylation is therefore important in biopharmaceutical development. In early development, e.g. during pool or clone selection, however, only minute protein amounts of multiple samples are available for analytics. High sensitivity and high throughput methods are thus needed. An approach based on 96-well plate sample preparation and nanoLC-MS of 2- anthranilic acid or 2-aminobenzoic acid (AA) labeled N-glycans for the characterization of biopharmaceuticals in early development is reported here. With this approach, 192 samples can be processed simultaneously from complex matrices (e.g., cell culture supernatant) to purified 2-AA glycans, which are then analyzed by reversed phase nanoLC-MS. Attomolar sensitivity has been achieved by use of nanoelectrospray ionization, resulting in detailed glycan maps of mAbs and fusion proteins that are exemplarily shown in this work. Reproducibility, robustness and linearity of the approach are demonstrated, making use in a routine manner during pool or clone selection possible. Other potential fields of application, such as glycan biomarker discovery from serum samples, are also presented.

  4. 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.

  5. 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...

  6. 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...

  7. 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

  8. 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.

  9. 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...

  10. 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.

  11. Further insight into the roles of the glycans attached to human blood protein C inhibitor

    DEFF Research Database (Denmark)

    Sun, Wei; Parry, Simon; Ubhayasekera, Wimal

    2010-01-01

    Protein C inhibitor (PCI) is a 57-kDa glycoprotein that exists in many tissues and secretions in human. As a member of the serpin superfamily of proteins it displays unusually broad protease specificity. PCI is implicated in the regulation of a wide range of processes, including blood coagulation......, fertilization, prevention of tumors and pathogen defence. It has been reported that PCI isolated from human blood plasma is highly heterogeneous, and that this heterogeneity is caused by differences in N-glycan structures, N-glycosylation occupancy, and the presence of two forms that differ by the presence...... or absence of 6 amino acids at the amino-terminus. In this study we have verified that such heterogeneity exists in PCI purified from single individuals, and that individuals of two different ethnicities possess a similar PCI pattern, verifying that the micro-heterogeneity is conserved among humans...

  12. N-linked glycans do not affect plasma membrane localization of multidrug resistance protein 4 (MRP4) but selectively alter its prostaglandin E2 transport activity.

    Science.gov (United States)

    Miah, M Fahad; Conseil, Gwenaëlle; Cole, Susan P C

    2016-01-22

    Multidrug resistance protein 4 (MRP4) is a member of subfamily C of the ATP-binding cassette superfamily of membrane transport proteins. MRP4 mediates the ATP-dependent efflux of many endogenous and exogenous solutes across the plasma membrane, and in polarized cells, it localizes to the apical or basolateral plasma membrane depending on the tissue type. MRP4 is a 170 kDa glycoprotein and here we show that MRP4 is simultaneously N-glycosylated at Asn746 and Asn754. Furthermore, confocal immunofluorescence studies showed that N-glycans do not affect MRP4's apical membrane localization in polarized LLC-PK1 cells or basolateral membrane localization in polarized MDCKI cells. However, vesicular transport assays showed that N-glycans differentially affect MRP4's ability to transport prostaglandin E2, but not estradiol glucuronide. Together these data indicate that N-glycosylation at Asn746 and Asn754 is not essential for plasma membrane localization of MRP4 but cause substrate-selective effects on its transport activity. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Glycosylation of Candida albicans cell wall proteins is critical for induction of innate immune responses and apoptosis of epithelial cells.

    Directory of Open Access Journals (Sweden)

    Jeanette Wagener

    Full Text Available C. albicans is one of the most common fungal pathogen of humans, causing local and superficial mucosal infections in immunocompromised individuals. Given that the key structure mediating host-C. albicans interactions is the fungal cell wall, we aimed to identify features of the cell wall inducing epithelial responses and be associated with fungal pathogenesis. We demonstrate here the importance of cell wall protein glycosylation in epithelial immune activation with a predominant role for the highly branched N-glycosylation residues. Moreover, these glycan moieties induce growth arrest and apoptosis of epithelial cells. Using an in vitro model of oral candidosis we demonstrate, that apoptosis induction by C. albicans wild-type occurs in early stage of infection and strongly depends on intact cell wall protein glycosylation. These novel findings demonstrate that glycosylation of the C. albicans cell wall proteins appears essential for modulation of epithelial immunity and apoptosis induction, both of which may promote fungal pathogenesis in vivo.

  14. 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.

  15. Diversity in protein glycosylation among insect species.

    Directory of Open Access Journals (Sweden)

    Gianni Vandenborre

    Full Text Available BACKGROUND: A very common protein modification in multicellular organisms is protein glycosylation or the addition of carbohydrate structures to the peptide backbone. Although the Class of the Insecta is the largest animal taxon on Earth, almost all information concerning glycosylation in insects is derived from studies with only one species, namely the fruit fly Drosophila melanogaster. METHODOLOGY/PRINCIPAL FINDINGS: In this report, the differences in glycoproteomes between insects belonging to several economically important insect orders were studied. Using GNA (Galanthus nivalis agglutinin affinity chromatography, different sets of glycoproteins with mannosyl-containing glycan structures were purified from the flour beetle (Tribolium castaneum, the silkworm (Bombyx mori, the honeybee (Apis mellifera, the fruit fly (D. melanogaster and the pea aphid (Acyrthosiphon pisum. To identify and characterize the purified glycoproteins, LC-MS/MS analysis was performed. For all insect species, it was demonstrated that glycoproteins were related to a broad range of biological processes and molecular functions. Moreover, the majority of glycoproteins retained on the GNA column were unique to one particular insect species and only a few glycoproteins were present in the five different glycoprotein sets. Furthermore, these data support the hypothesis that insect glycoproteins can be decorated with mannosylated O-glycans. CONCLUSIONS/SIGNIFICANCE: The results presented here demonstrate that oligomannose N-glycosylation events are highly specific depending on the insect species. In addition, we also demonstrated that protein O-mannosylation in insect species may occur more frequently than currently believed.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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

  6. Abundance estimation and Conservation Biology

    Directory of Open Access Journals (Sweden)

    Nichols, J. D.

    2004-06-01

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

  7. N-glycosylation of asparagine 8 regulates surface expression of major histocompatibility complex class I chain-related protein A (MICA) alleles dependent on threonine 24

    DEFF Research Database (Denmark)

    Pedersen, Maiken Mellergaard; Skovbakke, Sarah Line; Schneider, Christine L.

    2014-01-01

    for cell-surface expression and sought to identify the essential residues. We found that a single N-glycosylation site (N8) was important for MICA018 surface expression. The frequently expressed MICA allele 008, with an altered transmembrane and intracellular domain, was not affected by mutation of this N......-glycosylation site. Mutational analysis revealed that a single amino acid (T24) in the extracellular domain of MICA018 was essential for the N-glycosylation dependency, while the intracellular domain was not involved. The HHV7 immunoevasin, U21, was found to inhibit MICA018 surface expression by affecting N......-glycosylation and the retention was rescued by T24A substitution. Our study reveals N-glycosylation as an allele-specific regulatory mechanism important for regulation of surface expression of MICA018 and we pinpoint the residues essential for this N-glycosylation dependency. In addition we show that this regulatory mechanism...

  8. Synthesis of hydrazide-functionalized hydrophilic polymer hybrid graphene oxide for highly efficient N-glycopeptide enrichment and identification by mass spectrometry.

    Science.gov (United States)

    Bai, Haihong; Pan, Yiting; Guo, Cong; Zhao, Xinyuan; Shen, Bingquan; Wang, Xinghe; Liu, Zeyuan; Cheng, Yuanguo; Qin, Weijie; Qian, Xiaohong

    2017-08-15

    Protein N-glycosylation is one of the most important post-translational modifications, participating in many key biological and pathological processes. Large-scale and precise identification of N-glycosylated proteins and peptides is especially beneficial for understanding their biological functions and for discovery of new clinical biomarkers and therapeutic drug targets. However, protein N-glycosylation is microheterogeneous and low abundant in living organisms, therefore specific enrichment of N-glycosylated proteins/peptides before mass spectrometry analysis is a prerequisite. In this work, we developed a new type of polymer hybrid graphene oxide (GO) by in situ growth of hydrazide-functionalized hydrophilic polymer chains on the GO surface (GO-PAAH) for selective N-glycopeptide enrichment and identification by mass spectrometry. The densely attached and low steric hindrance hydrazide groups as well as the highly hydrophilic nature of GO-PAAH facilitate N-glycopeptide enrichment by the combination of hydrazide capturing and HILIC interaction. Taking advantage of the unique features of GO-PAAH, all of the three N-glycopeptides of bovine fetuin were successfully enriched and identified with significantly enhanced signal intensities from a digest mixture of bovine fetuin and bovine serum albumin at a mass ratio of 1:100, demonstrating the excellent enrichment selectivity of GO-PAAH. Furthermore, a total of 507 N-glycosylation sites and 480 N-glycopeptides in 232 N-glycoproteins were enriched and identified from 10μL of human serum by three replicates using this novel enrichment material, which is nearly two times higher than the commercial hydrazide resin based method (280 N-glycosylation sites, 261 N-glycopeptides and 144 N-glycoproteins in three experiments). Among the identified, 95 N-glycosylation sites were not reported in the Uniprot database, and 106 N-glycoproteins were disease related in the Nextprot database, indicating the potential of this new

  9. Identification of a protein glycosylation operon from Campylobacter jejuni JCM 2013 and its heterologous expression in Escherichia coli.

