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Sample records for defense reveal quantitative

  1. Quantitative defense theory and patterns of feeding by oak insects.

    Science.gov (United States)

    Faeth, Stanley H

    1985-12-01

    Patterns of herbivory over a two year period on Quercus emoryi (Fagaceae) were correlated with seasonal and yearly changes in tannin and protein content. Quantitative defense theory predicts that tannin and protein content in apparent plants should be negatively and positively correlated, respectively, with degree of herbivory. Most herbivory occurred early in the growing season, but the pattern varied between the two years. Tannin and protein content sometimes varied negatively and sometimes positively with degree of herbivory; they did not consistently covary with herbivory. Protein content was positively correlated with herbivory in 1981-1982 but not in 1982-1983. Condensed tannin content was negatively correlated with herbivory in 1981-1982 but not in 1982-1983. Hydrolysable tannin content was positively correlated with herbivory activity. Multiple regression analyses indicated these phytochemical variables explained either no significant variation in herbivory (1982-1983) or did so in a fashion opposite (1981-1982) to the predictions of the theory of quantitative defense.Feeding by oak insects was not solely a function of seasonal changes in quantitative defenses and nutrients. Obviously, population dynamics of the insects are sensitive to factors other than phytochemistry of the trees and I discuss other factors that can influence patterns of herbivory.

  2. Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze)

    Science.gov (United States)

    Jayaswall, Kuldip; Mahajan, Pallavi; Singh, Gagandeep; Parmar, Rajni; Seth, Romit; Raina, Aparnashree; Swarnkar, Mohit Kumar; Singh, Anil Kumar; Shankar, Ravi; Sharma, Ram Kumar

    2016-07-01

    To unravel the molecular mechanism of defense against blister blight (BB) disease caused by an obligate biotrophic fungus, Exobasidium vexans, transcriptome of BB interaction with resistance and susceptible tea genotypes was analysed through RNA-seq using Illumina GAIIx at four different stages during ~20-day disease cycle. Approximately 69 million high quality reads were assembled de novo, yielding 37,790 unique transcripts with more than 55% being functionally annotated. Differentially expressed, 149 defense related transcripts/genes, namely defense related enzymes, resistance genes, multidrug resistant transporters, transcription factors, retrotransposons, metacaspases and chaperons were observed in RG, suggesting their role in defending against BB. Being present in the major hub, putative master regulators among these candidates were identified from predetermined protein-protein interaction network of Arabidopsis thaliana. Further, confirmation of abundant expression of well-known RPM1, RPS2 and RPP13 in quantitative Real Time PCR indicates salicylic acid and jasmonic acid, possibly induce synthesis of antimicrobial compounds, required to overcome the virulence of E. vexans. Compendiously, the current study provides a comprehensive gene expression and insights into the molecular mechanism of tea defense against BB to serve as a resource for unravelling the possible regulatory mechanism of immunity against various biotic stresses in tea and other crops.

  3. Multiple Identified Neurons and Peripheral Nerves Innervating the Prothoracic Defense Glands in Stick Insects Reveal Evolutionary Conserved and Novel Elements of a Chemical Defense System

    Directory of Open Access Journals (Sweden)

    Johannes Strauß

    2017-11-01

    Full Text Available The defense glands in the dorsal prothorax are an important autapomorphic trait of stick insects (Phasmatodea. Here, we study the functional anatomy and neuronal innervation of the defense glands in Anisomorpha paromalus (Westwood, 1859 (Pseudophasmatinae, a species which sprays its defense secretions when disturbed or attacked. We use a neuroanatomical approach to identify the nerves innervating the gland muscles and the motoneurons with axons in the different nerves. The defense gland is innervated by nerves originating from two segments, the subesophageal ganglion (SOG, and the prothoracic ganglion. Axonal tracing confirms the gland innervation via the anterior subesophageal nerve, and two intersegmental nerves, the posterior subesophageal nerve, and the anterior prothoracic nerve. Axonal tracing of individual nerves reveals eight identified neuron types in the subesophageal or prothoracic ganglion. The strongest innervating nerve of the gland is the anterior subesophageal nerve, which also supplies dorsal longitudinal thorax muscles (neck muscles by separate nerve branches. Tracing of individual nerve branches reveals different sets of motoneurons innervating the defense gland (one ipsilateral and one contralateral subesophageal neuron or the neck muscle (ventral median neurons. The ipsilateral and contralateral subesophageal neurons have no homologs in related taxa like locusts and crickets, and thus evolved within stick insects with the differentiation of the defense glands. The overall innervation pattern suggests that the longitudinal gland muscles derived from dorsal longitudinal neck muscles. In sum, the innervating nerves for dorsal longitudinal muscles are conserved in stick insects, while the neuronal control system was specialized with conserved motoneurons for the persisting neck muscles, and evolutionarily novel subesophageal and prothoracic motoneurons innervating the defense gland.

  4. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Brunak, Søren; Olsen, JV

    2010-01-01

    and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20% of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global...

  5. Papillon-Lefèvre syndrome patient reveals species-dependent requirements for neutrophil defenses

    DEFF Research Database (Denmark)

    Sørensen, Ole E.; Clemmensen, Stine N; Dahl, Sara L

    2014-01-01

    immunodeficiency. Here, we characterized a 24-year-old woman who had suffered from severe juvenile periodontal disease, but was otherwise healthy, and identified a homozygous missense mutation in CTSC indicative of PLS. Proteome analysis of patient neutrophil granules revealed that several proteins that normally......Papillon-Lefèvre syndrome (PLS) results from mutations that inactivate cysteine protease cathepsin C (CTSC), which processes a variety of serine proteases considered essential for antimicrobial defense. Despite serine protease-deficient immune cell populations, PLS patients do not exhibit marked......CAP-18 into the antibacterial peptide LL-37 in response to ionomycin. In immature myeloid cells from patient bone marrow, biosynthesis of CTSC and neutrophil serine proteases appeared normal along with initial processing and sorting to cellular storage. In contrast, these proteins were completely absent...

  6. Coincidence in map positions between pathogen-induced defense-responsive genes and quantitative resistance loci in rice

    Institute of Scientific and Technical Information of China (English)

    熊敏; 王石平; 张启发

    2002-01-01

    Quantitative disease resistance conferred by quantitative trait loci (QTLs) is presumably of wider spectrum and durable. Forty-four cDNA clones, representing 44 defense-responsive genes, were fine mapped to 56 loci distributed on 9 of the 12 rice chromosomes. The locations of 32 loci detected by 27 cDNA clones were associated with previously identified resistance QTLs for different rice diseases, including blast, bacterial blight, sheath blight and yellow mottle virus. The loci detected by the same multiple-copy cDNA clones were frequently located on similar locations of different chromosomes. Some of the multiple loci detected by the same clones were all associated with resistance QTLs. These results suggest that some of the genes may be important components in regulation of defense responses against pathogen invasion and they may be the candidates for studying the mechanism of quantitative disease resistance in rice.

  7. Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis.

    Science.gov (United States)

    Wen, Chengping; Zheng, Zhijun; Shao, Tiejuan; Liu, Lin; Xie, Zhijun; Le Chatelier, Emmanuelle; He, Zhixing; Zhong, Wendi; Fan, Yongsheng; Zhang, Linshuang; Li, Haichang; Wu, Chunyan; Hu, Changfeng; Xu, Qian; Zhou, Jia; Cai, Shunfeng; Wang, Dawei; Huang, Yun; Breban, Maxime; Qin, Nan; Ehrlich, Stanislav Dusko

    2017-07-27

    The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease. To investigate the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study based on deep shotgun sequencing was performed, using gut microbial DNA from 211 Chinese individuals. A total of 23,709 genes and 12 metagenomic species were shown to be differentially abundant between ankylosing spondylitis patients and healthy controls. Patients were characterized by a form of gut microbial dysbiosis that is more prominent than previously reported cases with inflammatory bowel disease. Specifically, the ankylosing spondylitis patients demonstrated increases in the abundance of Prevotella melaninogenica, Prevotella copri, and Prevotella sp. C561 and decreases in Bacteroides spp. It is noteworthy that the Bifidobacterium genus, which is commonly used in probiotics, accumulated in the ankylosing spondylitis patients. Diagnostic algorithms were established using a subset of these gut microbial biomarkers. Alterations of the gut microbiome are associated with development of ankylosing spondylitis. Our data suggest biomarkers identified in this study might participate in the pathogenesis or development process of ankylosing spondylitis, providing new leads for the development of new diagnostic tools and potential treatments.

  8. Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization.

    Science.gov (United States)

    Slaby, Beate M; Hackl, Thomas; Horn, Hannes; Bayer, Kristina; Hentschel, Ute

    2017-11-01

    Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes involved in host colonization and extracellular matrix utilization in sponge symbionts. A within-symbionts genome comparison revealed a nutritional specialization of at least two symbiont guilds, where one appears to metabolize carnitine and the other sulfated polysaccharides, both of which are abundant molecules in the sponge extracellular matrix. A third guild of symbionts may be viewed as nutritional generalists that perform largely the same metabolic pathways but lack such extraordinary numbers of the relevant genes. This study characterizes the genomic repertoire of sponge symbionts at an unprecedented resolution and it provides greater insights into the molecular mechanisms underlying microbial-sponge symbiosis.

  9. Quantitative flux analysis reveals folate-dependent NADPH production

    Science.gov (United States)

    Fan, Jing; Ye, Jiangbin; Kamphorst, Jurre J.; Shlomi, Tomer; Thompson, Craig B.; Rabinowitz, Joshua D.

    2014-06-01

    ATP is the dominant energy source in animals for mechanical and electrical work (for example, muscle contraction or neuronal firing). For chemical work, there is an equally important role for NADPH, which powers redox defence and reductive biosynthesis. The most direct route to produce NADPH from glucose is the oxidative pentose phosphate pathway, with malic enzyme sometimes also important. Although the relative contribution of glycolysis and oxidative phosphorylation to ATP production has been extensively analysed, similar analysis of NADPH metabolism has been lacking. Here we demonstrate the ability to directly track, by liquid chromatography-mass spectrometry, the passage of deuterium from labelled substrates into NADPH, and combine this approach with carbon labelling and mathematical modelling to measure NADPH fluxes. In proliferating cells, the largest contributor to cytosolic NADPH is the oxidative pentose phosphate pathway. Surprisingly, a nearly comparable contribution comes from serine-driven one-carbon metabolism, in which oxidation of methylene tetrahydrofolate to 10-formyl-tetrahydrofolate is coupled to reduction of NADP+ to NADPH. Moreover, tracing of mitochondrial one-carbon metabolism revealed complete oxidation of 10-formyl-tetrahydrofolate to make NADPH. As folate metabolism has not previously been considered an NADPH producer, confirmation of its functional significance was undertaken through knockdown of methylenetetrahydrofolate dehydrogenase (MTHFD) genes. Depletion of either the cytosolic or mitochondrial MTHFD isozyme resulted in decreased cellular NADPH/NADP+ and reduced/oxidized glutathione ratios (GSH/GSSG) and increased cell sensitivity to oxidative stress. Thus, although the importance of folate metabolism for proliferating cells has been long recognized and attributed to its function of producing one-carbon units for nucleic acid synthesis, another crucial function of this pathway is generating reducing power.

  10. Review of Department of Defense Education Activity (DODEA) Schools. Volume II: Quantitative Analysis of Educational Quality

    National Research Council Canada - National Science Library

    Anderson, Lowell

    2000-01-01

    This volume compiles, and presents in integrated form, IDA's quantitative analysis of educational quality provided by DoD's dependent schools, It covers the quantitative aspects of volume I in greater...

  11. Relative Quantitative Proteomic Analysis of Brucella abortus Reveals Metabolic Adaptation to Multiple Environmental Stresses.

    Science.gov (United States)

    Zai, Xiaodong; Yang, Qiaoling; Yin, Ying; Li, Ruihua; Qian, Mengying; Zhao, Taoran; Li, Yaohui; Zhang, Jun; Fu, Ling; Xu, Junjie; Chen, Wei

    2017-01-01

    Brucella spp. are facultative intracellular pathogens that cause chronic brucellosis in humans and animals. The virulence of Brucella primarily depends on its successful survival and replication in host cells. During invasion of the host tissue, Brucella is simultaneously subjected to a variety of harsh conditions, including nutrient limitation, low pH, antimicrobial defenses, and extreme levels of reactive oxygen species (ROS) via the host immune response. This suggests that Brucella may be able to regulate its metabolic adaptation in response to the distinct stresses encountered during its intracellular infection of the host. An investigation into the differential proteome expression patterns of Brucella grown under the relevant stress conditions may contribute toward a better understanding of its pathogenesis and adaptive response. Here, we utilized a mass spectrometry-based label-free relative quantitative proteomics approach to investigate and compare global proteomic changes in B. abortus in response to eight different stress treatments. The 3 h short-term in vitro single-stress and multi-stress conditions mimicked the in vivo conditions of B. abortus under intracellular infection, with survival rates ranging from 3.17 to 73.17%. The proteomic analysis identified and quantified a total of 2,272 proteins and 74% of the theoretical proteome, thereby providing wide coverage of the B. abortus proteome. By including eight distinct growth conditions and comparing these with a control condition, we identified a total of 1,221 differentially expressed proteins (DEPs) that were significantly changed under the stress treatments. Pathway analysis revealed that most of the proteins were involved in oxidative phosphorylation, ABC transporters, two-component systems, biosynthesis of secondary metabolites, the citrate cycle, thiamine metabolism, and nitrogen metabolism; constituting major response mechanisms toward the reconstruction of cellular homeostasis and metabolic

  12. Relative Quantitative Proteomic Analysis of Brucella abortus Reveals Metabolic Adaptation to Multiple Environmental Stresses

    Directory of Open Access Journals (Sweden)

    Xiaodong Zai

    2017-11-01

    Full Text Available Brucella spp. are facultative intracellular pathogens that cause chronic brucellosis in humans and animals. The virulence of Brucella primarily depends on its successful survival and replication in host cells. During invasion of the host tissue, Brucella is simultaneously subjected to a variety of harsh conditions, including nutrient limitation, low pH, antimicrobial defenses, and extreme levels of reactive oxygen species (ROS via the host immune response. This suggests that Brucella may be able to regulate its metabolic adaptation in response to the distinct stresses encountered during its intracellular infection of the host. An investigation into the differential proteome expression patterns of Brucella grown under the relevant stress conditions may contribute toward a better understanding of its pathogenesis and adaptive response. Here, we utilized a mass spectrometry-based label-free relative quantitative proteomics approach to investigate and compare global proteomic changes in B. abortus in response to eight different stress treatments. The 3 h short-term in vitro single-stress and multi-stress conditions mimicked the in vivo conditions of B. abortus under intracellular infection, with survival rates ranging from 3.17 to 73.17%. The proteomic analysis identified and quantified a total of 2,272 proteins and 74% of the theoretical proteome, thereby providing wide coverage of the B. abortus proteome. By including eight distinct growth conditions and comparing these with a control condition, we identified a total of 1,221 differentially expressed proteins (DEPs that were significantly changed under the stress treatments. Pathway analysis revealed that most of the proteins were involved in oxidative phosphorylation, ABC transporters, two-component systems, biosynthesis of secondary metabolites, the citrate cycle, thiamine metabolism, and nitrogen metabolism; constituting major response mechanisms toward the reconstruction of cellular

  13. Root defense analysis against Fusarium oxysporum reveals new regulators to confer resistance

    Science.gov (United States)

    Chen, Yi Chung; Wong, Chin Lin; Muzzi, Frederico; Vlaardingerbroek, Ido; Kidd, Brendan N.; Schenk, Peer M.

    2014-01-01

    Fusarium oxysporum is a root-infecting fungal pathogen that causes wilt disease on a broad range of plant species, including Arabidopsis thaliana. Investigation of the defense response against this pathogen had primarily been conducted using leaf tissue and little was known about the root defense response. In this study, we profiled the expression of root genes after infection with F. oxysporum by microarray analysis. In contrast to the leaf response, root tissue did not show a strong induction of defense-associated gene expression and instead showed a greater proportion of repressed genes. Screening insertion mutants from differentially expressed genes in the microarray uncovered a role for the transcription factor ETHYLENE RESPONSE FACTOR72 (ERF72) in susceptibility to F. oxysporum. Due to the role of ERF72 in suppressing programmed cell death and detoxifying reactive oxygen species (ROS), we examined the pub22/pub23/pub24 U-box type E3 ubiquitin ligase triple mutant which is known to possess enhanced ROS production in response to pathogen challenge. We found that the pub22/23/24 mutant is more resistant to F. oxysporum infection, suggesting that a heightened innate immune response provides protection against F. oxysporum. We conclude that root-mediated defenses against soil-borne pathogens can be provided at multiple levels. PMID:24998294

  14. Changes in plant defense chemistry (pyrrolizidine alkaloids) revealed through high-resolution spectroscopy

    NARCIS (Netherlands)

    Carvalho, S.; Macel, M.; Schlerf, M.; Eghbali Moghaddam, F.; Mulder, P.P.J.; Skidmore, A.K.; Van der Putten, W.H.

    2013-01-01

    Plant toxic biochemicals play an important role in defense against natural enemies and often are toxic to humans and livestock. Hyperspectral reflectance is an established method for primary chemical detection and could be further used to determine plant toxicity in the field. In order to make a

  15. Molecular Dynamics Simulation and Statistics Analysis Reveals the Defense Response Mechanism in Plants

    Science.gov (United States)

    Liu, Zhichao; Zhao, Yunjie; Zeng, Chen; Computational Biophysics Lab Team

    As the main protein of the bacterial flagella, flagellin plays an important role in perception and defense response. The newly discovered locus, FLS2, is ubiquitously expressed. FLS2 encodes a putative receptor kinase and shares many homologies with some plant resistance genes and even with some components of immune system of mammals and insects. In Arabidopsis, FLS2 perception is achieved by the recognition of epitope flg22, which induces FLS2 heteromerization with BAK1 and finally the plant immunity. Here we use both analytical methods such as Direct Coupling Analysis (DCA) and Molecular Dynamics (MD) Simulations to get a better understanding of the defense mechanism of FLS2. This may facilitate a redesign of flg22 or de-novo design for desired specificity and potency to extend the immune properties of FLS2 to other important crops and vegetables.

  16. Changes in plant defense chemistry (pyrrolizidine alkaloids) revealed through high-resolution spectroscopy

    Science.gov (United States)

    Carvalho, Sabrina; Macel, Mirka; Schlerf, Martin; Moghaddam, Fatemeh Eghbali; Mulder, Patrick P. J.; Skidmore, Andrew K.; van der Putten, Wim H.

    2013-06-01

    Plant toxic biochemicals play an important role in defense against natural enemies and often are toxic to humans and livestock. Hyperspectral reflectance is an established method for primary chemical detection and could be further used to determine plant toxicity in the field. In order to make a first step for pyrrolizidine alkaloids detection (toxic defense compound against mammals and many insects) we studied how such spectral data can estimate plant defense chemistry under controlled conditions. In a greenhouse, we grew three related plant species that defend against generalist herbivores through pyrrolizidine alkaloids: Jacobaea vulgaris, Jacobaea erucifolia and Senecio inaequidens, and analyzed the relation between spectral measurements and chemical concentrations using multivariate statistics. Nutrient addition enhanced tertiary-amine pyrrolizidine alkaloids contents of J. vulgaris and J. erucifolia and decreased N-oxide contents in S. inaequidens and J. vulgaris. Pyrrolizidine alkaloids could be predicted with a moderate accuracy. Pyrrolizidine alkaloid forms tertiary-amines and epoxides were predicted with 63% and 56% of the variation explained, respectively. The most relevant spectral regions selected for prediction were associated with electron transitions and Csbnd H, Osbnd H, and Nsbnd H bonds in the 1530 and 2100 nm regions. Given the relatively low concentration in pyrrolizidine alkaloids concentration (in the order of mg g-1) and resultant predictions, it is promising that pyrrolizidine alkaloids interact with incident light. Further studies should be considered to determine if such a non-destructive method may predict changes in PA concentration in relation to plant natural enemies. Spectroscopy may be used to study plant defenses in intact plant tissues, and may provide managers of toxic plants, food industry and multitrophic-interaction researchers with faster and larger monitoring possibilities.

  17. Simultaneous transcriptome analysis of Colletotrichum gloeosporioides and tomato fruit pathosystem reveals novel fungal pathogenicity and fruit defense strategies.

    Science.gov (United States)

    Alkan, Noam; Friedlander, Gilgi; Ment, Dana; Prusky, Dov; Fluhr, Robert

    2015-01-01

    The fungus Colletotrichum gloeosporioides breaches the fruit cuticle but remains quiescent until fruit ripening signals a switch to necrotrophy, culminating in devastating anthracnose disease. There is a need to understand the distinct fungal arms strategy and the simultaneous fruit response. Transcriptome analysis of fungal-fruit interactions was carried out concurrently in the appressoria, quiescent and necrotrophic stages. Conidia germinating on unripe fruit cuticle showed stage-specific transcription that was accompanied by massive fruit defense responses. The subsequent quiescent stage showed the development of dendritic-like structures and swollen hyphae within the fruit epidermis. The quiescent fungal transcriptome was characterized by activation of chromatin remodeling genes and unsuspected environmental alkalization. Fruit response was portrayed by continued highly integrated massive up-regulation of defense genes. During cuticle infection of green or ripe fruit, fungi recapitulate the same developmental stages but with differing quiescent time spans. The necrotrophic stage showed a dramatic shift in fungal metabolism and up-regulation of pathogenicity factors. Fruit response to necrotrophy showed activation of the salicylic acid pathway, climaxing in cell death. Transcriptome analysis of C. gloeosporioides infection of fruit reveals its distinct stage-specific lifestyle and the concurrent changing fruit response, deepening our perception of the unfolding fungal-fruit arms and defenses race. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  18. The Transcriptome and Terpene Profile of Eucalyptus grandis Reveals Mechanisms of Defense Against the Insect Pest, Leptocybe invasa.

    Science.gov (United States)

    Oates, Caryn N; Külheim, Carsten; Myburg, Alexander A; Slippers, Bernard; Naidoo, Sanushka

    2015-07-01

    Plants have evolved complex defenses that allow them to protect themselves against pests and pathogens. However, there is relatively little information regarding the Eucalyptus defensome. Leptocybe invasa is one of the most damaging pests in global Eucalyptus forestry, and essentially nothing is known regarding the molecular mechanisms governing the interaction between the pest and host. The aim of the study was to investigate changes in the transcriptional landscape and terpene profile of a resistant and susceptible Eucalyptus genotype in an effort to improve our understanding of this interaction. We used RNA-seqencing to investigate transcriptional changes following L. invasa oviposition. Expression levels were validated using real-time quantitative PCR. Terpene profiles were investigated using gas chromatography coupled to mass spectometry on uninfested and oviposited leaves. We found 698 and 1,115 significantly differentially expressed genes from the resistant and susceptible interactions, respectively. Gene Ontology enrichment and Mapman analyses identified putative defense mechanisms including cell wall reinforcement, protease inhibitors, cell cycle suppression and regulatory hormone signaling pathways. There were significant differences in the mono- and sesquiterpene profiles between genotypes and between control and infested material. A model of the interaction between Eucalyptus and L. invasa was proposed from the transcriptomic and chemical data. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  19. Quantitative proteomics reveals the central changes of wheat in response to powdery mildew.

    Science.gov (United States)

    Fu, Ying; Zhang, Hong; Mandal, Siddikun Nabi; Wang, Changyou; Chen, Chunhuan; Ji, Wanquan

    2016-01-01

    Powdery mildew (Pm), caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most important crop diseases, causing severe economic losses to wheat production worldwide. However, there are few reports about the proteomic response to Bgt infection in resistant wheat. Hence, quantitative proteomic analysis of N9134, a resistant wheat line, was performed to explore the molecular mechanism of wheat in defense against Bgt. Comparing the leaf proteins of Bgt-inoculated N9134 with that of mock-inoculated controls, a total of 2182 protein-species were quantified by iTRAQ at 24, 48 and 72h postinoculation (hpi) with Bgt, of which 394 showed differential accumulation. These differentially accumulated protein-species (DAPs) mainly included pathogenesis-related (PR) polypeptides, oxidative stress responsive proteins and components involved in primary metabolic pathways. KEGG enrichment analysis showed that phenylpropanoid biosynthesis, phenylalanine metabolism and photosynthesis-antenna proteins were the key pathways in response to Bgt infection. InterProScan 5 and the Gibbs Motif Sampler cluster 394 DAPs into eight conserved motifs, which shared leucine repeats and histidine sites in the sequence motifs. Moreover, eight separate protein-protein interaction (PPI) networks were predicted from STRING database. This study provides a powerful platform for further exploration of the molecular mechanism underlying resistant wheat responding to Bgt. Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a destructive pathogenic disease in wheat-producing regions worldwide, resulting in severe yield reductions. Although many resistant wheat varieties have been cultivated, there are few reports about the proteomic response to Bgt infection in resistant wheat. Therefore, an iTRAQ-based quantitative proteomic analysis of a resistant wheat line (N9134) in response to Bgt infection has been performed. This paper provides new insights into the underlying molecular

  20. A quantitative infrared spectral library of vapor phase chemicals: applications to environmental monitoring and homeland defense

    Science.gov (United States)

    Sharpe, Steven W.; Johnson, Timothy J.; Sams, Robert L.

    2004-12-01

    The utility of infrared spectroscopy for monitoring and early warning of accidental or deliberate chemical releases to the atmosphere is well documented. Regardless of the monitoring technique (open-path or extractive) or weather the spectrometer is passive or active (Fourier transform or lidar) a high quality, quantitative reference library is essential for meaningful interpretation of the data. Pacific Northwest National Laboratory through the support of the Department of Energy has been building a library of pure, vapor phase chemical species for the last 4 years. This infrared spectral library currently contains over 300 chemicals and is expected to grow to over 400 chemicals before completion. The library spectra are based on a statistical fit to many spectra at different concentrations, allowing for rigorous error analysis. The contents of the library are focused on atmospheric pollutants, naturally occurring chemicals, toxic industrial chemicals and chemicals specifically designed to do damage. Applications, limitations and technical details of the spectral library will be discussed.

  1. Transcriptome of Dickeya dadantii infecting Acyrthosiphon pisum reveals a strong defense against antimicrobial peptides.

    Science.gov (United States)

    Costechareyre, Denis; Chich, Jean-François; Strub, Jean-Marc; Rahbé, Yvan; Condemine, Guy

    2013-01-01

    The plant pathogenic bacterium Dickeya dadantii has recently been shown to be able to kill the aphid Acyrthosiphon pisum. While the factors required to cause plant disease are now well characterized, those required for insect pathogeny remain mostly unknown. To identify these factors, we analyzed the transcriptome of the bacteria isolated from infected aphids. More than 150 genes were upregulated and 300 downregulated more than 5-fold at 3 days post infection. No homologue to known toxin genes could be identified in the upregulated genes. The upregulated genes reflect the response of the bacteria to the conditions encountered inside aphids. While only a few genes involved in the response to oxidative stress were induced, a strong defense against antimicrobial peptides (AMP) was induced. Expression of a great number of efflux proteins and transporters was increased. Besides the genes involved in LPS modification by addition of 4-aminoarabinose (the arnBCADTEF operon) and phosphoethanolamine (pmrC, eptB) usually induced in Gram negative bacteria in response to AMPs, dltBAC and pbpG genes, which confer Gram positive bacteria resistance to AMPs by adding alanine to teichoic acids, were also induced. Both types of modification confer D. dadantii resistance to the AMP polymyxin. A. pisum harbors symbiotic bacteria and it is thought that it has a very limited immune system to maintain these populations and do not synthesize AMPs. The arnB mutant was less pathogenic to A. pisum, which suggests that, in contrast to what has been supposed, aphids do synthesize AMP.

  2. Transcriptome of Dickeya dadantii infecting Acyrthosiphon pisum reveals a strong defense against antimicrobial peptides.

    Directory of Open Access Journals (Sweden)

    Denis Costechareyre

    Full Text Available The plant pathogenic bacterium Dickeya dadantii has recently been shown to be able to kill the aphid Acyrthosiphon pisum. While the factors required to cause plant disease are now well characterized, those required for insect pathogeny remain mostly unknown. To identify these factors, we analyzed the transcriptome of the bacteria isolated from infected aphids. More than 150 genes were upregulated and 300 downregulated more than 5-fold at 3 days post infection. No homologue to known toxin genes could be identified in the upregulated genes. The upregulated genes reflect the response of the bacteria to the conditions encountered inside aphids. While only a few genes involved in the response to oxidative stress were induced, a strong defense against antimicrobial peptides (AMP was induced. Expression of a great number of efflux proteins and transporters was increased. Besides the genes involved in LPS modification by addition of 4-aminoarabinose (the arnBCADTEF operon and phosphoethanolamine (pmrC, eptB usually induced in Gram negative bacteria in response to AMPs, dltBAC and pbpG genes, which confer Gram positive bacteria resistance to AMPs by adding alanine to teichoic acids, were also induced. Both types of modification confer D. dadantii resistance to the AMP polymyxin. A. pisum harbors symbiotic bacteria and it is thought that it has a very limited immune system to maintain these populations and do not synthesize AMPs. The arnB mutant was less pathogenic to A. pisum, which suggests that, in contrast to what has been supposed, aphids do synthesize AMP.

  3. Escherichia coli K-12 pathogenicity in the pea aphid, Acyrthosiphon pisum, reveals reduced antibacterial defense in aphids.

    Science.gov (United States)

    Altincicek, Boran; Ter Braak, Bas; Laughton, Alice M; Udekwu, Klas I; Gerardo, Nicole M

    2011-10-01

    To better understand the molecular basis underlying aphid immune tolerance to beneficial bacteria and immune defense to pathogenic bacteria, we characterized how the pea aphid Acyrthosiphon pisum responds to Escherichia coli K-12 infections. E. coli bacteria, usually cleared in the hemolymph of other insect species, were capable of growing exponentially and killing aphids within a few days. Red fluorescence protein expressing E. coli K-12 laboratory strain multiplied in the aphid hemolymph as well as in the digestive tract, resulting in death of infected aphids. Selected gene deletion mutants of the E. coli K-12 predicted to have reduced virulence during systemic infections showed no difference in either replication or killing rate when compared to the wild type E. coli strain. Of note, however, the XL1-Blue E. coli K-12 strain exhibited a significant lag phase before multiplying and killing aphids. This bacterial strain has recently been shown to be more sensitive to oxidative stress than other E. coli K-12 strains, revealing a potential role for reactive oxygen species-mediated defenses in the otherwise reduced aphid immune system. Copyright © 2011 Elsevier Ltd. All rights reserved.

  4. Quantitative proteomic study of Aspergillus Fumigatus secretome revealed deamidation of secretory enzymes.

    Science.gov (United States)

    Adav, Sunil S; Ravindran, Anita; Sze, Siu Kwan

    2015-04-24

    Aspergillus sp. plays an essential role in lignocellulosic biomass recycling and is also exploited as cell factories for the production of industrial enzymes. This study profiled the secretome of Aspergillus fumigatus when grown with cellulose, xylan and starch by high throughput quantitative proteomics using isobaric tags for relative and absolute quantification (iTRAQ). Post translational modifications (PTMs) of proteins play a critical role in protein functions. However, our understanding of the PTMs in secretory proteins is limited. Here, we present the identification of PTMs such as deamidation of secreted proteins of A. fumigatus. This study quantified diverse groups of extracellular secreted enzymes and their functional classification revealed cellulases and glycoside hydrolases (32.9%), amylases (0.9%), hemicellulases (16.2%), lignin degrading enzymes (8.1%), peptidases and proteases (11.7%), chitinases, lipases and phosphatases (7.6%), and proteins with unknown function (22.5%). The comparison of quantitative iTRAQ results revealed that cellulose and xylan stimulates expression of specific cellulases and hemicellulases, and their abundance level as a function of substrate. In-depth data analysis revealed deamidation as a major PTM of key cellulose hydrolyzing enzymes like endoglucanases, cellobiohydrolases and glucosidases. Hemicellulose degrading endo-1,4-beta-xylanase, monosidases, xylosidases, lignin degrading laccase, isoamyl alcohol oxidase and oxidoreductases were also found to be deamidated. The filamentous fungi play an essential role in lignocellulosic biomass recycling and fungal strains belonging to Aspergillus were also exploited as cell factories for the production of organic acids, pharmaceuticals, and industrially important enzymes. In this study, extracellular proteins secreted by thermophilic A. fumigatus when grown with cellulose, xylan and starch were profiled using isobaric tags for relative and absolute quantification (iTRAQ) by

  5. Quantitative protein localization signatures reveal an association between spatial and functional divergences of proteins.

    Science.gov (United States)

    Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

    2014-03-01

    Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein

  6. New quantitative approaches reveal the spatial preference of nuclear compartments in mammalian fibroblasts.

    Science.gov (United States)

    Weston, David J; Russell, Richard A; Batty, Elizabeth; Jensen, Kirsten; Stephens, David A; Adams, Niall M; Freemont, Paul S

    2015-03-06

    The nuclei of higher eukaryotic cells display compartmentalization and certain nuclear compartments have been shown to follow a degree of spatial organization. To date, the study of nuclear organization has often involved simple quantitative procedures that struggle with both the irregularity of the nuclear boundary and the problem of handling replicate images. Such studies typically focus on inter-object distance, rather than spatial location within the nucleus. The concern of this paper is the spatial preference of nuclear compartments, for which we have developed statistical tools to quantitatively study and explore nuclear organization. These tools combine replicate images to generate 'aggregate maps' which represent the spatial preferences of nuclear compartments. We present two examples of different compartments in mammalian fibroblasts (WI-38 and MRC-5) that demonstrate new knowledge of spatial preference within the cell nucleus. Specifically, the spatial preference of RNA polymerase II is preserved across normal and immortalized cells, whereas PML nuclear bodies exhibit a change in spatial preference from avoiding the centre in normal cells to exhibiting a preference for the centre in immortalized cells. In addition, we show that SC35 splicing speckles are excluded from the nuclear boundary and localize throughout the nucleoplasm and in the interchromatin space in non-transformed WI-38 cells. This new methodology is thus able to reveal the effect of large-scale perturbation on spatial architecture and preferences that would not be obvious from single cell imaging.

  7. Quantitative proteomics of the tonoplast reveals a role for glycolytic enzymes in salt tolerance.

    Science.gov (United States)

    Barkla, Bronwyn J; Vera-Estrella, Rosario; Hernández-Coronado, Marcela; Pantoja, Omar

    2009-12-01

    To examine the role of the tonoplast in plant salt tolerance and identify proteins involved in the regulation of transporters for vacuolar Na(+) sequestration, we exploited a targeted quantitative proteomics approach. Two-dimensional differential in-gel electrophoresis analysis of free flow zonal electrophoresis separated tonoplast fractions from control, and salt-treated Mesembryanthemum crystallinum plants revealed the membrane association of glycolytic enzymes aldolase and enolase, along with subunits of the vacuolar H(+)-ATPase V-ATPase. Protein blot analysis confirmed coordinated salt regulation of these proteins, and chaotrope treatment indicated a strong tonoplast association. Reciprocal coimmunoprecipitation studies revealed that the glycolytic enzymes interacted with the V-ATPase subunit B VHA-B, and aldolase was shown to stimulate V-ATPase activity in vitro by increasing the affinity for ATP. To investigate a physiological role for this association, the Arabidopsis thaliana cytoplasmic enolase mutant, los2, was characterized. These plants were salt sensitive, and there was a specific reduction in enolase abundance in the tonoplast from salt-treated plants. Moreover, tonoplast isolated from mutant plants showed an impaired ability for aldolase stimulation of V-ATPase hydrolytic activity. The association of glycolytic proteins with the tonoplast may not only channel ATP to the V-ATPase, but also directly upregulate H(+)-pump activity.

  8. Quantitative Proteomics Reveals the Regulatory Networks of Circular RNA CDR1as in Hepatocellular Carcinoma Cells.

    Science.gov (United States)

    Yang, Xue; Xiong, Qian; Wu, Ying; Li, Siting; Ge, Feng

    2017-10-06

    Circular RNAs (circRNAs), a class of widespread endogenous RNAs, play crucial roles in diverse biological processes and are potential biomarkers in diverse human diseases and cancers. Cerebellar-degeneration-related protein 1 antisense RNA (CDR1as), an oncogenic circRNA, is involved in human tumorigenesis and is dysregulated in hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying CDR1as functions in HCC remain unclear. Here we explored the functions of CDR1as and searched for CDR1as-regulated proteins in HCC cells. A quantitative proteomics strategy was employed to globally identify CDR1as-regulated proteins in HCC cells. In total, we identified 330 differentially expressed proteins (DEPs) upon enhanced CDR1as expression in HepG2 cells, indicating that they could be proteins regulated by CDR1as. Bioinformatic analysis revealed that many DEPs were involved in cell proliferation and the cell cycle. Further functional studies of epidermal growth factor receptor (EGFR) found that CDR1as exerts its effects on cell proliferation at least in part through the regulation of EGFR expression. We further confirmed that CDR1as could inhibit the expression of microRNA-7 (miR-7). EGFR is a validated target of miR-7; therefore, CDR1as may exert its function by regulating EGFR expression via targeting miR-7 in HCC cells. Taken together, we revealed novel functions and underlying mechanisms of CDR1as in HCC cells. This study serves as the first proteome-wide analysis of a circRNA-regulated protein in cells and provides a reliable and highly efficient method for globally identifying circRNA-regulated proteins.

  9. Quantitative proteomics reveals dynamic responses of Synechocystis sp. PCC 6803 to next-generation biofuel butanol.

    Science.gov (United States)

    Tian, Xiaoxu; Chen, Lei; Wang, Jiangxin; Qiao, Jianjun; Zhang, Weiwen

    2013-01-14

    Butanol is a promising biofuel, and recent metabolic engineering efforts have demonstrated the use of photosynthetic cyanobacterial hosts for its production. However, cyanobacteria have very low tolerance to butanol, limiting the economic viability of butanol production from these renewable producing systems. The existing knowledge of molecular mechanism involved in butanol tolerance in cyanobacteria is very limited. To build a foundation necessary to engineer robust butanol-producing cyanobacterial hosts, in this study, the responses of Synechocystis PCC 6803 to butanol were investigated using a quantitative proteomics approach with iTRAQ - LC-MS/MS technologies. The resulting high-quality dataset consisted of 25,347 peptides corresponding to 1452 unique proteins, a coverage of approximately 40% of the predicted proteins in Synechocystis. Comparative quantification of protein abundances led to the identification of 303 differentially regulated proteins by butanol. Annotation and GO term enrichment analysis showed that multiple biological processes were regulated, suggesting that Synechocystis probably employed multiple and synergistic resistance mechanisms in dealing with butanol stress. Notably, the analysis revealed the induction of heat-shock protein and transporters, along with modification of cell membrane and envelope were the major protection mechanisms against butanol. A conceptual cellular model of Synechocystis PCC 6803 responses to butanol stress was constructed to illustrate the putative molecular mechanisms employed to defend against butanol stress. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. Quantitative phosphoproteomics reveals new roles for the protein phosphatase PP6 in mitotic cells.

    Science.gov (United States)

    Rusin, Scott F; Schlosser, Kate A; Adamo, Mark E; Kettenbach, Arminja N

    2015-10-13

    Protein phosphorylation is an important regulatory mechanism controlling mitotic progression. Protein phosphatase 6 (PP6) is an essential enzyme with conserved roles in chromosome segregation and spindle assembly from yeast to humans. We applied a baculovirus-mediated gene silencing approach to deplete HeLa cells of the catalytic subunit of PP6 (PP6c) and analyzed changes in the phosphoproteome and proteome in mitotic cells by quantitative mass spectrometry-based proteomics. We identified 408 phosphopeptides on 272 proteins that increased and 298 phosphopeptides on 220 proteins that decreased in phosphorylation upon PP6c depletion in mitotic cells. Motif analysis of the phosphorylated sites combined with bioinformatics pathway analysis revealed previously unknown PP6c-dependent regulatory pathways. Biochemical assays demonstrated that PP6c opposed casein kinase 2-dependent phosphorylation of the condensin I subunit NCAP-G, and cellular analysis showed that depletion of PP6c resulted in defects in chromosome condensation and segregation in anaphase, consistent with dysregulation of condensin I function in the absence of PP6 activity. Copyright © 2015, American Association for the Advancement of Science.

  11. Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community.

    Science.gov (United States)

    Mayali, Xavier; Weber, Peter K

    2018-05-01

    To quantitatively link microbial identity with biogeochemical function, we carried out 14 simultaneous stable isotope probing experiments with organic and inorganic C and N substrates to measure the isotope incorporation by over one hundred co-occurring eukaryotic and prokaryotic populations in a coastal community. We found that nitrate was the most commonly incorporated substrate, and that light-driven carbon fixation was carried out by some bacterial taxa from the Flavobacteriales and OM60 (NOR5) clade, in addition to photoautotrophic phytoplankton. We found that organisms that incorporated starch, maltose, glucose, lactose and bicarbonate were phylogenetically clustered, suggesting that specific bacterial lineages specialized in the incorporation of these substrates. The data further revealed that coastal microorganisms spanned a range of resource utilization strategies from generalists to specialists and demonstrated a high level of substrate partitioning, with two thirds of taxa exhibiting unique substrate incorporation patterns and the remaining third shared by no more than three OTUs each. Specialists exhibited more extreme incorporation levels (high or low), whereas generalists displayed more intermediate activity levels. These results shed valuable insights into the bottom-up ecological strategies enabling the persistence of high microbial diversity in aquatic ecosystems.

  12. Stochasticity in the enterococcal sex pheromone response revealed by quantitative analysis of transcription in single cells.

    Science.gov (United States)

    Breuer, Rebecca J; Bandyopadhyay, Arpan; O'Brien, Sofie A; Barnes, Aaron M T; Hunter, Ryan C; Hu, Wei-Shou; Dunny, Gary M

    2017-07-01

    In Enterococcus faecalis, sex pheromone-mediated transfer of antibiotic resistance plasmids can occur under unfavorable conditions, for example, when inducing pheromone concentrations are low and inhibiting pheromone concentrations are high. To better understand this paradox, we adapted fluorescence in situ hybridization chain reaction (HCR) methodology for simultaneous quantification of multiple E. faecalis transcripts at the single cell level. We present direct evidence for variability in the minimum period, maximum response level, and duration of response of individual cells to a specific inducing condition. Tracking of induction patterns of single cells temporally using a fluorescent reporter supported HCR findings. It also revealed subpopulations of rapid responders, even under low inducing pheromone concentrations where the overall response of the entire population was slow. The strong, rapid induction of small numbers of cells in cultures exposed to low pheromone concentrations is in agreement with predictions of a stochastic model of the enterococcal pheromone response. The previously documented complex regulatory circuitry controlling the pheromone response likely contributes to stochastic variation in this system. In addition to increasing our basic understanding of the biology of a horizontal gene transfer system regulated by cell-cell signaling, demonstration of the stochastic nature of the pheromone response also impacts any future efforts to develop therapeutic agents targeting the system. Quantitative single cell analysis using HCR also has great potential to elucidate important bacterial regulatory mechanisms not previously amenable to study at the single cell level, and to accelerate the pace of functional genomic studies.

  13. Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome

    DEFF Research Database (Denmark)

    Grassl, Niklas; Kulak, Nils Alexander; Pichler, Garwin

    2016-01-01

    BACKGROUND: The oral cavity is home to one of the most diverse microbial communities of the human body and a major entry portal for pathogens. Its homeostasis is maintained by saliva, which fulfills key functions including lubrication of food, pre-digestion, and bacterial defense. Consequently, d...

  14. Quantitative Phosphoproteomics Reveals Wee1 Kinase as a Therapeutic Target in a Model of Proneural Glioblastoma.

    Science.gov (United States)

    Lescarbeau, Rebecca S; Lei, Liang; Bakken, Katrina K; Sims, Peter A; Sarkaria, Jann N; Canoll, Peter; White, Forest M

    2016-06-01

    Glioblastoma (GBM) is the most common malignant primary brain cancer. With a median survival of about a year, new approaches to treating this disease are necessary. To identify signaling molecules regulating GBM progression in a genetically engineered murine model of proneural GBM, we quantified phosphotyrosine-mediated signaling using mass spectrometry. Oncogenic signals, including phosphorylated ERK MAPK, PI3K, and PDGFR, were found to be increased in the murine tumors relative to brain. Phosphorylation of CDK1 pY15, associated with the G2 arrest checkpoint, was identified as the most differentially phosphorylated site, with a 14-fold increase in phosphorylation in the tumors. To assess the role of this checkpoint as a potential therapeutic target, syngeneic primary cell lines derived from these tumors were treated with MK-1775, an inhibitor of Wee1, the kinase responsible for CDK1 Y15 phosphorylation. MK-1775 treatment led to mitotic catastrophe, as defined by increased DNA damage and cell death by apoptosis. To assess the extensibility of targeting Wee1/CDK1 in GBM, patient-derived xenograft (PDX) cell lines were also treated with MK-1775. Although the response was more heterogeneous, on-target Wee1 inhibition led to decreased CDK1 Y15 phosphorylation and increased DNA damage and apoptosis in each line. These results were also validated in vivo, where single-agent MK-1775 demonstrated an antitumor effect on a flank PDX tumor model, increasing mouse survival by 1.74-fold. This study highlights the ability of unbiased quantitative phosphoproteomics to reveal therapeutic targets in tumor models, and the potential for Wee1 inhibition as a treatment approach in preclinical models of GBM. Mol Cancer Ther; 15(6); 1332-43. ©2016 AACR. ©2016 American Association for Cancer Research.

  15. Quantitative X-ray Diffraction (QXRD) analysis for revealing thermal transformations of red mud.

    Science.gov (United States)

    Liao, Chang-Zhong; Zeng, Lingmin; Shih, Kaimin

    2015-07-01

    Red mud is a worldwide environmental problem, and many authorities are trying to find an economic solution for its beneficial application or/and safe disposal. Ceramic production is one of the potential waste-to-resource strategies for using red mud as a raw material. Before implementing such a strategy, an unambiguous understanding of the reaction behavior of red mud under thermal conditions is essential. In this study, the phase compositions and transformation processes were revealed for the Pingguo red mud (PRM) heat-treated at different sintering temperatures. Hematite, perovskite, andradite, cancrinite, kaolinite, diaspore, gibbsite and calcite phases were observed in the samples. However, unlike those red mud samples from the other regions, no TiO2 (rutile or anatase) or quartz were observed. Titanium was found to exist mainly in perovskite and andradite while the iron mainly existed in hematite and andradite. A new silico-ferrite of calcium and aluminum (SFCA) phase was found in samples treated at temperatures above 1100°C, and two possible formation pathways for SFCA were suggested. This is the first SFCA phase to be reported in thermally treated red mud, and this finding may turn PRM waste into a material resource for the iron-making industry. Titanium was found to be enriched in the perovskite phase after 1200°C thermal treatment, and this observation indicated a potential strategy for the recovery of titanium from PRM. In addition to noting these various resource recovery opportunities, this is also the first study to quantitatively summarize the reaction details of PRM phase transformations at various temperatures. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Fagen Li

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

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

    Science.gov (United States)

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

    2015-01-01

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

  18. What Is "Good" Research? Revealing the Paradigmatic Tensions in Quantitative Criticalist Work

    Science.gov (United States)

    Hernández, Ebelia

    2014-01-01

    If quantitative criticalism is thought to be a bridge between positivist epistemologies prevalent in quantitative work and social constructionism often found in critical qualitative work, then this bridge is fraught with challenges and tensions. This chapter examines the methodological issues, questions, and tensions that emerged from a research…

  19. Identification of Host Defense-Related Proteins Using Label-Free Quantitative Proteomic Analysis of Milk Whey from Cows with Staphylococcus aureus Subclinical Mastitis

    Directory of Open Access Journals (Sweden)

    Shaimaa Abdelmegid

    2017-12-01

    Full Text Available Staphylococcus aureus is the most common contagious pathogen associated with bovine subclinical mastitis. Current diagnosis of S. aureus mastitis is based on bacteriological culture of milk samples and somatic cell counts, which lack either sensitivity or specificity. Identification of milk proteins that contribute to host defense and their variable responses to pathogenic stimuli would enable the characterization of putative biomarkers of subclinical mastitis. To accomplish this, milk whey samples from healthy and mastitic dairy cows were analyzed using a label-free quantitative proteomics approach. In total, 90 proteins were identified, of which 25 showed significant differential abundance between healthy and mastitic samples. In silico functional analyses indicated the involvement of the differentially abundant proteins in biological mechanisms and signaling pathways related to host defense including pathogen-recognition, direct antimicrobial function, and the acute-phase response. This proteomics and bioinformatics analysis not only facilitates the identification of putative biomarkers of S. aureus subclinical mastitis but also recapitulates previous findings demonstrating the abundance of host defense proteins in intramammary infection. All mass spectrometry data are available via ProteomeXchange with identifier PXD007516.

  20. Agonistic interactions between the honeybee (Apis mellifera ligustica and the European wasp (Vespula germanica reveal context-dependent defense strategies.

    Directory of Open Access Journals (Sweden)

    Michelina Pusceddu

    Full Text Available Predator-prey relationships between sympatric species allow the evolution of defense behaviors, such as honeybee colonies defending their nests against predatory wasps. We investigated the predator-prey relationship between the honeybee (Apis mellifera ligustica and the European wasp (Vespula germanica by evaluating the effectiveness of attack and defense behaviors, which have coevolved in these sympatric species, as well as the actual damage and disturbance caused to the colonies under attack. Attack and defense behaviors were recorded in front of the hive to observe attacks at the hive entrance (68 attacks in 279 h and at ground level on isolated and weakened honeybees close to the hive (465 attacks in 32 h. We found that V. germanica attacked the hive entrance infrequently due to the low success rate of this strategy and instead preferred a specialized attack method targeting adult honeybees at ground level, demonstrating opportunistic scavenger behavior. Individual honeybees usually responded effectively to an attack by recruiting an average of two nestmates, causing the wasp to flee, whereas collective balling behavior was only observed on four occasions. V. germanica does not appear to disrupt the foraging activity of the colonies under attack. We found that agonistic events supported by other nestmates were typically the most intense ones, involving physical combat and prolonged attacks at the entrance to the hive. These observations support the hypothesis that A. mellifera ligustica can adapt its behavior to match the severity of the threat and the context of the attack.

  1. Agonistic interactions between the honeybee (Apis mellifera ligustica) and the European wasp (Vespula germanica) reveal context-dependent defense strategies.

    Science.gov (United States)

    Pusceddu, Michelina; Floris, Ignazio; Buffa, Franco; Salaris, Emanuele; Satta, Alberto

    2017-01-01

    Predator-prey relationships between sympatric species allow the evolution of defense behaviors, such as honeybee colonies defending their nests against predatory wasps. We investigated the predator-prey relationship between the honeybee (Apis mellifera ligustica) and the European wasp (Vespula germanica) by evaluating the effectiveness of attack and defense behaviors, which have coevolved in these sympatric species, as well as the actual damage and disturbance caused to the colonies under attack. Attack and defense behaviors were recorded in front of the hive to observe attacks at the hive entrance (68 attacks in 279 h) and at ground level on isolated and weakened honeybees close to the hive (465 attacks in 32 h). We found that V. germanica attacked the hive entrance infrequently due to the low success rate of this strategy and instead preferred a specialized attack method targeting adult honeybees at ground level, demonstrating opportunistic scavenger behavior. Individual honeybees usually responded effectively to an attack by recruiting an average of two nestmates, causing the wasp to flee, whereas collective balling behavior was only observed on four occasions. V. germanica does not appear to disrupt the foraging activity of the colonies under attack. We found that agonistic events supported by other nestmates were typically the most intense ones, involving physical combat and prolonged attacks at the entrance to the hive. These observations support the hypothesis that A. mellifera ligustica can adapt its behavior to match the severity of the threat and the context of the attack.

  2. Quantitative proteomics reveals the mechanism and consequence of gliotoxin-mediated dysregulation of the methionine cycle in Aspergillus niger

    OpenAIRE

    Manzanares-Miralles, Lara; Bayram, Ozgur; Sarikaya-Bayram, Ozlem; Smith, Elizabeth B.; Dolan, Stephen K.; Jones, Gary W.; Doyle, Sean

    2016-01-01

    Gliotoxin (GT) is a redox-active metabolite, produced by Aspergillus fumigatus,which inhibits the growth of other fungi. Here we demonstrate how Aspergillus niger responds to GT exposure. Quantitative proteomics revealed that GT dysregulated the abundance of 378 proteins including those involved in methionine metabolism and induced de novo abundance of two S-adenosylmethionine (SAM)-dependent methyltransferases. Increased abundance of enzymes S-adenosylhomocysteinase (p = 0.0018) ...

  3. Infrared spectroscopy reveals both qualitative and quantitative differences in equine subchondral bone during maturation

    Science.gov (United States)

    Kobrina, Yevgeniya; Isaksson, Hanna; Sinisaari, Miikka; Rieppo, Lassi; Brama, Pieter A.; van Weeren, René; Helminen, Heikki J.; Jurvelin, Jukka S.; Saarakkala, Simo

    2010-11-01

    The collagen phase in bone is known to undergo major changes during growth and maturation. The objective of this study is to clarify whether Fourier transform infrared (FTIR) microspectroscopy, coupled with cluster analysis, can detect quantitative and qualitative changes in the collagen matrix of subchondral bone in horses during maturation and growth. Equine subchondral bone samples (n = 29) from the proximal joint surface of the first phalanx are prepared from two sites subjected to different loading conditions. Three age groups are studied: newborn (0 days old), immature (5 to 11 months old), and adult (6 to 10 years old) horses. Spatial collagen content and collagen cross-link ratio are quantified from the spectra. Additionally, normalized second derivative spectra of samples are clustered using the k-means clustering algorithm. In quantitative analysis, collagen content in the subchondral bone increases rapidly between the newborn and immature horses. The collagen cross-link ratio increases significantly with age. In qualitative analysis, clustering is able to separate newborn and adult samples into two different groups. The immature samples display some nonhomogeneity. In conclusion, this is the first study showing that FTIR spectral imaging combined with clustering techniques can detect quantitative and qualitative changes in the collagen matrix of subchondral bone during growth and maturation.

  4. A genetic screen reveals Arabidopsis stomatal and/or apoplastic defenses against Pseudomonas syringae pv. tomato DC3000.

    Directory of Open Access Journals (Sweden)

    Weiqing Zeng

    2011-10-01

    Full Text Available Bacterial infection of plants often begins with colonization of the plant surface, followed by entry into the plant through wounds and natural openings (such as stomata, multiplication in the intercellular space (apoplast of the infected tissues, and dissemination of bacteria to other plants. Historically, most studies assess bacterial infection based on final outcomes of disease and/or pathogen growth using whole infected tissues; few studies have genetically distinguished the contribution of different host cell types in response to an infection. The phytotoxin coronatine (COR is produced by several pathovars of Pseudomonas syringae. COR-deficient mutants of P. s. tomato (Pst DC3000 are severely compromised in virulence, especially when inoculated onto the plant surface. We report here a genetic screen to identify Arabidopsis mutants that could rescue the virulence of COR-deficient mutant bacteria. Among the susceptible to coronatine-deficient Pst DC3000 (scord mutants were two that were defective in stomatal closure response, two that were defective in apoplast defense, and four that were defective in both stomatal and apoplast defense. Isolation of these three classes of mutants suggests that stomatal and apoplastic defenses are integrated in plants, but are genetically separable, and that COR is important for Pst DC3000 to overcome both stomatal guard cell- and apoplastic mesophyll cell-based defenses. Of the six mutants defective in bacterium-triggered stomatal closure, three are defective in salicylic acid (SA-induced stomatal closure, but exhibit normal stomatal closure in response to abscisic acid (ABA, and scord7 is compromised in both SA- and ABA-induced stomatal closure. We have cloned SCORD3, which is required for salicylic acid (SA biosynthesis, and SCORD5, which encodes an ATP-binding cassette (ABC protein, AtGCN20/AtABCF3, predicted to be involved in stress-associated protein translation control. Identification of SCORD5 begins to

  5. Intake and transformation to a glycoside of (Z)-3-hexenol from infested neighbors reveals a mode of plant odor reception and defense

    Science.gov (United States)

    Sugimoto, Koichi; Matsui, Kenji; Iijima, Yoko; Akakabe, Yoshihiko; Muramoto, Shoko; Ozawa, Rika; Uefune, Masayoshi; Sasaki, Ryosuke; Alamgir, Kabir Md.; Akitake, Shota; Nobuke, Tatsunori; Galis, Ivan; Aoki, Koh; Shibata, Daisuke; Takabayashi, Junji

    2014-01-01

    Plants receive volatile compounds emitted by neighboring plants that are infested by herbivores, and consequently the receiver plants begin to defend against forthcoming herbivory. However, to date, how plants receive volatiles and, consequently, how they fortify their defenses, is largely unknown. In this study, we found that undamaged tomato plants exposed to volatiles emitted by conspecifics infested with common cutworms (exposed plants) became more defensive against the larvae than those exposed to volatiles from uninfested conspecifics (control plants) in a constant airflow system under laboratory conditions. Comprehensive metabolite analyses showed that only the amount of (Z)-3-hexenylvicianoside (HexVic) was higher in exposed than control plants. This compound negatively affected the performance of common cutworms when added to an artificial diet. The aglycon of HexVic, (Z)-3-hexenol, was obtained from neighboring infested plants via the air. The amount of jasmonates (JAs) was not higher in exposed plants, and HexVic biosynthesis was independent of JA signaling. The use of (Z)-3-hexenol from neighboring damaged conspecifics for HexVic biosynthesis in exposed plants was also observed in an experimental field, indicating that (Z)-3-hexenol intake occurred even under fluctuating environmental conditions. Specific use of airborne (Z)-3-hexenol to form HexVic in undamaged tomato plants reveals a previously unidentified mechanism of plant defense. PMID:24778218

  6. Quantitative iTRAQ secretome analysis of Aspergillus niger reveals novel hydrolytic enzymes.

    Science.gov (United States)

    Adav, Sunil S; Li, An A; Manavalan, Arulmani; Punt, Peter; Sze, Siu Kwan

    2010-08-06

    The natural lifestyle of Aspergillus niger made them more effective secretors of hydrolytic proteins and becomes critical when this species were exploited as hosts for the commercial secretion of heterologous proteins. The protein secretion profile of A. niger and its mutant at different pH was explored using iTRAQ-based quantitative proteomics approach coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). This study characterized 102 highly confident unique proteins in the secretome with zero false discovery rate based on decoy strategy. The iTRAQ technique identified and relatively quantified many hydrolyzing enzymes such as cellulases, hemicellulases, glycoside hydrolases, proteases, peroxidases, and protein translocating transporter proteins during fermentation. The enzymes have potential application in lignocellulosic biomass hydrolysis for biofuel production, for example, the cellulolytic and hemicellulolytic enzymes glucan 1,4-alpha-glucosidase, alpha-glucosidase C, endoglucanase, alpha l-arabinofuranosidase, beta-mannosidase, glycosyl hydrolase; proteases such as tripeptidyl-peptidase, aspergillopepsin, and other enzymes including cytochrome c oxidase, cytochrome c oxidase, glucose oxidase were highly expressed in A. niger and its mutant secretion. In addition, specific enzyme production can be stimulated by controlling pH of the culture medium. Our results showed comprehensive unique secretory protein profile of A. niger, its regulation at different pH, and the potential application of iTRAQ-based quantitative proteomics for the microbial secretome analysis.

  7. Comparative mapping reveals quantitative trait loci that affect spawning time in coho salmon (Oncorhynchus kisutch

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    Cristian Araneda

    2012-01-01

    Full Text Available Spawning time in salmonids is a sex-limited quantitative trait that can be modified by selection. In rainbow trout (Oncorhynchus mykiss, various quantitative trait loci (QTL that affect the expression of this trait have been discovered. In this study, we describe four microsatellite loci associated with two possible spawning time QTL regions in coho salmon (Oncorhynchus kisutch. The four loci were identified in females from two populations (early and late spawners produced by divergent selection from the same base population. Three of the loci (OmyFGT34TUF, One2ASC and One19ASC that were strongly associated with spawning time in coho salmon (p < 0.0002 were previously associated with QTL for the same trait in rainbow trout; a fourth loci (Oki10 with a suggestive association (p = 0.00035 mapped 10 cM from locus OmyFGT34TUF in rainbow trout. The changes in allelic frequency observed after three generations of selection were greater than expected because of genetic drift. This work shows that comparing information from closely-related species is a valid strategy for identifying QTLs for marker-assisted selection in species whose genomes are poorly characterized or lack a saturated genetic map.

  8. Serum quantitative proteomic analysis reveals potential zinc-associated biomarkers for nonbacterial prostatitis.

    Science.gov (United States)

    Yang, Xiaoli; Li, Hongtao; Zhang, Chengdong; Lin, Zhidi; Zhang, Xinhua; Zhang, Youjie; Yu, Yanbao; Liu, Kun; Li, Muyan; Zhang, Yuening; Lv, Wenxin; Xie, Yuanliang; Lu, Zheng; Wu, Chunlei; Teng, Ruobing; Lu, Shaoming; He, Min; Mo, Zengnan

    2015-10-01

    Prostatitis is one of the most common urological problems afflicting adult men. The etiology and pathogenesis of nonbacterial prostatitis, which accounts for 90-95% of cases, is largely unknown. As serum proteins often indicate the overall pathologic status of patients, we hypothesized that protein biomarkers of prostatitis might be identified by comparing the serum proteomes of patients with and without nonbacterial prostatitis. All untreated samples were collected from subjects attending the Fangchenggang Area Male Health and Examination Survey (FAMHES). We profiled pooled serum samples from four carefully selected groups of patients (n = 10/group) representing the various categories of nonbacterial prostatitis (IIIa, IIIb, and IV) and matched healthy controls using a mass spectrometry-based 4-plex iTRAQ proteomic approach. More than 160 samples were validated by ELISA. Overall, 69 proteins were identified. Among them, 42, 52, and 37 proteins were identified with differential expression in Category IIIa, IIIb, and IV prostatitis, respectively. The 19 common proteins were related to immunity and defense, ion binding, transport, and proteolysis. Two zinc-binding proteins, superoxide dismutase 3 (SOD3), and carbonic anhydrase I (CA1), were significantly higher in all types of prostatitis than in the control. A receiver operating characteristic curve estimated sensitivities of 50.4 and 68.1% and specificities of 92.1 and 83.8% for CA1 and SOD3, respectively, in detecting nonbacterial prostatitis. The serum CA1 concentration was inversely correlated to the zinc concentration in expressed-prostatic secretions. Our findings suggest that SOD3 and CA1 are potential diagnostic markers of nonbacterial prostatitis, although further large-scale studies are required. The molecular profiles of nonbacterial prostatitis pathogenesis may lay a foundation for discovery of new therapies. © 2015 Wiley Periodicals, Inc.

  9. Transcriptomics of the rice blast fungus Magnaporthe oryzae in response to the bacterial antagonist Lysobacter enzymogenes reveals candidate fungal defense response genes.

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    Sandra M Mathioni

    Full Text Available Plants and animals have evolved a first line of defense response to pathogens called innate or basal immunity. While basal defenses in these organisms are well studied, there is almost a complete lack of understanding of such systems in fungal species, and more specifically, how they are able to detect and mount a defense response upon pathogen attack. Hence, the goal of the present study was to understand how fungi respond to biotic stress by assessing the transcriptional profile of the rice blast pathogen, Magnaporthe oryzae, when challenged with the bacterial antagonist Lysobacter enzymogenes. Based on microscopic observations of interactions between M. oryzae and wild-type L. enzymogenes strain C3, we selected early and intermediate stages represented by time-points of 3 and 9 hours post-inoculation, respectively, to evaluate the fungal transcriptome using RNA-seq. For comparative purposes, we also challenged the fungus with L. enzymogenes mutant strain DCA, previously demonstrated to be devoid of antifungal activity. A comparison of transcriptional data from fungal interactions with the wild-type bacterial strain C3 and the mutant strain DCA revealed 463 fungal genes that were down-regulated during attack by C3; of these genes, 100 were also found to be up-regulated during the interaction with DCA. Functional categorization of genes in this suite included those with roles in carbohydrate metabolism, cellular transport and stress response. One gene in this suite belongs to the CFEM-domain class of fungal proteins. Another CFEM class protein called PTH11 has been previously characterized, and we found that a deletion in this gene caused advanced lesion development by C3 compared to its growth on the wild-type fungus. We discuss the characterization of this suite of 100 genes with respect to their role in the fungal defense response.

  10. Strigolactone-Regulated Proteins Revealed by iTRAQ-Based Quantitative Proteomics in Arabidopsis

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhou [ORNL; Czarnecki, Olaf [ORNL; Chourey, Karuna [ORNL; Yang, Jun [ORNL; Tuskan, Gerald A [ORNL; Hurst, Gregory {Greg} B [ORNL; Pan, Chongle [ORNL; Chen, Jay [ORNL

    2014-01-01

    Strigolactones (SLs) are a new class of plant hormones. In addition to acting as a key inhibitor of shoot branching, SLs stimulate seed germination of root parasitic plants and promote hyphal branching and root colonization of symbiotic arbuscular mycorrhizal fungi. They also regulate many other aspects of plant growth and development. At the transcription level, SL-regulated genes have been reported. However, nothing is known about the proteome regulated by this new class of plant hormones. Here, a quantitative proteomics approach using an isobaric chemical labeling reagent, iTRAQ, to identify the proteome regulated by SLs in Arabidopsis seedlings is presented. It was found SLs regulate the expression of about three dozens of proteins that have not been previously assigned to SL pathways. These findings provide a new tool to investigate the molecular mechanism of action of SLs.

  11. Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis.

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    Daniela Beisser

    Full Text Available Aquatic environments are heavily impacted by human activities including climate warming and the introduction of xenobiotics. Due to the application of silver nanoparticles as bactericidal agent the introduction of silver into the environment strongly has increased during the past years. Silver ions affect the primary metabolism of algae, in particular photosynthesis. Mixotrophic algae are an interesting test case as they do not exclusively rely on photosynthesis which may attenuate the harmful effect of silver. In order to study the effect of silver ions on mixotrophs, cultures of the chrysophyte Poterioochromonas malhamensis were treated in a replicate design in light and darkness with silver nitrate at a sub-lethal concentration. At five time points samples were taken for the identification and quantitation of proteins by mass spectrometry. In our analysis, relative quantitative protein mass spectrometry has shown to be a useful tool for functional analyses in conjunction with transcriptome reference sequences. A total of 3,952 proteins in 63 samples were identified and quantified, mapping to 4,829 transcripts of the sequenced and assembled transcriptome. Among them, 720 and 104 proteins performing various cellular functions were differentially expressed after eight days in light versus darkness and after three days of silver treatment, respectively. Specifically pathways of the energy and primary carbon metabolism were differentially affected by light and the utilization of expensive reactions hints to an energy surplus of P. malhamensis under light conditions. The excess energy is not invested in growth, but in the synthesis of storage metabolites. The effects of silver were less explicit, observable especially in the dark treatments where the light effect could not mask coinciding but weaker effects of silver. Photosynthesis, particularly the light harvesting complexes, and several sulphur containing enzymes were affected presumably due to

  12. Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

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    Takahiro Tsujikawa

    2017-04-01

    Full Text Available Here, we describe a multiplexed immunohistochemical platform with computational image processing workflows, including image cytometry, enabling simultaneous evaluation of 12 biomarkers in one formalin-fixed paraffin-embedded tissue section. To validate this platform, we used tissue microarrays containing 38 archival head and neck squamous cell carcinomas and revealed differential immune profiles based on lymphoid and myeloid cell densities, correlating with human papilloma virus status and prognosis. Based on these results, we investigated 24 pancreatic ductal adenocarcinomas from patients who received neoadjuvant GVAX vaccination and revealed that response to therapy correlated with degree of mono-myelocytic cell density and percentages of CD8+ T cells expressing T cell exhaustion markers. These data highlight the utility of in situ immune monitoring for patient stratification and provide digital image processing pipelines to the community for examining immune complexity in precious tissue sections, where phenotype and tissue architecture are preserved to improve biomarker discovery and assessment.

  13. Quantitative transcription dynamic analysis reveals candidate genes and key regulators for ethanol tolerance in Saccharomyces cerevisiae

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    Ma Menggen

    2010-06-01

    Full Text Available Abstract Background Derived from our lignocellulosic conversion inhibitor-tolerant yeast, we generated an ethanol-tolerant strain Saccharomyces cerevisiae NRRL Y-50316 by enforced evolutionary adaptation. Using a newly developed robust mRNA reference and a master equation unifying gene expression data analyses, we investigated comparative quantitative transcription dynamics of 175 genes selected from previous studies for an ethanol-tolerant yeast and its closely related parental strain. Results A highly fitted master equation was established and applied for quantitative gene expression analyses using pathway-based qRT-PCR array assays. The ethanol-tolerant Y-50316 displayed significantly enriched background of mRNA abundance for at least 35 genes without ethanol challenge compared with its parental strain Y-50049. Under the ethanol challenge, the tolerant Y-50316 responded in consistent expressions over time for numerous genes belonging to groups of heat shock proteins, trehalose metabolism, glycolysis, pentose phosphate pathway, fatty acid metabolism, amino acid biosynthesis, pleiotropic drug resistance gene family and transcription factors. The parental strain showed repressed expressions for many genes and was unable to withstand the ethanol stress and establish a viable culture and fermentation. The distinct expression dynamics between the two strains and their close association with cell growth, viability and ethanol fermentation profiles distinguished the tolerance-response from the stress-response in yeast under the ethanol challenge. At least 82 genes were identified as candidate and key genes for ethanol-tolerance and subsequent fermentation under the stress. Among which, 36 genes were newly recognized by the present study. Most of the ethanol-tolerance candidate genes were found to share protein binding motifs of transcription factors Msn4p/Msn2p, Yap1p, Hsf1p and Pdr1p/Pdr3p. Conclusion Enriched background of transcription abundance

  14. Assigning Quantitative Function to Post-Translational Modifications Reveals Multiple Sites of Phosphorylation That Tune Yeast Pheromone Signaling Output

    Energy Technology Data Exchange (ETDEWEB)

    Pincus, David; Ryan, Christopher J.; Smith, Richard D.; Brent, Roger; Resnekov, Orna; Hakimi, Mohamed Ali

    2013-03-12

    Cell signaling systems transmit information by post-­translationally modifying signaling proteins, often via phosphorylation. While thousands of sites of phosphorylation have been identified in proteomic studies, the vast majority of sites have no known function. Assigning functional roles to the catalog of uncharacterized phosphorylation sites is a key research challenge. Here we present a general approach to address this challenge and apply it to a prototypical signaling pathway, the pheromone response pathway in Saccharomyces cerevisiae. The pheromone pathway includes a mitogen activated protein kinase (MAPK) cascade activated by a G-­protein coupled receptor (GPCR). We used mass spectrometry-based proteomics to identify sites whose phosphorylation changed when the system was active, and evolutionary conservation to assign priority to a list of candidate MAPK regulatory sites. We made targeted alterations in those sites, and measured the effects of the mutations on pheromone pathway output in single cells. Our work identified six new sites that quantitatively tuned system output. We developed simple computational models to find system architectures that recapitulated the quantitative phenotypes of the mutants. Our results identify a number of regulated phosphorylation events that contribute to adjust the input-­output relationship of this model eukaryotic signaling system. We believe this combined approach constitutes a general means not only to reveal modification sites required to turn a pathway on and off, but also those required for more subtle quantitative effects that tune pathway output. Our results further suggest that relatively small quantitative influences from individual regulatory phosphorylation events endow signaling systems with plasticity that evolution may exploit to quantitatively tailor signaling outcomes.

  15. Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion.

    Science.gov (United States)

    Pan, Yanbo; Cheng, Kai; Mao, Jiawei; Liu, Fangjie; Liu, Jing; Ye, Mingliang; Zou, Hanfa

    2014-10-01

    Trypsin is the popular protease to digest proteins into peptides in shotgun proteomics, but few studies have attempted to systematically investigate the kinetics of trypsin-catalyzed protein digestion in proteome samples. In this study, we applied quantitative proteomics via triplex stable isotope dimethyl labeling to investigate the kinetics of trypsin-catalyzed cleavage. It was found that trypsin cleaves the C-terminal to lysine (K) and arginine (R) residues with higher rates for R. And the cleavage sites surrounded by neutral residues could be quickly cut, while those with neighboring charged residues (D/E/K/R) or proline residue (P) could be slowly cut. In a proteome sample, a huge number of proteins with different physical chemical properties coexists. If any type of protein could be preferably digested, then limited digestion could be applied to reduce the sample complexity. However, we found that protein abundance and other physicochemical properties, such as molecular weight (Mw), grand average of hydropathicity (GRAVY), aliphatic index, and isoelectric point (pI) have no notable correlation with digestion priority of proteins.

  16. Fiber architecture in remodeled myocardium revealed with a quantitative diffusion CMR tractography framework and histological validation.

    Science.gov (United States)

    Mekkaoui, Choukri; Huang, Shuning; Chen, Howard H; Dai, Guangping; Reese, Timothy G; Kostis, William J; Thiagalingam, Aravinda; Maurovich-Horvat, Pal; Ruskin, Jeremy N; Hoffmann, Udo; Jackowski, Marcel P; Sosnovik, David E

    2012-10-12

    The study of myofiber reorganization in the remote zone after myocardial infarction has been performed in 2D. Microstructural reorganization in remodeled hearts, however, can only be fully appreciated by considering myofibers as continuous 3D entities. The aim of this study was therefore to develop a technique for quantitative 3D diffusion CMR tractography of the heart, and to apply this method to quantify fiber architecture in the remote zone of remodeled hearts. Diffusion Tensor CMR of normal human, sheep, and rat hearts, as well as infarcted sheep hearts was performed ex vivo. Fiber tracts were generated with a fourth-order Runge-Kutta integration technique and classified statistically by the median, mean, maximum, or minimum helix angle (HA) along the tract. An index of tract coherence was derived from the relationship between these HA statistics. Histological validation was performed using phase-contrast microscopy. In normal hearts, the subendocardial and subepicardial myofibers had a positive and negative HA, respectively, forming a symmetric distribution around the midmyocardium. However, in the remote zone of the infarcted hearts, a significant positive shift in HA was observed. The ratio between negative and positive HA variance was reduced from 0.96 ± 0.16 in normal hearts to 0.22 ± 0.08 in the remote zone of the remodeled hearts (p layers of the myocardium. Tractography-based quantification, performed here for the first time in remodeled hearts, may provide a framework for assessing regional changes in the left ventricle following infarction.

  17. Quantitative Susceptibility Mapping Reveals an Association between Brain Iron Load and Depression Severity

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    Shun Yao

    2017-08-01

    Full Text Available Previous studies have detected abnormal serum ferritin levels in patients with depression; however, the results have been inconsistent. This study used quantitative susceptibility mapping (QSM for the first time to examine brain iron concentration in depressed patients and evaluated whether it is related to severity. We included three groups of age- and gender-matched participants: 30 patients with mild-moderate depression (MD, 14 patients with major depression disorder (MDD and 20 control subjects. All participants underwent MR scans with a 3D gradient-echo sequence reconstructing for QSM and performed the 17-item Hamilton Depression Rating Scale (HDRS test. In MDD, the susceptibility value in the bilateral putamen was significantly increased compared with MD or control subjects. In addition, a significant difference was also observed in the left thalamus in MDD patients compared with controls. However, the susceptibility values did not differ between MD patients and controls. The susceptibility values positively correlated with the severity of depression as indicated by the HDRS scores. Our results provide evidence that brain iron deposition may be associated with depression and may even be a biomarker for investigating the pathophysiological mechanism of depression.

  18. Quantitative Proteomics Reveals Membrane Protein-Mediated Hypersaline Sensitivity and Adaptation in Halophilic Nocardiopsis xinjiangensis.

    Science.gov (United States)

    Zhang, Yao; Li, Yanchang; Zhang, Yongguang; Wang, Zhiqiang; Zhao, Mingzhi; Su, Na; Zhang, Tao; Chen, Lingsheng; Wei, Wei; Luo, Jing; Zhou, Yanxia; Xu, Yongru; Xu, Ping; Li, Wenjun; Tao, Yong

    2016-01-04

    The genus Nocardiopsis is one of the most dominant Actinobacteria that survives in hypersaline environments. However, the adaptation mechanisms for halophilism are still unclear. Here, we performed isobaric tags for relative and absolute quantification based quantitative proteomics to investigate the functions of the membrane proteome after salt stress. A total of 683 membrane proteins were identified and quantified, of which 126 membrane proteins displayed salt-induced changes in abundance. Intriguingly, bioinformatics analyses indicated that these differential proteins showed two expression patterns, which were further validated by phenotypic changes and functional differences. The majority of ABC transporters, secondary active transporters, cell motility proteins, and signal transduction kinases were up-regulated with increasing salt concentration, whereas cell differentiation, small molecular transporter (ions and amino acids), and secondary metabolism proteins were significantly up-regulated at optimum salinity, but down-regulated or unchanged at higher salinity. The small molecule transporters and cell differentiation-related proteins acted as sensing proteins that played a more important biological role at optimum salinity. However, the ABC transporters for compatible solutes, Na(+)-dependent transporters, and cell motility proteins acted as adaptive proteins that actively counteracted higher salinity stress. Overall, regulation of membrane proteins may provide a major protection strategy against hyperosmotic stress.

  19. Context influences on TALE-DNA binding revealed by quantitative profiling.

    Science.gov (United States)

    Rogers, Julia M; Barrera, Luis A; Reyon, Deepak; Sander, Jeffry D; Kellis, Manolis; Joung, J Keith; Bulyk, Martha L

    2015-06-11

    Transcription activator-like effector (TALE) proteins recognize DNA using a seemingly simple DNA-binding code, which makes them attractive for use in genome engineering technologies that require precise targeting. Although this code is used successfully to design TALEs to target specific sequences, off-target binding has been observed and is difficult to predict. Here we explore TALE-DNA interactions comprehensively by quantitatively assaying the DNA-binding specificities of 21 representative TALEs to ∼5,000-20,000 unique DNA sequences per protein using custom-designed protein-binding microarrays (PBMs). We find that protein context features exert significant influences on binding. Thus, the canonical recognition code does not fully capture the complexity of TALE-DNA binding. We used the PBM data to develop a computational model, Specificity Inference For TAL-Effector Design (SIFTED), to predict the DNA-binding specificity of any TALE. We provide SIFTED as a publicly available web tool that predicts potential genomic off-target sites for improved TALE design.

  20. Context influences on TALE–DNA binding revealed by quantitative profiling

    Science.gov (United States)

    Rogers, Julia M.; Barrera, Luis A.; Reyon, Deepak; Sander, Jeffry D.; Kellis, Manolis; Joung, J Keith; Bulyk, Martha L.

    2015-01-01

    Transcription activator-like effector (TALE) proteins recognize DNA using a seemingly simple DNA-binding code, which makes them attractive for use in genome engineering technologies that require precise targeting. Although this code is used successfully to design TALEs to target specific sequences, off-target binding has been observed and is difficult to predict. Here we explore TALE–DNA interactions comprehensively by quantitatively assaying the DNA-binding specificities of 21 representative TALEs to ∼5,000–20,000 unique DNA sequences per protein using custom-designed protein-binding microarrays (PBMs). We find that protein context features exert significant influences on binding. Thus, the canonical recognition code does not fully capture the complexity of TALE–DNA binding. We used the PBM data to develop a computational model, Specificity Inference For TAL-Effector Design (SIFTED), to predict the DNA-binding specificity of any TALE. We provide SIFTED as a publicly available web tool that predicts potential genomic off-target sites for improved TALE design. PMID:26067805

  1. Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation.

    Science.gov (United States)

    Naboulsi, Wael; Bracht, Thilo; Megger, Dominik A; Reis, Henning; Ahrens, Maike; Turewicz, Michael; Eisenacher, Martin; Tautges, Stephanie; Canbay, Ali E; Meyer, Helmut E; Weber, Frank; Baba, Hideo A; Sitek, Barbara

    2016-11-01

    The majority of poorly differentiated hepatocellular carcinomas (HCCs) develop from well-differentiated tumors. Endocytosis is a cellular function which is likely to take part in this development due to its important role in regulating the abundances of vital signaling receptors. Here, we aimed to investigate the abundance of endocytosis-associated proteins in HCCs with various differentiation grades. Therefore, we analyzed 36 tissue specimens from HCC patients via LC-MS/MS-based label-free quantitative proteomics including 19 HCC tissue samples with different degrees of histological grades and corresponding non-tumorous tissue controls. As a result, 277 proteins were differentially regulated between well-differentiated tumors and controls. In moderately and poorly differentiated tumors, 278 and 1181 proteins, respectively, were significantly differentially regulated compared to non-tumorous tissue. We explored the regulated proteins based on their functions and identified thirty endocytosis-associated proteins, mostly overexpressed in poorly differentiated tumors. These included proteins that have been shown to be up-regulated in HCC like clathrin heavy chain-1 (CLTC) as well as unknown proteins, such as secretory carrier-associated membrane protein 3 (SCAMP3). The abundances of SCAMP3 and CLTC were immunohistochemically examined in tissue sections of 84 HCC patients. We demonstrate the novel association of several endocytosis-associated proteins, in particular, SCAMP3 with HCC progression. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

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    David A. Orlando

    2014-11-01

    Full Text Available Epigenomic profiling by chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq is a prevailing methodology used to investigate chromatin-based regulation in biological systems such as human disease, but the lack of an empirical methodology to enable normalization among experiments has limited the precision and usefulness of this technique. Here, we describe a method called ChIP with reference exogenous genome (ChIP-Rx that allows one to perform genome-wide quantitative comparisons of histone modification status across cell populations using defined quantities of a reference epigenome. ChIP-Rx enables the discovery and quantification of dynamic epigenomic profiles across mammalian cells that would otherwise remain hidden using traditional normalization methods. We demonstrate the utility of this method for measuring epigenomic changes following chemical perturbations and show how reference normalization of ChIP-seq experiments enables the discovery of disease-relevant changes in histone modification occupancy.

  3. Quantitative mass spectrometry reveals changes in SNAP-25 isoforms in schizophrenia

    Science.gov (United States)

    Barakauskas, Vilte E; Moradian, Annie; Barr, Alasdair M.; Beasley, Clare L; Rosoklija, Gorazd; Mann, J John; Ilievski, Boro; Stankov, Aleksandar; Dwork, Andrew J; Falkai, Peter; Morin, Gregg B; Honer, William G

    2016-01-01

    SNAP-25 and syntaxin are presynaptic terminal SNARE proteins altered in amount and function in schizophrenia. In the ventral caudate, we observed 32% lower SNAP-25 and 26% lower syntaxin, but greater interaction between the two proteins using an in vitro assay. SNAP-25 has two isoforms, SNAP-25A and B, differing by only 9 amino acids, but with different effects on neurotransmission. A quantitative mass spectrometry assay was developed to measure total SNAP-25, and proportions of SNAP-25A and B. The assay had a good linear range (50- to 150-fold) and coefficient of variation (4.5%). We studied ventral caudate samples from patients with schizophrenia (n=15) previously reported to have lower total SNAP-25 than controls (n=13). We confirmed 27% lower total SNAP-25 in schizophrenia, and observed 31% lower SNAP-25A (P = 0.002) with 20% lower SNAP-25B amounts (P = 0.10). Lower SNAP-25A amount correlated with greater SNAP-25-syntaxin protein-protein interactions (r = -0.41, P = 0.03); the level of SNAP-25B did not. Administration of haloperidol or clozapine to rats did not mimic the changes found in schizophrenia. The findings suggest that lower levels of SNAP-25 in schizophrenia may represent a greater effect of the illness on the SNAP-25A isoform. This in turn could contribute to the greater interaction between SNAP25 and syntaxin, and possibly disturb neurotransmission in the illness. PMID:26971072

  4. Quantitative image analysis reveals distinct structural transitions during aging in Caenorhabditis elegans tissues.

    Science.gov (United States)

    Johnston, Josiah; Iser, Wendy B; Chow, David K; Goldberg, Ilya G; Wolkow, Catherine A

    2008-07-30

    Aging is associated with functional and structural declines in many body systems, even in the absence of underlying disease. In particular, skeletal muscles experience severe declines during aging, a phenomenon termed sarcopenia. Despite the high incidence and severity of sarcopenia, little is known about contributing factors and development. Many studies focus on functional aspects of aging-related tissue decline, while structural details remain understudied. Traditional approaches for quantifying structural changes have assessed individual markers at discrete intervals. Such approaches are inadequate for the complex changes associated with aging. An alternative is to consider changes in overall morphology rather than in specific markers. We have used this approach to quantitatively track tissue architecture during adulthood and aging in the C. elegans pharynx, the neuromuscular feeding organ. Using pattern recognition to analyze aged-grouped pharynx images, we identified discrete step-wise transitions between distinct morphologies. The morphology state transitions were maintained in mutants with pharynx neurotransmission defects, although the pace of the transitions was altered. Longitudinal measurements of pharynx function identified a predictive relationship between mid-life pharynx morphology and function at later ages. These studies demonstrate for the first time that adult tissues undergo distinct structural transitions reflecting postdevelopmental events. The processes that underlie these architectural changes may contribute to increased disease risk during aging, and may be targets for factors that alter the aging rate. This work further demonstrates that pattern analysis of an image series offers a novel and generally accessible approach for quantifying morphological changes and identifying structural biomarkers.

  5. Nucleophosmin in the pathogenesis of arsenic-related bladder carcinogenesis revealed by quantitative proteomics

    International Nuclear Information System (INIS)

    Chen Shuhui; Wang Yiwen; Hsu Jueliang; Chang Hongyi; Wang Chiyun; Shen Potsun; Chiang Chiwu; Chuang Jingjing; Tsai Hungwen; Gu Powen; Chang Fangchih; Liu Hsiaosheng; Chow Nanhaw

    2010-01-01

    To investigate the molecular mechanisms of arsenic (As)-associated carcinogenesis, we performed proteomic analysis on E7 immortalized human uroepithelial cells after treatment with As in vitro. Quantitative proteomics was performed using stable isotope dimethyl labeling coupled with two-dimensional liquid chromatography peptide separation and mass spectrometry (MS)/MS analysis. Among 285 proteins, a total of 26 proteins were upregulated (ratio > 2.0) and 18 proteins were downregulated (ratio < 0.65) by As treatment, which are related to nucleotide binding, lipid metabolism, protein folding, protein biosynthesis, transcription, DNA repair, cell cycle control, and signal transduction. This study reports the potential significance of nucleophosmin (NPM) in the As-related bladder carcinogenesis. NPM was universally expressed in all of uroepithelial cell lines examined, implying that NPM may play a role in human bladder carcinogenesis. Upregulation of NPM tends to be dose- and time-dependent after As treatment. Expression of NPM was associated with cell proliferation, migration and anti-apoptosis. On the contrary, soy isoflavones inhibited the expression of NPM in vitro. The results suggest that NPM may play a role in the As-related bladder carcinogenesis, and soybean-based foods may have potential in the suppression of As/NPM-related tumorigenesis.

  6. Quantitative phosphoproteomics reveals the role of protein arginine phosphorylation in the bacterial stress response.

    Science.gov (United States)

    Schmidt, Andreas; Trentini, Débora Broch; Spiess, Silvia; Fuhrmann, Jakob; Ammerer, Gustav; Mechtler, Karl; Clausen, Tim

    2014-02-01

    Arginine phosphorylation is an emerging protein modification implicated in the general stress response of Gram-positive bacteria. The modification is mediated by the arginine kinase McsB, which phosphorylates and inactivates the heat shock repressor CtsR. In this study, we developed a mass spectrometric approach accounting for the peculiar chemical properties of phosphoarginine. The improved methodology was used to analyze the dynamic changes in the Bacillus subtilis arginine phosphoproteome in response to different stress situations. Quantitative analysis showed that a B. subtilis mutant lacking the YwlE arginine phosphatase accumulated a strikingly large number of arginine phosphorylations (217 sites in 134 proteins), however only a minor fraction of these sites was increasingly modified during heat shock or oxidative stress. The main targets of McsB-mediated arginine phosphorylation comprise central factors of the stress response system including the CtsR and HrcA heat shock repressors, as well as major components of the protein quality control system such as the ClpCP protease and the GroEL chaperonine. These findings highlight the impact of arginine phosphorylation in orchestrating the bacterial stress response.

  7. Mass Spectrometry-Based Quantitative Metabolomics Revealed a Distinct Lipid Profile in Breast Cancer Patients

    Directory of Open Access Journals (Sweden)

    Yun Yen

    2013-04-01

    Full Text Available Breast cancer accounts for the largest number of newly diagnosed cases in female cancer patients. Although mammography is a powerful screening tool, about 20% of breast cancer cases cannot be detected by this method. New diagnostic biomarkers for breast cancer are necessary. Here, we used a mass spectrometry-based quantitative metabolomics method to analyze plasma samples from 55 breast cancer patients and 25 healthy controls. A number of 30 patients and 20 age-matched healthy controls were used as a training dataset to establish a diagnostic model and to identify potential biomarkers. The remaining samples were used as a validation dataset to evaluate the predictive accuracy for the established model. Distinct separation was obtained from an orthogonal partial least squares-discriminant analysis (OPLS-DA model with good prediction accuracy. Based on this analysis, 39 differentiating metabolites were identified, including significantly lower levels of lysophosphatidylcholines and higher levels of sphingomyelins in the plasma samples obtained from breast cancer patients compared with healthy controls. Using logical regression, a diagnostic equation based on three metabolites (lysoPC a C16:0, PC ae C42:5 and PC aa C34:2 successfully differentiated breast cancer patients from healthy controls, with a sensitivity of 98.1% and a specificity of 96.0%.

  8. Data-Independent Acquisition-Based Quantitative Proteomic Analysis Reveals Potential Biomarkers of Kidney Cancer.

    Science.gov (United States)

    Song, Yimeng; Zhong, Lijun; Zhou, Juntuo; Lu, Min; Xing, Tianying; Ma, Lulin; Shen, Jing

    2017-12-01

    Renal cell carcinoma (RCC) is a malignant and metastatic cancer with 95% mortality, and clear cell RCC (ccRCC) is the most observed among the five major subtypes of RCC. Specific biomarkers that can distinguish cancer tissues from adjacent normal tissues should be developed to diagnose this disease in early stages and conduct a reliable prognostic evaluation. Data-independent acquisition (DIA) strategy has been widely employed in proteomic analysis because of various advantages, including enhanced protein coverage and reliable data acquisition. In this study, a DIA workflow is constructed on a quadrupole-Orbitrap LC-MS platform to reveal dysregulated proteins between ccRCC and adjacent normal tissues. More than 4000 proteins are identified, 436 of these proteins are dysregulated in ccRCC tissues. Bioinformatic analysis reveals that multiple pathways and Gene Ontology items are strongly associated with ccRCC. The expression levels of L-lactate dehydrogenase A chain, annexin A4, nicotinamide N-methyltransferase, and perilipin-2 examined through RT-qPCR, Western blot, and immunohistochemistry confirm the validity of the proteomic analysis results. The proposed DIA workflow yields optimum time efficiency and data reliability and provides a good choice for proteomic analysis in biological and clinical studies, and these dysregulated proteins might be potential biomarkers for ccRCC diagnosis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Stiffness and evolution of interfacial micropancakes revealed by AFM quantitative nanomechanical imaging.

    Science.gov (United States)

    Zhao, Binyu; Wang, Xingya; Song, Yang; Hu, Jun; Lü, Junhong; Zhou, Xingfei; Tai, Renzhong; Zhang, Xuehua; Zhang, Lijuan

    2015-05-28

    Micropancakes are quasi-two-dimensional micron-sized domains on crystalline substrates (e.g. highly oriented pyrolytic graphite (HOPG)) immersed in water. They are only a few nanometers thick, and are suspected to come from the accumulation of dissolved air at the solid-water interface. However, the exact chemical nature and basic physical properties of micropancakes have been under debate ever since their first observation, primarily due to the lack of a suitable characterization technique. In this study, the stiffness of micropancakes at the interface between HOPG and ethanol-water solutions was investigated by using PeakForce Quantitative NanoMechanics (PF-QNM) mode Atomic Force Microscopy (AFM). Our measurements showed that micropancakes were stiffer than nanobubbles, and for bilayer micropancakes, the bottom layer in contact with the substrate was stiffer than the top one. Interestingly, the micropancakes became smaller and softer with an increase in the ethanol concentration in the solution, and were undetectable by AFM above a critical concentration of ethanol. But they re-appeared after the ethanol concentration in the solution was reduced. Clearly the evolution and stiffness of the micropancakes were dependent on the chemical composition in the solution, which could be attributed to the correlation of the mechanical properties of the micropancakes with the surface tension of the liquid phase. Based on the "go-and-come" behaviors of micropancakes with the ethanol concentration, we found that the micropancakes could actually tolerate the ethanol concentration much higher than 5%, a value reported in the literature. The results from this work may be helpful in alluding the chemical nature of micropancakes.

  10. Fiber architecture in remodeled myocardium revealed with a quantitative diffusion CMR tractography framework and histological validation

    Directory of Open Access Journals (Sweden)

    Mekkaoui Choukri

    2012-10-01

    Full Text Available Abstract Background The study of myofiber reorganization in the remote zone after myocardial infarction has been performed in 2D. Microstructural reorganization in remodeled hearts, however, can only be fully appreciated by considering myofibers as continuous 3D entities. The aim of this study was therefore to develop a technique for quantitative 3D diffusion CMR tractography of the heart, and to apply this method to quantify fiber architecture in the remote zone of remodeled hearts. Methods Diffusion Tensor CMR of normal human, sheep, and rat hearts, as well as infarcted sheep hearts was performed ex vivo. Fiber tracts were generated with a fourth-order Runge-Kutta integration technique and classified statistically by the median, mean, maximum, or minimum helix angle (HA along the tract. An index of tract coherence was derived from the relationship between these HA statistics. Histological validation was performed using phase-contrast microscopy. Results In normal hearts, the subendocardial and subepicardial myofibers had a positive and negative HA, respectively, forming a symmetric distribution around the midmyocardium. However, in the remote zone of the infarcted hearts, a significant positive shift in HA was observed. The ratio between negative and positive HA variance was reduced from 0.96 ± 0.16 in normal hearts to 0.22 ± 0.08 in the remote zone of the remodeled hearts (p Conclusions A significant reorganization of the 3D fiber continuum is observed in the remote zone of remodeled hearts. The positive (rightward shift in HA in the remote zone is greatest in the subepicardium, but involves all layers of the myocardium. Tractography-based quantification, performed here for the first time in remodeled hearts, may provide a framework for assessing regional changes in the left ventricle following infarction.

  11. Quantitative image analysis reveals distinct structural transitions during aging in Caenorhabditis elegans tissues.

    Directory of Open Access Journals (Sweden)

    Josiah Johnston

    2008-07-01

    Full Text Available Aging is associated with functional and structural declines in many body systems, even in the absence of underlying disease. In particular, skeletal muscles experience severe declines during aging, a phenomenon termed sarcopenia. Despite the high incidence and severity of sarcopenia, little is known about contributing factors and development. Many studies focus on functional aspects of aging-related tissue decline, while structural details remain understudied. Traditional approaches for quantifying structural changes have assessed individual markers at discrete intervals. Such approaches are inadequate for the complex changes associated with aging. An alternative is to consider changes in overall morphology rather than in specific markers. We have used this approach to quantitatively track tissue architecture during adulthood and aging in the C. elegans pharynx, the neuromuscular feeding organ. Using pattern recognition to analyze aged-grouped pharynx images, we identified discrete step-wise transitions between distinct morphologies. The morphology state transitions were maintained in mutants with pharynx neurotransmission defects, although the pace of the transitions was altered. Longitudinal measurements of pharynx function identified a predictive relationship between mid-life pharynx morphology and function at later ages. These studies demonstrate for the first time that adult tissues undergo distinct structural transitions reflecting postdevelopmental events. The processes that underlie these architectural changes may contribute to increased disease risk during aging, and may be targets for factors that alter the aging rate. This work further demonstrates that pattern analysis of an image series offers a novel and generally accessible approach for quantifying morphological changes and identifying structural biomarkers.

  12. Quantitative proteomics and dynamic imaging of the nucleolus reveal distinct responses to UV and ionizing radiation.

    Science.gov (United States)

    Moore, Henna M; Bai, Baoyan; Boisvert, François-Michel; Latonen, Leena; Rantanen, Ville; Simpson, Jeremy C; Pepperkok, Rainer; Lamond, Angus I; Laiho, Marikki

    2011-10-01

    The nucleolus is a nuclear organelle that coordinates rRNA transcription and ribosome subunit biogenesis. Recent proteomic analyses have shown that the nucleolus contains proteins involved in cell cycle control, DNA processing and DNA damage response and repair, in addition to the many proteins connected with ribosome subunit production. Here we study the dynamics of nucleolar protein responses in cells exposed to stress and DNA damage caused by ionizing and ultraviolet (UV) radiation in diploid human fibroblasts. We show using a combination of imaging and quantitative proteomics methods that nucleolar substructure and the nucleolar proteome undergo selective reorganization in response to UV damage. The proteomic responses to UV include alterations of functional protein complexes such as the SSU processome and exosome, and paraspeckle proteins, involving both decreases and increases in steady state protein ratios, respectively. Several nonhomologous end-joining proteins (NHEJ), such as Ku70/80, display similar fast responses to UV. In contrast, nucleolar proteomic responses to IR are both temporally and spatially distinct from those caused by UV, and more limited in terms of magnitude. With the exception of the NHEJ and paraspeckle proteins, where IR induces rapid and transient changes within 15 min of the damage, IR does not alter the ratios of most other functional nucleolar protein complexes. The rapid transient decrease of NHEJ proteins in the nucleolus indicates that it may reflect a response to DNA damage. Our results underline that the nucleolus is a specific stress response organelle that responds to different damage and stress agents in a unique, damage-specific manner.

  13. Quantitative Proteomics Reveals Temporal Proteomic Changes in Signaling Pathways during BV2 Mouse Microglial Cell Activation.

    Science.gov (United States)

    Woo, Jongmin; Han, Dohyun; Wang, Joseph Injae; Park, Joonho; Kim, Hyunsoo; Kim, Youngsoo

    2017-09-01

    The development of systematic proteomic quantification techniques in systems biology research has enabled one to perform an in-depth analysis of cellular systems. We have developed a systematic proteomic approach that encompasses the spectrum from global to targeted analysis on a single platform. We have applied this technique to an activated microglia cell system to examine changes in the intracellular and extracellular proteomes. Microglia become activated when their homeostatic microenvironment is disrupted. There are varying degrees of microglial activation, and we chose to focus on the proinflammatory reactive state that is induced by exposure to such stimuli as lipopolysaccharide (LPS) and interferon-gamma (IFN-γ). Using an improved shotgun proteomics approach, we identified 5497 proteins in the whole-cell proteome and 4938 proteins in the secretome that were associated with the activation of BV2 mouse microglia by LPS or IFN-γ. Of the differentially expressed proteins in stimulated microglia, we classified pathways that were related to immune-inflammatory responses and metabolism. Our label-free parallel reaction monitoring (PRM) approach made it possible to comprehensively measure the hyper-multiplex quantitative value of each protein by high-resolution mass spectrometry. Over 450 peptides that corresponded to pathway proteins and direct or indirect interactors via the STRING database were quantified by label-free PRM in a single run. Moreover, we performed a longitudinal quantification of secreted proteins during microglial activation, in which neurotoxic molecules that mediate neuronal cell loss in the brain are released. These data suggest that latent pathways that are associated with neurodegenerative diseases can be discovered by constructing and analyzing a pathway network model of proteins. Furthermore, this systematic quantification platform has tremendous potential for applications in large-scale targeted analyses. The proteomics data for

  14. Atomic-scale Ge diffusion in strained Si revealed by quantitative scanning transmission electron microscopy

    Science.gov (United States)

    Radtke, G.; Favre, L.; Couillard, M.; Amiard, G.; Berbezier, I.; Botton, G. A.

    2013-05-01

    Aberration-corrected scanning transmission electron microscopy is employed to investigate the local chemistry in the vicinity of a Si0.8Ge0.2/Si interface grown by molecular-beam epitaxy. Atomic-resolution high-angle annular dark field contrast reveals the presence of a nonuniform diffusion of Ge from the substrate into the strained Si thin film. On the basis of multislice calculations, a model is proposed to quantify the experimental contrast, showing that the Ge concentration in the thin film reaches about 4% at the interface and decreases monotonically on a typical length scale of 10 nm. Diffusion occurring during the growth process itself therefore appears as a major factor limiting the abruptness of interfaces in the Si-Ge system.

  15. Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs

    DEFF Research Database (Denmark)

    Drag, Markus; Hansen, Mathias B.; Kadarmideen, Haja N.

    2018-01-01

    Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed...... to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at similar to 100 kg. Gene...... and SSC14. Functional characterisation of eQTLs revealed functions within regulation of androgen and the intracellular steroid hormone receptor signalling pathway and of xenobiotic metabolism by cytochrome P450 system and cellular response to oestradiol. A QTL enrichment test revealed 89 QTL traits...

  16. Quantitative analysis of diet structure by real-time PCR, reveals different feeding patterns by two dominant grasshopper species

    Science.gov (United States)

    Huang, Xunbing; Wu, Huihui; McNeill, Mark Richard; Qin, Xinghu; Ma, Jingchuan; Tu, Xiongbing; Cao, Guangchun; Wang, Guangjun; Nong, Xiangqun; Zhang, Zehua

    2016-01-01

    Studies on grasshopper diets have historically employed a range of methodologies, each with certain advantages and disadvantages. For example, some methodologies are qualitative instead of quantitative. Others require long experimental periods or examine population-level effects, only. In this study, we used real-time PCR to examine diets of individual grasshoppers. The method has the advantage of being both fast and quantitative. Using two grasshopper species, Oedaleus asiaticus and Dasyhippus barbipes, we designed ITS primer sequences for their three main host plants, Stipa krylovii, Leymus chinensis and Cleistogenes squarrosa and used real-time PCR method to test diet structure both qualitatively and quantitatively. The lowest detection efficiency of the three grass species was ~80% with a strong correlation between actual and PCR-measured food intake. We found that Oedaleus asiaticus maintained an unchanged diet structure across grasslands with different grass communities. By comparison, Dasyhippus barbipes changed its diet structure. These results revealed why O. asiaticus distribution is mainly confined to Stipa-dominated grassland, and D. barbipes is more widely distributed across Inner Mongolia. Overall, real-time PCR was shown to be a useful tool for investigating grasshopper diets, which in turn offers some insight into grasshopper distributions and improved pest management. PMID:27562455

  17. Quantitative Tissue Proteomics Analysis Reveals Versican as Potential Biomarker for Early-Stage Hepatocellular Carcinoma.

    Science.gov (United States)

    Naboulsi, Wael; Megger, Dominik A; Bracht, Thilo; Kohl, Michael; Turewicz, Michael; Eisenacher, Martin; Voss, Don Marvin; Schlaak, Jörg F; Hoffmann, Andreas-Claudius; Weber, Frank; Baba, Hideo A; Meyer, Helmut E; Sitek, Barbara

    2016-01-04

    Hepatocellular carcinoma (HCC) is one of the most aggressive tumors, and the treatment outcome of this disease is improved when the cancer is diagnosed at an early stage. This requires biomarkers allowing an accurate and early tumor diagnosis. To identify potential markers for such applications, we analyzed a patient cohort consisting of 50 patients (50 HCC and 50 adjacent nontumorous tissue samples as controls) using two independent proteomics approaches. We performed label-free discovery analysis on 19 HCC and corresponding tissue samples. The data were analyzed considering events known to take place in early events of HCC development, such as abnormal regulation of Wnt/b-catenin and activation of receptor tyrosine kinases (RTKs). 31 proteins were selected for verification experiments. For this analysis, the second set of the patient cohort (31 HCC and corresponding tissue samples) was analyzed using selected (multiple) reaction monitoring (SRM/MRM). We present the overexpression of ATP-dependent RNA helicase (DDX39), Fibulin-5 (FBLN5), myristoylated alanine-rich C-kinase substrate (MARCKS), and Serpin H1 (SERPINH1) in HCC for the first time. We demonstrate Versican core protein (VCAN) to be significantly associated with well differentiated and low-stage HCC. We revealed for the first time the evidence of VCAN as a potential biomarker for early-HCC diagnosis.

  18. Quantitative proteomics reveals that peroxidases play key roles in post-flooding recovery in soybean roots.

    Science.gov (United States)

    Khan, Mudassar Nawaz; Sakata, Katsumi; Hiraga, Susumu; Komatsu, Setsuko

    2014-12-05

    Soybean is an important legume crop that exhibits markedly reduced growth and yields under flooding conditions. To unravel the mechanisms involved in recovery after flooding in soybean root, gel-free proteomic analysis was performed. Morphological analysis revealed that growth suppression was more severe with increased flooding duration. Out of a total of 1645 and 1707 identified proteins, 73 and 21 proteins were changed significantly during the recovery stage following 2 and 4 days flooding, respectively. Based on the proteomic, clustering, and in silico protein-protein interaction analyses, six key enzymes were analyzed at the mRNA level. Lipoxygenase 1, which was increased at the protein level during the recovery period, was steadily down-regulated at the mRNA level. The peroxidase superfamily protein continuously increased in abundance during the course of recovery and was up-regulated at the mRNA level. HAD acid phosphatase was decreased at the protein level and down-regulated at the transcript level, while isoflavone reductase and an unknown protein were increased at both the protein and mRNA levels. Consistent with these findings, the enzymatic activity of peroxidase was decreased under flooding stress but increased significantly during the recovery sage. These results suggest that peroxidases might play key roles in post-flooding recovery in soybean roots through the scavenging of toxic radicals.

  19. Quantitative proteomics reveals middle infrared radiation-interfered networks in breast cancer cells.

    Science.gov (United States)

    Chang, Hsin-Yi; Li, Ming-Hua; Huang, Tsui-Chin; Hsu, Chia-Lang; Tsai, Shang-Ru; Lee, Si-Chen; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

    2015-02-06

    Breast cancer is one of the leading cancer-related causes of death worldwide. Treatment of triple-negative breast cancer (TNBC) is complex and challenging, especially when metastasis has developed. In this study, we applied infrared radiation as an alternative approach for the treatment of TNBC. We used middle infrared (MIR) with a wavelength range of 3-5 μm to irradiate breast cancer cells. MIR significantly inhibited cell proliferation in several breast cancer cells but did not affect the growth of normal breast epithelial cells. We performed iTRAQ-coupled LC-MS/MS analysis to investigate the MIR-triggered molecular mechanisms in breast cancer cells. A total of 1749 proteins were identified, quantified, and subjected to functional enrichment analysis. From the constructed functionally enriched network, we confirmed that MIR caused G2/M cell cycle arrest, remodeled the microtubule network to an astral pole arrangement, altered the actin filament formation and focal adhesion molecule localization, and reduced cell migration activity and invasion ability. Our results reveal the coordinative effects of MIR-regulated physiological responses in concentrated networks, demonstrating the potential implementation of infrared radiation in breast cancer therapy.

  20. Integrative Analysis of Subcellular Quantitative Proteomics Studies Reveals Functional Cytoskeleton Membrane-Lipid Raft Interactions in Cancer.

    Science.gov (United States)

    Shah, Anup D; Inder, Kerry L; Shah, Alok K; Cristino, Alexandre S; McKie, Arthur B; Gabra, Hani; Davis, Melissa J; Hill, Michelle M

    2016-10-07

    Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and renal cell carcinoma. This analysis revealed that cancer development is associated with increased membrane raft-cytoskeleton interactions, with ∼40% of elevated lipid raft proteins being cytoskeletal components. Previous studies suggest a potential functional role for the raft-cytoskeleton in the action of the putative tumor suppressors PTRF/Cavin-1 and Merlin. To extend the observation, we examined lipid raft proteome modulation by an unrelated tumor suppressor opioid binding protein cell-adhesion molecule (OPCML) in ovarian cancer SKOV3 cells. In agreement with the other model systems, quantitative proteomics revealed that 39% of OPCML-depleted lipid raft proteins are cytoskeletal components, with microfilaments and intermediate filaments specifically down-regulated. Furthermore, protein-protein interaction network and simulation analysis showed significantly higher interactions among cancer raft proteins compared with general human raft proteins. Collectively, these results suggest increased cytoskeleton-mediated stabilization of lipid raft domains with greater molecular interactions as a common, functional, and reversible feature of cancer cells.

  1. Quantitative membrane proteomics reveals a role for tetraspanin enriched microdomains during entry of human cytomegalovirus.

    Directory of Open Access Journals (Sweden)

    Kasinath Viswanathan

    Full Text Available Human cytomegalovirus (HCMV depends on and modulates multiple host cell membrane proteins during each stage of the viral life cycle. To gain a global view of the impact of HCMV-infection on membrane proteins, we analyzed HCMV-induced changes in the abundance of membrane proteins in fibroblasts using stable isotope labeling with amino acids (SILAC, membrane fractionation and protein identification by two-dimensional liquid chromatography and tandem mass spectrometry. This systematic approach revealed that CD81, CD44, CD98, caveolin-1 and catenin delta-1 were down-regulated during infection whereas GRP-78 was up-regulated. Since CD81 downregulation was also observed during infection with UV-inactivated virus we hypothesized that this tetraspanin is part of the viral entry process. Interestingly, additional members of the tetraspanin family, CD9 and CD151, were also downregulated during HCMV-entry. Since tetraspanin-enriched microdomains (TEM cluster host cell membrane proteins including known CMV receptors such as integrins, we studied whether TEMs are required for viral entry. When TEMs were disrupted with the cholesterol chelator methyl-β-cylcodextrin, viral entry was inhibited and this inhibition correlated with reduced surface levels of CD81, CD9 and CD151, whereas integrin levels remained unchanged. Furthermore, simultaneous siRNA-mediated knockdown of multiple tetraspanins inhibited viral entry whereas individual knockdown had little effect suggesting essential, but redundant roles for individual tetraspanins during entry. Taken together, our data suggest that TEM act as platforms for receptors utilized by HCMV for entry into cells.

  2. Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics

    Directory of Open Access Journals (Sweden)

    Yadetie Fekadu

    2012-02-01

    Full Text Available Abstract Background Animals have developed extensive mechanisms of response to xenobiotic chemical attacks. Although recent genome surveys have suggested a broad conservation of the chemical defensome across metazoans, global gene expression responses to xenobiotics have not been well investigated in most invertebrates. Here, we performed genome survey for key defensome genes in Oikopleura dioica genome, and explored genome-wide gene expression using high density tiling arrays with over 2 million probes, in response to two model xenobiotic chemicals - the carcinogenic polycyclic aromatic hydrocarbon benzo[a]pyrene (BaP the pharmaceutical compound Clofibrate (Clo. Results Oikopleura genome surveys for key genes of the chemical defensome suggested a reduced repertoire. Not more than 23 cytochrome P450 (CYP genes could be identified, and neither CYP1 family genes nor their transcriptional activator AhR was detected. These two genes were present in deuterostome ancestors. As in vertebrates, the genotoxic compound BaP induced xenobiotic biotransformation and oxidative stress responsive genes. Notable exceptions were genes of the aryl hydrocarbon receptor (AhR signaling pathway. Clo also affected the expression of many biotransformation genes and markedly repressed genes involved in energy metabolism and muscle contraction pathways. Conclusions Oikopleura has the smallest number of CYP genes among sequenced animal genomes and lacks the AhR signaling pathway. However it appears to have basic xenobiotic inducible biotransformation genes such as a conserved genotoxic stress response gene set. Our genome survey and expression study does not support a role of AhR signaling pathway in the chemical defense of metazoans prior to the emergence of vertebrates.

  3. Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses.

    Science.gov (United States)

    Ehret, Totta; Spork, Simone; Dieterich, Christoph; Lucius, Richard; Heitlinger, Emanuel

    2017-09-05

    Parasites can either respond to differences in immune defenses that exist between individual hosts plastically or, alternatively, follow a genetically canalized ("hard wired") program of infection. Assuming that large-scale functional plasticity would be discernible in the parasite transcriptome we have performed a dual RNA-seq study of the lifecycle of Eimeria falciformis using infected mice with different immune status as models for coccidian infections. We compared parasite and host transcriptomes (dual transcriptome) between naïve and challenge infected mice, as well as between immune competent and immune deficient ones. Mice with different immune competence show transcriptional differences as well as differences in parasite reproduction (oocyst shedding). Broad gene categories represented by differently abundant host genes indicate enrichments for immune reaction and tissue repair functions. More specifically, TGF-beta, EGF, TNF and IL-1 and IL-6 are examples of functional annotations represented differently depending on host immune status. Much in contrast, parasite transcriptomes were neither different between Coccidia isolated from immune competent and immune deficient mice, nor between those harvested from naïve and challenge infected mice. Instead, parasite transcriptomes have distinct profiles early and late in infection, characterized largely by biosynthesis or motility associated functional gene groups, respectively. Extracellular sporozoite and oocyst stages showed distinct transcriptional profiles and sporozoite transcriptomes were found enriched for species specific genes and likely pathogenicity factors. We propose that the niche and host-specific parasite E. falciformis uses a genetically canalized program of infection. This program is likely fixed in an evolutionary process rather than employing phenotypic plasticity to interact with its host. This in turn might limit the potential of the parasite to adapt to new host species or niches, forcing

  4. Isotopic Zonation Within Sulfate Evaporite Mineral Crystals Reveal Quantitative Paleoenvironment Details

    Science.gov (United States)

    Coleman, M.; Rhorssen, M.; Mielke, R. E.

    2008-12-01

    developed a new analytical method [2]. We use a modification of the standard TC/EA continuous-flow protocol to measure both hydrogen and oxygen of water of hydration from the same small sample. We have proved the concept of this new approach by analyzing zones within crystals and individual grains, growing epsomite (magnesium sulfate heptahydrate) in the laboratory and by analysis of natural gypsum evaporites. We are now exploring the effects of varying the controlling parameters. Eventual application to Martian sulfates will reveal amount of water involved in sulfate formation, its isotopic composition(s) and details of the paleo-atmospheric humidity. [1] Gat JR and Gonfiantini R, (Eds) (1981) IAEA Technical Report Series. [2] Rohrssen MK, Brunner B Mielke RE and Coleman M (2008) Analyt. Chem. (in press).

  5. Quantitative ligand and receptor binding studies reveal the mechanism of interleukin-36 (IL-36) pathway activation.

    Science.gov (United States)

    Zhou, Li; Todorovic, Viktor; Kakavas, Steve; Sielaff, Bernhard; Medina, Limary; Wang, Leyu; Sadhukhan, Ramkrishna; Stockmann, Henning; Richardson, Paul L; DiGiammarino, Enrico; Sun, Chaohong; Scott, Victoria

    2018-01-12

    IL-36 cytokines signal through the IL-36 receptor (IL-36R) and a shared subunit, IL-1RAcP (IL-1 receptor accessory protein). The activation mechanism for the IL-36 pathway is proposed to be similar to that of IL-1 in that an IL-36R agonist (IL-36α, IL-36β, or IL-36γ) forms a binary complex with IL-36R, which then recruits IL-1RAcP. Recent studies have shown that IL-36R interacts with IL-1RAcP even in the absence of an agonist. To elucidate the IL-36 activation mechanism, we considered all possible binding events for IL-36 ligands/receptors and examined these events in direct binding assays. Our results indicated that the agonists bind the IL-36R extracellular domain with micromolar affinity but do not detectably bind IL-1RAcP. Using surface plasmon resonance (SPR), we found that IL-1RAcP also does not bind IL-36R when no agonist is present. In the presence of IL-36α, however, IL-1RAcP bound IL-36R strongly. These results suggested that the main pathway to the IL-36R·IL-36α·IL-1RAcP ternary complex is through the IL-36R·IL-36α binary complex, which recruits IL-1RAcP. We could not measure the binding affinity of IL-36R to IL-1RAcP directly, so we engineered a fragment crystallizable-linked construct to induce IL-36R·IL-1RAcP heterodimerization and predicted the binding affinity during a complete thermodynamic cycle to be 74 μm The SPR analysis also indicated that the IL-36R antagonist IL-36Ra binds IL-36R with higher affinity and a much slower off rate than the IL-36R agonists, shedding light on IL-36 pathway inhibition. Our results reveal the landscape of IL-36 ligand and receptor interactions, improving our understanding of IL-36 pathway activation and inhibition. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Comparative proteomic analysis of oil palm leaves infected with Ganoderma boninense revealed changes in proteins involved in photosynthesis, carbohydrate metabolism, and immunity and defense.

    Science.gov (United States)

    Jeffery Daim, Leona Daniela; Ooi, Tony Eng Keong; Ithnin, Nalisha; Mohd Yusof, Hirzun; Kulaveerasingam, Harikrishna; Abdul Majid, Nazia; Karsani, Saiful Anuar

    2015-08-01

    The basidiomycete fungal pathogen Ganoderma boninense is the causative agent for the incurable basal stem rot (BSR) disease in oil palm. This disease causes significant annual crop losses in the oil palm industry. Currently, there is no effective method for disease control and elimination, nor is any molecular marker for early detection of the disease available. An understanding of how BSR affects protein expression in plants may help identify and/or assist in the development of an early detection protocol. Although the mode of infection of BSR disease is primarily via the root system, defense-related genes have been shown to be expressed in both the root and leafs. Thus, to provide an insight into the changes in the global protein expression profile in infected plants, comparative 2DE was performed on leaf tissues sampled from palms with and without artificial inoculation of the Ganoderma fungus. Comparative 2DE revealed that 54 protein spots changed in abundance. A total of 51 protein spots were successfully identified by LC-QTOF MS/MS. The majority of these proteins were those involved in photosynthesis, carbohydrate metabolism as well as immunity and defense. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Quantitative proteomics reveals the mechanism and consequence of gliotoxin-mediated dysregulation of the methionine cycle in Aspergillus niger.

    Science.gov (United States)

    Manzanares-Miralles, Lara; Sarikaya-Bayram, Özlem; Smith, Elizabeth B; Dolan, Stephen K; Bayram, Özgür; Jones, Gary W; Doyle, Sean

    2016-01-10

    Gliotoxin (GT) is a redox-active metabolite, produced by Aspergillus fumigatus, which inhibits the growth of other fungi. Here we demonstrate how Aspergillus niger responds to GT exposure. Quantitative proteomics revealed that GT dysregulated the abundance of 378 proteins including those involved in methionine metabolism and induced de novo abundance of two S-adenosylmethionine (SAM)-dependent methyltransferases. Increased abundance of enzymes S-adenosylhomocysteinase (p=0.0018) required for homocysteine generation from S-adenosylhomocysteine (SAH), and spermidine synthase (p=0.0068), involved in the recycling of Met, was observed. Analysis of Met-related metabolites revealed significant increases in the levels of Met and adenosine, in correlation with proteomic data. Methyltransferase MT-II is responsible for bisthiobis(methylthio)gliotoxin (BmGT) formation, deletion of MT-II abolished BmGT formation and led to increased GT sensitivity in A. niger. Proteomic analysis also revealed that GT exposure also significantly (pniger. Thus, it provides new opportunities to exploit the response of GT-naïve fungi to GT. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Quantitative Proteomics of the Tonoplast Reveals a Role for Glycolytic Enzymes in Salt Tolerance[C][W

    Science.gov (United States)

    Barkla, Bronwyn J.; Vera-Estrella, Rosario; Hernández-Coronado, Marcela; Pantoja, Omar

    2009-01-01

    To examine the role of the tonoplast in plant salt tolerance and identify proteins involved in the regulation of transporters for vacuolar Na+ sequestration, we exploited a targeted quantitative proteomics approach. Two-dimensional differential in-gel electrophoresis analysis of free flow zonal electrophoresis separated tonoplast fractions from control, and salt-treated Mesembryanthemum crystallinum plants revealed the membrane association of glycolytic enzymes aldolase and enolase, along with subunits of the vacuolar H+-ATPase V-ATPase. Protein blot analysis confirmed coordinated salt regulation of these proteins, and chaotrope treatment indicated a strong tonoplast association. Reciprocal coimmunoprecipitation studies revealed that the glycolytic enzymes interacted with the V-ATPase subunit B VHA-B, and aldolase was shown to stimulate V-ATPase activity in vitro by increasing the affinity for ATP. To investigate a physiological role for this association, the Arabidopsis thaliana cytoplasmic enolase mutant, los2, was characterized. These plants were salt sensitive, and there was a specific reduction in enolase abundance in the tonoplast from salt-treated plants. Moreover, tonoplast isolated from mutant plants showed an impaired ability for aldolase stimulation of V-ATPase hydrolytic activity. The association of glycolytic proteins with the tonoplast may not only channel ATP to the V-ATPase, but also directly upregulate H+-pump activity. PMID:20028841

  9. 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

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

    Science.gov (United States)

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

    2009-06-01

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

  11. Quantitative Analysis of MicroRNAs in Vaccinia virus Infection Reveals Diversity in Their Susceptibility to Modification and Suppression.

    Directory of Open Access Journals (Sweden)

    Amy H Buck

    Full Text Available Vaccinia virus (VACV is a large cytoplasmic DNA virus that causes dramatic alterations to many cellular pathways including microRNA biogenesis. The virus encodes a poly(A polymerase which was previously shown to add poly(A tails to the 3' end of cellular miRNAs, resulting in their degradation by 24 hours post infection (hpi. Here we used small RNA sequencing to quantify the impact of VACV infection on cellular miRNAs in human cells at both early (6 h and late (24 h times post infection. A detailed quantitative analysis of individual miRNAs revealed marked diversity in the extent of their modification and relative change in abundance during infection. Some miRNAs became highly modified (e.g. miR-29a-3p, miR-27b-3p whereas others appeared resistant (e.g. miR-16-5p. Furthermore, miRNAs that were highly tailed at 6 hpi were not necessarily among the most reduced at 24 hpi. These results suggest that intrinsic features of human cellular miRNAs cause them to be differentially polyadenylated and altered in abundance during VACV infection. We also demonstrate that intermediate and late VACV gene expression are required for optimal repression of some miRNAs including miR-27-3p. Overall this work reveals complex and varied consequences of VACV infection on host miRNAs and identifies miRNAs which are largely resistant to VACV-induced polyadenylation and are therefore present at functional levels during the initial stages of infection and replication.

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

    Directory of Open Access Journals (Sweden)

    Fangfang Chen

    2018-01-01

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

  13. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Mohan Babu

    2014-02-01

    Full Text Available Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI screens can provide insights into the biological role(s of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.

  14. Protein content and functional characteristics of serum-purified exosomes from patients with colorectal cancer revealed by quantitative proteomics.

    Science.gov (United States)

    Chen, Yanyu; Xie, Yong; Xu, Lai; Zhan, Shaohua; Xiao, Yi; Gao, Yanpan; Wu, Bin; Ge, Wei

    2017-02-15

    Tumor cells of colorectal cancer (CRC) release exosomes into the circulation. These exosomes can mediate communication between cells and affect various tumor-related processes in their target cells. We present a quantitative proteomics analysis of the exosomes purified from serum of patients with CRC and normal volunteers; data are available via ProteomeXchange with identifier PXD003875. We identified 918 proteins with an overlap of 725 Gene IDs in the Exocarta proteins list. Compared with the serum-purified exosomes (SPEs) of normal volunteers, we found 36 proteins upregulated and 22 proteins downregulated in the SPEs of CRC patients. Bioinformatics analysis revealed that upregulated proteins are involved in processes that modulate the pretumorigenic microenvironment for metastasis. In contrast, differentially expressed proteins (DEPs) that play critical roles in tumor growth and cell survival were principally downregulated. Our study demonstrates that SPEs of CRC patients play a pivotal role in promoting the tumor invasiveness, but have minimal influence on putative alterations in tumor survival or proliferation. According to bioinformatics analysis, we speculate that the protein contents of exosomes might be associated with whether they are involved in premetastatic niche establishment or growth and survival of metastatic tumor cells. This information will be helpful in elucidating the pathophysiological functions of tumor-derived exosomes, and aid in the development of CRC diagnostics and therapeutics. © 2016 UICC.

  15. Quantitative proteomics of seed filling in castor: comparison with soybean and rapeseed reveals differences between photosynthetic and nonphotosynthetic seed metabolism.

    Science.gov (United States)

    Houston, Norma L; Hajduch, Martin; Thelen, Jay J

    2009-10-01

    Seed maturation or seed filling is a phase of development that plays a major role in the storage reserve composition of a seed. In many plant seeds photosynthesis plays a major role in this process, although oilseeds, such as castor (Ricinus communis), are capable of accumulating oil without the benefit of photophosphorylation to augment energy demands. To characterize seed filling in castor, a systematic quantitative proteomics study was performed. Two-dimensional gel electrophoresis was used to resolve and quantify Cy-dye-labeled proteins expressed at 2, 3, 4, 5, and 6 weeks after flowering in biological triplicate. Expression profiles for 660 protein spot groups were established, and of these, 522 proteins were confidently identified by liquid chromatography-tandem mass spectrometry by mining against the castor genome. Identified proteins were classified according to function, and the most abundant groups of proteins were involved in protein destination and storage (34%), energy (19%), and metabolism (15%). Carbon assimilatory pathways in castor were compared with previous studies of photosynthetic oilseeds, soybean (Glycine max) and rapeseed (Brassica napus). These comparisons revealed differences in abundance and number of protein isoforms at numerous steps in glycolysis. One such difference was the number of enolase isoforms and their sum abundance; castor had approximately six times as many isoforms as soy and rapeseed. Furthermore, Rubisco was 11-fold less prominent in castor compared to rapeseed. These and other differences suggest some aspects of carbon flow, carbon recapture, as well as ATP and NADPH production in castor differs from photosynthetic oilseeds.

  16. Quantitative PCR Profiling of Escherichia coli in Livestock Feces Reveals Increased Population Resilience Relative to Culturable Counts under Temperature Extremes.

    Science.gov (United States)

    Oliver, David M; Bird, Clare; Burd, Emmy; Wyman, Michael

    2016-09-06

    The relationship between culturable counts (CFU) and quantitative PCR (qPCR) cell equivalent counts of Escherichia coli in dairy feces exposed to different environmental conditions and temperature extremes was investigated. Fecal samples were collected in summer and winter from dairy cowpats held under two treatments: field-exposed versus polytunnel-protected. A significant correlation in quantified E. coli was recorded between the qPCR and culture-based methods (r = 0.82). Evaluation of the persistence profiles of E. coli over time revealed no significant difference in the E. coli numbers determined as either CFU or gene copies during the summer for the field-exposed cowpats, whereas significantly higher counts were observed by qPCR for the polytunnel-protected cowpats, which were exposed to higher ambient temperatures. In winter, the qPCR returned significantly higher counts of E. coli for the field-exposed cowpats, thus representing a reversal of the findings from the summer sampling campaign. Results from this study suggest that with increasing time post-defecation and with the onset of challenging environmental conditions, such as extremes in temperature, culture-based counts begin to underestimate the true resilience of viable E. coli populations in livestock feces. This is important not only in the long term as the Earth changes in response to climate-change drivers but also in the short term during spells of extremely cold or hot weather.

  17. Enhanced Botrytis cinerea resistance of Arabidopsis plants grown in compost may be explained by increased expression of defense-related genes, as revealed by microarray analysis.

    Directory of Open Access Journals (Sweden)

    Guillem Segarra

    Full Text Available Composts are the products obtained after the aerobic degradation of different types of organic matter waste and can be used as substrates or substrate/soil amendments for plant cultivation. There is a small but increasing number of reports that suggest that foliar diseases may be reduced when using compost, rather than standard substrates, as growing medium. The purpose of this study was to examine the gene expression alteration produced by the compost to gain knowledge of the mechanisms involved in compost-induced systemic resistance. A compost from olive marc and olive tree leaves was able to induce resistance against Botrytis cinerea in Arabidopsis, unlike the standard substrate, perlite. Microarray analyses revealed that 178 genes were differently expressed, with a fold change cut-off of 1, of which 155 were up-regulated and 23 were down-regulated in compost-grown, as against perlite-grown plants. A functional enrichment study of up-regulated genes revealed that 38 Gene Ontology terms were significantly enriched. Response to stress, biotic stimulus, other organism, bacterium, fungus, chemical and abiotic stimulus, SA and ABA stimulus, oxidative stress, water, temperature and cold were significantly enriched, as were immune and defense responses, systemic acquired resistance, secondary metabolic process and oxireductase activity. Interestingly, PR1 expression, which was equally enhanced by growing the plants in compost and by B. cinerea inoculation, was further boosted in compost-grown pathogen-inoculated plants. Compost triggered a plant response that shares similarities with both systemic acquired resistance and ABA-dependent/independent abiotic stress responses.