    Science.gov (United States)

    Srichaisupakit, Akkaraphol; Ohashi, Takao; Fujiyama, Kazuhito

    2014-09-01

    Campylobacter jejuni is a human enteropathogenic bacterium possessing an N-glycosylation system. In this work, a protein glycosylation (pgl) operon conferring prokaryotic N-glycosylation in C. jejuni JCM 2013 was cloned and identified. Fourteen open reading frames (ORFs) were found in the pgl operon. The operon organization was similar to that of C. jejuni NCTC 11168, with 98% and 99% identities in overall nucleotide sequence and amino acid sequence, respectively. The pgl operon was heterologously co-expressed with model protein CmeA in the Escherichia coli BL21 ΔwaaL mutant. The immuno- and lectin-blotting analysis indicated the protein glycosylation on the recombinant CmeA. In addition, to analyze the glycan composition, the recombinant CmeA was purified and subjected to in-gel trypsin digestion followed by mass spectrometry analysis. The mass spectrometry analysis showed the presence of the N-acetylhexosamine residue at the reducing end but not the predicted di-N-acetylbacillosamine (diNAcBac) residue. Further glycan structural study using the conventional fluorophore-labeling method revealed the GalNAcα-GalNAcα-(Hex-)HexNAc-HexNAc-HexNAc-HexNAc structure. Transcriptional analysis showed that UDP-diNAcBac synthases and diNAcBac transferase are transcribed but might not function in the constructed system. In conclusion, a pgl operon from C. jejuni JCM 2013 successfully functioned in E. coli, resulting in the observed prokaryotic glycosylation. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  10. Structural Insights into Triglyceride Storage Mediated by Fat Storage-Inducing Transmembrane (FIT) Protein 2

    Science.gov (United States)

    Gross, David A.; Snapp, Erik L.; Silver, David L.

    2010-01-01

    Fat storage-Inducing Transmembrane proteins 1 & 2 (FIT1/FITM1 and FIT2/FITM2) belong to a unique family of evolutionarily conserved proteins localized to the endoplasmic reticulum that are involved in triglyceride lipid droplet formation. FIT proteins have been shown to mediate the partitioning of cellular triglyceride into lipid droplets, but not triglyceride biosynthesis. FIT proteins do not share primary sequence homology with known proteins and no structural information is available to inform on the mechanism by which FIT proteins function. Here, we present the experimentally-solved topological models for FIT1 and FIT2 using N-glycosylation site mapping and indirect immunofluorescence techniques. These methods indicate that both proteins have six-transmembrane-domains with both N- and C-termini localized to the cytosol. Utilizing this model for structure-function analysis, we identified and characterized a gain-of-function mutant of FIT2 (FLL(157-9)AAA) in transmembrane domain 4 that markedly augmented the total number and mean size of lipid droplets. Using limited-trypsin proteolysis we determined that the FLL(157-9)AAA mutant has enhanced trypsin cleavage at K86 relative to wild-type FIT2, indicating a conformational change. Taken together, these studies indicate that FIT2 is a 6 transmembrane domain-containing protein whose conformation likely regulates its activity in mediating lipid droplet formation. PMID:20520733

  11. Structural insights into triglyceride storage mediated by fat storage-inducing transmembrane (FIT protein 2.

    Directory of Open Access Journals (Sweden)

    David A Gross

    2010-05-01

    Full Text Available Fat storage-Inducing Transmembrane proteins 1 & 2 (FIT1/FITM1 and FIT2/FITM2 belong to a unique family of evolutionarily conserved proteins localized to the endoplasmic reticulum that are involved in triglyceride lipid droplet formation. FIT proteins have been shown to mediate the partitioning of cellular triglyceride into lipid droplets, but not triglyceride biosynthesis. FIT proteins do not share primary sequence homology with known proteins and no structural information is available to inform on the mechanism by which FIT proteins function. Here, we present the experimentally-solved topological models for FIT1 and FIT2 using N-glycosylation site mapping and indirect immunofluorescence techniques. These methods indicate that both proteins have six-transmembrane-domains with both N- and C-termini localized to the cytosol. Utilizing this model for structure-function analysis, we identified and characterized a gain-of-function mutant of FIT2 (FLL(157-9AAA in transmembrane domain 4 that markedly augmented the total number and mean size of lipid droplets. Using limited-trypsin proteolysis we determined that the FLL(157-9AAA mutant has enhanced trypsin cleavage at K86 relative to wild-type FIT2, indicating a conformational change. Taken together, these studies indicate that FIT2 is a 6 transmembrane domain-containing protein whose conformation likely regulates its activity in mediating lipid droplet formation.

  12. Molecular cloning and protein structure of a human blood group Rh polypeptide

    International Nuclear Information System (INIS)

    Cherif-Zahar, B.; Bloy, C.; Le Van Kim, C.; Blanchard, D.; Bailly, P.; Hermand, P.; Salmon, C.; Cartron, J.P.; Colin, Y.

    1990-01-01

    cDNA clones encoding a human blood group Rh polypeptide were isolated from a human bone marrow cDNA library by using a polymerase chain reaction-amplified DNA fragment encoding the known common N-terminal region of the Rh proteins. The entire primary structure of the Rh polypeptide has been deduced from the nucleotide sequence of a 1384-base-pair-long cDNA clone. Translation of the open reading frame indicates that the Rh protein is composed of 417 amino acids, including the initiator methionine, which is removed in the mature protein, lacks a cleavable N-terminal sequence, and has no consensus site for potential N-glycosylation. The predicted molecular mass of the protein is 45,500, while that estimated for the Rh protein analyzed in NaDodSO 4 /polyacrylamide gels is in the range of 30,000-32,000. These findings suggest either that the hydrophobic Rh protein behaves abnormally on NaDodSO 4 gels or that the Rh mRNA may encode a precursor protein, which is further matured by a proteolytic cleavage of the C-terminal region of the polypeptide. Hydropathy analysis and secondary structure predictions suggest the presence of 13 membrane-spanning domains, indicating that the Rh polypeptide is highly hydrophobic and deeply buried within the phospholipid bilayer. These results suggest that the expression of the Rh gene(s) might be restricted to tissues or cell lines expressing erythroid characters

  13. Protein and Glycoprotein Patterns Related to Morphogenesis in Mammillaria gracillis Pfeiff. Tissue Culture

    Directory of Open Access Journals (Sweden)

    Biljana Balen

    2002-01-01

    Full Text Available As plants with Crassulacean Acid Metabolism (CAM, cacti are highly affected by artificial environmental conditions in tissue culture. Plants of Mammillaria gracillis Pfeiff. (Cactaceae propagated in vitro produced callus spontaneously. This habituated callus regenerated normal and hyperhydric shoots without the addition of growth regulators. In order to compare habituated callus with the tumorous one, cactus cells were transformed with two strains of Agrobacterium tumefaciens: the wild strain B6S3 (tumour line TW and the rooty mutant GV3101 (tumour line TR. Gene expression in cactus plants, habituated callus, regenerated shoots and two tumour lines was analysed at the level of cellular and extracellular protein and glycoprotein profiles. Proteins were separated by SDS-polyacrylamide gel electrophoresis and 2-D PAGE electrophoresis and silver stained. Concavalin A-peroxidase staining detected glycoproteins with D-manose in their glycan component on protein blots. Developmentally specific protein patterns of Mammillaria gracillis tissue lines were detected. The 2-D PAGE electrophoresis revealed some tissue specific protein groups. The cellular glycoprotein of 42 kDa detected by ConA was highly expressed in undifferentiated tissues (habituated callus, TW and TR tumours and in hyperhydric regenerants. Tumours produced extracellular proteins of 33, 23 and 22 kDa. The N glycosylation of cellular and extracellular proteins was related to specific developmental stage of cactus tissue.

  14. 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.