  18. Quantitative proteomic analysis of human testis reveals system-wide molecular and cellular pathways associated with non-obstructive azoospermia.

    Science.gov (United States)

    Alikhani, Mehdi; Mirzaei, Mehdi; Sabbaghian, Marjan; Parsamatin, Pouria; Karamzadeh, Razieh; Adib, Samane; Sodeifi, Niloofar; Gilani, Mohammad Ali Sadighi; Zabet-Moghaddam, Masoud; Parker, Lindsay; Wu, Yunqi; Gupta, Vivek; Haynes, Paul A; Gourabi, Hamid; Baharvand, Hossein; Salekdeh, Ghasem Hosseini

    2017-06-06

    Male infertility accounts for half of the infertility problems experienced by couples. Azoospermia, having no measurable level of sperm in seminal fluid, is one of the known conditions resulting in male infertility. In order to elucidate the complex molecular mechanisms causing male azoospermia, label-free quantitative shotgun proteomics was carried out on testicular tissue specimens from patients with obstructive azoospermia and non-obstructive azoospermia, including maturation arrest (MA) and Sertoli cell only syndrome (SCOS). The abundance of 520 proteins was significantly changed across three groups of samples. We were able to identify several functional biological pathways enriched in azoospermia samples and confirm selected differentially abundant proteins, using multiple histological methods. The results revealed that cell cycle and proteolysis, and RNA splicing were the most significant biological processes impaired by the substantial suppression of proteins related to the aforementioned categories in SCOS tissues. In the MA patient testes, generation of precursor metabolites and energy as well as oxidation-reduction were the most significantly altered processes. Novel candidate proteins identified in this study include key transcription factors, many of which have not previously been shown to be associated with azoospermia. Our findings can provide substantial insights into the molecular regulation of spermatogenesis and human reproduction. The obtained data showed a drastic suppression of proteins involved in spliceosome, cell cycle and proteasome proteins, as well as energy and metabolic production in Sertoli cell only syndrome testis tissue, and to a lesser extent in maturation arrest samples. Moreover, we identified new transcription factors that are highly down-regulated in SCOS and MA patients, thus helping to understand the molecular complexity of spermatogenesis in male infertility. Our findings provide novel candidate protein targets associated

  19. Quantitative Imaging of Cholinergic Interneurons Reveals a Distinctive Spatial Organization and a Functional Gradient across the Mouse Striatum.

    Directory of Open Access Journals (Sweden)

    Miriam Matamales

    Full Text Available Information processing in the striatum requires the postsynaptic integration of glutamatergic and dopaminergic signals, which are then relayed to the output nuclei of the basal ganglia to influence behavior. Although cellularly homogeneous in appearance, the striatum contains several rare interneuron populations which tightly modulate striatal function. Of these, cholinergic interneurons (CINs have been recently shown to play a critical role in the control of reward-related learning; however how the striatal cholinergic network is functionally organized at the mesoscopic level and the way this organization influences striatal function remains poorly understood. Here, we systematically mapped and digitally reconstructed the entire ensemble of CINs in the mouse striatum and quantitatively assessed differences in densities, spatial arrangement and neuropil content across striatal functional territories. This approach demonstrated that the rostral portion of the striatum contained a higher concentration of CINs than the caudal striatum and that the cholinergic content in the core of the ventral striatum was significantly lower than in the rest of the regions. Additionally, statistical comparison of spatial point patterns in the striatal cholinergic ensemble revealed that only a minor portion of CINs (17% aggregated into cluster and that they were predominantly organized in a random fashion. Furthermore, we used a fluorescence reporter to estimate the activity of over two thousand CINs in naïve mice and found that there was a decreasing gradient of CIN overall function along the dorsomedial-to-ventrolateral axis, which appeared to be independent of their propensity to aggregate within the striatum. Altogether this work suggests that the regulation of striatal function by acetylcholine across the striatum is highly heterogeneous, and that signals originating in external afferent systems may be principally determining the function of CINs in the

  20. Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs.

    Directory of Open Access Journals (Sweden)

    Markus Drag

    Full Text Available Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS were slaughtered at ~100 kg. Gene expression profiles were obtained by RNA-Seq, and genotype data were obtained by an Illumina 60K Porcine SNP chip. Following quality control and filtering, 10,545 and 12,731 genes from liver and testis were included in the eQTL analysis, together with 20,827 SNP variants. A total of 205 and 109 single-tissue eQTLs associated with 102 and 58 unique genes were identified in liver and testis, respectively. By employing a multivariate Bayesian hierarchical model, 26 eQTLs were identified as significant multi-tissue eQTLs. The highest densities of eQTLs were found on pig chromosomes SSC12, SSC1, SSC13, SSC9 and SSC14. Functional characterisation of eQTLs revealed functions within regulation of androgen and the intracellular steroid hormone receptor signalling pathway and of xenobiotic metabolism by cytochrome P450 system and cellular response to oestradiol. A QTL enrichment test revealed 89 QTL traits curated by the Animal Genome PigQTL database to be significantly overlapped by the genomic coordinates of cis-acting eQTLs. Finally, a subset of 35 cis-acting eQTLs overlapped with known boar taint QTL traits. These eQTLs could be useful in the development of a DNA test for boar taint but careful monitoring of other overlapping QTL traits should be performed to avoid any negative consequences of selection.

  1. BAC and RNA sequencing reveal the brown planthopper resistance gene BPH15 in a recombination cold spot that mediates a unique defense mechanism.

    Science.gov (United States)

    Lv, Wentang; Du, Ba; Shangguan, Xinxin; Zhao, Yan; Pan, Yufang; Zhu, Lili; He, Yuqing; He, Guangcun

    2014-08-11

    Brown planthopper (BPH, Nilaparvata lugens Stål), is the most destructive phloem-feeding insect pest of rice (Oryza sativa). The BPH-resistance gene BPH15 has been proved to be effective in controlling the pest and widely applied in rice breeding programs. Nevertheless, molecular mechanism of the resistance remain unclear. In this study, we narrowed down the position of BPH15 on chromosome 4 and investigated the transcriptome of BPH15 rice after BPH attacked. We analyzed 13,000 BC2F2 plants of cross between susceptible rice TN1 and the recombinant inbred line RI93 that carrying the BPH15 gene from original resistant donor B5. BPH15 was mapped to a 0.0269 cM region on chromosome 4, which is 210-kb in the reference genome of Nipponbare. Sequencing bacterial artificial chromosome (BAC) clones that span the BPH15 region revealed that the physical size of BPH15 region in resistant rice B5 is 580-kb, much bigger than the corresponding region in the reference genome of Nipponbare. There were 87 predicted genes in the BPH15 region in resistant rice. The expression profiles of predicted genes were analyzed. Four jacalin-related lectin proteins genes and one LRR protein gene were found constitutively expressed in resistant parent and considered the candidate genes of BPH15. The transcriptomes of resistant BPH15 introgression line and the susceptible recipient line were analyzed using high-throughput RNA sequencing. In total, 2,914 differentially expressed genes (DEGs) were identified. BPH-responsive transcript profiles were distinct between resistant and susceptible plants and between the early stage (6 h after infestation, HAI) and late stage (48 HAI). The key defense mechanism was related to jasmonate signaling, ethylene signaling, receptor kinase, MAPK cascades, Ca(2+) signaling, PR genes, transcription factors, and protein posttranslational modifications. Our work combined BAC and RNA sequencing to identify candidate genes of BPH15 and revealed the resistance mechanism

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  3. Quantitative analysis of an engineered CO2-fixing Escherichia coli reveals great potential of heterotrophic CO2 fixation.

    Science.gov (United States)

    Gong, Fuyu; Liu, Guoxia; Zhai, Xiaoyun; Zhou, Jie; Cai, Zhen; Li, Yin

    2015-01-01

    Production of fuels from the abundant and wasteful CO2 is a promising approach to reduce carbon emission and consumption of fossil fuels. Autotrophic microbes naturally assimilate CO2 using energy from light, hydrogen, and/or sulfur. However, their slow growth rates call for investigation of the possibility of heterotrophic CO2 fixation. Although preliminary research has suggested that CO2 fixation in heterotrophic microbes is feasible after incorporation of a CO2-fixing bypass into the central carbon metabolic pathway, it remains unclear how much and how efficient that CO2 can be fixed by a heterotrophic microbe. A simple metabolic flux index was developed to indicate the relative strength of the CO2-fixation flux. When two sequential enzymes of the cyanobacterial Calvin cycle were incorporated into an E. coli strain, the flux of the CO2-fixing bypass pathway accounts for 13 % of that of the central carbon metabolic pathway. The value was increased to 17 % when the carbonic anhydrase involved in the cyanobacterial carbon concentrating mechanism was introduced, indicating that low intracellular CO2 concentration is one limiting factor for CO2 fixation in E. coli. The engineered CO2-fixing E. coli with carbonic anhydrase was able to fix CO2 at a rate of 19.6 mg CO2 L(-1) h(-1) or the specific rate of 22.5 mg CO2 g DCW(-1) h(-1). This CO2-fixation rate is comparable with the reported rates of 14 autotrophic cyanobacteria and algae (10.5-147.0 mg CO2 L(-1) h(-1) or the specific rates of 3.5-23.7 mg CO2 g DCW(-1) h(-1)). The ability of CO2 fixation was created and improved in E. coli by incorporating partial cyanobacterial Calvin cycle and carbon concentrating mechanism, respectively. Quantitative analysis revealed that the CO2-fixation rate of this strain is comparable with that of the autotrophic cyanobacteria and algae, demonstrating great potential of heterotrophic CO2 fixation.

  4. iTRAQ-Based Quantitative Proteomics Analysis of Black Rice Grain Development Reveals Metabolic Pathways Associated with Anthocyanin Biosynthesis.

    Science.gov (United States)

    Chen, Linghua; Huang, Yining; Xu, Ming; Cheng, Zuxin; Zhang, Dasheng; Zheng, Jingui

    2016-01-01

    Black rice (Oryza sativa L.), whose pericarp is rich in anthocyanins (ACNs), is considered as a healthier alternative to white rice. Molecular species of ACNs in black rice have been well documented in previous studies; however, information about the metabolic mechanisms underlying ACN biosynthesis during black rice grain development is unclear. The aim of the present study was to determine changes in the metabolic pathways that are involved in the dynamic grain proteome during the development of black rice indica cultivar, (Oryza sativa L. indica var. SSP). Isobaric tags for relative and absolute quantification (iTRAQ) MS/MS were employed to identify statistically significant alterations in the grain proteome. Approximately 928 proteins were detected, of which 230 were differentially expressed throughout 5 successive developmental stages, starting from 3 to 20 days after flowering (DAF). The greatest number of differentially expressed proteins was observed on 7 and 10 DAF, including 76 proteins that were upregulated and 39 that were downregulated. The biological process analysis of gene ontology revealed that the 230 differentially expressed proteins could be sorted into 14 functional groups. Proteins in the largest group were related to metabolic process, which could be integrated into multiple biochemical pathways. Specifically, proteins with a role in ACN biosynthesis, sugar synthesis, and the regulation of gene expression were upregulated, particularly from the onset of black rice grain development and during development. In contrast, the expression of proteins related to signal transduction, redox homeostasis, photosynthesis and N-metabolism decreased during grain maturation. Finally, 8 representative genes encoding different metabolic proteins were verified via quantitative real-time polymerase chain reaction (qRT-PCR) analysis, these genes had differed in transcriptional and translational expression during grain development. Expression analyses of

  5. Early transcriptome analyses of Z-3-Hexenol-treated zea mays revealed distinct transcriptional networks and anti-herbivore defense potential of green leaf volatiles.

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    Jurgen Engelberth

    Full Text Available Green leaf volatiles (GLV, which are rapidly emitted by plants in response to insect herbivore damage, are now established as volatile defense signals. Receiving plants utilize these molecules to prime their defenses and respond faster and stronger when actually attacked. To further characterize the biological activity of these compounds we performed a microarray analysis of global gene expression. The focus of this project was to identify early transcriptional events elicited by Z-3-hexenol (Z-3-HOL as our model GLV in maize (Zea mays seedlings. The microarray results confirmed previous studies on Z-3-HOL -induced gene expression but also provided novel information about the complexity of Z-3-HOL -induced transcriptional networks. Besides identifying a distinct set of genes involved in direct and indirect defenses we also found significant expression of genes involved in transcriptional regulation, Ca(2+-and lipid-related signaling, and cell wall reinforcement. By comparing these results with those obtained by treatment of maize seedlings with insect elicitors we found a high degree of correlation between the two expression profiles at this early time point, in particular for those genes related to defense. We further analyzed defense gene expression induced by other volatile defense signals and found Z-3-HOL to be significantly more active than methyl jasmonate, methyl salicylate, and ethylene. The data presented herein provides important information on early genetic networks that are activated by Z-3-HOL and demonstrates the effectiveness of this compound in the regulation of typical plant defenses against insect herbivores in maize.

  6. Transforming Defense

    National Research Council Canada - National Science Library

    Lamb, Christopher J; Bunn, M. E; Lutes, Charles; Cavoli, Christopher

    2005-01-01

    .... Despite the resources and attention consumed by the war on terror, and recent decisions by the White House to curtail the growth of defense spending, the senior leadership of the Department of Defense (DoD...

  7. Can the Analytical Hierarchy Process Model Be Effectively Applied in the Prioritization of Information Assurance Defense In-Depth Measures? --A Quantitative Study

    Science.gov (United States)

    Alexander, Rodney T.

    2017-01-01

    Organizational computing devices are increasingly becoming targets of cyber-attacks, and organizations have become dependent on the safety and security of their computer networks and their organizational computing devices. Business and government often use defense in-depth information assurance measures such as firewalls, intrusion detection…

  8. Growth of solid domains in model membranes: quantitative image analysis reveals a strong correlation between domain shape and spatial position

    DEFF Research Database (Denmark)

    Bernchou, Uffe; Ipsen, John Hjort; Simonsen, Adam Cohen

    2009-01-01

    . To analyze this effect, the nucleation points were used as generators in a Voronoi construction. Associated with each generator is a Voronoi polygon that contains all points closer to this generator than to any other. Through a detailed quantitative analysis of the Voronoi cells and the domains, we have...

  9. Novel Fungal Pathogenicity and Leaf Defense Strategies Are Revealed by Simultaneous Transcriptome Analysis of Colletotrichum fructicola and Strawberry Infected by This Fungus

    Directory of Open Access Journals (Sweden)

    Liqing Zhang

    2018-04-01

    Full Text Available Colletotrichum fructicola, which is part of the C. gloeosporioides species complex, can cause anthracnose diseases in strawberries worldwide. However, the molecular interactions between C. fructicola and strawberry are largely unknown. A deep RNA-sequencing approach was applied to gain insights into the pathogenicity mechanisms of C. fructicola and the defense response of strawberry plants at different stages of infection. The transcriptome data showed stage-specific transcription accompanied by a step-by-step strawberry defense response and the evasion of this defense system by fungus. Fungal genes involved in plant cell wall degradation, secondary metabolism, and detoxification were up-regulated at different stage of infection. Most importantly, C. fructicola infection was accompanied by a large number of highly expressed effectors. Four new identified effectors function in the suppression of Bax-mediated programmed cell death. Strawberry utilizes pathogen-associated molecular patterns (PAMP-triggered immunity and effector-triggered immunity to prevent C. fructicola invasion, followed by the initiation of downstream innate immunity. The up-regulation of genes related to salicylic acid provided evidence that salicylic acid signaling may serve as the core defense signaling mechanism, while jasmonic acid and ethylene pathways were largely inhibited by C. fructicola. The necrotrophic stage displayed a significant up-regulation of genes involved in reactive oxygen species activation. Collectively, the transcriptomic data of both C. fructicola and strawberry shows that even though plants build a multilayered defense against infection, C. fructicola employs a series of escape or antagonizing mechanisms to successfully infect host cells.

  10. Natural history-driven, plant-mediated RNAi-based study reveals CYP6B46's role in a nicotine-mediated antipredator herbivore defense.

    Science.gov (United States)

    Kumar, Pavan; Pandit, Sagar S; Steppuhn, Anke; Baldwin, Ian T

    2014-01-28

    Manduca sexta (Ms) larvae are known to efficiently excrete ingested nicotine when feeding on their nicotine-producing native hostplant, Nicotiana attenuata. Here we describe how ingested nicotine is co-opted for larval defense by a unique mechanism. Plant-mediated RNAi was used to silence a midgut-expressed, nicotine-induced cytochrome P450 6B46 (CYP6B46) in larvae consuming transgenic N. attenuata plants producing MsCYP6B46 dsRNA. These and transgenic nicotine-deficient plants were planted into native habitats to study the phenotypes of larvae feeding on these plants and the behavior of their predators. The attack-behavior of a native wolf spider (Camptocosa parallela), a major nocturnal predator, provided the key to understanding MsCYP6B46's function: spiders clearly preferred CYP6B46-silenced larvae, just as they had preferred larvae fed nicotine-deficient plants. MsCYP6B46 redirects a small amount (0.65%) of ingested nicotine from the midgut into hemolymph, from which nicotine is exhaled through the spiracles as an antispider signal. CYP6B46-silenced larvae were more susceptible to spider-attack because they exhaled less nicotine because of lower hemolymph nicotine concentrations. CYP6B46-silenced larvae were impaired in distributing ingested nicotine from midgut to hemolymph, but not in the clearing of hemolymph nicotine or in the exhalation of nicotine from hemolymph. MsCYP6B46 could be a component of a previously hypothesized pump that converts nicotine to a short-lived, transportable, metabolite. Other predators, big-eyed bugs, and antlion larvae were insensitive to this defense. Thus, chemical defenses, too toxic to sequester, can be repurposed for defensive functions through respiration as a form of defensive halitosis, and predators can assist the functional elucidation of herbivore genes.

  11. Quantitative Molecular Imaging with a Single Gd-Based Contrast Agent Reveals Specific Tumor Binding and Retention in Vivo.

    Science.gov (United States)

    Johansen, Mette L; Gao, Ying; Hutnick, Melanie A; Craig, Sonya E L; Pokorski, Jonathan K; Flask, Chris A; Brady-Kalnay, Susann M

    2017-06-06

    Magnetic resonance imaging (MRI) has become an indispensable tool in the diagnosis and treatment of many diseases, especially cancer. However, the poor sensitivity of MRI relative to other imaging modalities, such as PET, has hindered the development and clinical use of molecular MRI contrast agents that could provide vital diagnostic information by specifically locating a molecular target altered in the disease process. This work describes the specific and sustained in vivo binding and retention of a protein tyrosine phosphatase mu (PTPμ)-targeted, molecular magnetic resonance (MR) contrast agent with a single gadolinium (Gd) chelate using a quantitative MRI T 1 mapping technique in glioma xenografts. Quantitative T 1 mapping is an imaging method used to measure the longitudinal relaxation time, the T 1 relaxation time, of protons in a magnetic field after excitation by a radiofrequency pulse. T 1 relaxation times can in turn be used to calculate the concentration of a gadolinium-containing contrast agent in a region of interest, thereby allowing the retention or clearance of an agent to be quantified. In this context, retention is a measure of molecular contrast agent binding. Using conventional peptide chemistry, a PTPμ-targeted peptide was linked to a chelator that had been conjugated to a lysine residue. Following complexation with Gd, this PTPμ-targeted molecular contrast agent containing a single Gd ion showed significant tumor enhancement and a sustained increase in Gd concentration in both heterotopic and orthotopic tumors using dynamic quantitative MRI. This single Gd-containing PTPμ agent was more effective than our previous version with three Gd ions. Differences between nonspecific and specific agents, due to specific tumor binding, can be determined within the first 30 min after agent administration by examining clearance rates. This more facile chemistry, when combined with quantitative MR techniques, allows for widespread adoption by academic

  12. Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics.

    Science.gov (United States)

    Burkhart, Julia Maria; Schumbrutzki, Cornelia; Wortelkamp, Stefanie; Sickmann, Albert; Zahedi, René Peiman

    2012-02-02

    Trypsin is the most frequently used proteolytic enzyme in mass spectrometry-based proteomics. Beside its good availability, it also offers some major advantages such as an optimal average peptide length of ~14 amino acids, and typically the presence of at least two defined positive charges at the N-terminus as well as the C-terminal Arg/Lys, rendering tryptic peptides well suited for CID-based LC-MS/MS. Here, we conducted a systematic study of different types of commercially available trypsin in order to qualitatively and quantitatively compare cleavage specificity, efficiency as well as reproducibility and the potential impact on quantitation and proteome coverage. We present a straightforward strategy applied to complex digests of human platelets, comprising (1) digest controls using a monolithic column HPLC-setup, (2) SCX enrichment of semitryptic/nonspecific peptides, (3) targeted MRM analysis of corresponding full cleavage/missed cleavage peptide pairs as well as (4) LC-MS analyses of complete digests with a three-step data interpretation. Thus, differences in digest performance can be readily assessed, rendering these procedures extremely beneficial to quality control not only the trypsin of choice, but also to effectively compare as well as optimize different digestion conditions and to evaluate the reproducibility of a dedicated digest protocol for all kinds of quantitative proteome studies. Copyright © 2011 Elsevier B.V. All rights reserved.

  13. Transcriptome and quantitative proteome analysis reveals molecular processes associated with larval metamorphosis in the polychaete pseudopolydora vexillosa

    KAUST Repository

    Chandramouli, Kondethimmanahalli; Sun, Jin; Mok, FloraSy; Liu, Lingli; Qiu, Jianwen; Ravasi, Timothy; Qian, Peiyuan

    2013-01-01

    Larval growth of the polychaete worm Pseudopolydora vexillosa involves the formation of segment-specific structures. When larvae attain competency to settle, they discard swimming chaetae and secrete mucus. The larvae build tubes around themselves and metamorphose into benthic juveniles. Understanding the molecular processes, which regulate this complex and unique transition, remains a major challenge because of the limited molecular information available. To improve this situation, we conducted high-throughput RNA sequencing and quantitative proteome analysis of the larval stages of P. vexillosa. Based on gene ontology (GO) analysis, transcripts related to cellular and metabolic processes, binding, and catalytic activities were highly represented during larval-adult transition. Mitogen-activated protein kinase (MAPK), calcium-signaling, Wnt/β-catenin, and notch signaling metabolic pathways were enriched in transcriptome data. Quantitative proteomics identified 107 differentially expressed proteins in three distinct larval stages. Fourteen and 53 proteins exhibited specific differential expression during competency and metamorphosis, respectively. Dramatic up-regulation of proteins involved in signaling, metabolism, and cytoskeleton functions were found during the larval-juvenile transition. Several proteins involved in cell signaling, cytoskeleton and metabolism were up-regulated, whereas proteins related to transcription and oxidative phosphorylation were down-regulated during competency. The integration of high-throughput RNA sequencing and quantitative proteomics allowed a global scale analysis of larval transcripts/proteins associated molecular processes in the metamorphosis of polychaete worms. Further, transcriptomic and proteomic insights provide a new direction to understand the fundamental mechanisms that regulate larval metamorphosis in polychaetes. © 2013 American Chemical Society.

  14. Transcriptome and quantitative proteome analysis reveals molecular processes associated with larval metamorphosis in the polychaete pseudopolydora vexillosa

    KAUST Repository

    Chandramouli, Kondethimmanahalli

    2013-03-01

    Larval growth of the polychaete worm Pseudopolydora vexillosa involves the formation of segment-specific structures. When larvae attain competency to settle, they discard swimming chaetae and secrete mucus. The larvae build tubes around themselves and metamorphose into benthic juveniles. Understanding the molecular processes, which regulate this complex and unique transition, remains a major challenge because of the limited molecular information available. To improve this situation, we conducted high-throughput RNA sequencing and quantitative proteome analysis of the larval stages of P. vexillosa. Based on gene ontology (GO) analysis, transcripts related to cellular and metabolic processes, binding, and catalytic activities were highly represented during larval-adult transition. Mitogen-activated protein kinase (MAPK), calcium-signaling, Wnt/β-catenin, and notch signaling metabolic pathways were enriched in transcriptome data. Quantitative proteomics identified 107 differentially expressed proteins in three distinct larval stages. Fourteen and 53 proteins exhibited specific differential expression during competency and metamorphosis, respectively. Dramatic up-regulation of proteins involved in signaling, metabolism, and cytoskeleton functions were found during the larval-juvenile transition. Several proteins involved in cell signaling, cytoskeleton and metabolism were up-regulated, whereas proteins related to transcription and oxidative phosphorylation were down-regulated during competency. The integration of high-throughput RNA sequencing and quantitative proteomics allowed a global scale analysis of larval transcripts/proteins associated molecular processes in the metamorphosis of polychaete worms. Further, transcriptomic and proteomic insights provide a new direction to understand the fundamental mechanisms that regulate larval metamorphosis in polychaetes. © 2013 American Chemical Society.

  15. Novel Fungal Pathogenicity and Leaf Defense Strategies Are Revealed by Simultaneous Transcriptome Analysis of Colletotrichum fructicola and Strawberry Infected by This Fungus

    OpenAIRE

    Liqing Zhang; Xin Huang; Chengyong He; Chengyong He; Qing-Yu Zhang; Xiaohua Zou; Ke Duan; Ke Duan; Qinghua Gao

    2018-01-01

    Colletotrichum fructicola, which is part of the C. gloeosporioides species complex, can cause anthracnose diseases in strawberries worldwide. However, the molecular interactions between C. fructicola and strawberry are largely unknown. A deep RNA-sequencing approach was applied to gain insights into the pathogenicity mechanisms of C. fructicola and the defense response of strawberry plants at different stages of infection. The transcriptome data showed stage-specific transcription accompanied...

  16. RNA-Seq analysis of Citrus reticulata in the early stages of Xylella fastidiosa infection reveals auxin-related genes as a defense response.

    Science.gov (United States)

    Rodrigues, Carolina M; de Souza, Alessandra A; Takita, Marco A; Kishi, Luciano T; Machado, Marcos A

    2013-10-03

    Citrus variegated chlorosis (CVC), caused by Xylella fastidiosa, is one the most important citrus diseases, and affects all varieties of sweet orange (Citrus sinensis L. Osb). On the other hand, among the Citrus genus there are different sources of resistance against X. fastidiosa. For these species identifying these defense genes could be an important step towards obtaining sweet orange resistant varieties through breeding or genetic engineering. To assess these genes we made use of mandarin (C. reticulata Blanco) that is known to be resistant to CVC and shares agronomical characteristics with sweet orange. Thus, we investigated the gene expression in Ponkan mandarin at one day after infection with X. fastidiosa, using RNA-seq. A set of genes considered key elements in the resistance was used to confirm its regulation in mandarin compared with the susceptible sweet orange. Gene expression analysis of mock inoculated and infected tissues of Ponkan mandarin identified 667 transcripts repressed and 724 significantly induced in the later. Among the induced transcripts, we identified genes encoding proteins similar to Pattern Recognition Receptors. Furthermore, many genes involved in secondary metabolism, biosynthesis and cell wall modification were upregulated as well as in synthesis of abscisic acid, jasmonic acid and auxin. This work demonstrated that the defense response to the perception of bacteria involves cell wall modification and activation of hormone pathways, which probably lead to the induction of other defense-related genes. We also hypothesized the induction of auxin-related genes indicates that resistant plants initially recognize X. fastidiosa as a necrotrophic pathogen.

  17. Benchmarking sample preparation/digestion protocols reveals tube-gel being a fast and repeatable method for quantitative proteomics.

    Science.gov (United States)

    Muller, Leslie; Fornecker, Luc; Van Dorsselaer, Alain; Cianférani, Sarah; Carapito, Christine

    2016-12-01

    Sample preparation, typically by in-solution or in-gel approaches, has a strong influence on the accuracy and robustness of quantitative proteomics workflows. The major benefit of in-gel procedures is their compatibility with detergents (such as SDS) for protein solubilization. However, SDS-PAGE is a time-consuming approach. Tube-gel (TG) preparation circumvents this drawback as it involves directly trapping the sample in a polyacrylamide gel matrix without electrophoresis. We report here the first global label-free quantitative comparison between TG, stacking gel (SG), and basic liquid digestion (LD). A series of UPS1 standard mixtures (at 0.5, 1, 2.5, 5, 10, and 25 fmol) were spiked in a complex yeast lysate background. TG preparation allowed more yeast proteins to be identified than did the SG and LD approaches, with mean numbers of 1979, 1788, and 1323 proteins identified, respectively. Furthermore, the TG method proved equivalent to SG and superior to LD in terms of the repeatability of the subsequent experiments, with mean CV for yeast protein label-free quantifications of 7, 9, and 10%. Finally, known variant UPS1 proteins were successfully detected in the TG-prepared sample within a complex background with high sensitivity. All the data from this study are accessible on ProteomeXchange (PXD003841). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    DEFF Research Database (Denmark)

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

    2018-01-01

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

  19. Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs

    DEFF Research Database (Denmark)

    Drag, Markus; Hansen, Mathias B.; Kadarmideen, Haja N.

    2018-01-01

    Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed...... to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at similar to 100 kg. Gene...... monitoring of other overlapping QTL traits should be performed to avoid any negative consequences of selection....

  20. Genetic control of environmental variation of two quantitative traits of Drosophila melanogaster revealed by whole-genome sequencing

    DEFF Research Database (Denmark)

    Sørensen, Peter; de los Campos, Gustavo; Morgante, Fabio

    2015-01-01

    and others more volatile performance. Understanding the mechanisms responsible for environmental variability not only informs medical questions but is relevant in evolution and in agricultural science. In this work fully sequenced inbred lines of Drosophila melanogaster were analyzed to study the nature...... of genetic control of environmental variance for two quantitative traits: starvation resistance (SR) and startle response (SL). The evidence for genetic control of environmental variance is compelling for both traits. Sequence information is incorporated in random regression models to study the underlying...... genetic signals, which are shown to be different in the two traits. Genomic variance in sexual dimorphism was found for SR but not for SL. Indeed, the proportion of variance captured by sequence information and the contribution to this variance from four chromosome segments differ between sexes in SR...

  1. Quantitative Live Imaging of Human Embryonic Stem Cell Derived Neural Rosettes Reveals Structure-Function Dynamics Coupled to Cortical Development.

    Science.gov (United States)

    Ziv, Omer; Zaritsky, Assaf; Yaffe, Yakey; Mutukula, Naresh; Edri, Reuven; Elkabetz, Yechiel

    2015-10-01

    Neural stem cells (NSCs) are progenitor cells for brain development, where cellular spatial composition (cytoarchitecture) and dynamics are hypothesized to be linked to critical NSC capabilities. However, understanding cytoarchitectural dynamics of this process has been limited by the difficulty to quantitatively image brain development in vivo. Here, we study NSC dynamics within Neural Rosettes--highly organized multicellular structures derived from human pluripotent stem cells. Neural rosettes contain NSCs with strong epithelial polarity and are expected to perform apical-basal interkinetic nuclear migration (INM)--a hallmark of cortical radial glial cell development. We developed a quantitative live imaging framework to characterize INM dynamics within rosettes. We first show that the tendency of cells to follow the INM orientation--a phenomenon we referred to as radial organization, is associated with rosette size, presumably via mechanical constraints of the confining structure. Second, early forming rosettes, which are abundant with founder NSCs and correspond to the early proliferative developing cortex, show fast motions and enhanced radial organization. In contrast, later derived rosettes, which are characterized by reduced NSC capacity and elevated numbers of differentiated neurons, and thus correspond to neurogenesis mode in the developing cortex, exhibit slower motions and decreased radial organization. Third, later derived rosettes are characterized by temporal instability in INM measures, in agreement with progressive loss in rosette integrity at later developmental stages. Finally, molecular perturbations of INM by inhibition of actin or non-muscle myosin-II (NMII) reduced INM measures. Our framework enables quantification of cytoarchitecture NSC dynamics and may have implications in functional molecular studies, drug screening, and iPS cell-based platforms for disease modeling.

  2. Quantitative Live Imaging of Human Embryonic Stem Cell Derived Neural Rosettes Reveals Structure-Function Dynamics Coupled to Cortical Development.

    Directory of Open Access Journals (Sweden)

    Omer Ziv

    2015-10-01

    Full Text Available Neural stem cells (NSCs are progenitor cells for brain development, where cellular spatial composition (cytoarchitecture and dynamics are hypothesized to be linked to critical NSC capabilities. However, understanding cytoarchitectural dynamics of this process has been limited by the difficulty to quantitatively image brain development in vivo. Here, we study NSC dynamics within Neural Rosettes--highly organized multicellular structures derived from human pluripotent stem cells. Neural rosettes contain NSCs with strong epithelial polarity and are expected to perform apical-basal interkinetic nuclear migration (INM--a hallmark of cortical radial glial cell development. We developed a quantitative live imaging framework to characterize INM dynamics within rosettes. We first show that the tendency of cells to follow the INM orientation--a phenomenon we referred to as radial organization, is associated with rosette size, presumably via mechanical constraints of the confining structure. Second, early forming rosettes, which are abundant with founder NSCs and correspond to the early proliferative developing cortex, show fast motions and enhanced radial organization. In contrast, later derived rosettes, which are characterized by reduced NSC capacity and elevated numbers of differentiated neurons, and thus correspond to neurogenesis mode in the developing cortex, exhibit slower motions and decreased radial organization. Third, later derived rosettes are characterized by temporal instability in INM measures, in agreement with progressive loss in rosette integrity at later developmental stages. Finally, molecular perturbations of INM by inhibition of actin or non-muscle myosin-II (NMII reduced INM measures. Our framework enables quantification of cytoarchitecture NSC dynamics and may have implications in functional molecular studies, drug screening, and iPS cell-based platforms for disease modeling.

  3. Ultrasonography of the nail unit reveals quantitative and qualitative alterations in patients with psoriasis and psoriatic arthritis.

    Science.gov (United States)

    Idolazzi, Luca; Gisondi, Paolo; Fassio, Angelo; Viapiana, Ombretta; Giollo, Alessandro; Rossini, Maurizio; Girolomoni, Giampiero; Gatti, Davide

    2018-05-02

    The nail unit is a matter of interest both for dermatologist and rheumatologist. The nail is considered one of the possible targets of assessment, especially when ultrasonography is performed. The aim of the study is to highlight peculiar features and alterations of the nail unit in patients affected by psoriasis and psoriatic arthritis versus healthy controls using ultrasonography. The study sample included 82 patients affected by psoriasis and/or psoriatic arthritis and 50 healthy controls. The patients were consecutively enrolled during their routine visit in the outpatient clinic and they performed clinical and ultrasonographic evaluation of the nail. The evaluationof disease activity was done using Disease Activity in Psoriatic Arthritis (DAPSA), Psoriasis Activity Severity Index (PASI), and Nail Psoriasi Severity Index (NAPSI). Multivariate analysis of variance was performed between groups. Post hoc analysis underlined the differences between healthy and affected regarding nail plate thickness (0.063±0.011 cm for patients with psoriasis, 0.065±0.014 cm for patients with psoriatic arthritis and 0.051±0.006 cm for healthy controls, p<0.05). Elementary lesions of nail plate and nail bed were compared using Pearson's chi square test between patients in psoriasis and psoriatic arthritis groups, with no differences except for a trend for onycholisis and crumbling (p=0.07 and 0.06, respectively) in the psoriatic arthritis group. ROC curves were calculated (AUC = 0.68) obtaining also quantitative cut offs for nail plate andnail bed thickness in the affected vs healthy patients. Our study shows that ultrasonography may be a potential advantage in clinical practice. Our results strengthen the information already available in the literature and add quantitative parameters for ultrasonography of the nail.

  4. Elevated host lipid metabolism revealed by iTRAQ-based quantitative proteomic analysis of cerebrospinal fluid of tuberculous meningitis patients

    Energy Technology Data Exchange (ETDEWEB)

    Mu, Jun [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing (China); Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing (China); Chongqing Key Laboratory of Neurobiology, Chongqing (China); Yang, Yongtao [Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing (China); Chongqing Key Laboratory of Neurobiology, Chongqing (China); Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing (China); Chen, Jin; Cheng, Ke; Li, Qi; Wei, Yongdong; Zhu, Dan; Shao, Weihua; Zheng, Peng [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing (China); Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing (China); Chongqing Key Laboratory of Neurobiology, Chongqing (China); Xie, Peng, E-mail: xiepeng@cqmu.edu.cn [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing (China); Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing (China); Chongqing Key Laboratory of Neurobiology, Chongqing (China); Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing (China)

    2015-10-30

    Purpose: Tuberculous meningitis (TBM) remains to be one of the most deadly infectious diseases. The pathogen interacts with the host immune system, the process of which is largely unknown. Various cellular processes of Mycobacterium tuberculosis (MTB) centers around lipid metabolism. To determine the lipid metabolism related proteins, a quantitative proteomic study was performed here to identify differential proteins in the cerebrospinal fluid (CSF) obtained from TBM patients (n = 12) and healthy controls (n = 12). Methods: CSF samples were desalted, concentrated, labelled with isobaric tags for relative and absolute quantitation (iTRAQ™), and analyzed by multi-dimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gene ontology and proteomic phenotyping analysis of the differential proteins were conducted using Database for Annotation, Visualization, and Integrated Discovery (DAVID) Bioinformatics Resources. ApoE and ApoB were selected for validation by ELISA. Results: Proteomic phenotyping of the 4 differential proteins was invloved in the lipid metabolism. ELISA showed significantly increased ApoB levels in TBM subjects compared to healthy controls. Area under the receiver operating characteristic curve analysis demonstrated ApoB levels could distinguish TBM subjects from healthy controls and viral meningitis subjects with 89.3% sensitivity and 92% specificity. Conclusions: CSF lipid metabolism disregulation, especially elevated expression of ApoB, gives insights into the pathogenesis of TBM. Further evaluation of these findings in larger studies including anti-tuberculosis medicated and unmedicated patient cohorts with other center nervous system infectious diseases is required for successful clinical translation. - Highlights: • The first proteomic study on the cerebrospinal fluid of tuberculous meningitis patients using iTRAQ. • Identify 4 differential proteins invloved in the lipid metabolism. • Elevated expression of ApoB gives

  5. Elevated host lipid metabolism revealed by iTRAQ-based quantitative proteomic analysis of cerebrospinal fluid of tuberculous meningitis patients.

    Science.gov (United States)

    Mu, Jun; Yang, Yongtao; Chen, Jin; Cheng, Ke; Li, Qi; Wei, Yongdong; Zhu, Dan; Shao, Weihua; Zheng, Peng; Xie, Peng

    2015-10-30

    Tuberculous meningitis (TBM) remains to be one of the most deadly infectious diseases. The pathogen interacts with the host immune system, the process of which is largely unknown. Various cellular processes of Mycobacterium tuberculosis (MTB) centers around lipid metabolism. To determine the lipid metabolism related proteins, a quantitative proteomic study was performed here to identify differential proteins in the cerebrospinal fluid (CSF) obtained from TBM patients (n = 12) and healthy controls (n = 12). CSF samples were desalted, concentrated, labelled with isobaric tags for relative and absolute quantitation (iTRAQ™), and analyzed by multi-dimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gene ontology and proteomic phenotyping analysis of the differential proteins were conducted using Database for Annotation, Visualization, and Integrated Discovery (DAVID) Bioinformatics Resources. ApoE and ApoB were selected for validation by ELISA. Proteomic phenotyping of the 4 differential proteins was invloved in the lipid metabolism. ELISA showed significantly increased ApoB levels in TBM subjects compared to healthy controls. Area under the receiver operating characteristic curve analysis demonstrated ApoB levels could distinguish TBM subjects from healthy controls and viral meningitis subjects with 89.3% sensitivity and 92% specificity. CSF lipid metabolism disregulation, especially elevated expression of ApoB, gives insights into the pathogenesis of TBM. Further evaluation of these findings in larger studies including anti-tuberculosis medicated and unmedicated patient cohorts with other center nervous system infectious diseases is required for successful clinical translation. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Elevated host lipid metabolism revealed by iTRAQ-based quantitative proteomic analysis of cerebrospinal fluid of tuberculous meningitis patients

    International Nuclear Information System (INIS)

    Mu, Jun; Yang, Yongtao; Chen, Jin; Cheng, Ke; Li, Qi; Wei, Yongdong; Zhu, Dan; Shao, Weihua; Zheng, Peng; Xie, Peng

    2015-01-01

    Purpose: Tuberculous meningitis (TBM) remains to be one of the most deadly infectious diseases. The pathogen interacts with the host immune system, the process of which is largely unknown. Various cellular processes of Mycobacterium tuberculosis (MTB) centers around lipid metabolism. To determine the lipid metabolism related proteins, a quantitative proteomic study was performed here to identify differential proteins in the cerebrospinal fluid (CSF) obtained from TBM patients (n = 12) and healthy controls (n = 12). Methods: CSF samples were desalted, concentrated, labelled with isobaric tags for relative and absolute quantitation (iTRAQ™), and analyzed by multi-dimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gene ontology and proteomic phenotyping analysis of the differential proteins were conducted using Database for Annotation, Visualization, and Integrated Discovery (DAVID) Bioinformatics Resources. ApoE and ApoB were selected for validation by ELISA. Results: Proteomic phenotyping of the 4 differential proteins was invloved in the lipid metabolism. ELISA showed significantly increased ApoB levels in TBM subjects compared to healthy controls. Area under the receiver operating characteristic curve analysis demonstrated ApoB levels could distinguish TBM subjects from healthy controls and viral meningitis subjects with 89.3% sensitivity and 92% specificity. Conclusions: CSF lipid metabolism disregulation, especially elevated expression of ApoB, gives insights into the pathogenesis of TBM. Further evaluation of these findings in larger studies including anti-tuberculosis medicated and unmedicated patient cohorts with other center nervous system infectious diseases is required for successful clinical translation. - Highlights: • The first proteomic study on the cerebrospinal fluid of tuberculous meningitis patients using iTRAQ. • Identify 4 differential proteins invloved in the lipid metabolism. • Elevated expression of ApoB gives

  7. iTRAQ-based quantitative proteomic analysis reveals proteomic changes in leaves of cultivated tobacco (Nicotiana tabacum) in response to drought stress.

    Science.gov (United States)

    Xie, He; Yang, Da-Hai; Yao, Heng; Bai, Ge; Zhang, Yi-Han; Xiao, Bing-Guang

    2016-01-15

    Drought is one of the most severe forms of abiotic stresses that threaten the survival of plants, including crops. In turn, plants dramatically change their physiology to increase drought tolerance, including reconfiguration of proteomes. Here, we studied drought-induced proteomic changes in leaves of cultivated tobacco (Nicotiana tabacum), a solanaceous plant, using the isobaric tags for relative and absolute quantitation (iTRAQ)-based protein labeling technology. Of identified 5570 proteins totally, drought treatment increased and decreased abundance of 260 and 206 proteins, respectively, compared with control condition. Most of these differentially regulated proteins are involved in photosynthesis, metabolism, and stress and defense. Although abscisic acid (ABA) levels greatly increased in drought-treated tobacco leaves, abundance of detected ABA biosynthetic enzymes showed no obvious changes. In contrast, heat shock proteins (HSPs), thioredoxins, ascorbate-, glutathione-, and hydrogen peroxide (H2O2)-related proteins were up- or down-regulated in drought-treated tobacco leaves, suggesting that chaperones and redox signaling are important for tobacco tolerance to drought, and it is likely that redox-induced posttranslational modifications play an important role in modulating protein activity. This study not only provides a comprehensive dataset on overall protein changes in drought-treated tobacco leaves, but also shed light on the mechanism by which solanaceous plants adapt to drought stress. Copyright © 2015 Yunnan Academy of Tobacco Agricultural Sciences. Published by Elsevier Inc. All rights reserved.

  8. Quantitative Proteomic Analysis of Mosquito C6/36 Cells Reveals Host Proteins Involved in Zika Virus Infection.

    Science.gov (United States)

    Xin, Qi-Lin; Deng, Cheng-Lin; Chen, Xi; Wang, Jun; Wang, Shao-Bo; Wang, Wei; Deng, Fei; Zhang, Bo; Xiao, Gengfu; Zhang, Lei-Ke

    2017-06-15

    Zika virus (ZIKV) is an emerging arbovirus belonging to the genus Flavivirus of the family Flaviviridae During replication processes, flavivirus manipulates host cell systems to facilitate its replication, while the host cells activate antiviral responses. Identification of host proteins involved in the flavivirus replication process may lead to the discovery of antiviral targets. The mosquitoes Aedes aegypti and Aedes albopictus are epidemiologically important vectors for ZIKV, and effective restrictions of ZIKV replication in mosquitoes will be vital in controlling the spread of virus. In this study, an iTRAQ-based quantitative proteomic analysis of ZIKV-infected Aedes albopictus C6/36 cells was performed to investigate host proteins involved in the ZIKV infection process. A total of 3,544 host proteins were quantified, with 200 being differentially regulated, among which CHCHD2 can be upregulated by ZIKV infection in both mosquito C6/36 and human HeLa cells. Our further study indicated that CHCHD2 can promote ZIKV replication and inhibit beta interferon (IFN-β) production in HeLa cells, suggesting that ZIKV infection may upregulate CHCHD2 to inhibit IFN-I production and thus promote virus replication. Bioinformatics analysis of regulated host proteins highlighted several ZIKV infection-regulated biological processes. Further study indicated that the ubiquitin proteasome system (UPS) plays roles in the ZIKV entry process and that an FDA-approved inhibitor of the 20S proteasome, bortezomib, can inhibit ZIKV infection in vivo Our study illustrated how host cells respond to ZIKV infection and also provided a candidate drug for the control of ZIKV infection in mosquitoes and treatment of ZIKV infection in patients. IMPORTANCE ZIKV infection poses great threats to human health, and there is no FDA-approved drug available for the treatment of ZIKV infection. During replication, ZIKV manipulates host cell systems to facilitate its replication, while host cells activate

  9. Quantitative evaluation of protocorm growth and fungal colonization in Bletilla striata (Orchidaceae) reveals less-productive symbiosis with a non-native symbiotic fungus.

    Science.gov (United States)

    Yamamoto, Tatsuki; Miura, Chihiro; Fuji, Masako; Nagata, Shotaro; Otani, Yuria; Yagame, Takahiro; Yamato, Masahide; Kaminaka, Hironori

    2017-02-21

    In nature, orchid plants depend completely on symbiotic fungi for their nutrition at the germination and the subsequent seedling (protocorm) stages. However, only limited quantitative methods for evaluating the orchid-fungus interactions at the protocorm stage are currently available, which greatly constrains our understanding of the symbiosis. Here, we aimed to improve and integrate quantitative evaluations of the growth and fungal colonization in the protocorms of a terrestrial orchid, Blettila striata, growing on a plate medium. We achieved both symbiotic and asymbiotic germinations for the terrestrial orchid B. striata. The protocorms produced by the two germination methods grew almost synchronously for the first three weeks. At week four, however, the length was significantly lower in the symbiotic protocorms. Interestingly, the dry weight of symbiotic protocorms did not significantly change during the growth period, which implies that there was only limited transfer of carbon compounds from the fungus to the protocorms in this relationship. Next, to evaluate the orchid-fungus interactions, we developed an ink-staining method to observe the hyphal coils in protocorms without preparing thin sections. Crushing the protocorm under the coverglass enables us to observe all hyphal coils in the protocorms with high resolution. For this observation, we established a criterion to categorize the stages of hyphal coils, depending on development and degradation. By counting the symbiotic cells within each stage, it was possible to quantitatively evaluate the orchid-fungus symbiosis. We describe a method for quantitative evaluation of orchid-fungus symbiosis by integrating the measurements of plant growth and fungal colonization. The current study revealed that although fungal colonization was observed in the symbiotic protocorms, the weight of the protocorm did not significantly increase, which is probably due to the incompatibility of the fungus in this symbiosis. These

  10. Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

    Energy Technology Data Exchange (ETDEWEB)

    Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; Kong, Betty Y.; Gleber, Sophie C.; Vogt, Stefan; Chen, Si; Garwin, Seth A.; Bayer, Amanda R.; Dravid, Vinayak P.; Woodruff, Teresa K.; O' Halloran, Thomas V.

    2014-12-15

    Fertilization of a mammalian egg initiates a series of 'zinc sparks' that are necessary to induce the egg-to-embryo transition. Despite the importance of these zinc-efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches that resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy-dispersive spectroscopy, X-ray fluorescence microscopy and three-dimensional elemental tomography for high-resolution elemental mapping. We show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each of which contains, on average, 10(6) zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. The discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes

  11. The Pseudomonas community in metal-contaminated sediments as revealed by quantitative PCR: a link with metal bioavailability.

    Science.gov (United States)

    Roosa, Stéphanie; Wauven, Corinne Vander; Billon, Gabriel; Matthijs, Sandra; Wattiez, Ruddy; Gillan, David C

    2014-10-01

    Pseudomonas bacteria are ubiquitous Gram-negative and aerobic microorganisms that are known to harbor metal resistance mechanisms such as efflux pumps and intracellular redox enzymes. Specific Pseudomonas bacteria have been quantified in some metal-contaminated environments, but the entire Pseudomonas population has been poorly investigated under these conditions, and the link with metal bioavailability was not previously examined. In the present study, quantitative PCR and cell cultivation were used to monitor and characterize the Pseudomonas population at 4 different sediment sites contaminated with various levels of metals. At the same time, total metals and metal bioavailability (as estimated using an HCl 1 m extraction) were measured. It was found that the total level of Pseudomonas, as determined by qPCR using two different genes (oprI and the 16S rRNA gene), was positively and significantly correlated with total and HCl-extractable Cu, Co, Ni, Pb and Zn, with high correlation coefficients (>0.8). Metal-contaminated sediments featured isolates of the Pseudomonas putida, Pseudomonas fluorescens, Pseudomonas lutea and Pseudomonas aeruginosa groups, with other bacterial genera such as Mycobacterium, Klebsiella and Methylobacterium. It is concluded that Pseudomonas bacteria do proliferate in metal-contaminated sediments, but are still part of a complex community. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  12. SAFER, an Analysis Method of Quantitative Proteomic Data, Reveals New Interactors of the C. elegans Autophagic Protein LGG-1.

    Science.gov (United States)

    Yi, Zhou; Manil-Ségalen, Marion; Sago, Laila; Glatigny, Annie; Redeker, Virginie; Legouis, Renaud; Mucchielli-Giorgi, Marie-Hélène

    2016-05-06

    Affinity purifications followed by mass spectrometric analysis are used to identify protein-protein interactions. Because quantitative proteomic data are noisy, it is necessary to develop statistical methods to eliminate false-positives and identify true partners. We present here a novel approach for filtering false interactors, named "SAFER" for mass Spectrometry data Analysis by Filtering of Experimental Replicates, which is based on the reproducibility of the replicates and the fold-change of the protein intensities between bait and control. To identify regulators or targets of autophagy, we characterized the interactors of LGG1, a ubiquitin-like protein involved in autophagosome formation in C. elegans. LGG-1 partners were purified by affinity, analyzed by nanoLC-MS/MS mass spectrometry, and quantified by a label-free proteomic approach based on the mass spectrometric signal intensity of peptide precursor ions. Because the selection of confident interactions depends on the method used for statistical analysis, we compared SAFER with several statistical tests and different scoring algorithms on this set of data. We show that SAFER recovers high-confidence interactors that have been ignored by the other methods and identified new candidates involved in the autophagy process. We further validated our method on a public data set and conclude that SAFER notably improves the identification of protein interactors.

  13. Quantitative mass spectrometry analysis reveals similar substrate consensus motif for human Mps1 kinase and Plk1.

    Directory of Open Access Journals (Sweden)

    Zhen Dou

    Full Text Available BACKGROUND: Members of the Mps1 kinase family play an essential and evolutionarily conserved role in the spindle assembly checkpoint (SAC, a surveillance mechanism that ensures accurate chromosome segregation during mitosis. Human Mps1 (hMps1 is highly phosphorylated during mitosis and many phosphorylation sites have been identified. However, the upstream kinases responsible for these phosphorylations are not presently known. METHODOLOGY/PRINCIPAL FINDINGS: Here, we identify 29 in vivo phosphorylation sites in hMps1. While in vivo analyses indicate that Aurora B and hMps1 activity are required for mitotic hyper-phosphorylation of hMps1, in vitro kinase assays show that Cdk1, MAPK, Plk1 and hMps1 itself can directly phosphorylate hMps1. Although Aurora B poorly phosphorylates hMps1 in vitro, it positively regulates the localization of Mps1 to kinetochores in vivo. Most importantly, quantitative mass spectrometry analysis demonstrates that at least 12 sites within hMps1 can be attributed to autophosphorylation. Remarkably, these hMps1 autophosphorylation sites closely resemble the consensus motif of Plk1, demonstrating that these two mitotic kinases share a similar substrate consensus. CONCLUSIONS/SIGNIFICANCE: hMps1 kinase is regulated by Aurora B kinase and its autophosphorylation. Analysis on hMps1 autophosphorylation sites demonstrates that hMps1 has a substrate preference similar to Plk1 kinase.

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

    Science.gov (United States)

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

    2017-08-01

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

  15. Quantitative FLIM-FRET Microscopy to Monitor Nanoscale Chromatin Compaction In Vivo Reveals Structural Roles of Condensin Complexes

    Directory of Open Access Journals (Sweden)

    David Llères

    2017-02-01

    Full Text Available How metazoan genomes are structured at the nanoscale in living cells and tissues remains unknown. Here, we adapted a quantitative FRET (Förster resonance energy transfer-based fluorescence lifetime imaging microscopy (FLIM approach to assay nanoscale chromatin compaction in living organisms. Caenorhabditis elegans was chosen as a model system. By measuring FRET between histone-tagged fluorescent proteins, we visualized distinct chromosomal regions and quantified the different levels of nanoscale compaction in meiotic cells. Using RNAi and repetitive extrachromosomal array approaches, we defined the heterochromatin state and showed that its architecture presents a nanoscale-compacted organization controlled by Heterochromatin Protein-1 (HP1 and SETDB1 H3-lysine-9 methyltransferase homologs in vivo. Next, we functionally explored condensin complexes. We found that condensin I and condensin II are essential for heterochromatin compaction and that condensin I additionally controls lowly compacted regions. Our data show that, in living animals, nanoscale chromatin compaction is controlled not only by histone modifiers and readers but also by condensin complexes.

  16. Transcriptome analysis of tobacco BY-2 cells elicited by cryptogein reveals new potential actors of calcium-dependent and calcium-independent plant defense pathways.

    Science.gov (United States)

    Amelot, Nicolas; Dorlhac de Borne, François; San Clemente, Hélène; Mazars, Christian; Grima-Pettenati, Jacqueline; Brière, Christian

    2012-02-01

    Cryptogein is a proteinaceous elicitor secreted by the oomycete Phytophthora cryptogea, which induces a hypersensitive response in tobacco plants. We have previously reported that in tobacco BY-2 cells treated with cryptogein, most of the genes of the phenylpropanoid pathway were upregulated and cell wall-bound phenolics accumulated. Both events were Ca(2+) dependent. In this study, we designed a microarray covering a large proportion of the tobacco genome and monitored gene expression in cryptogein-elicited BY-2 cells to get a more complete view of the transcriptome changes and to assess their Ca(2+) dependence. The predominant functional gene categories affected by cryptogein included stress- and disease-related proteins, phenylpropanoid pathway, signaling components, transcription factors and cell wall reinforcement. Among the 3819 unigenes whose expression changed more than fourfold, 90% were Ca(2+) dependent, as determined by their sensitivity to lanthanum chloride. The most Ca(2+)-dependent transcripts upregulated by cryptogein were involved in defense responses or the oxylipin pathway. This genome-wide study strongly supports the importance of Ca(2+)-dependent transcriptional regulation of regulatory and defense-related genes contributing to cryptogein responses in tobacco. Copyright © 2011 Elsevier Ltd. All rights reserved.

  17. Quantitative proteomic analysis of cabernet sauvignon grape cells exposed to thermal stresses reveals alterations in sugar and phenylpropanoid metabolism.

    Science.gov (United States)

    George, Iniga S; Pascovici, Dana; Mirzaei, Mehdi; Haynes, Paul A

    2015-09-01

    Grapes (Vitis vinifera) are a valuable fruit crop and wine production is a major industry. Global warming and expanded range of cultivation will expose grapes to more temperature stresses in future. Our study investigated protein level responses to abiotic stresses, with particular reference to proteomic changes induced by the impact of four different temperature stress regimes, including both hot and cold temperatures, on cultured grape cells. Cabernet Sauvignon cell suspension cultures grown at 26°C were subjected to 14 h of exposure to 34 and 42°C for heat stress, and 18 and 10°C for cold stress. Cells from the five temperatures were harvested in biological triplicates and label-free quantitative shotgun proteomic analysis was performed. A total of 2042 non-redundant proteins were identified from the five temperature points. Fifty-five proteins were only detected in extreme heat stress conditions (42°C) and 53 proteins were only detected at extreme cold stress conditions (10°C). Gene Ontology (GO) annotations of differentially expressed proteins provided insights into the metabolic pathways that are involved in temperature stress in grape cells. Sugar metabolism displayed switching between alternative and classical pathways during temperature stresses. Additionally, nine proteins involved in the phenylpropanoid pathway were greatly increased in abundance at extreme cold stress, and were thus found to be cold-responsive proteins. All MS data have been deposited in the ProteomeXchange with identifier PXD000977 (http://proteomecentral.proteomexchange.org/dataset/PXD000977). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Quantitative Proteomic Analysis Reveals that Antioxidation Mechanisms Contribute to Cold Tolerance in Plantain (Musa paradisiaca L.; ABB Group) Seedlings*

    Science.gov (United States)

    Yang, Qiao-Song; Wu, Jun-Hua; Li, Chun-Yu; Wei, Yue-Rong; Sheng, Ou; Hu, Chun-Hua; Kuang, Rui-Bin; Huang, Yong-Hong; Peng, Xin-Xiang; McCardle, James A.; Chen, Wei; Yang, Yong; Rose, Jocelyn K. C.; Zhang, Sheng; Yi, Gan-Jun

    2012-01-01

    Banana and its close relative, plantain are globally important crops and there is considerable interest in optimizing their cultivation. Plantain has superior cold tolerance compared with banana and a thorough understanding of the molecular mechanisms and responses of plantain to cold stress has great potential value for developing cold tolerant banana cultivars. In this study, we used iTRAQ-based comparative proteomic analysis to investigate the temporal responses of plantain to cold stress. Plantain seedlings were exposed for 0, 6, and 24 h of cold stress at 8 °C and subsequently allowed to recover for 24 h at 28 °C. A total of 3477 plantain proteins were identified, of which 809 showed differential expression from the three treatments. The majority of differentially expressed proteins were predicted to be involved in oxidation-reduction, including oxylipin biosynthesis, whereas others were associated with photosynthesis, photorespiration, and several primary metabolic processes, such as carbohydrate metabolic process and fatty acid beta-oxidation. Western blot analysis and enzyme activity assays were performed on seven differentially expressed, cold-response candidate plantain proteins to validate the proteomics data. Similar analyses of the seven candidate proteins were performed in cold-sensitive banana to examine possible functional conservation, and to compare the results to equivalent responses between the two species. Consistent results were achieved by Western blot and enzyme activity assays, demonstrating that the quantitative proteomics data collected in this study are reliable. Our results suggest that an increase of antioxidant capacity through adapted ROS scavenging capability, reduced production of ROS, and decreased lipid peroxidation contribute to molecular mechanisms for the increased cold tolerance in plantain. To the best of our knowledge, this is the first report of a global investigation on molecular responses of plantain to cold stress by

  19. Quantitative proteomic analysis reveals that antioxidation mechanisms contribute to cold tolerance in plantain (Musa paradisiaca L.; ABB Group) seedlings.

    Science.gov (United States)

    Yang, Qiao-Song; Wu, Jun-Hua; Li, Chun-Yu; Wei, Yue-Rong; Sheng, Ou; Hu, Chun-Hua; Kuang, Rui-Bin; Huang, Yong-Hong; Peng, Xin-Xiang; McCardle, James A; Chen, Wei; Yang, Yong; Rose, Jocelyn K C; Zhang, Sheng; Yi, Gan-Jun

    2012-12-01

    Banana and its close relative, plantain are globally important crops and there is considerable interest in optimizing their cultivation. Plantain has superior cold tolerance compared with banana and a thorough understanding of the molecular mechanisms and responses of plantain to cold stress has great potential value for developing cold tolerant banana cultivars. In this study, we used iTRAQ-based comparative proteomic analysis to investigate the temporal responses of plantain to cold stress. Plantain seedlings were exposed for 0, 6, and 24 h of cold stress at 8 °C and subsequently allowed to recover for 24 h at 28 °C. A total of 3477 plantain proteins were identified, of which 809 showed differential expression from the three treatments. The majority of differentially expressed proteins were predicted to be involved in oxidation-reduction, including oxylipin biosynthesis, whereas others were associated with photosynthesis, photorespiration, and several primary metabolic processes, such as carbohydrate metabolic process and fatty acid beta-oxidation. Western blot analysis and enzyme activity assays were performed on seven differentially expressed, cold-response candidate plantain proteins to validate the proteomics data. Similar analyses of the seven candidate proteins were performed in cold-sensitive banana to examine possible functional conservation, and to compare the results to equivalent responses between the two species. Consistent results were achieved by Western blot and enzyme activity assays, demonstrating that the quantitative proteomics data collected in this study are reliable. Our results suggest that an increase of antioxidant capacity through adapted ROS scavenging capability, reduced production of ROS, and decreased lipid peroxidation contribute to molecular mechanisms for the increased cold tolerance in plantain. To the best of our knowledge, this is the first report of a global investigation on molecular responses of plantain to cold stress by

  20. Quantitative Proteomics Reveals Dynamic Interactions of the Minichromosome Maintenance Complex (MCM) in the Cellular Response to Etoposide Induced DNA Damage.

    Science.gov (United States)

    Drissi, Romain; Dubois, Marie-Line; Douziech, Mélanie; Boisvert, François-Michel

    2015-07-01

    The minichromosome maintenance complex (MCM) proteins are required for processive DNA replication and are a target of S-phase checkpoints. The eukaryotic MCM complex consists of six proteins (MCM2-7) that form a heterohexameric ring with DNA helicase activity, which is loaded on chromatin to form the pre-replication complex. Upon entry in S phase, the helicase is activated and opens the DNA duplex to recruit DNA polymerases at the replication fork. The MCM complex thus plays a crucial role during DNA replication, but recent work suggests that MCM proteins could also be involved in DNA repair. Here, we employed a combination of stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomics with immunoprecipitation of green fluorescent protein-tagged fusion proteins to identify proteins interacting with the MCM complex, and quantify changes in interactions in response to DNA damage. Interestingly, the MCM complex showed very dynamic changes in interaction with proteins such as Importin7, the histone chaperone ASF1, and the Chromodomain helicase DNA binding protein 3 (CHD3) following DNA damage. These changes in interactions were accompanied by an increase in phosphorylation and ubiquitination on specific sites on the MCM proteins and an increase in the co-localization of the MCM complex with γ-H2AX, confirming the recruitment of these proteins to sites of DNA damage. In summary, our data indicate that the MCM proteins is involved in chromatin remodeling in response to DNA damage. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. Asynchrony of the early maturation of white matter bundles in healthy infants: Quantitative landmarks revealed noninvasively by diffusion tensor imaging

    International Nuclear Information System (INIS)

    Dubois, J.; Perrin, M.; Mangin, J.F.; Cointepas, Y.; Duchesnay, E.; Le Bihan, D.; Hertz-Pannier, L.; Dehaene-Lambertz, G.; Dubois, J.; Dehaene-Lambertz, G.; Perrin, M.; Mangin, J.F.; Cointepas, Y.; Duchesnay, E.; Le Bihan, D.; Hertz-Pannier, L.