  15. The p36 Isoform of Murine Cytomegalovirus m152 Protein Suffices for Mediating Innate and Adaptive Immune Evasion

    Science.gov (United States)

    Fink, Annette; Renzaho, Angeliqué; Reddehase, Matthias J.; Lemmermann, Niels A. W.

    2013-01-01

    The MHC-class I (MHC-I)-like viral (MHC-Iv) m152 gene product of murine cytomegalovirus (mCMV) was the first immune evasion molecule described for a member of the β-subfamily of herpesviruses as a paradigm for analogous functions of human cytomegalovirus proteins. Notably, by interacting with classical MHC-I molecules and with MHC-I-like RAE1 family ligands of the activatory natural killer (NK) cell receptor NKG2D, it inhibits presentation of antigenic peptides to CD8 T cells and the NKG2D-dependent activation of NK cells, respectively, thus simultaneously interfering with adaptive and innate immune recognition of infected cells. Although the m152 gene product exists in differentially glycosylated isoforms whose individual contributions to immune evasion are unknown, it has entered the scientific literature as m152/gp40, based on the quantitatively most prominent isoform but with no functional justification. By construction of a recombinant mCMV in which all three N-glycosylation sites are mutated (N61Q, N208Q, and N241Q), we show here that N-linked glycosylation is not essential for functional interaction of the m152 immune evasion protein with either MHC-I or RAE1. These data add an important functional detail to recent structural analysis of the m152/RAE1γ complex that has revealed N-glycosylations at positions Asn61 and Asn208 of m152 distant from the m152/RAE1γ interface. PMID:24351798

  16. The p36 Isoform of Murine Cytomegalovirus m152 Protein Suffices for Mediating Innate and Adaptive Immune Evasion

    Directory of Open Access Journals (Sweden)

    Annette Fink

    2013-12-01

    Full Text Available The MHC-class I (MHC-I-like viral (MHC-Iv m152 gene product of murine cytomegalovirus (mCMV was the first immune evasion molecule described for a member of the β-subfamily of herpesviruses as a paradigm for analogous functions of human cytomegalovirus proteins. Notably, by interacting with classical MHC-I molecules and with MHC-I-like RAE1 family ligands of the activatory natural killer (NK cell receptor NKG2D, it inhibits presentation of antigenic peptides to CD8 T cells and the NKG2D-dependent activation of NK cells, respectively, thus simultaneously interfering with adaptive and innate immune recognition of infected cells. Although the m152 gene product exists in differentially glycosylated isoforms whose individual contributions to immune evasion are unknown, it has entered the scientific literature as m152/gp40, based on the quantitatively most prominent isoform but with no functional justification. By construction of a recombinant mCMV in which all three N-glycosylation sites are mutated (N61Q, N208Q, and N241Q, we show here that N-linked glycosylation is not essential for functional interaction of the m152 immune evasion protein with either MHC-I or RAE1. These data add an important functional detail to recent structural analysis of the m152/RAE1g complex that has revealed N-glycosylations at positions Asn61 and Asn208 of m152 distant from the m152/RAE1g interface.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae

    Directory of Open Access Journals (Sweden)

    Atsushi Kurotani

    2015-08-01

    Full Text Available Recent proteome analyses have reported that intrinsically disordered regions (IDRs of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups.

  2. In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae.

    Science.gov (United States)

    Kurotani, Atsushi; Sakurai, Tetsuya

    2015-08-20

    Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups.

  3. Advanced technologies for improved expression of recombinant proteins in bacteria: perspectives and applications.

    Science.gov (United States)

    Gupta, Sanjeev K; Shukla, Pratyoosh

    2016-12-01

    Prokaryotic expression systems are superior in producing valuable recombinant proteins, enzymes and therapeutic products. Conventional microbial technology is evolving gradually and amalgamated with advanced technologies in order to give rise to improved processes for the production of metabolites, recombinant biopharmaceuticals and industrial enzymes. Recently, several novel approaches have been employed in a bacterial expression platform to improve recombinant protein expression. These approaches involve metabolic engineering, use of strong promoters, novel vector elements such as inducers and enhancers, protein tags, secretion signals, high-throughput devices for cloning and process screening as well as fermentation technologies. Advancement of the novel technologies in E. coli systems led to the production of "difficult to express" complex products including small peptides, antibody fragments, few proteins and full-length aglycosylated monoclonal antibodies in considerable large quantity. Wacker's secretion technologies, Pfenex system, inducers, cell-free systems, strain engineering for post-translational modification, such as disulfide bridging and bacterial N-glycosylation, are still under evaluation for the production of complex proteins and peptides in E. coli in an efficient manner. This appraisal provides an impression of expression technologies developed in recent times for enhanced production of heterologous proteins in E. coli which are of foremost importance for diverse applications in microbiology and biopharmaceutical production.

  4. High-throughput peptide mass fingerprinting and protein macroarray analysis using chemical printing strategies

    International Nuclear Information System (INIS)

    Sloane, A.J.; Duff, J.L.; Hopwood, F.G.; Wilson, N.L.; Smith, P.E.; Hill, C.J.; Packer, N.H.; Williams, K.L.; Gooley, A.A.; Cole, R.A.; Cooley, P.W.; Wallace, D.B.

    2001-01-01

    We describe a 'chemical printer' that uses piezoelectric pulsing for rapid and accurate microdispensing of picolitre volumes of fluid for proteomic analysis of 'protein macroarrays'. Unlike positive transfer and pin transfer systems, our printer dispenses fluid in a non-contact process that ensures that the fluid source cannot be contaminated by substrate during a printing event. We demonstrate automated delivery of enzyme and matrix solutions for on-membrane protein digestion and subsequent peptide mass fingerprinting (pmf) analysis directly from the membrane surface using matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). This approach bypasses the more commonly used multi-step procedures, thereby permitting a more rapid procedure for protein identification. We also highlight the advantage of printing different chemistries onto an individual protein spot for multiple microscale analyses. This ability is particularly useful when detailed characterisation of rare and valuable sample is required. Using a combination of PNGase F and trypsin we have mapped sites of N-glycosylation using on-membrane digestion strategies. We also demonstrate the ability to print multiple serum samples in a micro-ELISA format and rapidly screen a protein macroarray of human blood plasma for pathogen-derived antigens. We anticipate that the 'chemical printer' will be a major component of proteomic platforms for high-throughput protein identification and characterisation with widespread applications in biomedical and diagnostic discovery

  5. How Egg Case Proteins Can Protect Cuttlefish Offspring?

    Science.gov (United States)

    Cornet, Valérie; Henry, Joël; Goux, Didier; Duval, Emilie; Bernay, Benoit; Le Corguillé, Gildas; Corre, Erwan; Zatylny-Gaudin, Céline

    2015-01-01

    Sepia officinalis egg protection is ensured by a complex capsule produced by the female accessory genital glands and the ink bag. Our study is focused on the proteins constituting the main egg case. De novo transcriptomes from female genital glands provided essential databases for protein identification. A proteomic approach in SDS-PAGE coupled with MS unveiled a new egg case protein family: SepECPs, for Sepia officinalis Egg Case Proteins. N-glycosylation was demonstrated by PAS staining SDS-PAGE gels. These glycoproteins are mainly produced in the main nidamental glands. SepECPs share high sequence homology, especially in the signal peptide and the three cysteine-rich domains. SepECPs have a high number of cysteines, with conserved motifs involved in 3D-structure. SDS-PAGE showed that SepECPs could form dimers; this result was confirmed by TEM observations, which also revealed a protein network. This network is similar to the capsule network, and it associates these structural proteins with polysaccharides, melanin and bacteria to form a tight mesh. Its hardness and elasticity provide physical protection to the embryo. In addition, SepECPs also have bacteriostatic antimicrobial activity on GRAM- bacteria. By observing the SepECP / Vibrio aestuarianus complex in SEM, we demonstrated the ability of these proteins to agglomerate bacteria and thus inhibit their growth. These original proteins identified from the outer egg case ensure the survival of the species by providing physical and chemical protection to the embryos released in the environment without any maternal protection. PMID:26168161

  6. How Egg Case Proteins Can Protect Cuttlefish Offspring?

    Directory of Open Access Journals (Sweden)

    Valérie Cornet

    Full Text Available Sepia officinalis egg protection is ensured by a complex capsule produced by the female accessory genital glands and the ink bag. Our study is focused on the proteins constituting the main egg case. De novo transcriptomes from female genital glands provided essential databases for protein identification. A proteomic approach in SDS-PAGE coupled with MS unveiled a new egg case protein family: SepECPs, for Sepia officinalis Egg Case Proteins. N-glycosylation was demonstrated by PAS staining SDS-PAGE gels. These glycoproteins are mainly produced in the main nidamental glands. SepECPs share high sequence homology, especially in the signal peptide and the three cysteine-rich domains. SepECPs have a high number of cysteines, with conserved motifs involved in 3D-structure. SDS-PAGE showed that SepECPs could form dimers; this result was confirmed by TEM observations, which also revealed a protein network. This network is similar to the capsule network, and it associates these structural proteins with polysaccharides, melanin and bacteria to form a tight mesh. Its hardness and elasticity provide physical protection to the embryo. In addition, SepECPs also have bacteriostatic antimicrobial activity on GRAM- bacteria. By observing the SepECP / Vibrio aestuarianus complex in SEM, we demonstrated the ability of these proteins to agglomerate bacteria and thus inhibit their growth. These original proteins identified from the outer egg case ensure the survival of the species by providing physical and chemical protection to the embryos released in the environment without any maternal protection.