    2008-01-01

    Normal cognitive development in infants follows a well-known temporal sequence, which is assumed to be correlated with the structural maturation of underlying functional networks. Postmortem studies and, more recently, structural MR imaging studies have described qualitatively the heterogeneous spatio-temporal progression of white matter myelination. However, in vivo quantification of the maturation phases of fiber bundles is still lacking. We used noninvasive diffusion tensor MR imaging and tractography in twenty-three 1-4-month-old healthy infants to quantify the early maturation of the main cerebral fascicles. A specific maturation model, based on the respective roles of different maturational processes on the diffusion phenomena, was designed to highlight asynchronous maturation across bundles by evaluating the time-course of mean diffusivity and anisotropy changes over the considered developmental period. Using an original approach, a progression of maturation in four relative stages was determined in each tract by estimating the maturation state and speed, from the diffusion indices over the infants group compared with an adults group on one hand, and in each tract compared with the average over bundles on the other hand. Results were coherent with, and extended previous findings in 8 of 11 bundles, showing the anterior limb of the internal capsule and cingulum as the most immature, followed by the optic radiations, arcuate and inferior longitudinal fascicles, then the spino-thalamic tract and fornix, and finally the cortico-spinal tract as the most mature bundle. Thus, this approach provides new quantitative landmarks for further noninvasive research on brain-behavior relationships during normal and abnormal development. (authors)

  2. Quantitative proteomics reveals divergent responses in Apis mellifera worker and drone pupae to parasitization by Varroa destructor.

    Science.gov (United States)

    Surlis, Carla; Carolan, James C; Coffey, Mary; Kavanagh, Kevin

    Varroa destructor is a haemophagous ectoparasite of honeybees and is considered a major causal agent of colony losses in Europe and North America. Although originating in Eastern Asia where it parasitizes Apis cerana, it has shifted hosts to the western honeybee Apis mellifera on which it has a greater deleterious effect on the individual and colony level. To investigate this important host-parasite interaction and to determine whether Varroa causes different effects on different castes we conducted a label free quantitative proteomic analysis of Varroa-parasitized and non-parasitized drone and worker Apis mellifera pupae. 1195 proteins were identified in total, of which 202 and 250 were differentially abundant in parasitized drone and worker pupae, respectively. Both parasitized drone and worker pupae displayed reduced abundance in proteins associated with the cuticle, lipid transport and innate immunity. Proteins involved in metabolic processes were more abundant in both parasitized castes although the response in workers was more pronounced. A number of caste specific responses were observed including differential abundance of numerous cytoskeletal and muscle proteins, which were of higher abundance in parasitized drones in comparison to parasitized workers. Proteins involved in fatty acid and carbohydrate metabolism were more abundant in parasitized workers as were a large number of ribosomal proteins highlighting either potentially divergent responses to Varroa or a different strategy by the mite when parasitizing the different castes. This data improves our understanding of this interaction and may provide a basis for future studies into improvements to therapy and control of Varroasis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Quantitative PCR analysis reveals a high incidence of large intragenic deletions in the FANCA gene in Spanish Fanconi anemia patients.

    Science.gov (United States)

    Callén, E; Tischkowitz, M D; Creus, A; Marcos, R; Bueren, J A; Casado, J A; Mathew, C G; Surrallés, J

    2004-01-01

    Fanconi anaemia is an autosomal recessive disease characterized by chromosome fragility, multiple congenital abnormalities, progressive bone marrow failure and a high predisposition to develop malignancies. Most of the Fanconi anaemia patients belong to complementation group FA-A due to mutations in the FANCA gene. This gene contains 43 exons along a 4.3-kb coding sequence with a very heterogeneous mutational spectrum that makes the mutation screening of FANCA a difficult task. In addition, as the FANCA gene is rich in Alu sequences, it was reported that Alu-mediated recombination led to large intragenic deletions that cannot be detected in heterozygous state by conventional PCR, SSCP analysis, or DNA sequencing. To overcome this problem, a method based on quantitative fluorescent multiplex PCR was proposed to detect intragenic deletions in FANCA involving the most frequently deleted exons (exons 5, 11, 17, 21 and 31). Here we apply the proposed method to detect intragenic deletions in 25 Spanish FA-A patients previously assigned to complementation group FA-A by FANCA cDNA retroviral transduction. A total of eight heterozygous deletions involving from one to more than 26 exons were detected. Thus, one third of the patients carried a large intragenic deletion that would have not been detected by conventional methods. These results are in agreement with previously published data and indicate that large intragenic deletions are one of the most frequent mutations leading to Fanconi anaemia. Consequently, this technology should be applied in future studies on FANCA to improve the mutation detection rate. Copyright 2003 S. Karger AG, Basel

  4. Quantitative N-linked Glycoproteomics of Myocardial Ischemia and Reperfusion Injury Reveals Early Remodeling in the Extracellular Environment

    DEFF Research Database (Denmark)

    Parker, Benjamin L; Palmisano, Giuseppe; Edwards, Alistair V G

    2011-01-01

    , while dimethyl labeling confirmed 46 of these and revealed an additional 62 significant changes. These were mainly from predicted extracellular matrix and basement membrane proteins that are implicated in cardiac remodeling. Analysis of N-glycans released from myocardial proteins suggest...... that the observed changes were not due to significant alterations in N-glycan structures. Altered proteins included the collagen-laminin-integrin complexes and collagen assembly enzymes, cadherins, mast cell proteases, proliferation-associated secreted protein acidic and rich in cysteine, and microfibril......Extracellular and cell surface proteins are generally modified with N-linked glycans and glycopeptide enrichment is an attractive tool to analyze these proteins. The role of N-linked glycoproteins in cardiovascular disease, particularly ischemia and reperfusion injury, is poorly understood...

  5. Quantitative analysis of DNA methylation at all human imprinted regions reveals preservation of epigenetic stability in adult somatic tissue

    Directory of Open Access Journals (Sweden)

    Woodfine Kathryn

    2011-01-01

    Full Text Available Abstract Background Genes subject to genomic imprinting are mono-allelically expressed in a parent-of-origin dependent manner. Each imprinted locus has at least one differentially methylated region (DMR which has allele specific DNA methylation and contributes to imprinted gene expression. Once DMRs are established, they are potentially able to withstand normal genome reprogramming events that occur during cell differentiation and germ-line DMRs are stably maintained throughout development. These DMRs, in addition to being either maternally or paternally methylated, have differences in whether methylation was acquired in the germ-line or post fertilization and are present in a variety of genomic locations with different Cytosine-phosphate guanine (CpG densities and CTCF binding capacities. We therefore examined the stability of maintenance of DNA methylation imprints and determined the normal baseline DNA methylation levels in several adult tissues for all imprinted genes. In order to do this, we first developed and validated 50 highly specific, quantitative DNA methylation pyrosequencing assays for the known DMRs associated with human imprinted genes. Results Remarkable stability of the DNA methylation imprint was observed in all germ-line DMRs and paternally methylated somatic DMRs (which maintained average methylation levels of between 35% - 65% in all somatic tissues, independent of gene expression. Maternally methylated somatic DMRs were found to have more variation with tissue specific methylation patterns. Most DMRs, however, showed some intra-individual variability for DNA methylation levels in peripheral blood, suggesting that more than one DMR needs to be examined in order to get an overall impression of the epigenetic stability in a tissue. The plasticity of DNA methylation at imprinted genes was examined in a panel of normal and cancer cell lines. All cell lines showed changes in DNA methylation, especially at the paternal germ

  6. A quantitative multiplex nuclease protection assay reveals immunotoxicity gene expression profiles in the rabbit model for vaginal drug safety evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Fichorova, Raina N., E-mail: rfichorova@rics.bwh.harvard.edu [Laboratory of Genital Tract Biology, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women' s Hospital and Harvard Medical School, Boston, MA (United States); Mendonca, Kevin; Yamamoto, Hidemi S.; Murray, Ryan [Laboratory of Genital Tract Biology, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women' s Hospital and Harvard Medical School, Boston, MA (United States); Chandra, Neelima; Doncel, Gustavo F. [CONRAD, Department of Obstetrics and Gynecology, Eastern Virginia Medical School, Norfolk, VA (United States)

    2015-06-15

    Any vaginal product that alters the mucosal environment and impairs the immune barrier increases the risk of sexually transmitted infections, especially HIV infection, which thrives on mucosal damage and inflammation. The FDA-recommended rabbit vaginal irritation (RVI) model serves as a first line selection tool for vaginal products; however, for decades it has been limited to histopathology scoring, insufficient to select safe anti-HIV microbicides. In this study we incorporate to the RVI model a novel quantitative nuclease protection assay (qNPA) to quantify mRNA levels of 25 genes representing leukocyte differentiation markers, toll-like receptors (TLR), cytokines, chemokines, epithelial repair, microbicidal and vascular markers, by designing two multiplex arrays. Tissue sections were obtained from 36 rabbits (6 per treatment arm) after 14 daily applications of a placebo gel, saline, 4% nonoxynol-9 (N-9), and three combinations of the anti-HIV microbicides tenofovir (TFV) and UC781 in escalating concentrations (highest: 10% TFV + 2.5%UC781). Results showed that increased expression levels of toll-like receptor (TLR)-4, interleukin (IL)-1β, CXCL8, epithelial membrane protein (EMP)-1 (P < 0.05), and decreased levels of TLR2 (P < 0.05), TLR3 and bactericidal permeability increasing protein (BPI) (P < 0.001) were associated with cervicovaginal mucosal alteration (histopathology). Seven markers showed a significant linear trend predicting epithelial damage (up with CD4, IL-1β, CXCL8, CCL2, CCL21, EMP1 and down with BPI). Despite the low tissue damage RVI scores, the high-dose microbicide combination gel caused activation of HIV host cells (SLC and CD4) while N-9 caused proinflammatory gene upregulation (IL-8 and TLR4) suggesting a potential for increasing risk of HIV via different mechanisms depending on the chemical nature of the test product. - Highlights: • A transcriptome nuclease protection assay assessed microbicides for vaginal safety. • Biomarkers were

  7. A quantitative multiplex nuclease protection assay reveals immunotoxicity gene expression profiles in the rabbit model for vaginal drug safety evaluation

    International Nuclear Information System (INIS)

    Fichorova, Raina N.; Mendonca, Kevin; Yamamoto, Hidemi S.; Murray, Ryan; Chandra, Neelima; Doncel, Gustavo F.

    2015-01-01

    Any vaginal product that alters the mucosal environment and impairs the immune barrier increases the risk of sexually transmitted infections, especially HIV infection, which thrives on mucosal damage and inflammation. The FDA-recommended rabbit vaginal irritation (RVI) model serves as a first line selection tool for vaginal products; however, for decades it has been limited to histopathology scoring, insufficient to select safe anti-HIV microbicides. In this study we incorporate to the RVI model a novel quantitative nuclease protection assay (qNPA) to quantify mRNA levels of 25 genes representing leukocyte differentiation markers, toll-like receptors (TLR), cytokines, chemokines, epithelial repair, microbicidal and vascular markers, by designing two multiplex arrays. Tissue sections were obtained from 36 rabbits (6 per treatment arm) after 14 daily applications of a placebo gel, saline, 4% nonoxynol-9 (N-9), and three combinations of the anti-HIV microbicides tenofovir (TFV) and UC781 in escalating concentrations (highest: 10% TFV + 2.5%UC781). Results showed that increased expression levels of toll-like receptor (TLR)-4, interleukin (IL)-1β, CXCL8, epithelial membrane protein (EMP)-1 (P < 0.05), and decreased levels of TLR2 (P < 0.05), TLR3 and bactericidal permeability increasing protein (BPI) (P < 0.001) were associated with cervicovaginal mucosal alteration (histopathology). Seven markers showed a significant linear trend predicting epithelial damage (up with CD4, IL-1β, CXCL8, CCL2, CCL21, EMP1 and down with BPI). Despite the low tissue damage RVI scores, the high-dose microbicide combination gel caused activation of HIV host cells (SLC and CD4) while N-9 caused proinflammatory gene upregulation (IL-8 and TLR4) suggesting a potential for increasing risk of HIV via different mechanisms depending on the chemical nature of the test product. - Highlights: • A transcriptome nuclease protection assay assessed microbicides for vaginal safety. • Biomarkers were

  8. Quantitative proteomics revealed partial fungistatic mechanism of ammonia against conidial germination of nematode-trapping fungus Arthrobotrys oligospora ATCC24927.

    Science.gov (United States)

    Liu, Tong; Tian, Dong-Wei; Zou, Li-Juan; Liu, Fang-Yu; Can, Qi-Yan; Yang, Jin-Kui; Xu, Jian-Ping; Huang, Xiao-Wei; Xi, Jia-Qin; Zhu, Ming-Liang; Mo, Ming-He; Zhang, Ke-Qin

    2018-05-01

    Ammonia is one of the fungistatic factors in soil that can suppress conidial germination, but the molecular mechanism underlying the suppression is unknown. In this study, the proteomes of fungistatic conidia, fresh conidia and germinated conidia of Arthrobotrys oligospora ATCC24927 were determined and quantified. The protein expression profile of fungistatic conidia was significantly different from those in the other two conditions. 281 proteins were down expressed in fungistatic conidia and characterized by GO annotation. Gene transcription analysis and inhibition of puromycin (a protein translation inhibitor) on conidial germination suggested that down expression of 33 protein translation related proteins might well result in repression of protein synthesis and inhibition of conidial germination. In addition, 16 down-expressed proteins were mapped to the Ras/mitogen-activated protein (Ras/MAP) regulatory networks which regulate conidial DNA synthesis. The conidial DNA synthesis was found to be definitely inhibited under by ammonia, and function studies of two Ras/MAP proteins by using knock-out strains provided partial evidence that Ras/MAP pathway regulate the conidial germination. These results suggested that down-expression of Ras/MAP related proteins might result in inhibition of DNA synthesis and finally result in inhibition conidial germination. This study revealed partial fungistatic mechanism of ammonia against conidial germination. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level.

    Science.gov (United States)

    Smati, Mounira; Clermont, Olivier; Bleibtreu, Alexandre; Fourreau, Frédéric; David, Anthony; Daubié, Anne-Sophie; Hignard, Cécile; Loison, Odile; Picard, Bertrand; Denamur, Erick

    2015-08-01

    The primary habitat of the Escherichia coli species is the gut of warm-blooded vertebrates. The E. coli species is structured into four main phylogenetic groups A, B1, B2, and D. We estimated the relative proportions of these phylogroups in the feces of 137 wild and domesticated animals with various diets living in the Ile de France (Paris) region by real-time PCR. We distinguished three main clusters characterized by a particular abundance of two or more phylogroups within the E. coli animal commensal populations, which we called "enterocolitypes" by analogy with the enterotypes defined in the human gut microbiota at the genus level. These enterocolitypes were characterized by a dominant (>50%) B2, B1, or A phylogroup and were associated with different host species, diets, and habitats: wild and herbivorous species (wild rabbits and deer), domesticated herbivorous species (domesticated rabbits, horses, sheep, and cows), and omnivorous species (boar, pigs, and chickens), respectively. By analyzing retrospectively the data obtained using the same approach from 98 healthy humans living in Ile de France (Smati et al. 2013, Appl. Environ. Microbiol. 79, 5005-5012), we identified a specific human enterocolitype characterized by the dominant and/or exclusive (>90%) presence of phylogroup B2. We then compared B2 strains isolated from animals and humans, and revealed that human and animal strains differ regarding O-type and B2 subgroup. Moreover, two genes, sfa/foc and clbQ, were associated with the exclusive character of strains, observed only in humans. In conclusion, a complex network of interactions exists at several levels (genus and intra-species) within the intestinal microbiota. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  10. Planetary Defense

    Science.gov (United States)

    2016-05-01

    4 Abstract Planetary defense against asteroids should be a major concern for every government in the world . Millions of asteroids and...helps make Planetary Defense viable because defending the Earth against asteroids benefits from all the above technologies. So if our planet security...information about their physical characteristics so we can employ the right strategies. It is a crucial difference if asteroids are made up of metal

  11. The Chemistry of Plant–Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance

    Science.gov (United States)

    Mhlongo, Msizi I.; Piater, Lizelle A.; Madala, Ntakadzeni E.; Labuschagne, Nico; Dubery, Ian A.

    2018-01-01

    Plant roots communicate with microbes in a sophisticated manner through chemical communication within the rhizosphere, thereby leading to biofilm formation of beneficial microbes and, in the case of plant growth-promoting rhizomicrobes/-bacteria (PGPR), resulting in priming of defense, or induced resistance in the plant host. The knowledge of plant–plant and plant–microbe interactions have been greatly extended over recent years; however, the chemical communication leading to priming is far from being well understood. Furthermore, linkage between below- and above-ground plant physiological processes adds to the complexity. In metabolomics studies, the main aim is to profile and annotate all exo- and endo-metabolites in a biological system that drive and participate in physiological processes. Recent advances in this field has enabled researchers to analyze 100s of compounds in one sample over a short time period. Here, from a metabolomics viewpoint, we review the interactions within the rhizosphere and subsequent above-ground ‘signalomics’, and emphasize the contributions that mass spectrometric-based metabolomic approaches can bring to the study of plant-beneficial – and priming events. PMID:29479360

  12. Involvement of the US Department of Defense in Civilian Assistance, Part I: a quantitative description of the projects funded by the Overseas Humanitarian, Disaster, and Civic Aid Program.

    Science.gov (United States)

    Bourdeaux, Margaret Ellis; Lawry, Lynn; Bonventre, Eugene V; Burkle, Frederick M

    2010-03-01

    To review the history and goals of the US Department of Defense's largest civilian assistance program, the Overseas Humanitarian, Disaster and Civic Aid Program and to describe the number, geographic regions, years, key words, countries, and types of projects carried out under this program since 2001. Using the program's central database, we reviewed all approved projects since 2001 and tabulated them by year, combatant command, country, and key word. We also reviewed the project descriptions of projects funded between January 1, 2006, and February 9, 2008, and examined how their activities varied by combatant command and year. Of the 5395 projects in the database, 2097 were funded. Projects took place in more than 90 countries, with Southern, Pacific, and Africa Command hosting the greatest number. The most common types of projects were school, health, disaster response, and water infrastructure construction, and disaster-response training. The "global war on terror" was the key word most frequently tagged to project descriptions. Project descriptions lacked stated goals as well as implementation and coordination strategies with potential partners, and did not report outcome or impact indicators. The geographic reach of the program is vast and projects take place in a wide variety of public sectors. Yet their security and civilian assistance value remains unclear given the lack of stated project goals, implementation strategies, or measures of effectiveness. To facilitate transparency and policy discussion, we recommend project proposals include hypotheses as to how they will enhance US security, their relevance to the public sector they address, and outcome and impact indicators that can assess their value and effectiveness.

  13. Comparing quantitative analysis on revealed comparative advantages of aquatic products trade of china and ASEAN based on 21st century maritime silk road

    Science.gov (United States)

    Luo, X. F.; Han, Y. H.; Li, Z. W.

    2017-11-01

    As the world’s leading aquaculture, aquatic production and trading country, China’s development of aquatic products trade with ASEAN is facing a historic opportunity in the favourable circumstances of construction of the 21st century Maritime Silk Road. In order to make guidance of the product selection and transformation for corresponding export enterprises, this article makes a quantitative analysis the Revealed Comparative Advantage of aquatic products trade from China and ASEAN respectively based on the HS classification and thoroughly compares the RCA indices. The comparison results show that the international competitiveness of aquatic products structures of China and ASEAN are quite different with few overlaps of strong competitive products, and there is a great gap between the two areas in many kinds of products.

  14. Defense Business Board

    Science.gov (United States)

    Skip to main content (Press Enter). Toggle navigation Defense Business Board Search Search Defense Business Board: Search Search Defense Business Board: Search Defense Business Board Business Excellence in Defense of the Nation Defense Business Board Home Charter Members Meetings Studies Contact Us The Defense

  15. Sequence and Expression Analysis of Interferon Regulatory Factor 10 (IRF10 in Three Diverse Teleost Fish Reveals Its Role in Antiviral Defense.

    Directory of Open Access Journals (Sweden)

    Qiaoqing Xu

    Full Text Available Interferon regulatory factor (IRF 10 was first found in birds and is present in the genome of other tetrapods (but not humans and mice, as well as in teleost fish. The functional role of IRF10 in vertebrate immunity is relatively unknown compared to IRF1-9. The target of this research was to clone and characterize the IRF10 genes in three economically important fish species that will facilitate future evaluation of this molecule in fish innate and adaptive immunity.In the present study, a single IRF10 gene was cloned in grass carp Ctenopharyngodon idella and Asian swamp eel Monopterus albus, and two, named IRF10a and IRF10b, in rainbow trout Oncorhynchus mykiss. The fish IRF10 molecules share highest identities to other vertebrate IRF10s, and have a well conserved DNA binding domain, IRF-associated domain, and an 8 exon/7 intron structure with conserved intron phase. The presence of an upstream ATG or open reading frame (ORF in the 5'-untranslated region of different fish IRF10 cDNA sequences suggests potential regulation at the translational level, and this has been verified by in vitro transcription/translation experiments of the trout IRF10a cDNA, but would still need to be validated in fish cells.Both trout IRF10 paralogues are highly expressed in thymus, blood and spleen but are relatively low in head kidney and caudal kidney. Trout IRF10b expression is significantly higher than IRF10a in integumentary tissues i.e. gills, scales, skin, intestine, adipose fin and tail fins, suggesting that IRF10b may be more important in mucosal immunity. The expression of both trout IRF10 paralogues is up-regulated by recombinant IFN-γ. The expression of the IRF10 genes is highly induced by Poly I:C in vitro and in vivo, and by viral infection, but is less responsive to peptidoglycan and bacterial infection, suggesting an important role of fish IRF10 in antiviral defense.

  16. Quantitative proteomics reveals altered expression of extracellular matrix related proteins of human primary dermal fibroblasts in response to sulfated hyaluronan and collagen applied as artificial extracellular matrix.

    Science.gov (United States)

    Müller, Stephan A; van der Smissen, Anja; von Feilitzsch, Margarete; Anderegg, Ulf; Kalkhof, Stefan; von Bergen, Martin

    2012-12-01

    Fibroblasts are the main matrix producing cells of the dermis and are also strongly regulated by their matrix environment which can be used to improve and guide skin wound healing processes. Here, we systematically investigated the molecular effects on primary dermal fibroblasts in response to high-sulfated hyaluronan [HA] (hsHA) by quantitative proteomics. The comparison of non- and high-sulfated HA revealed regulation of 84 of more than 1,200 quantified proteins. Based on gene enrichment we found that sulfation of HA alters extracellular matrix remodeling. The collagen degrading enzymes cathepsin K, matrix metalloproteinases-2 and -14 were found to be down-regulated on hsHA. Additionally protein expression of thrombospondin-1, decorin, collagen types I and XII were reduced, whereas the expression of trophoblast glycoprotein and collagen type VI were slightly increased. This study demonstrates that global proteomics provides a valuable tool for revealing proteins involved in molecular effects of growth substrates for further material optimization.

  17. Quantitative Proteomics Analysis Reveals Novel Insights into Mechanisms of Action of Long Noncoding RNA Hox Transcript Antisense Intergenic RNA (HOTAIR) in HeLa Cells*

    Science.gov (United States)

    Zheng, Peng; Xiong, Qian; Wu, Ying; Chen, Ying; Chen, Zhuo; Fleming, Joy; Gao, Ding; Bi, Lijun; Ge, Feng

    2015-01-01

    Long noncoding RNAs (lncRNAs), which have emerged in recent years as a new and crucial layer of gene regulators, regulate various biological processes such as carcinogenesis and metastasis. HOTAIR (Hox transcript antisense intergenic RNA), a lncRNA overexpressed in most human cancers, has been shown to be an oncogenic lncRNA. Here, we explored the role of HOTAIR in HeLa cells and searched for proteins regulated by HOTAIR. To understand the mechanism of action of HOTAIR from a systems perspective, we employed a quantitative proteomic strategy to systematically identify potential targets of HOTAIR. The expression of 170 proteins was significantly dys-regulated after inhibition of HOTAIR, implying that they could be potential targets of HOTAIR. Analysis of this data at the systems level revealed major changes in proteins involved in diverse cellular components, including the cytoskeleton and the respiratory chain. Further functional studies on vimentin (VIM), a key protein involved in the cytoskeleton, revealed that HOTAIR exerts its effects on migration and invasion of HeLa cells, at least in part, through the regulation of VIM expression. Inhibition of HOTAIR leads to mitochondrial dysfunction and ultrastructural alterations, suggesting a novel role of HOTAIR in maintaining mitochondrial function in cancer cells. Our results provide novel insights into the mechanisms underlying the function of HOTAIR in cancer cells. We expect that the methods used in this study will become an integral part of functional studies of lncRNAs. PMID:25762744

  18. Trade Costs, Conflicts, and Defense Spending

    OpenAIRE

    Seitz, Michael; Tarasov, Alexander; Zakharenko, Roman

    2013-01-01

    This paper develops a quantitative model of trade, military conflicts, and defense spending. Trade liberalization between two countries reduces probability of an armed conflict between them, causing both to cut defense spending. This in turn causes a domino effect on defense spending by other countries. As a result, both countries and the rest of the world are better off. We estimate the model using data on trade, conflicts, and military spending. We find that, after reduction of costs of tra...

  19. High-resolution mapping of a fruit firmness-related quantitative trait locus in tomato reveals epistatic interactions associated with a complex combinatorial locus.

    Science.gov (United States)

    Chapman, Natalie H; Bonnet, Julien; Grivet, Laurent; Lynn, James; Graham, Neil; Smith, Rebecca; Sun, Guiping; Walley, Peter G; Poole, Mervin; Causse, Mathilde; King, Graham J; Baxter, Charles; Seymour, Graham B

    2012-08-01

    Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir(s.p.)QTL2.1 to Fir(s.p.)QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir(s.p.)QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir(s.p.)QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.

  20. Clusters of Insomnia Disorder: An Exploratory Cluster Analysis of Objective Sleep Parameters Reveals Differences in Neurocognitive Functioning, Quantitative EEG, and Heart Rate Variability

    Science.gov (United States)

    Miller, Christopher B.; Bartlett, Delwyn J.; Mullins, Anna E.; Dodds, Kirsty L.; Gordon, Christopher J.; Kyle, Simon D.; Kim, Jong Won; D'Rozario, Angela L.; Lee, Rico S.C.; Comas, Maria; Marshall, Nathaniel S.; Yee, Brendon J.; Espie, Colin A.; Grunstein, Ronald R.

    2016-01-01

    Study Objectives: To empirically derive and evaluate potential clusters of Insomnia Disorder through cluster analysis from polysomnography (PSG). We hypothesized that clusters would differ on neurocognitive performance, sleep-onset measures of quantitative (q)-EEG and heart rate variability (HRV). Methods: Research volunteers with Insomnia Disorder (DSM-5) completed a neurocognitive assessment and overnight PSG measures of total sleep time (TST), wake time after sleep onset (WASO), and sleep onset latency (SOL) were used to determine clusters. Results: From 96 volunteers with Insomnia Disorder, cluster analysis derived at least two clusters from objective sleep parameters: Insomnia with normal objective sleep duration (I-NSD: n = 53) and Insomnia with short sleep duration (I-SSD: n = 43). At sleep onset, differences in HRV between I-NSD and I-SSD clusters suggest attenuated parasympathetic activity in I-SSD (P insomnia clusters derived from cluster analysis differ in sleep onset HRV. Preliminary data suggest evidence for three clusters in insomnia with differences for sustained attention and sleep-onset q-EEG. Clinical Trial Registration: Insomnia 100 sleep study: Australia New Zealand Clinical Trials Registry (ANZCTR) identification number 12612000049875. URL: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=347742. Citation: Miller CB, Bartlett DJ, Mullins AE, Dodds KL, Gordon CJ, Kyle SD, Kim JW, D'Rozario AL, Lee RS, Comas M, Marshall NS, Yee BJ, Espie CA, Grunstein RR. Clusters of Insomnia Disorder: an exploratory cluster analysis of objective sleep parameters reveals differences in neurocognitive functioning, quantitative EEG, and heart rate variability. SLEEP 2016;39(11):1993–2004. PMID:27568796

  1. SWATH label-free proteomics analyses revealed the roles of oxidative stress and antioxidant defensing system in sclerotia formation of Polyporus umbellatus

    Science.gov (United States)

    Li, Bing; Tian, Xiaofang; Wang, Chunlan; Zeng, Xu; Xing, Yongmei; Ling, Hong; Yin, Wanqiang; Tian, Lixia; Meng, Zhixia; Zhang, Jihui; Guo, Shunxing

    2017-01-01

    Understanding the initiation and maturing mechanisms is important for rational manipulating sclerotia differentiation and growth from hypha of Polyporus umbellatus. Proteomes in P. umbellatus sclerotia and hyphae at initial, developmental and mature phases were studied. 1391 proteins were identified by nano-liquid chromatograph-mass spectrometry (LC-MS) in Data Dependant Acquisition mode, and 1234 proteins were quantified successfully by Sequential Window Acquisition of all THeoretical fragment ion spectra-MS (SWATH-MS) technology. There were 347 differentially expressed proteins (DEPs) in sclerotia at initial phase compared with those in hypha, and the DEP profiles were dynamically changing with sclerotia growth. Oxidative stress (OS) in sclerotia at initial phase was indicated by the repressed proteins of respiratory chain, tricarboxylic acid cycle and the activation of glycolysis/gluconeogenesis pathways were determined based on DEPs. The impact of glycolysis/gluconeogenesis on sclerotium induction was further verified by glycerol addition assays, in which 5% glycerol significantly increased sclerotial differentiation rate and biomass. It can be speculated that OS played essential roles in triggering sclerotia differentiation from hypha of P. umbellatus, whereas antioxidant activity associated with glycolysis is critical for sclerotia growth. These findings reveal a mechanism for sclerotial differentiation in P. umbellatus, which may also be applicable for other fungi.

  2. Chemical Genomic Screening of a Saccharomyces cerevisiae Genomewide Mutant Collection Reveals Genes Required for Defense against Four Antimicrobial Peptides Derived from Proteins Found in Human Saliva

    Science.gov (United States)

    Bhatt, Sanjay; Schoenly, Nathan E.; Lee, Anna Y.; Nislow, Corey; Bobek, Libuse A.

    2013-01-01

    To compare the effects of four antimicrobial peptides (MUC7 12-mer, histatin 12-mer, cathelicidin KR20, and a peptide containing lactoferricin amino acids 1 to 11) on the yeast Saccharomyces cerevisiae, we employed a genomewide fitness screen of combined collections of mutants with homozygous deletions of nonessential genes and heterozygous deletions of essential genes. When an arbitrary fitness score cutoffs of 1 (indicating a fitness defect, or hypersensitivity) and −1 (indicating a fitness gain, or resistance) was used, 425 of the 5,902 mutants tested exhibited altered fitness when treated with at least one peptide. Functional analysis of the 425 strains revealed enrichment among the identified deletions in gene groups associated with the Gene Ontology (GO) terms “ribosomal subunit,” “ribosome biogenesis,” “protein glycosylation,” “vacuolar transport,” “Golgi vesicle transport,” “negative regulation of transcription,” and others. Fitness profiles of all four tested peptides were highly similar, particularly among mutant strains exhibiting the greatest fitness defects. The latter group included deletions in several genes involved in induction of the RIM101 signaling pathway, including several components of the ESCRT sorting machinery. The RIM101 signaling regulates response of yeasts to alkaline and neutral pH and high salts, and our data indicate that this pathway also plays a prominent role in regulating protective measures against all four tested peptides. In summary, the results of the chemical genomic screens of S. cerevisiae mutant collection suggest that the four antimicrobial peptides, despite their differences in structure and physical properties, share many interactions with S. cerevisiae cells and consequently a high degree of similarity between their modes of action. PMID:23208710

  3. Transcriptomic and Proteomic Profiling Revealed High Proportions of Odorant Binding and Antimicrobial Defense Proteins in Olfactory Tissues of the House Mouse

    Directory of Open Access Journals (Sweden)

    Barbora Kuntová

    2018-02-01

    Full Text Available Mammalian olfaction depends on chemosensory neurons of the main olfactory epithelia (MOE, and/or of the accessory olfactory epithelia in the vomeronasal organ (VNO. Thus, we have generated the VNO and MOE transcriptomes and the nasal cavity proteome of the house mouse, Mus musculus musculus. Both transcriptomes had low levels of sexual dimorphisms, while the soluble proteome of the nasal cavity revealed high levels of sexual dimorphism similar to that previously reported in tears and saliva. Due to low levels of sexual dimorphism in the olfactory receptors in MOE and VNO, the sex-specific sensing seems less likely to be dependent on receptor repertoires. However, olfaction may also depend on a continuous removal of background compounds from the sites of detection. Odorant binding proteins (OBPs are thought to be involved in this process and in our study Obp transcripts were most expressed along other lipocalins (e.g., Lcn13, Lcn14 and antimicrobial proteins. At the level of proteome, OBPs were highly abundant with only few being sexually dimorphic. We have, however, detected the major urinary proteins MUP4 and MUP5 in males and females and the male-biased central/group-B MUPs that were thought to be abundant mainly in the urine. The exocrine gland-secreted peptides ESP1 and ESP22 were male-biased but not male-specific in the nose. For the first time, we demonstrate that the expression of nasal lipocalins correlates with antimicrobial proteins thus suggesting that their individual variation may be linked to evolvable mechanisms that regulate natural microbiota and pathogens that regularly enter the body along the ‘eyes-nose-oral cavity’ axis.

  4. Quantitative imaging reveals heterogeneous growth dynamics and treatment-dependent residual tumor distributions in a three-dimensional ovarian cancer model

    Science.gov (United States)

    Celli, Jonathan P.; Rizvi, Imran; Evans, Conor L.; Abu-Yousif, Adnan O.; Hasan, Tayyaba

    2010-09-01

    Three-dimensional tumor models have emerged as valuable in vitro research tools, though the power of such systems as quantitative reporters of tumor growth and treatment response has not been adequately explored. We introduce an approach combining a 3-D model of disseminated ovarian cancer with high-throughput processing of image data for quantification of growth characteristics and cytotoxic response. We developed custom MATLAB routines to analyze longitudinally acquired dark-field microscopy images containing thousands of 3-D nodules. These data reveal a reproducible bimodal log-normal size distribution. Growth behavior is driven by migration and assembly, causing an exponential decay in spatial density concomitant with increasing mean size. At day 10, cultures are treated with either carboplatin or photodynamic therapy (PDT). We quantify size-dependent cytotoxic response for each treatment on a nodule by nodule basis using automated segmentation combined with ratiometric batch-processing of calcein and ethidium bromide fluorescence intensity data (indicating live and dead cells, respectively). Both treatments reduce viability, though carboplatin leaves micronodules largely structurally intact with a size distribution similar to untreated cultures. In contrast, PDT treatment disrupts micronodular structure, causing punctate regions of toxicity, shifting the distribution toward smaller sizes, and potentially increasing vulnerability to subsequent chemotherapeutic treatment.

  5. Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression.

    Science.gov (United States)

    Megger, Dominik A; Philipp, Jos; Le-Trilling, Vu Thuy Khanh; Sitek, Barbara; Trilling, Mirko

    2017-01-01

    Interferons (IFNs) are pleotropic cytokines secreted upon encounter of pathogens and tumors. Applying their antipathogenic, antiproliferative, and immune stimulatory capacities, recombinant IFNs are frequently prescribed as drugs to treat different diseases. IFNs act by changing the gene expression profile of cells. Due to characteristics such as rapid gene induction and signaling, IFNs also represent prototypical model systems for various aspects of biomedical research (e.g., signal transduction). In regard to the signaling and activated promoters, IFNs can be subdivided into two groups. Here, alterations of the cellular proteome of human cells treated with IFNα and IFNγ were elucidated in a time-resolved manner by quantitative proteome analysis. The majority of protein regulations were strongly IFN type and time dependent. In addition to the expected upregulation of IFN-responsive proteins, an astonishing number of proteins became profoundly repressed especially by IFNγ. Thus, our comprehensive analysis revealed important insights into the human IFN-regulated proteome and its dynamics of protein induction and repression. Interestingly, the new class of IFN-repressed genes comprises known host factors for highly relevant pathogens such as HIV, dengue virus, and hepatitis C virus.

  6. Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression

    Directory of Open Access Journals (Sweden)

    Dominik A. Megger

    2017-09-01

    Full Text Available Interferons (IFNs are pleotropic cytokines secreted upon encounter of pathogens and tumors. Applying their antipathogenic, antiproliferative, and immune stimulatory capacities, recombinant IFNs are frequently prescribed as drugs to treat different diseases. IFNs act by changing the gene expression profile of cells. Due to characteristics such as rapid gene induction and signaling, IFNs also represent prototypical model systems for various aspects of biomedical research (e.g., signal transduction. In regard to the signaling and activated promoters, IFNs can be subdivided into two groups. Here, alterations of the cellular proteome of human cells treated with IFNα and IFNγ were elucidated in a time-resolved manner by quantitative proteome analysis. The majority of protein regulations were strongly IFN type and time dependent. In addition to the expected upregulation of IFN-responsive proteins, an astonishing number of proteins became profoundly repressed especially by IFNγ. Thus, our comprehensive analysis revealed important insights into the human IFN-regulated proteome and its dynamics of protein induction and repression. Interestingly, the new class of IFN-repressed genes comprises known host factors for highly relevant pathogens such as HIV, dengue virus, and hepatitis C virus.

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

    Science.gov (United States)

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

    2012-11-02

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

  8. Expression quantitative trait loci and genetic regulatory network analysis reveals that Gabra2 is involved in stress responses in the mouse.

    Science.gov (United States)

    Dai, Jiajuan; Wang, Xusheng; Chen, Ying; Wang, Xiaodong; Zhu, Jun; Lu, Lu

    2009-11-01

    Previous studies have revealed that the subunit alpha 2 (Gabra2) of the gamma-aminobutyric acid receptor plays a critical role in the stress response. However, little is known about the gentetic regulatory network for Gabra2 and the stress response. We combined gene expression microarray analysis and quantitative trait loci (QTL) mapping to characterize the genetic regulatory network for Gabra2 expression in the hippocampus of BXD recombinant inbred (RI) mice. Our analysis found that the expression level of Gabra2 exhibited much variation in the hippocampus across the BXD RI strains and between the parental strains, C57BL/6J, and DBA/2J. Expression QTL (eQTL) mapping showed three microarray probe sets of Gabra2 to have highly significant linkage likelihood ratio statistic (LRS) scores. Gene co-regulatory network analysis showed that 10 genes, including Gria3, Chka, Drd3, Homer1, Grik2, Odz4, Prkag2, Grm5, Gabrb1, and Nlgn1 are directly or indirectly associated with stress responses. Eleven genes were implicated as Gabra2 downstream genes through mapping joint modulation. The genetical genomics approach demonstrates the importance and the potential power of the eQTL studies in identifying genetic regulatory networks that contribute to complex traits, such as stress responses.

  9. Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition.

    Directory of Open Access Journals (Sweden)

    Thomas Hoffmann

    2015-07-01

    Full Text Available T-cell receptors (TCR play an important role in the adaptive immune system as they recognize pathogen- or cancer-based epitopes and thus initiate the cell-mediated immune response. Therefore there exists a growing interest in the optimization of TCRs for medical purposes like adoptive T-cell therapy. However, the molecular mechanisms behind T-cell signaling are still predominantly unknown. For small sets of TCRs it was observed that the angle between their Vα- and Vβ-domains, which bind the epitope, can vary and might be important for epitope recognition. Here we present a comprehensive, quantitative study of the variation in the Vα/Vβ interdomain-angle and its influence on epitope recognition, performing a systematic bioinformatics analysis based on a representative set of experimental TCR structures. For this purpose we developed a new, cuboid-based superpositioning method, which allows a unique, quantitative analysis of the Vα/Vβ-angles. Angle-based clustering led to six significantly different clusters. Analysis of these clusters revealed the unexpected result that the angle is predominantly influenced by the TCR-clonotype, whereas the bound epitope has only a minor influence. Furthermore we could identify a previously unknown center of rotation (CoR, which is shared by all TCRs. All TCR geometries can be obtained by rotation around this center, rendering it a new, common TCR feature with the potential of improving the accuracy of TCR structure prediction considerably. The importance of Vα/Vβ rotation for signaling was confirmed as we observed larger variances in the Vα/Vβ-angles in unbound TCRs compared to epitope-bound TCRs. Our results strongly support a two-step mechanism for TCR-epitope: First, preformation of a flexible TCR geometry in the unbound state and second, locking of the Vα/Vβ-angle in a TCR-type specific geometry upon epitope-MHC association, the latter being driven by rotation around the unique center of rotation.

  10. Defense Human Resources Activity > PERSEREC

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    Skip to main content (Press Enter). Toggle navigation Defense Human Resources Activity Search Search Defense Human Resources Activity: Search Search Defense Human Resources Activity: Search Defense Human Resources Activity U.S. Department of Defense Defense Human Resources Activity Overview

  11. Role of DNA Repair Factor Xeroderma Pigmentosum Protein Group C in Response to Replication Stress As Revealed by DNA Fragile Site Affinity Chromatography and Quantitative Proteomics.

    Science.gov (United States)

    Beresova, Lucie; Vesela, Eva; Chamrad, Ivo; Voller, Jiri; Yamada, Masayuki; Furst, Tomas; Lenobel, Rene; Chroma, Katarina; Gursky, Jan; Krizova, Katerina; Mistrik, Martin; Bartek, Jiri

    2016-12-02

    Replication stress (RS) fuels genomic instability and cancer development and may contribute to aging, raising the need to identify factors involved in cellular responses to such stress. Here, we present a strategy for identification of factors affecting the maintenance of common fragile sites (CFSs), which are genomic loci that are particularly sensitive to RS and suffer from increased breakage and rearrangements in tumors. A DNA probe designed to match the high flexibility island sequence typical for the commonly expressed CFS (FRA16D) was used as specific DNA affinity bait. Proteins significantly enriched at the FRA16D fragment under normal and replication stress conditions were identified using stable isotope labeling of amino acids in cell culture-based quantitative mass spectrometry. The identified proteins interacting with the FRA16D fragment included some known CFS stabilizers, thereby validating this screening approach. Among the hits from our screen so far not implicated in CFS maintenance, we chose Xeroderma pigmentosum protein group C (XPC) for further characterization. XPC is a key factor in the DNA repair pathway known as global genomic nucleotide excision repair (GG-NER), a mechanism whose several components were enriched at the FRA16D fragment in our screen. Functional experiments revealed defective checkpoint signaling and escape of DNA replication intermediates into mitosis and the next generation of XPC-depleted cells exposed to RS. Overall, our results provide insights into an unexpected biological role of XPC in response to replication stress and document the power of proteomics-based screening strategies to elucidate mechanisms of pathophysiological significance.

  12. Quantitative iTRAQ LC-MS/MS proteomics reveals metabolic responses to biofuel ethanol in cyanobacterial Synechocystis sp. PCC 6803.

    Science.gov (United States)

    Qiao, Jianjun; Wang, Jiangxin; Chen, Lei; Tian, Xiaoxu; Huang, Siqiang; Ren, Xiaoyue; Zhang, Weiwen

    2012-11-02

    Recent progress in metabolic engineering has led to autotrophic production of ethanol in various cyanobacterial hosts. However, cyanobacteria are known to be sensitive to ethanol, which restricts further efforts to increase ethanol production levels in these renewable host systems. To understand the mechanisms of ethanol tolerance so that engineering more robust cyanobacterial hosts can be possible, in this study, the responses of model cyanobacterial Synechocystis sp. PCC 6803 to ethanol were determined using a quantitative proteomics approach with iTRAQ LC-MS/MS technologies. The resulting high-quality proteomic data set consisted of 24,887 unique peptides corresponding to 1509 identified proteins, a coverage of approximately 42% of the predicted proteins in the Synechocystis genome. Using a cutoff of 1.5-fold change and a p-value less than 0.05, 135 and 293 unique proteins with differential abundance levels were identified between control and ethanol-treated samples at 24 and 48 h, respectively. Functional analysis showed that the Synechocystis cells employed a combination of induced common stress response, modifications of cell membrane and envelope, and induction of multiple transporters and cell mobility-related proteins as protection mechanisms against ethanol toxicity. Interestingly, our proteomic analysis revealed that proteins related to multiple aspects of photosynthesis were up-regulated in the ethanol-treated Synechocystis cells, consistent with increased chlorophyll a concentration in the cells upon ethanol exposure. The study provided the first comprehensive view of the complicated molecular mechanisms against ethanol stress and also provided a list of potential gene targets for further engineering ethanol tolerance in Synechocystis PCC 6803.

  13. The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures.

    Science.gov (United States)

    Chung, Oksung; Jin, Seondeok; Cho, Yun Sung; Lim, Jeongheui; Kim, Hyunho; Jho, Sungwoong; Kim, Hak-Min; Jun, JeHoon; Lee, HyeJin; Chon, Alvin; Ko, Junsu; Edwards, Jeremy; Weber, Jessica A; Han, Kyudong; O'Brien, Stephen J; Manica, Andrea; Bhak, Jong; Paek, Woon Kee

    2015-10-21

    The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging. We sequenced the genome of a cinereous vulture, and mapped it to the bald eagle reference genome, a close relative with a divergence time of 18 million years. By comparing the cinereous vulture to other avian genomes, we find positively selected genetic variations in this species associated with respiration, likely linked to their ability of immune defense responses and gastric acid secretion, consistent with their ability to digest carcasses. Comparisons between the Old World and New World vulture groups suggest convergent gene evolution. We assemble the cinereous vulture blood transcriptome from a second individual, and annotate genes. Finally, we infer the demographic history of the cinereous vulture which shows marked fluctuations in effective population size during the late Pleistocene. We present the first genome and transcriptome analyses of the cinereous vulture compared to other avian genomes and transcriptomes, revealing genetic signatures of dietary and environmental adaptations accompanied by possible convergent evolution between the Old World and New World vultures.

  14. Quantitative habitability.

    Science.gov (United States)

    Shock, Everett L; Holland, Melanie E

    2007-12-01

    A framework is proposed for a quantitative approach to studying habitability. Considerations of environmental supply and organismal demand of energy lead to the conclusions that power units are most appropriate and that the units for habitability become watts per organism. Extreme and plush environments are revealed to be on a habitability continuum, and extreme environments can be quantified as those where power supply only barely exceeds demand. Strategies for laboratory and field experiments are outlined that would quantify power supplies, power demands, and habitability. An example involving a comparison of various metabolisms pursued by halophiles is shown to be well on the way to a quantitative habitability analysis.

  15. Home - Defense Technology Security Administration

    Science.gov (United States)

    by @dtsamil Defense Technology Security Administration Mission, Culture, and History Executive Official seal of Defense Technology Security Administration Official seal of Defense Technology Security Administration OFFICE of the SECRETARY of DEFENSE Defense Technology Security Administration

  16. Ballistic missile defense effectiveness

    Science.gov (United States)

    Lewis, George N.

    2017-11-01

    The potential effectiveness of ballistic missile defenses today remains a subject of debate. After a brief discussion of terminal and boost phase defenses, this chapter will focus on long-range midcourse defenses. The problems posed by potential countermeasures to such midcourse defenses are discussed as are the sensor capabilities a defense might have available to attempt to discriminate the actual missile warhead in a countermeasures environment. The role of flight testing in assessing ballistic missile defense effectiveness is discussed. Arguments made about effectiveness by missile defense supporters and critics are summarized.

  17. Optimizing Active Cyber Defense

    OpenAIRE

    Lu, Wenlian; Xu, Shouhuai; Yi, Xinlei

    2016-01-01

    Active cyber defense is one important defensive method for combating cyber attacks. Unlike traditional defensive methods such as firewall-based filtering and anti-malware tools, active cyber defense is based on spreading "white" or "benign" worms to combat against the attackers' malwares (i.e., malicious worms) that also spread over the network. In this paper, we initiate the study of {\\em optimal} active cyber defense in the setting of strategic attackers and/or strategic defenders. Specific...

  18. Quantitative proteomics of fractionated membrane and lumen exosome proteins from isogenic metastatic and nonmetastatic bladder cancer cells reveal differential expression of EMT factors

    DEFF Research Database (Denmark)

    Jeppesen, Dennis Kjølhede; Nawrocki, Arkadiusz; Jensen, Steffen Grann

    2014-01-01

    Cancer cells secrete soluble factors and various extracellular vesicles, including exosomes, into their tissue microenvironment. The secretion of exosomes is speculated to facilitate local invasion and metastatic spread. Here, we used an in vivo metastasis model of human bladder carcinoma cell line...... T24 without metastatic capacity and its two isogenic derivate cell lines SLT4 and FL3, which form metastases in the lungs and liver of mice, respectively. Cultivation in CLAD1000 bioreactors rather than conventional culture flasks resulted in a 13-16-fold increased exosome yield and facilitated...... quantitative proteomics of fractionated exosomes. Exosomes from T24, SLT4, and FL3 cells were partitioned into membrane and luminal fractions and changes in protein abundance related to the gain of metastatic capacity were identified by quantitative iTRAQ- proteomics. We identified several proteins linked...

  19. Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population.

    OpenAIRE

    Timothée Bonnet; Peter Wandeler; Glauco Camenisch; Erik Postma

    2017-01-01

    In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions: Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called ‘stasis paradox’ highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic enviro...

  20. Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population.

    Directory of Open Access Journals (Sweden)

    Timothée Bonnet

    2017-01-01

    Full Text Available In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called "stasis paradox" highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative genetic models are able to provide us with an understanding of the causes and consequences of

  1. Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population

    Science.gov (United States)

    Wandeler, Peter; Camenisch, Glauco

    2017-01-01

    In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called “stasis paradox” highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is

  2. Which is more effective for suppressing an infectious disease: imperfect vaccination or defense against contagion?

    Science.gov (United States)

    Kuga, Kazuki; Tanimoto, Jun

    2018-02-01

    We consider two imperfect ways to protect against an infectious disease such as influenza, namely vaccination giving only partial immunity and a defense against contagion such as wearing a mask. We build up a new analytic framework considering those two cases instead of perfect vaccination, conventionally assumed as a premise, with the assumption of an infinite and well-mixed population. Our framework also considers three different strategy-updating rules based on evolutionary game theory: conventional pairwise comparison with one randomly selected agent, another concept of pairwise comparison referring to a social average, and direct alternative selection not depending on the usual copying concept. We successfully obtain a phase diagram in which vaccination coverage at equilibrium can be compared when assuming the model of either imperfect vaccination or a defense against contagion. The obtained phase diagram reveals that a defense against contagion is marginally inferior to an imperfect vaccination as long as the same coefficient value is used. Highlights - We build a new analytical framework for a vaccination game combined with the susceptible-infected-recovered (SIR) model. - Our model can evaluate imperfect provisions such as vaccination giving only partial immunity and a defense against contagion. - We obtain a phase diagram with which to compare the quantitative effects of partial vaccination and a defense against contagion.

  3. Strategic Defense Initiative Overview

    National Research Council Canada - National Science Library

    1990-01-01

    ... to Third World and other nations. I will then discuss the scope of the SDI effort, the evolving strategic defense system architectures and theater defense, our compliancy with the ABM Treaty, technology spinoffs resulting from SDI...

  4. Quantitative Proteome Analysis Reveals Increased Content of Basement Membrane Proteins in Arteries from Patients with Type 2 Diabetes and Lower Levels among Metformin Users

    DEFF Research Database (Denmark)

    Rørdam Preil, Simone; Kristensen, Lars P; Beck, Hans C

    2015-01-01

    hypothesized that metformin intake influences the protein composition. METHODS AND RESULTS: -We analyzed non-atherosclerotic repair arteries gathered at coronary by-pass operations from 30 patients with type 2 diabetes, as well as from 30 age- and gender-matched non-diabetic individuals. Quantitative proteome......BACKGROUND: -The increased risk of cardiovascular diseases (CVD) in type 2 diabetes has been extensively documented, but the origins of the association remain largely unknown. We sought to determine changes in protein expressions in arterial tissue from patients with type 2 diabetes and moreover...... analysis was done by iTRAQ-labelling and LC-MS/MS analysis on individual arterial samples. The amounts of the basement membrane (BM) components, alpha-1- and alpha-2- type IV collagen, gamma-1- and beta-2-laminin were significantly increased in patients with diabetes. Moreover, the expressions of basement...

  5. Research resource: new and diverse substrates for the insulin receptor isoform a revealed by quantitative proteomics after stimulation with igf-ii or insulin

    DEFF Research Database (Denmark)

    Morcavallo, Alaide; Gaspari, Marco; Pandini, Giuseppe

    2011-01-01

    progression. We hypothesized that IGF-II binding to the IR-A elicits a unique signaling pathway. In order to obtain an unbiased evaluation of IR-A substrates differentially involved after IGF-II and insulin stimulation, we performed quantitative proteomics of IR-A substrates recruited to tyrosine......-phosphorylated protein complexes using stable isotope labeling with amino acids in cell culture in combination with antiphosphotyrosine antibody pull down and mass spectrometry. Using cells expressing only the human IR-A and lacking the IGF-I receptor, we identified 38 IR-A substrates. Only 10 were known IR mediators......, whereas 28 substrates were not previously related to IR signaling. Eleven substrates were recruited by stimulation with both ligands: two equally recruited by IGF-II and insulin, three more strongly recruited by IGF-II, and six more strongly recruited by insulin. Moreover, 14 substrates were recruited...

  6. An anti-phospholipase A2 receptor quantitative immunoassay and epitope analysis in membranous nephropathy reveals different antigenic domains of the receptor.

    Directory of Open Access Journals (Sweden)

    Astrid Behnert

    Full Text Available The phospholipase A2 receptor (PLA2R was recently discovered as a target autoantigen in patients with idiopathic membranous nephropathy (IMN. Published evidence suggests that the autoantibodies directed towards a conformation dependent epitope are currently effectively detected by a cell based assay (CBA utilizing indirect immunofluorescence (IIF on tissue culture cells transfected with the PLA2R cDNA. Limitations of such IIF-CBA assays include observer dependent subjective evaluation of semi-quantitative test results and the protocols are not amenable to high throughput diagnostic testing. We developed a quantitative, observer independent, high throughput capture immunoassay for detecting PLA2R autoantibodies on an addressable laser bead immunoassay (ALBIA platform. Since reactive domains of PLA2R (i.e. epitopes could be used to improve diagnostic tests by using small peptides in various high throughput diagnostic platforms, we identified PLA2R epitopes that bound autoantibodies of IMN patients. These studies confirmed that inter-molecular epitope spreading occurs in IMN but use of the cognate synthetic peptides in immunoassays was unable to conclusively distinguish between IMN patients and normal controls. However, combinations of these peptides were able to effectively absorb anti-PLA2R reactivity in IIF-CBA and an immunoassay that employed a lysate derived from HEK cells tranfected with and overexpressing PLA2R. While we provide evidence of intermolecular epitope spreading, our data indicates that in addition to conformational epitopes, human anti-PLA2R reactivity in a commercially available CBA and an addressable laser bead immunoassay is significantly absorbed by peptides representing epitopes of PLA2R.

  7. Rethinking Defensive Information Warfare

    National Research Council Canada - National Science Library

    French, Geoffrey S

    2004-01-01

    .... This paper examines defensive tactics and strategies from the German defense in depth that emerged from World War I to the American Active Defense that developed in the Cold War and proposes a new mindset for DIW that draws on these operational concepts from military history.

  8. Recognizing Plant Defense Priming

    NARCIS (Netherlands)

    Martinez-Medina, Ainhoa; Flors, Victor; Heil, Martin; Mauch-Mani, Brigitte; Pieterse, Corné M J|info:eu-repo/dai/nl/113115113; Pozo, Maria J; Ton, Jurriaan; van Dam, Nicole M; Conrath, Uwe

    2016-01-01

    Defense priming conditions diverse plant species for the superinduction of defense, often resulting in enhanced pest and disease resistance and abiotic stress tolerance. Here, we propose a guideline that might assist the plant research community in a consistent assessment of defense priming in

  9. Recognizing Plant Defense Priming.

    Science.gov (United States)

    Martinez-Medina, Ainhoa; Flors, Victor; Heil, Martin; Mauch-Mani, Brigitte; Pieterse, Corné M J; Pozo, Maria J; Ton, Jurriaan; van Dam, Nicole M; Conrath, Uwe

    2016-10-01

    Defense priming conditions diverse plant species for the superinduction of defense, often resulting in enhanced pest and disease resistance and abiotic stress tolerance. Here, we propose a guideline that might assist the plant research community in a consistent assessment of defense priming in plants. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Recognizing plant defense priming

    NARCIS (Netherlands)

    Martinez-Medina, A.; Flors, V.; Heil, M.; Mauch-Mani, B.; Pieterse, C.M.J.; Pozo, M.J.; Ton, J.; Van Dam, N.M.; Conrath, U.

    2016-01-01

    Defense priming conditions diverse plant species for the superinduction of defense, often resulting in enhanced pest and disease resistance and abiotic stress tolerance. Here, we propose a guideline that might assist the plant research community in a consistent assessment of defense priming in

  11. Partial activation of SA- and JA-defensive pathways in strawberry upon Colletotrichum acutatum interaction

    Directory of Open Access Journals (Sweden)

    FRANCISCO AMIL-RUIZ

    2016-07-01

    Full Text Available Understanding the nature of pathogen host interaction may help improve strawberry (Fragaria × ananassa cultivars. Plant resistance to pathogenic agents usually operates through a complex network of defense mechanisms mediated by a diverse array of signaling molecules. In strawberry, resistance to a variety of pathogens has been reported to be mostly polygenic and quantitatively inherited, making it difficult to associate molecular markers with disease resistance genes. Colletotrichum acutatum spp. is a major strawberry pathogen, and completely resistant cultivars have not been reported. Moreover, strawberry defense network components and mechanisms remain largely unknown and poorly understood. Assessment of the strawberry response to C. acutatum included a global transcript analysis, and acidic hormones SA and JA measurements were analyzed after challenge with the pathogen. Induction of transcripts corresponding to the SA and JA signaling pathways and key genes controlling major steps within these defense pathways was detected. Accordingly, SA and JA accumulated in strawberry after infection. Contrastingly, induction of several important SA, JA, and oxidative stress-responsive defense genes, including FaPR1-1, FaLOX2, FaJAR1, FaPDF1, and FaGST1, was not detected, which suggests that specific branches in these defense pathways (those leading to FaPR1-2, FaPR2-1, FaPR2-2, FaAOS, FaPR5 and FaPR10 were activated. Our results reveal that specific aspects in SA and JA dependent signaling pathways are activated in strawberry upon interaction with C. acutatum. Certain described defense-associated transcripts related to these two known signaling pathways do not increase in abundance following infection. This finding suggests new insight into a specific putative molecular strategy for defense against this pathogen.

  12. Quantitative trait loci for resistance to stripe rust of wheat revealed using global field nurseries and opportunities for stacking resistance genes.

    Science.gov (United States)

    Bokore, Firdissa E; Cuthbert, Richard D; Knox, Ron E; Randhawa, Harpinder S; Hiebert, Colin W; DePauw, Ron M; Singh, Asheesh K; Singh, Arti; Sharpe, Andrew G; N'Diaye, Amidou; Pozniak, Curtis J; McCartney, Curt; Ruan, Yuefeng; Berraies, Samia; Meyer, Brad; Munro, Catherine; Hay, Andy; Ammar, Karim; Huerta-Espino, Julio; Bhavani, Sridhar

    2017-12-01

    Quantitative trait loci controlling stripe rust resistance were identified in adapted Canadian spring wheat cultivars providing opportunity for breeders to stack loci using marker-assisted breeding. Stripe rust or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss., is a devastating disease of common wheat (Triticum aestivum L.) in many regions of the world. The objectives of this research were to identify and map quantitative trait loci (QTL) associated with stripe rust resistance in adapted Canadian spring wheat cultivars that are effective globally, and investigate opportunities for stacking resistance. Doubled haploid (DH) populations from the crosses Vesper/Lillian, Vesper/Stettler, Carberry/Vesper, Stettler/Red Fife and Carberry/AC Cadillac were phenotyped for stripe rust severity and infection response in field nurseries in Canada (Lethbridge and Swift Current), New Zealand (Lincoln), Mexico (Toluca) and Kenya (Njoro), and genotyped with SNP markers. Six QTL for stripe rust resistance in the population of Vesper/Lillian, five in Vesper/Stettler, seven in Stettler/Red Fife, four in Carberry/Vesper and nine in Carberry/AC Cadillac were identified. Lillian contributed stripe rust resistance QTL on chromosomes 4B, 5A, 6B and 7D, AC Cadillac on 2A, 2B, 3B and 5B, Carberry on 1A, 1B, 4A, 4B, 7A and 7D, Stettler on 1A, 2A, 3D, 4A, 5B and 6A, Red Fife on 2D, 3B and 4B, and Vesper on 1B, 2B and 7A. QTL on 1A, 1B, 2A, 2B, 3B, 4A, 4B, 5B, 7A and 7D were observed in multiple parents. The populations are compelling sources of recombination of many stripe rust resistance QTL for stacking disease resistance. Gene pyramiding should be possible with little chance of linkage drag of detrimental genes as the source parents were mostly adapted cultivars widely grown in Canada.

  13. Quantitative proteomics and network analysis of SSA1 and SSB1 deletion mutants reveals robustness of chaperone HSP70 network in Saccharomyces cerevisiae.

    Science.gov (United States)

    Jarnuczak, Andrew F; Eyers, Claire E; Schwartz, Jean-Marc; Grant, Christopher M; Hubbard, Simon J

    2015-09-01

    Molecular chaperones play an important role in protein homeostasis and the cellular response to stress. In particular, the HSP70 chaperones in yeast mediate a large volume of protein folding through transient associations with their substrates. This chaperone interaction network can be disturbed by various perturbations, such as environmental stress or a gene deletion. Here, we consider deletions of two major chaperone proteins, SSA1 and SSB1, from the chaperone network in Sacchromyces cerevisiae. We employ a SILAC-based approach to examine changes in global and local protein abundance and rationalise our results via network analysis and graph theoretical approaches. Although the deletions result in an overall increase in intracellular protein content, correlated with an increase in cell size, this is not matched by substantial changes in individual protein concentrations. Despite the phenotypic robustness to deletion of these major hub proteins, it cannot be simply explained by the presence of paralogues. Instead, network analysis and a theoretical consideration of folding workload suggest that the robustness to perturbation is a product of the overall network structure. This highlights how quantitative proteomics and systems modelling can be used to rationalise emergent network properties, and how the HSP70 system can accommodate the loss of major hubs. © 2015 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. High abundance of JS-1- and Chloroflexi-related Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR.

    Science.gov (United States)

    Blazejak, Anna; Schippers, Axel

    2010-05-01

    Sequences of members of the bacterial candidate division JS-1 and the classes Anaerolineae and Caldilineae of the phylum Chloroflexi are frequently found in 16S rRNA gene clone libraries obtained from marine sediments. Using a newly designed quantitative, real-time PCR assay, these bacterial groups were jointly quantified in samples from near-surface and deeply buried marine sediments from the Peru margin, the Black Sea, and a forearc basin off the island of Sumatra. In near-surface sediments, sequences of the JS-1 as well as Anaerolineae- and Caldilineae-related Bacteria were quantified with significantly lower 16S rRNA gene copy numbers than the sequences of total Bacteria. In contrast, in deeply buried sediments below approximately 1 m depth, similar quantities of the 16S rRNA gene copies of these specific groups and Bacteria were found. This finding indicates that JS-1 and Anaerolineae- and Caldilineae-related Bacteria might dominate the bacterial community in deeply buried marine sediments and thus seem to play an important ecological role in the deep biosphere.

  15. Quantitative proteomic analysis of paired colorectal cancer and non-tumorigenic tissues reveals signature proteins and perturbed pathways involved in CRC progression and metastasis.