  7. 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.

  8. 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

  9. 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 ...

  10. 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

  11. 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 ...

  12. 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

  13. Emergence of canine distemper virus strains with two amino acid substitutions in the haemagglutinin protein, detected from vaccinated carnivores in North-Eastern China in 2012-2013.

    Science.gov (United States)

    Zhao, Jianjun; Zhang, Hailing; Bai, Xue; Martella, Vito; Hu, Bo; Sun, Yangang; Zhu, Chunsheng; Zhang, Lei; Liu, Hao; Xu, Shujuan; Shao, Xiqun; Wu, Wei; Yan, Xijun

    2014-04-01

    A total of 16 strains of canine distemper virus (CDV) were detected from vaccinated minks, foxes, and raccoon dogs in four provinces in North-Eastern China between the end of 2011 and 2013. Upon sequence analysis of the haemagglutinin gene and comparison with wild-type CDV from different species in the same geographical areas, two non-synonymous single nucleotide polymorphisms were identified in 10 CDV strains, which led to amino acid changes at positions 542 (isoleucine to asparagine) and 549 (tyrosine to histidine) of the haemagglutinin protein coding sequence. The change at residue 542 generated a potentially novel N-glycosylation site. Masking of antigenic epitopes by sugar moieties might represent a mechanism for evasion of virus neutralising antibodies and reduced protection by vaccination. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Cell culture media supplementation of infrequently used sugars for the targeted shifting of protein glycosylation profiles.

    Science.gov (United States)

    Hossler, Patrick; Racicot, Christopher; Chumsae, Christopher; McDermott, Sean; Cochran, Keith

    2017-03-01

    Mammalian cells in culture rely on sources of carbohydrates to supply the energy requirements for proliferation. In addition, carbohydrates provide a large source of the carbon supply for supporting various other metabolic activities, including the intermediates involved in the protein glycosylation pathway. Glucose and galactose, in particular, are commonly used sugars in culture media for these purposes. However, there exists a very large repertoire of other sugars in nature, and many that have been chemically synthesized. These sugars are particularly interesting because they can be utilized by cells in culture in distinct ways. In the present work it has been found that many infrequently used sugars, and the corresponding cellular response towards them as substrates, led to differences in the protein N-glycosylation profile of a recombinant glycoprotein. The selective media supplementation of raffinose, trehalose, turanose, palatinose, melezitose, psicose, lactose, lactulose, and mannose were found to be capable of redirecting N-glycan oligosaccharide profiles. Despite this shifting of protein glycosylation, there were no other adverse changes in culture performance, including both cell growth and cellular productivity over a wide range of supplemented sugar concentrations. The approach presented highlights a potential means towards both the targeted shifting of protein glycosylation profiles and ensuring recombinant protein comparability, which up to this point in time has remained under-appreciated for these under-utilized compounds. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:511-522, 2017. © 2017 American Institute of Chemical Engineers.

  15. 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...

  16. 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

  17. 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

  18. Characterisation of different forms of the accessory gp3 canine coronavirus type I protein identified in cats.

    Science.gov (United States)

    d'Orengiani, Anne-Laure Pham-Hung d'Alexandry; Duarte, Lidia; Pavio, Nicole; Le Poder, Sophie

    2015-04-16

    ORF3 is a supplemental open reading frame coding for an accessory glycoprotein gp3 of unknown function, only present in genotype I canine strain (CCoV-I) and some atypical feline FCoV strains. In these latter hosts, the ORF3 gene systematically displays one or two identical deletions leading to the synthesis of truncated proteins gp3-Δ1 and gp3-Δ2. As deletions in CoV accessory proteins have already been involved in tissue or host switch, studies of these different gp3 proteins were conducted in canine and feline cell. All proteins oligomerise through covalent bonds, are N-glycosylated and are maintained in the ER in non-infected but also in CCoV-II infected cells, without any specific retention signal. However, deletions influence their level of expression. In canine cells, all proteins are expressed with similar level whereas in feline cells, the expression of gp3-Δ1 is higher than the two other forms of gp3. None of the gp3 proteins modulate the viral replication cycle of heterologous genotype II CCoV in canine cell line, leading to the conclusion that the gp3 proteins are probably advantageous only for CCoV-I and atypical FCoV strains. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. 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.

  20. 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.

  1. 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...

  2. Identification and characterization of a stage specific membrane protein involved in flagellar attachment in Trypanosoma brucei.

    Directory of Open Access Journals (Sweden)

    Katherine Woods

    Full Text Available Flagellar attachment is a visibly striking morphological feature of African trypanosomes but little is known about the requirements for attachment at a molecular level. This study characterizes a previously undescribed membrane protein, FLA3, which plays an essential role in flagellar attachment in Trypanosoma brucei. FLA3 is heavily N-glycosylated, locates to the flagellar attachment zone and appears to be a bloodstream stage specific protein. Ablation of the FLA3 mRNA rapidly led to flagellar detachment and a concomitant failure of cytokinesis in the long slender bloodstream form but had no effect on the procyclic form. Flagellar detachment was obvious shortly after induction of the dsRNA and the newly synthesized flagellum was often completely detached after it emerged from the flagellar pocket. Within 12 h most cells possessed detached flagella alongside the existing attached flagellum. These results suggest that proteins involved in attachment are not shared between the new and old attachment zones. In other respects the detached flagella appear normal, they beat rapidly although directional motion was lost, and they possess an apparently normal axoneme and paraflagellar rod structure. The flagellar attachment zone appeared to be disrupted when FLA3 was depleted. Thus, while flagellar attachment is a constitutive feature of the life cycle of trypanosomes, attachment requires stage specific elements at the protein level.

  3. Role of protein glycosylation on the expression of muscarinic receptors of N4TG1 neuroblastoma cells

    International Nuclear Information System (INIS)

    Ahmad, A.; Chiang, P.K.

    1986-01-01

    Muscarinic acetylcholine receptors (mAChR) are glycoproteins. Experiments were conducted to determine whether active glycosylation of proteins in N4TG1 neuroblastoma cells could affect the expression of muscarinic receptors on the cell surface. The binding of radioactive N-methylscopolamine, a membrane impermeable ligand, to intact cells was used as a measure of mAChR. In the presence of the inhibitors of glycosylation, such as tunicamycin, monensin and amphomycin, N-linked glycosylation of proteins in the N4TG1 cells was inhibited, as measured by the incorporation of radioactive glucosamine or mannose in proteins. At the concentrations of tunicamycin and monensin used, the glycosylation of proteins after 3 hours were drastically reduced, but the number of mAChR in the cells was not altered. The apparent lack of effect within a short incubation period could be attributed to the presence of preformed oligosaccharide dolichol readily available for N-glycosylation. However, after 24 hours, tunicamycin (0.05 μg/ml) caused a decrease in the number of mAChR by 17% without having any effect on protein synthesis. Therefore, de novo glycosylation of proteins may be required for the expression of mAChR receptors in the N4TG1 neuroblastoma cell surface

  4. 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.)

  5. 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 ...

  6. 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...

  7. 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...

  8. 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...

  9. 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

  10. 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

  11. 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...

  12. 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)...

  13. 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

  14. Accessibility and contribution to glucan masking of natural and genetically tagged versions of yeast wall protein 1 of Candida albicans.

    Science.gov (United States)

    Granger, Bruce L

    2018-01-01

    Yeast wall protein 1 (Ywp1) is an abundant glycoprotein of the cell wall of the yeast form of Candida albicans, the most prevalent fungal pathogen of humans. Antibodies that bind to the polypeptide backbone of isolated Ywp1 show little binding to intact yeast cells, presumably because the Ywp1 epitopes are masked by the polysaccharides of the mannoproteins that form the outer layer of the cell wall. Rare cells do exhibit much greater anti-Ywp1 binding, however, and one of these was isolated and characterized. No differences were seen in its Ywp1, but it exhibited greater adhesiveness, sensitivity to wall perturbing agents, and exposure of its underlying β-1,3-glucan layer to external antibodies. The molecular basis for this greater epitope accessibility has not been determined, but has facilitated exploration of how these properties change as a function of cell growth and morphology. In addition, previously engineered strains with reduced quantities of Ywp1 in their cell walls were also found to have greater β-1,3-glucan exposure, indicating that Ywp1 itself contributes to the masking of wall epitopes, which may be important for understanding the anti-adhesive effect of Ywp1. Ectopic production of Ywp1 by hyphae, which reduces the adhesivity of these filamentous forms of C. albicans, was similarly found to reduce exposure of the β-1,3-glucan in their walls. To monitor Ywp1 in the cell wall irrespective of its accessibility, green fluorescent protein (Gfp) was genetically inserted into wall-anchored Ywp1 using a bifunctional cassette that also allowed production from a single transfection of a soluble, anchor-free version. The wall-anchored Ywp1-Gfp-Ywp1 accumulated in the wall of the yeast forms but not hyphae, and appeared to have properties similar to native Ywp1, including its adhesion-inhibiting effect. Some pseudohyphal walls also detectably accumulated this probe. Strains of C. albicans with tandem hemagglutinin (HA) epitopes inserted into wall

  15. Accessibility and contribution to glucan masking of natural and genetically tagged versions of yeast wall protein 1 of Candida albicans.

    Directory of Open Access Journals (Sweden)

    Bruce L Granger

    Full Text Available Yeast wall protein 1 (Ywp1 is an abundant glycoprotein of the cell wall of the yeast form of Candida albicans, the most prevalent fungal pathogen of humans. Antibodies that bind to the polypeptide backbone of isolated Ywp1 show little binding to intact yeast cells, presumably because the Ywp1 epitopes are masked by the polysaccharides of the mannoproteins that form the outer layer of the cell wall. Rare cells do exhibit much greater anti-Ywp1 binding, however, and one of these was isolated and characterized. No differences were seen in its Ywp1, but it exhibited greater adhesiveness, sensitivity to wall perturbing agents, and exposure of its underlying β-1,3-glucan layer to external antibodies. The molecular basis for this greater epitope accessibility has not been determined, but has facilitated exploration of how these properties change as a function of cell growth and morphology. In addition, previously engineered strains with reduced quantities of Ywp1 in their cell walls were also found to have greater β-1,3-glucan exposure, indicating that Ywp1 itself contributes to the masking of wall epitopes, which may be important for understanding the anti-adhesive effect of Ywp1. Ectopic production of Ywp1 by hyphae, which reduces the adhesivity of these filamentous forms of C. albicans, was similarly found to reduce exposure of the β-1,3-glucan in their walls. To monitor Ywp1 in the cell wall irrespective of its accessibility, green fluorescent protein (Gfp was genetically inserted into wall-anchored Ywp1 using a bifunctional cassette that also allowed production from a single transfection of a soluble, anchor-free version. The wall-anchored Ywp1-Gfp-Ywp1 accumulated in the wall of the yeast forms but not hyphae, and appeared to have properties similar to native Ywp1, including its adhesion-inhibiting effect. Some pseudohyphal walls also detectably accumulated this probe. Strains of C. albicans with tandem hemagglutinin (HA epitopes inserted into

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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)

  2. 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

  3. Glycoprotein folding and quality-control mechanisms in protein-folding diseases

    Directory of Open Access Journals (Sweden)

    Sean P. Ferris

    2014-03-01

    Full Text Available Biosynthesis of proteins – from translation to folding to export – encompasses a complex set of events that are exquisitely regulated and scrutinized to ensure the functional quality of the end products. Cells have evolved to capitalize on multiple post-translational modifications in addition to primary structure to indicate the folding status of nascent polypeptides to the chaperones and other proteins that assist in their folding and export. These modifications can also, in the case of irreversibly misfolded candidates, signal the need for dislocation and degradation. The current Review focuses on the glycoprotein quality-control (GQC system that utilizes protein N-glycosylation and N-glycan trimming to direct nascent glycopolypeptides through the folding, export and dislocation pathways in the endoplasmic reticulum (ER. A diverse set of pathological conditions rooted in defective as well as over-vigilant ER quality-control systems have been identified, underlining its importance in human health and disease. We describe the GQC pathways and highlight disease and animal models that have been instrumental in clarifying our current understanding of these processes.

  4. 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

  5. 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.

  6. 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

  7. The mitochondrial translocator protein, TSPO, inhibits HIV-1 envelope glycoprotein biosynthesis via the endoplasmic reticulum-associated protein degradation pathway.

    Science.gov (United States)

    Zhou, Tao; Dang, Ying; Zheng, Yong-Hui

    2014-03-01

    are folded in the ER and secreted through the classical secretory pathway. The Env folding process involves extensive cross-linking of 10 Cys residues by disulfide bond formation and heavy N-glycosylation on ∼30 Asn residues. Currently, it is still unclear how this process is regulated. Here, we studied this mechanism in the HIV nonpermissive human CD4(+) T cell line CEM.NKR. We found that Env proteins were rapidly degraded through a cellular pathway that specifically targets misfolded proteins, resulting in inhibition of Env expression. Importantly, we have identified a mitochondrial translocator protein, TSPO, which could trigger this degradation by interfering with the Env folding process. Further characterization of TSPO antiviral activity will reveal a novel antiretroviral mechanism that targets the Env protein.

  8. 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

  9. 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

  10. 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 ...

  11. 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

  12. 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

  13. 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.

  14. 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...

  15. 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...

  16. 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.

  17. 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 ...

  18. 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

  19. 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 ...

  20. 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

  1. 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 ...

  2. 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.

  3. 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 &.

  4. Classical Galactosaemia and CDG, the N-Glycosylation Interface. A Review

    OpenAIRE

    Maratha, Ashwini; Colhoun, Hugh-Owen; Knerr, Ina; Coss, Karen P.; Doran, Peter; Treacy, Eileen P.

    2016-01-01

    Classical galactosaemia is a rare disorder of carbohydrate metabolism caused by galactose-1-phosphate uridyltransferase (GALT) deficiency (EC 2.7.7.12). The disease is life threatening if left untreated in neonates and the only available treatment option is a long-term galactose restricted diet. While this is lifesaving in the neonate, complications persist in treated individuals, and the cause of these, despite early initiation of treatment, and shared GALT genotypes remain poorly understood...

  5. Therapeutic monoclonal antibody N-glycosylation - Structure, function and therapeutic potential.

    Science.gov (United States)

    Cymer, Florian; Beck, Hermann; Rohde, Adelheid; Reusch, Dietmar

    2018-03-01

    Therapeutic antibodies (IgG-type) contain several post-translational modifications (PTMs) whereby introducing a large heterogeneity, both structural and functional, into this class of therapeutics. Of these modifications, glycosylation in the fragment crystallizable (Fc) region is the most heterogeneous PTM, which can affect the stability of the molecule and interactions with Fc-receptors in vivo. Hence, the glycoform distribution can affect the mode of action and have implications for bioactivity, safety and efficacy of the drug. Main topics of the manuscript include: What factors influence the (Fc) glycan pattern in therapeutic antibodies and how can these glycans be characterized? How does structure of the Fc-glycan relate to function and what methods are available to characterize those functions? Although heterogeneous in their scope, the different sections are intended to combine current knowledge on structure-function correlations of IgG glycan structures with regard to Fc (effector) functions, as well as basic aspects and methodologies for their assessment. Copyright © 2017. Published by Elsevier Ltd.

  6. 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

  7. 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.