    Science.gov (United States)

    Sethi, Manveen K; Thaysen-Andersen, Morten; Kim, Hoguen; Park, Cheol Keun; Baker, Mark S; Packer, Nicolle H; Paik, Young-Ki; Hancock, William S; Fanayan, Susan

    2015-08-03

    Modern proteomics has proven instrumental in our understanding of the molecular deregulations associated with the development and progression of cancer. Herein, we profile membrane-enriched proteome of tumor and adjacent normal tissues from eight CRC patients using label-free nanoLC-MS/MS-based quantitative proteomics and advanced pathway analysis. Of the 948 identified proteins, 184 proteins were differentially expressed (P1.5) between the tumor and non-tumor tissue (69 up-regulated and 115 down-regulated in tumor tissues). The CRC tumor and non-tumor tissues clustered tightly in separate groups using hierarchical cluster analysis of the differentially expressed proteins, indicating a strong CRC-association of this proteome subset. Specifically, cancer associated proteins such as FN1, TNC, DEFA1, ITGB2, MLEC, CDH17, EZR and pathways including actin cytoskeleton and RhoGDI signaling were deregulated. Stage-specific proteome signatures were identified including up-regulated ribosomal proteins and down-regulated annexin proteins in early stage CRC. Finally, EGFR(+) CRC tissues showed an EGFR-dependent down-regulation of cell adhesion molecules, relative to EGFR(-) tissues. Taken together, this study provides a detailed map of the altered proteome and associated protein pathways in CRC, which enhances our mechanistic understanding of CRC biology and opens avenues for a knowledge-driven search for candidate CRC protein markers. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Quantitative measures of sexual selection reveal no evidence for sex-role reversal in a sea spider with prolonged paternal care.

    Science.gov (United States)

    Barreto, Felipe S; Avise, John C

    2010-10-07

    Taxa in which males alone invest in postzygotic care of offspring are often considered good models for investigating the proffered relationships between sexual selection and mating systems. In the pycnogonid sea spider Pycnogonum stearnsi, males carry large egg masses on their bodies for several weeks, so this species is a plausible candidate for sex-role reversal (greater intensity of sexual selection on females than on males). Here, we couple a microsatellite-based assessment of the mating system in a natural population with formal quantitative measures of genetic fitness to investigate the direction of sexual selection in P. stearnsi. Both sexes proved to be highly polygamous and showed similar standardized variances in reproductive and mating successes. Moreover, the fertility (number of progeny) of males and females appeared to be equally and highly dependent on mate access, as shown by similar Bateman gradients for the two sexes. The absence of sex-role reversal in this population of P. stearnsi is probably attributable to the fact that males are not limited by brooding space but have evolved an ability to carry large numbers of progeny. Body length was not a good predictor of male mating or reproductive success, so the aim of future studies should be to determine what traits are the targets of sexual selection in this species.

  17. Clusters of Insomnia Disorder: An Exploratory Cluster Analysis of Objective Sleep Parameters Reveals Differences in Neurocognitive Functioning, Quantitative EEG, and Heart Rate Variability.

    Science.gov (United States)

    Miller, Christopher B; Bartlett, Delwyn J; Mullins, Anna E; Dodds, Kirsty L; Gordon, Christopher J; Kyle, Simon D; Kim, Jong Won; D'Rozario, Angela L; Lee, Rico S C; Comas, Maria; Marshall, Nathaniel S; Yee, Brendon J; Espie, Colin A; Grunstein, Ronald R

    2016-11-01

    To empirically derive and evaluate potential clusters of Insomnia Disorder through cluster analysis from polysomnography (PSG). We hypothesized that clusters would differ on neurocognitive performance, sleep-onset measures of quantitative ( q )-EEG and heart rate variability (HRV). Research volunteers with Insomnia Disorder (DSM-5) completed a neurocognitive assessment and overnight PSG measures of total sleep time (TST), wake time after sleep onset (WASO), and sleep onset latency (SOL) were used to determine clusters. From 96 volunteers with Insomnia Disorder, cluster analysis derived at least two clusters from objective sleep parameters: Insomnia with normal objective sleep duration (I-NSD: n = 53) and Insomnia with short sleep duration (I-SSD: n = 43). At sleep onset, differences in HRV between I-NSD and I-SSD clusters suggest attenuated parasympathetic activity in I-SSD (P insomnia clusters derived from cluster analysis differ in sleep onset HRV. Preliminary data suggest evidence for three clusters in insomnia with differences for sustained attention and sleep-onset q -EEG. Insomnia 100 sleep study: Australia New Zealand Clinical Trials Registry (ANZCTR) identification number 12612000049875. URL: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=347742. © 2016 Associated Professional Sleep Societies, LLC.

  18. Quantitative Phospho-proteomic Analysis of TNFα/NFκB Signaling Reveals a Role for RIPK1 Phosphorylation in Suppressing Necrotic Cell Death.

    Science.gov (United States)

    Mohideen, Firaz; Paulo, Joao A; Ordureau, Alban; Gygi, Steve P; Harper, J Wade

    2017-07-01

    TNFα is a potent inducer of inflammation due to its ability to promote gene expression, in part via the NFκB pathway. Moreover, in some contexts, TNFα promotes Caspase-dependent apoptosis or RIPK1/RIPK3/MLKL-dependent necrosis. Engagement of the TNF Receptor Signaling Complex (TNF-RSC), which contains multiple kinase activities, promotes phosphorylation of several downstream components, including TAK1, IKKα/IKKβ, IκBα, and NFκB. However, immediate downstream phosphorylation events occurring in response to TNFα signaling are poorly understood at a proteome-wide level. Here we use Tandem Mass Tagging-based proteomics to quantitatively characterize acute TNFα-mediated alterations in the proteome and phosphoproteome with or without inhibition of the cIAP-dependent survival arm of the pathway with a SMAC mimetic. We identify and quantify over 8,000 phosphorylated peptides, among which are numerous known sites in the TNF-RSC, NFκB, and MAP kinase signaling systems, as well as numerous previously unrecognized phosphorylation events. Functional analysis of S320 phosphorylation in RIPK1 demonstrates a role for this event in suppressing its kinase activity, association with CASPASE-8 and FADD proteins, and subsequent necrotic cell death during inflammatory TNFα stimulation. This study provides a resource for further elucidation of TNFα-dependent signaling pathways. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

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

    Directory of Open Access Journals (Sweden)

    Thomas Nebl

    2011-09-01

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

  20. In-vivo nonlinear optical microscopy (NLOM) of epithelial-connective tissue interface (ECTI) reveals quantitative measures of neoplasia in hamster oral mucosa.

    Science.gov (United States)

    Pal, Rahul; Yang, Jinping; Ortiz, Daniel; Qiu, Suimin; Resto, Vicente; McCammon, Susan; Vargas, Gracie

    2015-01-01

    The epithelial-connective tissue interface (ECTI) plays an integral role in epithelial neoplasia, including oral squamous cell carcinoma (OSCC). This interface undergoes significant alterations due to hyperproliferating epithelium that supports the transformation of normal epithelium to precancers and cancer. We present a method based on nonlinear optical microscopy to directly assess the ECTI and quantify dysplastic alterations using a hamster model for oral carcinogenesis. Neoplastic and non-neoplastic normal mucosa were imaged in-vivo by both multiphoton autofluorescence microscopy (MPAM) and second harmonic generation microscopy (SHGM) to obtain cross-sectional reconstructions of the oral epithelium and lamina propria. Imaged sites were biopsied and processed for histopathological grading and measurement of ECTI parameters. An ECTI shape parameter was calculated based on deviation from the linear geometry (ΔLinearity) seen in normal mucosa was measured using MPAM-SHGM and histology. The ECTI was readily visible in MPAM-SHGM and quantitative shape analysis showed ECTI deformation in dysplasia but not in normal mucosa. ΔLinearity was significantly (p tissue with 87.9% sensitivity and 97.6% specificity, while calculations from histology provided 96.4% sensitivity and 85.7% specificity. Among other quantifiable architectural changes, a progressive statistically significant increase in epithelial thickness was seen with increasing grade of dysplasia. MPAM-SHGM provides new noninvasive ways for direct characterization of ECTI which may be used in preclinical studies to investigate the role of this interface in early transformation. Further development of the method may also lead to new diagnostic approaches to differentiate non-neoplastic tissue from precancers and neoplasia, possibly with other cellular and layer based indicators of abnormality.

  1. Quantitative proteomics analysis reveals perturbation of lipid metabolic pathways in the liver of Atlantic cod (Gadus morhua) treated with PCB 153.

    Science.gov (United States)

    Yadetie, Fekadu; Oveland, Eystein; Døskeland, Anne; Berven, Frode; Goksøyr, Anders; Karlsen, Odd André

    2017-04-01

    PCB 153 is one of the most abundant PCB congeners detected in biological samples. It is a persistent compound that is still present in the environment despite the ban on production and use of PCBs in the late 1970s. It has strong tendencies to bioaccumulate and biomagnify in biota, and studies have suggested that it is an endocrine and metabolic disruptor. In order to study mechanisms of toxicity, we exposed Atlantic cod (Gadus morhua) to various doses of PCB 153 (0, 0.5, 2 and 8mg/kg body weight) for two weeks and examined the effects on expression of liver proteins using label-free quantitative proteomics. Label-free liquid chromatography-mass spectrometry analysis of the liver proteome resulted in the quantification of 1272 proteins, of which 78 proteins were differentially regulated in the PCB 153-treated dose groups compared to the control group. Functional enrichment analysis showed that pathways significantly affected are related to lipid metabolism, cytoskeletal remodeling, cell cycle and cell adhesion. Importantly, the main effects appear to be on lipid metabolism, with up-regulation of enzymes in the de novo fatty acid synthesis pathway, consistent with previous transcriptomics results. Increased plasma triglyceride levels were also observed in the PCB 153 treated fish, in agreement with the induction of the lipogenic genes and proteins. The results suggest that PCB 153 perturbs lipid metabolism in the Atlantic cod liver. Elevated levels of lipogenic enzymes and plasma triglycerides further suggest increased synthesis of fatty acids and triglycerides. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Parallel β-sheet vibrational couplings revealed by 2D IR spectroscopy of an isotopically labeled macrocycle: quantitative benchmark for the interpretation of amyloid and protein infrared spectra.

    Science.gov (United States)

    Woys, Ann Marie; Almeida, Aaron M; Wang, Lu; Chiu, Chi-Cheng; McGovern, Michael; de Pablo, Juan J; Skinner, James L; Gellman, Samuel H; Zanni, Martin T

    2012-11-21

    Infrared spectroscopy is playing an important role in the elucidation of amyloid fiber formation, but the coupling models that link spectra to structure are not well tested for parallel β-sheets. Using a synthetic macrocycle that enforces a two stranded parallel β-sheet conformation, we measured the lifetimes and frequency for six combinations of doubly (13)C═(18)O labeled amide I modes using 2D IR spectroscopy. The average vibrational lifetime of the isotope labeled residues was 550 fs. The frequencies of the labels ranged from 1585 to 1595 cm(-1), with the largest frequency shift occurring for in-register amino acids. The 2D IR spectra of the coupled isotope labels were calculated from molecular dynamics simulations of a series of macrocycle structures generated from replica exchange dynamics to fully sample the conformational distribution. The models used to simulate the spectra include through-space coupling, through-bond coupling, and local frequency shifts caused by environment electrostatics and hydrogen bonding. The calculated spectra predict the line widths and frequencies nearly quantitatively. Historically, the characteristic features of β-sheet infrared spectra have been attributed to through-space couplings such as transition dipole coupling. We find that frequency shifts of the local carbonyl groups due to nearest neighbor couplings and environmental factors are more important, while the through-space couplings dictate the spectral intensities. As a result, the characteristic absorption spectra empirically used for decades to assign parallel β-sheet secondary structure arises because of a redistribution of oscillator strength, but the through-space couplings do not themselves dramatically alter the frequency distribution of eigenstates much more than already exists in random coil structures. Moreover, solvent exposed residues have amide I bands with >20 cm(-1) line width. Narrower line widths indicate that the amide I backbone is solvent

  3. Quantitative proteomics of heavy metal exposure in Arabidopsis thaliana reveals alterations in one-carbon metabolism enzymes upon exposure to zinc.

    Science.gov (United States)

    Barkla, Bronwyn J; Vera-Estrella, Rosario; Miranda-Vergara, María Cristina; Pantoja, Omar

    2014-12-05

    Plant zinc (Zn) homeostasis must be tightly regulated as the requirement for this micronutrient necessitates its uptake. However, excessive Zn can lead to toxicity and the plant must respond rapidly and effectively within its capacity to minimize damage. To detect mechanisms that may be important for coping with excess Zn we carried out a quantitative proteomics approach using 2D-DIGE to identify Zn-responsive proteins in microsomal fractions from leaves of 4day, 200μM Zn-treated, Arabidopsis thaliana plants. Of the eight proteins which showed significant changes in abundance in the Zn-treated samples and which met all of the selection criteria following statistical analysis, six were successfully identified by LC-MS/MS with 2 or more unique peptides. Three of the proteins were found to be involved in the one-carbon metabolism pathway; including glycine decarboxylase P protein, serine hydroxymethyltransferase (SHMT) and methionine synthase, all of which showed reduced abundance in the Zn-treated samples. Western blot analysis confirmed the decrease in SHMT, while changes in metal tolerance protein indicated plants were most likely actively sequestering Zn. Interestingly, excess Zn led to increased petiole length, a phenotype which may reflect the reduced levels of methionine, a key product of the one-carbon metabolism pathway. Metal contamination is becoming an increasingly common environmental problem. High levels of zinc can be found in certain soils naturally or as a result of long-term anthropogenic activity which leads to its accumulation; i.e. use of fertilizers or industrial waste. The study of metal tolerant plants, particularly those classified as hyperaccumulators has been driven by the potential use of these plants for bioremediation purposes. However, the effects of heavy metal exposure on sensitive plants and the different cellular processes that are affected have received significantly less attention. We are interested in identifying proteins in A

  4. Quantitative Tyrosine Phosphoproteomics of Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitor-treated Lung Adenocarcinoma Cells Reveals Potential Novel Biomarkers of Therapeutic Response.

    Science.gov (United States)

    Zhang, Xu; Maity, Tapan; Kashyap, Manoj K; Bansal, Mukesh; Venugopalan, Abhilash; Singh, Sahib; Awasthi, Shivangi; Marimuthu, Arivusudar; Charles Jacob, Harrys Kishore; Belkina, Natalya; Pitts, Stephanie; Cultraro, Constance M; Gao, Shaojian; Kirkali, Guldal; Biswas, Romi; Chaerkady, Raghothama; Califano, Andrea; Pandey, Akhilesh; Guha, Udayan

    2017-05-01

    Mutations in the Epidermal growth factor receptor (EGFR) kinase domain, such as the L858R missense mutation and deletions spanning the conserved sequence 747 LREA 750 , are sensitive to tyrosine kinase inhibitors (TKIs). The gatekeeper site residue mutation, T790M accounts for around 60% of acquired resistance to EGFR TKIs. The first generation EGFR TKIs, erlotinib and gefitinib, and the second generation inhibitor, afatinib are FDA approved for initial treatment of EGFR mutated lung adenocarcinoma. The predominant biomarker of EGFR TKI responsiveness is the presence of EGFR TKI-sensitizing mutations. However, 30-40% of patients with EGFR mutations exhibit primary resistance to these TKIs, underscoring the unmet need of identifying additional biomarkers of treatment response. Here, we sought to characterize the dynamics of tyrosine phosphorylation upon EGFR TKI treatment of mutant EGFR-driven human lung adenocarcinoma cell lines with varying sensitivity to EGFR TKIs, erlotinib and afatinib. We employed stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative mass spectrometry to identify and quantify tyrosine phosphorylated peptides. The proportion of tyrosine phosphorylated sites that had reduced phosphorylation upon erlotinib or afatinib treatment correlated with the degree of TKI-sensitivity. Afatinib, an irreversible EGFR TKI, more effectively inhibited tyrosine phosphorylation of a majority of the substrates. The phosphosites with phosphorylation SILAC ratios that correlated with the TKI-sensitivity of the cell lines include sites on kinases, such as EGFR-Y1197 and MAPK7-Y221, and adaptor proteins, such as SHC1-Y349/350, ERRFI1-Y394, GAB1-Y689, STAT5A-Y694, DLG3-Y705, and DAPP1-Y139, suggesting these are potential biomarkers of TKI sensitivity. DAPP1, is a novel target of mutant EGFR signaling and Y-139 is the major site of DAPP1 tyrosine phosphorylation. We also uncovered several off-target effects of these TKIs, such as MST1R-Y1238

  5. A genome-wide association study for equine recurrent airway obstruction in European Warmblood horses reveals a suggestive new quantitative trait locus on chromosome 13.

    Science.gov (United States)

    Schnider, D; Rieder, S; Leeb, T; Gerber, V; Neuditschko, M

    2017-12-01

    Recurrent airway obstruction (RAO), also known as heaves, is an asthma-like respiratory disease. Its development is strongly influenced by environmental risk factors such as sensitization and exposure to moldy hay, straw bedding and stabling indoors. A hereditary component has been documented in previous studies; however, so far no causative genetic variant that influences the risk of developing RAO has been identified. In this study, we revised an existing dataset and selected 384 horses for genotyping on the Affymetrix high-density equine SNP array. We performed an allelic case-control genome-wide association study, which revealed a suggestively significant association on equine chromosome 13 at 32 843 309 bp. This SNP is located in the protein-coding gene TXNDC11, which is possibly involved in the folding process of the multiprotein complexes DUOX1 and DUOX2. In humans, these proteins are known to take part in regulating the production of H 2 O 2 in the respiratory tract epithelium as well as in MUC5AC mucin expression. Therefore, TXNDC11 may be considered a functional candidate gene, and further research is needed to explore its potential role in RAO-affected horses. © 2017 Stichting International Foundation for Animal Genetics.

  6. [Study on psychiatric disorders and defensive process assessed by the "defense style questionnaire" in sterile males SAMPLE consulting in andrology].

    Science.gov (United States)

    Bellone, M; Cottencin, O; Rigot, J M; Goudemand, M

    2005-01-01

    The literature about artificial insemination and the associated psychological, psychiatric and sexual disorders is relatively rich. But the majority of these studies is made in gynaecology, with a feminine approach of the disorder. There are very few works led in andrology. This justified the investigation of new trails in order to understand better the clinical context of the sterile man. We undertake a study about the psychiatric disorders among sterile men and about the defense styles. These are a clinical entity recently introduced in the quantitative psychopathology research. The defense style questionnaire (DSQ) is a psychometric scale used in common practice in order to measure the defense styles. We made this study in order to examine the psychiatric state of a sterile males sample consulting in andrology; to assess the defense style by means of the Bond and al DSQ-88 ; to look into a difference between the defensive process according to their clinical situation of azoospermic males or as the oligoazoospermic males and finally, to reveal a correlation between the psychiatric disorders developed in this sample of sterile males and the defensive process they used. There were 42 people (22 azoospermic males and 20 oligoazoospermic males) aged between 23 and 49 years old in the analysed sample. These have been selected at the surgery of andrology at the RUHC of Lille, depending on their arrival order for 6 months. There was no significant difference between the two groups as far as the age and the education standard are concerned. The selection criteria were medical and somatic. Our sample population were divided into two groups: azoospermia (no spermatozoon found in the semen analysis) and oligoasthenospermia (decrease of the number and the mobility of the spermatozoa and an increase of the percentage of atypical forms). The method first consisted in the DSQ, followed by the analysis of the psychiatric state according to the DSM IV, a hetero questionnaire to

  7. A comparison of two common sample preparation techniques for lipid and fatty acid analysis in three different coral morphotypes reveals quantitative and qualitative differences.

    Science.gov (United States)

    Conlan, Jessica A; Rocker, Melissa M; Francis, David S

    2017-01-01

    Lipids are involved in a host of biochemical and physiological processes in corals. Therefore, changes in lipid composition reflect changes in the ecology, nutrition, and health of corals. As such, accurate lipid extraction, quantification, and identification is critical to obtain comprehensive insight into a coral's condition. However, discrepancies exist in sample preparation methodology globally, and it is currently unknown whether these techniques generate analogous results. This study compared the two most common sample preparation techniques for lipid analysis in corals: (1) tissue isolation by air-spraying and (2) crushing the coral in toto . Samples derived from each preparation technique were subsequently analysed to quantify lipids and their constituent classes and fatty acids in four common, scleractinian coral species representing three distinct morphotypes ( Acropora millepora , Montipora crassotuberculata , Porites cylindrica , and Pocillopora damicornis ). Results revealed substantial amounts of organic material, including lipids, retained in the skeletons of all species following air-spraying, causing a marked underestimation of total lipid concentration using this method. Moreover, lipid class and fatty acid compositions between the denuded skeleton and sprayed tissue were substantially different. In particular, the majority of the total triacylglycerol and total fatty acid concentrations were retained in the skeleton (55-69% and 56-64%, respectively). As such, the isolated, sprayed tissue cannot serve as a reliable proxy for lipid quantification or identification in the coral holobiont. The in toto crushing method is therefore recommended for coral sample preparation prior to lipid analysis to capture the lipid profile of the entire holobiont, permitting accurate diagnoses of coral condition.

  8. A comparison of two common sample preparation techniques for lipid and fatty acid analysis in three different coral morphotypes reveals quantitative and qualitative differences

    Directory of Open Access Journals (Sweden)

    Jessica A. Conlan

    2017-08-01

    Full Text Available Lipids are involved in a host of biochemical and physiological processes in corals. Therefore, changes in lipid composition reflect changes in the ecology, nutrition, and health of corals. As such, accurate lipid extraction, quantification, and identification is critical to obtain comprehensive insight into a coral’s condition. However, discrepancies exist in sample preparation methodology globally, and it is currently unknown whether these techniques generate analogous results. This study compared the two most common sample preparation techniques for lipid analysis in corals: (1 tissue isolation by air-spraying and (2 crushing the coral in toto. Samples derived from each preparation technique were subsequently analysed to quantify lipids and their constituent classes and fatty acids in four common, scleractinian coral species representing three distinct morphotypes (Acropora millepora, Montipora crassotuberculata, Porites cylindrica, and Pocillopora damicornis. Results revealed substantial amounts of organic material, including lipids, retained in the skeletons of all species following air-spraying, causing a marked underestimation of total lipid concentration using this method. Moreover, lipid class and fatty acid compositions between the denuded skeleton and sprayed tissue were substantially different. In particular, the majority of the total triacylglycerol and total fatty acid concentrations were retained in the skeleton (55–69% and 56–64%, respectively. As such, the isolated, sprayed tissue cannot serve as a reliable proxy for lipid quantification or identification in the coral holobiont. The in toto crushing method is therefore recommended for coral sample preparation prior to lipid analysis to capture the lipid profile of the entire holobiont, permitting accurate diagnoses of coral condition.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-09-01

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

  10. Quantitative proteome-level analysis of paulownia witches’ broom disease with methyl methane sulfonate assistance reveals diverse metabolic changes during the infection and recovery processes

    Directory of Open Access Journals (Sweden)

    Zhe Wang

    2017-07-01

    Full Text Available Paulownia witches’ broom (PaWB disease caused by phytoplasma is a fatal disease that leads to considerable economic losses. Although there are a few reports describing studies of PaWB pathogenesis, the molecular mechanisms underlying phytoplasma pathogenicity in Paulownia trees remain uncharacterized. In this study, after building a transcriptome database containing 67,177 sequences, we used isobaric tags for relative and absolute quantification (iTRAQ to quantify and analyze the proteome-level changes among healthy P. fortunei (PF, PaWB-infected P. fortunei (PFI, and PaWB-infected P. fortunei treated with 20 mg L−1 or 60 mg L−1 methyl methane sulfonate (MMS (PFI-20 and PFI-60, respectively. A total of 2,358 proteins were identified. We investigated the proteins profiles in PF vs. PFI (infected process and PFI-20 vs. PFI-60 (recovered process, and further found that many of the MMS-response proteins mapped to “photosynthesis” and “ribosome” pathways. Based on our comparison scheme, 36 PaWB-related proteins were revealed. Among them, 32 proteins were classified into three functional groups: (1 carbohydrate and energy metabolism, (2 protein synthesis and degradation, and (3 stress resistance. We then investigated the PaWB-related proteins involved in the infected and recovered processes, and discovered that carbohydrate and energy metabolism was inhibited, and protein synthesis and degradation decreased, as the plant responded to PaWB. Our observations may be useful for characterizing the proteome-level changes that occur at different stages of PaWB disease. The data generated in this study may serve as a valuable resource for elucidating the pathogenesis of PaWB disease during phytoplasma infection and recovery stages.

  11. Quantitative proteomics reveals new insights into calcium-mediated resistance mechanisms in Aspergillus flavus against the antifungal protein PgAFP in cheese.

    Science.gov (United States)

    Delgado, Josué; Owens, Rebecca A; Doyle, Sean; Núñez, Félix; Asensio, Miguel A

    2017-09-01

    The ability of Aspergillus flavus to produce aflatoxins in dairy products presents a potential hazard. The antifungal protein PgAFP from Penicillium chrysogenum inhibits various foodborne toxigenic fungi, including Aspergillus flavus. However, PgAFP did not inhibit A. flavus growth in cheese, which was related to the associated cation content. CaCl 2 increased A. flavus permeability and prevented PgAFP-mediated inhibition in potato dextrose broth (PDB). PgAFP did not elicit any additional increase in permeability of CaCl 2 -incubated A. flavus. Furthermore, PgAFP did not alter metabolic capability, chitin deposition, or hyphal viability of A. flavus grown with CaCl 2 . Comparative proteomic analysis after PgAFP treatment of A. flavus in calcium-enriched PDB revealed increased abundance of 125 proteins, including oxidative stress-related proteins, as determined by label-free mass spectrometry (MS)-based proteomics. Seventy proteins were found at lower abundance, with most involved in metabolic pathways and biosynthesis of secondary metabolites. These changes do not support the blockage of potential PgAFP receptors in A. flavus by calcium as the main cause of the protective role. A. flavus resistance appears to be mediated by calcineurin, G-protein, and γ-glutamyltranspeptidase that combat oxidative stress and impede apoptosis. These findings could serve to design strategies to improve PgAFP activity against aflatoxigenic moulds in dairy products. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Quantitative aspects and dynamic modelling of glucosinolate metabolism

    DEFF Research Database (Denmark)

    Vik, Daniel

    . This enables comparison of transcript and protein levels across mutants and upon induction. I find that unchallenged plants show good correspondence between protein and transcript, but that treatment with methyljasmonate results in significant differences (chapter 1). Functional genomics are used to study......). The construction a dynamic quantitative model of GLS hydrolysis is described. Simulations reveal potential effects on auxin signalling that could reflect defensive strategies (chapter 4). The results presented grant insights into, not only the dynamics of GLS biosynthesis and hydrolysis, but also the relationship...

  13. Technologies for distributed defense

    Science.gov (United States)

    Seiders, Barbara; Rybka, Anthony

    2002-07-01

    For Americans, the nature of warfare changed on September 11, 2001. Our national security henceforth will require distributed defense. One extreme of distributed defense is represented by fully deployed military troops responding to a threat from a hostile nation state. At the other extreme is a country of 'citizen soldiers', with families and communities securing their common defense through heightened awareness, engagement as good neighbors, and local support of and cooperation with local law enforcement, emergency and health care providers. Technologies - for information exploitation, biological agent detection, health care surveillance, and security - will be critical to ensuring success in distributed defense.

  14. Dynamic defense workshop :

    Energy Technology Data Exchange (ETDEWEB)

    Crosby, Sean Michael; Doak, Justin E.; Haas, Jason Juedes.; Helinski, Ryan; Lamb, Christopher C.

    2013-02-01

    On September 5th and 6th, 2012, the Dynamic Defense Workshop: From Research to Practice brought together researchers from academia, industry, and Sandia with the goals of increasing collaboration between Sandia National Laboratories and external organizations, de ning and un- derstanding dynamic, or moving target, defense concepts and directions, and gaining a greater understanding of the state of the art for dynamic defense. Through the workshop, we broadened and re ned our de nition and understanding, identi ed new approaches to inherent challenges, and de ned principles of dynamic defense. Half of the workshop was devoted to presentations of current state-of-the-art work. Presentation topics included areas such as the failure of current defenses, threats, techniques, goals of dynamic defense, theory, foundations of dynamic defense, future directions and open research questions related to dynamic defense. The remainder of the workshop was discussion, which was broken down into sessions on de ning challenges, applications to host or mobile environments, applications to enterprise network environments, exploring research and operational taxonomies, and determining how to apply scienti c rigor to and investigating the eld of dynamic defense.

  15. PTSD as a criminal defense: a review of case law.

    Science.gov (United States)

    Berger, Omri; McNiel, Dale E; Binder, Renée L

    2012-01-01

    Posttraumatic stress disorder (PTSD) has been offered as a basis for criminal defenses, including insanity, unconsciousness, self-defense, diminished capacity, and sentencing mitigation. Examination of case law (e.g., appellate decisions) involving PTSD reveals that when offered as a criminal defense, PTSD has received mixed treatment in the judicial system. Courts have often recognized testimony about PTSD as scientifically reliable. In addition, PTSD has been recognized by appellate courts in U.S. jurisdictions as a valid basis for insanity, unconsciousness, and self-defense. However, the courts have not always found the presentation of PTSD testimony to be relevant, admissible, or compelling in such cases, particularly when expert testimony failed to show how PTSD met the standard for the given defense. In cases that did not meet the standard for one of the complete defenses, PTSD has been presented as a partial defense or mitigating circumstance, again with mixed success.

  16. Defense response in non-genomic model species: methyl jasmonate exposure reveals the passion fruit leaves' ability to assemble a cocktail of functionally diversified Kunitz-type trypsin inhibitors and recruit two of them against papain.

    Science.gov (United States)

    Botelho-Júnior, Sylvio; Machado, Olga L T; Fernandes, Kátia V S; Lemos, Francisco J A; Perdizio, Viviane A; Oliveira, Antônia E A; Monteiro, Leandro R; Filho, Mauri L; Jacinto, Tânia

    2014-08-01

    Multiplicity of protease inhibitors induced by predators may increase the understanding of a plant's intelligent behavior toward environmental challenges. Information about defense mechanisms of non-genomic model plant passion fruit (Passiflora edulis Sims) in response to predator attack is still limited. Here, via biochemical approaches, we showed its flexibility to build-up a broad repertoire of potent Kunitz-type trypsin inhibitors (KTIs) in response to methyl jasmonate. Seven inhibitors (20-25 kDa) were purified from exposed leaves by chromatographic techniques. Interestingly, the KTIs possessed truncated Kunitz motif in their N-terminus and some of them also presented non-consensus residues. Gelatin-Native-PAGE established multiple isoforms for each inhibitor. Significant differences regarding inhibitors' activity toward trypsin and chymotrypsin were observed, indicating functional polymorphism. Despite its rarity, two of them also inhibited papain, and such bifunctionality suggests a recruiting process onto another mechanistic class of target protease (cysteine-type). All inhibitors acted strongly on midgut proteases from sugarcane borer, Diatraea saccharalis (a lepidopteran insect) while in vivo assays supported their insecticide properties. Moreover, the bifunctional inhibitors displayed activity toward midgut proteases from cowpea weevil, Callosobruchus maculatus (a coleopteran insect). Unexpectedly, all inhibitors were highly effective against midgut proteases from Aedes aegypti a dipteran insect (vector of neglected tropical diseases) opening new avenues for plant-derived PIs for vector control-oriented research. Our results reflect the KTIs' complexities in passion fruit which could be wisely exploited by influencing plant defense conditions. Therefore, the potential of passion fruit as source of bioactive compounds with diversified biotechnological application was strengthened.

  17. Defense Mechanisms: A Bibliography.

    Science.gov (United States)

    Pedrini, D. T.; Pedrini, Bonnie C.

    This bibliography includes studies of defense mechanisms, in general, and studies of multiple mechanisms. Defense mechanisms, briefly and simply defined, are the unconscious ego defendants against unpleasure, threat, or anxiety. Sigmund Freud deserves the clinical credit for studying many mechanisms and introducing them in professional literature.…

  18. Defense Business Transformation

    Science.gov (United States)

    2009-12-01

    Defense Business Transformation by Jacques S. Gansler and William Lucyshyn The Center for Technology and National...REPORT TYPE 3. DATES COVERED 00-00-2009 to 00-00-2009 4. TITLE AND SUBTITLE Defense Business Transformation 5a. CONTRACT NUMBER 5b. GRANT NUMBER...vii Part One: DoD Business Transformation

  19. Unfolding Green Defense

    DEFF Research Database (Denmark)

    Larsen, Kristian Knus

    2015-01-01

    In recent years, many states have developed and implemented green solutions for defense. Building on these initiatives NATO formulated the NATO Green Defence Framework in 2014. The framework provides a broad basis for cooperation within the Alliance on green solutions for defense. This report aims...... to inform and support the further development of green solutions by unfolding how green technologies and green strategies have been developed and used to handle current security challenges. The report, initially, focuses on the security challenges that are being linked to green defense, namely fuel...... consumption in military operations, defense expenditure, energy security, and global climate change. The report then proceeds to introduce the NATO Green Defence Framework before exploring specific current uses of green technologies and green strategies for defense. The report concludes that a number...

  20. Department of Defense perspective

    International Nuclear Information System (INIS)

    Devine, R.

    1985-01-01

    This paper examines radiation instrumentation from the Department of Defense perspective. Radiation survey instruments and calibration, or RADIAC, as it is called in the services, while administratively falling under the Assistant Secretary of Defense for Atomic Energy, has generally been managed at a lower level. The Naval Electronics Systems Command and Army Signal Corp are the two principles in the Department of Defense for RADIAC. The actions of the services are coordinated through the tri-service RADIAC working group, which meets about every year and a half. Several points from this organization are highlighted

  1. The hsp 16 Gene of the Probiotic Lactobacillus acidophilus Is Differently Regulated by Salt, High Temperature and Acidic Stresses, as Revealed by Reverse Transcription Quantitative PCR (qRT-PCR Analysis

    Directory of Open Access Journals (Sweden)

    Daniela Fiocco

    2011-08-01

    Full Text Available Small heat shock proteins (sHsps are ubiquitous conserved chaperone-like proteins involved in cellular proteins protection under stressful conditions. In this study, a reverse transcription quantitative PCR (RT-qPCR procedure was developed and used to quantify the transcript level of a small heat shock gene (shs in the probiotic bacterium Lactobacillus acidophilus NCFM, under stress conditions such as heat (45 °C and 53 °C, bile (0.3% w/v, hyperosmosis (1 M and 2.5 M NaCl, and low pH value (pH 4. The shs gene of L. acidophilus NCFM was induced by salt, high temperature and acidic stress, while repression was observed upon bile stress. Analysis of the 5' noncoding region of the hsp16 gene reveals the presence of an inverted repeat (IR sequence (TTAGCACTC-N9-GAGTGCTAA homologue to the controlling IR of chaperone expression (CIRCE elements found in the upstream regulatory region of Gram-positive heat shock operons, suggesting that the hsp16 gene of L. acidophilus might be transcriptionally controlled by HrcA. In addition, the alignment of several small heat shock proteins identified so far in lactic acid bacteria, reveals that the Hsp16 of L. acidophilus exhibits a strong evolutionary relationship with members of the Lactobacillus acidophilus group.

  2. Analysis of morphine responses in mice reveals a QTL on Chromosome 7 [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Wim E. Crusio

    2016-09-01

    Full Text Available In this study we identified a quantitative trait locus (QTL on mouse Chromosome 7 associated with locomotor activity and rearing post morphine treatment. This QTL was revealed after correcting for the effects of another QTL peak on Chromosome 10 using composite interval mapping. The positional candidate genes are Syt9 and Ppfibp2. Several other genes within the interval are linked to neural processes, locomotor activity, and the defensive response to harmful stimuli.

  3. Analysis of morphine responses in mice reveals a QTL on Chromosome 7 [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Wim E. Crusio

    2016-10-01

    Full Text Available In this study we identified a quantitative trait locus (QTL on mouse Chromosome 7 associated with locomotor activity and rearing post morphine treatment. This QTL was revealed after correcting for the effects of another QTL peak on Chromosome 10 using composite interval mapping. The positional candidate genes are Syt9 and Ppfibp2. Several other genes within the interval are linked to neural processes, locomotor activity, and the defensive response to harmful stimuli.

  4. Cruise Missile Defense

    National Research Council Canada - National Science Library

    Hichkad, Ravi R; Bolkcom, Christopher

    2005-01-01

    Congress has expressed interest in cruise missile defense for years. Cruise missiles (CMs) are essentially unmanned attack aircraft -- vehicles composed of an airframe, propulsion system, guidance system, and weapons payload...

  5. Cruise Missile Defense

    National Research Council Canada - National Science Library

    Hichkad, Ravi R; Bolkcom, Christopher

    2004-01-01

    Congress has expressed interest in cruise missile defense for years. Cruise missiles (CMs) are essentially unmanned attack aircraft -- vehicles composed of an airframe, propulsion system, guidance system, and weapons payload...

  6. Defense Transportation; The Army

    National Research Council Canada - National Science Library

    1998-01-01

    .... The statement of managers in the conference report on the Department of Defense Appropriations Act, 1997, directed us to validate the results and savings achieved from this and any other personal property pilot program...

  7. Infection and cellular defense dynamics in a novel 17β-estradiol murine model of chronic human group B streptococcus genital tract colonization reveal a role for hemolysin in persistence and neutrophil accumulation.

    Science.gov (United States)

    Carey, Alison J; Tan, Chee Keong; Mirza, Shaper; Irving-Rodgers, Helen; Webb, Richard I; Lam, Alfred; Ulett, Glen C

    2014-02-15

    Genital tract carriage of group B streptococcus (GBS) is prevalent among adult women; however, the dynamics of chronic GBS genital tract carriage, including how GBS persists in this immunologically active host niche long term, are not well defined. To our knowledge, in this study, we report the first animal model of chronic GBS genital tract colonization using female mice synchronized into estrus by delivery of 17β-estradiol prior to intravaginal challenge with wild-type GBS 874391. Cervicovaginal swabs, which were used to measure bacterial persistence, showed that GBS colonized the vaginal mucosa of mice at high numbers (10(6)-10(7) CFU/swab) for at least 90 d. Cellular and histological analyses showed that chronic GBS colonization of the murine genital tract caused significant lymphocyte and PMN cell infiltrates, which were localized to the vaginal mucosal surface. Long-term colonization was independent of regular hormone cycling. Immunological analyses of 23 soluble proteins related to chemotaxis and inflammation showed that the host response to GBS in the genital tract comprised markers of innate immune activation including cytokines such as GM-CSF and TNF-α. A nonhemolytic isogenic mutant of GBS 874391, Δcyle9, was impaired for colonization and was associated with amplified local PMN responses. Induction of DNA neutrophil extracellular traps, which was observed in GBS-infected human PMNs in vitro in a hemolysin-dependent manner, appeared to be part of this response. Overall, this study defines key infection dynamics in a novel murine model of chronic GBS genital tract colonization and establishes previously unknown cellular and soluble defense responses to GBS in the female genital tract.

  8. Defense Primer: DOD Contractors

    Science.gov (United States)

    2017-02-10

    functions, from intelligence analysis or software development to landscaping or food service. Why does DOD use individual contractors? Going back to...that provide professional services, from research to management support. The bulk of contractors—more than 70%—provide products, and these include...10 U.S.C. Part IV: Service, Supply, and Procurement. CRS Products CRS In Focus IF10548, Defense Primer: U.S. Defense Industrial Base, by Daniel

  9. Ballistic Missile Defense

    OpenAIRE

    Mayer, Michael

    2011-01-01

    At the 2010 NATO summit in Lisbon, the alliance decided to move forward on the development of a territorial ballistic missile defense (BMD) system and explore avenues for cooperation with Russia in this endeavor. Substantial progress on BMD has been made over the past decade, but some questions remain regarding the ultimate strategic utility of such a system and whether its benefi ts outweigh the possible opportunity costs. Missile defense has been a point of contention between the US and its...

  10. 76 FR 72391 - Defense Logistics Agency Revised Regulation 1000.22, Environmental Considerations in Defense...

    Science.gov (United States)

    2011-11-23

    ... DEPARTMENT OF DEFENSE Office of the Secretary [Docket ID DOD-2011-OS-0055] Defense Logistics Agency Revised Regulation 1000.22, Environmental Considerations in Defense Logistics Agency Actions AGENCY: Defense Logistics Agency, Department of Defense. ACTION: Revised Defense Logistics Agency...

  11. 75 FR 76423 - Defense Intelligence Agency National Defense Intelligence College Board of Visitors Closed Meeting

    Science.gov (United States)

    2010-12-08

    ... DEPARTMENT OF DEFENSE Office of the Secretary Defense Intelligence Agency National Defense Intelligence College Board of Visitors Closed Meeting AGENCY: National Defense Intelligence College, Defense Intelligence Agency, Department of Defense. ACTION: Notice of Closed Meeting. SUMMARY: Pursuant to the...

  12. 76 FR 28960 - Defense Intelligence Agency National Defense Intelligence College Board of Visitors Closed Meeting

    Science.gov (United States)

    2011-05-19

    ... DEPARTMENT OF DEFENSE Office of the Secretary Defense Intelligence Agency National Defense Intelligence College Board of Visitors Closed Meeting AGENCY: National Defense Intelligence College, Defense Intelligence Agency, Department of Defense. ACTION: Notice of Closed Meeting. SUMMARY: Pursuant to the...

  13. Quantitative mass spectrometry of histones H3.2 and H3.3 in Suz12-deficient mouse embryonic stem cells reveals distinct, dynamic post-translational modifications at Lys-27 and Lys-36

    DEFF Research Database (Denmark)

    Jung, Hye Ryung; Pasini, Diego; Helin, Kristian

    2010-01-01

    distinct coexisting modifications. In certain cases, high mass accuracy LTQ-Orbitrap MS/MS allowed precise localization of near isobaric coexisting PTMs such as trimethylation and acetylation within individual peptides. ETD MS/MS facilitated sequencing and annotation of phosphorylated histone peptides....... The combined use of ETD and CID MS/MS increased the total number of identified modified peptides. Comparative quantitative analysis of histones from wild type and Suz12-deficient ESCs using stable isotope labeling with amino acids in cell culture and LC-MS/MS revealed a dramatic reduction of H3K27me2 and H3K27......me3 and an increase of H3K27ac, thereby uncovering an antagonistic methyl/acetyl switch at H3K27. The reduction in H3K27 methylation and increase in H3K27 acetylation was accompanied by H3K36 acetylation and methylation. Estimation of the global isoform percentage of unmodified and modified histone...

  14. COP21: defense stakes

    International Nuclear Information System (INIS)

    Coldefy, Alain; Hulot, Nicolas; Aichi, Leila; Tertrais, Bruno; Paillard, Christophe-Alexandre; Piodi, Jerome; Regnier, Serge; Volpi, Jean-Luc; Descleves, Emmanuel; Garcin, Thierry; Granholm, Niklas; Wedin, Lars; Pouvreau, Ana; Henninger, Laurent

    2015-01-01

    The 21. Conference of the Parties (COP21) from the UN Framework Convention took place in Paris between November 30 and December 11, 2015. The challenge is to reach a universal agreement of fight against global warming and to control the carbon footprint of human activities. This topic is in the core of the Defense Ministry preoccupations. This special dossier takes stock of the question of defense issues linked with global warming. The dossier comprises 13 papers dealing with: 1 - COP21: defense stakes (Coldefy, A.); 2 - Warfare climate, a chance for peace (Hulot, N.); 3 - COP21 and defense (Aichi, L.); 4 - A war climate? (Tertrais, B.); 5 - Challenges the World has to face in the 21. century (Paillard, C.A.); 6 - Desertification: a time bomb in the heart of Sahel (Piodi, J.); 7 - The infrastructure department of defense in the fight against climate disturbance (Regnier, S.); 8 - Fight against global warming, a chance for the forces? (Volpi, J.L.); 9 - Sea and sustainable development (Descleves, E.); 10 - Rationales of Arctic's surrounding powers (Garcin, T.); 11 - Arctic: strategic stake (Granholm, N.; Wedin, L.); 12 - Strategic impact of Turkey's new energy choices (Pouvreau, A.); 13 - Climate and war: a brief historical outlook (Henninger, L.)

  15. Defense waste management plan

    International Nuclear Information System (INIS)

    1983-06-01

    Defense high-level waste (HLW) and defense transuranic (TRU) waste are in interim storage at three sites, namely: at the Savannah River Plant, in South Carolina; at the Hanford Reservation, in Washington; and at the Idaho National Engineering Laboratory, in Idaho. Defense TRU waste is also in interim storage at the Oak Ridge National Laboratory, in Tennessee; at the Los Alamos National Laboratory, in New Mexico; and at the Nevada Test Site, in Nevada. (Figure E-2). This document describes a workable approach for the permanent disposal of high-level and transuranic waste from atomic energy defense activities. The plan does not address the disposal of suspect waste which has been conservatively considered to be high-level or transuranic waste but which can be shown to be low-level waste. This material will be processed and disposed of in accordance with low-level waste practices. The primary goal of this program is to utilize or dispose of high-level and transuranic waste routinely, safely, and effectively. This goal will include the disposal of the backlog of stored defense waste. A Reference Plan for each of the sites describes the sequence of steps leading to permanent disposal. No technological breakthroughs are required to implement the reference plan. Not all final decisions concerning the activities described in this document have been made. These decisions will depend on: completion of the National Environmental Policy Act process, authorization and appropriation of funds, agreements with states as appropriate, and in some cases, the results of pilot plant experiments and operational experience. The major elements of the reference plan for permanent disposal of defense high-level and transuranic waste are summarized

  16. Defensive Federal Litigation

    Science.gov (United States)

    1998-08-20

    requires that all affirmative defenses be pleaded in the answer. The rule lists 19 specific affirmative defenses, such as estoppel , laches, res judicata...Brown, 22 F.3d 516 (2d Cir. 1994); Poole v. Rourke, 779 F. Supp. 1546 (E.D. Cal. 1991). 3-40 potential collateral estoppel .4. effect of the district...the back pay claim, which was over $10,000, to the Court of Claims. The court of appeals found that ൸Collateral estoppel prohibits relitigation of

  17. Defense styles of pedophilic offenders.

    Science.gov (United States)

    Drapeau, Martin; Beretta, Véronique; de Roten, Yves; Koerner, Annett; Despland, Jean-Nicolas

    2008-04-01

    This pilot study investigated the defense styles of pedophile sexual offenders. Interviews with 20 pedophiles and 20 controls were scored using the Defense Mechanisms Rating Scales. Results showed that pedophiles had a significantly lower overall defensive functioning score than the controls. Pedophiles used significantly fewer obsessional-level defenses but more major image-distorting and action-level defenses. Results also suggested differences in the prevalence of individual defenses where pedophiles used more dissociation, displacement, denial, autistic fantasy, splitting of object, projective identification, acting out, and passive aggressive behavior but less intellectualization and rationalization.

  18. Defense mutualisms enhance plant diversification.

    Science.gov (United States)

    Weber, Marjorie G; Agrawal, Anurag A

    2014-11-18

    The ability of plants to form mutualistic relationships with animal defenders has long been suspected to influence their evolutionary success, both by decreasing extinction risk and by increasing opportunity for speciation through an expanded realized niche. Nonetheless, the hypothesis that defense mutualisms consistently enhance plant diversification across lineages has not been well tested due to a lack of phenotypic and phylogenetic information. Using a global analysis, we show that the >100 vascular plant families in which species have evolved extrafloral nectaries (EFNs), sugar-secreting organs that recruit arthropod mutualists, have twofold higher diversification rates than families that lack species with EFNs. Zooming in on six distantly related plant clades, trait-dependent diversification models confirmed the tendency for lineages with EFNs to display increased rates of diversification. These results were consistent across methodological approaches. Inference using reversible-jump Markov chain Monte Carlo (MCMC) to model the placement and number of rate shifts revealed that high net diversification rates in EFN clades were driven by an increased number of positive rate shifts following EFN evolution compared with sister clades, suggesting that EFNs may be indirect facilitators of diversification. Our replicated analysis indicates that defense mutualisms put lineages on a path toward increased diversification rates within and between clades, and is concordant with the hypothesis that mutualistic interactions with animals can have an impact on deep macroevolutionary patterns and enhance plant diversity.

  19. The biocontrol endophytic bacterium Pseudomonas fluorescens PICF7 induces systemic defense responses in aerial tissues upon colonization of olive roots

    Directory of Open Access Journals (Sweden)

    Carmen eGómez-Lama Cabanás

    2014-09-01

    Full Text Available Pseudomonas fluorescens PICF7, a native olive root endophyte and effective biocontrol agent (BCA against Verticillium wilt of olive, is able to trigger a broad range of defense responses in root tissues of this woody plant. In order to elucidate whether strain PICF7 also induces systemic defense responses in above-ground organs, aerial tissues of olive plants grown under non-gnotobiotic conditions were collected at different time points after root bacterization with this endophytic BCA. A suppression subtractive hybridization (SSH cDNA library, enriched in up-regulated genes, was generated. This strategy enabled the identification of 376 ESTs (99 contigs and 277 singlets, many of them related to response to different stresses. Five ESTs, involved in defense responses, were selected to carry out time-course quantitative real-time PCR (qRT-PCR experiments aiming to: (i validate the induction of these genes, and (ii shed light on their expression pattern along time (from 1 to 15 days. Induction of olive genes potentially coding for lypoxigenase 2, catalase, 1-aminocyclopropane-1-carboxylate oxidase and phenylananine ammonia-lyase was thus confirmed at some time points. Computational analysis also revealed that different transcription factors were up-regulated in olive aerial tissues (i.e. jerf, bHLH, WRKYs, as previously reported for roots. Results confirmed that root colonization by this endophytic bacterium does not only trigger defense responses in this organ but also mount a wide array of systemic defense responses in distant tissues (stems, leaves. This sheds light on how olive plants respond to the ‘non-hostile’ colonization by a bacterial endophyte and how induced defense response can contribute to the biocontrol activity of strain PICF7.

  20. Strategic Framework for the Defense Acquisition System Understanding Defense Consolidation

    National Research Council Canada - National Science Library

    Potts, Anthony W

    2007-01-01

    The 1993 policy to promote the consolidation of the United States defense industry began a series of acquisitions and mergers that went beyond the intent of the policy and left the Department of Defense (DoD...

  1. Strategic Framework for the Defense Acquisition System Understanding Defense Consolidation

    National Research Council Canada - National Science Library

    Potts, Anthony W

    2007-01-01

    ...% of defense product sales annually. Defense consolidation has diminished the flexibility required for surge capacity, diminished competitive innovations in products, and reduced competitive pricing based on multiple sources for products...

  2. Defensive Passivity in Adolescence

    Science.gov (United States)

    Rosenheim, Eliyahu; Gaoni, Bracha

    1977-01-01

    There are potentially healthy adolescents who display excessive reluctance to move toward independent decision and action. This research presents a clinical description of this "syndrome", conceptualizes it as a defensive maneuver against mourning over cherished childhood dreams and offers steps for therapeutic intervention. (Editor/RK)

  3. Defense radioactive waste management

    International Nuclear Information System (INIS)

    Hindman, T.B. Jr.

    1988-01-01

    The Office of Defense Programs (DP), U.S. Department of Energy, is responsible for the production of nuclear weapons and materials for national defense. Pursuant to this mission, DP operates a large industrial complex that employs over 60,000 people at various installations across the country. As a byproduct of their activities, these installations generate radioactive, hazardous, or mixed wastes that must be managed in a safe and cost-effective manner in compliance with all applicable Federal and STate environmental requirements. At the Federal level such requirements derive primarily from the Atomic Energy Act, the Resource Conservation and Recovery Act (RCRA), the comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) and the Superfund Amendments and Reauthorization Act (SARA). Responsibility for DP activities in connection with the disposal of defense wastes is consolidated within the Office of Defense Waste and Transportation Management (DWTM). This paper discusses these activities which consist of five principal elements: the environmental restoration of inactive DP facilities and sites, the processing storage and disposal of wastes associated with ongoing operations at active DP facilities, research and development directed toward the long-term disposal of radioactive, hazardous, mixed wastes, technology development directly supporting regulatory compliance, and the development of policies, procedures, and technologies for assuring the safe transportation of radioactive and hazardous materials

  4. Auxins in defense strategies

    Czech Academy of Sciences Publication Activity Database

    Čarná, Mária; Repka, V.; Skůpa, Petr; Šturdík, E.

    2014-01-01

    Roč. 69, č. 10 (2014), s. 1255-1263 ISSN 0006-3088 R&D Projects: GA TA ČR TA01011802 Institutional support: RVO:61389030 Keywords : auxin * defense responses * JA Subject RIV: GF - Plant Pathology, Vermin, Weed, Plant Protection Impact factor: 0.827, year: 2014

  5. Hanford defense waste studies

    International Nuclear Information System (INIS)

    Napier, B.A.; Zimmerman, M.G.; Soldat, J.K.

    1981-01-01

    PNL is assisting Rockwell Hanford Operations to prepare a programmatic environmental impact statement for the management of Hanford defense nuclear waste. The Ecological Sciences Department is leading the task of calculation of public radiation doses from a large matrix of potential routine and accidental releases of radionuclides to the environment

  6. Rethinking Defensive Information Warfare

    Science.gov (United States)

    2004-06-01

    Countless studies, however, have demonstrated the weakness in this system.15 The tension between easily remembered passwords and suffi...vulnerabilities Undiscovered flaws The patch model for Internet security has failed spectacularly. Caida , 2004 Signature-Based Defense Anti virus, intrusion

  7. Oxidative stress provokes distinct transcriptional responses in the stress-tolerant atr7 and stress-sensitive loh2 Arabidopsis thaliana mutants as revealed by multi-parallel quantitative real-time PCR analysis of ROS marker and antioxidant genes.

    Science.gov (United States)

    Mehterov, Nikolay; Balazadeh, Salma; Hille, Jacques; Toneva, Valentina; Mueller-Roeber, Bernd; Gechev, Tsanko

    2012-10-01

    The Arabidopsis thaliana atr7 mutant is tolerant to oxidative stress induced by paraquat (PQ) or the catalase inhibitor aminotriazole (AT), while its original background loh2 and wild-type plants are sensitive. Both, AT and PQ, which stimulate the intracellular formation of H₂O₂ or superoxide anions, respectively, trigger cell death in loh2 but do not lead to visible damage in atr7. To study gene expression during oxidative stress and ROS-induced programmed cell death, two platforms for multi-parallel quantitative real-time PCR (qRT-PCR) analysis of 217 antioxidant and 180 ROS marker genes were employed. The qRT-PCR analyses revealed AT- and PQ-induced expression of many ROS-responsive genes mainly in loh2, confirming that an oxidative burst plays a role in the activation of the cell death in this mutant. Some of the genes were specifically regulated by either AT or PQ, serving as markers for particular types of ROS. Genes significantly induced by both AT and PQ in loh2 included transcription factors (ANAC042/JUB1, ANAC102, DREB19, HSFA2, RRTF1, ZAT10, ZAT12, ethylene-responsive factors), signaling compounds, ferritins, alternative oxidases, and antioxidant enzymes. Many of these genes were upregulated in atr7 compared to loh2 under non-stress conditions at the first time point, indicating that higher basal levels of ROS and higher antioxidant capacity in atr7 are responsible for the enhanced tolerance to oxidative stress and suggesting a possible tolerance against multiple stresses of this mutant. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

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

    Science.gov (United States)

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

    2018-03-15

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

  9. Defense Logistics Agency Revenue Eliminations

    National Research Council Canada - National Science Library

    1996-01-01

    The issue of revenue eliminations was identified during our work on the Defense Logistics Agency portion of the Audit of Revenue Accounts in the FY 1996 Financial Statements of the Defense Business Operations Fund...

  10. ADTool: Security Analysis with Attack-Defense Trees

    NARCIS (Netherlands)

    Kordy, Barbara; Kordy, P.T.; Mauw, Sjouke; Schweitzer, Patrick; Joshi, Kaustubh; Siegle, Markus; Stoelinga, Mariëlle Ida Antoinette; d' Argenio, P.R.

    ADTool is free, open source software assisting graphical modeling and quantitative analysis of security, using attack–defense trees. The main features of ADTool are easy creation, efficient editing, and automated bottom-up evaluation of security-relevant measures. The tool also supports the usage of

  11. Defense Primer: Procurement

    Science.gov (United States)

    2017-02-10

    Usually, incremental funding is used to mitigate peaks and valleys in annual budgets caused by the cost of one item significantly changing the...base defense budget . DOD uses these funds to buy several different types of materiel, including  new items easily recognizable as military...pursues a policy of full funding for procurement, meaning that the total estimated cost of each unit must be funded in the year it is budgeted . In a

  12. Quadrennial Defense Review Report

    Science.gov (United States)

    2010-02-01

    medicine , and computer network operations. While we continue to employ a mix of programs and incentives to recruit quality personnel, we are also...Lithuania* Singapore Australia Finland Luxembourg* Slovakia* Austria France* Macedonia Slovenia* Azerbaijan Georgia Montenegro Spain* Belgium...20,000 positions by 2015. We will continue to significantly enhance Secretary of Defense Robert M. Gates meets with plant workers during a tour of an

  13. Whither Ballistic Missile Defense?

    Science.gov (United States)

    1992-11-30

    important that technology today is placing enormous power in the many camps-not only information that enables timely decision-making, but also the...WHITHER BALLISTIC MISSILE DEFENSE? BY AMBASSADOR HENRY F. COOPER NOVEMBER 30,1992 TECHNICAL MARKETING SOCIETY OF AMERICA WASHINGTON, DC...Conference on Technical Marketing 2000: Opportunities and Strategies for a Changing World) I intend to discuss the prospects for SDI in a changing

  14. Plant defense against insect herbivores

    DEFF Research Database (Denmark)

    Fürstenberg-Hägg, Joel; Zagrobelny, Mika; Bak, Søren

    2013-01-01

    , defense compounds. These bioactive specialized plant defense compounds may repel or intoxicate insects, while defense proteins often interfere with their digestion. Volatiles are released upon herbivory to repel herbivores, attract predators or for communication between leaves or plants, and to induce......Plants have been interacting with insects for several hundred million years, leading to complex defense approaches against various insect feeding strategies. Some defenses are constitutive while others are induced, although the insecticidal defense compound or protein classes are often similar...... defense responses. Plants also apply morphological features like waxes, trichomes and latices to make the feeding more difficult for the insects. Extrafloral nectar, food bodies and nesting or refuge sites are produced to accommodate and feed the predators of the herbivores. Meanwhile, herbivorous insects...

  15. Quantitative Non-canonical Amino Acid Tagging (QuaNCAT) Proteomics Identifies Distinct Patterns of Protein Synthesis Rapidly Induced by Hypertrophic Agents in Cardiomyocytes, Revealing New Aspects of Metabolic Remodeling*

    Science.gov (United States)

    Liu, Rui; Kenney, Justin W.; Manousopoulou, Antigoni; Johnston, Harvey E.; Kamei, Makoto; Woelk, Christopher H.; Xie, Jianling; Schwarzer, Michael; Proud, Christopher G.

    2016-01-01

    Cardiomyocytes undergo growth and remodeling in response to specific pathological or physiological conditions. In the former, myocardial growth is a risk factor for cardiac failure and faster protein synthesis is a major factor driving cardiomyocyte growth. Our goal was to quantify the rapid effects of different pro-hypertrophic stimuli on the synthesis of specific proteins in ARVC and to determine whether such effects are caused by alterations on mRNA abundance or the translation of specific mRNAs. Cardiomyocytes have very low rates of protein synthesis, posing a challenging problem in terms of studying changes in the synthesis of specific proteins, which also applies to other nondividing primary cells. To study the rates of accumulation of specific proteins in these cells, we developed an optimized version of the Quantitative Noncanonical Amino acid Tagging LC/MS proteomic method to label and selectively enrich newly synthesized proteins in these primary cells while eliminating the suppressive effects of pre-existing and highly abundant nonisotope-tagged polypeptides. Our data revealed that a classical pathologic (phenylephrine; PE) and the recently identified insulin stimulus that also contributes to the development of pathological cardiac hypertrophy (insulin), both increased the synthesis of proteins involved in, e.g. glycolysis, the Krebs cycle and beta-oxidation, and sarcomeric components. However, insulin increased synthesis of many metabolic enzymes to a greater extent than PE. Using a novel validation method, we confirmed that synthesis of selected candidates is indeed up-regulated by PE and insulin. Synthesis of all proteins studied was up-regulated by signaling through mammalian target of rapamycin complex 1 without changes in their mRNA levels, showing the key importance of translational control in the rapid effects of hypertrophic stimuli. Expression of PKM2 was up-regulated in rat hearts following TAC. This isoform possesses specific regulatory

  16. Quantitative expression of defense-related genes induced in ...

    African Journals Online (AJOL)

    XP LITE

    2013-03-20

    Mar 20, 2013 ... immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. RNA extraction. Total RNA was extracted from 4 g of the pooled technical replicates based on the protocol described by Chang et al. (1993) with modifications, as .... endogenous control present in the same reaction. Ct is defined ...

  17. Battle through signaling between wheat and the fungal pathogen Septoria tritici revealed by proteomics and phosphoproteomics

    DEFF Research Database (Denmark)

    Yang, Fen; Braga, Marcella Nunes de Melo; Larsen, Martin Røssel

    2013-01-01

    The fungus Septoria tritici causes the disease septoria tritici blotch in wheat, one of the most economically devastating foliar diseases in this crop. To investigate signaling events and defense responses in the wheat-S. tritici interaction, we performed a time-course study of S. tritici infection...... in resistant and susceptible wheat using quantitative proteomics and phosphoproteomics, with special emphasis on the initial biotrophic phase of interactions. Our study revealed an accumulation of defense and stress-related proteins, suppression of photosynthesis, and changes in sugar metabolism during...... compatible and incompatible interactions. However, differential regulation of the phosphorylation status of signaling proteins, transcription and translation regulators, and membrane-associated proteins was observed between two interactions. The proteomic data were correlated with a more rapid or stronger...

  18. Quantitative research.

    Science.gov (United States)

    Watson, Roger

    2015-04-01

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

  19. DEFENSE PROGRAMS RISK MANAGEMENT FRAMEWORK

    Directory of Open Access Journals (Sweden)

    Constantin PREDA

    2012-01-01

    Full Text Available For the past years defense programs have faced delays in delivering defense capabilities and budget overruns. Stakeholders are looking for ways to improve program management and the decision making process given the very fluid and uncertain economic and political environment. Consequently, they have increasingly resorted to risk management as the main management tool for achieving defense programs objectives and for delivering the defense capabilities strongly needed for the soldiers on the ground on time and within limited defense budgets. Following a risk management based decision-making approach the stakeholders are expected not only to protect program objectives against a wide range of risks but, at the same time, to take advantage of the opportunities to increase the likelihood of program success. The prerequisite for making risk management the main tool for achieving defense programs objectives is the design and implementation of a strong risk management framework as a foundation providing an efficient and effective application of the best risk management practices. The aim of this paper is to examine the risk management framework for defense programs based on the ISO 31000:2009 standard, best risk management practices and the defense programs’ needs and particularities. For the purposes of this article, the term of defense programs refers to joint defense programs.

  20. Nanomaterials for Defense Applications

    Science.gov (United States)

    Turaga, Uday; Singh, Vinitkumar; Lalagiri, Muralidhar; Kiekens, Paul; Ramkumar, Seshadri S.

    Nanotechnology has found a number of applications in electronics and healthcare. Within the textile field, applications of nanotechnology have been limited to filters, protective liners for chemical and biological clothing and nanocoatings. This chapter presents an overview of the applications of nanomaterials such as nanofibers and nanoparticles that are of use to military and industrial sectors. An effort has been made to categorize nanofibers based on the method of production. This chapter particularly focuses on a few latest developments that have taken place with regard to the application of nanomaterials such as metal oxides in the defense arena.

  1. Phenomenon of Psychological Defense

    Directory of Open Access Journals (Sweden)

    Elena T. Sokolova

    2011-01-01

    Full Text Available The author discusses the controversial issues of formation and functioning of psy¬chological defense mechanisms in ontogenesis and in personality disorders as they are represented in classical and contemporary psychoanalysis, in cognitivism and communication theory. The paper emphasizes the role of cognitive organi¬zation (style, sign-symbolic mediation, representative system of object relations and attachments in individual typological variability of the level organization of ciency of personal and social adaptation, in maturity and mental health of personality

  2. Defense Treaty Inspection Readiness Program

    International Nuclear Information System (INIS)

    Cronin, J.J.; Kohen, M.D.; Rivers, J.D.

    1996-01-01

    The Defense Treaty Inspection Readiness Program (DTIRP) was established by the Department of Defense in 1990 to assist defense facilities in preparing for treaty verification activities. Led by the On-Site Inspection Agency (OSIA), an element of the Department of Defense, DTIRP''s membership includes representatives from other Department of Defense agencies, the Department of Energy (DOE), the Central Intelligence Agency, the Federal Bureau of Investigation, the Department of Commerce, and others. The Office of Safeguards and Security has a significant interest in this program, due to the number of national defense facilities within its purview that are candidates for future inspections. As a result, the Office of Safeguards and Security has taken a very active role in DTIRP. This paper discusses the Office of Safeguards and Security''s increasing involvement in various elements of the DTIRP, ranging from facility assessments to training development and implementation

  3. Ballistic Missile Defense in Europe

    OpenAIRE

    Sarihan, Ali; Bush, Amy; Summers, Lawrence; Thompson, Brent; Tomasszewski, Steven

    2009-01-01

    This paper will build on ballistic missile defense in Europe. In the first part, a brief historical overview will place the current public management issue into light. This is followed by a discussion of the main actors in the international debate, the problems that arise and the available options and recommendations to address missile defense. In the second part, differences between George W. Bush and Barack H. Obama will analyze under the title “Ballistic Missile Defense in Europe: Evolving...

  4. Extracellular Alkalinization as a Defense Response in Potato Cells.

    Science.gov (United States)

    Moroz, Natalia; Fritch, Karen R; Marcec, Matthew J; Tripathi, Diwaker; Smertenko, Andrei; Tanaka, Kiwamu

    2017-01-01

    A quantitative and robust bioassay to assess plant defense response is important for studies of disease resistance and also for the early identification of disease during pre- or non-symptomatic phases. An increase in extracellular pH is known to be an early defense response in plants. In this study, we demonstrate extracellular alkalinization as a defense response in potatoes. Using potato suspension cell cultures, we observed an alkalinization response against various pathogen- and plant-derived elicitors in a dose- and time-dependent manner. We also assessed the defense response against a variety of potato pathogens, such as protists ( Phytophthora infestans and Spongospora subterranea ) and fungi ( Verticillium dahliae and Colletotrichum coccodes ). Our results show that extracellular pH increases within 30 min in proportion to the number of pathogen spores added. Consistently with the alkalinization effect, the higher transcription level of several defense-related genes and production of reactive oxygen species was observed. Our results demonstrate that the alkalinization response is an effective marker to study early stages of defense response in potatoes.

  5. Defense Programs and Budget Risk

    National Research Council Canada - National Science Library

    Troutman, Mark D

    2006-01-01

    .... Therefore the Defense Department has set before itself a requirement to modernize a large conventional force structure engaged in ongoing combat operations while simultaneously developing deeper...

  6. Defense.gov Special Report: Defense Officials Release Operational Energy

    Science.gov (United States)

    , DOD Operational Energy Strategy DOD's Operational Energy Strategy will guide the Defense Department to operations are among the goals of the Defense Department's operational energy strategy, a senior Pentagon operational energy footprint, experts in solar power, microgrids and "smart" generators recently

  7. Induction of defensive enzymes (isozymes) during defense against ...

    African Journals Online (AJOL)

    user

    2012-09-06

    Sep 6, 2012 ... defense against two different fungal pathogens in pear calli ... study the biochemical changes in relation to plant defense ... relatively easy to manipulate by empirical means, allowing for a ... earlier phase, and the degree of rot was significantly ..... resistance of fruit, and they play an important role in the.

  8. Quantitative Finance

    Science.gov (United States)

    James, Jessica

    2017-01-01

    Quantitative finance is a field that has risen to prominence over the last few decades. It encompasses the complex models and calculations that value financial contracts, particularly those which reference events in the future, and apply probabilities to these events. While adding greatly to the flexibility of the market available to corporations and investors, it has also been blamed for worsening the impact of financial crises. But what exactly does quantitative finance encompass, and where did these ideas and models originate? We show that the mathematics behind finance and behind games of chance have tracked each other closely over the centuries and that many well-known physicists and mathematicians have contributed to the field.

  9. Antipredator defenses predict diversification rates

    Science.gov (United States)

    Arbuckle, Kevin; Speed, Michael P.

    2015-01-01

    The “escape-and-radiate” hypothesis predicts that antipredator defenses facilitate adaptive radiations by enabling escape from constraints of predation, diversified habitat use, and subsequently speciation. Animals have evolved diverse strategies to reduce the direct costs of predation, including cryptic coloration and behavior, chemical defenses, mimicry, and advertisement of unprofitability (conspicuous warning coloration). Whereas the survival consequences of these alternative defenses for individuals are well-studied, little attention has been given to the macroevolutionary consequences of alternative forms of defense. Here we show, using amphibians as the first, to our knowledge, large-scale empirical test in animals, that there are important macroevolutionary consequences of alternative defenses. However, the escape-and-radiate hypothesis does not adequately describe them, due to its exclusive focus on speciation. We examined how rates of speciation and extinction vary across defensive traits throughout amphibians. Lineages that use chemical defenses show higher rates of speciation as predicted by escape-and-radiate but also show higher rates of extinction compared with those without chemical defense. The effect of chemical defense is a net reduction in diversification compared with lineages without chemical defense. In contrast, acquisition of conspicuous coloration (often used as warning signals or in mimicry) is associated with heightened speciation rates but unchanged extinction rates. We conclude that predictions based on the escape-and-radiate hypothesis must incorporate the effect of traits on both speciation and extinction, which is rarely considered in such studies. Our results also suggest that knowledge of defensive traits could have a bearing on the predictability of extinction, perhaps especially important in globally threatened taxa such as amphibians. PMID:26483488

  10. Defense Reutilization and Marketing Manual

    Science.gov (United States)

    1990-03-01

    H -3 E Responsibilities of Defense Reutilization and Marketing Regions (D R M s...at Defense electronic products which produce radiation Reutilization and Marketing Offices, para- when energized. Among the principal radi- graph F... Sporting Equipment 7820 Games , Toys, and Wheeled Goods 7830 Recreational and Gymnastic Equipment 7910 Floor Polishers and Vacuum Cleaning Equipment

  11. Defense Acquisitions Acronyms and Terms

    Science.gov (United States)

    2012-12-01

    DR Decision Review DRMO Defense Reutilization Marketing Office DRPM Direct Reporting Program Manager DSAA Defense Security Assistance Agency...STE Special Test Equipment STEP Simulation, Test, and Evaluation Process STLDD Software Top Level Design Document STP Software Test Plan STPR...established catalog or market prices for specific tasks under standard commercial terms and conditions; this does not include services sold based

  12. Anorexia and Attachment: Dysregulated Defense and Pathological Mourning

    Directory of Open Access Journals (Sweden)

    elisa edelvecchio

    2014-10-01

    Full Text Available The role of Defensive exclusion (Deactivation and Segregated Systems in the development of early relationships and related to subsequent manifestations of symptoms of eating disorders was assessed using the Adult Attachment Projective Picture System (AAP. Fifty-one DSM-IV diagnosed women with anorexia participated in the study. Anorexic patients were primarily classified as dismissing or unresolved. Quantitative and qualitative analyses of defensive exclusion were carried out. Results showed potential benefits of using the AAP defense exclusion coding system, in addition to the main attachment classifications, in order to better understand the developmental issues involved in anorexia. Discussion concerned the processes, such as pathological mourning, that may underlie the associations between dismissing and unresolved attachment and anorexia. Implications for developmental research and clinical nosology are discussed.

  13. Quantitative Trait Loci Mapping in Brassica rapa Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of Brassica Species

    Science.gov (United States)

    Li, Xiaonan; Ramchiary, Nirala; Dhandapani, Vignesh; Choi, Su Ryun; Hur, Yoonkang; Nou, Ill-Sup; Yoon, Moo Kyoung; Lim, Yong Pyo

    2013-01-01

    Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species. PMID:23223793

  14. Defense Agencies Cash Management in the Defense Business Operations Fund

    National Research Council Canada - National Science Library

    Lane, F

    1997-01-01

    The primary audit objective was to determine whether the Fund Balance With Treasury Account on the Consolidated Financial Statements of the Defense Business Operations Fund for FY 1996 was presented...

  15. Quantitative radiography

    International Nuclear Information System (INIS)

    Brase, J.M.; Martz, H.E.; Waltjen, K.E.; Hurd, R.L.; Wieting, M.G.

    1986-01-01

    Radiographic techniques have been used in nondestructive evaluation primarily to develop qualitative information (i.e., defect detection). This project applies and extends the techniques developed in medical x-ray imaging, particularly computed tomography (CT), to develop quantitative information (both spatial dimensions and material quantities) on the three-dimensional (3D) structure of solids. Accomplishments in FY 86 include (1) improvements in experimental equipment - an improved microfocus system that will give 20-μm resolution and has potential for increased imaging speed, and (2) development of a simple new technique for displaying 3D images so as to clearly show the structure of the object. Image reconstruction and data analysis for a series of synchrotron CT experiments conducted by LLNL's Chemistry Department has begun

  16. Quantitative lymphography

    International Nuclear Information System (INIS)

    Mostbeck, A.; Lofferer, O.; Kahn, P.; Partsch, H.; Koehn, H.; Bialonczyk, Ch.; Koenig, B.

    1984-01-01

    Labelled colloids and macromolecules are removed lymphatically. The uptake of tracer in the regional lymphnodes is a parameter of lymphatic flow. Due to great variations in patient shape - obesity, cachexia - and accompanying variations in counting efficiencies quantitative measurements with reasonable accuracy have not been reported to date. A new approach to regional absorption correction is based on the combination of transmission and emission scans for each patient. The transmission scan is used for calculation of an absorption correction matrix. Accurate superposition of the correction matrix and the emission scan is achieved by computing the centers of gravity of point sources and - in the case of aligning opposite views - by cross correlation of binary images. In phantom studies the recovery was high (98.3%) and the coefficient of variation of repeated measurement below 1%. In patient studies a standardized stress is a prerequisite for reliable and comparable results. Discrimination between normals (14.3 +- 4.2D%) and patients with lymphedema (2.05 +- 2.5D%) was highly significant using praefascial lymphography and sc injection. Clearence curve analysis of the activities at the injection site, however, gave no reliable data for this purpose. In normals, the uptake in lymphnodes after im injection is by one order of magnitude lower then the uptake after sc injection. The discrimination between normals and patients with postthromboic syndrome was significant. Lymphography after ic injection was in the normal range in 2/3 of the patients with lymphedema and is therefore of no diagnostic value. The difference in uptake after ic and sc injection demonstrated for the first time by our quantitative method provides new insights into the pathophysiology of lymphedema and needs further investigation. (Author)

  17. Analysis of collective defense in finals of 2012. Radivoj Korac Cup

    Directory of Open Access Journals (Sweden)

    Stanković Aleksandar

    2013-01-01

    Full Text Available The aim of this research was to determine and analyze use, the way of organization and successfulness of collective defense, as well as effects of use of specific defense types. In this case of study, empirically non experimental method and monitoring technique which enables research of technically tactical activities in basketball were used. The sample of research included eight basketball teams, competitors in finals of Radivoj Korac Cup, held in Nis in 2012. In the research seven games were analyzed - four quarterfinal games, two semifinal games and one finals game. The data was collected by the monitoring technique, and analysis of collective defense is done based on variables on which, organization and successfulness of collective defense depends on. Five general variables, seven that refers to the type of defense and five variables of defense activities were included in this analysis and the results of the survey were expressed with quantitative values. With data analysis, it was realized that the team that had higher percentage of general defense efficiency was winning the game. While watching the games an impression that, the players on outer positions were significantly contributing to the efficiency of defense was made, while inner positions players showed much less mobility in defense.

  18. 78 FR 13543 - Defense Federal Acquisition Regulation Supplement; Technical Amendments

    Science.gov (United States)

    2013-02-28

    ..., 204, 215, 225, 227, 242, 245 and 252 Government procurement. Manuel Quinones, Editor, Defense...) shall be conducted only when-- (i) A contractor has $50 million of qualifying sales to the Government... circumstance(s) may result in a material impact on Government contract costs: (1) Information or data reveals a...

  19. Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires

    DEFF Research Database (Denmark)

    Bergseng, Elin; Dørum, Siri; Arntzen, Magnus Ø.

    2014-01-01

    Celiac disease is caused by intolerance to cereal gluten proteins, and HLA-DQ molecules are involved in the disease pathogenesis by presentation of gluten peptides to CD4+ T cells. The α- or β-chain sharing HLA molecules DQ2.5, DQ2.2, and DQ7.5 display different risks for the disease...... established binding motifs. The binding motif of DQ2.2 was strikingly different from that of DQ2.5 with position P3 being a major anchor having a preference for threonine and serine. This is notable as three recently identified epitopes of gluten recognized by T cells of DQ2.2 celiac patients harbor serine...... at position P3. This study demonstrates that relative quantitative comparison of endogenous peptides sampled from our protein metabolism by HLA molecules provides clues to understand HLA association with disease....

  20. Tyraminergic and Octopaminergic Modulation of Defensive Behavior in Termite Soldier.

    Directory of Open Access Journals (Sweden)

    Yuki Ishikawa

    Full Text Available In termites, i.e. a major group of eusocial insects, the soldier caste exhibits specific morphological characteristics and extremely high aggression against predators. Although the genomic background is identical to the other non-aggressive castes, they acquire the soldier-specific behavioral character during the course of caste differentiation. The high aggressiveness and defensive behavior is essential for colony survival, but the neurophysiological bases are completely unknown. In the present study, using the damp-wood termite Hodotermopsis sjostedti, we focused on two biogenic amines, octopamine (OA and tyramine (TA, as candidate neuromodulators for the defensive behavior in soldiers. High-performance liquid chromatographic analysis revealed that TA levels in the brain and suboesophageal ganglion (SOG and the OA level in brain were increased in soldiers than in pseudergates (worker caste. Immunohistochemical analysis revealed that TA/OA neurons that innervate specific areas, including the mandibular muscles, antennal nerve, central complex, suboesophageal ganglion, and thoracic and/or abdominal ganglia, were enlarged in a soldier-specific manner. Together with the results that pharmacological application of TA promoted the defensive behavior in pseudergates, these findings suggest that the increased TA/OA levels induce the higher aggressiveness and defensive behavior in termite soldiers. The projection targets of these soldier-specific enlarged TA/OA neurons may have important roles in the higher aggressiveness and defensive behavior of the termite soldiers, inducing the neuronal transition that accompanies external morphological changes.

  1. Japan and Ballistic Missile Defense

    National Research Council Canada - National Science Library

    Swaine, Michael

    2001-01-01

    Spurred by a perceived growing ballistic missile threat from within the Asia-Pacific region and requests from the United States to support research and development on components of a missile defense...

  2. Proactive Self Defense in Cyberspace

    National Research Council Canada - National Science Library

    Caulkins, Bruce D

    2009-01-01

    ... and standards to properly secure and defend the Global Information Grid (GIG) from cyber attacks. This paper will discuss the strategic requirements for enacting a proactive self-defense mechanism in cyberspace...

  3. Defense Meteorological Satellite Program (DMSP)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Defense Meteorological Satellite Program (DMSP) satellites collect visible and infrared cloud imagery as well as monitoring the atmospheric, oceanographic,...

  4. A PR-4 gene identified from Malus domestica is involved in the defense responses against Botryosphaeria dothidea.

    Science.gov (United States)

    Bai, Suhua; Dong, Chaohua; Li, Baohua; Dai, Hongyi

    2013-01-01

    Pathogenesis-related protein-4 (PR-4) family is a group of proteins with a Barwin domain in C-terminus and generally thought to be involved in plant defense responses. However, their detailed roles are poorly understood in defense of apple plant against pathogenic infection. In the present study, a new PR-4 gene (designated as MdPR-4) was identified from Malus domestica, and its roles in defense responses of apple were investigated. The open reading frame of MdPR-4 gene is of 447 bp encoding a protein of 148 amino acids with a Barwin domain in C-terminus and a signal peptide of 26 amino acids in N-terminus. Sequence and structural analysis indicated that MdPR-4 protein belongs to class II of PR-4 family. The high-level expression of MdPR-4 was observed in flowers and leaves as revealed by quantitative real time PCR. The temporal expression analysis demonstrated that MdPR-4 expression could be up-regulated by Botryosphaeria dothidea infection and salicylic acid (SA) or methyl jasmonate (MeJA) treatment, but suppressed by diethyldithiocarbamic acid (DIECA). In vitro assays, recombinant MdPR-4 protein exhibited ribonuclease activity specific for single strand RNA and significant inhibition to hyphal growth of three apple pathogenic fungi B. dothidea, Valsa ceratosperma and Glomerella cingulata. Moreover, the inhibition was reduced by the presence of 5'-ADP. Taken all together, the results indicate that MdPR-4 protein is involved in the defense responses of apple against pathogenic attack by directly inhibiting hyphal growth, and the inhibition is correlated with its ribonuclease activity, where as MdPR-4 expression is regulated by both SA and JA signaling pathway. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  5. Strategic Missile Defense & Nuclear Deterrence

    Science.gov (United States)

    Grego, Laura

    The United States has pursued defenses against nuclear-armed long-range ballistic missiles since at least the 1950s. At the same time, concerns that missile defenses could undermine nuclear deterrence and potentially spark an arms race led the United States and Soviet Union to negotiate limits on these systems. The 1972 Anti-Ballistic Missile Treaty constrained strategic missile defenses for thirty years. After abandoning the treaty in 2002, President George W. Bush began fielding the Ground-based Midcourse Defense (GMD) homeland missile defense system on an extremely aggressive schedule, nominally to respond to threats from North Korea and Iran. Today, nearly fifteen years after its initial deployment, the potential and the limits of this homeland missile defense are apparent. Its test record is poor and it has no demonstrated ability to stop an incoming missile under real-world conditions. No credible strategy is in place to solve the issue of discriminating countermeasures. Insufficient oversight has not only exacerbated the GMD system's problems, but has obscured their full extent, which could encourage politicians and military leaders to make decisions that actually increase the risk of a missile attack against the United States. These are not the only costs. Both Russia and China have repeatedly expressed concerns that U.S. missile defenses adversely affect their own strategic capabilities and interests, particularly taken in light of the substantial US nuclear forces. This in turn affects these countries' nuclear modernization priorities. This talk will provide a technical overview of the US strategic missile defense system, and how it relates to deterrence against non-peer adversaries as well as how it affects deterrence with Russia and China and the long-term prospects for nuclear reductions

  6. Quantitative Thermochronology

    Science.gov (United States)

    Braun, Jean; van der Beek, Peter; Batt, Geoffrey

    2006-05-01

    Thermochronology, the study of the thermal history of rocks, enables us to quantify the nature and timing of tectonic processes. Quantitative Thermochronology is a robust review of isotopic ages, and presents a range of numerical modeling techniques to allow the physical implications of isotopic age data to be explored. The authors provide analytical, semi-analytical, and numerical solutions to the heat transfer equation in a range of tectonic settings and under varying boundary conditions. They then illustrate their modeling approach built around a large number of case studies. The benefits of different thermochronological techniques are also described. Computer programs on an accompanying website at www.cambridge.org/9780521830577 are introduced through the text and provide a means of solving the heat transport equation in the deforming Earth to predict the ages of rocks and compare them directly to geological and geochronological data. Several short tutorials, with hints and solutions, are also included. Numerous case studies help geologists to interpret age data and relate it to Earth processes Essential background material to aid understanding and using thermochronological data Provides a thorough treatise on numerical modeling of heat transport in the Earth's crust Supported by a website hosting relevant computer programs and colour slides of figures from the book for use in teaching

  7. Tactile defensiveness and stereotyped behaviors.

    Science.gov (United States)

    Baranek, G T; Foster, L G; Berkson, G

    1997-02-01

    This study explores the constructs of stereotyped behaviors (e.g., repetitive motor patterns, object manipulations, behavioral rigidities) and tactile defensiveness as relevant to occupational therapy theory and practice and attempts to test their purported relationships in children with developmental disabilities. Twenty-eight children with developmental disabilities and autism were assessed on eight factors of stereotyped behavior via a questionnaire and by four measures of tactile defensiveness. The subjects' scores from the questionnaire were correlated with their scores on the tactile defensiveness measures to see what, if any, relationship among these behaviors exists. Significant relationships emerged from the data, indicating that subjects with higher levels of tactile defensiveness were also more likely to evidence rigid or inflexible behaviors, repetitive verbalizations, visual stereotypes, and abnormal focused affections that are often associated with autism. No significant association was found between motor and object stereotypes and tactile defensiveness. These relationships could not be explained solely by maturational factors. The results suggest that clinicians should include observations of stereotyped behaviors, particularly behavioral rigidities, in conjunction with assessments of sensory defensiveness because these are related phenomena that may pose unique challenges for children with developmental disabilities and autism. Further study is needed to determine the causal mechanisms responsible for these relationships.

  8. THE PROGNOSIS OF RUSSIAN DEFENSE INDUSTRY DEVELOPMENT IMPLEMENTED THROUGH REGRESSION ANALYSIS

    Directory of Open Access Journals (Sweden)

    L.M. Kapustina

    2007-03-01

    Full Text Available The article illustrates the results of investigation the major internal and external factors which influence the development of the defense industry, as well as the results of regression analysis which quantitatively displays the factorial contribution in the growth rate of Russian defense industry. On the basis of calculated regression dependences the authors fulfilled the medium-term prognosis of defense industry. Optimistic and inertial versions of defense product growth rate for the period up to 2009 are based on scenario conditions in Russian economy worked out by the Ministry of economy and development. In conclusion authors point out which factors and conditions have the largest impact on successful and stable operation of Russian defense industry.

  9. Acquisition Planning at the Defense Communications Agency.

    Science.gov (United States)

    1984-04-01

    guidelines for interaction are developed under the leadership of DCA agencywide integrators with the participation of personnel from DCA, the Services...Communications System DCSO - Defense Communications System Organizatin . DDN - Defense Data Network DEC - Decision Making DG - Defense Guidance DIA - Defense

  10. Mapping of quantitative adult plant field resistance to leaf rust and stripe rust in two European winter wheat populations reveals co-location of three QTL conferring resistance to both rust pathogens.

    Science.gov (United States)

    Buerstmayr, Maria; Matiasch, Lydia; Mascher, Fabio; Vida, Gyula; Ittu, Marianna; Robert, Olivier; Holdgate, Sarah; Flath, Kerstin; Neumayer, Anton; Buerstmayr, Hermann

    2014-09-01

    We detected several, most likely novel QTL for adult plant resistance to rusts. Notably three QTL improved resistance to leaf rust and stripe rust simultaneously indicating broad spectrum resistance QTL. The rusts of wheat (Puccinia spp.) are destructive fungal wheat diseases. The deployment of resistant cultivars plays a central role in integrated rust disease management. Durability of resistance would be preferred, but is difficult to analyse. The Austrian winter wheat cultivar Capo was released in the 1989 and grown on a large acreage during more than two decades and maintained a good level of quantitative leaf rust and stripe rust resistance. Two bi-parental mapping populations: Capo × Arina and Capo × Furore were tested in multiple environments for severity of leaf rust and stripe rust at the adult plant stage in replicated field experiments. Quantitative trait loci associated with leaf rust and stripe rust severity were mapped using DArT and SSR markers. Five QTL were detected in multiple environments associated with resistance to leaf rust designated as QLr.ifa-2AL, QLr.ifa-2BL, QLr.ifa-2BS, QLr.ifa-3BS, and QLr.ifa-5BL, and five for resistance to stripe rust QYr.ifa-2AL, QYr.ifa-2BL, QYr.ifa-3AS, QYr.ifa-3BS, and QYr.ifa-5A. For all QTL apart from two (QYr.ifa-3AS, QLr.ifa-5BL) Capo contributed the resistance improving allele. The leaf rust and stripe rust resistance QTL on 2AL, 2BL and 3BS mapped to the same chromosome positions, indicating either closely linked genes or pleiotropic gene action. These three multiple disease resistance QTL (QLr.ifa-2AL/QYr.ifa-2AL, QLr.ifa.2BL/QYr.ifa-2BL, QLr.ifa-3BS/QYr.ifa.3BS) potentially contribute novel resistance sources for stripe rust and leaf rust. The long-lasting resistance of Capo apparently rests upon a combination of several genes. The described germplasm, QTL and markers are applicable for simultaneous resistance improvement against leaf rust and stripe rust.

  11. Report of the Defense Science Board/Defense Policy Board Task Force On Theater Missile Defense

    National Research Council Canada - National Science Library

    1996-01-01

    ... also tackled the controversial subject of the ABM Treaty and its effect on theater missile defenses Subsequent to its interim report, which expressed strong concerns about the demarcation path the US...

  12. The quantitative Morse theorem

    OpenAIRE

    Loi, Ta Le; Phien, Phan

    2013-01-01

    In this paper, we give a proof of the quantitative Morse theorem stated by {Y. Yomdin} in \\cite{Y1}. The proof is based on the quantitative Sard theorem, the quantitative inverse function theorem and the quantitative Morse lemma.

  13. Mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1979-01-01

    Mathematics Revealed focuses on the principles, processes, operations, and exercises in mathematics.The book first offers information on whole numbers, fractions, and decimals and percents. Discussions focus on measuring length, percent, decimals, numbers as products, addition and subtraction of fractions, mixed numbers and ratios, division of fractions, addition, subtraction, multiplication, and division. The text then examines positive and negative numbers and powers and computation. Topics include division and averages, multiplication, ratios, and measurements, scientific notation and estim

  14. Information Warfare: Issues Associated with the Defense of DOD Computers and Computer Networks

    National Research Council Canada - National Science Library

    Franklin, Derek

    2002-01-01

    ... that may threaten the critical information pathways of the armed forces An analysis of the history of computer information warfare reveals that there was an embarrassing lack of readiness and defense...

  15. Quantitative proteomic analysis of HIV-1 infected CD4+ T cells reveals an early host response in important biological pathways: Protein synthesis, cell proliferation, and T-cell activation

    Energy Technology Data Exchange (ETDEWEB)

    Navare, Arti T.; Sova, Pavel; Purdy, David E.; Weiss, Jeffrey M. [Department of Microbiology, University of Washington, Seattle, WA (United States); Wolf-Yadlin, Alejandro [Department of Genome Sciences, University of Washington, Seattle, WA (United States); Korth, Marcus J.; Chang, Stewart T.; Proll, Sean C. [Department of Microbiology, University of Washington, Seattle, WA (United States); Jahan, Tahmina A. [Proteomics Resource, UW Medicine at South Lake Union, Seattle, WA (United States); Krasnoselsky, Alexei L.; Palermo, Robert E. [Department of Microbiology, University of Washington, Seattle, WA (United States); Katze, Michael G., E-mail: honey@uw.edu [Department of Microbiology, University of Washington, Seattle, WA (United States); Washington National Primate Research Center, University of Washington, Seattle, WA (United States)

    2012-07-20

    Human immunodeficiency virus (HIV-1) depends upon host-encoded proteins to facilitate its replication while at the same time inhibiting critical components of innate and/or intrinsic immune response pathways. To characterize the host cell response on protein levels in CD4+ lymphoblastoid SUP-T1 cells after infection with HIV-1 strain LAI, we used mass spectrometry (MS)-based global quantitation with iTRAQ (isobaric tag for relative and absolute quantification). We found 266, 60 and 22 proteins differentially expressed (DE) (P-value{<=}0.05) at 4, 8, and 20 hours post-infection (hpi), respectively, compared to time-matched mock-infected samples. The majority of changes in protein abundance occurred at an early stage of infection well before the de novo production of viral proteins. Functional analyses of these DE proteins showed enrichment in several biological pathways including protein synthesis, cell proliferation, and T-cell activation. Importantly, these early changes before the time of robust viral production have not been described before.

  16. 76 FR 28757 - Defense Logistics Agency Revised Regulation 1000.22, Environmental Considerations in Defense...

    Science.gov (United States)

    2011-05-18

    ... DEPARTMENT OF DEFENSE Office of the Secretary [DOCKET ID DOD-2011-OS-0055] Defense Logistics Agency Revised Regulation 1000.22, Environmental Considerations in Defense Logistics Agency Actions AGENCY: Defense Logistics Agency, Department of Defense. ACTION: Notice of Availability (NOA) of Revised...

  17. 76 FR 53119 - Defense Logistics Agency Revised Regulation 1000.22, Environmental Considerations in Defense...

    Science.gov (United States)

    2011-08-25

    ... DEPARTMENT OF DEFENSE Office of the Secretary [Docket ID: DOD-2011-OS-0055] Defense Logistics Agency Revised Regulation 1000.22, Environmental Considerations in Defense Logistics Agency Actions AGENCY: Defense Logistics Agency, Department of Defense. ACTION: Comment Addressed on Notice of...

  18. 75 FR 52732 - Renewal of Department of Defense Federal Advisory Committee; Missile Defense Advisory Committee

    Science.gov (United States)

    2010-08-27

    ... Committee; Missile Defense Advisory Committee AGENCY: Department of Defense (DoD). ACTION: Renewal of..., the Department of Defense gives notice that it is renewing the charter for the Missile Defense... Director, Missile Defense Agency, independent advice and recommendations on all matters relating to missile...

  19. Technical Soddi Defenses: The Trojan Horse Defense Revisited

    Directory of Open Access Journals (Sweden)

    Chad Steel

    2014-12-01

    Full Text Available In 2004, the Trojan horse defense was at a crossroads, with two child pornography cases where it was successfully employed in the United Kingdom, resulting in acquittals.  The original Trojan horse defense has now become part of the more general “technical SODDI” defense, which includes the possibility of unknown actors using unsecured Wi-Fi connections or having physical access to a computer to perform criminal acts.  In the past ten years, it has failed to be effective in the United States for criminal cases, with no published acquittals in cases where it was the primary defense.  In the criminal cases where it has been used as leverage in plea negotiations, there has been either poor forensics performed by the prosecution or political pressure to resolve a matter.  On the civil side, however, the defense has been wildly successful, effectively shutting down large John Doe copyright infringement litigation against non-commercial violators.  

  20. Host Defense Mechanisms against Bark Beetle Attack Differ between Ponderosa and Lodgepole Pines

    Directory of Open Access Journals (Sweden)

    Daniel R. West

    2016-10-01

    Full Text Available Conifer defenses against bark beetle attack include, but are not limited to, quantitative and qualitative defenses produced prior to attack. Our objective was to assess host defenses of lodgepole pine and ponderosa pine from ecotone stands. These stands provide a transition of host species for mountain pine beetle (Dendroctonus ponderosae; MPB. We asked two questions: (1 do the preformed quantitative host defenses (amount of resin and (2 the preformed qualitative host defenses (monoterpene constituents differ between lodgepole and ponderosa pines. We collected oleoresins at three locations in the Southern Rocky Mountains from 56 pairs of the pine species of similar size and growing conditions. The amount of preformed-ponderosa pine oleoresins exuded in 24 h (mg was almost four times that of lodgepole pine. Total qualitative preformed monoterpenes did not differ between the two hosts, though we found differences in all but three monoterpenes. No differences were detected in α-pinene, γ-terpinene, and bornyl acetate. We found greater concentrations of limonene, β-phellandrene, and cymene in lodgepole pines, whereas β-pinene, 3-carene, myrcene, and terpinolene were greater in ponderosa pine. Although we found differences both in quantitative and qualitative preformed oleoresin defenses, the ecological relevance of these differences to bark beetle susceptibility have not been fully tested.

  1. TMV-Cg Coat Protein stabilizes DELLA proteins and in turn negatively modulates salicylic acid-mediated defense pathway during Arabidopsis thaliana viral infection.

    Science.gov (United States)

    Rodriguez, Maria Cecilia; Conti, Gabriela; Zavallo, Diego; Manacorda, Carlos Augusto; Asurmendi, Sebastian

    2014-08-03

    Plant viral infections disturb defense regulatory networks during tissue invasion. Emerging evidence demonstrates that a significant proportion of these alterations are mediated by hormone imbalances. Although the DELLA proteins have been reported to be central players in hormone cross-talk, their role in the modulation of hormone signaling during virus infections remains unknown. This work revealed that TMV-Cg coat protein (CgCP) suppresses the salicylic acid (SA) signaling pathway without altering defense hormone SA or jasmonic acid (JA) levels in Arabidopsis thaliana. Furthermore, it was observed that the expression of CgCP reduces plant growth and delays the timing of floral transition. Quantitative RT-qPCR analysis of DELLA target genes showed that CgCP alters relative expression of several target genes, indicating that the DELLA proteins mediate transcriptional changes produced by CgCP expression. Analyses by fluorescence confocal microscopy showed that CgCP stabilizes DELLA proteins accumulation in the presence of gibberellic acid (GA) and that the DELLA proteins are also stabilized during TMV-Cg virus infections. Moreover, DELLA proteins negatively modulated defense transcript profiles during TMV-Cg infection. As a result, TMV-Cg accumulation was significantly reduced in the quadruple-DELLA mutant Arabidopsis plants compared to wild type plants. Taken together, these results demonstrate that CgCP negatively regulates the salicylic acid-mediated defense pathway by stabilizing the DELLA proteins during Arabidopsis thaliana viral infection, suggesting that CgCP alters the stability of DELLAs as a mechanism of negative modulation of antiviral defense responses.

  2. Quantitative evaluation of high intensity signal on MIP images of carotid atherosclerotic plaques from routine TOF-MRA reveals elevated volumes of intraplaque hemorrhage and lipid rich necrotic core.

    Science.gov (United States)

    Yamada, Kiyofumi; Song, Yan; Hippe, Daniel S; Sun, Jie; Dong, Li; Xu, Dongxiang; Ferguson, Marina S; Chu, Baocheng; Hatsukami, Thomas S; Chen, Min; Zhou, Cheng; Yuan, Chun

    2012-11-29

    Carotid intraplaque hemorrhage (IPH) and lipid rich necrotic core (LRNC) have been associated with accelerated plaque growth, luminal narrowing, future surface disruption and development of symptomatic events. The aim of this study was to evaluate the quantitative relationships between high intensity signals (HIS) in the plaque on TOF-MRA and IPH or LRNC volumes as measured by multicontrast weighted CMR. Seventy six patients with a suspected carotid artery stenosis or carotid plaque by ultrasonography underwent multicontrast carotid CMR. HIS presence and volume were measured from TOF-MRA MIP images while IPH and LRNC volumes were separately measured from multicontrast CMR. For detecting IPH, HIS on MIP images overall had high specificity (100.0%, 95% CI: 93.0 - 100.0%) but relatively low sensitivity (32%, 95% CI: 20.8 - 47.9%). However, the sensitivity had a significant increasing relationship with underlying IPH volume (p = 0.033) and degree of stenosis (p = 0.022). Mean IPH volume was 2.7 times larger in those with presence of HIS than in those without (142.8 ± 97.7 mm(3) vs. 53.4 ± 56.3 mm(3), p = 0.014). Similarly, mean LRNC volume was 3.4 times larger in those with HIS present (379.8 ± 203.4 mm(3) vs. 111.3 ± 122.7 mm(3), p = 0.001). There was a strong correlation between the volume of the HIS region and the IPH volume measured from multicontrast CMR (r = 0.96, p routine, clinical TOF sequences. High intensity signals in carotid plaque on TOF-MRA MIP images are associated with increased intraplaque hemorrhage and lipid-rich necrotic core volumes. The technique is most sensitive in patients with moderate to severe stenosis.

  3. Expression patterns of WRKY genes in di-haploid Populus simonii × P. nigra in response to salinity stress revealed by quantitative real-time PCR and RNA sequencing.

    Science.gov (United States)

    Wang, Shengji; Wang, Jiying; Yao, Wenjing; Zhou, Boru; Li, Renhua; Jiang, Tingbo

    2014-10-01

    Spatio-temporal expression patterns of 13 out of 119 poplar WRKY genes indicated dynamic and tissue-specific roles of WRKY family proteins in salinity stress tolerance. To understand the expression patterns of poplar WRKY genes under salinity stress, 51 of the 119 WRKY genes were selected from di-haploid Populus simonii × P. nigra by quantitative real-time PCR (qRT-PCR). We used qRT-PCR to profile the expression of the top 13 genes under salinity stress across seven time points, and employed RNA-Seq platforms to cross-validate it. Results demonstrated that all the 13 WRKY genes were expressed in root, stem, and leaf tissues, but their expression levels and overall patterns varied notably in these tissues. Regarding overall gene expression in roots, the 13 genes were significantly highly expressed at all six time points after the treatment, reaching the plateau of expression at hour 9. In leaves, the 13 genes were similarly up-regulated from 3 to 12 h in response to NaCl treatment. In stems, however, expression levels of the 13 genes did not show significant changes after the NaCl treatment. Regarding individual gene expression across the time points and the three tissues, the 13 genes can be classified into three clusters: the lowly expressed Cluster 1 containing PthWRKY28, 45 and 105; intermediately expressed Clusters 2 including PthWRKY56, 88 and 116; and highly expressed Cluster 3 consisting of PthWRKY41, 44, 51, 61, 62, 75 and 106. In general, genes in Cluster 2 and 3 displayed a dynamic pattern of "induced amplification-recovering", suggesting that these WRKY genes and corresponding pathways may play a critical role in mediating salt response and tolerance in a dynamic and tissue-specific manner.

  4. Quantitative Proteomics of Gut-Derived Th1 and Th1/Th17 Clones Reveal the Presence of CD28+ NKG2D- Th1 Cytotoxic CD4+ T cells.

    Science.gov (United States)

    Riaz, Tahira; Sollid, Ludvig Magne; Olsen, Ingrid; de Souza, Gustavo Antonio

    2016-03-01

    T-helper cells are differentiated from CD4+ T cells and are traditionally characterized by inflammatory or immunosuppressive responses in contrast to cytotoxic CD8+ T cells. Mass-spectrometry studies on T-helper cells are rare. In this study, we aimed to identify the proteomes of human Th1 and Th1/Th17 clones derived from intestinal biopsies of Crohn's disease patients and to identify differentially expressed proteins between the two phenotypes. Crohn's disease is an inflammatory bowel disease, with predominantly Th1- and Th17-mediated response where cells of the "mixed" phenotype Th1/Th17 have also been commonly found. High-resolution mass spectrometry was used for protein identification and quantitation. In total, we identified 7401 proteins from Th1 and Th1/Th17 clones, where 334 proteins were differentially expressed. Major differences were observed in cytotoxic proteins that were overrepresented in the Th1 clones. The findings were validated by flow cytometry analyses using staining with anti-granzyme B and anti-perforin and by a degranulation assay, confirming higher cytotoxic features of Th1 compared with Th1/Th17 clones. By testing a larger panel of T-helper cell clones from seven different Crohn's disease patients, we concluded that only a subgroup of the Th1 cell clones had cytotoxic features, and these expressed the surface markers T-cell-specific surface glycoprotein CD28 and were negative for expression of natural killer group 2 member D. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Basal host resistance of barley to powdery mildew: connecting quantitative trait loci and candidate genes

    NARCIS (Netherlands)

    Aghnoum, R.; Marcel, T.C.; Johrde, A.; Pecchioni, N.; Schweizer, P.; Niks, R.E.

    2010-01-01

    The basal resistance of barley to powdery mildew (Blumeria graminis f. sp. hordei) is a quantitatively inherited trait that is based on nonhypersensitive mechanisms of defense. A functional genomic approach indicates that many plant candidate genes are involved in the defense against formation of

  6. Exploring the Caste-Specific Multi-Layer Defense Mechanism of Formosan Subterranean Termites, Coptotermes formosanus Shiraki

    Directory of Open Access Journals (Sweden)

    Abid Hussain

    2017-12-01

    Full Text Available The survival and foraging of Coptotermes formosanus Shiraki in a microbe-rich environment reflect the adaptation of an extraordinary, sophisticated defense mechanism by the nest-mates. We aimed to explore the host pathogen interaction by studying caste-specific volatile chemistry and genes encoding the antioxidant defense of winged imagoes, nymphs, soldiers and workers of Formosan subterranean termites. Qualitative analyses of C. formosanus Shiraki performed by HS-SPME/GC-MS showed considerable variations in the chemical composition of volatile organic compounds (VOCs and their proportions among all the castes. Winged imagoes produced the most important compounds such as naphthalene and n-hexanoic acid. The antifungal activity of these compounds along with nonanal, n-pentadecane, n-tetradecane, n-heptadecane and methyl octanoate against the conidial suspensions of Metarhizium anisopliae and Beauveria bassiana isolates enable us to suggest that the failure of natural fungal infection in the nest is due to the antiseptic environment of the nest, which is mainly controlled by the VOCs of nest-mates. In addition, conidial germination of M. anisopliae and B. bassiana isolates evaluated on the cuticle of each caste showed significant variations among isolates and different castes. Our results showed that the conidia of M. anisopliae 02049 exhibited the highest germination on the cuticle of all the inoculated castes. Moreover, we recorded the lowest germination of the conidia of B. bassiana 200436. Caste-specific germination variations enabled us to report for the first time that the cuticle of winged imagoes was found to be the most resistant cuticle. The analysis of the transcriptome of C. formosanus Shiraki revealed the identification of 17 genes directly involved in antioxidant defense. Expression patterns of the identified antioxidant genes by quantitative real-time PCR (qPCR revealed the significantly highest upregulation of CAT, GST, PRXSL, Cu

  7. Optimal defense resource allocation in scale-free networks

    Science.gov (United States)

    Zhang, Xuejun; Xu, Guoqiang; Xia, Yongxiang

    2018-02-01

    The robustness research of networked systems has drawn widespread attention in the past decade, and one of the central topics is to protect the network from external attacks through allocating appropriate defense resource to different nodes. In this paper, we apply a specific particle swarm optimization (PSO) algorithm to optimize the defense resource allocation in scale-free networks. Results reveal that PSO based resource allocation shows a higher robustness than other resource allocation strategies such as uniform, degree-proportional, and betweenness-proportional allocation strategies. Furthermore, we find that assigning less resource to middle-degree nodes under small-scale attack while more resource to low-degree nodes under large-scale attack is conductive to improving the network robustness. Our work provides an insight into the optimal defense resource allocation pattern in scale-free networks and is helpful for designing a more robust network.

  8. Quantitative evaluation of high intensity signal on MIP images of carotid atherosclerotic plaques from routine TOF-MRA reveals elevated volumes of intraplaque hemorrhage and lipid rich necrotic core

    Directory of Open Access Journals (Sweden)

    Yamada Kiyofumi

    2012-11-01

    Full Text Available Abstract Background Carotid intraplaque hemorrhage (IPH and lipid rich necrotic core (LRNC have been associated with accelerated plaque growth, luminal narrowing, future surface disruption and development of symptomatic events. The aim of this study was to evaluate the quantitative relationships between high intensity signals (HIS in the plaque on TOF-MRA and IPH or LRNC volumes as measured by multicontrast weighted CMR. Methods Seventy six patients with a suspected carotid artery stenosis or carotid plaque by ultrasonography underwent multicontrast carotid CMR. HIS presence and volume were measured from TOF-MRA MIP images while IPH and LRNC volumes were separately measured from multicontrast CMR. Results For detecting IPH, HIS on MIP images overall had high specificity (100.0%, 95% CI: 93.0 – 100.0% but relatively low sensitivity (32%, 95% CI: 20.8 – 47.9%. However, the sensitivity had a significant increasing relationship with underlying IPH volume (p = 0.033 and degree of stenosis (p = 0.022. Mean IPH volume was 2.7 times larger in those with presence of HIS than in those without (142.8 ± 97.7 mm3 vs. 53.4 ± 56.3 mm3, p = 0.014. Similarly, mean LRNC volume was 3.4 times larger in those with HIS present (379.8 ± 203.4 mm3 vs. 111.3 ± 122.7 mm3, p = 0.001. There was a strong correlation between the volume of the HIS region and the IPH volume measured from multicontrast CMR (r = 0.96, p  Conclusion MIP images are easily reformatted from three minute, routine, clinical TOF sequences. High intensity signals in carotid plaque on TOF-MRA MIP images are associated with increased intraplaque hemorrhage and lipid-rich necrotic core volumes. The technique is most sensitive in patients with moderate to severe stenosis.

  9. Major Quantitative Trait Loci and Putative Candidate Genes for Powdery Mildew Resistance and Fruit-Related Traits Revealed by an Intraspecific Genetic Map for Watermelon (Citrullus lanatus var. lanatus)

    Science.gov (United States)

    Kim, Kwang-Hwan; Hwang, Ji-Hyun; Han, Dong-Yeup; Park, Minkyu; Kim, Seungill; Choi, Doil; Kim, Yongjae; Lee, Gung Pyo; Kim, Sun-Tae; Park, Young-Hoon

    2015-01-01

    An intraspecific genetic map for watermelon was constructed using an F2 population derived from ‘Arka Manik’ × ‘TS34’ and transcript sequence variants and quantitative trait loci (QTL) for resistance to powdery mildew (PMR), seed size (SS), and fruit shape (FS) were analyzed. The map consists of 14 linkage groups (LGs) defined by 174 cleaved amplified polymorphic sequences (CAPS), 2 derived-cleaved amplified polymorphic sequence markers, 20 sequence-characterized amplified regions, and 8 expressed sequence tag-simple sequence repeat markers spanning 1,404.3 cM, with a mean marker interval of 6.9 cM and an average of 14.6 markers per LG. Genetic inheritance and QTL analyses indicated that each of the PMR, SS, and FS traits is controlled by an incompletely dominant effect of major QTLs designated as pmr2.1, ss2.1, and fsi3.1, respectively. The pmr2.1, detected on chromosome 2 (Chr02), explained 80.0% of the phenotypic variation (LOD = 30.76). This QTL was flanked by two CAPS markers, wsb2-24 (4.00 cM) and wsb2-39 (13.97 cM). The ss2.1, located close to pmr2.1 and CAPS marker wsb2-13 (1.00 cM) on Chr02, explained 92.3% of the phenotypic variation (LOD = 68.78). The fsi3.1, detected on Chr03, explained 79.7% of the phenotypic variation (LOD = 31.37) and was flanked by two CAPS, wsb3-24 (1.91 cM) and wsb3-9 (7.00 cM). Candidate gene-based CAPS markers were developed from the disease resistance and fruit shape gene homologs located on Chr.02 and Chr03 and were mapped on the intraspecific map. Colocalization of these markers with the major QTLs indicated that watermelon orthologs of a nucleotide-binding site-leucine-rich repeat class gene containing an RPW8 domain and a member of SUN containing the IQ67 domain are candidate genes for pmr2.1 and fsi3.1, respectively. The results presented herein provide useful information for marker-assisted breeding and gene cloning for PMR and fruit-related traits. PMID:26700647

  10. Major Quantitative Trait Loci and Putative Candidate Genes for Powdery Mildew Resistance and Fruit-Related Traits Revealed by an Intraspecific Genetic Map for Watermelon (Citrullus lanatus var. lanatus).

    Science.gov (United States)

    Kim, Kwang-Hwan; Hwang, Ji-Hyun; Han, Dong-Yeup; Park, Minkyu; Kim, Seungill; Choi, Doil; Kim, Yongjae; Lee, Gung Pyo; Kim, Sun-Tae; Park, Young-Hoon

    2015-01-01

    An intraspecific genetic map for watermelon was constructed using an F2 population derived from 'Arka Manik' × 'TS34' and transcript sequence variants and quantitative trait loci (QTL) for resistance to powdery mildew (PMR), seed size (SS), and fruit shape (FS) were analyzed. The map consists of 14 linkage groups (LGs) defined by 174 cleaved amplified polymorphic sequences (CAPS), 2 derived-cleaved amplified polymorphic sequence markers, 20 sequence-characterized amplified regions, and 8 expressed sequence tag-simple sequence repeat markers spanning 1,404.3 cM, with a mean marker interval of 6.9 cM and an average of 14.6 markers per LG. Genetic inheritance and QTL analyses indicated that each of the PMR, SS, and FS traits is controlled by an incompletely dominant effect of major QTLs designated as pmr2.1, ss2.1, and fsi3.1, respectively. The pmr2.1, detected on chromosome 2 (Chr02), explained 80.0% of the phenotypic variation (LOD = 30.76). This QTL was flanked by two CAPS markers, wsb2-24 (4.00 cM) and wsb2-39 (13.97 cM). The ss2.1, located close to pmr2.1 and CAPS marker wsb2-13 (1.00 cM) on Chr02, explained 92.3% of the phenotypic variation (LOD = 68.78). The fsi3.1, detected on Chr03, explained 79.7% of the phenotypic variation (LOD = 31.37) and was flanked by two CAPS, wsb3-24 (1.91 cM) and wsb3-9 (7.00 cM). Candidate gene-based CAPS markers were developed from the disease resistance and fruit shape gene homologs located on Chr.02 and Chr03 and were mapped on the intraspecific map. Colocalization of these markers with the major QTLs indicated that watermelon orthologs of a nucleotide-binding site-leucine-rich repeat class gene containing an RPW8 domain and a member of SUN containing the IQ67 domain are candidate genes for pmr2.1 and fsi3.1, respectively. The results presented herein provide useful information for marker-assisted breeding and gene cloning for PMR and fruit-related traits.

  11. Evaluation of health and safety impacts of defense high-level waste in geologic repositories

    International Nuclear Information System (INIS)

    Smith, E.D.; Kocher, D.C.; Witherspoon, J.P.

    1985-02-01

    Pursuant to the requirement of the Nuclear Waste Policy Act of 1982 that the President evaluate the use of commercial high-level waste repositories for the disposal of defense high-level wastes, a comparative assessment has been performed of the potential health and safety impacts of disposal of defense wastes in commercial or defense-only repositories. Simplified models were used to make quantitative estimates of both long- and short-term health and safety impacts of several options for defense high-level waste disposal. The results indicate that potential health and safety impacts are not likely to vary significantly among the different disposal options for defense wastes. Estimated long-term health and safety impacts from all defense-waste disposal options are somewhat less than those from commercial waste disposal, while short-term health and safety impacts appear to be insensitive to the differences between defense and commercial wastes. In all cases, potential health and safety impacts are small because of the need to meet stringent standards promulgated by the US Environmental Protection Agency and the US Nuclear Regulatory Commission. We conclude that health and safety impacts should not be a significant factor in the choice of a disposal option for defense high-level wastes. 20 references, 14 tables

  12. Organizing Defense Logistics: What Strategic Structures Should Exist for the Defense Supply Chain

    National Research Council Canada - National Science Library

    Maddox, Edward D

    2005-01-01

    .... The primary research question of this study was: What strategic organizational structures should exist within the Department of Defense to facilitate further integration of the defense supply chain...

  13. The Inflammasome in Host Defense

    Directory of Open Access Journals (Sweden)

    Gang Chen

    2009-12-01

    Full Text Available Nod-like receptors have emerged as an important family of sensors in host defense. These receptors are expressed in macrophages, dendritic cells and monocytes and play an important role in microbial immunity. Some Nod-like receptors form the inflammasome, a protein complex that activates caspase-1 in response to several stimuli. Caspase-1 activation leads to processing and secretion of pro-inflammatory cytokines such as interleukin (IL-1β and IL-18. Here, we discuss recent advances in the inflammasome field with an emphasis on host defense. We also compare differential requirements for inflammasome activation in dendritic cells, macrophages and monocytes.

  14. On Three Defenses of Sentimentalism

    OpenAIRE

    Iwasa, Noriaki

    2013-01-01

    This essay shows that a moral sense or moral sentiments alone cannot identify appropriate morals. To this end, the essay analyzes three defenses of Francis Hutcheson’s, David Hume’s, and Adam Smith’s moral sense theories against the relativism charge that a moral sense or moral sentiments vary across people, societies, cultures, or times. The first defense is the claim that there is a universal moral sense or universal moral sentiments. However, even if they exist, a moral sense or moral sent...

  15. Defense Primer: The National Defense Budget Function (050)

    Science.gov (United States)

    2017-03-17

    individual policy activities. Subfunctions are assigned a numeric identifier (ending in a single digit ) related to the function to which they belong...operations, equipment repair, and maintenance of defense facilities, healthcare costs, and administration. 24% Military Personnel (MILPERS) Pay and

  16. Report on Defense Business Operations to the Congressional Defense Committees

    Science.gov (United States)

    2009-03-15

    Department’s strategic framework for planning and decision-making, and acknowledged the need to establish clear, actionable strategic goals and...Business Operations Department of Defense Business Transformation 5 2. Business Enterprise Priorities Six Business Enterprise Priorities ( BEPs ... framework products that facilitate the interoperability and integration of the operational activities, processes, data, information exchanges

  17. Quantitative Risk - Phase 1

    Science.gov (United States)

    2013-09-03

    November 2002 29. Ward, D., “The Comic Guide To Improving Defense Acquisitions”, Department of Defense, 2012 30. Nilsson, P.,Ohlsson, E...Professional Education Program, 2002 UNCLASSIFIED Contract Number: H98230-08-D-0171 TO 0030, RT 040 Report No. SERC-2013-TR-040-2 Revised

  18. Does investment in leaf defenses drive changes in leaf economic strategy? A focus on whole-plant ontogeny.

    Science.gov (United States)

    Mason, Chase M; Donovan, Lisa A

    2015-04-01

    Leaf defenses have long been studied in the context of plant growth rate, resource availability, and optimal investment theory. Likewise, one of the central modern paradigms of plant ecophysiology, the leaf economics spectrum (LES), has been extensively studied in the context of these factors across ecological scales ranging from global species data sets to temporal shifts within individuals. Despite strong physiological links between LES strategy and leaf defenses in structure, function, and resource investment, the relationship between these trait classes has not been well explored. This study investigates the relationship between leaf defenses and LES strategy across whole-plant ontogeny in three diverse Helianthus species known to exhibit dramatic ontogenetic shifts in LES strategy, focusing primarily on physical and quantitative chemical defenses. Plants were grown under controlled environmental conditions and sampled for LES and defense traits at four ontogenetic stages. Defenses were found to shift strongly with ontogeny, and to correlate strongly with LES strategy. More advanced ontogenetic stages with more conservative LES strategy leaves had higher tannin activity and toughness in all species, and higher leaf dry matter content in two of three species. Modeling results in two species support the conclusion that changes in defenses drive changes in LES strategy through ontogeny, and in one species that changes in defenses and LES strategy are likely independently driven by ontogeny. Results of this study support the hypothesis that leaf-level allocation to defenses might be an important determinant of leaf economic traits, where high investment in defenses drives a conservative LES strategy.

  19. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

    Full Text Available The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI. Our results emphasised the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt’s portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings.

  20. Financial Reporting Procedures for Defense Distribution Depots - Defense Logistics Agency Business Area of the Defense Business Operations Fund

    National Research Council Canada - National Science Library

    Young, Shelton

    1994-01-01

    In our audit of the FY 1993 Financial Statements for the Distribution Depots--Defense Logistics Agency Business Mea of the Defense Business Operations Fund, we evaluated procedures and controls used...

  1. An observational study of defensible space in the neighbourhood park

    Science.gov (United States)

    Marzukhi, M. A.; Afiq, M. A.; Zaki, S. Ahmad; Ling, O. H. L.

    2018-02-01

    The planning of neighborhood park is important to provide space for interaction, leisure, and recreation among residents in any neighbourhood area. However, on an almost daily basis, newspapers report inappropriate incidents such as snatch theft, robbery and street attack that occurred in the neighborhood park. These cases reflect the significance of physical planning and design of neighborhood park that directly affect the safety and comfort of the users. Thus, this study attempts to engage with the defensible space concept in ensuring the security elements be applied in the planning of the recreational area. This study adopts a qualitative method form of research that is retrofitted to an observational study. The observational study is significant for revealing the condition of a neighbourhood park in the ‘real-world,’ in which direct observation is conducted on Taman Tasik Puchong Perdana. The observer focused on four elements or variables of defensible space concept including the provision of facilities in the neighborhood park, territoriality, surveillance, image and milieu. The findings revealed that the planning of Taman Tasik Puchong Perdana does not deliberate the defensible space elements, which may contribute to the crime activities in the park. In these circumstances, the planning of neighbourhood park needs to include proposals for the implementation of defensible space in response to the challenges underpinned by crime problems. Besides, the awareness among the residents needs to be emphasized with the support from local authorities and other organizations to manage and sustain the safety environment in the neighborhood park.

  2. Battle through signaling between wheat and the fungal pathogen Septoria tritici revealed by proteomics and phosphoproteomics.

    Science.gov (United States)

    Yang, Fen; Melo-Braga, Marcella N; Larsen, Martin R; Jørgensen, Hans J L; Palmisano, Giuseppe

    2013-09-01

    The fungus Septoria tritici causes the disease septoria tritici blotch in wheat, one of the most economically devastating foliar diseases in this crop. To investigate signaling events and defense responses in the wheat-S. tritici interaction, we performed a time-course study of S. tritici infection in resistant and susceptible wheat using quantitative proteomics and phosphoproteomics, with special emphasis on the initial biotrophic phase of interactions. Our study revealed an accumulation of defense and stress-related proteins, suppression of photosynthesis, and changes in sugar metabolism during compatible and incompatible interactions. However, differential regulation of the phosphorylation status of signaling proteins, transcription and translation regulators, and membrane-associated proteins was observed between two interactions. The proteomic data were correlated with a more rapid or stronger accumulation of signal molecules, including calcium, H2O2, NO, and sugars, in the resistant than in the susceptible cultivar in response to the infection. Additionally, 31 proteins and 5 phosphoproteins from the pathogen were identified, including metabolic proteins and signaling proteins such as GTP-binding proteins, 14-3-3 proteins, and calcium-binding proteins. Quantitative PCR analysis showed the expression of fungal signaling genes and genes encoding a superoxide dismutase and cell-wall degrading enzymes. These results indicate roles of signaling, antioxidative stress mechanisms, and nutrient acquisition in facilitating the initial symptomless growth. Taken in its entirety, our dataset suggests interplay between the plant and S. tritici through complex signaling networks and downstream molecular events. Resistance is likely related to several rapidly and intensively triggered signal transduction cascades resulting in a multiple-level activation of transcription and translation processes of defense responses. Our sensitive approaches and model provide a comprehensive

  3. Soviet debate on missile defense

    Energy Technology Data Exchange (ETDEWEB)

    Parrott, B.

    1987-04-01

    Although the Strategic Defense Initiative (SDI) is meant to cope with the danger of a Soviet nuclear attack, the recent US debate over SDI has paid surprisingly little attention to Soviet views of ballistic missile defense. Despite the existence of a substantial body of pertinent scholarship, the debate has failed to take adequate account of major changes in Soviet ballistic missile defense policy since the mid-1960s. It has also neglected the links between current Soviet military policy and broader Soviet political and economic choices. The Soviets regard SDI not as a novel undertaking to reduce the risks of nuclear war but as an extension of the geopolitical competition between the superpowers. This competition has been dominated in the 1980s, in the Soviet view, by sharply increased US assertiveness and the decline of detente. Viewing SDI as a manifestation of these general trends, Soviet decision makers find the prospect of an unregulated race in ballistic missile defenses and military space technologies deeply unsettling. The deterioration of superpower relations has raised serious doubts in Moscow about the wisdom of Soviet external policy during the 1970s and has provoked sharp internal differences over policy toward the US. Already highly suspicious of the Reagan administration, the elite is united by a general conviction that SDI is an American gambit that may ultimately undercut past Soviet strategic gains and pose a grave new threat to Soviet security. 14 references.

  4. Managing Quadrennial Defense Review Integration: An Overview

    National Research Council Canada - National Science Library

    Schrader, John

    2001-01-01

    ...). The lessons learned from the 1997 Quadrennial Defense Review (QDR 1997) included the need for leadership guidance and integration of analytic activities to sort through the myriad issues that are always confronting the Department of Defense...

  5. Department of Defense PERSEREC (DOD PERSEREC)

    Data.gov (United States)

    Social Security Administration — The purpose of this agreement is for SSA to verify SSN information for Defense Manpower Data Center (DMDC) of the Department of Defense. DMDC will use the SSA data...

  6. The Art and Science of Defense Logistics

    Science.gov (United States)

    1995-04-01

    The Art And Science Of Defense Logistics CSC 1995 SUBJECT AREA - Logistics THE ART AND SCIENCE OF DEFENSE LOGISTICS...Government EXECUTIVE SUMMARY Title: The Art and Science of Defense Logistics Author: Major S. I. Schuler, USMC Research Questions: 1...00-1995 4. TITLE AND SUBTITLE The Art And Science Of Defense Logistics 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6

  7. Missile defense in the United States

    OpenAIRE

    Heurlin, Bertil

    2004-01-01

    The basic arguments of this paper are, first, that the current US-missile defense, being operative from fall 2004, is based upon the former experiences with missile defense, second, that missile defense closely associated with weapons of mass destruction has gained the highest priority in American national security policy due to the 9.11 attacks, and third, that the superior argument for establishing an American missile defense is to maintain global, long term political-strategic superiority....

  8. Mood States Associated with Induced Defensiveness.

    Science.gov (United States)

    Jaderlund, Natasha Slesnick; Waldron, Holly Barrett

    1994-01-01

    Compared effects of neutral and defensive mood induction in 70 students reporting conflicted versus nonconflicted families for presence of hostility, aggression, fear, anxiety, and sadness. Found that defensive students from high-conflict families reported stronger negative emotions than did neutral high-conflict and defensive low-conflict…

  9. 22 CFR 120.6 - Defense article.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Defense article. 120.6 Section 120.6 Foreign Relations DEPARTMENT OF STATE INTERNATIONAL TRAFFIC IN ARMS REGULATIONS PURPOSE AND DEFINITIONS § 120.6 Defense article. Defense article means any item or technical data designated in § 121.1 of this subchapter...

  10. 22 CFR 120.9 - Defense service.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Defense service. 120.9 Section 120.9 Foreign... Defense service. (a) Defense service means: (1) The furnishing of assistance (including training) to..., educational, or information publications and media of all kinds, training aid, orientation, training exercise...

  11. 75 FR 65462 - Renewal of Department of Defense Federal Advisory Committee; Department of Defense Military...

    Science.gov (United States)

    2010-10-25

    ... Committee; Department of Defense Military Family Readiness Council AGENCY: Department of Defense (DoD... renewing the charter for the Department of Defense Military Family Readiness Council (hereafter referred to... requirements for the support of military family readiness by the Department of Defense; and (c) evaluate and...

  12. Integration of long-range planning for management of defense transuranic waste

    International Nuclear Information System (INIS)

    Gilbert, K.V.; McFadden, M.H.; Raudenbush, M.H.; Smith, L.J.

    1984-01-01

    As described in The Defense Waste Management Plan, the defense TRU program goal is to achieve permanent disposal and to end interim storage. TRU waste is currently stored at six Department of Energy (DOE) sites, and new waste is generated at several more sites. The Waste Isolation Pilot Plant (WIPP) project is well defined, and it has been necessary to integrate the activities of other parts of the TRU program in support of DOE Headquarters policy and the WIPP schedules and technical requirements. The strategy is described in the Defense Transuranic Waste Program Strategy Document. More detailed, quantitative plans have been developed through the use of several system models, with a Long-Range Master Plan for Defense Transuranic Waste Management as the focal point for coordination of proposed plans with all the parties involved

  13. Romania's Experiences with Defense Reform Since the December 1989 Revolution and the Dimensions of Civil-Military Relations Viewed as a Trinity

    National Research Council Canada - National Science Library

    Stan, Ramona

    2007-01-01

    ...) since the collapse of communism in December 1989. The purpose of the thesis is to identify relevant qualitative and quantitative indicators for measuring the progress of Romanian political and military authorities in implementing defense reform initiatives...

  14. Self-Handicapping and Defensive Pessimism: Exploring a Model of Predictors and Outcomes from a Self-Protection Perspective.

    Science.gov (United States)

    Martin, Andrew J.; Marsh, Herbert W.; Debus, Raymond L.