  8. A cathepsin F-like peptidase involved in barley grain protein mobilization, HvPap-1, is modulated by its own propeptide and by cystatins

    Science.gov (United States)

    Diaz, Isabel

    2012-01-01

    Among the C1A cysteine proteases, the plant cathepsin F-like group has been poorly studied. This paper describes the molecular and functional characterization of the HvPap-1 cathepsin F-like protein from barley. This peptidase is N-glycosylated and has to be processed to become active by its own propeptide being an important modulator of the peptidase activity. The expression pattern of its mRNA and protein suggest that it is involved in different proteolytic processes in the barley plant. HvPap-1 peptidase has been purified in Escherichia coli and the recombinant protein is able to degrade different substrates, including barley grain proteins (hordeins, albumins, and globulins) stored in the barley endosperm. It has been localized in protein bodies and vesicles of the embryo and it is induced in aleurones by gibberellin treatment. These three features support the implication of HvPap-1 in storage protein mobilization during grain germination. In addition, a complex regulation exerted by the barley cystatins, which are cysteine protease inhibitors, and by its own propeptide, is also described PMID:22791822

  9. 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

  10. A two-step recognition of signal sequences determines the translocation efficiency of proteins.

    Science.gov (United States)

    Belin, D; Bost, S; Vassalli, J D; Strub, K

    1996-02-01

    The cytosolic and secreted, N-glycosylated, forms of plasminogen activator inhibitor-2 (PAI-2) are generated by facultative translocation. To study the molecular events that result in the bi-topological distribution of proteins, we determined in vitro the capacities of several signal sequences to bind the signal recognition particle (SRP) during targeting, and to promote vectorial transport of murine PAI-2 (mPAI-2). Interestingly, the six signal sequences we compared (mPAI-2 and three mutated derivatives thereof, ovalbumin and preprolactin) were found to have the differential activities in the two events. For example, the mPAI-2 signal sequence first binds SRP with moderate efficiency and secondly promotes the vectorial transport of only a fraction of the SRP-bound nascent chains. Our results provide evidence that the translocation efficiency of proteins can be controlled by the recognition of their signal sequences at two steps: during SRP-mediated targeting and during formation of a committed translocation complex. This second recognition may occur at several time points during the insertion/translocation step. In conclusion, signal sequences have a more complex structure than previously anticipated, allowing for multiple and independent interactions with the translocation machinery.

  11. Glycoform-independent prion conversion by highly efficient, cell-based, protein misfolding cyclic amplification.

    Science.gov (United States)

    Moudjou, Mohammed; Chapuis, Jérôme; Mekrouti, Mériem; Reine, Fabienne; Herzog, Laetitia; Sibille, Pierre; Laude, Hubert; Vilette, Didier; Andréoletti, Olivier; Rezaei, Human; Dron, Michel; Béringue, Vincent

    2016-07-07

    Prions are formed of misfolded assemblies (PrP(Sc)) of the variably N-glycosylated cellular prion protein (PrP(C)). In infected species, prions replicate by seeding the conversion and polymerization of host PrP(C). Distinct prion strains can be recognized, exhibiting defined PrP(Sc) biochemical properties such as the glycotype and specific biological traits. While strain information is encoded within the conformation of PrP(Sc) assemblies, the storage of the structural information and the molecular requirements for self-perpetuation remain uncertain. Here, we investigated the specific role of PrP(C) glycosylation status. First, we developed an efficient protein misfolding cyclic amplification method using cells expressing the PrP(C) species of interest as substrate. Applying the technique to PrP(C) glycosylation mutants expressing cells revealed that neither PrP(C) nor PrP(Sc) glycoform stoichiometry was instrumental to PrP(Sc) formation and strainness perpetuation. Our study supports the view that strain properties, including PrP(Sc) glycotype are enciphered within PrP(Sc) structural backbone, not in the attached glycans.

  12. ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae.

    Science.gov (United States)

    Albornos, Lucía; Martín, Ignacio; Iglesias, Rebeca; Jiménez, Teresa; Labrador, Emilia; Dopico, Berta

    2012-11-07

    Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the described group of 20 to 40

  13. 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...

  14. 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...

  15. 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)

  16. 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

  17. 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

  18. 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.

  19. 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)

  20. 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)

  1. 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%

  2. 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

  3. 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

  4. 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...

  5. 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

  6. 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.

  7. 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)

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. Cellular repressor of E1A-stimulated genes is a bona fide lysosomal protein which undergoes proteolytic maturation during its biosynthesis

    International Nuclear Information System (INIS)

    Schaehs, Philipp; Weidinger, Petra; Probst, Olivia C.; Svoboda, Barbara; Stadlmann, Johannes; Beug, Hartmut; Waerner, Thomas; Mach, Lukas

    2008-01-01

    Cellular repressor of E1A-stimulated genes (CREG) has been reported to be a secretory glycoprotein implicated in cellular growth and differentiation. We now show that CREG is predominantly localized within intracellular compartments. Intracellular CREG was found to lack an N-terminal peptide present in the secreted form of the protein. In contrast to normal cells, CREG is largely secreted by fibroblasts missing both mannose 6-phosphate receptors. This is not observed in cells lacking only one of them. Mass spectrometric analysis of recombinant CREG revealed that the protein contains phosphorylated oligosaccharides at either of its two N-glycosylation sites. Cellular CREG was found to cosediment with lysosomal markers upon subcellular fractionation by density-gradient centrifugation. In fibroblasts expressing a CREG-GFP fusion construct, the heterologous protein was detected in compartments containing lysosomal proteins. Immunolocalization of endogenous CREG confirmed that intracellular CREG is localized in lysosomes. Proteolytic processing of intracellular CREG involves the action of lysosomal cysteine proteinases. These results establish that CREG is a lysosomal protein that undergoes proteolytic maturation in the course of its biosynthesis, carries the mannose 6-phosphate recognition marker and depends on the interaction with mannose 6-phosphate receptors for efficient delivery to lysosomes

  16. 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

  17. RT-PCR and sequence analysis of the full-length fusion protein of Canine Distemper Virus from domestic dogs.

    Science.gov (United States)

    Romanutti, Carina; Gallo Calderón, Marina; Keller, Leticia; Mattion, Nora; La Torre, José

    2016-02-01

    During 2007-2014, 84 out of 236 (35.6%) samples from domestic dogs submitted to our laboratory for diagnostic purposes were positive for Canine Distemper Virus (CDV), as analyzed by RT-PCR amplification of a fragment of the nucleoprotein gene. Fifty-nine of them (70.2%) were from dogs that had been vaccinated against CDV. The full-length gene encoding the Fusion (F) protein of fifteen isolates was sequenced and compared with that of those of other CDVs, including wild-type and vaccine strains. Phylogenetic analysis using the F gene full-length sequences grouped all the Argentinean CDV strains in the SA2 clade. Sequence identity with the Onderstepoort vaccine strain was 89.0-90.6%, and the highest divergence was found in the 135 amino acids corresponding to the F protein signal-peptide, Fsp (64.4-66.7% identity). In contrast, this region was highly conserved among the local strains (94.1-100% identity). One extra putative N-glycosylation site was identified in the F gene of CDV Argentinean strains with respect to the vaccine strain. The present report is the first to analyze full-length F protein sequences of CDV strains circulating in Argentina, and contributes to the knowledge of molecular epidemiology of CDV, which may help in understanding future disease outbreaks. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Mammalian protein secretion without signal peptide removal. Biosynthesis of plasminogen activator inhibitor-2 in U-937 cells

    International Nuclear Information System (INIS)

    Ye, R.D.; Wun, T.C.; Sadler, J.E.

    1988-01-01

    Plasminogen activator inhibitor-2 (PAI-2) is a serine protease inhibitor that regulates plasmin generation by inhibiting urokinase and tissue plasminogen activator. The primary structure of PAI-2 suggests that it may be secreted without cleavage of a single peptide. To confirm this hypothesis we have studied the glycosylation and secretion of PAI-2 in human monocytic U-937 cells by metabolic labeling, immunoprecipitation, glycosidase digestion, and protein sequencing. PAI-2 is variably glycosylated on asparagine residues to yield intracellular intermediates with zero, one, two, or three high mannose-type oligosaccharide units. Secretion of the N-glycosylated species began by 1 h of chase and the secreted molecules contained both complex-type N-linked and O-linked oligosaccharides. Enzymatically deglycosylated PAI-2 had an electrophoretic mobility identical to that of the nonglycosylated precursor and also to that of PAI-2 synthesized in vitro in a rabbit reticulocyte lysate from synthetic mRNA derived from full length PAI-2 cDNA. The amino-terminal protein sequence of secreted PAI-2 began with the initiator methionine residue. These results indicate that PAI-2 is glycosylated and secreted efficiently without the cleavage of a signal peptide. PAI-2 shares this property with its nearest homologue in the serine protease inhibitor family, chicken ovalbumin, and appears to be the first well characterized example of this phenomenon among natural mammalian proteins

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Simultaneous analysis of proteome, phospho- and glycoproteome of rat kidney tissue with electrostatic repulsion hydrophilic interaction chromatography.

    Directory of Open Access Journals (Sweden)

    Piliang Hao

    Full Text Available Protein post-translational modifications (PTMs are regulated separately from protein expression levels. Thus, simultaneous characterization of the proteome and its PTMs is pivotal to an understanding of protein regulation, function and activity. However, concurrent analysis of the proteome and its PTMs by mass spectrometry is a challenging task because the peptides bearing PTMs are present in sub-stoichiometric amounts and their ionization is often suppressed by unmodified peptides of high abundance. We describe here a method for concurrent analysis of phosphopeptides, glycopeptides and unmodified peptides in a tryptic digest of rat kidney tissue with a sequence of ERLIC and RP-LC-MS/MS in a single experimental run, thereby avoiding inter-experimental variation. Optimization of loading solvents and elution gradients permitted ERLIC to be performed with totally volatile solvents. Two SCX and four ERLIC gradients were compared in details, and one ERLIC gradient was found to perform the best, which identified 2929 proteins, 583 phosphorylation sites in 338 phosphoproteins and 722 N-glycosylation sites in 387 glycoproteins from rat kidney tissue. Two hundred low-abundance proteins with important functions were identified only from the glyco- or phospho-subproteomes, reflecting the importance of the enrichment and separation of modified peptides by ERLIC. In addition, this strategy enables identification of unmodified and corresponding modified peptides (partial phosphorylation and N-glycosylation from the same protein. Interestingly, partially modified proteins tend to occur on proteins involved in transport. Moreover, some membrane or extracellular proteins, such as versican core protein and fibronectin, were found to have both phosphorylation and N-glycosylation, which may permit an assessment of the potential for cross talk between these two vital PTMs and their roles in regulation.

  6. 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)

  7. 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.

  8. 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...

  9. 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...

  10. 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 ...

  11. 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)

  12. 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.

  13. 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)

  14. 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.

  15. 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...

  16. 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...

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

    Directory of Open Access Journals (Sweden)

    Guilai Liu

    2015-11-01

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

  18. 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.

  19. 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...

  20. 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...

  1. Safety evaluation of the phosphinothricin acetyltransferase proteins encoded by the pat and bar sequences that confer tolerance to glufosinate-ammonium herbicide in transgenic plants.

    Science.gov (United States)

    Hérouet, Corinne; Esdaile, David J; Mallyon, Bryan A; Debruyne, Eric; Schulz, Arno; Currier, Thomas; Hendrickx, Koen; van der Klis, Robert-Jan; Rouan, Dominique

    2005-03-01

    Transgenic plant varieties, which are tolerant to glufosinate-ammonium, were developed. The herbicide tolerance is based upon the presence of either the bar or the pat gene, which encode for two homologous phosphinothricin acetyltransferases (PAT), in the plant genome. Based on both a review of published literature and experimental studies, the safety assessment reviews the first step of a two-step-approach for the evaluation of the safety of the proteins expressed in plants. It can be used to support the safety of food or feed products derived from any crop that contains and expresses these PAT proteins. The safety evaluation supports the conclusion that the genes and the donor microorganisms (Streptomyces) are innocuous. The PAT enzymes are highly specific and do not possess the characteristics associated with food toxins or allergens, i.e., they have no sequence homology with any known allergens or toxins, they have no N-glycosylation sites, they are rapidly degraded in gastric and intestinal fluids, and they are devoid of adverse effects in mice after intravenous administration at a high dose level. In conclusion, there is a reasonable certainty of no harm resulting from the inclusion of the PAT proteins in human food or in animal feed.

  2. Computational Biophysical, Biochemical, and Evolutionary Signature of Human R-Spondin Family Proteins, the Member of Canonical Wnt/β-Catenin Signaling Pathway

    Directory of Open Access Journals (Sweden)

    Ashish Ranjan Sharma

    2014-01-01

    Full Text Available In human, Wnt/β-catenin signaling pathway plays a significant role in cell growth, cell development, and disease pathogenesis. Four human (Rspos are known to activate canonical Wnt/β-catenin signaling pathway. Presently, (Rspos serve as therapeutic target for several human diseases. Henceforth, basic understanding about the molecular properties of (Rspos is essential. We approached this issue by interpreting the biochemical and biophysical properties along with molecular evolution of (Rspos thorough computational algorithm methods. Our analysis shows that signal peptide length is roughly similar in (Rspos family along with similarity in aa distribution pattern. In Rspo3, four N-glycosylation sites were noted. All members are hydrophilic in nature and showed alike GRAVY values, approximately. Conversely, Rspo3 contains the maximum positively charged residues while Rspo4 includes the lowest. Four highly aligned blocks were recorded through Gblocks. Phylogenetic analysis shows Rspo4 is being rooted with Rspo2 and similarly Rspo3 and Rspo1 have the common point of origin. Through phylogenomics study, we developed a phylogenetic tree of sixty proteins (n=60 with the orthologs and paralogs seed sequences. Protein-protein network was also illustrated. Results demonstrated in our study may help the future researchers to unfold significant physiological and therapeutic properties of (Rspos in various disease models.

  3. A disease-causing mutation illuminates the protein membrane topology of the kidney-expressed prohibitin homology (PHB) domain protein podocin.

    Science.gov (United States)

    Schurek, Eva-Maria; Völker, Linus A; Tax, Judit; Lamkemeyer, Tobias; Rinschen, Markus M; Ungrue, Denise; Kratz, John E; Sirianant, Lalida; Kunzelmann, Karl; Chalfie, Martin; Schermer, Bernhard; Benzing, Thomas; Höhne, Martin

    2014-04-18

    Mutations in the NPHS2 gene are a major cause of steroid-resistant nephrotic syndrome, a severe human kidney disorder. The NPHS2 gene product podocin is a key component of the slit diaphragm cell junction at the kidney filtration barrier and part of a multiprotein-lipid supercomplex. A similar complex with the podocin ortholog MEC-2 is required for touch sensation in Caenorhabditis elegans. Although podocin and MEC-2 are membrane-associated proteins with a predicted hairpin-like structure and amino and carboxyl termini facing the cytoplasm, this membrane topology has not been convincingly confirmed. One particular mutation that causes kidney disease in humans (podocin(P118L)) has also been identified in C. elegans in genetic screens for touch insensitivity (MEC-2(P134S)). Here we show that both mutant proteins, in contrast to the wild-type variants, are N-glycosylated because of the fact that the mutant C termini project extracellularly. Podocin(P118L) and MEC-2(P134S) did not fractionate in detergent-resistant membrane domains. Moreover, mutant podocin failed to activate the ion channel TRPC6, which is part of the multiprotein-lipid supercomplex, indicative of the fact that cholesterol recruitment to the ion channels, an intrinsic function of both proteins, requires C termini facing the cytoplasmic leaflet of the plasma membrane. Taken together, this study demonstrates that the carboxyl terminus of podocin/MEC-2 has to be placed at the inner leaflet of the plasma membrane to mediate cholesterol binding and contribute to ion channel activity, a prerequisite for mechanosensation and the integrity of the kidney filtration barrier.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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)

  9. 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.

  10. 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

  11. 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.

  12. 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 .

  13. 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.

  14. 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.

  15. 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....

  16. 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

  17. In vivo subcellular localization of Mal de Rio Cuarto virus (MRCV) non-structural proteins in insect cells reveals their putative functions

    Energy Technology Data Exchange (ETDEWEB)

    Maroniche, Guillermo A.; Mongelli, Vanesa C.; Llauger, Gabriela; Alfonso, Victoria; Taboga, Oscar [Instituto de Biotecnologia, CICVyA, Instituto Nacional de Tecnologia Agropecuaria (IB-INTA), Las cabanas y Los Reseros s/n. Hurlingham Cp 1686, Buenos Aires (Argentina); Vas, Mariana del, E-mail: mdelvas@cnia.inta.gov.ar [Instituto de Biotecnologia, CICVyA, Instituto Nacional de Tecnologia Agropecuaria (IB-INTA), Las cabanas y Los Reseros s/n. Hurlingham Cp 1686, Buenos Aires (Argentina)

    2012-09-01

    The in vivo subcellular localization of Mal de Rio Cuarto virus (MRCV, Fijivirus, Reoviridae) non-structural proteins fused to GFP was analyzed by confocal microscopy. P5-1 showed a cytoplasmic vesicular-like distribution that was lost upon deleting its PDZ binding TKF motif, suggesting that P5-1 interacts with cellular PDZ proteins. P5-2 located at the nucleus and its nuclear import was affected by the deletion of its basic C-termini. P7-1 and P7-2 also entered the nucleus and therefore, along with P5-2, could function as regulators of host gene expression. P6 located in the cytoplasm and in perinuclear cloud-like inclusions, was driven to P9-1 viroplasm-like structures and co-localized with P7-2, P10 and {alpha}-tubulin, suggesting its involvement in viroplasm formation and viral intracellular movement. Finally, P9-2 was N-glycosylated and located at the plasma membrane in association with filopodia-like protrusions containing actin, suggesting a possible role in virus cell-to-cell movement and spread.

  18. 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.

  19. 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.