    2001-01-01

    Examines self-handicapping and defensive pessimism, the factors that predict these strategies, and the associations between these strategies and a variety of academic outcomes. Findings reveal that task orientation negatively predicts both self-handicapping and defensive expectations and positively predicts reflectivity. Students high in…

  15. Missile Defense: Ballistic Missile Defense System Testing Delays Affect Delivery of Capabilities

    Science.gov (United States)

    2016-04-28

    Page 1 GAO-16-339R Ballistic Missile Defense 441 G St. N.W. Washington, DC 20548 April 28, 2016 Congressional Committees Missile Defense... Ballistic Missile Defense System Testing Delays Affect Delivery of Capabilities For over half a century, the Department of Defense (DOD) has been...funding efforts to develop a system to detect, track, and defeat enemy ballistic missiles. The current system—the Ballistic Missile Defense System

  16. Defense bill: Earmarking as usual

    Science.gov (United States)

    Earmarked funds in the $268 billion defense appropriations bill for fiscal year 1991 stirred congressional debate in late October. Senator Sam Nunn (D-Ga.), chairman of the Senate Armed Services Committee, charged that the defense bill contains questionable projects totaling tens of millions of dollars. AGU opposes legislative earmarking of money for particular institutions, maintaining that the practice prevents the best use of federal funding by circumventing competitive review. Nunn noted on the Senate floor that the appropriations bill provided specific funds for cited institutions—contravening a federal law promoting competition. “ If these programs have merit, they will succeed in a fair and competent review in competition,” Nunn said. “If no other institution in the country is able to compete, there should be no fear whatever of competition… But no one else in the world is allowed to compete to work on these projects.”

  17. Redesigning the Structure of Republic Indonesian Defense System; An Analysis of Systems Thinking

    Directory of Open Access Journals (Sweden)

    Ade Muhammad

    2013-09-01

    Full Text Available The phenomenon of Shrinking Defense Capabilities is only the tip of the iceberg of Indonesian Defense System’s problem. The root of the problem that lies beneath and outside is keep untouched. This journal is the part of the efforts to reveal the phenomenon’s structure that binding as a system. The present structure is a cause of that phenomenon and the basis of the current organization responsible for Republic Indonesia Defense sector. With the Systems thinking analysis, the research has revealed the structure that become the problem cause and give a holistic solution trough redesigning new structure based on two theories namely the Strategic-Operational Management with Vision Dissemination of Prof. Dr. Jürgen Strohhecker and the Defense System Generic Dr. Ir. Muhammad Tasrif, M.Eng and Ir. Ade Muhammad, M.Han. The logical consequences would also changing of formation of Indonesian Defense Organization. Keywords : Design, Redesigning, Defense System, System, Defense, Holistic

  18. Cyber Defense: An International View

    Science.gov (United States)

    2015-09-01

    and Mathematics at the Royal Institute of Tech- nology, Stockholm, Sweden; and Otto von Guericke University, Magdeburg , Germany . viii ix SUMMARY...and analysis to influence policy debate and bridge the gap between military and academia. The Center for Strategic Leadership and Development...provide an overview of four different national approaches to cyber defense: those of Nor- way, Estonia, Germany , and Sweden. While provid- ing a

  19. Defense Programs Transportation Risk Assessment

    International Nuclear Information System (INIS)

    Clauss, D.B.

    1994-01-01

    This paper provides an overview of the methodology used in a probabilistic transportation risk assessment conducted to assess the probabilities and consequences of inadvertent dispersal of radioactive materials arising from severe transportation accidents. The model was developed for the Defense Program Transportation Risk Assessment (DPTRA) study. The analysis incorporates several enhancements relative to previous risk assessments of hazardous materials transportation including newly-developed statistics on the frequencies and severities of tractor semitrailer accidents and detailed route characterization using the 1990 Census data

  20. Priming of antiherbivore defensive responses in plants

    Institute of Scientific and Technical Information of China (English)

    Jinwon Kim; Gary W.Felton

    2013-01-01

    Defense priming is defined as increased readiness of defense induction.A growing body of literature indicates that plants (or intact parts of a plant) are primed in anticipation of impending environmental stresses,both biotic and abiotic,and upon the following stimulus,induce defenses more quickly and strongly.For instance,some plants previously exposed to herbivore-inducible plant volatiles (HIPVs) from neighboring plants under herbivore attack show faster or stronger defense activation and enhanced insect resistance when challenged with secondary insect feeding.Research on priming of antiherbivore defense has been limited to the HIPV-mediated mechanism until recently,but significant advances were made in the past three years,including non-HIPV-mediated defense priming,epigenetic modifications as the molecular mechanism of priming,and others.It is timely to consider the advances in research on defense priming in the plantinsect interactions.

  1. Defense of a space elevator

    Energy Technology Data Exchange (ETDEWEB)

    Laubscher, B. E. (Bryan E.)

    2004-01-01

    The Space Elevator (SE) represents a major paradigm shift in space access. If the SE's promise of low-cost access is to be realized, everything becomes economically more feasible to accomplish in space. In this paper we describe a defensive system of the SE. The primary scenario adopted for this analysis is the SE based on a floating platform in the ocean along the equator. A second possible scenario is the SE stationed on land (island or continent) on or near the equator. The SE will capture the imaginations of people around the world. It will become a symbol of power, capability, wealth and prestige for the country that builds it. As such, it will become a prime terrorist target. Moreover, the tremendous economic leverage afforded by the SE might motivate rogue nations to plot its destruction. Therefore, it is necessary to consider the requirements for defense of the SE. For the purposes of this paper it is assumed that the SE is to be deployed by the United States or one of its companies, and the resources of the US are available for its defense.

  2. Genetic constraints and sexual dimorphism in immune defense

    DEFF Research Database (Denmark)

    Rolff, Jens; Armitage, Sophie Alice Octavia; Coltman, David W.

    2005-01-01

    The absence of continued evolutionary change despite the presence of genetic variation and directional selection is very common. Genetic correlations between traits can reduce the evolvability of traits. One intriguing example might be found in a sexual conflict over sexually dimorphic traits......: a common genetic architecture constrains the response to selection on a trait subjected to sexually asymmetric selection pressures. Here we show that males and females of the mealworm beetle Tenebrio molitor differ in the quantitative genetic architecture of four traits related to immune defense...

  3. Chemical and genetic defenses against disease in insect societies.

    Science.gov (United States)

    Stow, Adam; Beattie, Andrew

    2008-10-01

    The colonies of ants, bees, wasps and termites, the social insects, consist of large numbers of closely related individuals; circumstances ideal for contagious diseases. Antimicrobial assays of these animals have demonstrated a wide variety of chemical defenses against both bacteria and fungi that can be broadly classified as either external antiseptic compounds or internal immune molecules. Reducing the disease risks inherent in colonies of social insects is also achieved by behaviors, such as multiple mating or dispersal, that lower genetic relatedness both within- and among colonies. The interactions between social insects and their pathogens are complex, as illustrated by some ants that require antimicrobial and behavioral defenses against highly specialized fungi, such as those in the genus Cordyceps that attack larvae and adults and species in the genus Escovopsis that attack their food supplies. Studies of these defenses, especially in ants, have revealed remarkably sophisticated immune systems, including peptides induced by, and specific to, individual bacterial strains. The latter may be the result of the recruitment by the ants of antibiotic-producing bacteria but the extent of such three-way interactions remains unknown. There is strong experimental evidence that the evolution of sociality required dramatic increases in antimicrobial defenses and that microbes have been powerful selective agents. The antimicrobial chemicals and the insect-killing fungi may be useful in medicine and agriculture, respectively.

  4. Qualitative discussion of quantitative radiography

    International Nuclear Information System (INIS)

    Berger, H.; Motz, J.W.

    1975-01-01

    Since radiography yields an image that can be easily related to the tested object, it is superior to many nondestructive testing techniques in revealing the size, shape, and location of certain types of discontinuities. The discussion is limited to a description of the radiographic process, examination of some of the quantitative aspects of radiography, and an outline of some of the new ideas emerging in radiography. The advantages of monoenergetic x-ray radiography and neutron radiography are noted

  5. Contribution to the improvement of management in defense logistics

    Directory of Open Access Journals (Sweden)

    Srđan D. Ljubojević

    2013-12-01

    Full Text Available Introduction Changes in social environment require adequate answers of all organizational systems, including defense systems and their logistic systems. Improvement of management in defense logistics involves good knowledge of management theory and practice, knowledge of the impact of ownership and market on management, knowledge of public and other macroeconomic sectors functioning, broader opening towards environment and the exchange of knowledge, information and lessons learned with international environment. The paper presents theoretical and practical knowledge that is prerequisite for improving the management of defense and the management of defense logistic systems.   Definition and the essence of management   Regarding its complexity and a lack of a comprehensive definition, the concept of management is nowadays considered in three ways: as a skill, as social categories - structure of management, as well as a theory - a scientific discipline. When we aanalyze the phenomenon of management, with respect to the historical aspect of its development, there is a necessity to distinguish between management as a scientific discipline and management practice.   Relation between organizational science and management In theory and practice, management is associated with the achievements of many other scientific fields. One of the areas closest to management is organizational science. Today, in the management theory and organization theory, the prevailing attitudes state that these two areas are non-separable and that they are focused on the explaination of the same phenomenon, with the same desire to improve effectivity and development of different purpose systems. There is no clear boundary between organizational science and management, both from theoretical and practical aspects.   Achievements and shortcomings of organizational schools   As a result of solving problems in real systems, a number of opinions and different organizational

  6. INSTITUTIONAL BASIS OF MANAGEMENT AND EVALUATION OF UKRAINIAN DEFENSE LANDS

    Directory of Open Access Journals (Sweden)

    Garazhа Y.P

    2017-02-01

    Full Text Available The management and evaluation of defense land was revealed in the article. Specific institution is the military institutе in the institutional framework for defense land. A special regime and zoning, evaluation, payment and exclusion conditions were established for these lands. The market economy has changed the land-property relations in the country. Lands for defense used only in the framework that established the state. Recently there was a tendency of land release this subcategory. This has led to their misuse, belonging to other owners. The research problem consists of the setting clear boundaries of defense land and legal regulation mechanisms of land relations. Public ownership rights applies only to the defense lands. They are located only in the state ownership. The subject is the state that implements ownership (right to possess, use and dispose of the lands of Defense. It ensures the defense of the country and territory for military sites, airfields, parts, ammunition depots. Functional use of defense land is divided into public (military schools, socio-cultural (health centers, recreation centers, industrial (military and industrial objects, residential (cantonment, commercial (commissary, special (military installations, transport ( carpark, bridges, engineering (antennas, radars, storage (defense deport. The land for military unit were given for permanent use with the justification of the project design documentation sizes. The military part of the land for permanent use with the justification sizes by the project design documentation. Safety, security and other areas are created around military and other defense installations. There are restricted areas, prohibited areas. They have a special regime. Reform of the Armed Forces of Ukraine, the State Special Transport Service leads to the release of land and real estate. Reform of the Armed Forces of Ukraine, the State Special Transport Service leads to the release of land and real

  7. SQL Injection Attacks and Defense

    CERN Document Server

    Clarke, Justin

    2012-01-01

    SQL Injection Attacks and Defense, First Edition: Winner of the Best Book Bejtlich Read Award "SQL injection is probably the number one problem for any server-side application, and this book unequaled in its coverage." -Richard Bejtlich, Tao Security blog SQL injection represents one of the most dangerous and well-known, yet misunderstood, security vulnerabilities on the Internet, largely because there is no central repository of information available for penetration testers, IT security consultants and practitioners, and web/software developers to turn to for help. SQL Injection Att

  8. Territorial Defense, Education, and Interculturalism

    Directory of Open Access Journals (Sweden)

    Claudia Patricia Sierra Pardo

    2011-10-01

    Full Text Available The article carries out a series of reflections regarding the social and economic conditions in which the cultivation of oil palm affected the Bajo Atrato region of the Department of Chocó at the end of the nineteen nineties. It also discusses the actions carried out by communities, companies, and organizations in solidarity with the region’s cause, since these expressions make it possible to understand the role of organization and education in territorial defense processes. Finally, the article examines the different tensions, struggles, challenges, and contradictions inherent to these types of processes.

  9. Cyber defense and situational awareness

    CERN Document Server

    Kott, Alexander; Erbacher, Robert F

    2015-01-01

    This book is the first publication to give a comprehensive, structured treatment to the important topic of situational awareness in cyber defense. It presents the subject in a logical, consistent, continuous discourse, covering key topics such as formation of cyber situational awareness, visualization and human factors, automated learning and inference, use of ontologies and metrics, predicting and assessing impact of cyber attacks, and achieving resilience of cyber and physical mission. Chapters include case studies, recent research results and practical insights described specifically for th

  10. Disposal of Hanford defense waste

    International Nuclear Information System (INIS)

    Holten, R.A.; Burnham, J.B.; Nelson, I.C.

    1986-01-01

    An Environmental Impact Statement (EIS) on the disposal of Hanford Defense Waste is scheduled to be released near the end of March, 1986. This EIS will evaluate the impacts of alternatives for disposal of high-level, tank, and transuranic wastes which are now stored at the Department of Energy's Hanford Site or will be produced there in the future. In addition to releasing the EIS, the Department of Energy is conducting an extensive public participation process aimed at providing information to the public and receiving comments on the EIS

  11. Quantitative investment analysis

    CERN Document Server

    DeFusco, Richard

    2007-01-01

    In the "Second Edition" of "Quantitative Investment Analysis," financial experts Richard DeFusco, Dennis McLeavey, Jerald Pinto, and David Runkle outline the tools and techniques needed to understand and apply quantitative methods to today's investment process.

  12. THE DEFENSE PLANNING SYSTEMS AND THEIR IMPLICATIONS

    Directory of Open Access Journals (Sweden)

    Laszlo STICZ

    2010-01-01

    Full Text Available Defense planning in the Alliance is a fundamental element of the arrangements which enable its member countries to enjoy the crucial political, military and resource advantages of collective defense and other common military efforts to enhance security and stability. In this respect, the aim of this paper is to outline the role of the Armed Forces and the specific processes aiming to achieve the ultimate goal of a nation regarding national security, with focus on defense planning and the PDPS.

  13. Student Papers on Strategic Defense Initiative.

    Science.gov (United States)

    1985-01-01

    895. 3. "Scientific Canvas" AWST, p. 19. 4. Halliday, p. 548. 5. William Shiner, Lasers (New York: Mc Graw -Hill, 1980), p. 21. - 30...and Design. New York: Mc Graw -Hill, 1980. U.S. Department of Defense. The Strategic Defense Ini- tiative: Defensive Technologies Study. Washington...Armageddon," Armed Forces Journal, February 1983, p. 30. 7. David Baker, The Shape of Wars to Come (Cambridge: Patrick Stephens , Ltd, 1981), p. 109

  14. Defense Transuranic Waste Program Strategy Document

    International Nuclear Information System (INIS)

    1984-01-01

    The Defense Transuranic Waste Program (DTWP) Strategy Document presents the general strategy for managing transuranic (TRU) waste materials generated during defense and research activities regulated by the US Department of Energy. The Strategy Document includes discussion of objectives and activities relating to the entire Defense Transuranic Waste Program. However, the primary focus is on the specific management responsibilities of the Transuranic Waste Lead Organization (TLO). The document also includes an updated summary of progress on TLO-managed activities over the past year

  15. Status of DOE defense waste management policy

    International Nuclear Information System (INIS)

    Oertel, K.G.; Scott, R.S.

    1983-01-01

    This paper very briefly traces the statutory basis for DOE management of atomic energy defense activity wastes, touches on the authority of the Federal agencies involved in the regulation of defense nuclear waste management, and addresses the applicable regulations and their status. This background sets the stage for a fairly detailed discussion of management and disposal strategies of the Defense Waste and Byproducts Management Program

  16. Active Computer Network Defense: An Assessment

    Science.gov (United States)

    2001-04-01

    sufficient base of knowledge in information technology can be assumed to be working on some form of computer network warfare, even if only defensive in...the Defense Information Infrastructure (DII) to attack. Transmission Control Protocol/ Internet Protocol (TCP/IP) networks are inherently resistant to...aims to create this part of information superiority, and computer network defense is one of its fundamental components. Most of these efforts center

  17. Rigour in quantitative research.

    Science.gov (United States)

    Claydon, Leica Sarah

    2015-07-22

    This article which forms part of the research series addresses scientific rigour in quantitative research. It explores the basis and use of quantitative research and the nature of scientific rigour. It examines how the reader may determine whether quantitative research results are accurate, the questions that should be asked to determine accuracy and the checklists that may be used in this process. Quantitative research has advantages in nursing, since it can provide numerical data to help answer questions encountered in everyday practice.

  18. SELF-DEFENSE IN KARABAKH CONFLICT?

    Directory of Open Access Journals (Sweden)

    Saeed Bagheri

    2015-01-01

    Full Text Available Use of force is one of the principles of international law which has been banned by the UN Charter and modern constitutions. However, since the enforcement of the UN Charter, self-defense has become the preferred excuse for states to justify their use of force. But applying self-defense requires some conditions. Immediacy is one of the important conditions of self-defense. Immediacy defined as the time span between armed attacks and reaction to it, is the main discourse. This condition requires self defense immediately after the armed conflict or during a rational time span since its occurance.In this respect, the emerging Karabakh Conflict between Armenia and Azerbaijan in the 1990s is important. After Armenia’s armed attacks, Azerbaijan has acted within the scope of legitimate self-defense. But in accordance with UN Security Council cease-fire resolution Azerbaijan has suspended its self-defense actions. However, today, still twenty percent of Azerbaijani territory is still under Armenian occupation. Accordingly, after a long time the validity of Azerbaijan’s right to legitimate self-defense is still subject to arguments.In this article, by comparing two different approaches (strict and board interpretation approaches on the temporal link between the measures of self-defense and the armed attacks (immediacy, the temporal link between the self-defense countermeasures of Azerbaijan and armed attacks by Armenia in Karabakh Conflict will be examined.

  19. Variation in plant defense suppresses herbivore performance

    Science.gov (United States)

    Pearse, Ian; Paul, Ryan; Ode, Paul J.

    2018-01-01

    Defensive variability of crops and natural systems can alter herbivore communities and reduce herbivory. However, it is still unknown how defense variability translates into herbivore suppression. Nonlinear averaging and constraints in physiological tracking (also more generally called time-dependent effects) are the two mechanisms by which defense variability might impact herbivores. We conducted a set of experiments manipulating the mean and variability of a plant defense, showing that defense variability does suppress herbivore performance and that it does so through physiological tracking effects that cannot be explained by nonlinear averaging. While nonlinear averaging predicted higher or the same herbivore performance on a variable defense than on an invariable defense, we show that variability actually decreased herbivore performance and population growth rate. Defense variability reduces herbivore performance in a way that is more than the average of its parts. This is consistent with constraints in physiological matching of detoxification systems for herbivores experiencing variable toxin levels in their diet and represents a more generalizable way of understanding the impacts of variability on herbivory. Increasing defense variability in croplands at a scale encountered by individual herbivores can suppress herbivory, even if that is not anticipated by nonlinear averaging.

  20. Defense Business Operations Fund Inventory Record Accuracy

    National Research Council Canada - National Science Library

    1998-01-01

    .... The overall objective of the audit was to determine whether inventory amounts on the FY 1996 Defense Business Operations Fund Consolidated Financial Statements were presented fairly in accordance...

  1. Quantitation: clinical applications

    International Nuclear Information System (INIS)

    Britton, K.E.

    1982-01-01

    Single photon emission tomography may be used quantitatively if its limitations are recognized and quantitation is made in relation to some reference area on the image. Relative quantitation is discussed in outline in relation to the liver, brain and pituitary, thyroid, adrenals, and heart. (U.K.)

  2. Defense Agency Travel Payments at Defense Finance and Accounting Service Indianapolis Center

    National Research Council Canada - National Science Library

    1997-01-01

    The audit objective was to assess the effectiveness of Defense Finance and Accounting Service Indianapolis Center management controls over payments to Defense agency personnel for temporary duty and local travel...

  3. Report to the Congressional Defense Committees: Status of the Department of Defense's Business Transformation Efforts

    National Research Council Canada - National Science Library

    2008-01-01

    ...). It directs the Secretary of Defense to provide the Congressional Defense Committees with an annual report on the Department's business transformation efforts and compliance with the requirements of the law...

  4. For a NATO defensive deterrent

    International Nuclear Information System (INIS)

    Smoke, R.

    1988-01-01

    This paper proposes that NATO should adopt, in a gradual and orderly fashion, a grand strategy and accompanying posture distinctly different from its present one. The strategy the author recommends has variously been termed non-provocative defence, defence-only defence, or defensive deterrence, employs the latter term here. By it the author means a militarily sound strategy relying solely on conventional weapons so long as the enemy uses only conventional weapons, and a posture that is unambiguously capable only of defence. Secure, second-strike nuclear forces would be retained for deterrence of any nuclear use by the opponent. This goal is consistent with the goal stated in Frank Barnaby's companion paper in this volume; here however the author lays the emphasis on political and politico-military rationales for a defensive deterrent. The paper begins with two brief arguments why a shift in NATO strategy is needed, advances some distinctions among the possible alternatives, and then presents some seven rationales for its recommended policy

  5. Energetic Techniques For Planetary Defense

    Science.gov (United States)

    Barbee, B.; Bambacus, M.; Bruck Syal, M.; Greenaugh, K. C.; Leung, R. Y.; Plesko, C. S.

    2017-12-01

    Near-Earth Objects (NEOs) are asteroids and comets whose heliocentric orbits tend to approach or cross Earth's heliocentric orbit. NEOs of various sizes periodically collide with Earth, and efforts are currently underway to discover, track, and characterize NEOs so that those on Earth-impacting trajectories are discovered far enough in advance that we would have opportunities to deflect or destroy them prior to Earth impact, if warranted. We will describe current efforts by the National Aeronautics and Space Administration (NASA) and the National Nuclear Security Administration (NNSA) to assess options for energetic methods of deflecting or destroying hazardous NEOs. These methods include kinetic impactors, which are spacecraft designed to collide with an NEO and thereby alter the NEO's trajectory, and nuclear engineering devices, which are used to rapidly vaporize a layer of NEO surface material. Depending on the amount of energy imparted, this can result in either deflection of the NEO via alteration of its trajectory, or robust disruption of the NEO and dispersal of the remaining fragments. We have studied the efficacies and limitations of these techniques in simulations, and have combined the techniques with corresponding spacecraft designs and mission designs. From those results we have generalized planetary defense mission design strategies and drawn conclusions that are applicable to a range of plausible scenarios. We will present and summarize our research efforts to date, and describe approaches to carrying out planetary defense missions with energetic NEO deflection or disruption techniques.

  6. Verification of excess defense material

    International Nuclear Information System (INIS)

    Fearey, B.L.; Pilat, J.F.; Eccleston, G.W.; Nicholas, N.J.; Tape, J.W.

    1997-01-01

    The international community in the post-Cold War period has expressed an interest in the International Atomic Energy Agency (IAEA) using its expertise in support of the arms control and disarmament process in unprecedented ways. The pledges of the US and Russian presidents to place excess defense materials under some type of international inspections raises the prospect of using IAEA safeguards approaches for monitoring excess materials, which include both classified and unclassified materials. Although the IAEA has suggested the need to address inspections of both types of materials, the most troublesome and potentially difficult problems involve approaches to the inspection of classified materials. The key issue for placing classified nuclear components and materials under IAEA safeguards is the conflict between these traditional IAEA materials accounting procedures and the US classification laws and nonproliferation policy designed to prevent the disclosure of critical weapon-design information. Possible verification approaches to classified excess defense materials could be based on item accountancy, attributes measurements, and containment and surveillance. Such approaches are not wholly new; in fact, they are quite well established for certain unclassified materials. Such concepts may be applicable to classified items, but the precise approaches have yet to be identified, fully tested, or evaluated for technical and political feasibility, or for their possible acceptability in an international inspection regime. Substantial work remains in these areas. This paper examines many of the challenges presented by international inspections of classified materials

  7. Light-dependent expression of flg22-induced defense genes in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Satoshi eSano

    2014-10-01

    Full Text Available Chloroplasts have been reported to generate retrograde immune signals that activate defense gene expression in the nucleus. However, the roles of light and photosynthesis in plant immunity remain largely elusive. In this study, we evaluated the effects of light on the expression of defense genes induced by flg22, a peptide derived from bacterial flagellins which acts as a potent elicitor in plants. Whole-transcriptome analysis of flg22-treated Arabidopsis thaliana seedlings under light and dark conditions for 30 min revealed that a number of (30% genes strongly induced by flg22 (>4.0 require light for their rapid expression, whereas flg22-repressed genes include a significant number of genes that are down-regulated by light. Furthermore, light is responsible for the flg22-induced accumulation of salicylic acid, indicating that light is indispensable for basal defense responses in plants. To elucidate the role of photosynthesis in defense, we further examined flg22-induced defense gene expression in the presence of specific inhibitors of photosynthetic electron transport: 3-(3,4-dichlorophenyl-1,1-dimethylurea (DCMU and 2,5-dibromo-3-methyl-6-isopropyl-benzoquinone (DBMIB. Light-dependent expression of defense genes was largely suppressed by DBMIB, but only partially suppressed by DCMU. These findings suggest that photosynthetic electron flow plays a role in controling the light-dependent expression of flg22-inducible defense genes.

  8. The role of defensive ecological interactions in the evolution of conotoxins.

    Science.gov (United States)

    Prashanth, J R; Dutertre, S; Jin, A H; Lavergne, V; Hamilton, B; Cardoso, F C; Griffin, J; Venter, D J; Alewood, P F; Lewis, R J

    2016-01-01

    Venoms comprise of complex mixtures of peptides evolved for predation and defensive purposes. Remarkably, some carnivorous cone snails can inject two distinct venoms in response to predatory or defensive stimuli, providing a unique opportunity to study separately how different ecological pressures contribute to toxin diversification. Here, we report the extraordinary defensive strategy of the Rhizoconus subgenus of cone snails. The defensive venom from this worm-hunting subgenus is unusually simple, almost exclusively composed of αD-conotoxins instead of the ubiquitous αA-conotoxins found in the more complex defensive venom of mollusc- and fish-hunting cone snails. A similarly compartmentalized venom gland as those observed in the other dietary groups facilitates the deployment of this defensive venom. Transcriptomic analysis of a Conus vexillum venom gland revealed the αD-conotoxins as the major transcripts, with lower amounts of 15 known and four new conotoxin superfamilies also detected with likely roles in prey capture. Our phylogenetic and molecular evolution analysis of the αD-conotoxins from five subgenera of cone snails suggests they evolved episodically as part of a defensive strategy in the Rhizoconus subgenus. Thus, our results demonstrate an important role for defence in the evolution of conotoxins. © 2015 John Wiley & Sons Ltd.

  9. Other Defense Organizations and Defense Finance and Accounting Service Controls Over High-Risk Transactions Were Not Effective

    Science.gov (United States)

    2016-03-28

    Defense Organizations and Defense Finance and Accounting Service Controls Over High-Risk Transactions Were Not Effective M A R C H 2 8 , 2 0 1 6...Defense Organizations and Defense Finance and Accounting Service Controls Over High-Risk Transactions Were Not Effective Visit us at www.dodig.mil... FINANCE AND ACCOUNTING SERVICE DIRECTOR, DEFENSE HEALTH AGENCY SUBJECT: Other Defense Organizations and Defense Finance and Accounting Service

  10. The US-Russia missile defense dialogue as a factor of the Russian defense policy

    OpenAIRE

    Dmitry Suslov

    2013-01-01

    To a big extent the Russian defense policy and, as a consequence, development of the Russian defense industrial complex, is determined by the prospects of the US missile defense policy and fate of the US-Russia negotiations in this area. As a cooperative solution seems improbable in the observable future, Russia plans to develop certain response measures of military nature, including creation of a new heavy ICBM, and to create its own missile defense by 2015. However, this policy does not see...

  11. Strategic Defense Initiative: Splendid Defense or Pipe Dream? Headline Series No. 275.

    Science.gov (United States)

    Armstrong, Scott; Grier, Peter

    This pamphlet presents a discussion of the various components of President Reagan's Strategic Defense Initiative (SDI) including the problem of pulling together various new technologies into an effective defensive system and the politics of the so-called "star wars" system. An important part of the defense initiative is the…

  12. Defense pattern of Chinese cork oak across latitudinal gradients: influences of ontogeny, herbivory, climate and soil nutrients

    Science.gov (United States)

    Wang, Xiao-Fei; Liu, Jian-Feng; Gao, Wen-Qiang; Deng, Yun-Peng; Ni, Yan-Yan; Xiao, Yi-Hua; Kang, Feng-Feng; Wang, Qi; Lei, Jing-Pin; Jiang, Ze-Ping

    2016-06-01

    Knowledge of latitudinal patterns in plant defense and herbivory is crucial for understanding the mechanisms that govern ecosystem functioning and for predicting their responses to climate change. Using a widely distributed species in East Asia, Quercus variabilis, we aim to reveal defense patterns of trees with respect to ontogeny along latitudinal gradients. Six leaf chemical (total phenolics and total condensed tannin concentrations) and physical (cellulose, hemicellulose, lignin and dry mass concentration) defensive traits as well as leaf herbivory (% leaf area loss) were investigated in natural Chinese cork oak (Q. variabilis) forests across two ontogenetic stages (juvenile and mature trees) along a ~14°-latitudinal gradient. Our results showed that juveniles had higher herbivory values and a higher concentration of leaf chemical defense substances compared with mature trees across the latitudinal gradient. In addition, chemical defense and herbivory in both ontogenetic stages decreased with increasing latitude, which supports the latitudinal herbivory-defense hypothesis and optimal defense theory. The identified trade-offs between chemical and physical defense were primarily determined by environmental variation associated with the latitudinal gradient, with the climatic factors (annual precipitation, minimum temperature of the coldest month) largely contributing to the latitudinal defense pattern in both juvenile and mature oak trees.

  13. 76 FR 22681 - Defense Logistics Agency (DLA) Address Directory

    Science.gov (United States)

    2011-04-22

    ... DEPARTMENT OF DEFENSE Office of the Secretary Defense Logistics Agency (DLA) Address Directory AGENCY: Department of Defense. ACTION: Notice. SUMMARY: The Defense Logistics Agency (DLA) is updating... Directory: Defense Logistics Agency Headquarters, Andrew T. McNamara Building, 8725 John J. Kingman Road...

  14. 2015 Assessment of the Ballistic Missile Defense System (BMDS)

    Science.gov (United States)

    2016-04-01

    Director, Operational Test and Evaluation 2015 Assessment of the Ballistic Missile Defense System (BMDS...Evaluation (DOT&E) as they pertain to the Ballistic Missile Defense System (BMDS). Congress specified these requirements in the fiscal year 2002 (FY02...systems are the Ground-based Midcourse Defense (GMD), Aegis Ballistic Missile Defense (Aegis BMD), Terminal High-Altitude Area Defense (THAAD), and

  15. 78 FR 17176 - Federal Acquisition Regulation; Defense Base Act

    Science.gov (United States)

    2013-03-20

    ... Regulation; Defense Base Act AGENCIES: Department of Defense (DoD), General Services Administration (GSA... the Defense Base Act. DATES: Interested parties should submit written comments to the Regulatory... Act as extended by the Defense Base Act. II. Discussion and Analysis The Defense Base Act of 1941...

  16. 75 FR 43156 - Federal Advisory Committee; Missile Defense Advisory Committee

    Science.gov (United States)

    2010-07-23

    ... DEPARTMENT OF DEFENSE Office of the Secretary Federal Advisory Committee; Missile Defense Advisory Committee AGENCY: Missile Defense Agency (MDA), DoD. ACTION: Notice of closed meeting. SUMMARY: Under the... Defense announces that the Missile Defense Advisory Committee will meet on August 4 and 5, 2010, in...

  17. Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems.

    Science.gov (United States)

    Iranzo, Jaime; Lobkovsky, Alexander E; Wolf, Yuri I; Koonin, Eugene V

    2015-03-13

    Parasite-host arms race is one of the key factors in the evolution of life. Most cellular life forms, in particular prokaryotes, possess diverse forms of defense against pathogens including innate immunity, adaptive immunity and programmed cell death (altruistic suicide). Coevolution of these different but interacting defense strategies yields complex evolutionary regimes. We develop and extensively analyze a computational model of coevolution of different defense strategies to show that suicide as a defense mechanism can evolve only in structured populations and when the attainable degree of immunity against pathogens is limited. The general principle of defense evolution seems to be that hosts do not evolve two costly defense mechanisms when one is sufficient. Thus, the evolutionary interplay of innate immunity, adaptive immunity and suicide, leads to an equilibrium state where the combination of all three defense strategies is limited to a distinct, small region of the parameter space. The three strategies can stably coexist only if none of them are highly effective. Coupled adaptive immunity-suicide systems, the existence of which is implied by the colocalization of genes for the two types of defense in prokaryotic genomes, can evolve either when immunity-associated suicide is more efficacious than other suicide systems or when adaptive immunity functionally depends on the associated suicide system. Computational modeling reveals a broad range of outcomes of coevolution of anti-pathogen defense strategies depending on the relative efficacy of different mechanisms and population structure. Some of the predictions of the model appear compatible with recent experimental evolution results and call for additional experiments.

  18. Defensive effects of extrafloral nectaries in quaking aspen differ with scale.

    Science.gov (United States)

    Mortensen, Brent; Wagner, Diane; Doak, Patricia

    2011-04-01

    The effects of plant defenses on herbivory can differ among spatial scales. This may be particularly common with indirect defenses, such as extrafloral nectaries (EFNs), that attract predatory arthropods and are dependent on predator distribution, abundance, and behavior. We tested the defensive effects of EFNs in quaking aspen (Populus tremuloides Michx.) against damage by a specialist herbivore, the aspen leaf miner (Phyllocnistis populiella Cham.), at the scale of individual leaves and entire ramets (i.e., stems). Experiments excluding crawling arthropods revealed that the effects of aspen EFNs differed at the leaf and ramet scales. Crawling predators caused similar reductions in the percent leaf area mined on individual leaves with and without EFNs. However, the extent to which crawling predators increased leaf miner mortality and, consequently, reduced mining damage increased with EFN expression at the ramet scale. Thus, aspen EFNs provided a diffuse defense, reducing damage to leaves across a ramet regardless of leaf-scale EFN expression. We detected lower leaf miner damage and survival unassociated with crawling predators on EFN-bearing leaves, suggesting that direct defenses (e.g., chemical defenses) were stronger on leaves with than without EFNs. Greater direct defenses on EFN-bearing leaves may reduce the probability of losing these leaves and thus weakening ramet-scale EFN defense. Aspen growth was not related to EFN expression or the presence of crawling predators over the course of a single season. Different effects of aspen EFNs at the leaf and ramet scales suggest that future studies may benefit from examining indirect defenses simultaneously at multiple scales.

  19. Website Fingerprinting Defenses at the Application Layer

    Directory of Open Access Journals (Sweden)

    Cherubin Giovanni

    2017-04-01

    Full Text Available Website Fingerprinting (WF allows a passive network adversary to learn the websites that a client visits by analyzing traffic patterns that are unique to each website. It has been recently shown that these attacks are particularly effective against .onion sites, anonymous web servers hosted within the Tor network. Given the sensitive nature of the content of these services, the implications of WF on the Tor network are alarming. Prior work has only considered defenses at the client-side arguing that web servers lack of incentives to adopt countermeasures. Furthermore, most of these defenses have been designed to operate on the stream of network packets, making practical deployment difficult. In this paper, we propose two application-level defenses including the first server-side defense against WF, as .onion services have incentives to support it. The other defense is a lightweight client-side defense implemented as a browser add-on, improving ease of deployment over previous approaches. In our evaluations, the server-side defense is able to reduce WF accuracy on Tor .onion sites from 69.6% to 10% and the client-side defense reduces accuracy from 64% to 31.5%.

  20. Strengthening Nordic-Baltic Defense Capabilities

    DEFF Research Database (Denmark)

    Breitenbauch, Henrik Ø.

    2014-01-01

    and troubling challenge to the way international security has been structured in Europe since the end of the Cold War. While most of the existing defense cooperation with a view of strengthening defense capabilities has been carried out within the internationally renowned framework of NORDEFCO...

  1. Policy implications of the Strategic Defense Initiative

    International Nuclear Information System (INIS)

    Goodwin, R.C.

    1991-01-01

    Specific topics include: the technological feasibility of proposed components and architectures; the compatibility of the proposed systems with existing and proposed arms control agreements, with special emphasis upon the ABM Treaty, Outer Space Treaty, the Defense and Space Treaty, and the START Treaty; the compatibility of proposed systems with classical warfare doctrine and the four modern strategic nuclear doctrines of Massive Retaliation, Assured Destruction, Countervailing and Flexible Response; the economics of strategic defense including an assessment of overall governmental spending, of the suballocation for defense, and of the feasibility of defensive systems which are cost-effective at the margin; and, in summary, an assessment of the New Strategic Concept which balances arms control, offensive forces, and defensive forces. This study falls within the realm of defense policy analysis in that it attempts to determine whether the administration's proposed Strategic Defense Initiative, as well as the long-term strategic defensive systems derived from SDI research, constitute efficient, desirable allocation of scarce government resources - especially in a period of seemingly relaxed superpower tensions and numerous demands upon those resources

  2. Civil defense should be mandatory

    International Nuclear Information System (INIS)

    Kearney, C.H.

    1985-01-01

    In this paper, the author exposes myths about the effects of nuclear weapons so that the U.S. can begin the necessary task of a mandatory civil defense program. An all-out nuclear war between Russia and the United States would be the worst catastrophe in history, a tragedy so huge it is difficult to comprehend. Even so, it would be far from the end of human life on earth. The dangers from nuclear weapons have been distorted and exaggerated for varied reasons. These exaggerations have become demoralizing myths, believed by millions of Americans. The author has found that many people see no sense in talking about details of survival skills. Only after they have begun to question the truth of these myths do they become interested, under normal peacetime conditions, in acquiring nuclear war survival skills. The author examines the most harmful of the myths about nuclear war dangers, along with some of the grim facts

  3. Defense program pushes microchip frontiers

    Science.gov (United States)

    Julian, K.

    1985-05-01

    The very-high-speed integrated circuit (VHSIC) program of the Department of Defense will have a significant effect on the expansion of integrated circuit technology. This program, which is to cost several hundred million dollars, is accelerating the trend toward higher-speed, denser circuitry for microchips through innovative design and fabrication techniques. Teams in six different American companies are to design and fabricate a military useful 'brassboard' system which would employ chips developed in the first phase of the VHSIC program. Military objectives envisaged include automatic monitoring of displays in tactical aircraft by means of an artificial intelligence system, a brassboard used in airborne electronic warfare system, and antisubmarine warfare applications. After a fivefold improvement in performance achieved in the first phase, the second phase is concerned with a further 20-fold increase. The entire VHSIC program is, therefore, to produce a 100-fold gain over the state of the art found when the program started.

  4. Low power unattended defense reactor

    International Nuclear Information System (INIS)

    Kirchner, W.L.; Meier, K.L.

    1984-01-01

    A small, low power, passive, nuclear reactor electric power supply has been designed for unattended defense applications. Through innovative utilization of existing proven technologies and components, a highly reliable, ''walk-away safe'' design has been obtained. Operating at a thermal power level of 200 kWt, the reactor uses low enrichment uranium fuel in a graphite block core to generate heat that is transferred through heat pipes to a thermoelectric (TE) converter. Waste heat is removed from the TEs by circulation of ambient air. Because such a power supply offers the promise of minimal operation and maintenance (OandM) costs as well as no fuel logistics, it is particularly attractive for remote, unattended applications such as the North Warning System

  5. Low power unattended defense reactor

    International Nuclear Information System (INIS)

    Kirchner, W.L.; Meier, K.L.

    1984-01-01

    A small, low power, passive, nuclear reactor electric power supply has been designed for unattended defense applications. Through innovative utilization of existing proven technologies and components, a highly reliable, walk-away safe design has been obtained. Operating at a thermal power level of 200 kWt, the reactor uses low enrichment uranium fuel in a graphite block core to generate heat that is transferred through heat pipes to a thermoelectric (TE) converter. Waste heat is removed from the TEs by circulation of ambient air. Because such a power supply offers the promise of minimal operation and maintenance (O and M) costs as well as no fuel logistics, it is particularly attractive for remote, unattended applications such as the North Warning System

  6. Physics of a ballistic missile defense - The chemical laser boost-phase defense

    Science.gov (United States)

    Grabbe, Crockett L.

    1988-01-01

    The basic physics involved in proposals to use a chemical laser based on satellites for a boost-phase defense are investigated. After a brief consideration of simple physical conditions for the defense, a calculation of an equation for the number of satellites needed for the defense is made along with some typical values of this for possible future conditions for the defense. Basic energy and power requirements for the defense are determined. A sumary is made of probable minimum conditions that must be achieved for laser power, targeting accuracy, number of satellites, and total sources for power needed.

  7. Immune defense in leaf-cutting ants

    DEFF Research Database (Denmark)

    Armitage, Sophie A O; Broch, Jens F; Marín, Hermogenes Fernández

    2011-01-01

    To ameliorate the impact of disease, social insects combine individual innate immune defenses with collective social defenses. This implies that there are different levels of selection acting on investment in immunity, each with their own trade-offs. We present the results of a cross......-fostering experiment designed to address the influences of genotype and social rearing environment upon individual and social immune defenses. We used a multiply mating leaf-cutting ant, enabling us to test for patriline effects within a colony, as well as cross-colony matriline effects. The worker's father influenced...... both individual innate immunity (constitutive antibacterial activity) and the size of the metapleural gland, which secretes antimicrobial compounds and functions in individual and social defense, indicating multiple mating could have important consequences for both defense types. However, the primarily...

  8. Study on defensive security concepts and policies

    International Nuclear Information System (INIS)

    1993-01-01

    The report begins by describing the background against which the proposal for the study emerged-the welcome developments brought about by the end of the cold war but also the emergence of new threats and the reappearance of long-standing problems. The study proceeds to examine current trends in the international security environment and how they may influence the peaceful settlement of dispute and the effecting of restraint and a defensive orientation in the development, maintenance and use of armed forces. A discussion of the substance and main features of defensive security concepts and policies follows. Existing studies and models designed to eliminate the offensive character of military force postures by effecting a defensive orientation of capabilities are surveyed. In addition, the study discusses political and military aspects of defensive security, pointing out how defensive security differs from those existing models

  9. Status of defense radioactive waste disposal activities

    International Nuclear Information System (INIS)

    Wade, T.W.

    1988-01-01

    The Office of Defense Programs, U.S. Department of Energy, is responsible for the production of nuclear weapons and materials for national defense. As a byproduct to their activities, nuclear production facilities have generated, and will continue to generate, certain radioactive, hazardous, or mixed wastes that must be managed and disposed of in a safe and cost-effective manner. Compliance with all applicable Federal and State regulations is required. This paper describes the principal elements that comprise Defense Programs' approach to waste management and disposal. The status of high-level, transuranic, and low-level radioactive waste disposal is set forth. Defense Programs' activities in connection with the environmental restoration of inactive facilities and with the safe transport of waste materials are summarized. Finally, the principal challenges to realizing the goals set for the defense waste program are discussed in terms of regulatory, public acceptance, technical, and budget issues

  10. Silverleaf whitefly induces salicylic acid defenses and suppresses effectual jasmonic acid defenses.

    Science.gov (United States)

    Zarate, Sonia I; Kempema, Louisa A; Walling, Linda L

    2007-02-01

    The basal defenses important in curtailing the development of the phloem-feeding silverleaf whitefly (Bemisia tabaci type B; SLWF) on Arabidopsis (Arabidopsis thaliana) were investigated. Sentinel defense gene RNAs were monitored in SLWF-infested and control plants. Salicylic acid (SA)-responsive gene transcripts accumulated locally (PR1, BGL2, PR5, SID2, EDS5, PAD4) and systemically (PR1, BGL2, PR5) during SLWF nymph feeding. In contrast, jasmonic acid (JA)- and ethylene-dependent RNAs (PDF1.2, VSP1, HEL, THI2.1, FAD3, ERS1, ERF1) were repressed or not modulated in SLWF-infested leaves. To test for a role of SA and JA pathways in basal defense, SLWF development on mutant and transgenic lines that constitutively activate or impair defense pathways was determined. By monitoring the percentage of SLWF nymphs in each instar, we show that mutants that activate SA defenses (cim10) or impair JA defenses (coi1) accelerated SLWF nymphal development. Reciprocally, mutants that activate JA defenses (cev1) or impair SA defenses (npr1, NahG) slowed SLWF nymphal development. Furthermore, when npr1 plants, which do not activate downstream SA defenses, were treated with methyl jasmonate, a dramatic delay in nymph development was observed. Collectively, these results showed that SLWF-repressed, JA-regulated defenses were associated with basal defense to the SLWF.

  11. Silverleaf Whitefly Induces Salicylic Acid Defenses and Suppresses Effectual Jasmonic Acid Defenses1[W][OA

    Science.gov (United States)

    Zarate, Sonia I.; Kempema, Louisa A.; Walling, Linda L.

    2007-01-01

    The basal defenses important in curtailing the development of the phloem-feeding silverleaf whitefly (Bemisia tabaci type B; SLWF) on Arabidopsis (Arabidopsis thaliana) were investigated. Sentinel defense gene RNAs were monitored in SLWF-infested and control plants. Salicylic acid (SA)-responsive gene transcripts accumulated locally (PR1, BGL2, PR5, SID2, EDS5, PAD4) and systemically (PR1, BGL2, PR5) during SLWF nymph feeding. In contrast, jasmonic acid (JA)- and ethylene-dependent RNAs (PDF1.2, VSP1, HEL, THI2.1, FAD3, ERS1, ERF1) were repressed or not modulated in SLWF-infested leaves. To test for a role of SA and JA pathways in basal defense, SLWF development on mutant and transgenic lines that constitutively activate or impair defense pathways was determined. By monitoring the percentage of SLWF nymphs in each instar, we show that mutants that activate SA defenses (cim10) or impair JA defenses (coi1) accelerated SLWF nymphal development. Reciprocally, mutants that activate JA defenses (cev1) or impair SA defenses (npr1, NahG) slowed SLWF nymphal development. Furthermore, when npr1 plants, which do not activate downstream SA defenses, were treated with methyl jasmonate, a dramatic delay in nymph development was observed. Collectively, these results showed that SLWF-repressed, JA-regulated defenses were associated with basal defense to the SLWF. PMID:17189328

  12. Investment in defense and cost of predator-induced defense along a resource gradient

    DEFF Research Database (Denmark)

    Steiner, Uli

    2007-01-01

    An organism's investment in different traits to reduce predation is determined by the fitness benefit of the defense relative to the fitness costs associated with the allocation of time and resources to the defense. Inherent tradeoffs in time and resource allocation should result in differential...... investment in defense along a resource gradient, but competing models predict different patterns of investment. There are currently insufficient empirical data on changes in investment in defensive traits or their costs along resource gradients to differentiate between the competing allocation models....... In this study, I exposed tadpoles to caged predators along a resource gradient in order to estimate investment in defense and costs of defense by assessing predator-induced plasticity. Induced defenses included increased tail depth, reduced feeding, and reduced swimming activity; costs associated...

  13. Sandia National Laboratories: National Security Missions: Defense Systems

    Science.gov (United States)

    ; Technology Defense Systems & Assessments About Defense Systems & Assessments Program Areas Audit Sandia's Economic Impact Licensing & Technology Transfer Browse Technology Portfolios ; Culture Work-Life Balance Special Programs Nuclear Weapons Defense Systems Global Security Energy Facebook

  14. Analysis of Defense Industry Consolidation Effects on Program Acquisition Costs

    National Research Council Canada - National Science Library

    Hoff, Russell V

    2007-01-01

    .... This thesis examines whether cost changes are evident following consolidation within the defense industry by conducting a regression analysis of Major Defense Acquisition Programs across 13 broad defense market sectors...

  15. HOMA: Israel's National Missile Defense Strategy (Abridged Version)

    National Research Council Canada - National Science Library

    Lailari, Guermantes

    2002-01-01

    ... (Hebrew for Fortress Wall), Chapter 1 discusses the fundamentals of missile defense and the reason why Israel's missile defense system affects US national security interests, Chapter 2 describes Israel's missile defense...

  16. Defensive Medicine in U.S. Spine Neurosurgery.

    Science.gov (United States)

    Din, Ryan S; Yan, Sandra C; Cote, David J; Acosta, Michael A; Smith, Timothy R

    2017-02-01

    Observational cross-sectional survey. To compare defensive practices of U.S. spine and nonspine neurosurgeons in the context of state medical liability risk. Defensive medicine is a commonly reported and costly phenomenon in neurosurgery. Although state liability risk is thought to contribute greatly to defensive practice, variation within neurosurgical specialties has not been well explored. A validated, online survey was sent via email to 3344 members of the American Board of Neurological Surgeons. The instrument contained eight question domains: surgeon characteristics, patient characteristics, practice type, insurance type, surgeon liability profile, basic surgeon reimbursement, surgeon perceptions of medical legal environment, and the practice of defensive medicine. The overall response rate was 30.6% (n = 1026), including 499 neurosurgeons performing mainly spine procedures (48.6%). Spine neurosurgeons had a similar average practice duration as nonspine neurosurgeons (16.6 vs 16.9 years, P = 0.64) and comparable lifetime case volume (4767 vs 4,703, P = 0.71). The average annual malpractice premium for spine neurosurgeons was similar to nonspine neurosurgeons ($104,480.52 vs $101,721.76, P = 0.60). On average, spine neurosurgeons had a significantly higher rate of ordering labs, medications, referrals, procedures, and imaging solely for liability concerns compared with nonspine neurosurgeons (89.2% vs 84.6%, P = 0.031). Multivariate analysis revealed that spine neurosurgeons were roughly 3 times more likely to practice defensively compared with nonspine neurosurgeons (odds ratio, OR = 2.9, P = 0.001) when controlling for high-risk procedures (OR = 7.8, P < 0.001), annual malpractice premium (OR = 3.3, P = 0.01), percentage of patients publicly insured (OR = 1.1, P = 0.80), malpractice claims in the last 3 years (OR = 1.13, P = 0.71), and state medical-legal environment (OR = 1.3, P = 0

  17. Physcomitrella patens Activates Defense Responses against the Pathogen Colletotrichum gloeosporioides

    Directory of Open Access Journals (Sweden)

    Guillermo Reboledo

    2015-09-01

    Full Text Available The moss Physcomitrella patens is a suitable model plant to analyze the activation of defense mechanisms after pathogen assault. In this study, we show that Colletotrichum gloeosporioides isolated from symptomatic citrus fruit infects P. patens and cause disease symptoms evidenced by browning and maceration of tissues. After C. gloeosporioides infection, P. patens reinforces the cell wall by the incorporation of phenolic compounds and induces the expression of a Dirigent-protein-like encoding gene that could lead to the formation of lignin-like polymers. C. gloeosporioides-inoculated protonemal cells show cytoplasmic collapse, browning of chloroplasts and modifications of the cell wall. Chloroplasts relocate in cells of infected tissues toward the initially infected C. gloeosporioides cells. P. patens also induces the expression of the defense genes PAL and CHS after fungal colonization. P. patens reporter lines harboring the auxin-inducible promoter from soybean (GmGH3 fused to β-glucuronidase revealed an auxin response in protonemal tissues, cauloids and leaves of C. gloeosporioides-infected moss tissues, indicating the activation of auxin signaling. Thus, P. patens is an interesting plant to gain insight into defense mechanisms that have evolved in primitive land plants to cope with microbial pathogens.

  18. Quantitative analysis chemistry

    International Nuclear Information System (INIS)

    Ko, Wansuk; Lee, Choongyoung; Jun, Kwangsik; Hwang, Taeksung

    1995-02-01

    This book is about quantitative analysis chemistry. It is divided into ten chapters, which deal with the basic conception of material with the meaning of analysis chemistry and SI units, chemical equilibrium, basic preparation for quantitative analysis, introduction of volumetric analysis, acid-base titration of outline and experiment examples, chelate titration, oxidation-reduction titration with introduction, titration curve, and diazotization titration, precipitation titration, electrometric titration and quantitative analysis.

  19. Quantitative Algebraic Reasoning

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Panangaden, Prakash; Plotkin, Gordon

    2016-01-01

    We develop a quantitative analogue of equational reasoning which we call quantitative algebra. We define an equality relation indexed by rationals: a =ε b which we think of as saying that “a is approximately equal to b up to an error of ε”. We have 4 interesting examples where we have a quantitative...... equational theory whose free algebras correspond to well known structures. In each case we have finitary and continuous versions. The four cases are: Hausdorff metrics from quantitive semilattices; pWasserstein metrics (hence also the Kantorovich metric) from barycentric algebras and also from pointed...

  20. Quantitative autoradiography of neurochemicals

    International Nuclear Information System (INIS)

    Rainbow, T.C.; Biegon, A.; Bleisch, W.V.

    1982-01-01

    Several new methods have been developed that apply quantitative autoradiography to neurochemistry. These methods are derived from the 2-deoxyglucose (2DG) technique of Sokoloff (1), which uses quantitative autoradiography to measure the rate of glucose utilization in brain structures. The new methods allow the measurement of the rate of cerbral protein synthesis and the levels of particular neurotransmitter receptors by quantitative autoradiography. As with the 2DG method, the new techniques can measure molecular levels in micron-sized brain structures; and can be used in conjunction with computerized systems of image processing. It is possible that many neurochemical measurements could be made by computerized analysis of quantitative autoradiograms

  1. 'Secret' Shuttle payloads revealed

    Science.gov (United States)

    Powell, Joel W.

    1993-05-01

    A secret military payload carried by the orbiter Discovery launched on January 24 1985 is discussed. Secondary payloads on the military Shuttle flights are briefly reviewed. Most of the military middeck experiments were sponsored by the Space Test Program established at the Pentagon to oversee all Defense Department space research projects.

  2. Defense and Regional Integration: Brazil’s Weapons Industry Case

    Directory of Open Access Journals (Sweden)

    Suzeley Kalil Mathias

    2009-06-01

    Full Text Available This paper works with the relation between technological development and weapons industry in Brazil, pointing out the dependence of this to that one. One reveals as the changes in the commerce of armaments that currently privileges the production of small weapons for exportation. The conclusion is that to keep projects of this nature, is using to advantage the industrial park for the dual production, that is, that one takes care the civil and the military demands. At last, it defends the possibility of the defense industry works as mechanism of regional integration.

  3. Accounting for Unliquidated Obligations for the Defense Fuel Supply Center

    National Research Council Canada - National Science Library

    1996-01-01

    .... The Defense Finance and Accounting Service (DFAS) Columbus Center, Columbus, Ohio, and the Defense Fuel Supply Center share responsibility for accurate accounting information and financial reporting...

  4. Selected General Controls Over the Defense Business Management System

    National Research Council Canada - National Science Library

    1996-01-01

    .... The Defense Business Management System performs appropriation accounting, cost accounting, personnel, payroll, manpower, and management information functions for the Navy, the Air Force, five Defense...

  5. Defense Contract Management Command Capitalization of Fixed Assets

    National Research Council Canada - National Science Library

    Young, Shelton

    1997-01-01

    The audit objective was to determine whether the Defense Logistics Agency and the Defense Finance and Accounting Service had implemented effective management control procedures and complied with laws...

  6. FY 1997 Financial Reporting by The Defense Automated Printing Service

    National Research Council Canada - National Science Library

    1998-01-01

    .... The accuracy of information in the financial systems and reported on financial statements is the joint responsibility of the Defense Automated Printing Service and the Defense Logistics Agency...

  7. Defense Finance and Accounting Service Commercial Activities Program

    National Research Council Canada - National Science Library

    1999-01-01

    .... This report evaluated the Defense Finance and Accounting Service competitive sourcing process and reviewed the adequacy of the Defense Finance and Accounting Service management control program...

  8. NAD Acts as an Integral Regulator of Multiple Defense Layers.

    Science.gov (United States)

    Pétriacq, Pierre; Ton, Jurriaan; Patrit, Oriane; Tcherkez, Guillaume; Gakière, Bertrand

    2016-11-01

    Pyridine nucleotides, such as NAD, are crucial redox carriers and have emerged as important signaling molecules in stress responses. Previously, we have demonstrated in Arabidopsis (Arabidopsis thaliana) that the inducible NAD-overproducing nadC lines are more resistant to an avirulent strain of Pseudomonas syringae pv tomato (Pst-AvrRpm1), which was associated with salicylic acid-dependent defense. Here, we have further characterized the NAD-dependent immune response in Arabidopsis. Quinolinate-induced stimulation of intracellular NAD in transgenic nadC plants enhanced resistance against a diverse range of (a)virulent pathogens, including Pst-AvrRpt2, Dickeya dadantii, and Botrytis cinerea Characterization of the redox status demonstrated that elevated NAD levels induce reactive oxygen species (ROS) production and the expression of redox marker genes of the cytosol and mitochondrion. Using pharmacological and reverse genetics approaches, we show that NAD-induced ROS production functions independently of NADPH oxidase activity and light metabolism but depends on mitochondrial respiration, which was increased at higher NAD. We further demonstrate that NAD primes pathogen-induced callose deposition and cell death. Mass spectrometry analysis reveals that NAD simultaneously induces different defense hormones and that the NAD-induced metabolic profiles are similar to those of defense-expressing plants after treatment with pathogen-associated molecular patterns. We thus conclude that NAD triggers metabolic profiles rather similar to that of pathogen-associated molecular patterns and discuss how signaling cross talk between defense hormones, ROS, and NAD explains the observed resistance to pathogens. © 2016 American Society of Plant Biologists. All Rights Reserved.

  9. System justification and the defense of committed relationship ideology.

    Science.gov (United States)

    Day, Martin V; Kay, Aaron C; Holmes, John G; Napier, Jaime L

    2011-08-01

    A consequential ideology in Western society is the uncontested belief that a committed relationship is the most important adult relationship and that almost all people want to marry or seriously couple (DePaulo & Morris, 2005). In the present article, we investigated the extent to which the system justification motive may contribute to the adoption of this ideology. In Studies 1 and 2, we examined whether a heightened motive to maintain the status quo would increase defense of committed relationship values. In Study 3, we examined the reverse association, that is, whether a threat to committed relationship ideology would also affect sociopolitical system endorsement. As past research has found that the justification of political systems depends upon how much these systems are perceived as controlling, in Study 4 we tested whether the defense of the system of committed relationships would also increase when framed as controlling. Results from Studies 1-4 were consistent with our hypotheses, but only for men. In Study 5, using cross-cultural data, we sought to replicate these findings correlationally and probe for a cause of the gender effect. Results from more than 33,000 respondents indicated a relationship (for men) between defense of the sociopolitical system and defense of marriage in countries where the traditional advantages of men over women were most threatened. In Studies 6 and 7, we investigated when this gender difference disappears. Results revealed that when we measured (Study 6) or manipulated (Study 7) personal relationship identity rather than relationship ideology, effects also emerge for women.

  10. Defense islands in bacterial and archaeal genomes and prediction of novel defense systems.

    Science.gov (United States)

    Makarova, Kira S; Wolf, Yuri I; Snir, Sagi; Koonin, Eugene V

    2011-11-01

    The arms race between cellular life forms and viruses is a major driving force of evolution. A substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. We analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. The defense islands are enriched in putative operons and contain numerous overrepresented gene families. A detailed sequence analysis of the proteins encoded by genes in these families shows that many of them are diverged variants of known defense system components, whereas others show features, such as characteristic operonic organization, that are suggestive of novel defense systems. Thus, genomic islands provide abundant material for the experimental study of bacterial and archaeal antivirus defense. Except for the CRISPR-Cas systems, different classes of defense systems, in particular toxin-antitoxin and restriction-modification systems, show nonrandom clustering in defense islands. It remains unclear to what extent these associations reflect functional cooperation between different defense systems and to what extent the islands are genomic "sinks" that accumulate diverse nonessential genes, particularly those acquired via horizontal gene transfer. The characteristics of defense islands resemble those of mobilome islands. Defense and mobilome genes are nonrandomly associated in islands, suggesting nonadaptive evolution of the islands via a preferential attachment-like mechanism underpinned by the addictive properties of defense systems such as toxins-antitoxins and an important role of horizontal mobility in the evolution of these islands.

  11. Why even good defenses may be bad

    International Nuclear Information System (INIS)

    Glaser, C.L.

    1984-01-01

    The current debate over whether an effective ballistic missile defense (BMD) is technically feasible and whether it could be developed and deployed has left most of the advocacy up to those supporting a BMD program. The author emphasizes the issues beyond technical feasibility in his conclusion that assured destruction may still be preferable to perfect defense in terms of reducing the probability of nuclear war. After examining a number of possible scenarios involving the US and Soviet Union, the positions of allies, and the possibility of clandestine bombs, he sees no reason to expect that a defense system would be less vulnerable or have fewer uncertainties. 29 references

  12. Should the Department of Defense Transfer the Defense Logistics Agency's Map Functions to the Defense Working Capital Fund

    National Research Council Canada - National Science Library

    Zimmerman, Donald

    2000-01-01

    .... The functions cost about $25 million annually and are funded by operations and maintenance (O&M) dollars. This study analyzed if the functions should be transferred to the Defense Working Capital Fund...

  13. Isonitrosoacetophenone drives transcriptional reprogramming in Nicotiana tabacum cells in support of innate immunity and defense.

    Directory of Open Access Journals (Sweden)

    Arnaud T Djami-Tchatchou

    Full Text Available Plants respond to various stress stimuli by activating broad-spectrum defense responses both locally as well as systemically. As such, identification of expressed genes represents an important step towards understanding inducible defense responses and assists in designing appropriate intervention strategies for disease management. Genes differentially expressed in tobacco cell suspensions following elicitation with isonitrosoacetophenone (INAP were identified using mRNA differential display and pyro-sequencing. Sequencing data produced 14579 reads, which resulted in 198 contigs and 1758 singletons. Following BLAST analyses, several inducible plant defense genes of interest were identified and classified into functional categories including signal transduction, transcription activation, transcription and protein synthesis, protein degradation and ubiquitination, stress-responsive, defense-related, metabolism and energy, regulation, transportation, cytoskeleton and cell wall-related. Quantitative PCR was used to investigate the expression of 17 selected target genes within these categories. Results indicate that INAP has a sensitising or priming effect through activation of salicylic acid-, jasmonic acid- and ethylene pathways that result in an altered transcriptome, with the expression of genes involved in perception of pathogens and associated cellular re-programming in support of defense. Furthermore, infection assays with the pathogen Pseudomonas syringae pv. tabaci confirmed the establishment of a functional anti-microbial environment in planta.

  14. Virtual Leadership: The Influence of Transformational Leadership Style on Employee Satisfaction at the Defense Contract Management Agency

    Science.gov (United States)

    Johnson, Kevin A.

    2012-01-01

    The purpose of this quantitative correlational study was to examine the possible relationship between transformational leadership style behaviors and the influence it had on employee satisfaction. The information presented in this study involved virtual team members at the Defense Contract Management Agency, Navy Special Emphasis Operations. The…

  15. [Study of defense styles, defenses and coping strategies in alcohol-dependent population].

    Science.gov (United States)

    Ribadier, A; Varescon, I

    2017-05-01

    Defense mechanisms have been seen to greatly change over time and across different definitions made by different theoretical currents. Recently with the definition provided by the DSM IV, defense mechanisms have integrated the concept of coping as a defensive factor. These mechanisms are no longer considered just through a psychodynamic approach but also through a cognitive and behavioral one. In recent years, new theories have therefore integrated these two components of the defensive operation. According to Chabrol and Callahan (2013), defense mechanisms precede coping strategies. In individuals with psychopathological disorders, these authors indicate a relative stability of these mechanisms. Also, we asked about the presence of unique characteristics among people with alcohol dependence. Indeed, studies conducted with people with alcohol dependence highlight the presence of a neurotic defense style and some highly immature defenses (projection, acting out, splitting and somatization). In terms of coping strategies, persons with alcohol dependence preferentially use avoidant strategies and strategies focused on emotion. However, although several studies have been conducted to assess coping strategies and defense styles within a population of individuals with an alcohol problem, at the present time none of them has taken into account all these aspects of defense mechanisms. The aim of this study is therefore to study the defenses and defense styles and coping strategies in an alcohol-dependent population. This multicenter study (3 CHU, 1 center of supportive care and prevention in addiction and 1 clinic) received a favorable opinion of an Institutional Review Board (IRB Registration #: 00001072). Eighty alcohol-dependent individuals responded to a questionnaire assessing sociodemographic characteristics and elements related to the course of consumption. Coping strategies were assessed by means of a questionnaire validated in French: the Brief Cope. The Defense

  16. Capitalization of Defense Technology Security Administration Equipment

    National Research Council Canada - National Science Library

    Gimble, Thomas

    1996-01-01

    ... $5.2 million in the Equipment in Use account on its trial balance. Starting with FY 1996, Defense Technology Security Administration financial data will be included in consolidated DoD financial statements...

  17. 29 CFR 1630.15 - Defenses.

    Science.gov (United States)

    2010-07-01

    ... safety of the individual or others in the workplace. (See § 1630.2(r) defining direct threat.) (c) Other...) Conflict with other Federal laws. It may be a defense to a charge of discrimination under this part that a...

  18. Strategic Defense Initiative Organization: Corporate Plan

    National Research Council Canada - National Science Library

    1992-01-01

    ... requires a flexible yet focused approach to attain its mission; namely, to research, develop, acquire, and deploy systems and technologies which provide ballistic missile defense to include Global Protection Against Limited Strikes (OPALS...

  19. Defense Contract Audit Agency Compensation Audits

    National Research Council Canada - National Science Library

    1999-01-01

    .... The Defense Contract Audit Agency (DCAA) assists the administrative contracting officer in accomplishing that responsibility by determining whether the contractor's compensation system is sound, reliable, consistently applied, and results...

  20. Defensive Swarm: An Agent Based Modeling Analysis

    Science.gov (United States)

    2017-12-01

    32  1.  System Dynamics .........................................................................33  2.  Variables...CONSIDERATIONS AND RECOMMENDATIONS ..........................83  1.  Prolonged Time of Operations ....................................................83...LIST OF FIGURES Figure 1.  Unmanned Aircraft System ..........................................................................8  Figure 2.  Defensive

  1. Defense Meteorological Satellite Program (DMSP) Film

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The United States Air Force Defense Meteorological Satellite Program (DMSP) Operational Linescan System (OLS) is a polar orbiting meteorological sensor with two...

  2. Defense Science Board Task Force on Mobility

    National Research Council Canada - National Science Library

    Tuttle, Jr, William G

    2005-01-01

    .... national security objectives as it is today. Both the 2001 and 2005 National Defense Strategy objectives place greater emphasis than in the past on the nation's worldwide commitments, increasing the demand for responsive forces capable...

  3. Formerly Used Defense Sites (FUDS) Public Properties

    Data.gov (United States)

    Department of Homeland Security — The FUDS Public GIS dataset contains point location information for the 2,709 Formerly Used Defense Sites (FUDS) properties where the U.S. Army Corps of Engineers is...

  4. Happiness and Defense Styles in Psychiatrists.

    Science.gov (United States)

    Machado, Leonardo; Tavares, Hermano; Petribú, Kátia; Pinto, Tiago; Cantilino, Amaury

    2016-03-01

    The aim of this study was to measure happiness in a sample of Brazilian psychiatrists and correlate it with the defense styles used by them and sociodemographic data. This study was observational, cross-sectional, and analytical. Data were collected through self-administered questionnaires by Brazilian psychiatrists who participated in the XXXII Brazilian Congress of Psychiatry, 2014. In this sample of psychiatrists, happiness levels were high (scoring 5.69 of a total of 7), and mature defense styles prevailed, especially humor and anticipation. In a multivariate analysis, having children, good sleep quality, increased sexual interest, and use of defense styles such as humor, anticipation, and idealization all showed a positive relationship with happiness; on the other hand, using defense style such as acting out or annulment demonstrated a negative relationship with happiness. Despite the well-known professional burden that they bear, Brazilian psychiatrists surveyed presented, in general, high levels of subjective well-being and happiness.

  5. Ballistic Missile Defense and ABM Treaty Limitations

    National Research Council Canada - National Science Library

    Robinson, Brian

    1998-01-01

    The U.S. must critically evaluate our current ballistic missile defense (BMD) strategy. In today's geostrategic context, is it sound strategy to continue to impose 1972 ABM Treaty restrictions on BMD systems development...

  6. Ballistic Missile Defense: An Administration Perspective

    National Research Council Canada - National Science Library

    Bell, Robert

    1995-01-01

    ...: "What is our strategy?" What the Clinton Administration is doing with regard to strategic offensive systems provides an instructive context for what we re now trying to do on the strategic defensive side...

  7. Deploying Missile Defense: Major Operational Challenges

    National Research Council Canada - National Science Library

    Bunn, M

    2004-01-01

    By October 2004, the United States will have begun initial deployment of a missile defense capability albeit a modest, limited, and not completely proven one to defend the homeland against a limited...

  8. Lease vs. Purchase in Defense Acquisition

    National Research Council Canada - National Science Library

    Hensley, Carlton L; Tinjum, Archie L

    2008-01-01

    With declining budgets and consolidation in the defense industry, should competition between prime and sub-prime contractors be fostered through innovative lease arrangements similar to the Navy's TAKX...

  9. Photovoltaics in the Department of Defense

    International Nuclear Information System (INIS)

    Chapman, R.N.

    1997-01-01

    This paper documents the history of photovoltaic use within the Department of Defense leading up to the installation of 2.1 MW of photovoltaics underway today. This history describes the evolution of the Department of Defense's Tri-Service Photovoltaic Review Committee and the committee's strategic plan to realize photovoltaic's full potential through outreach, conditioning of the federal procurement system, and specific project development. The Photovoltaic Review Committee estimates photovoltaic's potential at nearly 4,000 MW, of which about 700 MW are considered to be cost-effective at today's prices. The paper describes photovoltaic's potential within the Department of Defense, the status and features of the 2.1-MW worth of photovoltaic systems under installation, and how these systems are selected and implemented. The paper also documents support provided to the Department of Defense by the Department of Energy dating back to the late 70s. copyright 1997 American Institute of Physics

  10. Cost Effective Regional Ballistic Missile Defense

    Science.gov (United States)

    2016-02-16

    deploying advanced air defense systems18, such as the Russian S-300 and S-500, and concealing them in hardened, camouflaged sites, such as extensive... Russian objections to the European Phased Adaptive Approach (EPAA) and fund homeland defense priorities.39 Furthermore, the PTSS system was also... Theatre Ballistic Missile Defence Capability Becomes Operational,” Jane’s Missiles & Rockets, 1 February 2011. 55 Joseph W. Kirschbaum, REGIONAL MISSILE

  11. Carp erythrodermatitis : host defense-pathogen interaction

    OpenAIRE

    Pourreau, C.N.

    1990-01-01

    The outcome of a bacterial infection depends on the interaction between pathogen and host. The ability of the microbe to survive in the host depends on its invasive potential (i.e. spreading and multiplication), and its ability to obtain essential nutrients and to resist the host's defense system. On the other hand, the host's resistance to a bacterial attack depends on its physiological state, the intensity of the bacterial attack and the efficacy of the defense system to ...

  12. Defense Acquisition Reform, 19602009: An Elusive Goal

    Science.gov (United States)

    2011-10-31

    the seven largest economies of the world (United States, China, Japan, Germany, France, United Kingdom, and Italy ).11 Major weapon systems...the Federal Acquisition Regulation.96 95 Ibid., pp. 20, 21. 96 Joseph Ferrara , “DoD’s 5000 Documents: Evolution and Change in Defense Acquisition...Wayne Smith. How Much Is Enough: Shaping the Defense Program, 1961–1969. New York: Harper & Row, 1971. Ferrara , Joseph. “DoD’s 5000 Documents

  13. Integrating the Department of Defense Supply Chain

    Science.gov (United States)

    2012-01-01

    Defense for Logistics and Materiel Readiness, DoD Supply Chain Materiel Management Procedures , DoD Manual 4140.01, Volumes 1 through 11, draft as of March...this is summarized in R. Glenn Richey, Jr., Anthony S. Roath, Judith M. Whipple , and Stanley E. Fawcett, “Exploring a Governance Theory of Supply...of this report, DoD Supply Chain Materiel Management Procedures (Assistant Secretary of Defense for Logis- tics and Materiel Readiness, DoD Manual

  14. A New Department of Defense Framework for Efficient Defense Support of Civil Authorities

    National Research Council Canada - National Science Library

    Liberato, Rodney

    2007-01-01

    ...) capabilities support to civilian authorities during emergencies. Hurricane Katrina added to this national attention on the role the Department of Defense should play in responding to emergencies...

  15. Acquisition: Allegations to the Defense Hotline on the Management of the Defense Travel System

    National Research Council Canada - National Science Library

    2002-01-01

    .... The Defense Travel System was envisioned as a general support system designed to make business travel quicker, easier, and more efficient by providing automated commercial and Government travel...

  16. Self-Defense in Karabakh Conflict?

    Directory of Open Access Journals (Sweden)

    Saeed Bagheri

    2015-01-01

    Full Text Available Use of force is one of the principles of international law that has been banned by the UN Charter and modern constitutions. However, since the enforcement of the UN Charter, self-defense has become the preferred excuse for states to justify their use of force. Applying self-defense, however, requires some conditions. Immediacy is one of the important conditions of self-defense. This is defined as the timeframe between armed attacks and reaction to it. This situation requires self-defense immediately after the armed conflict or during a reasonable timeframe since its occurance.In this respect, emerging Karabakh Conflict between Armenia and Azerbaijan in the 1990s is important. In this article, by comparing two different approaches (strict and board interpretation of the temporal link between the measures of self-defense and the armed attacks (immediacy, the temporal link between the self-defense countermeasures of Azerbaijan and attacks by Armenia in Karabakh Conflict will be examined.

  17. Soviet civil defense is inadequate and meaningless

    International Nuclear Information System (INIS)

    Kaplan, F.M.

    1985-01-01

    In this paper, the author argues that Soviet civil defense plans exist primarily on paper and are used to pacify the Soviet people, not as plans to survive and prevail in a nuclear confrontation with the U.S. The author describes how the Soviet people have little faith in the civil defense programs. They don't believe they can survive an attack. Furthermore, he says the Soviets have never staged an evacuation exercise in any major city nor, even in smaller towns, has an entire community been evacuated. The author says there are numerous problems with the shelter programs as well. Very few existing shelters have any food stocks, only a few more have any water. There is little evidence that Soviet leaders have planned their economy with civil defense in mind. Nor - given the blatant inadequacies of Soviet civil defense programs, the marked vulnerabilities of the Soviet economy, and the intrinsic limitation and uncertainties about civil defense generally - is there much basis for claiming that Soviet leaders, even in desperate straits, would risk war with the United States while counting on civil defense measures to limit the damage wreaked on the Soviet Union

  18. The methodological defense of realism scrutinized.

    Science.gov (United States)

    Wray, K Brad

    2015-12-01

    I revisit an older defense of scientific realism, the methodological defense, a defense developed by both Popper and Feyerabend. The methodological defense of realism concerns the attitude of scientists, not philosophers of science. The methodological defense is as follows: a commitment to realism leads scientists to pursue the truth, which in turn is apt to put them in a better position to get at the truth. In contrast, anti-realists lack the tenacity required to develop a theory to its fullest. As a consequence, they are less likely to get at the truth. My aim is to show that the methodological defense is flawed. I argue that a commitment to realism does not always benefit science, and that there is reason to believe that a research community with both realists and anti-realists in it may be better suited to advancing science. A case study of the Copernican Revolution in astronomy supports this claim. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Cometary Defense with Directed Energy

    Science.gov (United States)

    Zhang, Q.; Lubin, P. M.; Hughes, G. B.

    2016-12-01

    Cometary impacts pose a long-term hazard to humans on Earth. Due to their comparative rarity, most planetary defense schemes neglect the comet threat, choosing instead to focus exclusively on mitigating asteroid impacts. Methods like kinetic impactors may be suitable for deflecting near-Earth asteroids (NEAs) and Jupiter-family comets (JFCs), both of which are characterized by low inclination orbits and short orbital periods which favor early detection—characteristics ideal for an interception mission. In contrast, Halley-type comets (HTCs) and long-period comets (LPCs) are often found in high inclination orbits rarely more than 2 yr prior to reaching Earth's orbit. Unless discovered and identified in a prior apparition—often centuries or millennia earlier, if ever—timely interception of a threatening HTC or LPC is improbable even with preparation, with missions demanding delta-v budgets often in excess of 30 km/s. Active comets, however, are already naturally perturbed from purely gravitational trajectories through solar-driven sublimation of volatiles. Further deflection may be achieved by supplementing the solar radiation with an artificial directed energy source such as by one or more laser arrays positioned on or near Earth. Simulations were developed with models derived from the known solar nongravitational perturbations of typical comets. Results suggest that a diffraction-limited 500 m array operating at 10 GW for 10 min/day may be sufficient to divert a typical active 500 m comet from an impact given 1 yr. A larger 1 km array operating at 100 GW for 100 s/day is similarly effective. Care must be taken to ensure the target remains intact throughout the deflection period due to comets' low compressive strength and resulting propensity for disintegration at high incident flux.

  20. 47 CFR 90.411 - Civil defense communications.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 5 2010-10-01 2010-10-01 false Civil defense communications. 90.411 Section 90... PRIVATE LAND MOBILE RADIO SERVICES Operating Requirements § 90.411 Civil defense communications. The... necessary for the implementation of civil defense activities assigned such station by local civil defense...

  1. 75 FR 9588 - Defense Intelligence Agency Advisory Board; Closed Meeting

    Science.gov (United States)

    2010-03-03

    ... DEPARTMENT OF DEFENSE Office of the Secretary Defense Intelligence Agency Advisory Board; Closed Meeting AGENCY: Defense Intelligence Agency, DoD. ACTION: Notice of closed meeting. SUMMARY: Pursuant to... Law 94-409, notice is hereby given that the Defense Intelligence Agency Advisory Board, will meet on...

  2. Quantitative film radiography

    International Nuclear Information System (INIS)

    Devine, G.; Dobie, D.; Fugina, J.; Hernandez, J.; Logan, C.; Mohr, P.; Moss, R.; Schumacher, B.; Updike, E.; Weirup, D.

    1991-01-01

    We have developed a system of quantitative radiography in order to produce quantitative images displaying homogeneity of parts. The materials that we characterize are synthetic composites and may contain important subtle density variations not discernible by examining a raw film x-radiograph. In order to quantitatively interpret film radiographs, it is necessary to digitize, interpret, and display the images. Our integrated system of quantitative radiography displays accurate, high-resolution pseudo-color images in units of density. We characterize approximately 10,000 parts per year in hundreds of different configurations and compositions with this system. This report discusses: the method; film processor monitoring and control; verifying film and processor performance; and correction of scatter effects

  3. Quantitative Risk - Phases 1 & 2

    Science.gov (United States)

    2013-11-12

    No. 4, November 2002 29. Ward, D., “The Comic Guide To Improving Defense Acquisitions”, Department of Defense, 2012 30. Nilsson, P.,Ohlsson, E...Conference Professional Education Program, 2002 Contract Number: H98230-08-D-0171 TO 0030, RT 040 Report No. SERC-2013-TR-040-3 Volume I November

  4. Expression of tomato prosystemin gene in Arabidopsis reveals systemic translocation of its mRNA and confers necrotrophic fungal resistance.

    Science.gov (United States)

    Zhang, Haiyan; Yu, Pengli; Zhao, Jiuhai; Jiang, Hongling; Wang, Haiyang; Zhu, Yingfang; Botella, Miguel A; Šamaj, Jozef; Li, Chuanyou; Lin, Jinxing

    2018-01-01

    Systemin (SYS), an octadecapeptide hormone processed from a 200-amino-acid precursor (prosystemin, PS), plays a central role in the systemic activation of defense genes in tomato in response to herbivore and pathogen attacks. However, whether PS mRNA is transferable and its role in systemic defense responses remain unknown. We created the transgenic tomato PS gene tagged with the green fluorescent protein (PS-GFP) using a shoot- or root-specific promoter, and the constitutive 35S promoter in Arabidopsis. Subcellular localization of PS-/SYS-GFP was observed using confocal laser scanning microscopy and gene transcripts were determined using quantitative real-time PCR. In Arabidopsis, PS protein can be processed and SYS is secreted. Shoot-/root-specific expression of PS-GFP in Arabidopsis, and grafting experiments, revealed that the PS mRNA moves in a bi-directional manner. We also found that ectopic expression of PS improves Arabidopsis resistance to the necrotrophic fungus Botrytis cinerea, consistent with substantial upregulation of the transcript levels of specific pathogen-responsive genes. Our results provide novel insights into the multifaceted mechanism of SYS signaling transport and its potential application in genetic engineering for increasing pathogen resistance across diverse plant families. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  5. The Lipopolysaccharide-Induced Metabolome Signature in Arabidopsis thaliana Reveals Dynamic Reprogramming of Phytoalexin and Phytoanticipin Pathways

    Science.gov (United States)

    Finnegan, Tarryn; Steenkamp, Paul A.; Piater, Lizelle A.

    2016-01-01

    Lipopolysaccharides (LPSs), as MAMP molecules, trigger the activation of signal transduction pathways involved in defence. Currently, plant metabolomics is providing new dimensions into understanding the intracellular adaptive responses to external stimuli. The effect of LPS on the metabolomes of Arabidopsis thaliana cells and leaf tissue was investigated over a 24 h period. Cellular metabolites and those secreted into the medium were extracted with methanol and liquid chromatography coupled to mass spectrometry was used for quantitative and qualitative analyses. Multivariate statistical data analyses were used to extract interpretable information from the generated multidimensional LC-MS data. The results show that LPS perception triggered differential changes in the metabolomes of cells and leaves, leading to variation in the biosynthesis of specialised secondary metabolites. Time-dependent changes in metabolite profiles were observed and biomarkers associated with the LPS-induced response were tentatively identified. These include the phytohormones salicylic acid and jasmonic acid, and also the associated methyl esters and sugar conjugates. The induced defensive state resulted in increases in indole—and other glucosinolates, indole derivatives, camalexin as well as cinnamic acid derivatives and other phenylpropanoids. These annotated metabolites indicate dynamic reprogramming of metabolic pathways that are functionally related towards creating an enhanced defensive capacity. The results reveal new insights into the mode of action of LPS as an activator of plant innate immunity, broadens knowledge about the defence metabolite pathways involved in Arabidopsis responses to LPS, and identifies specialised metabolites of functional importance that can be employed to enhance immunity against pathogen infection. PMID:27656890

  6. Dynamics of a stabilized motor defense conditioned reflex at different levels of motivation in irradiated rats

    Energy Technology Data Exchange (ETDEWEB)

    Shtemberg, A S

    1982-05-01

    Postradiation dynamics of strengthened motor-defense conditioned reflex in rats-males irradiated with the doses of 94.111 and 137 Gy was studied. Phase disturbances of conditioned-reflex activity increased with enhancing irradiation dose have been revealed. Rapid recovery of conditioned reflex after short primary aggravation was a characteristic peculiarity. At that, the dynamics of relation of main nervous processes in cortex was noted for significant instability increasing with radiation syndrome development. Enhancement of force of electro-defense support promoted more effective strengthening of temporary connections and conditioned high stability of trained-reflex reactions during serious functional disturbances resulted from sublethal dose irradiation.

  7. Is flood defense changing in nature? Shifts in the flood defense strategy in six European countries

    Directory of Open Access Journals (Sweden)

    Mathilde Gralepois

    2016-12-01

    Full Text Available In many countries, flood defense has historically formed the core of flood risk management but this strategy is now evolving with the changing approach to risk management. This paper focuses on the neglected analysis of institutional changes within the flood defense strategies formulated and implemented in six European countries (Belgium, England, France, the Netherlands, Poland, and Sweden. The evolutions within the defense strategy over the last 30 years have been analyzed with the help of three mainstream institutional theories: a policy dynamics-oriented framework, a structure-oriented institutional theory on path dependency, and a policy actors-oriented analysis called the advocacy coalitions framework. We characterize the stability and evolution of the trends that affect the defense strategy in the six countries through four dimensions of a policy arrangement approach: actors, rules, resources, and discourses. We ask whether the strategy itself is changing radically, i.e., toward a discontinuous situation, and whether the processes of change are more incremental or radical. Our findings indicate that in the European countries studied, the position of defense strategy is continuous, as the classical role of flood defense remains dominant. With changing approaches to risk, integrated risk management, climate change, urban growth, participation in governance, and socioeconomic challenges, the flood defense strategy is increasingly under pressure to change. However, these changes can be defined as part of an adaptation of the defense strategy rather than as a real change in the nature of flood risk management.

  8. Defense Dollars and Sense: A Common Cause Guide to the Defense Budget Process.

    Science.gov (United States)

    Rovner, Mark

    Designed to increase public awareness of military spending, this 5-part guide examines the process and problems of preparing the national defense budget. The publication begins with a brief overview of the 1984 defense budget. Major military programs, trends in budgeting, and key concerns in budget formulation are explored. Graphs and charts…

  9. 76 FR 71467 - Defense Federal Acquisition Regulation Supplement; Extension of Department of Defense Mentor...

    Science.gov (United States)

    2011-11-18

    ... Defense Mentor-Prot[eacute]g[eacute] Pilot Program (DFARS Case 2011-D050) AGENCY: Defense Acquisition... applications under the DoD Mentor-Prot[eacute]g[eacute] Pilot Program for new mentor-prot[eacute]g[eacute] agreements and the date mentors may incur costs and/or receive credit towards fulfilling their small business...

  10. 77 FR 11367 - Defense Federal Acquisition Regulation Supplement; Extension of the Department of Defense Mentor...

    Science.gov (United States)

    2012-02-24

    ... Defense Mentor-Prot[eacute]g[eacute] Pilot Program (DFARS Case 2012-D024) AGENCY: Defense Acquisition... applications under the DoD Mentor-Prot[eacute]g[eacute] Pilot Program for new mentor-prot[eacute]g[eacute] agreements and the date mentors may incur costs and/or receive credit towards fulfilling their small business...

  11. Summary Report on the Audit of Defense Logistics Agency 1995 Defense Base Realignment and Closure Data Collection Process.

    Science.gov (United States)

    1995-06-19

    VXW-ÄVAVKVX’AWXW/XVXV:*: OFFICE OF THE INSPECTOR GENERAL SUMMARY REPORT ON THE AUDIT OF DEFENSE LOGISTICS AGENCY 1995 DEFENSE BASE REALIGNMENT...FOR DIRECTOR, DEFENSE LOGISTICS AGENCY SUBJECT: Summary Report on the Audit of Defense Logistics Agency 1995 Defense Base Realignment and Closure...the data that DLA provides to support recommendations for the 1995 Commission. The specific objective for the audits was to determine whether the

  12. MicroRNA-Mediated Gene Silencing in Plant Defense and Viral Counter-Defense

    Directory of Open Access Journals (Sweden)

    Sheng-Rui Liu

    2017-09-01

    Full Text Available MicroRNAs (miRNAs are non-coding RNAs of approximately 20–24 nucleotides in length that serve as central regulators of eukaryotic gene expression by targeting mRNAs for cleavage or translational repression. In plants, miRNAs are associated with numerous regulatory pathways in growth and development processes, and defensive responses in plant–pathogen interactions. Recently, significant progress has been made in understanding miRNA-mediated gene silencing and how viruses counter this defense mechanism. Here, we summarize the current knowledge and recent advances in understanding the roles of miRNAs involved in the plant defense against viruses and viral counter-defense. We also document the application of miRNAs in plant antiviral defense. This review discusses the current understanding of the mechanisms of miRNA-mediated gene silencing and provides insights on the never-ending arms race between plants and viruses.

  13. Peripheral and central mediators of lipopolysaccharide induced suppression of defensive rage behavior in the cat.

    Science.gov (United States)

    Bhatt, S; Bhatt, R S; Zalcman, S S; Siegel, A

    2009-11-10

    Based upon recent findings in our laboratory that cytokines microinjected into the medial hypothalamus or periaqueductal gray (PAG) powerfully modulate defensive rage behavior in cat, the present study determined the effects of peripherally released cytokines following lipopolysaccharide (LPS) challenge upon defensive rage. The study involved initial identification of the effects of peripheral administration of LPS upon defensive rage by electrical stimulation from PAG and subsequent determination of the peripheral and central mechanisms governing this process. The results revealed significant elevation in response latencies for defensive rage from 60 to 300 min, post LPS injection, with no detectable signs of sickness behavior present at 60 min. In contrast, head turning behavior elicited by stimulation of adjoining midbrain sites was not affected by LPS administration, suggesting a specificity of the effects of LPS upon defensive rage. Direct administration of LPS into the medial hypothalamus had no effect on defensive rage, suggesting that the effects of LPS were mediated by peripheral cytokines rather than by any direct actions upon hypothalamic neurons. Complete blockade of the suppressive effects of LPS by peripheral pretreatment with an Anti-tumor necrosis factor-alpha (TNFalpha) antibody but not with an anti- interleukin-1 (IL-1) antibody demonstrated that the effects of LPS were mediated through TNF-alpha rather than through an IL-1 mechanism. A determination of the central mechanisms governing LPS suppression revealed that pretreatment of the medial hypothalamus with PGE(2) or 5-HT(1A) receptor antagonists each completely blocked the suppressive effects of LPS, while microinjections of a TNF-alpha antibody into the medial hypothalamus were ineffective. Microinjections of -Iodo-N-[2-[4-(methoxyphenyl)-1-piperazinyl]ethyl]-N-(2-pyridinyl) benzamide monohydrochloride (p-MPPI) into lateral hypothalamus (to test for anatomical specificity) had no effect upon

  14. Review of defense display research programs

    Science.gov (United States)

    Tulis, Robert W.; Hopper, Darrel G.; Morton, David C.; Shashidhar, Ranganathan

    2001-09-01

    Display research has comprised a substantial portion of the defense investment in new technology for national security for the past 13 years. These investments have been made by the separate service departments and, especially, via several Defense Research Projects Agency (DARPA) programs, known collectively as the High Definition Systems (HDS) Program (which ended in 2001) and via the Office of the Secretary of Defense (OSD) Defense Production Act (DPA) Title III Program (efforts ended in 2000). Using input from the Army, Navy, and Air Force to focus research and identify insertion opportunities, DARPA and the Title III Program Office have made investments to develop the national technology base and manufacturing infrastructure necessary to meet the twin challenge of providing affordable displays in current systems and enabling the DoD strategy of winning future conflicts by getting more information to all participants during the battle. These completed DARPA and DPA research and infrastructure programs are reviewed. Service investments have been and are being made to transition display technology; examples are described. Display science and technology (S&T) visions are documented for each service to assist the identification of areas meriting consideration for future defense research.

  15. Immune defense and host life history.

    Science.gov (United States)

    Zuk, Marlene; Stoehr, Andrew M

    2002-10-01

    Recent interest has focused on immune response in an evolutionary context, with particular attention to disease resistance as a life-history trait, subject to trade-offs against other traits such as reproductive effort. Immune defense has several characteristics that complicate this approach, however; for example, because of the risk of autoimmunity, optimal immune defense is not necessarily maximum immune defense. Two important types of cost associated with immunity in the context of life history are resource costs, those related to the allocation of essential but limited resources, such as energy or nutrients, and option costs, those paid not in the currency of resources but in functional or structural components of the organism. Resource and option costs are likely to apply to different aspects of resistance. Recent investigations into possible trade-offs between reproductive effort, particularly sexual displays, and immunity have suggested interesting functional links between the two. Although all organisms balance the costs of immune defense against the requirements of reproduction, this balance works out differently for males than it does for females, creating sex differences in immune response that in turn are related to ecological factors such as the mating system. We conclude that immune response is indeed costly and that future work would do well to include invertebrates, which have sometimes been neglected in studies of the ecology of immune defense.

  16. Space-based ballistic-missile defense

    International Nuclear Information System (INIS)

    Bethe, H.A.; Garwin, R.L.; Gottfried, K.; Kendall, H.W.

    1984-01-01

    This article, based on a forthcoming book by the Union for Concerned Scientists, focuses on the technical aspects of the issue of space-based ballistic-missile defense. After analysis, the authors conclude that the questionable performance of the proposed defense, the ease with which it could be overwhelmed or circumvented, and its potential as an antisatellite system would cause grievous damage to the security of the US if the Strategic Defense Initiative were to be pursued. The path toward greater security lies in quite another direction, they feel. Although research on ballistic-missile defense should continue at the traditional level of expenditure and within the constraints of the ABM Treaty, every effort should be made to negotiate a bilateral ban on the testing and use of space weapons. The authors think it is essential that such an agreement cover all altitudes, because a ban on high-altitude antisatellite weapons alone would not viable if directed energy weapons were developed for ballistic-missile defense. Further, the Star Wars program, unlikely ever to protect the entire nation against a nuclear attack, would nonetheless trigger a major expansion of the arms race

  17. DCT-based cyber defense techniques

    Science.gov (United States)

    Amsalem, Yaron; Puzanov, Anton; Bedinerman, Anton; Kutcher, Maxim; Hadar, Ofer

    2015-09-01

    With the increasing popularity of video streaming services and multimedia sharing via social networks, there is a need to protect the multimedia from malicious use. An attacker may use steganography and watermarking techniques to embed malicious content, in order to attack the end user. Most of the attack algorithms are robust to basic image processing techniques such as filtering, compression, noise addition, etc. Hence, in this article two novel, real-time, defense techniques are proposed: Smart threshold and anomaly correction. Both techniques operate at the DCT domain, and are applicable for JPEG images and H.264 I-Frames. The defense performance was evaluated against a highly robust attack, and the perceptual quality degradation was measured by the well-known PSNR and SSIM quality assessment metrics. A set of defense techniques is suggested for improving the defense efficiency. For the most aggressive attack configuration, the combination of all the defense techniques results in 80% protection against cyber-attacks with PSNR of 25.74 db.

  18. Precipitation affects plant communication and defense.

    Science.gov (United States)

    Pezzola, Enrico; Mancuso, Stefano; Karban, Richard

    2017-06-01

    Anti-herbivore defense shows high levels of both inter- and intraspecific variability. Defending against herbivores may be costly to the plant when it requires a tradeoff in allocation between defense and other missed opportunities, such as reproduction. Indeed, the plastic expression of defensive traits allows the plant to invest resources in defense only when the risk of being damaged actually increases, avoiding wasted resources. Plants may assess risk by responding to volatile cues emitted by neighbors that are under attack. Most plastic responses likely depend on environmental conditions. In this experiment, we investigated the effect of water availability on resistance induced by volatile cues in sagebrush. We found that plants receiving additional water over summer and/or volatile cues from neighbor donor plants showed reduced herbivore damage compared to control plants. Interestingly, we found no evidence of interactions between additional water and volatile cues. We performed an inferential analysis comparing historical records of the levels of herbivore damage during different years that had different temperature and precipitation accumulations. Results confirmed findings from the experiment, as the regression model indicated that sagebrush was better defended during wetter and hotter seasons. Reports from the literature indicated that sagebrush is extremely sensitive to water availability in the soil. We suggest that water availability may directly affect resistance of herbivory as well as sensitivity to cues of damage. Costs and benefits of allocating resources to defensive traits may vary with environmental conditions. © 2017 by the Ecological Society of America.

  19. Water extracts from winery by-products as tobacco defense inducers.

    Science.gov (United States)

    Benouaret, Razik; Goujon, Eric; Trivella, Aurélien; Richard, Claire; Ledoigt, Gérard; Joubert, Jean-Marie; Mery-Bernardon, Aude; Goupil, Pascale

    2014-10-01

    Water extracts from winery by-products exhibited significant plant defense inducer properties. Experiments were conducted on three marc extracts containing various amounts of polyphenols and anthocyanins. Infiltration of red, white and seed grape marc extracts into tobacco leaves induced hypersensitive reaction-like lesions with cell death evidenced by Evans Blue staining. The infiltration zones and the surrounding areas revealed accumulation of autofluorescent compounds under UV light. Leaf infiltration of the three winery by-product extracts induced defense gene expression. The antimicrobial PR1, β-1,3-glucanase PR2, and chitinase PR3 target genes were upregulated locally in tobacco plants following grape marc extract treatments. The osmotin PR5 transcripts accumulated as well in red marc extract treated-tobacco leaves. Overall, the winery by-product extracts elicited an array of plant defense responses making the grape residues a potential use of high value compounds.

  20. Reentrant phase transitions and defensive alliances in social dilemmas with informed strategies

    Science.gov (United States)

    Szolnoki, Attila; Perc, Matjaž

    2015-05-01

    Knowing the strategy of an opponent in a competitive environment conveys obvious evolutionary advantages. But this information is costly, and the benefit of being informed may not necessarily offset the additional cost. Here we introduce social dilemmas with informed strategies, and we show that this gives rise to two cyclically dominant triplets that form defensive alliances. The stability of these two alliances is determined by the rotation velocity of the strategies within each triplet. A weaker strategy in a faster rotating triplet can thus overcome an individually stronger competitor. Fascinating spatial patterns favor the dominance of a single defensive alliance, but enable also the stable coexistence of both defensive alliances in very narrow regions of the parameter space. A continuous reentrant phase transition reveals before unseen complexity behind the stability of strategic alliances in evolutionary social dilemmas.

  1. A Quantitative Analysis of the Effect of Simulation on Medication Administration in Nursing Students

    Science.gov (United States)

    Scudmore, Casey

    2013-01-01

    Medication errors are a leading cause of injury and death in health care, and nurses are the last line of defense for patient safety. Nursing educators must develop curriculum to effectively teach nursing students to prevent medication errors and protect the public. The purpose of this quantitative, quasi-experimental study was to determine if…

  2. Quantitative assessment of target dependence of pion fluctuation in ...

    Indian Academy of Sciences (India)

    journal of. December 2012 physics pp. 1395–1405. Quantitative assessment ... The analysis reveals the erratic behaviour of the produced pions signifying ..... authors (Sitaram Pal) gratefully acknowledges the financial help from the University.

  3. Quantitative Data Analysis--In the Graduate Curriculum

    Science.gov (United States)

    Albers, Michael J.

    2017-01-01

    A quantitative research study collects numerical data that must be analyzed to help draw the study's conclusions. Teaching quantitative data analysis is not teaching number crunching, but teaching a way of critical thinking for how to analyze the data. The goal of data analysis is to reveal the underlying patterns, trends, and relationships of a…

  4. Qualitative and Quantitative Integrated Modeling for Stochastic Simulation and Optimization

    Directory of Open Access Journals (Sweden)

    Xuefeng Yan

    2013-01-01

    Full Text Available The simulation and optimization of an actual physics system are usually constructed based on the stochastic models, which have both qualitative and quantitative characteristics inherently. Most modeling specifications and frameworks find it difficult to describe the qualitative model directly. In order to deal with the expert knowledge, uncertain reasoning, and other qualitative information, a qualitative and quantitative combined modeling specification was proposed based on a hierarchical model structure framework. The new modeling approach is based on a hierarchical model structure which includes the meta-meta model, the meta-model and the high-level model. A description logic system is defined for formal definition and verification of the new modeling specification. A stochastic defense simulation was developed to illustrate how to model the system and optimize the result. The result shows that the proposed method can describe the complex system more comprehensively, and the survival probability of the target is higher by introducing qualitative models into quantitative simulation.

  5. Collective defense of Aphis nerii and Uroleucon hypochoeridis (Homoptera, Aphididae against natural enemies.

    Directory of Open Access Journals (Sweden)

    Manfred Hartbauer

    2010-04-01

    Full Text Available The prevalent way aphids accomplish colony defense against natural enemies is a mutualistic relationship with ants or the occurrence of a specialised soldier caste typical for eusocial aphids, or even both. Despite a group-living life style of those aphid species lacking these defense lines, communal defense against natural predators has not yet been observed there. Individuals of Aphis nerii (Oleander aphid and Uroleucon hypochoeridis, an aphid species feeding on Hypochoeris radicata (hairy cat's ear, show a behavioral response to visual stimulation in the form of spinning or twitching, which is often accompanied by coordinated kicks executed with hind legs. Interestingly, this behaviour is highly synchronized among members of a colony and repetitive visual stimulation caused strong habituation. Observations of natural aphid colonies revealed that a collective twitching and kicking response (CTKR was frequently evoked during oviposition attempts of the parasitoid wasp Aphidius colemani and during attacks of aphidophagous larvae. CTKR effectively interrupted oviposition attempts of this parasitoid wasp and even repelled this parasitoid from colonies after evoking consecutive CTKRs. In contrast, solitary feeding A. nerii individuals were not able to successfully repel this parasitoid wasp. In addition, CTKR was also evoked through gentle substrate vibrations. Laser vibrometry of the substrate revealed twitching-associated vibrations that form a train of sharp acceleration peaks in the course of a CTKR. This suggests that visual signals in combination with twitching-related substrate vibrations may play an important role in synchronising defense among members of a colony. In both aphid species collective defense in encounters with different natural enemies was executed in a stereotypical way and was similar to CTKR evoked through visual stimulation. This cooperative defense behavior provides an example of a surprising sociality that can be found

  6. Development of Information Technology for Smart Defense

    International Nuclear Information System (INIS)

    Chung, Kyoil; Lee, So Yeon; Park, Sangjoon; Park, Jonghyun; Han, Sangcheol

    2014-01-01

    Recently, there has been demand for the convergence of IT (Information and communication Technologies, ICT) with defense, as has already been achieved in civilian fields such as healthcare and construction. It is expected that completely new and common requirements would emerge from the civilian and military domains and that the shape of war field would change rapidly. Many military scientists forecast that future wars would be network-centric and be based on C4I(Command, Control, Communication and Computer, Intelligence), ISR(Intelligence, Surveillance and Reconnaissance), and PGM(Precision Guided Munitions). For realizing the smart defense concept, IT should act as a baseline technology even for simulating a real combat field using virtual reality. In this paper, we propose the concept of IT-based smart defense with a focus on accurate detection in real and cyber wars, effective data communication, automated and unmanned operation, and modeling and simulation

  7. Defensive medicine: No wonder policymakers are confused.

    Science.gov (United States)

    Kapp, Marshall B

    2016-01-01

    Discussions regarding defensive medical practice often result in proposals for public policy actions. Such proposals generally are premised on assumptions about defensive medicine, namely, that it (a) is driven by physicians' legal anxieties, (b) constitutes bad medical practice, (c) drives up health care costs, (d) varies depending on a jurisdiction's particular tort law climate, (e) depends on medical specialty and a physician's own prior experience as a malpractice defendant, and (f) is a rational response to actual legal risks confronting physicians. This article examines a sample of recent literature focusing on defensive medicine and finds that the messages conveyed vary widely, helping to explain the confusion experienced by many policymakers trying to improve the quality and affordability of health care.

  8. Antiviral Defense Mechanisms in Honey Bees

    Science.gov (United States)

    Brutscher, Laura M.; Daughenbaugh, Katie F.; Flenniken, Michelle L.

    2015-01-01

    Honey bees are significant pollinators of agricultural crops and other important plant species. High annual losses of honey bee colonies in North America and in some parts of Europe have profound ecological and economic implications. Colony losses have been attributed to multiple factors including RNA viruses, thus understanding bee antiviral defense mechanisms may result in the development of strategies that mitigate colony losses. Honey bee antiviral defense mechanisms include RNA-interference, pathogen-associated molecular pattern (PAMP) triggered signal transduction cascades, and reactive oxygen species generation. However, the relative importance of these and other pathways is largely uncharacterized. Herein we review the current understanding of honey bee antiviral defense mechanisms and suggest important avenues for future investigation. PMID:26273564

  9. Advanced thermal management technologies for defense electronics

    Science.gov (United States)

    Bloschock, Kristen P.; Bar-Cohen, Avram

    2012-05-01

    Thermal management technology plays a key role in the continuing miniaturization, performance improvements, and higher reliability of electronic systems. For the past decade, and particularly, the past 4 years, the Defense Advanced Research Projects Agency (DARPA) has aggressively pursued the application of micro- and nano-technology to reduce or remove thermal constraints on the performance of defense electronic systems. The DARPA Thermal Management Technologies (TMT) portfolio is comprised of five technical thrust areas: Thermal Ground Plane (TGP), Microtechnologies for Air-Cooled Exchangers (MACE), NanoThermal Interfaces (NTI), Active Cooling Modules (ACM), and Near Junction Thermal Transport (NJTT). An overview of the TMT program will be presented with emphasis on the goals and status of these efforts relative to the current State-of-the-Art. The presentation will close with future challenges and opportunities in the thermal management of defense electronics.

  10. Salt, chloride, bleach, and innate host defense

    Science.gov (United States)

    Wang, Guoshun; Nauseef, William M.

    2015-01-01

    Salt provides 2 life-essential elements: sodium and chlorine. Chloride, the ionic form of chlorine, derived exclusively from dietary absorption and constituting the most abundant anion in the human body, plays critical roles in many vital physiologic functions, from fluid retention and secretion to osmotic maintenance and pH balance. However, an often overlooked role of chloride is its function in innate host defense against infection. Chloride serves as a substrate for the generation of the potent microbicide chlorine bleach by stimulated neutrophils and also contributes to regulation of ionic homeostasis for optimal antimicrobial activity within phagosomes. An inadequate supply of chloride to phagocytes and their phagosomes, such as in CF disease and other chloride channel disorders, severely compromises host defense against infection. We provide an overview of the roles that chloride plays in normal innate immunity, highlighting specific links between defective chloride channel function and failures in host defense. PMID:26048979

  11. Development of Information Technology for Smart Defense

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Kyoil; Lee, So Yeon; Park, Sangjoon; Park, Jonghyun [ETRI, Daejeon (Korea, Republic of); Han, Sangcheol [KEIT, Seoul (Korea, Republic of)

    2014-03-15

    Recently, there has been demand for the convergence of IT (Information and communication Technologies, ICT) with defense, as has already been achieved in civilian fields such as healthcare and construction. It is expected that completely new and common requirements would emerge from the civilian and military domains and that the shape of war field would change rapidly. Many military scientists forecast that future wars would be network-centric and be based on C4I(Command, Control, Communication and Computer, Intelligence), ISR(Intelligence, Surveillance and Reconnaissance), and PGM(Precision Guided Munitions). For realizing the smart defense concept, IT should act as a baseline technology even for simulating a real combat field using virtual reality. In this paper, we propose the concept of IT-based smart defense with a focus on accurate detection in real and cyber wars, effective data communication, automated and unmanned operation, and modeling and simulation.

  12. Salt, chloride, bleach, and innate host defense.

    Science.gov (United States)

    Wang, Guoshun; Nauseef, William M

    2015-08-01

    Salt provides 2 life-essential elements: sodium and chlorine. Chloride, the ionic form of chlorine, derived exclusively from dietary absorption and constituting the most abundant anion in the human body, plays critical roles in many vital physiologic functions, from fluid retention and secretion to osmotic maintenance and pH balance. However, an often overlooked role of chloride is its function in innate host defense against infection. Chloride serves as a substrate for the generation of the potent microbicide chlorine bleach by stimulated neutrophils and also contributes to regulation of ionic homeostasis for optimal antimicrobial activity within phagosomes. An inadequate supply of chloride to phagocytes and their phagosomes, such as in CF disease and other chloride channel disorders, severely compromises host defense against infection. We provide an overview of the roles that chloride plays in normal innate immunity, highlighting specific links between defective chloride channel function and failures in host defense. © Society for Leukocyte Biology.

  13. IBR5 Modulates Temperature-Dependent, R Protein CHS3-Mediated Defense Responses in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Jingyan Liu

    2015-10-01

    Full Text Available Plant responses to low temperature are tightly associated with defense responses. We previously characterized the chilling-sensitive mutant chs3-1 resulting from the activation of the Toll and interleukin 1 receptor-nucleotide binding-leucine-rich repeat (TIR-NB-LRR-type resistance (R protein harboring a C-terminal LIM (Lin-11, Isl-1 and Mec-3 domains domain. Here we report the identification of a suppressor of chs3, ibr5-7 (indole-3-butyric acid response 5, which largely suppresses chilling-activated defense responses. IBR5 encodes a putative dual-specificity protein phosphatase. The accumulation of CHS3 protein at chilling temperatures is inhibited by the IBR5 mutation. Moreover, chs3-conferred defense phenotypes were synergistically suppressed by mutations in HSP90 and IBR5. Further analysis showed that IBR5, with holdase activity, physically associates with CHS3, HSP90 and SGT1b (Suppressor of the G2 allele of skp1 to form a complex that protects CHS3. In addition to the positive role of IBR5 in regulating CHS3, IBR5 is also involved in defense responses mediated by R genes, including SNC1 (Suppressor of npr1-1, Constitutive 1, RPS4 (Resistance to P. syringae 4 and RPM1 (Resistance to Pseudomonas syringae pv. maculicola 1. Thus, the results of the present study reveal a role for IBR5 in the regulation of multiple R protein-mediated defense responses.

  14. Quantitative secondary electron detection

    Science.gov (United States)

    Agrawal, Jyoti; Joy, David C.; Nayak, Subuhadarshi

    2018-05-08

    Quantitative Secondary Electron Detection (QSED) using the array of solid state devices (SSD) based electron-counters enable critical dimension metrology measurements in materials such as semiconductors, nanomaterials, and biological samples (FIG. 3). Methods and devices effect a quantitative detection of secondary electrons with the array of solid state detectors comprising a number of solid state detectors. An array senses the number of secondary electrons with a plurality of solid state detectors, counting the number of secondary electrons with a time to digital converter circuit in counter mode.

  15. [Methods of quantitative proteomics].

    Science.gov (United States)

    Kopylov, A T; Zgoda, V G

    2007-01-01

    In modern science proteomic analysis is inseparable from other fields of systemic biology. Possessing huge resources quantitative proteomics operates colossal information on molecular mechanisms of life. Advances in proteomics help researchers to solve complex problems of cell signaling, posttranslational modification, structure and functional homology of proteins, molecular diagnostics etc. More than 40 various methods have been developed in proteomics for quantitative analysis of proteins. Although each method is unique and has certain advantages and disadvantages all these use various isotope labels (tags). In this review we will consider the most popular and effective methods employing both chemical modifications of proteins and also metabolic and enzymatic methods of isotope labeling.

  16. Magnetoresistive biosensors for quantitative proteomics

    Science.gov (United States)

    Zhou, Xiahan; Huang, Chih-Cheng; Hall, Drew A.

    2017-08-01

    Quantitative proteomics, as a developing method for study of proteins and identification of diseases, reveals more comprehensive and accurate information of an organism than traditional genomics. A variety of platforms, such as mass spectrometry, optical sensors, electrochemical sensors, magnetic sensors, etc., have been developed for detecting proteins quantitatively. The sandwich immunoassay is widely used as a labeled detection method due to its high specificity and flexibility allowing multiple different types of labels. While optical sensors use enzyme and fluorophore labels to detect proteins with high sensitivity, they often suffer from high background signal and challenges in miniaturization. Magnetic biosensors, including nuclear magnetic resonance sensors, oscillator-based sensors, Hall-effect sensors, and magnetoresistive sensors, use the specific binding events between magnetic nanoparticles (MNPs) and target proteins to measure the analyte concentration. Compared with other biosensing techniques, magnetic sensors take advantage of the intrinsic lack of magnetic signatures in biological samples to achieve high sensitivity and high specificity, and are compatible with semiconductor-based fabrication process to have low-cost and small-size for point-of-care (POC) applications. Although still in the development stage, magnetic biosensing is a promising technique for in-home testing and portable disease monitoring.

  17. 32 CFR 13.4 - Duties and responsibilities of the defense.

    Science.gov (United States)

    2010-07-01

    ... COMMISSIONS RESPONSIBILITIES OF THE CHIEF DEFENSE COUNSEL, DETAILED DEFENSE COUNSEL, AND CIVILIAN DEFENSE COUNSEL § 13.4 Duties and responsibilities of the defense. (a) Regular duties. The Defense shall perform... 32 National Defense 1 2010-07-01 2010-07-01 false Duties and responsibilities of the defense. 13.4...

  18. 77 FR 76938 - Defense Federal Acquisition Regulation Supplement: Contracting Activity Updates (DFARS Case 2012...

    Science.gov (United States)

    2012-12-31

    ... Security Cooperation Agency, the Defense Security Service, the Defense Threat Reduction Agency, the Missile... DEPARTMENT OF DEFENSE Defense Acquisition Regulations System 48 CFR Part 202 RIN 0750-AH81 Defense...: Defense Acquisition Regulations System, Department of Defense (DoD). ACTION: Final rule. SUMMARY: DoD is...

  19. Quantitative Decision Support Requires Quantitative User Guidance

    Science.gov (United States)

    Smith, L. A.

    2009-12-01

    Is it conceivable that models run on 2007 computer hardware could provide robust and credible probabilistic information for decision support and user guidance at the ZIP code level for sub-daily meteorological events in 2060? In 2090? Retrospectively, how informative would output from today’s models have proven in 2003? or the 1930’s? Consultancies in the United Kingdom, including the Met Office, are offering services to “future-proof” their customers from climate change. How is a US or European based user or policy maker to determine the extent to which exciting new Bayesian methods are relevant here? or when a commercial supplier is vastly overselling the insights of today’s climate science? How are policy makers and academic economists to make the closely related decisions facing them? How can we communicate deep uncertainty in the future at small length-scales without undermining the firm foundation established by climate science regarding global trends? Three distinct aspects of the communication of the uses of climate model output targeting users and policy makers, as well as other specialist adaptation scientists, are discussed. First, a brief scientific evaluation of the length and time scales at which climate model output is likely to become uninformative is provided, including a note on the applicability the latest Bayesian methodology to current state-of-the-art general circulation models output. Second, a critical evaluation of the language often employed in communication of climate model output, a language which accurately states that models are “better”, have “improved” and now “include” and “simulate” relevant meteorological processed, without clearly identifying where the current information is thought to be uninformative and misleads, both for the current climate and as a function of the state of the (each) climate simulation. And thirdly, a general approach for evaluating the relevance of quantitative climate model output

  20. Autonomous Aerial Ice Observation for Ice Defense

    Directory of Open Access Journals (Sweden)

    Joakim Haugen

    2014-10-01

    Full Text Available One of the tasks in ice defense is to gather information about the surrounding ice environment using various sensor platforms. In this manuscript we identify two monitoring tasks known in literature, namely dynamic coverage and target tracking, and motivate how these tasks are relevant in ice defense using RPAS. An optimization-based path planning concept is outlined for solving these tasks. A path planner for the target tracking problem is elaborated in more detail and a hybrid experiment, which consists of both a real fixed-wing aircraft and simulated objects, is included to show the applicability of the proposed framework.

  1. A characteristic study of CCF modeling techniques and optimization of CCF defense strategies

    International Nuclear Information System (INIS)

    Kim, Min Chull

    2000-02-01

    Common Cause Failures (CCFs ) are among the major contributors to risk and core damage frequency (CDF ) from operating nuclear power plants (NPPs ). Our study on CCF focused on the following aspects : 1) a characteristic study on the CCF modeling techniques and 2) development of the optimal CCF defense strategy. Firstly, the characteristics of CCF modeling techniques were studied through sensitivity study of CCF occurrence probability upon system redundancy. The modeling techniques considered in this study include those most widely used worldwide, i.e., beta factor, MGL, alpha factor, and binomial failure rate models. We found that MGL and alpha factor models are essentially identical in terms of the CCF probability. Secondly, in the study for CCF defense, the various methods identified in the previous studies for defending against CCF were classified into five different categories. Based on these categories, we developed a generic method by which the optimal CCF defense strategy can be selected. The method is not only qualitative but also quantitative in nature: the selection of the optimal strategy among candidates is based on the use of analytic hierarchical process (AHP). We applied this method to two motor-driven valves for containment sump isolation in Ulchin 3 and 4 nuclear power plants. The result indicates that the method for developing an optimal CCF defense strategy is effective

  2. Investigating an approach to the alliance based on interpersonal defense theory.

    Science.gov (United States)

    Westerman, Michael A; Muran, J Christopher

    2017-09-01

    Notwithstanding consistent findings of significant relationships between the alliance and outcome, questions remain to be answered about the relatively small magnitude of those correlations, the mechanisms underlying the association, and how to conceptualize the alliance construct. We conducted a preliminary study of an approach to the alliance based on interpersonal defense theory, which is an interpersonal reconceptualization of defense processes, to investigate the promise of this alternative approach as a way to address the outstanding issues. We employed qualitative, theory-building case study methodology, closely examining alliance processes at four time points in the treatment of a case in terms of a case formulation based on interpersonal defense theory. The results suggested that our approach made it possible to recognize key processes in the alliance and that it helps explain how the alliance influences outcome. Our analyses also provided a rich set of concrete illustrations of the alliance phenomena identified by the theory. The findings suggest that an approach to the alliance based on interpersonal defense theory holds promise. However, although the qualitative method we employed has advantages, it also has limitations. We offer suggestions about how future qualitative and quantitative investigations could build on this study.

  3. Extending Quantitative Easing

    DEFF Research Database (Denmark)

    Hallett, Andrew Hughes; Fiedler, Salomon; Kooths, Stefan

    The notes in this compilation address the pros and cons associated with the extension of ECB quantitative easing programme of asset purchases. The notes have been requested by the Committee on Economic and Monetary Affairs as an input for the February 2017 session of the Monetary Dialogue....

  4. Quantitative Moessbauer analysis

    International Nuclear Information System (INIS)

    Collins, R.L.

    1978-01-01

    The quantitative analysis of Moessbauer data, as in the measurement of Fe 3+ /Fe 2+ concentration, has not been possible because of the different mean square velocities (x 2 ) of Moessbauer nuclei at chemically different sites. A method is now described which, based on Moessbauer data at several temperatures, permits the comparison of absorption areas at (x 2 )=0. (Auth.)

  5. GNF Defense in Depth Update

    Energy Technology Data Exchange (ETDEWEB)

    Lingenfelter, Andrew A.; Schneider, Robert J.; Cantonwine, Paul E.; Moore, Brian; Rea, John; Crawford, Douglas C. [Global Nuclear Fuel, P.O. Box 780 M/C H25, Wilmington, NC 28402 (United States)

    2009-06-15

    Global Nuclear Fuel (GNF) has designed, fabricated, and placed into operation more than 9 million fuel rods in approximately 135 thousand assemblies. Customer satisfaction has always compelled GNF to reduce fuel rod failures (defined here as fuel rods that breach or leak in service), However, increasing success with and subsequent expectations for economic performance of nuclear reactor plants have raised broader Industry emphasis on fuel reliability. In 2005, GNF established its Defense-in-Depth (DID) Program for the purpose of focusing attention on the many aspects of fuel design, fabrication, performance, and utilization that affect fuel reliability as well as on the key methods that govern the utilization of GNF fuel. The Program is structured to address each of the identified in-service, fuel failure mechanisms. This paper provides a summary of GNF fuel performance, following previous updates. This paper will discuss recent GNF fuel reliability and channel performance, GNF2 introduction status, and methods. GNF's more recent fuel experience includes approximately 3.8 million GE11/13 (9x9) and GE12/14 (10x10) fuel rods, well over half of which are the GE12/14 design. (Those figures also include roughly 25,000 recently-introduced GNF2 fuel rods.) Reliability, expressed as annual, observed fuel failure rates (i.e., number of rods failed each year divided by the number of opportunities, or fuel rods in service), has improved for each year since 2005. The GNF fuel failure rate for years leading up to 2007 and 2008 has been on the order of 5 to 7 ppm (excluding the corrosion events of 2001-2003), and as of this writing (January 2009) the current in-service failure has decreased to around 1.5 ppm. Failures in GE14 fuel rod failures have been primarily due to debris-fretting (> 60%), with other failures being duty-related or yet undetermined. The only failure observed in GNF2 to date was a single, early-life debris failure in a bundle not equipped with GNF

  6. Critical Quantitative Inquiry in Context

    Science.gov (United States)

    Stage, Frances K.; Wells, Ryan S.

    2014-01-01

    This chapter briefly traces the development of the concept of critical quantitative inquiry, provides an expanded conceptualization of the tasks of critical quantitative research, offers theoretical explanation and justification for critical research using quantitative methods, and previews the work of quantitative criticalists presented in this…

  7. Structural evaluation of multifunctional flood defenses

    NARCIS (Netherlands)

    Voorendt, M.Z.; Kothuis, Baukje; Kok, Matthijs

    2017-01-01

    Flood risk reduction aims to minimize losses in low-lying areas. One of the ways to reduce flood risks is to protect land by means of flood defenses. The Netherlands has a long tradition of flood protection and, therefore, a wide variety of technical reports written

  8. Excessive Profits of German Defense Contractors

    Science.gov (United States)

    2014-09-01

    its business unit Thyssen Krupp Marine Systems, is a German defense contractor. (2) Tognom AG Tognum AG owned the MTU Friedrichshafen GmbH before... Friedrichshafen provided engines for many ships of the German Navy and for German battle tanks, such as the Leopard I and Leopard II. MTU refers to the

  9. The Transferability and Retraining of Defense Engineers.

    Science.gov (United States)

    Rittenhouse, Carl H.

    This study was undertaken to describe any special barriers to the transfer of engineers from defense to commercial work, and to evaluate retraining and reorientation techniques that might help ease the transfer. Interviews and questionnaires were used to obtain data from about 2,100 engineers and 100 managers in 14 industries. Characteristics,…

  10. Pathogen Pressure Puts Immune Defense into Perspective

    NARCIS (Netherlands)

    Horrocks, Nicholas P. C.; Matson, Kevin D.; Tieleman, B. Irene

    2011-01-01

    The extent to which organisms can protect themselves from disease depends on both the immune defenses they maintain and the pathogens they face. At the same time, immune systems are shaped by the antigens they encounter, both over ecological and evolutionary time. Ecological immunologists often

  11. DETERMINATION OF DEFENSE MECHANISM IN Phaseolus ...

    African Journals Online (AJOL)

    Administrator

    Field studies were conducted to determine the role of defense mechanism in various parameters associated with plant protection subjected to UV-B radiation in Phaseolus trilobus Ait. commonly used as green manure and fodder. Spectrophotometric analysis showed that UV-B radiation decreases the chlorophyll content ...

  12. Defense.gov Special Report: Fiscal Budget

    Science.gov (United States)

    Department of Defense Submit Search 2012 Fiscal Budget Published Feb. 15, 2011 Top Stories Commanders Cite Department is losing billions of dollars by Congress' failure to pass the department's fiscal 2011 budget . Gates told a Senate committee. Story Gates, Mullen Take Budget to Senate WASHINGTON, Feb. 17, 2011 - The

  13. Under Secretary of Defense (Comptroller) > Budget

    Science.gov (United States)

    functionalStatements OUSD(C) History FMR Budget Materials Budget Execution Financial Management Improving Financial Performance Reports Regulations Press Release | Budget Briefing | Transcripts: David L. Norquist, Under PDF document. Click on Excel icon for Excel document Overview - FY2019 Defense Budget Performance

  14. The fragility of the Brazilian Defense Ministry

    Directory of Open Access Journals (Sweden)

    Jorge Zaverucha

    2006-01-01

    Full Text Available The present article presents different phases that the Brazilian Defense Ministry has passed through, since its inception during Fernando Henrique Cardoso's second presidential term (1999-2002 until the current administration of Luís Inácio Lula da Silva (2003-2006, under its respective ministers of Defense. It has been seen as one of the important stages in the re-constitutionalization of the country, insofar as it establishes the submission of Armed Forces commanders to a civilian minister, and although some analysts have considered that such submission is actually achieved, we point here to the military resistance and insubordination to civil power that are the result of an authoritarian legacy. To the extent that the Ministry of Defense is unable to implement its own policies in which the military would be required to follow civilian guidance, this article concludes with considerations on the civil Defense Ministry's political and institutional fragility vis-a-vis military command. The latter has been able to retain high levels of decision making autonomy in its relationship to the Ministry and its structure.

  15. Defense waste transportation: cost and logistics studies

    International Nuclear Information System (INIS)

    Andrews, W.B.; Cole, B.M.; Engel, R.L.; Oylear, J.M.

    1982-08-01

    Transportation of nuclear wastes from defense programs is expected to significantly increase in the 1980s and 1990s as permanent waste disposal facilities come into operation. This report uses models of the defense waste transportation system to quantify potential transportation requirements for treated and untreated contact-handled transuranic (CH-TRU) wastes and high-level defense wastes (HLDW). Alternative waste management strategies in repository siting, waste retrieval and treatment, treatment facility siting, waste packaging and transportation system configurations were examined to determine their effect on transportation cost and hardware requirements. All cost estimates used 1980 costs. No adjustments were made for future changes in these costs relative to inflation. All costs are reported in 1980 dollars. If a single repository is used for defense wastes, transportation costs for CH-TRU waste currently in surface storage and similar wastes expected to be generated by the year 2000 were estimated to be 109 million dollars. Recovery and transport of the larger buried volumes of CH-TRU waste will increase CH-TRU waste transportation costs by a factor of 70. Emphasis of truck transportation and siting of multiple repositories would reduce CH-TRU transportation costs. Transportation of HLDW to repositories for 25 years beginning in 1997 is estimated to cost $229 M in 1980 costs and dollars. HLDW transportation costs could either increase or decrease with the selection of a final canister configuration. HLDW transportation costs are reduced when multiple repositories exist and emphasis is placed on truck transport

  16. Defense.gov - Special Report - Cybersecurity

    Science.gov (United States)

    reduce vulnerability to cyber-attack attempts that occur regularly and are likely to continue for the together to protect cyberspace. U.S. Cyber Command Preparations Under Way WASHINGTON, March 16, 2010 - Preparations for the formal establishment of U.S. Cyber Command, which will operate and defend the Defense

  17. Department of Defense Education Activity. An Overview.

    Science.gov (United States)

    US Department of Defense, 2004

    2004-01-01

    DoDEA operates 223 public schools in 16 districts located in seven states, Puerto Rico, Guam, and 13 foreign countries to serve the children of military service members and Department of Defense civilian employees. Approximately 104,935 students are enrolled in DoDEA schools, with approximately 73,200 students in the DoDDS system, and…

  18. COMPETITIVENESS OF DEFENSE INDUSTRY IN TURKEY

    Directory of Open Access Journals (Sweden)

    Hakki BILGEN

    2010-01-01

    Full Text Available Turkey has created some opportunities for the organisations in the defense industry to generate a suitable business and to ensure its sustainability. The domestic coverage ratio of defense system need in 2010 is aimed as 50%. To achieve this target depends on the defense industry competitiveness. In this study, the development plans, strategies and foreign trade are examined. Its contribution which has an important place in the research and development investment, is not at the level expected in Turkey’s economy. Turkey occupies 47th position in World Competitiveness Scoreboard, and 61st position in Global Competitiveness Index in 2009. The index factors are investigated to understand the competitiveness according to the Porter’s diamond model, applied in Turkey for the first time. As a result, the competitiveness analysis of Turkish defense industry is carried out and its global place and competitive advantage are exposed. Therefore, a framework is made to introduce a guide for decision-making by using a widely-accepted model, and to contribute to the plans and strategies

  19. Preemptive strikes: Fear, hope, and defensive aggression.

    Science.gov (United States)

    Halevy, Nir

    2017-02-01

    Preemptive strikes are costly and harmful. Existing models of defensive aggression focus narrowly on the role fear plays in motivating preemptive strikes. Theoretically integrating the literatures on conflict, decision making, and emotion, the current research investigated how specific emotions associated with certainty or uncertainty, including fear, anger, disgust, hope, and happiness, influence preemptive strikes. Study 1 demonstrated that hope negatively predicts defensive exits from relationships in choice dilemmas. Studies 2 and 3 experimentally manipulated risk of being attacked in an incentivized, interactive decision making task-the Preemptive Strike Game. Risk of being attacked fueled preemptive strikes; reduced feelings of hope partially mediated this effect in Study 3. Studies 4 and 5 investigated preemptive strikes under uncertainty (rather than risk). In Study 4, reasoning about the factors that make one trustful of others curbed preemptive strikes; cogitating about the factors that underlie discrete emotions, however, did not influence defensive aggression. Study 5 demonstrated that the valence and uncertainty appraisals of incidental emotions interact in shaping preemptive strikes. Specifically, recalling an autobiographical emotional experience that produced hope significantly decreased attack rates relative to fear, happiness, and a control condition. Fear, anger, disgust, and happiness were either unrelated to preemptive strikes or showed inconsistent relationships with preemptive strikes across the 5 studies. These findings shed light on how emotions shape defensive aggression, advance knowledge on strategic choice under risk and uncertainty, and demonstrate hope's positive effects on social interactions and relationships. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  20. Innovation in the Defense Acquisition Enterprise

    Science.gov (United States)

    2015-12-01

    uni- versities in the fields of innovation and entrepreneurship . Many books and articles have been written on innovation, perhaps none more well...partners has been the possible loss of freedom to make their own IR&D invest- ment decisions. That was never my intent . I once ran a major defense