  20. 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).

  1. 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 ...

  2. 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

  3. 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)

  4. 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.

  5. 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...

  6. 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 ...

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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...

  15. 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, ...

  16. 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

  17. 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

  18. Purification and characterization of bioactive his6-tagged recombinant human tissue inhibitor of metalloproteinases-1 (TIMP-1) protein expressed at high yields in mammalian cells

    DEFF Research Database (Denmark)

    Jensen, Lena Vinther; Lademann, Ulrik Axel; Andersen, Elisabeth Veyhe

    2014-01-01

    Tissue inhibitor of metalloproteinases-1 (TIMP-1) is an endogenous inhibitor of matrix metalloproteinases (MMPs) with reported tumor promoting, as well as inhibitory, effects. These paradoxical properties are presumably mediated by different biological functions, MMP-dependent as well as -indepen...... TIMP-1, which structurally and functionally is similar to endogenous human TIMP-1, while using an expression system that is adaptable to most biochemical and biomedical laboratories including those that do not perform protein purifications routinely.......Tissue inhibitor of metalloproteinases-1 (TIMP-1) is an endogenous inhibitor of matrix metalloproteinases (MMPs) with reported tumor promoting, as well as inhibitory, effects. These paradoxical properties are presumably mediated by different biological functions, MMP-dependent as well...... as -independent, and probably related to TIMP-1 levels of protein expression, post-translational modifications, and cellular localization. TIMP-1 is an N-glycosylated protein that folds into two functional domains, a C- and an N-terminal domain, with six disulfide bonds. Furthermore, TIMP-1 is processed in the N...

  19. 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.

  20. 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.

  1. Semisynthetic prion protein (PrP) variants carrying glycan mimics at position 181 and 197 do not form fibrils.

    Science.gov (United States)

    Araman, Can; Thompson, Robert E; Wang, Siyao; Hackl, Stefanie; Payne, Richard J; Becker, Christian F W

    2017-09-01

    The prion protein (PrP) is an N -glycosylated protein attached to the outer leaflet of eukaryotic cell membranes via a glycosylphosphatidylinositol (GPI) anchor. Different prion strains have distinct glycosylation patterns and the extent of glycosylation of potentially pathogenic misfolded prion protein (PrP Sc ) has a major impact on several prion-related diseases (transmissible spongiform encephalopathies, TSEs). Based on these findings it is hypothesized that posttranslational modifications (PTMs) of PrP influence conversion of cellular prion protein (PrP C ) into PrP Sc and, as such, modified PrP variants are critical tools needed to investigate the impact of PTMs on the pathogenesis of TSEs. Here we report a semisynthetic approach to generate PrP variants modified with monodisperse polyethyleneglycol (PEG) units as mimics of N-glycans. Incorporating PEG at glycosylation sites 181 and 197 in PrP induced only small changes to the secondary structure when compared to unmodified, wildtype PrP. More importantly, in vitro aggregation was abrogated for all PEGylated PrP variants under conditions at which wildtype PrP aggregated. Furthermore, the addition of PEGylated PrP as low as 10 mol% to wildtype PrP completely blocked aggregation. A similar effect was observed for synthetic PEGylated PrP segments comprising amino acids 179-231 alone if these were added to wildtype PrP in aggregation assays. This behavior raises the question if large N-glycans interfere with aggregation in vivo and if PEGylated PrP peptides could serve as potential therapeutics.

  2. 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.

  3. 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.

  4. 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

  5. Comparative studies of vertebrate endothelin-converting enzyme-like 1 genes and proteins

    Directory of Open Access Journals (Sweden)

    Holmes RS

    2013-01-01

    Full Text Available Roger S Holmes,1,2 Laura A Cox11Department of Genetics and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA; 2Eskitis Institute for Cell and Molecular Therapies and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, AustraliaAbstract: Endothelin-converting enzyme-like 1 (ECEL1 is a member of the M13 family of neutral endopeptidases which play an essential role in the neural regulation of vertebrate respiration. Genetic deficiency of this protein results in respiratory failure soon after birth. Comparative ECEL1 amino acid sequences and structures and ECEL1 gene locations were examined using data from several vertebrate genome projects. Vertebrate ECEL1 sequences shared 66%–99% identity as compared with 30%–63% sequence identities with other M13-like family members, ECE1, ECE2, and NEP (neprilysin or MME. Three N-glycosylation sites were conserved among most vertebrate ECEL1 proteins examined. Sequence alignments, conserved key amino acid residues, and predicted secondary and tertiary structures were also studied, including cytoplasmic, transmembrane, and luminal sequences and active site residues. Vertebrate ECEL1 genes usually contained 18 exons and 17 coding exons on the negative strand. Exons 1 and 2 of the human ECEL1 gene contained 5'-untranslated (5'-UTR regions, a large CpG island (CpG256, and several transcription factor binding sites which may contribute to the high levels of gene expression previously reported in neural tissues. Phylogenetic analyses examined the relationships and potential evolutionary origins of the vertebrate ECEL1 gene with six other vertebrate neutral endopeptidase M13 family genes. These suggested that ECEL1 originated in an ancestral vertebrate genome from a duplication event in an ancestral neutral endopeptidase M13-like gene.Keywords: vertebrates, amino acid sequence, ECEL1, ECE1, ECE2, KELL, NEP, NEPL1, PHEX

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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...

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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...

  1. 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...

  2. 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 ...

  3. 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, ...

  4. 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...

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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 ...

  10. 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.

  11. 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.

  12. 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 ...

  13. 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, ...

  14. 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 ...

  15. 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

  16. 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.

  17. 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

  18. 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

  19. 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)

  20. 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

  1. 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...

  2. Characterization of an Sf-rhabdovirus-negative Spodoptera frugiperda cell line as an alternative host for recombinant protein production in the baculovirus-insect cell system.

    Science.gov (United States)

    Maghodia, Ajay B; Geisler, Christoph; Jarvis, Donald L

    2016-06-01

    Cell lines derived from the fall armyworm, Spodoptera frugiperda (Sf), are widely used as hosts for recombinant protein production in the baculovirus-insect cell system (BICS). However, it was recently discovered that these cell lines are contaminated with a virus, now known as Sf-rhabdovirus [1]. The detection of this adventitious agent raised a potential safety issue that could adversely impact the BICS as a commercial recombinant protein production platform. Thus, we examined the properties of Sf-RVN, an Sf-rhabdovirus-negative Sf cell line, as a potential alternative host. Nested RT-PCR assays showed Sf-RVN cells had no detectable Sf-rhabdovirus over the course of 60 passages in continuous culture. The general properties of Sf-RVN cells, including their average growth rates, diameters, morphologies, and viabilities after baculovirus infection, were virtually identical to those of Sf9 cells. Baculovirus-infected Sf-RVN and Sf9 cells produced equivalent levels of three recombinant proteins, including an intracellular prokaryotic protein and two secreted eukaryotic glycoproteins, and provided similar N-glycosylation patterns. In fact, except for the absence of Sf-rhabdovirus, the only difference between Sf-RVN and Sf9 cells was SF-RVN produced higher levels of infectious baculovirus progeny. These results show Sf-RVN cells can be used as improved, alternative hosts to circumvent the potential safety hazard associated with the use of Sf-rhabdovirus-contaminated Sf cells for recombinant protein manufacturing with the BICS. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. 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

  4. 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.  .

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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 .

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. Clinical and biochemical presentation of siblings with COG-7 deficiency, a lethal multiple O- and N-glycosylation disorder.

    NARCIS (Netherlands)

    Spaapen, L.J.; Bakker, J.A.; Meer, S.B. van der; Sijstermans, H.J.; Steet, R.A.; Wevers, R.A.; Jaeken, J.

    2005-01-01

    Congenital disorders of glycosylation (CDG) represent a group of inherited multiorgan diseases caused by defects in the biosynthesis of glycoproteins. We report on two dysmorphic siblings with severe liver disease who died at the age of a few weeks. Increased activities of lysosomal enzymes in

  20. Three-dimensional structures of two heavily N-glycosylated Aspergillus sp family GH3 beta-D-glucosidases

    Czech Academy of Sciences Publication Activity Database

    Agirre, J.; Ariza, A.; Offen, W. A.; Turkenburg, J. P.; Roberts, S. M.; McNicholas, S.; Harris, P. V.; McBrayer, B.; Dohnálek, Jan; Cowtan, K. D.; Davies, G. J.; Wilson, K. S.

    2016-01-01

    Roč. 72, č. 2 (2016), s. 254-265 ISSN 2059-7983 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:86652036 Keywords : cellulose degradation * N-glycan * biofuels * glycoblocks Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.114, year: 2016